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@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ p = (\gamma - 1) \rho e
+$$
+
+\end{document}
diff --git a/doc/Eqs/pair_sph_tait.jpg b/doc/Eqs/pair_sph_tait.jpg
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+++ b/doc/Eqs/pair_sph_tait.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ p = B [(\frac{\rho}{\rho_0})^{\gamma} - 1]
+$$
+
+\end{document}
diff --git a/doc/Section_accelerate.html b/doc/Section_accelerate.html
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--- a/doc/Section_accelerate.html
+++ b/doc/Section_accelerate.html
@@ -1,534 +1,537 @@
<HTML>
<CENTER><A HREF = "Section_packages.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_howto.html">Next
Section</A>
</CENTER>
<HR>
<H3>5. Using accelerated CPU and GPU styles
</H3>
<P>Accelerated versions of various <A HREF = "pair_style.html">pair_style</A>,
<A HREF = "fix.html">fixes</A>, <A HREF = "compute.html">computes</A>, and other commands have
been added to LAMMPS, which will typically run faster than the
standard non-accelerated versions, if you have the appropriate
hardware on your system.
</P>
<P>The accelerated styles have the same name as the standard styles,
except that a suffix is appended. Otherwise, the syntax for the
command is identical, their functionality is the same, and the
numerical results it produces should also be identical, except for
precision and round-off issues.
</P>
<P>For example, all of these variants of the basic Lennard-Jones pair
style exist in LAMMPS:
</P>
<UL><LI><A HREF = "pair_lj.html">pair_style lj/cut</A>
<LI><A HREF = "pair_lj.html">pair_style lj/cut/opt</A>
<LI><A HREF = "pair_lj.html">pair_style lj/cut/omp</A>
<LI><A HREF = "pair_lj.html">pair_style lj/cut/gpu</A>
<LI><A HREF = "pair_lj.html">pair_style lj/cut/cuda</A>
</UL>
<P>Assuming you have built LAMMPS with the appropriate package, these
styles can be invoked by specifying them explicitly in your input
script. Or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> to invoke the accelerated versions
automatically, without changing your input script. The
<A HREF = "suffix.html">suffix</A> command allows you to set a suffix explicitly and
to turn off/on the comand-line switch setting, both from within your
input script.
</P>
<P>Styles with an "opt" suffix are part of the OPT package and typically
speed-up the pairwise calculations of your simulation by 5-25%.
</P>
<P>Styles with an "omp" suffix are part of the USER-OMP package and allow
a pair-style to be run in threaded mode using OpenMP. This can be
useful on nodes with high-core counts when using less MPI processes
than cores is advantageous, e.g. when running with PPPM so that FFTs
are run on fewer MPI processors.
</P>
<P>Styles with a "gpu" or "cuda" suffix are part of the GPU or USER-CUDA
packages, and can be run on NVIDIA GPUs associated with your CPUs.
The speed-up due to GPU usage depends on a variety of factors, as
discussed below.
</P>
<P>To see what styles are currently available in each of the accelerated
packages, see <A HREF = "Section_commands.html#cmd_5">this section</A> of the
manual. A list of accelerated styles is included in the pair, fix,
compute, and kspace sections.
</P>
<P>The following sections explain:
</P>
<UL><LI>what hardware and software the accelerated styles require
<LI>how to build LAMMPS with the accelerated packages in place
<LI>what changes (if any) are needed in your input scripts
<LI>guidelines for best performance
<LI>speed-ups you can expect
</UL>
<P>The final section compares and contrasts the GPU and USER-CUDA
packages, since they are both designed to use NVIDIA GPU hardware.
</P>
5.1 <A HREF = "#acc_1">OPT package</A><BR>
5.2 <A HREF = "#acc_2">USER-OMP package</A><BR>
5.3 <A HREF = "#acc_3">GPU package</A><BR>
5.4 <A HREF = "#acc_4">USER-CUDA package</A><BR>
5.5 <A HREF = "#acc_5">Comparison of GPU and USER-CUDA packages</A> <BR>
<HR>
<HR>
<H4><A NAME = "acc_1"></A>5.1 OPT package
</H4>
<P>The OPT package was developed by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
Technologies). It contains a handful of pair styles whose compute()
methods were rewritten in C++ templated form to reduce the overhead
due to if tests and other conditional code.
</P>
<P>The procedure for building LAMMPS with the OPT package is simple. It
is the same as for any other package which has no additional library
dependencies:
</P>
<PRE>make yes-opt
make machine
</PRE>
<P>If your input script uses one of the OPT pair styles,
you can run it as follows:
</P>
<PRE>lmp_machine -sf opt < in.script
mpirun -np 4 lmp_machine -sf opt < in.script
</PRE>
<P>You should see a reduction in the "Pair time" printed out at the end
of the run. On most machines and problems, this will typically be a 5
to 20% savings.
</P>
<HR>
<HR>
<H4><A NAME = "acc_2"></A>5.2 USER-OMP package
</H4>
<P>This section will be written when the USER-OMP package is released
in main LAMMPS.
</P>
<HR>
<HR>
<H4><A NAME = "acc_3"></A>5.3 GPU package
</H4>
<P>The GPU package was developed by Mike Brown at ORNL. It provides GPU
versions of several pair styles and for long-range Coulombics via the
PPPM command. It has the following features:
</P>
<UL><LI>The package is designed to exploit common GPU hardware configurations
where one or more GPUs are coupled with many cores of a multi-core
CPUs, e.g. within a node of a parallel machine.
<LI>Atom-based data (e.g. coordinates, forces) moves back-and-forth
between the CPU(s) and GPU every timestep.
<LI>Neighbor lists can be constructed on the CPU or on the GPU
<LI>The charge assignement and force interpolation portions of PPPM can be
run on the GPU. The FFT portion, which requires MPI communication
between processors, runs on the CPU.
<LI>Asynchronous force computations can be performed simultaneously on the
CPU(s) and GPU.
<LI>LAMMPS-specific code is in the GPU package. It makes calls to a
generic GPU library in the lib/gpu directory. This library provides
NVIDIA support as well as more general OpenCL support, so that the
same functionality can eventually be supported on a variety of GPU
hardware.
</UL>
<P><B>Hardware and software requirements:</B>
</P>
<P>To use this package, you currently need to have specific NVIDIA
hardware and install specific NVIDIA CUDA software on your system:
</P>
<UL><LI>Check if you have an NVIDIA card: cat /proc/driver/nvidia/cards/0
<LI>Go to http://www.nvidia.com/object/cuda_get.html
<LI>Install a driver and toolkit appropriate for your system (SDK is not necessary)
<LI>Follow the instructions in lammps/lib/gpu/README to build the library (see below)
<LI>Run lammps/lib/gpu/nvc_get_devices to list supported devices and properties
</UL>
<P><B>Building LAMMPS with the GPU package:</B>
</P>
<P>As with other packages that include a separately compiled library, you
need to first build the GPU library, before building LAMMPS itself.
General instructions for doing this are in <A HREF = "doc/Section_start.html#start_3">this
section</A> of the manual. For this
package, do the following, using a Makefile in lib/gpu appropriate for
your system:
</P>
<PRE>cd lammps/lib/gpu
make -f Makefile.linux
(see further instructions in lammps/lib/gpu/README)
</PRE>
<P>If you are successful, you will produce the file lib/libgpu.a.
</P>
<P>Now you are ready to build LAMMPS with the GPU package installed:
</P>
<PRE>cd lammps/src
make yes-gpu
make machine
</PRE>
<P>Note that the lo-level Makefile (e.g. src/MAKE/Makefile.linux) has
these settings: gpu_SYSINC, gpu_SYSLIB, gpu_SYSPATH. These need to be
set appropriately to include the paths and settings for the CUDA
system software on your machine. See src/MAKE/Makefile.g++ for an
example.
</P>
<P><B>GPU configuration</B>
</P>
<P>When using GPUs, you are restricted to one physical GPU per LAMMPS
process, which is an MPI process running on a single core or
processor. Multiple MPI processes (CPU cores) can share a single GPU,
and in many cases it will be more efficient to run this way.
</P>
<P><B>Input script requirements:</B>
</P>
<P>Additional input script requirements to run pair or PPPM styles with a
<I>gpu</I> suffix are as follows:
</P>
<UL><LI>To invoke specific styles from the GPU package, you can either append
"gpu" to the style name (e.g. pair_style lj/cut/gpu), or use the
<A HREF = "Section_start.html#start_6">-suffix command-line switch</A>, or use the
<A HREF = "suffix.html">suffix</A> command.
<LI>The <A HREF = "newton.html">newton pair</A> setting must be <I>off</I>.
<LI>The <A HREF = "package.html">package gpu</A> command must be used near the beginning
of your script to control the GPU selection and initialization
settings. It also has an option to enable asynchronous splitting of
force computations between the CPUs and GPUs.
</UL>
<P>As an example, if you have two GPUs per node and 8 CPU cores per node,
and would like to run on 4 nodes (32 cores) with dynamic balancing of
force calculation across CPU and GPU cores, you could specify
</P>
<PRE>package gpu force/neigh 0 1 -1
</PRE>
<P>In this case, all CPU cores and GPU devices on the nodes would be
utilized. Each GPU device would be shared by 4 CPU cores. The CPU
cores would perform force calculations for some fraction of the
particles at the same time the GPUs performed force calculation for
the other particles.
</P>
<P><B>Timing output:</B>
</P>
<P>As described by the <A HREF = "package.html">package gpu</A> command, GPU
accelerated pair styles can perform computations asynchronously with
CPU computations. The "Pair" time reported by LAMMPS will be the
maximum of the time required to complete the CPU pair style
computations and the time required to complete the GPU pair style
computations. Any time spent for GPU-enabled pair styles for
computations that run simultaneously with <A HREF = "bond_style.html">bond</A>,
<A HREF = "angle_style.html">angle</A>, <A HREF = "dihedral_style.html">dihedral</A>,
<A HREF = "improper_style.html">improper</A>, and <A HREF = "kspace_style.html">long-range</A>
calculations will not be included in the "Pair" time.
</P>
<P>When the <I>mode</I> setting for the package gpu command is force/neigh,
the time for neighbor list calculations on the GPU will be added into
the "Pair" time, not the "Neigh" time. An additional breakdown of the
times required for various tasks on the GPU (data copy, neighbor
calculations, force computations, etc) are output only with the LAMMPS
screen output (not in the log file) at the end of each run. These
timings represent total time spent on the GPU for each routine,
regardless of asynchronous CPU calculations.
</P>
<P><B>Performance tips:</B>
</P>
<P>Generally speaking, for best performance, you should use multiple CPUs
per GPU, as provided my most multi-core CPU/GPU configurations.
</P>
<P>Because of the large number of cores within each GPU device, it may be
more efficient to run on fewer processes per GPU when the number of
particles per MPI process is small (100's of particles); this can be
necessary to keep the GPU cores busy.
</P>
<P>See the lammps/lib/gpu/README file for instructions on how to build
the GPU library for single, mixed, or double precision. The latter
requires that your GPU card support double precision.
</P>
<HR>
<HR>
<H4><A NAME = "acc_4"></A>5.4 USER-CUDA package
</H4>
<P>The USER-CUDA package was developed by Christian Trott at U Technology
Ilmenau in Germany. It provides NVIDIA GPU versions of many pair
styles, many fixes, a few computes, and for long-range Coulombics via
the PPPM command. It has the following features:
</P>
<UL><LI>The package is designed to allow an entire LAMMPS calculation, for
many timesteps, to run entirely on the GPU (except for inter-processor
MPI communication), so that atom-based data (e.g. coordinates, forces)
do not have to move back-and-forth between the CPU and GPU.
+<LI>The speed-up advantage of this approach is typically better when the
+number of atoms per GPU is large
+
<LI>Data will stay on the GPU until a timestep where a non-GPU-ized fix or
compute is invoked. Whenever a non-GPU operation occurs (fix,
compute, output), data automatically moves back to the CPU as needed.
This may incur a performance penalty, but should otherwise work
transparently.
<LI>Neighbor lists for GPU-ized pair styles are constructed on the
GPU.
<LI>The package only supports use of a single CPU (core) with each
GPU.
</UL>
<P><B>Hardware and software requirements:</B>
</P>
<P>To use this package, you need to have specific NVIDIA hardware and
install specific NVIDIA CUDA software on your system.
</P>
<P>Your NVIDIA GPU needs to support Compute Capability 1.3. This list may
help you to find out the Compute Capability of your card:
</P>
<P>http://en.wikipedia.org/wiki/Comparison_of_Nvidia_graphics_processing_units
</P>
<P>Install the Nvidia Cuda Toolkit in version 3.2 or higher and the
corresponding GPU drivers. The Nvidia Cuda SDK is not required for
LAMMPSCUDA but we recommend it be installed. You can then make sure
that its sample projects can be compiled without problems.
</P>
<P><B>Building LAMMPS with the USER-CUDA package:</B>
</P>
<P>As with other packages that include a separately compiled library, you
need to first build the USER-CUDA library, before building LAMMPS
itself. General instructions for doing this are in <A HREF = "doc/Section_start.html#start_3">this
section</A> of the manual. For this
package, do the following, using settings in the lib/cuda Makefiles
appropriate for your system:
</P>
<UL><LI>Go to the lammps/lib/cuda directory
<LI>If your <I>CUDA</I> toolkit is not installed in the default system directoy
<I>/usr/local/cuda</I> edit the file <I>lib/cuda/Makefile.common</I>
accordingly.
<LI>Type "make OPTIONS", where <I>OPTIONS</I> are one or more of the following
options. The settings will be written to the
<I>lib/cuda/Makefile.defaults</I> and used in the next step.
<PRE><I>precision=N</I> to set the precision level
N = 1 for single precision (default)
N = 2 for double precision
N = 3 for positions in double precision
N = 4 for positions and velocities in double precision
<I>arch=M</I> to set GPU compute capability
M = 20 for CC2.0 (GF100/110, e.g. C2050,GTX580,GTX470) (default)
M = 21 for CC2.1 (GF104/114, e.g. GTX560, GTX460, GTX450)
M = 13 for CC1.3 (GF200, e.g. C1060, GTX285)
<I>prec_timer=0/1</I> to use hi-precision timers
0 = do not use them (default)
1 = use these timers
this is usually only useful for Mac machines
<I>dbg=0/1</I> to activate debug mode
0 = no debug mode (default)
1 = yes debug mode
this is only useful for developers
<I>cufft=1</I> to determine usage of CUDA FFT library
0 = no CUFFT support (default)
in the future other CUDA-enabled FFT libraries might be supported
</PRE>
<LI>Type "make" to build the library. If you are successful, you will
produce the file lib/libcuda.a.
</UL>
<P>Now you are ready to build LAMMPS with the USER-CUDA package installed:
</P>
<PRE>cd lammps/src
make yes-user-cuda
make machine
</PRE>
<P>Note that the LAMMPS build references the lib/cuda/Makefile.common
file to extract setting specific CUDA settings. So it is important
that you have first built the cuda library (in lib/cuda) using
settings appropriate to your system.
</P>
<P><B>Input script requirements:</B>
</P>
<P>Additional input script requirements to run styles with a <I>cuda</I>
suffix are as follows:
</P>
<UL><LI>To invoke specific styles from the USER-CUDA package, you can either
append "cuda" to the style name (e.g. pair_style lj/cut/cuda), or use
the <A HREF = "Section_start.html#start_6">-suffix command-line switch</A>, or use
the <A HREF = "suffix.html">suffix</A> command. One exception is that the
<A HREF = "kspace_style.html">kspace_style pppm/cuda</A> command has to be requested
explicitly.
<LI>To use the USER-CUDA package with its default settings, no additional
command is needed in your input script. This is because when LAMMPS
starts up, it detects if it has been built with the USER-CUDA package.
See the <A HREF = "Section_start.html#start_6">-cuda command-line switch</A> for
more details.
<LI>To change settings for the USER-CUDA package at run-time, the <A HREF = "package.html">package
cuda</A> command can be used near the beginning of your
input script. See the <A HREF = "package.html">package</A> command doc page for
details.
</UL>
<P><B>Performance tips:</B>
</P>
<P>The USER-CUDA package offers more speed-up relative to CPU performance
when the number of atoms per GPU is large, e.g. on the order of tens
or hundreds of 1000s.
</P>
<P>As noted above, this package will continue to run a simulation
entirely on the GPU(s) (except for inter-processor MPI communication),
for multiple timesteps, until a CPU calculation is required, either by
a fix or compute that is non-GPU-ized, or until output is performed
(thermo or dump snapshot or restart file). The less often this
occurs, the faster your simulation will run.
</P>
<HR>
<HR>
<H4><A NAME = "acc_5"></A>5.5 Comparison of GPU and USER-CUDA packages
</H4>
<P>Both the GPU and USER-CUDA packages accelerate a LAMMPS calculation
using NVIDIA hardware, but they do it in different ways.
</P>
<P>As a consequence, for a particular simulation on specific hardware,
one package may be faster than the other. We give guidelines below,
but the best way to determine which package is faster for your input
script is to try both of them on your machine. See the benchmarking
section below for examples where this has been done.
</P>
<P><B>Guidelines for using each package optimally:</B>
</P>
<UL><LI>The GPU package allows you to assign multiple CPUs (cores) to a single
GPU (a common configuration for "hybrid" nodes that contain multicore
CPU(s) and GPU(s)) and works effectively in this mode. The USER-CUDA
package does not allow this; you can only use one CPU per GPU.
<LI>The GPU package moves per-atom data (coordinates, forces)
back-and-forth between the CPU and GPU every timestep. The USER-CUDA
package only does this on timesteps when a CPU calculation is required
(e.g. to invoke a fix or compute that is non-GPU-ized). Hence, if you
can formulate your input script to only use GPU-ized fixes and
computes, and avoid doing I/O too often (thermo output, dump file
snapshots, restart files), then the data transfer cost of the
USER-CUDA package can be very low, causing it to run faster than the
GPU package.
<LI>The GPU package is often faster than the USER-CUDA package, if the
number of atoms per GPU is "small". The crossover point, in terms of
atoms/GPU at which the USER-CUDA package becomes faster depends
strongly on the pair style. For example, for a simple Lennard Jones
system the crossover (in single precision) is often about 50K-100K
atoms per GPU. When performing double precision calculations the
crossover point can be significantly smaller.
<LI>Both packages compute bonded interactions (bonds, angles, etc) on the
CPU. This means a model with bonds will force the USER-CUDA package
to transfer per-atom data back-and-forth between the CPU and GPU every
timestep. If the GPU package is running with several MPI processes
assigned to one GPU, the cost of computing the bonded interactions is
spread across more CPUs and hence the GPU package can run faster.
<LI>When using the GPU package with multiple CPUs assigned to one GPU, its
performance depends to some extent on high bandwidth between the CPUs
and the GPU. Hence its performance is affected if full 16 PCIe lanes
are not available for each GPU. In HPC environments this can be the
case if S2050/70 servers are used, where two devices generally share
one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide
full 16 lanes to each of the PCIe 2.0 16x slots.
</UL>
<P><B>Differences between the two packages:</B>
</P>
<UL><LI>The GPU package accelerates only pair force, neighbor list, and PPPM
calculations. The USER-CUDA package currently supports a wider range
of pair styles and can also accelerate many fix styles and some
compute styles, as well as neighbor list and PPPM calculations.
<LI>The GPU package uses more GPU memory than the USER-CUDA package. This
is generally not a problem since typical runs are computation-limited
rather than memory-limited.
</UL>
<P><B>Examples:</B>
</P>
<P>The LAMMPS distribution has two directories with sample input scripts
for the GPU and USER-CUDA packages.
</P>
<UL><LI>lammps/examples/gpu = GPU package files
<LI>lammps/examples/USER/cuda = USER-CUDA package files
</UL>
<P>These contain input scripts for identical systems, so they can be used
to benchmark the performance of both packages on your system.
</P>
<HR>
<P><B>Benchmark data:</B>
</P>
<P>NOTE: We plan to add some benchmark results and plots here for the
examples described in the previous section.
</P>
<P>Simulations:
</P>
<P>1. Lennard Jones
</P>
<UL><LI>256,000 atoms
<LI>2.5 A cutoff
<LI>0.844 density
</UL>
<P>2. Lennard Jones
</P>
<UL><LI>256,000 atoms
<LI>5.0 A cutoff
<LI>0.844 density
</UL>
<P>3. Rhodopsin model
</P>
<UL><LI>256,000 atoms
<LI>10A cutoff
<LI>Coulomb via PPPM
</UL>
<P>4. Lihtium-Phosphate
</P>
<UL><LI>295650 atoms
<LI>15A cutoff
<LI>Coulomb via PPPM
</UL>
<P>Hardware:
</P>
<P>Workstation:
</P>
<UL><LI>2x GTX470
<LI>i7 950@3GHz
<LI>24Gb DDR3 @ 1066Mhz
<LI>CentOS 5.5
<LI>CUDA 3.2
<LI>Driver 260.19.12
</UL>
<P>eStella:
</P>
<UL><LI>6 Nodes
<LI>2xC2050
<LI>2xQDR Infiniband interconnect(aggregate bandwidth 80GBps)
<LI>Intel X5650 HexCore @ 2.67GHz
<LI>SL 5.5
<LI>CUDA 3.2
<LI>Driver 260.19.26
</UL>
<P>Keeneland:
</P>
<UL><LI>HP SL-390 (Ariston) cluster
<LI>120 nodes
<LI>2x Intel Westmere hex-core CPUs
<LI>3xC2070s
<LI>QDR InfiniBand interconnect
</UL>
</HTML>
diff --git a/doc/Section_accelerate.txt b/doc/Section_accelerate.txt
index 30eefba2f..e98f7c85e 100644
--- a/doc/Section_accelerate.txt
+++ b/doc/Section_accelerate.txt
@@ -1,524 +1,527 @@
"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Section_howto.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
5. Using accelerated CPU and GPU styles :h3
Accelerated versions of various "pair_style"_pair_style.html,
"fixes"_fix.html, "computes"_compute.html, and other commands have
been added to LAMMPS, which will typically run faster than the
standard non-accelerated versions, if you have the appropriate
hardware on your system.
The accelerated styles have the same name as the standard styles,
except that a suffix is appended. Otherwise, the syntax for the
command is identical, their functionality is the same, and the
numerical results it produces should also be identical, except for
precision and round-off issues.
For example, all of these variants of the basic Lennard-Jones pair
style exist in LAMMPS:
"pair_style lj/cut"_pair_lj.html
"pair_style lj/cut/opt"_pair_lj.html
"pair_style lj/cut/omp"_pair_lj.html
"pair_style lj/cut/gpu"_pair_lj.html
"pair_style lj/cut/cuda"_pair_lj.html :ul
Assuming you have built LAMMPS with the appropriate package, these
styles can be invoked by specifying them explicitly in your input
script. Or you can use the "-suffix command-line
switch"_Section_start.html#start_6 to invoke the accelerated versions
automatically, without changing your input script. The
"suffix"_suffix.html command allows you to set a suffix explicitly and
to turn off/on the comand-line switch setting, both from within your
input script.
Styles with an "opt" suffix are part of the OPT package and typically
speed-up the pairwise calculations of your simulation by 5-25%.
Styles with an "omp" suffix are part of the USER-OMP package and allow
a pair-style to be run in threaded mode using OpenMP. This can be
useful on nodes with high-core counts when using less MPI processes
than cores is advantageous, e.g. when running with PPPM so that FFTs
are run on fewer MPI processors.
Styles with a "gpu" or "cuda" suffix are part of the GPU or USER-CUDA
packages, and can be run on NVIDIA GPUs associated with your CPUs.
The speed-up due to GPU usage depends on a variety of factors, as
discussed below.
To see what styles are currently available in each of the accelerated
packages, see "this section"_Section_commands.html#cmd_5 of the
manual. A list of accelerated styles is included in the pair, fix,
compute, and kspace sections.
The following sections explain:
what hardware and software the accelerated styles require
how to build LAMMPS with the accelerated packages in place
what changes (if any) are needed in your input scripts
guidelines for best performance
speed-ups you can expect :ul
The final section compares and contrasts the GPU and USER-CUDA
packages, since they are both designed to use NVIDIA GPU hardware.
5.1 "OPT package"_#acc_1
5.2 "USER-OMP package"_#acc_2
5.3 "GPU package"_#acc_3
5.4 "USER-CUDA package"_#acc_4
5.5 "Comparison of GPU and USER-CUDA packages"_#acc_5 :all(b)
:line
:line
5.1 OPT package :h4,link(acc_1)
The OPT package was developed by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
Technologies). It contains a handful of pair styles whose compute()
methods were rewritten in C++ templated form to reduce the overhead
due to if tests and other conditional code.
The procedure for building LAMMPS with the OPT package is simple. It
is the same as for any other package which has no additional library
dependencies:
make yes-opt
make machine :pre
If your input script uses one of the OPT pair styles,
you can run it as follows:
lmp_machine -sf opt < in.script
mpirun -np 4 lmp_machine -sf opt < in.script :pre
You should see a reduction in the "Pair time" printed out at the end
of the run. On most machines and problems, this will typically be a 5
to 20% savings.
:line
:line
5.2 USER-OMP package :h4,link(acc_2)
This section will be written when the USER-OMP package is released
in main LAMMPS.
:line
:line
5.3 GPU package :h4,link(acc_3)
The GPU package was developed by Mike Brown at ORNL. It provides GPU
versions of several pair styles and for long-range Coulombics via the
PPPM command. It has the following features:
The package is designed to exploit common GPU hardware configurations
where one or more GPUs are coupled with many cores of a multi-core
CPUs, e.g. within a node of a parallel machine. :ulb,l
Atom-based data (e.g. coordinates, forces) moves back-and-forth
between the CPU(s) and GPU every timestep. :l
Neighbor lists can be constructed on the CPU or on the GPU :l
The charge assignement and force interpolation portions of PPPM can be
run on the GPU. The FFT portion, which requires MPI communication
between processors, runs on the CPU. :l
Asynchronous force computations can be performed simultaneously on the
CPU(s) and GPU. :l
LAMMPS-specific code is in the GPU package. It makes calls to a
generic GPU library in the lib/gpu directory. This library provides
NVIDIA support as well as more general OpenCL support, so that the
same functionality can eventually be supported on a variety of GPU
hardware. :l,ule
[Hardware and software requirements:]
To use this package, you currently need to have specific NVIDIA
hardware and install specific NVIDIA CUDA software on your system:
Check if you have an NVIDIA card: cat /proc/driver/nvidia/cards/0
Go to http://www.nvidia.com/object/cuda_get.html
Install a driver and toolkit appropriate for your system (SDK is not necessary)
Follow the instructions in lammps/lib/gpu/README to build the library (see below)
Run lammps/lib/gpu/nvc_get_devices to list supported devices and properties :ul
[Building LAMMPS with the GPU package:]
As with other packages that include a separately compiled library, you
need to first build the GPU library, before building LAMMPS itself.
General instructions for doing this are in "this
section"_doc/Section_start.html#start_3 of the manual. For this
package, do the following, using a Makefile in lib/gpu appropriate for
your system:
cd lammps/lib/gpu
make -f Makefile.linux
(see further instructions in lammps/lib/gpu/README) :pre
If you are successful, you will produce the file lib/libgpu.a.
Now you are ready to build LAMMPS with the GPU package installed:
cd lammps/src
make yes-gpu
make machine :pre
Note that the lo-level Makefile (e.g. src/MAKE/Makefile.linux) has
these settings: gpu_SYSINC, gpu_SYSLIB, gpu_SYSPATH. These need to be
set appropriately to include the paths and settings for the CUDA
system software on your machine. See src/MAKE/Makefile.g++ for an
example.
[GPU configuration]
When using GPUs, you are restricted to one physical GPU per LAMMPS
process, which is an MPI process running on a single core or
processor. Multiple MPI processes (CPU cores) can share a single GPU,
and in many cases it will be more efficient to run this way.
[Input script requirements:]
Additional input script requirements to run pair or PPPM styles with a
{gpu} suffix are as follows:
To invoke specific styles from the GPU package, you can either append
"gpu" to the style name (e.g. pair_style lj/cut/gpu), or use the
"-suffix command-line switch"_Section_start.html#start_6, or use the
"suffix"_suffix.html command. :ulb,l
The "newton pair"_newton.html setting must be {off}. :l
The "package gpu"_package.html command must be used near the beginning
of your script to control the GPU selection and initialization
settings. It also has an option to enable asynchronous splitting of
force computations between the CPUs and GPUs. :l,ule
As an example, if you have two GPUs per node and 8 CPU cores per node,
and would like to run on 4 nodes (32 cores) with dynamic balancing of
force calculation across CPU and GPU cores, you could specify
package gpu force/neigh 0 1 -1 :pre
In this case, all CPU cores and GPU devices on the nodes would be
utilized. Each GPU device would be shared by 4 CPU cores. The CPU
cores would perform force calculations for some fraction of the
particles at the same time the GPUs performed force calculation for
the other particles.
[Timing output:]
As described by the "package gpu"_package.html command, GPU
accelerated pair styles can perform computations asynchronously with
CPU computations. The "Pair" time reported by LAMMPS will be the
maximum of the time required to complete the CPU pair style
computations and the time required to complete the GPU pair style
computations. Any time spent for GPU-enabled pair styles for
computations that run simultaneously with "bond"_bond_style.html,
"angle"_angle_style.html, "dihedral"_dihedral_style.html,
"improper"_improper_style.html, and "long-range"_kspace_style.html
calculations will not be included in the "Pair" time.
When the {mode} setting for the package gpu command is force/neigh,
the time for neighbor list calculations on the GPU will be added into
the "Pair" time, not the "Neigh" time. An additional breakdown of the
times required for various tasks on the GPU (data copy, neighbor
calculations, force computations, etc) are output only with the LAMMPS
screen output (not in the log file) at the end of each run. These
timings represent total time spent on the GPU for each routine,
regardless of asynchronous CPU calculations.
[Performance tips:]
Generally speaking, for best performance, you should use multiple CPUs
per GPU, as provided my most multi-core CPU/GPU configurations.
Because of the large number of cores within each GPU device, it may be
more efficient to run on fewer processes per GPU when the number of
particles per MPI process is small (100's of particles); this can be
necessary to keep the GPU cores busy.
See the lammps/lib/gpu/README file for instructions on how to build
the GPU library for single, mixed, or double precision. The latter
requires that your GPU card support double precision.
:line
:line
5.4 USER-CUDA package :h4,link(acc_4)
The USER-CUDA package was developed by Christian Trott at U Technology
Ilmenau in Germany. It provides NVIDIA GPU versions of many pair
styles, many fixes, a few computes, and for long-range Coulombics via
the PPPM command. It has the following features:
The package is designed to allow an entire LAMMPS calculation, for
many timesteps, to run entirely on the GPU (except for inter-processor
MPI communication), so that atom-based data (e.g. coordinates, forces)
do not have to move back-and-forth between the CPU and GPU. :ulb,l
+The speed-up advantage of this approach is typically better when the
+number of atoms per GPU is large :l
+
Data will stay on the GPU until a timestep where a non-GPU-ized fix or
compute is invoked. Whenever a non-GPU operation occurs (fix,
compute, output), data automatically moves back to the CPU as needed.
This may incur a performance penalty, but should otherwise work
transparently. :l
Neighbor lists for GPU-ized pair styles are constructed on the
GPU. :l
The package only supports use of a single CPU (core) with each
GPU. :l,ule
[Hardware and software requirements:]
To use this package, you need to have specific NVIDIA hardware and
install specific NVIDIA CUDA software on your system.
Your NVIDIA GPU needs to support Compute Capability 1.3. This list may
help you to find out the Compute Capability of your card:
http://en.wikipedia.org/wiki/Comparison_of_Nvidia_graphics_processing_units
Install the Nvidia Cuda Toolkit in version 3.2 or higher and the
corresponding GPU drivers. The Nvidia Cuda SDK is not required for
LAMMPSCUDA but we recommend it be installed. You can then make sure
that its sample projects can be compiled without problems.
[Building LAMMPS with the USER-CUDA package:]
As with other packages that include a separately compiled library, you
need to first build the USER-CUDA library, before building LAMMPS
itself. General instructions for doing this are in "this
section"_doc/Section_start.html#start_3 of the manual. For this
package, do the following, using settings in the lib/cuda Makefiles
appropriate for your system:
Go to the lammps/lib/cuda directory :ulb,l
If your {CUDA} toolkit is not installed in the default system directoy
{/usr/local/cuda} edit the file {lib/cuda/Makefile.common}
accordingly. :l
Type "make OPTIONS", where {OPTIONS} are one or more of the following
options. The settings will be written to the
{lib/cuda/Makefile.defaults} and used in the next step. :l
{precision=N} to set the precision level
N = 1 for single precision (default)
N = 2 for double precision
N = 3 for positions in double precision
N = 4 for positions and velocities in double precision
{arch=M} to set GPU compute capability
M = 20 for CC2.0 (GF100/110, e.g. C2050,GTX580,GTX470) (default)
M = 21 for CC2.1 (GF104/114, e.g. GTX560, GTX460, GTX450)
M = 13 for CC1.3 (GF200, e.g. C1060, GTX285)
{prec_timer=0/1} to use hi-precision timers
0 = do not use them (default)
1 = use these timers
this is usually only useful for Mac machines
{dbg=0/1} to activate debug mode
0 = no debug mode (default)
1 = yes debug mode
this is only useful for developers
{cufft=1} to determine usage of CUDA FFT library
0 = no CUFFT support (default)
in the future other CUDA-enabled FFT libraries might be supported :pre
Type "make" to build the library. If you are successful, you will
produce the file lib/libcuda.a. :l,ule
Now you are ready to build LAMMPS with the USER-CUDA package installed:
cd lammps/src
make yes-user-cuda
make machine :pre
Note that the LAMMPS build references the lib/cuda/Makefile.common
file to extract setting specific CUDA settings. So it is important
that you have first built the cuda library (in lib/cuda) using
settings appropriate to your system.
[Input script requirements:]
Additional input script requirements to run styles with a {cuda}
suffix are as follows:
To invoke specific styles from the USER-CUDA package, you can either
append "cuda" to the style name (e.g. pair_style lj/cut/cuda), or use
the "-suffix command-line switch"_Section_start.html#start_6, or use
the "suffix"_suffix.html command. One exception is that the
"kspace_style pppm/cuda"_kspace_style.html command has to be requested
explicitly. :ulb,l
To use the USER-CUDA package with its default settings, no additional
command is needed in your input script. This is because when LAMMPS
starts up, it detects if it has been built with the USER-CUDA package.
See the "-cuda command-line switch"_Section_start.html#start_6 for
more details. :l
To change settings for the USER-CUDA package at run-time, the "package
cuda"_package.html command can be used near the beginning of your
input script. See the "package"_package.html command doc page for
details. :l,ule
[Performance tips:]
The USER-CUDA package offers more speed-up relative to CPU performance
when the number of atoms per GPU is large, e.g. on the order of tens
or hundreds of 1000s.
As noted above, this package will continue to run a simulation
entirely on the GPU(s) (except for inter-processor MPI communication),
for multiple timesteps, until a CPU calculation is required, either by
a fix or compute that is non-GPU-ized, or until output is performed
(thermo or dump snapshot or restart file). The less often this
occurs, the faster your simulation will run.
:line
:line
5.5 Comparison of GPU and USER-CUDA packages :h4,link(acc_5)
Both the GPU and USER-CUDA packages accelerate a LAMMPS calculation
using NVIDIA hardware, but they do it in different ways.
As a consequence, for a particular simulation on specific hardware,
one package may be faster than the other. We give guidelines below,
but the best way to determine which package is faster for your input
script is to try both of them on your machine. See the benchmarking
section below for examples where this has been done.
[Guidelines for using each package optimally:]
The GPU package allows you to assign multiple CPUs (cores) to a single
GPU (a common configuration for "hybrid" nodes that contain multicore
CPU(s) and GPU(s)) and works effectively in this mode. The USER-CUDA
package does not allow this; you can only use one CPU per GPU. :ulb,l
The GPU package moves per-atom data (coordinates, forces)
back-and-forth between the CPU and GPU every timestep. The USER-CUDA
package only does this on timesteps when a CPU calculation is required
(e.g. to invoke a fix or compute that is non-GPU-ized). Hence, if you
can formulate your input script to only use GPU-ized fixes and
computes, and avoid doing I/O too often (thermo output, dump file
snapshots, restart files), then the data transfer cost of the
USER-CUDA package can be very low, causing it to run faster than the
GPU package. :l
The GPU package is often faster than the USER-CUDA package, if the
number of atoms per GPU is "small". The crossover point, in terms of
atoms/GPU at which the USER-CUDA package becomes faster depends
strongly on the pair style. For example, for a simple Lennard Jones
system the crossover (in single precision) is often about 50K-100K
atoms per GPU. When performing double precision calculations the
crossover point can be significantly smaller. :l
Both packages compute bonded interactions (bonds, angles, etc) on the
CPU. This means a model with bonds will force the USER-CUDA package
to transfer per-atom data back-and-forth between the CPU and GPU every
timestep. If the GPU package is running with several MPI processes
assigned to one GPU, the cost of computing the bonded interactions is
spread across more CPUs and hence the GPU package can run faster. :l
When using the GPU package with multiple CPUs assigned to one GPU, its
performance depends to some extent on high bandwidth between the CPUs
and the GPU. Hence its performance is affected if full 16 PCIe lanes
are not available for each GPU. In HPC environments this can be the
case if S2050/70 servers are used, where two devices generally share
one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide
full 16 lanes to each of the PCIe 2.0 16x slots. :l,ule
[Differences between the two packages:]
The GPU package accelerates only pair force, neighbor list, and PPPM
calculations. The USER-CUDA package currently supports a wider range
of pair styles and can also accelerate many fix styles and some
compute styles, as well as neighbor list and PPPM calculations. :ulb,l
The GPU package uses more GPU memory than the USER-CUDA package. This
is generally not a problem since typical runs are computation-limited
rather than memory-limited. :l,ule
[Examples:]
The LAMMPS distribution has two directories with sample input scripts
for the GPU and USER-CUDA packages.
lammps/examples/gpu = GPU package files
lammps/examples/USER/cuda = USER-CUDA package files :ul
These contain input scripts for identical systems, so they can be used
to benchmark the performance of both packages on your system.
:line
[Benchmark data:]
NOTE: We plan to add some benchmark results and plots here for the
examples described in the previous section.
Simulations:
1. Lennard Jones
256,000 atoms
2.5 A cutoff
0.844 density :ul
2. Lennard Jones
256,000 atoms
5.0 A cutoff
0.844 density :ul
3. Rhodopsin model
256,000 atoms
10A cutoff
Coulomb via PPPM :ul
4. Lihtium-Phosphate
295650 atoms
15A cutoff
Coulomb via PPPM :ul
Hardware:
Workstation:
2x GTX470
i7 950@3GHz
24Gb DDR3 @ 1066Mhz
CentOS 5.5
CUDA 3.2
Driver 260.19.12 :ul
eStella:
6 Nodes
2xC2050
2xQDR Infiniband interconnect(aggregate bandwidth 80GBps)
Intel X5650 HexCore @ 2.67GHz
SL 5.5
CUDA 3.2
Driver 260.19.26 :ul
Keeneland:
HP SL-390 (Ariston) cluster
120 nodes
2x Intel Westmere hex-core CPUs
3xC2070s
QDR InfiniBand interconnect :ul
diff --git a/doc/Section_commands.html b/doc/Section_commands.html
index eb16907d2..31c0ea631 100644
--- a/doc/Section_commands.html
+++ b/doc/Section_commands.html
@@ -1,565 +1,567 @@
<HTML>
<CENTER><A HREF = "Section_start.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_packages.html">Next Section</A>
</CENTER>
<HR>
<H3>3. Commands
</H3>
<P>This section describes how a LAMMPS input script is formatted and what
commands are used to define a LAMMPS simulation.
</P>
3.1 <A HREF = "#cmd_1">LAMMPS input script</A><BR>
3.2 <A HREF = "#cmd_2">Parsing rules</A><BR>
3.3 <A HREF = "#cmd_3">Input script structure</A><BR>
3.4 <A HREF = "#cmd_4">Commands listed by category</A><BR>
3.5 <A HREF = "#cmd_5">Commands listed alphabetically</A> <BR>
<HR>
<A NAME = "cmd_1"></A><H4>3.1 LAMMPS input script
</H4>
<P>LAMMPS executes by reading commands from a input script (text file),
one line at a time. When the input script ends, LAMMPS exits. Each
command causes LAMMPS to take some action. It may set an internal
variable, read in a file, or run a simulation. Most commands have
default settings, which means you only need to use the command if you
wish to change the default.
</P>
<P>In many cases, the ordering of commands in an input script is not
important. However the following rules apply:
</P>
<P>(1) LAMMPS does not read your entire input script and then perform a
simulation with all the settings. Rather, the input script is read
one line at a time and each command takes effect when it is read.
Thus this sequence of commands:
</P>
<PRE>timestep 0.5
run 100
run 100
</PRE>
<P>does something different than this sequence:
</P>
<PRE>run 100
timestep 0.5
run 100
</PRE>
<P>In the first case, the specified timestep (0.5 fmsec) is used for two
simulations of 100 timesteps each. In the 2nd case, the default
timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5
fmsec timestep is used for the 2nd one.
</P>
<P>(2) Some commands are only valid when they follow other commands. For
example you cannot set the temperature of a group of atoms until atoms
have been defined and a group command is used to define which atoms
belong to the group.
</P>
<P>(3) Sometimes command B will use values that can be set by command A.
This means command A must precede command B in the input script if it
is to have the desired effect. For example, the
<A HREF = "read_data.html">read_data</A> command initializes the system by setting
up the simulation box and assigning atoms to processors. If default
values are not desired, the <A HREF = "processors.html">processors</A> and
<A HREF = "boundary.html">boundary</A> commands need to be used before read_data to
tell LAMMPS how to map processors to the simulation box.
</P>
<P>Many input script errors are detected by LAMMPS and an ERROR or
WARNING message is printed. <A HREF = "Section_errors.html">This section</A> gives
more information on what errors mean. The documentation for each
command lists restrictions on how the command can be used.
</P>
<HR>
<A NAME = "cmd_2"></A><H4>3.2 Parsing rules
</H4>
<P>Each non-blank line in the input script is treated as a command.
LAMMPS commands are case sensitive. Command names are lower-case, as
are specified command arguments. Upper case letters may be used in
file names or user-chosen ID strings.
</P>
<P>Here is how each line in the input script is parsed by LAMMPS:
</P>
<P>(1) If the last printable character on the line is a "&" character
(with no surrounding quotes), the command is assumed to continue on
the next line. The next line is concatenated to the previous line by
removing the "&" character and newline. This allows long commands to
be continued across two or more lines.
</P>
<P>(2) All characters from the first "#" character onward are treated as
comment and discarded. See an exception in (6). Note that a
comment after a trailing "&" character will prevent the command from
continuing on the next line. Also note that for multi-line commands a
single leading "#" will comment out the entire command.
</P>
<P>(3) The line is searched repeatedly for $ characters, which indicate
variables that are replaced with a text string. See an exception in
(6). If the $ is followed by curly brackets, then the variable name
is the text inside the curly brackets. If no curly brackets follow
the $, then the variable name is the single character immediately
following the $. Thus ${myTemp} and $x refer to variable names
"myTemp" and "x". See the <A HREF = "variable.html">variable</A> command for
details of how strings are assigned to variables and how they are
substituted for in input script commands.
</P>
<P>(4) The line is broken into "words" separated by whitespace (tabs,
spaces). Note that words can thus contain letters, digits,
underscores, or punctuation characters.
</P>
<P>(5) The first word is the command name. All successive words in the
line are arguments.
</P>
<P>(6) If you want text with spaces to be treated as a single argument,
it can be enclosed in either double or single quotes. E.g.
</P>
<PRE>print "Volume = $v"
print 'Volume = $v'
</PRE>
<P>The quotes are removed when the single argument is stored internally.
See the <A HREF = "dump_modify.html">dump modify format</A> or <A HREF = "if.html">if</A> commands
for examples. A "#" or "$" character that is between quotes will not
be treated as a comment indicator in (2) or substituted for as a
variable in (3).
</P>
<P>IMPORTANT NOTE: If the argument is itself a command that requires a
quoted argument (e.g. using a <A HREF = "print.html">print</A> command as part of an
<A HREF = "if.html">if</A> or <A HREF = "run.html">run every</A> command), then the double and
single quotes can be nested in the usual manner. See the doc pages
for those commands for examples. Only one of level of nesting is
allowed, but that should be sufficient for most use cases.
</P>
<HR>
<H4><A NAME = "cmd_3"></A>3.3 Input script structure
</H4>
<P>This section describes the structure of a typical LAMMPS input script.
The "examples" directory in the LAMMPS distribution contains many
sample input scripts; the corresponding problems are discussed in
<A HREF = "Section_example.html">this section</A>, and animated on the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW
Site</A>.
</P>
<P>A LAMMPS input script typically has 4 parts:
</P>
<OL><LI>Initialization
<LI>Atom definition
<LI>Settings
<LI>Run a simulation
</OL>
<P>The last 2 parts can be repeated as many times as desired. I.e. run a
simulation, change some settings, run some more, etc. Each of the 4
parts is now described in more detail. Remember that almost all the
commands need only be used if a non-default value is desired.
</P>
<P>(1) Initialization
</P>
<P>Set parameters that need to be defined before atoms are created or
read-in from a file.
</P>
<P>The relevant commands are <A HREF = "units.html">units</A>,
<A HREF = "dimension.html">dimension</A>, <A HREF = "newton.html">newton</A>,
<A HREF = "processors.html">processors</A>, <A HREF = "boundary.html">boundary</A>,
<A HREF = "atom_style.html">atom_style</A>, <A HREF = "atom_modify.html">atom_modify</A>.
</P>
<P>If force-field parameters appear in the files that will be read, these
commands tell LAMMPS what kinds of force fields are being used:
<A HREF = "pair_style.html">pair_style</A>, <A HREF = "bond_style.html">bond_style</A>,
<A HREF = "angle_style.html">angle_style</A>, <A HREF = "dihedral_style.html">dihedral_style</A>,
<A HREF = "improper_style.html">improper_style</A>.
</P>
<P>(2) Atom definition
</P>
<P>There are 3 ways to define atoms in LAMMPS. Read them in from a data
or restart file via the <A HREF = "read_data.html">read_data</A> or
<A HREF = "read_restart.html">read_restart</A> commands. These files can contain
molecular topology information. Or create atoms on a lattice (with no
molecular topology), using these commands: <A HREF = "lattice.html">lattice</A>,
<A HREF = "region.html">region</A>, <A HREF = "create_box.html">create_box</A>,
<A HREF = "create_atoms.html">create_atoms</A>. The entire set of atoms can be
duplicated to make a larger simulation using the
<A HREF = "replicate.html">replicate</A> command.
</P>
<P>(3) Settings
</P>
<P>Once atoms and molecular topology are defined, a variety of settings
can be specified: force field coefficients, simulation parameters,
output options, etc.
</P>
<P>Force field coefficients are set by these commands (they can also be
set in the read-in files): <A HREF = "pair_coeff.html">pair_coeff</A>,
<A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "angle_coeff.html">angle_coeff</A>,
<A HREF = "dihedral_coeff.html">dihedral_coeff</A>,
<A HREF = "improper_coeff.html">improper_coeff</A>,
<A HREF = "kspace_style.html">kspace_style</A>, <A HREF = "dielectric.html">dielectric</A>,
<A HREF = "special_bonds.html">special_bonds</A>.
</P>
<P>Various simulation parameters are set by these commands:
<A HREF = "neighbor.html">neighbor</A>, <A HREF = "neigh_modify.html">neigh_modify</A>,
<A HREF = "group.html">group</A>, <A HREF = "timestep.html">timestep</A>,
<A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "run_style.html">run_style</A>,
<A HREF = "min_style.html">min_style</A>, <A HREF = "min_modify.html">min_modify</A>.
</P>
<P>Fixes impose a variety of boundary conditions, time integration, and
diagnostic options. The <A HREF = "fix.html">fix</A> command comes in many flavors.
</P>
<P>Various computations can be specified for execution during a
simulation using the <A HREF = "compute.html">compute</A>,
<A HREF = "compute_modify.html">compute_modify</A>, and <A HREF = "variable.html">variable</A>
commands.
</P>
<P>Output options are set by the <A HREF = "thermo.html">thermo</A>, <A HREF = "dump.html">dump</A>,
and <A HREF = "restart.html">restart</A> commands.
</P>
<P>(4) Run a simulation
</P>
<P>A molecular dynamics simulation is run using the <A HREF = "run.html">run</A>
command. Energy minimization (molecular statics) is performed using
the <A HREF = "minimize.html">minimize</A> command. A parallel tempering
(replica-exchange) simulation can be run using the
<A HREF = "temper.html">temper</A> command.
</P>
<HR>
<A NAME = "cmd_4"></A><H4>3.4 Commands listed by category
</H4>
<P>This section lists all LAMMPS commands, grouped by category. The
<A HREF = "#cmd_5">next section</A> lists the same commands alphabetically. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command's documentation.
</P>
<P>Initialization:
</P>
<P><A HREF = "atom_modify.html">atom_modify</A>, <A HREF = "atom_style.html">atom_style</A>,
<A HREF = "boundary.html">boundary</A>, <A HREF = "dimension.html">dimension</A>,
<A HREF = "newton.html">newton</A>, <A HREF = "processors.html">processors</A>, <A HREF = "units.html">units</A>
</P>
<P>Atom definition:
</P>
<P><A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "create_box.html">create_box</A>,
<A HREF = "lattice.html">lattice</A>, <A HREF = "read_data.html">read_data</A>,
<A HREF = "read_restart.html">read_restart</A>, <A HREF = "region.html">region</A>,
<A HREF = "replicate.html">replicate</A>
</P>
<P>Force fields:
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>, <A HREF = "angle_style.html">angle_style</A>,
<A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "bond_style.html">bond_style</A>,
<A HREF = "dielectric.html">dielectric</A>, <A HREF = "dihedral_coeff.html">dihedral_coeff</A>,
<A HREF = "dihedral_style.html">dihedral_style</A>,
<A HREF = "improper_coeff.html">improper_coeff</A>,
<A HREF = "improper_style.html">improper_style</A>,
<A HREF = "kspace_modify.html">kspace_modify</A>, <A HREF = "kspace_style.html">kspace_style</A>,
<A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_modify.html">pair_modify</A>,
<A HREF = "pair_style.html">pair_style</A>, <A HREF = "pair_write.html">pair_write</A>,
<A HREF = "special_bonds.html">special_bonds</A>
</P>
<P>Settings:
</P>
<P><A HREF = "communicate.html">communicate</A>, <A HREF = "group.html">group</A>, <A HREF = "mass.html">mass</A>,
<A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_style.html">min_style</A>,
<A HREF = "neigh_modify.html">neigh_modify</A>, <A HREF = "neighbor.html">neighbor</A>,
<A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "run_style.html">run_style</A>,
<A HREF = "set.html">set</A>, <A HREF = "timestep.html">timestep</A>, <A HREF = "velocity.html">velocity</A>
</P>
<P>Fixes:
</P>
<P><A HREF = "fix.html">fix</A>, <A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "unfix.html">unfix</A>
</P>
<P>Computes:
</P>
<P><A HREF = "compute.html">compute</A>, <A HREF = "compute_modify.html">compute_modify</A>,
<A HREF = "uncompute.html">uncompute</A>
</P>
<P>Output:
</P>
<P><A HREF = "dump.html">dump</A>, <A HREF = "dump_image.html">dump image</A>,
<A HREF = "dump_modify.html">dump_modify</A>, <A HREF = "restart.html">restart</A>,
<A HREF = "thermo.html">thermo</A>, <A HREF = "thermo_modify.html">thermo_modify</A>,
<A HREF = "thermo_style.html">thermo_style</A>, <A HREF = "undump.html">undump</A>,
<A HREF = "write_restart.html">write_restart</A>
</P>
<P>Actions:
</P>
<P><A HREF = "delete_atoms.html">delete_atoms</A>, <A HREF = "delete_bonds.html">delete_bonds</A>,
<A HREF = "displace_atoms.html">displace_atoms</A>,
<A HREF = "displace_box.html">displace_box</A>, <A HREF = "minimize.html">minimize</A>,
<A HREF = "neb.html">neb</A> <A HREF = "prd.html">prd</A>, <A HREF = "run.html">run</A>, <A HREF = "temper.html">temper</A>
</P>
<P>Miscellaneous:
</P>
<P><A HREF = "clear.html">clear</A>, <A HREF = "echo.html">echo</A>, <A HREF = "if.html">if</A>,
<A HREF = "include.html">include</A>, <A HREF = "jump.html">jump</A>, <A HREF = "label.html">label</A>,
<A HREF = "log.html">log</A>, <A HREF = "next.html">next</A>, <A HREF = "print.html">print</A>,
<A HREF = "shell.html">shell</A>, <A HREF = "variable.html">variable</A>
</P>
<HR>
<H4><A NAME = "cmd_5"></A><A NAME = "comm"></A>3.5 Individual commands
</H4>
<P>This section lists all LAMMPS commands alphabetically, with a separate
listing below of styles within certain commands. The <A HREF = "#cmd_4">previous
section</A> lists the same commands, grouped by category. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command's documentation.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "angle_coeff.html">angle_coeff</A></TD><TD ><A HREF = "angle_style.html">angle_style</A></TD><TD ><A HREF = "atom_modify.html">atom_modify</A></TD><TD ><A HREF = "atom_style.html">atom_style</A></TD><TD ><A HREF = "bond_coeff.html">bond_coeff</A></TD><TD ><A HREF = "bond_style.html">bond_style</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "boundary.html">boundary</A></TD><TD ><A HREF = "change_box.html">change_box</A></TD><TD ><A HREF = "clear.html">clear</A></TD><TD ><A HREF = "communicate.html">communicate</A></TD><TD ><A HREF = "compute.html">compute</A></TD><TD ><A HREF = "compute_modify.html">compute_modify</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "create_atoms.html">create_atoms</A></TD><TD ><A HREF = "create_box.html">create_box</A></TD><TD ><A HREF = "delete_atoms.html">delete_atoms</A></TD><TD ><A HREF = "delete_bonds.html">delete_bonds</A></TD><TD ><A HREF = "dielectric.html">dielectric</A></TD><TD ><A HREF = "dihedral_coeff.html">dihedral_coeff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "dihedral_style.html">dihedral_style</A></TD><TD ><A HREF = "dimension.html">dimension</A></TD><TD ><A HREF = "displace_atoms.html">displace_atoms</A></TD><TD ><A HREF = "displace_box.html">displace_box</A></TD><TD ><A HREF = "dump.html">dump</A></TD><TD ><A HREF = "dump_image.html">dump image</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "dump_modify.html">dump_modify</A></TD><TD ><A HREF = "echo.html">echo</A></TD><TD ><A HREF = "fix.html">fix</A></TD><TD ><A HREF = "fix_modify.html">fix_modify</A></TD><TD ><A HREF = "group.html">group</A></TD><TD ><A HREF = "if.html">if</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "improper_coeff.html">improper_coeff</A></TD><TD ><A HREF = "improper_style.html">improper_style</A></TD><TD ><A HREF = "include.html">include</A></TD><TD ><A HREF = "jump.html">jump</A></TD><TD ><A HREF = "kspace_modify.html">kspace_modify</A></TD><TD ><A HREF = "kspace_style.html">kspace_style</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "label.html">label</A></TD><TD ><A HREF = "lattice.html">lattice</A></TD><TD ><A HREF = "log.html">log</A></TD><TD ><A HREF = "mass.html">mass</A></TD><TD ><A HREF = "minimize.html">minimize</A></TD><TD ><A HREF = "min_modify.html">min_modify</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "min_style.html">min_style</A></TD><TD ><A HREF = "neb.html">neb</A></TD><TD ><A HREF = "neigh_modify.html">neigh_modify</A></TD><TD ><A HREF = "neighbor.html">neighbor</A></TD><TD ><A HREF = "newton.html">newton</A></TD><TD ><A HREF = "next.html">next</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "package.html">package</A></TD><TD ><A HREF = "pair_coeff.html">pair_coeff</A></TD><TD ><A HREF = "pair_modify.html">pair_modify</A></TD><TD ><A HREF = "pair_style.html">pair_style</A></TD><TD ><A HREF = "pair_write.html">pair_write</A></TD><TD ><A HREF = "prd.html">prd</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "print.html">print</A></TD><TD ><A HREF = "processors.html">processors</A></TD><TD ><A HREF = "read_data.html">read_data</A></TD><TD ><A HREF = "read_restart.html">read_restart</A></TD><TD ><A HREF = "region.html">region</A></TD><TD ><A HREF = "replicate.html">replicate</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "reset_timestep.html">reset_timestep</A></TD><TD ><A HREF = "restart.html">restart</A></TD><TD ><A HREF = "run.html">run</A></TD><TD ><A HREF = "run_style.html">run_style</A></TD><TD ><A HREF = "set.html">set</A></TD><TD ><A HREF = "shell.html">shell</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "special_bonds.html">special_bonds</A></TD><TD ><A HREF = "suffix.html">suffix</A></TD><TD ><A HREF = "tad.html">tad</A></TD><TD ><A HREF = "temper.html">temper</A></TD><TD ><A HREF = "thermo.html">thermo</A></TD><TD ><A HREF = "thermo_modify.html">thermo_modify</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "thermo_style.html">thermo_style</A></TD><TD ><A HREF = "timestep.html">timestep</A></TD><TD ><A HREF = "uncompute.html">uncompute</A></TD><TD ><A HREF = "undump.html">undump</A></TD><TD ><A HREF = "unfix.html">unfix</A></TD><TD ><A HREF = "units.html">units</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "variable.html">variable</A></TD><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_restart.html">write_restart</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Fix styles
</H4>
<P>See the <A HREF = "fix.html">fix</A> command for one-line descriptions
of each style or click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_adapt.html">adapt</A></TD><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_ave_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_correlate.html">ave/correlate</A></TD><TD ><A HREF = "fix_ave_histo.html">ave/histo</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_bond_break.html">bond/break</A></TD><TD ><A HREF = "fix_bond_create.html">bond/create</A></TD><TD ><A HREF = "fix_bond_swap.html">bond/swap</A></TD><TD ><A HREF = "fix_box_relax.html">box/relax</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_evaporate.html">evaporate</A></TD><TD ><A HREF = "fix_external.html">external</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gcmc.html">gcmc</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_move.html">move</A></TD><TD ><A HREF = "fix_msst.html">msst</A></TD><TD ><A HREF = "fix_neb.html">neb</A></TD><TD ><A HREF = "fix_nh.html">nph</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nph_asphere.html">nph/asphere</A></TD><TD ><A HREF = "fix_nph_sphere.html">nph/sphere</A></TD><TD ><A HREF = "fix_nh.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_npt_sphere.html">npt/sphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</A></TD><TD ><A HREF = "fix_nh.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_qeq_comb.html">qeq/comb</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_restrain.html">restrain</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nve</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nvt</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_srd.html">srd</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_store_state.html">store/state</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_region.html">wall/region</A></TD><TD ><A HREF = "fix_wall_srd.html">wall/srd</A>
</TD></TR></TABLE></DIV>
<P>These are fix styles contributed by users, which can be used if
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A>
+<TR ALIGN="center"><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD><TD ><A HREF = "fix_meso.html">meso</A></TD><TD ><A HREF = "fix_meso_stationary.html">meso/stationary</A></TD><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A>
</TD></TR></TABLE></DIV>
<P>These are accelerated fix styles, which can be used if LAMMPS is
built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_freeze.html">freeze/cuda</A></TD><TD ><A HREF = "fix_addforce.html">addforce/cuda</A></TD><TD ><A HREF = "fix_addtorque.html">addtorque</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce/cuda</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d/cuda</A></TD><TD ><A HREF = "fix_gravity.html">gravity/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nh.html">npt/cuda</A></TD><TD ><A HREF = "fix_nh.html">nve/cuda</A></TD><TD ><A HREF = "fix_nh.html">nvt/cuda</A></TD><TD ><A HREF = "fix_setforce.html">setforce/cuda</A></TD><TD ><A HREF = "fix_shake.html">shake/cuda</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale.html">temp/rescale/cuda</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale/limit/cuda</A></TD><TD ><A HREF = "fix_viscous.html">viscous/cuda</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Compute styles
</H4>
<P>See the <A HREF = "compute.html">compute</A> command for one-line descriptions of
each style or click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_angle_local.html">angle/local</A></TD><TD ><A HREF = "compute_atom_molecule.html">atom/molecule</A></TD><TD ><A HREF = "compute_bond_local.html">bond/local</A></TD><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_cluster_atom.html">cluster/atom</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_com.html">com</A></TD><TD ><A HREF = "compute_com_molecule.html">com/molecule</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD><TD ><A HREF = "compute_dihedral_local.html">dihedral/local</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_gyration_molecule.html">gyration/molecule</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_msd_molecule.html">msd/molecule</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_pair.html">pair</A></TD><TD ><A HREF = "compute_pair_local.html">pair/local</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_property_local.html">property/local</A></TD><TD ><A HREF = "compute_property_molecule.html">property/molecule</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_slice.html">slice</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A></TD><TD ><A HREF = "compute_ti.html">ti</A>
</TD></TR></TABLE></DIV>
<P>These are compute styles contributed by users, which can be used if
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
-<TR ALIGN="center"><TD ><A HREF = "compute_ackland_atom.html">ackland/atom</A></TD><TD ><A HREF = "compute_ke_eff.html">ke/eff</A></TD><TD ><A HREF = "compute_ke_atom_eff.html">ke/atom/eff</A></TD><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_temp_rotate.html">temp/rotate</A>
+<TR ALIGN="center"><TD ><A HREF = "compute_ackland_atom.html">ackland/atom</A></TD><TD ><A HREF = "compute_ke_eff.html">ke/eff</A></TD><TD ><A HREF = "compute_ke_atom_eff.html">ke/atom/eff</A></TD><TD ><A HREF = "compute_meso_e_atom.html">meso_e/atom</A></TD><TD ><A HREF = "compute_meso_rho_atom.html">meso_rho/atom</A></TD><TD ><A HREF = "compute_meso_t_atom.html">meso_t/atom</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A></TD><TD ><A HREF = "compute_temp_rotate.html">temp/rotate</A>
</TD></TR></TABLE></DIV>
<P>These are accelerated compute styles, which can be used if LAMMPS is
built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_pe.html">pe/cuda</A></TD><TD ><A HREF = "compute_pressure.html">pressure/cuda</A></TD><TD ><A HREF = "compute_temp.html">temp/cuda</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial/cuda</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Pair_style potentials
</H4>
<P>See the <A HREF = "pair_style.html">pair_style</A> command for an overview of pair
potentials. Click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_none.html">none</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid/overlay</A></TD><TD ><A HREF = "pair_adp.html">adp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_airebo.html">airebo</A></TD><TD ><A HREF = "pair_born.html">born</A></TD><TD ><A HREF = "pair_born.html">born/coul/long</A></TD><TD ><A HREF = "pair_buck.html">buck</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/cut</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long</A></TD><TD ><A HREF = "pair_colloid.html">colloid</A></TD><TD ><A HREF = "pair_comb.html">comb</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/cut</A></TD><TD ><A HREF = "pair_coul.html">coul/debye</A></TD><TD ><A HREF = "pair_coul.html">coul/long</A></TD><TD ><A HREF = "pair_dipole.html">dipole/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_dpd.html">dpd</A></TD><TD ><A HREF = "pair_dpd.html">dpd/tstat</A></TD><TD ><A HREF = "pair_dsmc.html">dsmc</A></TD><TD ><A HREF = "pair_eam.html">eam</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy</A></TD><TD ><A HREF = "pair_eam.html">eam/fs</A></TD><TD ><A HREF = "pair_eim.html">eim</A></TD><TD ><A HREF = "pair_gauss.html">gauss</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gayberne.html">gayberne</A></TD><TD ><A HREF = "pair_gran.html">gran/hertz/history</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long</A></TD><TD ><A HREF = "pair_class2.html">lj/class2</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_peri.html">peri/lps</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_airebo.html">rebo</A></TD><TD ><A HREF = "pair_resquared.html">resquared</A></TD><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
</TD></TR></TABLE></DIV>
<P>These are pair styles contributed by users, which can be used if
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_awpmd.html">awpmd/cut</A></TD><TD ><A HREF = "pair_buck_coul.html">buck/coul</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/long</A></TD><TD ><A HREF = "pair_dipole.html">dipole/sf</A></TD><TD ><A HREF = "pair_eam.html">eam/cd</A></TD><TD ><A HREF = "pair_eff.html">eff/cut</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_lj_coul.html">lj/coul</A></TD><TD ><A HREF = "pair_lj_sf.html">lj/sf</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A>
+<TR ALIGN="center"><TD ><A HREF = "pair_lj_coul.html">lj/coul</A></TD><TD ><A HREF = "pair_lj_sf.html">lj/sf</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A><A HREF = "pair_heatconduction.html">sph/heatconduction</A></TD><TD ><A HREF = "pair_idealgas.html">sph/idealgas</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">sph/lj</A></TD><TD ><A HREF = "pair_rhosum.html">sph/rhosum</A></TD><TD ><A HREF = "pair_taitwater.html">sph/taitwater</A></TD><TD ><A HREF = "pair_taitwater_morris.html">sph/taitwater/morris</A>
</TD></TR></TABLE></DIV>
<P>These are accelerated pair styles, which can be used if LAMMPS is
built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born/coul/long/cuda</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut/cuda</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long/cuda</A></TD><TD ><A HREF = "pair_buck.html">buck/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/cut/cuda</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/debye/cuda</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/long/cuda</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/coul/long/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_cmm.html">cg/cmm/cuda</A></TD><TD ><A HREF = "pair_cmm.html">cg/cmm/gpu</A></TD><TD ><A HREF = "pair_coul.html">coul/long/gpu</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/cuda</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/cuda</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/opt</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne/gpu</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/gpu</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/gpu</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/experimental/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/cuda</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs/cuda</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/cuda</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth/cuda</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj96.html">lj96/cut/gpu</A></TD><TD ><A HREF = "pair_morse.html">morse/cuda</A></TD><TD ><A HREF = "pair_morse.html">morse/gpu</A></TD><TD ><A HREF = "pair_morse.html">morse/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_resquared.html">resquared/gpu</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Bond_style potentials
</H4>
<P>See the <A HREF = "bond_style.html">bond_style</A> command for an overview of bond
potentials. Click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_none.html">none</A></TD><TD WIDTH="100"><A HREF = "bond_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "bond_class2.html">class2</A></TD><TD WIDTH="100"><A HREF = "bond_fene.html">fene</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_fene_expand.html">fene/expand</A></TD><TD WIDTH="100"><A HREF = "bond_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "bond_morse.html">morse</A></TD><TD WIDTH="100"><A HREF = "bond_nonlinear.html">nonlinear</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_quartic.html">quartic</A></TD><TD WIDTH="100"><A HREF = "bond_table.html">table</A>
</TD></TR></TABLE></DIV>
<P>These are bond styles contributed by users, which can be used if
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "bond_harmonic_shift.html">harmonic/shift</A></TD><TD ><A HREF = "bond_harmonic_shift_cut.html">harmonic/shift/cut</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Angle_style potentials
</H4>
<P>See the <A HREF = "angle_style.html">angle_style</A> command for an overview of
angle potentials. Click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_none.html">none</A></TD><TD WIDTH="100"><A HREF = "angle_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "angle_charmm.html">charmm</A></TD><TD WIDTH="100"><A HREF = "angle_class2.html">class2</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_cosine.html">cosine</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_delta.html">cosine/delta</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_periodic.html">cosine/periodic</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_squared.html">cosine/squared</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "angle_table.html">table</A>
</TD></TR></TABLE></DIV>
<P>These are angle styles contributed by users, which can be used if
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "angle_cmm.html">cg/cmm</A></TD><TD ><A HREF = "angle_cosine_shift.html">cosine/shift</A></TD><TD ><A HREF = "angle_cosine_shift_exp.html">cosine/shift/exp</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Dihedral_style potentials
</H4>
<P>See the <A HREF = "dihedral_style.html">dihedral_style</A> command for an overview
of dihedral potentials. Click on the style itself for a full
description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_none.html">none</A></TD><TD WIDTH="100"><A HREF = "dihedral_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "dihedral_charmm.html">charmm</A></TD><TD WIDTH="100"><A HREF = "dihedral_class2.html">class2</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "dihedral_helix.html">helix</A></TD><TD WIDTH="100"><A HREF = "dihedral_multi_harmonic.html">multi/harmonic</A></TD><TD WIDTH="100"><A HREF = "dihedral_opls.html">opls</A>
</TD></TR></TABLE></DIV>
<P>These are dihedral styles contributed by users, which can be used if
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "dihedral_cosine_shift_exp.html">cosine/shift/exp</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Improper_style potentials
</H4>
<P>See the <A HREF = "improper_style.html">improper_style</A> command for an overview
of improper potentials. Click on the style itself for a full
description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_none.html">none</A></TD><TD WIDTH="100"><A HREF = "improper_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "improper_class2.html">class2</A></TD><TD WIDTH="100"><A HREF = "improper_cvff.html">cvff</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "improper_umbrella.html">umbrella</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Kspace solvers
</H4>
<P>See the <A HREF = "kspace_style.html">kspace_style</A> command for an overview of
Kspace solvers. Click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "kspace_style.html">ewald</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">pppm</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">pppm/cg</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">pppm/tip4p</A>
</TD></TR></TABLE></DIV>
<P>These are Kspace solvers contributed by users, which can be used if
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "kspace_style.html">ewald/n</A>
</TD></TR></TABLE></DIV>
<P>These are accelerated Kspace solvers, which can be used if LAMMPS is
built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">pppm/cuda</A></TD><TD ><A HREF = "kspace_style.html">pppm/gpu</A>
</TD></TR></TABLE></DIV>
</HTML>
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt
index 496a5582f..9ff3449d5 100644
--- a/doc/Section_commands.txt
+++ b/doc/Section_commands.txt
@@ -1,846 +1,857 @@
"Previous Section"_Section_start.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_packages.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
3. Commands :h3
This section describes how a LAMMPS input script is formatted and what
commands are used to define a LAMMPS simulation.
3.1 "LAMMPS input script"_#cmd_1
3.2 "Parsing rules"_#cmd_2
3.3 "Input script structure"_#cmd_3
3.4 "Commands listed by category"_#cmd_4
3.5 "Commands listed alphabetically"_#cmd_5 :all(b)
:line
3.1 LAMMPS input script :link(cmd_1),h4
LAMMPS executes by reading commands from a input script (text file),
one line at a time. When the input script ends, LAMMPS exits. Each
command causes LAMMPS to take some action. It may set an internal
variable, read in a file, or run a simulation. Most commands have
default settings, which means you only need to use the command if you
wish to change the default.
In many cases, the ordering of commands in an input script is not
important. However the following rules apply:
(1) LAMMPS does not read your entire input script and then perform a
simulation with all the settings. Rather, the input script is read
one line at a time and each command takes effect when it is read.
Thus this sequence of commands:
timestep 0.5
run 100
run 100 :pre
does something different than this sequence:
run 100
timestep 0.5
run 100 :pre
In the first case, the specified timestep (0.5 fmsec) is used for two
simulations of 100 timesteps each. In the 2nd case, the default
timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5
fmsec timestep is used for the 2nd one.
(2) Some commands are only valid when they follow other commands. For
example you cannot set the temperature of a group of atoms until atoms
have been defined and a group command is used to define which atoms
belong to the group.
(3) Sometimes command B will use values that can be set by command A.
This means command A must precede command B in the input script if it
is to have the desired effect. For example, the
"read_data"_read_data.html command initializes the system by setting
up the simulation box and assigning atoms to processors. If default
values are not desired, the "processors"_processors.html and
"boundary"_boundary.html commands need to be used before read_data to
tell LAMMPS how to map processors to the simulation box.
Many input script errors are detected by LAMMPS and an ERROR or
WARNING message is printed. "This section"_Section_errors.html gives
more information on what errors mean. The documentation for each
command lists restrictions on how the command can be used.
:line
3.2 Parsing rules :link(cmd_2),h4
Each non-blank line in the input script is treated as a command.
LAMMPS commands are case sensitive. Command names are lower-case, as
are specified command arguments. Upper case letters may be used in
file names or user-chosen ID strings.
Here is how each line in the input script is parsed by LAMMPS:
(1) If the last printable character on the line is a "&" character
(with no surrounding quotes), the command is assumed to continue on
the next line. The next line is concatenated to the previous line by
removing the "&" character and newline. This allows long commands to
be continued across two or more lines.
(2) All characters from the first "#" character onward are treated as
comment and discarded. See an exception in (6). Note that a
comment after a trailing "&" character will prevent the command from
continuing on the next line. Also note that for multi-line commands a
single leading "#" will comment out the entire command.
(3) The line is searched repeatedly for $ characters, which indicate
variables that are replaced with a text string. See an exception in
(6). If the $ is followed by curly brackets, then the variable name
is the text inside the curly brackets. If no curly brackets follow
the $, then the variable name is the single character immediately
following the $. Thus $\{myTemp\} and $x refer to variable names
"myTemp" and "x". See the "variable"_variable.html command for
details of how strings are assigned to variables and how they are
substituted for in input script commands.
(4) The line is broken into "words" separated by whitespace (tabs,
spaces). Note that words can thus contain letters, digits,
underscores, or punctuation characters.
(5) The first word is the command name. All successive words in the
line are arguments.
(6) If you want text with spaces to be treated as a single argument,
it can be enclosed in either double or single quotes. E.g.
print "Volume = $v"
print 'Volume = $v' :pre
The quotes are removed when the single argument is stored internally.
See the "dump modify format"_dump_modify.html or "if"_if.html commands
for examples. A "#" or "$" character that is between quotes will not
be treated as a comment indicator in (2) or substituted for as a
variable in (3).
IMPORTANT NOTE: If the argument is itself a command that requires a
quoted argument (e.g. using a "print"_print.html command as part of an
"if"_if.html or "run every"_run.html command), then the double and
single quotes can be nested in the usual manner. See the doc pages
for those commands for examples. Only one of level of nesting is
allowed, but that should be sufficient for most use cases.
:line
3.3 Input script structure :h4,link(cmd_3)
This section describes the structure of a typical LAMMPS input script.
The "examples" directory in the LAMMPS distribution contains many
sample input scripts; the corresponding problems are discussed in
"this section"_Section_example.html, and animated on the "LAMMPS WWW
Site"_lws.
A LAMMPS input script typically has 4 parts:
Initialization
Atom definition
Settings
Run a simulation :ol
The last 2 parts can be repeated as many times as desired. I.e. run a
simulation, change some settings, run some more, etc. Each of the 4
parts is now described in more detail. Remember that almost all the
commands need only be used if a non-default value is desired.
(1) Initialization
Set parameters that need to be defined before atoms are created or
read-in from a file.
The relevant commands are "units"_units.html,
"dimension"_dimension.html, "newton"_newton.html,
"processors"_processors.html, "boundary"_boundary.html,
"atom_style"_atom_style.html, "atom_modify"_atom_modify.html.
If force-field parameters appear in the files that will be read, these
commands tell LAMMPS what kinds of force fields are being used:
"pair_style"_pair_style.html, "bond_style"_bond_style.html,
"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html,
"improper_style"_improper_style.html.
(2) Atom definition
There are 3 ways to define atoms in LAMMPS. Read them in from a data
or restart file via the "read_data"_read_data.html or
"read_restart"_read_restart.html commands. These files can contain
molecular topology information. Or create atoms on a lattice (with no
molecular topology), using these commands: "lattice"_lattice.html,
"region"_region.html, "create_box"_create_box.html,
"create_atoms"_create_atoms.html. The entire set of atoms can be
duplicated to make a larger simulation using the
"replicate"_replicate.html command.
(3) Settings
Once atoms and molecular topology are defined, a variety of settings
can be specified: force field coefficients, simulation parameters,
output options, etc.
Force field coefficients are set by these commands (they can also be
set in the read-in files): "pair_coeff"_pair_coeff.html,
"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html,
"dihedral_coeff"_dihedral_coeff.html,
"improper_coeff"_improper_coeff.html,
"kspace_style"_kspace_style.html, "dielectric"_dielectric.html,
"special_bonds"_special_bonds.html.
Various simulation parameters are set by these commands:
"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,
"group"_group.html, "timestep"_timestep.html,
"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
"min_style"_min_style.html, "min_modify"_min_modify.html.
Fixes impose a variety of boundary conditions, time integration, and
diagnostic options. The "fix"_fix.html command comes in many flavors.
Various computations can be specified for execution during a
simulation using the "compute"_compute.html,
"compute_modify"_compute_modify.html, and "variable"_variable.html
commands.
Output options are set by the "thermo"_thermo.html, "dump"_dump.html,
and "restart"_restart.html commands.
(4) Run a simulation
A molecular dynamics simulation is run using the "run"_run.html
command. Energy minimization (molecular statics) is performed using
the "minimize"_minimize.html command. A parallel tempering
(replica-exchange) simulation can be run using the
"temper"_temper.html command.
:line
3.4 Commands listed by category :link(cmd_4),h4
This section lists all LAMMPS commands, grouped by category. The
"next section"_#cmd_5 lists the same commands alphabetically. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command's documentation.
Initialization:
"atom_modify"_atom_modify.html, "atom_style"_atom_style.html,
"boundary"_boundary.html, "dimension"_dimension.html,
"newton"_newton.html, "processors"_processors.html, "units"_units.html
Atom definition:
"create_atoms"_create_atoms.html, "create_box"_create_box.html,
"lattice"_lattice.html, "read_data"_read_data.html,
"read_restart"_read_restart.html, "region"_region.html,
"replicate"_replicate.html
Force fields:
"angle_coeff"_angle_coeff.html, "angle_style"_angle_style.html,
"bond_coeff"_bond_coeff.html, "bond_style"_bond_style.html,
"dielectric"_dielectric.html, "dihedral_coeff"_dihedral_coeff.html,
"dihedral_style"_dihedral_style.html,
"improper_coeff"_improper_coeff.html,
"improper_style"_improper_style.html,
"kspace_modify"_kspace_modify.html, "kspace_style"_kspace_style.html,
"pair_coeff"_pair_coeff.html, "pair_modify"_pair_modify.html,
"pair_style"_pair_style.html, "pair_write"_pair_write.html,
"special_bonds"_special_bonds.html
Settings:
"communicate"_communicate.html, "group"_group.html, "mass"_mass.html,
"min_modify"_min_modify.html, "min_style"_min_style.html,
"neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html,
"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
"set"_set.html, "timestep"_timestep.html, "velocity"_velocity.html
Fixes:
"fix"_fix.html, "fix_modify"_fix_modify.html, "unfix"_unfix.html
Computes:
"compute"_compute.html, "compute_modify"_compute_modify.html,
"uncompute"_uncompute.html
Output:
"dump"_dump.html, "dump image"_dump_image.html,
"dump_modify"_dump_modify.html, "restart"_restart.html,
"thermo"_thermo.html, "thermo_modify"_thermo_modify.html,
"thermo_style"_thermo_style.html, "undump"_undump.html,
"write_restart"_write_restart.html
Actions:
"delete_atoms"_delete_atoms.html, "delete_bonds"_delete_bonds.html,
"displace_atoms"_displace_atoms.html,
"displace_box"_displace_box.html, "minimize"_minimize.html,
"neb"_neb.html "prd"_prd.html, "run"_run.html, "temper"_temper.html
Miscellaneous:
"clear"_clear.html, "echo"_echo.html, "if"_if.html,
"include"_include.html, "jump"_jump.html, "label"_label.html,
"log"_log.html, "next"_next.html, "print"_print.html,
"shell"_shell.html, "variable"_variable.html
:line
3.5 Individual commands :h4,link(cmd_5),link(comm)
This section lists all LAMMPS commands alphabetically, with a separate
listing below of styles within certain commands. The "previous
section"_#cmd_4 lists the same commands, grouped by category. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command's documentation.
"angle_coeff"_angle_coeff.html,
"angle_style"_angle_style.html,
"atom_modify"_atom_modify.html,
"atom_style"_atom_style.html,
"bond_coeff"_bond_coeff.html,
"bond_style"_bond_style.html,
"boundary"_boundary.html,
"change_box"_change_box.html,
"clear"_clear.html,
"communicate"_communicate.html,
"compute"_compute.html,
"compute_modify"_compute_modify.html,
"create_atoms"_create_atoms.html,
"create_box"_create_box.html,
"delete_atoms"_delete_atoms.html,
"delete_bonds"_delete_bonds.html,
"dielectric"_dielectric.html,
"dihedral_coeff"_dihedral_coeff.html,
"dihedral_style"_dihedral_style.html,
"dimension"_dimension.html,
"displace_atoms"_displace_atoms.html,
"displace_box"_displace_box.html,
"dump"_dump.html,
"dump image"_dump_image.html,
"dump_modify"_dump_modify.html,
"echo"_echo.html,
"fix"_fix.html,
"fix_modify"_fix_modify.html,
"group"_group.html,
"if"_if.html,
"improper_coeff"_improper_coeff.html,
"improper_style"_improper_style.html,
"include"_include.html,
"jump"_jump.html,
"kspace_modify"_kspace_modify.html,
"kspace_style"_kspace_style.html,
"label"_label.html,
"lattice"_lattice.html,
"log"_log.html,
"mass"_mass.html,
"minimize"_minimize.html,
"min_modify"_min_modify.html,
"min_style"_min_style.html,
"neb"_neb.html,
"neigh_modify"_neigh_modify.html,
"neighbor"_neighbor.html,
"newton"_newton.html,
"next"_next.html,
"package"_package.html,
"pair_coeff"_pair_coeff.html,
"pair_modify"_pair_modify.html,
"pair_style"_pair_style.html,
"pair_write"_pair_write.html,
"prd"_prd.html,
"print"_print.html,
"processors"_processors.html,
"read_data"_read_data.html,
"read_restart"_read_restart.html,
"region"_region.html,
"replicate"_replicate.html,
"reset_timestep"_reset_timestep.html,
"restart"_restart.html,
"run"_run.html,
"run_style"_run_style.html,
"set"_set.html,
"shell"_shell.html,
"special_bonds"_special_bonds.html,
"suffix"_suffix.html,
"tad"_tad.html,
"temper"_temper.html,
"thermo"_thermo.html,
"thermo_modify"_thermo_modify.html,
"thermo_style"_thermo_style.html,
"timestep"_timestep.html,
"uncompute"_uncompute.html,
"undump"_undump.html,
"unfix"_unfix.html,
"units"_units.html,
"variable"_variable.html,
"velocity"_velocity.html,
"write_restart"_write_restart.html :tb(c=6,ea=c)
:line
Fix styles :h4
See the "fix"_fix.html command for one-line descriptions
of each style or click on the style itself for a full description:
"adapt"_fix_adapt.html,
"addforce"_fix_addforce.html,
"aveforce"_fix_aveforce.html,
"ave/atom"_fix_ave_atom.html,
"ave/correlate"_fix_ave_correlate.html,
"ave/histo"_fix_ave_histo.html,
"ave/spatial"_fix_ave_spatial.html,
"ave/time"_fix_ave_time.html,
"bond/break"_fix_bond_break.html,
"bond/create"_fix_bond_create.html,
"bond/swap"_fix_bond_swap.html,
"box/relax"_fix_box_relax.html,
"deform"_fix_deform.html,
"deposit"_fix_deposit.html,
"drag"_fix_drag.html,
"dt/reset"_fix_dt_reset.html,
"efield"_fix_efield.html,
"enforce2d"_fix_enforce2d.html,
"evaporate"_fix_evaporate.html,
"external"_fix_external.html,
"freeze"_fix_freeze.html,
"gcmc"_fix_gcmc.html,
"gravity"_fix_gravity.html,
"heat"_fix_heat.html,
"indent"_fix_indent.html,
"langevin"_fix_langevin.html,
"lineforce"_fix_lineforce.html,
"momentum"_fix_momentum.html,
"move"_fix_move.html,
"msst"_fix_msst.html,
"neb"_fix_neb.html,
"nph"_fix_nh.html,
"nph/asphere"_fix_nph_asphere.html,
"nph/sphere"_fix_nph_sphere.html,
"npt"_fix_nh.html,
"npt/asphere"_fix_npt_asphere.html,
"npt/sphere"_fix_npt_sphere.html,
"nve"_fix_nve.html,
"nve/asphere"_fix_nve_asphere.html,
"nve/limit"_fix_nve_limit.html,
"nve/noforce"_fix_nve_noforce.html,
"nve/sphere"_fix_nve_sphere.html,
"nvt"_fix_nh.html,
"nvt/asphere"_fix_nvt_asphere.html,
"nvt/sllod"_fix_nvt_sllod.html,
"nvt/sphere"_fix_nvt_sphere.html,
"orient/fcc"_fix_orient_fcc.html,
"planeforce"_fix_planeforce.html,
"poems"_fix_poems.html,
"pour"_fix_pour.html,
"press/berendsen"_fix_press_berendsen.html,
"print"_fix_print.html,
"qeq/comb"_fix_qeq_comb.html,
"reax/bonds"_fix_reax_bonds.html,
"recenter"_fix_recenter.html,
"restrain"_fix_restrain.html,
"rigid"_fix_rigid.html,
"rigid/nve"_fix_rigid.html,
"rigid/nvt"_fix_rigid.html,
"setforce"_fix_setforce.html,
"shake"_fix_shake.html,
"spring"_fix_spring.html,
"spring/rg"_fix_spring_rg.html,
"spring/self"_fix_spring_self.html,
"srd"_fix_srd.html,
"store/force"_fix_store_force.html,
"store/state"_fix_store_state.html,
"temp/berendsen"_fix_temp_berendsen.html,
"temp/rescale"_fix_temp_rescale.html,
"thermal/conductivity"_fix_thermal_conductivity.html,
"tmd"_fix_tmd.html,
"ttm"_fix_ttm.html,
"viscosity"_fix_viscosity.html,
"viscous"_fix_viscous.html,
"wall/colloid"_fix_wall.html,
"wall/gran"_fix_wall_gran.html,
"wall/harmonic"_fix_wall.html,
"wall/lj126"_fix_wall.html,
"wall/lj93"_fix_wall.html,
"wall/reflect"_fix_wall_reflect.html,
"wall/region"_fix_wall_region.html,
"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c)
These are fix styles contributed by users, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"atc"_fix_atc.html,
"imd"_fix_imd.html,
"langevin/eff"_fix_langevin_eff.html,
+"meso"_fix_meso.html,
+"meso/stationary"_fix_meso_stationary.html,
"nph/eff"_fix_nh_eff.html,
"npt/eff"_fix_nh_eff.html,
"nve/eff"_fix_nve_eff.html,
"nvt/eff"_fix_nh_eff.html,
"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
"qeq/reax"_fix_qeq_reax.html,
"smd"_fix_smd.html,
"temp/rescale/eff"_fix_temp_rescale_eff.html :tb(c=6,ea=c)
These are accelerated fix styles, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"freeze/cuda"_fix_freeze.html,
"addforce/cuda"_fix_addforce.html,
"addtorque"_fix_addtorque.html,
"aveforce/cuda"_fix_aveforce.html,
"enforce2d/cuda"_fix_enforce2d.html,
"gravity/cuda"_fix_gravity.html,
"npt/cuda"_fix_nh.html,
"nve/cuda"_fix_nh.html,
"nvt/cuda"_fix_nh.html,
"setforce/cuda"_fix_setforce.html,
"shake/cuda"_fix_shake.html,
"temp/berendsen/cuda"_fix_temp_berendsen.html,
"temp/rescale/cuda"_fix_temp_rescale.html,
"temp/rescale/limit/cuda"_fix_temp_rescale.html,
"viscous/cuda"_fix_viscous.html :tb(c=6,ea=c)
:line
Compute styles :h4
See the "compute"_compute.html command for one-line descriptions of
each style or click on the style itself for a full description:
"angle/local"_compute_angle_local.html,
"atom/molecule"_compute_atom_molecule.html,
"bond/local"_compute_bond_local.html,
"centro/atom"_compute_centro_atom.html,
"cluster/atom"_compute_cluster_atom.html,
"cna/atom"_compute_cna_atom.html,
"com"_compute_com.html,
"com/molecule"_compute_com_molecule.html,
"coord/atom"_compute_coord_atom.html,
"damage/atom"_compute_damage_atom.html,
"dihedral/local"_compute_dihedral_local.html,
"displace/atom"_compute_displace_atom.html,
"erotate/asphere"_compute_erotate_asphere.html,
"erotate/sphere"_compute_erotate_sphere.html,
"event/displace"_compute_event_displace.html,
"group/group"_compute_group_group.html,
"gyration"_compute_gyration.html,
"gyration/molecule"_compute_gyration_molecule.html,
"heat/flux"_compute_heat_flux.html,
"improper/local"_compute_improper_local.html,
"ke"_compute_ke.html,
"ke/atom"_compute_ke_atom.html,
"msd"_compute_msd.html,
"msd/molecule"_compute_msd_molecule.html,
"pair"_compute_pair.html,
"pair/local"_compute_pair_local.html,
"pe"_compute_pe.html,
"pe/atom"_compute_pe_atom.html,
"pressure"_compute_pressure.html,
"property/atom"_compute_property_atom.html,
"property/local"_compute_property_local.html,
"property/molecule"_compute_property_molecule.html,
"rdf"_compute_rdf.html,
"reduce"_compute_reduce.html,
"reduce/region"_compute_reduce.html,
"slice"_compute_slice.html,
"stress/atom"_compute_stress_atom.html,
"temp"_compute_temp.html,
"temp/asphere"_compute_temp_asphere.html,
"temp/com"_compute_temp_com.html,
"temp/deform"_compute_temp_deform.html,
"temp/partial"_compute_temp_partial.html,
"temp/profile"_compute_temp_profile.html,
"temp/ramp"_compute_temp_ramp.html,
"temp/region"_compute_temp_region.html,
"temp/sphere"_compute_temp_sphere.html,
"ti"_compute_ti.html :tb(c=6,ea=c)
These are compute styles contributed by users, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"ackland/atom"_compute_ackland_atom.html,
"ke/eff"_compute_ke_eff.html,
"ke/atom/eff"_compute_ke_atom_eff.html,
+"meso_e/atom"_compute_meso_e_atom.html,
+"meso_rho/atom"_compute_meso_rho_atom.html,
+"meso_t/atom"_compute_meso_t_atom.html,
"temp/eff"_compute_temp_eff.html,
"temp/deform/eff"_compute_temp_deform_eff.html,
"temp/region/eff"_compute_temp_region_eff.html,
"temp/rotate"_compute_temp_rotate.html :tb(c=6,ea=c)
These are accelerated compute styles, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"pe/cuda"_compute_pe.html,
"pressure/cuda"_compute_pressure.html,
"temp/cuda"_compute_temp.html,
"temp/partial/cuda"_compute_temp_partial.html :tb(c=6,ea=c)
:line
Pair_style potentials :h4
See the "pair_style"_pair_style.html command for an overview of pair
potentials. Click on the style itself for a full description:
"none"_pair_none.html,
"hybrid"_pair_hybrid.html,
"hybrid/overlay"_pair_hybrid.html,
"adp"_pair_adp.html,
"airebo"_pair_airebo.html,
"born"_pair_born.html,
"born/coul/long"_pair_born.html,
"buck"_pair_buck.html,
"buck/coul/cut"_pair_buck.html,
"buck/coul/long"_pair_buck.html,
"colloid"_pair_colloid.html,
"comb"_pair_comb.html,
"coul/cut"_pair_coul.html,
"coul/debye"_pair_coul.html,
"coul/long"_pair_coul.html,
"dipole/cut"_pair_dipole.html,
"dpd"_pair_dpd.html,
"dpd/tstat"_pair_dpd.html,
"dsmc"_pair_dsmc.html,
"eam"_pair_eam.html,
"eam/alloy"_pair_eam.html,
"eam/fs"_pair_eam.html,
"eim"_pair_eim.html,
"gauss"_pair_gauss.html,
"gayberne"_pair_gayberne.html,
"gran/hertz/history"_pair_gran.html,
"gran/hooke"_pair_gran.html,
"gran/hooke/history"_pair_gran.html,
"hbond/dreiding/lj"_pair_hbond_dreiding.html,
"hbond/dreiding/morse"_pair_hbond_dreiding.html,
"lj/charmm/coul/charmm"_pair_charmm.html,
"lj/charmm/coul/charmm/implicit"_pair_charmm.html,
"lj/charmm/coul/long"_pair_charmm.html,
"lj/class2"_pair_class2.html,
"lj/class2/coul/cut"_pair_class2.html,
"lj/class2/coul/long"_pair_class2.html,
"lj/cut"_pair_lj.html,
"lj/cut/coul/cut"_pair_lj.html,
"lj/cut/coul/debye"_pair_lj.html,
"lj/cut/coul/long"_pair_lj.html,
"lj/cut/coul/long/tip4p"_pair_lj.html,
"lj/expand"_pair_lj_expand.html,
"lj/gromacs"_pair_gromacs.html,
"lj/gromacs/coul/gromacs"_pair_gromacs.html,
"lj/smooth"_pair_lj_smooth.html,
"lj96/cut"_pair_lj96.html,
"lubricate"_pair_lubricate.html,
"meam"_pair_meam.html,
"morse"_pair_morse.html,
"peri/lps"_pair_peri.html,
"peri/pmb"_pair_peri.html,
"reax"_pair_reax.html,
"rebo"_pair_airebo.html,
"resquared"_pair_resquared.html,
"soft"_pair_soft.html,
"sw"_pair_sw.html,
"table"_pair_table.html,
"tersoff"_pair_tersoff.html,
"tersoff/zbl"_pair_tersoff_zbl.html,
"yukawa"_pair_yukawa.html,
"yukawa/colloid"_pair_yukawa_colloid.html :tb(c=4,ea=c)
These are pair styles contributed by users, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"awpmd/cut"_pair_awpmd.html,
"buck/coul"_pair_buck_coul.html,
"cg/cmm"_pair_cmm.html,
"cg/cmm/coul/cut"_pair_cmm.html,
"cg/cmm/coul/long"_pair_cmm.html,
"dipole/sf"_pair_dipole.html,
"eam/cd"_pair_eam.html,
"eff/cut"_pair_eff.html,
"lj/coul"_pair_lj_coul.html,
"lj/sf"_pair_lj_sf.html,
-"reax/c"_pair_reax_c.html :tb(c=4,ea=c)
+"reax/c"_pair_reax_c.html
+"sph/heatconduction"_pair_heatconduction.html,
+"sph/idealgas"_pair_idealgas.html,
+"sph/lj"_pair_lj.html,
+"sph/rhosum"_pair_rhosum.html,
+"sph/taitwater"_pair_taitwater.html,
+"sph/taitwater/morris"_pair_taitwater_morris.html :tb(c=4,ea=c)
These are accelerated pair styles, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"born/coul/long/cuda"_pair_born.html,
"buck/coul/cut/cuda"_pair_buck.html,
"buck/coul/long/cuda"_pair_buck.html,
"buck/cuda"_pair_buck.html,
"cg/cmm/coul/cut/cuda"_pair_cmm.html,
"cg/cmm/coul/debye/cuda"_pair_cmm.html,
"cg/cmm/coul/long/cuda"_pair_cmm.html,
"cg/cmm/coul/long/gpu"_pair_cmm.html,
"cg/cmm/cuda"_pair_cmm.html,
"cg/cmm/gpu"_pair_cmm.html,
"coul/long/gpu"_pair_coul.html,
"eam/alloy/cuda"_pair_eam.html,
"eam/alloy/opt"_pair_eam.html,
"eam/cuda"_pair_eam.html,
"eam/fs/cuda"_pair_eam.html,
"eam/fs/opt"_pair_eam.html,
"eam/opt"_pair_eam.html,
"gayberne/gpu"_pair_gayberne.html,
"gran/hooke/cuda"_pair_gran.html,
"lj/charmm/coul/charmm/cuda"_pair_charmm.html,
"lj/charmm/coul/charmm/implicit/cuda"_pair_charmm.html,
"lj/charmm/coul/long/cuda"_pair_charmm.html,
"lj/charmm/coul/long/gpu"_pair_charmm.html,
"lj/charmm/coul/long/opt"_pair_charmm.html,
"lj/class2/coul/cut/cuda"_pair_class2.html,
"lj/class2/coul/long/cuda"_pair_class2.html,
"lj/class2/coul/long/gpu"_pair_class2.html,
"lj/class2/cuda"_pair_class2.html,
"lj/class2/gpu"_pair_class2.html,
"lj/cut/coul/cut/cuda"_pair_lj.html,
"lj/cut/coul/cut/gpu"_pair_lj.html,
"lj/cut/coul/debye/cuda"_pair_lj.html,
"lj/cut/coul/long/cuda"_pair_lj.html,
"lj/cut/coul/long/gpu"_pair_lj.html,
"lj/cut/cuda"_pair_lj.html,
"lj/cut/experimental/cuda"_pair_lj.html,
"lj/cut/gpu"_pair_lj.html,
"lj/cut/opt"_pair_lj.html,
"lj/expand/cuda"_pair_lj_expand.html,
"lj/expand/gpu"_pair_lj_expand.html,
"lj/gromacs/coul/gromacs/cuda"_pair_gromacs.html,
"lj/gromacs/cuda"_pair_gromacs.html,
"lj/smooth/cuda"_pair_lj_smooth.html,
"lj96/cut/cuda"_pair_lj96.html,
"lj96/cut/gpu"_pair_lj96.html,
"morse/cuda"_pair_morse.html,
"morse/gpu"_pair_morse.html,
"morse/opt"_pair_morse.html,
"resquared/gpu"_pair_resquared.html :tb(c=4,ea=c)
:line
Bond_style potentials :h4
See the "bond_style"_bond_style.html command for an overview of bond
potentials. Click on the style itself for a full description:
"none"_bond_none.html,
"hybrid"_bond_hybrid.html,
"class2"_bond_class2.html,
"fene"_bond_fene.html,
"fene/expand"_bond_fene_expand.html,
"harmonic"_bond_harmonic.html,
"morse"_bond_morse.html,
"nonlinear"_bond_nonlinear.html,
"quartic"_bond_quartic.html,
"table"_bond_table.html :tb(c=4,ea=c,w=100)
These are bond styles contributed by users, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"harmonic/shift"_bond_harmonic_shift.html,
"harmonic/shift/cut"_bond_harmonic_shift_cut.html :tb(c=4,ea=c)
:line
Angle_style potentials :h4
See the "angle_style"_angle_style.html command for an overview of
angle potentials. Click on the style itself for a full description:
"none"_angle_none.html,
"hybrid"_angle_hybrid.html,
"charmm"_angle_charmm.html,
"class2"_angle_class2.html,
"cosine"_angle_cosine.html,
"cosine/delta"_angle_cosine_delta.html,
"cosine/periodic"_angle_cosine_periodic.html,
"cosine/squared"_angle_cosine_squared.html,
"harmonic"_angle_harmonic.html,
"table"_angle_table.html :tb(c=4,ea=c,w=100)
These are angle styles contributed by users, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"cg/cmm"_angle_cmm.html,
"cosine/shift"_angle_cosine_shift.html,
"cosine/shift/exp"_angle_cosine_shift_exp.html :tb(c=4,ea=c)
:line
Dihedral_style potentials :h4
See the "dihedral_style"_dihedral_style.html command for an overview
of dihedral potentials. Click on the style itself for a full
description:
"none"_dihedral_none.html,
"hybrid"_dihedral_hybrid.html,
"charmm"_dihedral_charmm.html,
"class2"_dihedral_class2.html,
"harmonic"_dihedral_harmonic.html,
"helix"_dihedral_helix.html,
"multi/harmonic"_dihedral_multi_harmonic.html,
"opls"_dihedral_opls.html :tb(c=4,ea=c,w=100)
These are dihedral styles contributed by users, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"cosine/shift/exp"_dihedral_cosine_shift_exp.html :tb(c=4,ea=c)
:line
Improper_style potentials :h4
See the "improper_style"_improper_style.html command for an overview
of improper potentials. Click on the style itself for a full
description:
"none"_improper_none.html,
"hybrid"_improper_hybrid.html,
"class2"_improper_class2.html,
"cvff"_improper_cvff.html,
"harmonic"_improper_harmonic.html,
"umbrella"_improper_umbrella.html :tb(c=4,ea=c,w=100)
:line
Kspace solvers :h4
See the "kspace_style"_kspace_style.html command for an overview of
Kspace solvers. Click on the style itself for a full description:
"ewald"_kspace_style.html,
"pppm"_kspace_style.html,
"pppm/cg"_kspace_style.html,
"pppm/tip4p"_kspace_style.html :tb(c=4,ea=c,w=100)
These are Kspace solvers contributed by users, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"ewald/n"_kspace_style.html :tb(c=4,ea=c,w=100)
These are accelerated Kspace solvers, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"pppm/cuda"_kspace_style.html,
"pppm/gpu"_kspace_style.html :tb(c=4,ea=c)
diff --git a/doc/Section_intro.html b/doc/Section_intro.html
index 1e7001a9d..b77261945 100644
--- a/doc/Section_intro.html
+++ b/doc/Section_intro.html
@@ -1,634 +1,634 @@
<HTML>
<CENTER><A HREF = "Manual.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_start.html">Next Section</A>
</CENTER>
<HR>
<H3>1. Introduction
</H3>
<P>These sections provide an overview of what LAMMPS can and can't do,
describe what it means for LAMMPS to be an open-source code, and
acknowledge the funding and people who have contributed to LAMMPS over
the years.
</P>
1.1 <A HREF = "#intro_1">What is LAMMPS</A><BR>
1.2 <A HREF = "#intro_2">LAMMPS features</A><BR>
1.3 <A HREF = "#intro_3">LAMMPS non-features</A><BR>
1.4 <A HREF = "#intro_4">Open source distribution</A><BR>
1.5 <A HREF = "#intro_5">Acknowledgments and citations</A> <BR>
<HR>
<A NAME = "intro_1"></A><H4>1.1 What is LAMMPS
</H4>
<P>LAMMPS is a classical molecular dynamics code that models an ensemble
of particles in a liquid, solid, or gaseous state. It can model
atomic, polymeric, biological, metallic, granular, and coarse-grained
systems using a variety of force fields and boundary conditions.
</P>
<P>For examples of LAMMPS simulations, see the Publications page of the
<A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>.
</P>
<P>LAMMPS runs efficiently on single-processor desktop or laptop
machines, but is designed for parallel computers. It will run on any
parallel machine that compiles C++ and supports the <A HREF = "http://www-unix.mcs.anl.gov/mpi">MPI</A>
message-passing library. This includes distributed- or shared-memory
parallel machines and Beowulf-style clusters.
</P>
<P>LAMMPS can model systems with only a few particles up to millions or
billions. See <A HREF = "Section_perf.html">this section</A> for information on LAMMPS
performance and scalability, or the Benchmarks section of the <A HREF = "http://lammps.sandia.gov">LAMMPS
WWW Site</A>.
</P>
<P>LAMMPS is a freely-available open-source code, distributed under the
terms of the <A HREF = "http://www.gnu.org/copyleft/gpl.html">GNU Public License</A>, which means you can use or
modify the code however you wish. See <A HREF = "#intro_4">this section</A> for a brief
discussion of the open-source philosophy.
</P>
<P>LAMMPS is designed to be easy to modify or extend with new
capabilities, such as new force fields, atom types, boundary
conditions, or diagnostics. See <A HREF = "Section_modify.html">this section</A> for
more details.
</P>
<P>The current version of LAMMPS is written in C++. Earlier versions
were written in F77 and F90. See <A HREF = "Section_history.html">this section</A>
for more information on different versions. All versions can be
downloaded from the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>.
</P>
<P>LAMMPS was originally developed under a US Department of Energy CRADA
(Cooperative Research and Development Agreement) between two DOE labs
and 3 companies. It is distributed by <A HREF = "http://www.sandia.gov">Sandia National Labs</A>.
See <A HREF = "#intro_5">this section</A> for more information on LAMMPS funding and
individuals who have contributed to LAMMPS.
</P>
<P>In the most general sense, LAMMPS integrates Newton's equations of
motion for collections of atoms, molecules, or macroscopic particles
that interact via short- or long-range forces with a variety of
initial and/or boundary conditions. For computational efficiency
LAMMPS uses neighbor lists to keep track of nearby particles. The
lists are optimized for systems with particles that are repulsive at
short distances, so that the local density of particles never becomes
too large. On parallel machines, LAMMPS uses spatial-decomposition
techniques to partition the simulation domain into small 3d
sub-domains, one of which is assigned to each processor. Processors
communicate and store "ghost" atom information for atoms that border
their sub-domain. LAMMPS is most efficient (in a parallel sense) for
systems whose particles fill a 3d rectangular box with roughly uniform
density. Papers with technical details of the algorithms used in
LAMMPS are listed in <A HREF = "#intro_5">this section</A>.
</P>
<HR>
<A NAME = "intro_2"></A><H4>1.2 LAMMPS features
</H4>
<P>This section highlights LAMMPS features, with pointers to specific
commands which give more details. If LAMMPS doesn't have your
favorite interatomic potential, boundary condition, or atom type, see
<A HREF = "Section_modify.html">this section</A>, which describes how you can add it to
LAMMPS.
</P>
<H4>General features
</H4>
<UL><LI> runs on a single processor or in parallel
<LI> distributed-memory message-passing parallelism (MPI)
<LI> spatial-decomposition of simulation domain for parallelism
<LI> open-source distribution
<LI> highly portable C++
<LI> optional libraries used: MPI and single-processor FFT
<LI> easy to extend with new features and functionality
<LI> runs from an input script
<LI> syntax for defining and using variables and formulas
<LI> syntax for looping over runs and breaking out of loops
<LI> run one or multiple simulations simultaneously (in parallel) from one script
<LI> build as library, invoke LAMMPS thru library interface or provided Python wrapper
<LI> couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both
</UL>
<H4>Particle and model types
</H4>
<P>(<A HREF = "atom_style.html">atom style</A> command)
</P>
<UL><LI> atoms
<LI> coarse-grained particles (e.g. bead-spring polymers)
<LI> united-atom polymers or organic molecules
<LI> all-atom polymers, organic molecules, proteins, DNA
<LI> metals
<LI> granular materials
<LI> coarse-grained mesoscale models
<LI> extended spherical and ellipsoidal particles
<LI> point dipolar particles
<LI> rigid collections of particles
<LI> hybrid combinations of these
</UL>
<H4>Force fields
</H4>
<P>(<A HREF = "pair_style.html">pair style</A>, <A HREF = "bond_style.html">bond style</A>,
<A HREF = "angle_style.html">angle style</A>, <A HREF = "dihedral_style.html">dihedral style</A>,
<A HREF = "improper_style.html">improper style</A>, <A HREF = "kspace_style.html">kspace style</A>
commands)
</P>
<UL><LI> pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
<LI> charged pairwise potentials: Coulombic, point-dipole
<LI> manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), embedded ion method (EIM), ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB
<LI> electron force field (eFF, AWPMD)
<LI> coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
-<LI> mesoscopic potentials: granular, Peridynamics
+<LI> mesoscopic potentials: granular, Peridynamics, SPH
<LI> bond potentials: harmonic, FENE, Morse, nonlinear, class 2, quartic (breakable)
<LI> angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, class 2 (COMPASS)
<LI> dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, class 2 (COMPASS), OPLS
<LI> improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS)
<LI> polymer potentials: all-atom, united-atom, bead-spring, breakable
<LI> water potentials: TIP3P, TIP4P, SPC
<LI> implicit solvent potentials: hydrodynamic lubrication, Debye
<LI> long-range Coulombics and dispersion: Ewald, PPPM (similar to particle-mesh Ewald), Ewald/N for long-range Lennard-Jones
<LI> force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options
<LI> handful of GPU-enabled pair styles
</UL>
<P> hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
overlaid potentials: superposition of multiple pair potentials
</P>
<H4>Atom creation
</H4>
<P>(<A HREF = "read_data.html">read_data</A>, <A HREF = "lattice.html">lattice</A>,
<A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "delete_atoms.html">delete_atoms</A>,
<A HREF = "displace_atoms.html">displace_atoms</A>, <A HREF = "replicate.html">replicate</A> commands)
</P>
<UL><LI> read in atom coords from files
<LI> create atoms on one or more lattices (e.g. grain boundaries)
<LI> delete geometric or logical groups of atoms (e.g. voids)
<LI> replicate existing atoms multiple times
<LI> displace atoms
</UL>
<H4>Ensembles, constraints, and boundary conditions
</H4>
<P>(<A HREF = "fix.html">fix</A> command)
</P>
<UL><LI> 2d or 3d systems
<LI> orthogonal or non-orthogonal (triclinic symmetry) simulation domains
<LI> constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators
<LI> thermostatting options for groups and geometric regions of atoms
<LI> pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
<LI> simulation box deformation (tensile and shear)
<LI> harmonic (umbrella) constraint forces
<LI> rigid body constraints
<LI> SHAKE bond and angle constraints
<LI> bond breaking, formation, swapping
<LI> walls of various kinds
<LI> non-equilibrium molecular dynamics (NEMD)
<LI> variety of additional boundary conditions and constraints
</UL>
<H4>Integrators
</H4>
<P>(<A HREF = "run.html">run</A>, <A HREF = "run_style.html">run_style</A>, <A HREF = "minimize.html">minimize</A> commands)
</P>
<UL><LI> velocity-Verlet integrator
<LI> Brownian dynamics
<LI> rigid body integration
<LI> energy minimization via conjugate gradient or steepest descent relaxation
<LI> rRESPA hierarchical timestepping
</UL>
<H4>Diagnostics
</H4>
<UL><LI> see the various flavors of the <A HREF = "fix.html">fix</A> and <A HREF = "compute.html">compute</A> commands
</UL>
<H4>Output
</H4>
<P>(<A HREF = "dump.html">dump</A>, <A HREF = "restart.html">restart</A> commands)
</P>
<UL><LI> log file of thermodynamic info
<LI> text dump files of atom coords, velocities, other per-atom quantities
<LI> binary restart files
<LI> parallel I/O of dump and restart files
<LI> per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc)
<LI> user-defined system-wide (log file) or per-atom (dump file) calculations
<LI> spatial and time averaging of per-atom quantities
<LI> time averaging of system-wide quantities
<LI> atom snapshots in native, XYZ, XTC, DCD, CFG formats
</UL>
<H4>Multi-replica models
</H4>
<P><A HREF = "neb.html">nudged elastic band</A>
<A HREF = "prd.html">parallel replica dynamics</A>
<A HREF = "tad.html">temperature accelerated dynamics</A>
<A HREF = "temper.html">parallel tempering</A>
</P>
<H4>Pre- and post-processing
</H4>
<UL><LI>Various pre- and post-processing serial tools are packaged
with LAMMPS; see these <A HREF = "Section_tools.html">doc pages</A>.
<LI>Our group has also written and released a separate toolkit called
<A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which provides tools for doing setup, analysis,
plotting, and visualization for LAMMPS simulations. Pizza.py is
written in <A HREF = "http://www.python.org">Python</A> and is available for download from <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">the
Pizza.py WWW site</A>.
</UL>
<H4>Specialized features
</H4>
<P>These are LAMMPS capabilities which you may not think of as typical
molecular dynamics options:
</P>
<UL><LI><A HREF = "fix_srd.html">stochastic rotation dynamics (SRD)</A>
<LI><A HREF = "fix_imd.html">real-time visualization and interactive MD</A>
<LI><A HREF = "fix_atc.html">atom-to-continuum coupling</A> with finite elements
<LI>coupled rigid body integration via the <A HREF = "fix_poems.html">POEMS</A> library
<LI><A HREF = "doc/fix_gcmc.html">grand canonical Monte Carlo</A> insertions/deletions
<LI><A HREF = "pair_dsmc.html">Direct Simulation Monte Carlo</A> for low-density fluids
<LI><A HREF = "pair_peri.html">Peridynamics mesoscale modeling</A>
<LI><A HREF = "fix_tmd.html">targeted</A> and <A HREF = "fix_smd.html">steered</A> molecular dynamics
<LI><A HREF = "fix_ttm.html">two-temperature electron model</A>
</UL>
<HR>
<A NAME = "intro_3"></A><H4>1.3 LAMMPS non-features
</H4>
<P>LAMMPS is designed to efficiently compute Newton's equations of motion
for a system of interacting particles. Many of the tools needed to
pre- and post-process the data for such simulations are not included
in the LAMMPS kernel for several reasons:
</P>
<UL><LI>the desire to keep LAMMPS simple
<LI>they are not parallel operations
<LI>other codes already do them
<LI>limited development resources
</UL>
<P>Specifically, LAMMPS itself does not:
</P>
<UL><LI>run thru a GUI
<LI>build molecular systems
<LI>assign force-field coefficients automagically
<LI>perform sophisticated analyses of your MD simulation
<LI>visualize your MD simulation
<LI>plot your output data
</UL>
<P>A few tools for pre- and post-processing tasks are provided as part of
the LAMMPS package; they are described in <A HREF = "Section_tools.html">this
section</A>. However, many people use other codes or
write their own tools for these tasks.
</P>
<P>As noted above, our group has also written and released a separate
toolkit called <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which addresses some of the listed
bullets. It provides tools for doing setup, analysis, plotting, and
visualization for LAMMPS simulations. Pizza.py is written in
<A HREF = "http://www.python.org">Python</A> and is available for download from <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">the Pizza.py WWW
site</A>.
</P>
<P>LAMMPS requires as input a list of initial atom coordinates and types,
molecular topology information, and force-field coefficients assigned
to all atoms and bonds. LAMMPS will not build molecular systems and
assign force-field parameters for you.
</P>
<P>For atomic systems LAMMPS provides a <A HREF = "create_atoms.html">create_atoms</A>
command which places atoms on solid-state lattices (fcc, bcc,
user-defined, etc). Assigning small numbers of force field
coefficients can be done via the <A HREF = "pair_coeff.html">pair coeff</A>, <A HREF = "bond_coeff.html">bond
coeff</A>, <A HREF = "angle_coeff.html">angle coeff</A>, etc commands.
For molecular systems or more complicated simulation geometries, users
typically use another code as a builder and convert its output to
LAMMPS input format, or write their own code to generate atom
coordinate and molecular topology for LAMMPS to read in.
</P>
<P>For complicated molecular systems (e.g. a protein), a multitude of
topology information and hundreds of force-field coefficients must
typically be specified. We suggest you use a program like
<A HREF = "http://www.scripps.edu/brooks">CHARMM</A> or <A HREF = "http://amber.scripps.edu">AMBER</A> or other molecular builders to setup
such problems and dump its information to a file. You can then
reformat the file as LAMMPS input. Some of the tools in <A HREF = "Section_tools.html">this
section</A> can assist in this process.
</P>
<P>Similarly, LAMMPS creates output files in a simple format. Most users
post-process these files with their own analysis tools or re-format
them for input into other programs, including visualization packages.
If you are convinced you need to compute something on-the-fly as
LAMMPS runs, see <A HREF = "Section_modify.html">this section</A> for a discussion
of how you can use the <A HREF = "dump.html">dump</A> and <A HREF = "compute.html">compute</A> and
<A HREF = "fix.html">fix</A> commands to print out data of your choosing. Keep in
mind that complicated computations can slow down the molecular
dynamics timestepping, particularly if the computations are not
parallel, so it is often better to leave such analysis to
post-processing codes.
</P>
<P>A very simple (yet fast) visualizer is provided with the LAMMPS
package - see the <A HREF = "Section_tools.html#xmovie">xmovie</A> tool in <A HREF = "Section_tools.html">this
section</A>. It creates xyz projection views of
atomic coordinates and animates them. We find it very useful for
debugging purposes. For high-quality visualization we recommend the
following packages:
</P>
<UL><LI><A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>
<LI><A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A>
<LI><A HREF = "http://pymol.sourceforge.net">PyMol</A>
<LI><A HREF = "http://www.bmsc.washington.edu/raster3d/raster3d.html">Raster3d</A>
<LI><A HREF = "http://www.openrasmol.org">RasMol</A>
</UL>
<P>Other features that LAMMPS does not yet (and may never) support are
discussed in <A HREF = "Section_history.html">this section</A>.
</P>
<P>Finally, these are freely-available molecular dynamics codes, most of
them parallel, which may be well-suited to the problems you want to
model. They can also be used in conjunction with LAMMPS to perform
complementary modeling tasks.
</P>
<UL><LI><A HREF = "http://www.scripps.edu/brooks">CHARMM</A>
<LI><A HREF = "http://amber.scripps.edu">AMBER</A>
<LI><A HREF = "http://www.ks.uiuc.edu/Research/namd/">NAMD</A>
<LI><A HREF = "http://www.emsl.pnl.gov/docs/nwchem/nwchem.html">NWCHEM</A>
<LI><A HREF = "http://www.cse.clrc.ac.uk/msi/software/DL_POLY">DL_POLY</A>
<LI><A HREF = "http://dasher.wustl.edu/tinker">Tinker</A>
</UL>
<P>CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for
modeling biological molecules. CHARMM and AMBER use
atom-decomposition (replicated-data) strategies for parallelism; NAMD
and NWCHEM use spatial-decomposition approaches, similar to LAMMPS.
Tinker is a serial code. DL_POLY includes potentials for a variety of
biological and non-biological materials; both a replicated-data and
spatial-decomposition version exist.
</P>
<HR>
<A NAME = "intro_4"></A><H4>1.4 Open source distribution
</H4>
<P>LAMMPS comes with no warranty of any kind. As each source file states
in its header, it is a copyrighted code that is distributed free-of-
charge, under the terms of the <A HREF = "http://www.gnu.org/copyleft/gpl.html">GNU Public License</A> (GPL). This
is often referred to as open-source distribution - see
<A HREF = "http://www.gnu.org">www.gnu.org</A> or <A HREF = "http://www.opensource.org">www.opensource.org</A> for more
details. The legal text of the GPL is in the LICENSE file that is
included in the LAMMPS distribution.
</P>
<P>Here is a summary of what the GPL means for LAMMPS users:
</P>
<P>(1) Anyone is free to use, modify, or extend LAMMPS in any way they
choose, including for commercial purposes.
</P>
<P>(2) If you distribute a modified version of LAMMPS, it must remain
open-source, meaning you distribute it under the terms of the GPL.
You should clearly annotate such a code as a derivative version of
LAMMPS.
</P>
<P>(3) If you release any code that includes LAMMPS source code, then it
must also be open-sourced, meaning you distribute it under the terms
of the GPL.
</P>
<P>(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
source file headers (including the copyright and GPL notices) should
remain part of the code.
</P>
<P>In the spirit of an open-source code, these are various ways you can
contribute to making LAMMPS better. You can send email to the
<A HREF = "http://lammps.sandia.gov/authors.html">developers</A> on any of these
items.
</P>
<UL><LI>Point prospective users to the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>. Mention it in
talks or link to it from your WWW site.
<LI>If you find an error or omission in this manual or on the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW
Site</A>, or have a suggestion for something to clarify or include,
send an email to the
<A HREF = "http://lammps.sandia.gov/authors.html">developers</A>.
<LI>If you find a bug, <A HREF = "Section_errors.html#err_2">this section</A> describes
how to report it.
<LI>If you publish a paper using LAMMPS results, send the citation (and
any cool pictures or movies if you like) to add to the Publications,
Pictures, and Movies pages of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>, with links
and attributions back to you.
<LI>Create a new Makefile.machine that can be added to the src/MAKE
directory.
<LI>The tools sub-directory of the LAMMPS distribution has various
stand-alone codes for pre- and post-processing of LAMMPS data. More
details are given in <A HREF = "Section_tools.html">this section</A>. If you write
a new tool that users will find useful, it can be added to the LAMMPS
distribution.
<LI>LAMMPS is designed to be easy to extend with new code for features
like potentials, boundary conditions, diagnostic computations, etc.
<A HREF = "Section_modify.html">This section</A> gives details. If you add a
feature of general interest, it can be added to the LAMMPS
distribution.
<LI>The Benchmark page of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> lists LAMMPS
performance on various platforms. The files needed to run the
benchmarks are part of the LAMMPS distribution. If your machine is
sufficiently different from those listed, your timing data can be
added to the page.
<LI>You can send feedback for the User Comments page of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW
Site</A>. It might be added to the page. No promises.
<LI>Cash. Small denominations, unmarked bills preferred. Paper sack OK.
Leave on desk. VISA also accepted. Chocolate chip cookies
encouraged.
</UL>
<HR>
<H4><A NAME = "intro_5"></A>1.5 Acknowledgments and citations
</H4>
<P>LAMMPS development has been funded by the <A HREF = "http://www.doe.gov">US Department of
Energy</A> (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
programs and its <A HREF = "http://www.sc.doe.gov/ascr/home.html">OASCR</A> and <A HREF = "http://www.er.doe.gov/production/ober/ober_top.html">OBER</A> offices.
</P>
<P>Specifically, work on the latest version was funded in part by the US
Department of Energy's Genomics:GTL program
(<A HREF = "http://www.doegenomestolife.org">www.doegenomestolife.org</A>) under the <A HREF = "http://www.genomes2life.org">project</A>, "Carbon
Sequestration in Synechococcus Sp.: From Molecular Machines to
Hierarchical Modeling".
</P>
<P>The following papers describe the parallel algorithms used in LAMMPS.
</P>
<P>S. J. Plimpton, <B>Fast Parallel Algorithms for Short-Range Molecular
Dynamics</B>, J Comp Phys, 117, 1-19 (1995).
</P>
<P>S. J. Plimpton, R. Pollock, M. Stevens, <B>Particle-Mesh Ewald and
rRESPA for Parallel Molecular Dynamics Simulations</B>, in Proc of the
Eighth SIAM Conference on Parallel Processing for Scientific
Computing, Minneapolis, MN (March 1997).
</P>
<P>If you use LAMMPS results in your published work, please cite the J
Comp Phys reference and include a pointer to the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>
(http://lammps.sandia.gov).
</P>
<P>If you send is information about your publication, we'll be pleased to
add it to the Publications page of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>. Ditto
for a picture or movie for the Pictures or Movies pages.
</P>
<P>The core group of LAMMPS developers is at Sandia National Labs. They
include <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Paul Crozier, and Aidan Thompson and can
be contacted via email: sjplimp, pscrozi, athomps at sandia.gov.
</P>
<P>Here are various folks who have made significant contributions to
features in LAMMPS. The most recent contributions are at the top of
the list.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >pppm GPU single and double </TD><TD > Mike Brown (ORNL)</TD></TR>
<TR><TD >pair_style lj/cut/expand </TD><TD > Inderaj Bains (NVIDIA)</TD></TR>
<TR><TD >temperature accelerated dynamics (TAD) </TD><TD > Aidan Thompson (Sandia)</TD></TR>
<TR><TD >pair reax/c and fix qeq/reax </TD><TD > Metin Aktulga (Purdue, now LBNL)</TD></TR>
<TR><TD >DREIDING force field, pair_style hbond/dreiding, etc </TD><TD > Tod Pascal (CalTech)</TD></TR>
<TR><TD >fix adapt and compute ti for thermodynamic integreation for free energies </TD><TD > Sai Jayaraman (Sandia)</TD></TR>
<TR><TD >pair born and pair gauss </TD><TD > Sai Jayaraman (Sandia)</TD></TR>
<TR><TD >stochastic rotation dynamics (SRD) via fix srd </TD><TD > Jemery Lechman (Sandia) and Pieter in 't Veld (BASF)</TD></TR>
<TR><TD >ipp Perl script tool </TD><TD > Reese Jones (Sandia)</TD></TR>
<TR><TD >eam_database and createatoms tools </TD><TD > Xiaowang Zhou (Sandia)</TD></TR>
<TR><TD >electron force field (eFF) </TD><TD > Andres Jaramillo-Botero and Julius Su (Caltech)</TD></TR>
<TR><TD >embedded ion method (EIM) potential </TD><TD > Xiaowang Zhou (Sandia)</TD></TR>
<TR><TD >COMB potential with charge equilibration </TD><TD > Tzu-Ray Shan (U Florida)</TD></TR>
<TR><TD >fix ave/correlate </TD><TD > Benoit Leblanc, Dave Rigby, Paul Saxe (Materials Design) and Reese Jones (Sandia)</TD></TR>
<TR><TD >pair_style peri/lps </TD><TD > Mike Parks (Sandia)</TD></TR>
<TR><TD >fix msst </TD><TD > Lawrence Fried (LLNL), Evan Reed (LLNL, Stanford)</TD></TR>
<TR><TD >thermo_style custom tpcpu & spcpu keywords </TD><TD > Axel Kohlmeyer (Temple U) </TD></TR>
<TR><TD >fix rigid/nve, fix rigid/nvt </TD><TD > Tony Sheh and Trung Dac Nguyen (U Michigan)</TD></TR>
<TR><TD >public SVN & Git repositories for LAMMPS </TD><TD > Axel Kohlmeyer (Temple U) and Bill Goldman (Sandia)</TD></TR>
<TR><TD >fix nvt, fix nph, fix npt, Parinello/Rahman dynamics, fix box/relax </TD><TD > Aidan Thompson (Sandia)</TD></TR>
<TR><TD >compute heat/flux </TD><TD > German Samolyuk (ORNL) and Mario Pinto (Computational Research Lab, Pune, India)</TD></TR>
<TR><TD >pair yukawa/colloid </TD><TD > Randy Schunk (Sandia)</TD></TR>
<TR><TD >fix wall/colloid </TD><TD > Jeremy Lechman (Sandia)</TD></TR>
<TR><TD >pair_style dsmc for Direct Simulation Monte Carlo (DSMC) modeling </TD><TD > Paul Crozier (Sandia)</TD></TR>
<TR><TD >fix imd for real-time viz and interactive MD </TD><TD > Axel Kohlmeyer (Temple Univ)</TD></TR>
<TR><TD >concentration-dependent EAM potential </TD><TD > Alexander Stukowski (Technical University of Darmstadt)</TD></TR>
<TR><TD >parallel replica dymamics (PRD) </TD><TD > Mike Brown (Sandia)</TD></TR>
<TR><TD >min_style hftn </TD><TD > Todd Plantenga (Sandia)</TD></TR>
<TR><TD >fix atc </TD><TD > Reese Jones, Jon Zimmerman, Jeremy Templeton (Sandia)</TD></TR>
<TR><TD >dump cfg </TD><TD > Liang Wan (Chinese Academy of Sciences)</TD></TR>
<TR><TD >fix nvt with Nose/Hoover chains </TD><TD > Andy Ballard (U Maryland)</TD></TR>
<TR><TD >pair_style lj/cut/gpu, pair_style gayberne/gpu </TD><TD > Mike Brown (Sandia)</TD></TR>
<TR><TD >pair_style lj96/cut, bond_style table, angle_style table </TD><TD > Chuanfu Luo</TD></TR>
<TR><TD >fix langevin tally </TD><TD > Carolyn Phillips (U Michigan)</TD></TR>
<TR><TD >compute heat/flux for Green-Kubo </TD><TD > Reese Jones (Sandia), Philip Howell (Siemens), Vikas Varsney (AFRL)</TD></TR>
<TR><TD >region cone </TD><TD > Pim Schravendijk</TD></TR>
<TR><TD >fix reax/bonds </TD><TD > Aidan Thompson (Sandia)</TD></TR>
<TR><TD >pair born/coul/long </TD><TD > Ahmed Ismail (Sandia)</TD></TR>
<TR><TD >fix ttm </TD><TD > Paul Crozier (Sandia) and Carolyn Phillips (U Michigan)</TD></TR>
<TR><TD >fix box/relax </TD><TD > Aidan Thompson and David Olmsted (Sandia)</TD></TR>
<TR><TD >ReaxFF potential </TD><TD > Aidan Thompson (Sandia) and Hansohl Cho (MIT)</TD></TR>
<TR><TD >compute cna/atom </TD><TD > Wan Liang (Chinese Academy of Sciences)</TD></TR>
<TR><TD >Tersoff/ZBL potential </TD><TD > Dave Farrell (Northwestern U)</TD></TR>
<TR><TD >peridynamics </TD><TD > Mike Parks (Sandia)</TD></TR>
<TR><TD >fix smd for steered MD </TD><TD > Axel Kohlmeyer (U Penn)</TD></TR>
<TR><TD >GROMACS pair potentials </TD><TD > Mark Stevens (Sandia)</TD></TR>
<TR><TD >lmp2vmd tool </TD><TD > Axel Kohlmeyer (U Penn)</TD></TR>
<TR><TD >compute group/group </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
-<TR><TD >CG-CMM user package for coarse-graining </TD><TD > Axel Kohlmeyer (U Penn)</TD></TR>
+<TR><TD >USER-CG-CMM package for coarse-graining </TD><TD > Axel Kohlmeyer (U Penn)</TD></TR>
<TR><TD >cosine/delta angle potential </TD><TD > Axel Kohlmeyer (U Penn)</TD></TR>
<TR><TD >VIM editor add-ons for LAMMPS input scripts </TD><TD > Gerolf Ziegenhain</TD></TR>
<TR><TD >pair lubricate </TD><TD > Randy Schunk (Sandia)</TD></TR>
<TR><TD >compute ackland/atom </TD><TD > Gerolf Zeigenhain</TD></TR>
<TR><TD >kspace_style ewald/n, pair_style lj/coul, pair_style buck/coul </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
<TR><TD >AIREBO bond-order potential </TD><TD > Ase Henry (MIT)</TD></TR>
<TR><TD >making LAMMPS a true "object" that can be instantiated multiple times, e.g. as a library </TD><TD > Ben FrantzDale (RPI)</TD></TR>
<TR><TD >pymol_asphere viz tool </TD><TD > Mike Brown (Sandia)</TD></TR>
<TR><TD >NEMD SLLOD integration </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
<TR><TD >tensile and shear deformations </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
<TR><TD >GayBerne potential </TD><TD > Mike Brown (Sandia)</TD></TR>
<TR><TD >ellipsoidal particles </TD><TD > Mike Brown (Sandia)</TD></TR>
<TR><TD >colloid potentials </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
<TR><TD >fix heat </TD><TD > Paul Crozier and Ed Webb (Sandia)</TD></TR>
<TR><TD >neighbor multi and communicate multi </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
<TR><TD >MATLAB post-processing scripts </TD><TD > Arun Subramaniyan (Purdue)</TD></TR>
<TR><TD >triclinic (non-orthogonal) simulation domains </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
<TR><TD >thermo_extract tool</TD><TD > Vikas Varshney (Wright Patterson AFB)</TD></TR>
<TR><TD >fix ave/time and fix ave/spatial </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
<TR><TD >MEAM potential </TD><TD > Greg Wagner (Sandia)</TD></TR>
<TR><TD >optimized pair potentials for lj/cut, charmm/long, eam, morse </TD><TD > James Fischer (High Performance Technologies), David Richie and Vincent Natoli (Stone Ridge Technologies)</TD></TR>
<TR><TD >fix wall/lj126 </TD><TD > Mark Stevens (Sandia)</TD></TR>
<TR><TD >Stillinger-Weber and Tersoff potentials </TD><TD > Aidan Thompson and Xiaowang Zhou (Sandia)</TD></TR>
<TR><TD >region prism </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
<TR><TD >LJ tail corrections for energy/pressure </TD><TD > Paul Crozier (Sandia)</TD></TR>
<TR><TD >fix momentum and recenter </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
<TR><TD >multi-letter variable names </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
<TR><TD >OPLS dihedral potential</TD><TD > Mark Stevens (Sandia)</TD></TR>
<TR><TD >POEMS coupled rigid body integrator</TD><TD > Rudranarayan Mukherjee (RPI)</TD></TR>
<TR><TD >faster pair hybrid potential</TD><TD > James Fischer (High Performance Technologies, Inc), Vincent Natoli and David Richie (Stone Ridge Technology)</TD></TR>
<TR><TD >breakable bond quartic potential</TD><TD > Chris Lorenz and Mark Stevens (Sandia)</TD></TR>
<TR><TD >DCD and XTC dump styles</TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
<TR><TD >grain boundary orientation fix </TD><TD > Koenraad Janssens and David Olmsted (Sandia)</TD></TR>
<TR><TD >lj/smooth pair potential </TD><TD > Craig Maloney (UCSB) </TD></TR>
<TR><TD >radius-of-gyration spring fix </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U) and Paul Crozier (Sandia)</TD></TR>
<TR><TD >self spring fix </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
<TR><TD >EAM CoAl and AlCu potentials </TD><TD > Kwang-Reoul Lee (KIST, Korea)</TD></TR>
<TR><TD >cosine/squared angle potential </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
<TR><TD >helix dihedral potential </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U) and Mark Stevens (Sandia)</TD></TR>
<TR><TD >Finnis/Sinclair EAM</TD><TD > Tim Lau (MIT)</TD></TR>
<TR><TD >dissipative particle dynamics (DPD) potentials</TD><TD > Kurt Smith (U Pitt) and Frank van Swol (Sandia)</TD></TR>
<TR><TD >TIP4P potential (4-site water)</TD><TD > Ahmed Ismail and Amalie Frischknecht (Sandia)</TD></TR>
<TR><TD >uniaxial strain fix</TD><TD > Carsten Svaneborg (Max Planck Institute)</TD></TR>
<TR><TD >thermodynamics enhanced by fix quantities</TD><TD > Aidan Thompson (Sandia)</TD></TR>
<TR><TD >compressed dump files</TD><TD > Erik Luijten (U Illinois)</TD></TR>
<TR><TD >cylindrical indenter fix</TD><TD > Ravi Agrawal (Northwestern U)</TD></TR>
<TR><TD >electric field fix</TD><TD > Christina Payne (Vanderbilt U)</TD></TR>
<TR><TD >AMBER <-> LAMMPS tool</TD><TD > Keir Novik (Univ College London) and Vikas Varshney (U Akron)</TD></TR>
<TR><TD >CHARMM <-> LAMMPS tool</TD><TD > Pieter in 't Veld and Paul Crozier (Sandia)</TD></TR>
<TR><TD >Morse bond potential</TD><TD > Jeff Greathouse (Sandia)</TD></TR>
<TR><TD >radial distribution functions</TD><TD > Paul Crozier & Jeff Greathouse (Sandia)</TD></TR>
<TR><TD >force tables for long-range Coulombics</TD><TD > Paul Crozier (Sandia)</TD></TR>
<TR><TD >targeted molecular dynamics (TMD)</TD><TD > Paul Crozier (Sandia) and Christian Burisch (Bochum University, Germany)</TD></TR>
<TR><TD >FFT support for SGI SCSL (Altix)</TD><TD > Jim Shepherd (Ga Tech)</TD></TR>
<TR><TD >lmp2cfg and lmp2traj tools</TD><TD > Ara Kooser, Jeff Greathouse, Andrey Kalinichev (Sandia)</TD></TR>
<TR><TD >parallel tempering</TD><TD > Mark Sears (Sandia)</TD></TR>
<TR><TD >embedded atom method (EAM) potential</TD><TD > Stephen Foiles (Sandia)</TD></TR>
<TR><TD >multi-harmonic dihedral potential</TD><TD > Mathias Puetz (Sandia)</TD></TR>
<TR><TD >granular force fields and BC</TD><TD > Leo Silbert & Gary Grest (Sandia)</TD></TR>
<TR><TD >2d Ewald/PPPM</TD><TD > Paul Crozier (Sandia)</TD></TR>
<TR><TD >CHARMM force fields</TD><TD > Paul Crozier (Sandia)</TD></TR>
<TR><TD >msi2lmp tool</TD><TD > Steve Lustig (Dupont), Mike Peachey & John Carpenter (Cray)</TD></TR>
<TR><TD >HTFN energy minimizer</TD><TD > Todd Plantenga (Sandia)</TD></TR>
<TR><TD >class 2 force fields</TD><TD > Eric Simon (Cray)</TD></TR>
<TR><TD >NVT/NPT integrators</TD><TD > Mark Stevens (Sandia)</TD></TR>
<TR><TD >rRESPA</TD><TD > Mark Stevens & Paul Crozier (Sandia)</TD></TR>
<TR><TD >Ewald and PPPM solvers</TD><TD > Roy Pollock (LLNL) </TD><TD >
</TD></TR></TABLE></DIV>
<P>Other CRADA partners involved in the design and testing of LAMMPS were
</P>
<UL><LI>John Carpenter (Mayo Clinic, formerly at Cray Research)
<LI>Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
<LI>Steve Lustig (Dupont)
<LI>Jim Belak (LLNL)
</UL>
</HTML>
diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt
index 4c3a6be8a..9dde846b6 100644
--- a/doc/Section_intro.txt
+++ b/doc/Section_intro.txt
@@ -1,628 +1,628 @@
"Previous Section"_Manual.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_start.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
1. Introduction :h3
These sections provide an overview of what LAMMPS can and can't do,
describe what it means for LAMMPS to be an open-source code, and
acknowledge the funding and people who have contributed to LAMMPS over
the years.
1.1 "What is LAMMPS"_#intro_1
1.2 "LAMMPS features"_#intro_2
1.3 "LAMMPS non-features"_#intro_3
1.4 "Open source distribution"_#intro_4
1.5 "Acknowledgments and citations"_#intro_5 :all(b)
:line
1.1 What is LAMMPS :link(intro_1),h4
LAMMPS is a classical molecular dynamics code that models an ensemble
of particles in a liquid, solid, or gaseous state. It can model
atomic, polymeric, biological, metallic, granular, and coarse-grained
systems using a variety of force fields and boundary conditions.
For examples of LAMMPS simulations, see the Publications page of the
"LAMMPS WWW Site"_lws.
LAMMPS runs efficiently on single-processor desktop or laptop
machines, but is designed for parallel computers. It will run on any
parallel machine that compiles C++ and supports the "MPI"_mpi
message-passing library. This includes distributed- or shared-memory
parallel machines and Beowulf-style clusters.
:link(mpi,http://www-unix.mcs.anl.gov/mpi)
LAMMPS can model systems with only a few particles up to millions or
billions. See "this section"_Section_perf.html for information on LAMMPS
performance and scalability, or the Benchmarks section of the "LAMMPS
WWW Site"_lws.
LAMMPS is a freely-available open-source code, distributed under the
terms of the "GNU Public License"_gnu, which means you can use or
modify the code however you wish. See "this section"_#intro_4 for a brief
discussion of the open-source philosophy.
:link(gnu,http://www.gnu.org/copyleft/gpl.html)
LAMMPS is designed to be easy to modify or extend with new
capabilities, such as new force fields, atom types, boundary
conditions, or diagnostics. See "this section"_Section_modify.html for
more details.
The current version of LAMMPS is written in C++. Earlier versions
were written in F77 and F90. See "this section"_Section_history.html
for more information on different versions. All versions can be
downloaded from the "LAMMPS WWW Site"_lws.
LAMMPS was originally developed under a US Department of Energy CRADA
(Cooperative Research and Development Agreement) between two DOE labs
and 3 companies. It is distributed by "Sandia National Labs"_snl.
See "this section"_#intro_5 for more information on LAMMPS funding and
individuals who have contributed to LAMMPS.
:link(snl,http://www.sandia.gov)
In the most general sense, LAMMPS integrates Newton's equations of
motion for collections of atoms, molecules, or macroscopic particles
that interact via short- or long-range forces with a variety of
initial and/or boundary conditions. For computational efficiency
LAMMPS uses neighbor lists to keep track of nearby particles. The
lists are optimized for systems with particles that are repulsive at
short distances, so that the local density of particles never becomes
too large. On parallel machines, LAMMPS uses spatial-decomposition
techniques to partition the simulation domain into small 3d
sub-domains, one of which is assigned to each processor. Processors
communicate and store "ghost" atom information for atoms that border
their sub-domain. LAMMPS is most efficient (in a parallel sense) for
systems whose particles fill a 3d rectangular box with roughly uniform
density. Papers with technical details of the algorithms used in
LAMMPS are listed in "this section"_#intro_5.
:line
1.2 LAMMPS features :link(intro_2),h4
This section highlights LAMMPS features, with pointers to specific
commands which give more details. If LAMMPS doesn't have your
favorite interatomic potential, boundary condition, or atom type, see
"this section"_Section_modify.html, which describes how you can add it to
LAMMPS.
General features :h4
runs on a single processor or in parallel
distributed-memory message-passing parallelism (MPI)
spatial-decomposition of simulation domain for parallelism
open-source distribution
highly portable C++
optional libraries used: MPI and single-processor FFT
easy to extend with new features and functionality
runs from an input script
syntax for defining and using variables and formulas
syntax for looping over runs and breaking out of loops
run one or multiple simulations simultaneously (in parallel) from one script
build as library, invoke LAMMPS thru library interface or provided Python wrapper
couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul
Particle and model types :h4
("atom style"_atom_style.html command)
atoms
coarse-grained particles (e.g. bead-spring polymers)
united-atom polymers or organic molecules
all-atom polymers, organic molecules, proteins, DNA
metals
granular materials
coarse-grained mesoscale models
extended spherical and ellipsoidal particles
point dipolar particles
rigid collections of particles
hybrid combinations of these :ul
Force fields :h4
("pair style"_pair_style.html, "bond style"_bond_style.html,
"angle style"_angle_style.html, "dihedral style"_dihedral_style.html,
"improper style"_improper_style.html, "kspace style"_kspace_style.html
commands)
pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, \
Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
charged pairwise potentials: Coulombic, point-dipole
manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
embedded ion method (EIM), ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB
electron force field (eFF, AWPMD)
coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
- mesoscopic potentials: granular, Peridynamics
+ mesoscopic potentials: granular, Peridynamics, SPH
bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \
quartic (breakable)
angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, \
class 2 (COMPASS)
dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, \
class 2 (COMPASS), OPLS
improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS)
polymer potentials: all-atom, united-atom, bead-spring, breakable
water potentials: TIP3P, TIP4P, SPC
implicit solvent potentials: hydrodynamic lubrication, Debye
long-range Coulombics and dispersion: Ewald, \
PPPM (similar to particle-mesh Ewald), Ewald/N for long-range Lennard-Jones
force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options
handful of GPU-enabled pair styles :ul
hybrid potentials: multiple pair, bond, angle, dihedral, improper \
potentials can be used in one simulation
overlaid potentials: superposition of multiple pair potentials
Atom creation :h4
("read_data"_read_data.html, "lattice"_lattice.html,
"create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html,
"displace_atoms"_displace_atoms.html, "replicate"_replicate.html commands)
read in atom coords from files
create atoms on one or more lattices (e.g. grain boundaries)
delete geometric or logical groups of atoms (e.g. voids)
replicate existing atoms multiple times
displace atoms :ul
Ensembles, constraints, and boundary conditions :h4
("fix"_fix.html command)
2d or 3d systems
orthogonal or non-orthogonal (triclinic symmetry) simulation domains
constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators
thermostatting options for groups and geometric regions of atoms
pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions
simulation box deformation (tensile and shear)
harmonic (umbrella) constraint forces
rigid body constraints
SHAKE bond and angle constraints
bond breaking, formation, swapping
walls of various kinds
non-equilibrium molecular dynamics (NEMD)
variety of additional boundary conditions and constraints :ul
Integrators :h4
("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands)
velocity-Verlet integrator
Brownian dynamics
rigid body integration
energy minimization via conjugate gradient or steepest descent relaxation
rRESPA hierarchical timestepping :ul
Diagnostics :h4
see the various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul
Output :h4
("dump"_dump.html, "restart"_restart.html commands)
log file of thermodynamic info
text dump files of atom coords, velocities, other per-atom quantities
binary restart files
parallel I/O of dump and restart files
per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc)
user-defined system-wide (log file) or per-atom (dump file) calculations
spatial and time averaging of per-atom quantities
time averaging of system-wide quantities
atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul
Multi-replica models :h4
"nudged elastic band"_neb.html
"parallel replica dynamics"_prd.html
"temperature accelerated dynamics"_tad.html
"parallel tempering"_temper.html
Pre- and post-processing :h4
Various pre- and post-processing serial tools are packaged
with LAMMPS; see these "doc pages"_Section_tools.html. :ulb,l
Our group has also written and released a separate toolkit called
"Pizza.py"_pizza which provides tools for doing setup, analysis,
plotting, and visualization for LAMMPS simulations. Pizza.py is
written in "Python"_python and is available for download from "the
Pizza.py WWW site"_pizza. :l,ule
:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
:link(python,http://www.python.org)
Specialized features :h4
These are LAMMPS capabilities which you may not think of as typical
molecular dynamics options:
"stochastic rotation dynamics (SRD)"_fix_srd.html
"real-time visualization and interactive MD"_fix_imd.html
"atom-to-continuum coupling"_fix_atc.html with finite elements
coupled rigid body integration via the "POEMS"_fix_poems.html library
"grand canonical Monte Carlo"_doc/fix_gcmc.html insertions/deletions
"Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids
"Peridynamics mesoscale modeling"_pair_peri.html
"targeted"_fix_tmd.html and "steered"_fix_smd.html molecular dynamics
"two-temperature electron model"_fix_ttm.html :ul
:line
1.3 LAMMPS non-features :link(intro_3),h4
LAMMPS is designed to efficiently compute Newton's equations of motion
for a system of interacting particles. Many of the tools needed to
pre- and post-process the data for such simulations are not included
in the LAMMPS kernel for several reasons:
the desire to keep LAMMPS simple
they are not parallel operations
other codes already do them
limited development resources :ul
Specifically, LAMMPS itself does not:
run thru a GUI
build molecular systems
assign force-field coefficients automagically
perform sophisticated analyses of your MD simulation
visualize your MD simulation
plot your output data :ul
A few tools for pre- and post-processing tasks are provided as part of
the LAMMPS package; they are described in "this
section"_Section_tools.html. However, many people use other codes or
write their own tools for these tasks.
As noted above, our group has also written and released a separate
toolkit called "Pizza.py"_pizza which addresses some of the listed
bullets. It provides tools for doing setup, analysis, plotting, and
visualization for LAMMPS simulations. Pizza.py is written in
"Python"_python and is available for download from "the Pizza.py WWW
site"_pizza.
LAMMPS requires as input a list of initial atom coordinates and types,
molecular topology information, and force-field coefficients assigned
to all atoms and bonds. LAMMPS will not build molecular systems and
assign force-field parameters for you.
For atomic systems LAMMPS provides a "create_atoms"_create_atoms.html
command which places atoms on solid-state lattices (fcc, bcc,
user-defined, etc). Assigning small numbers of force field
coefficients can be done via the "pair coeff"_pair_coeff.html, "bond
coeff"_bond_coeff.html, "angle coeff"_angle_coeff.html, etc commands.
For molecular systems or more complicated simulation geometries, users
typically use another code as a builder and convert its output to
LAMMPS input format, or write their own code to generate atom
coordinate and molecular topology for LAMMPS to read in.
For complicated molecular systems (e.g. a protein), a multitude of
topology information and hundreds of force-field coefficients must
typically be specified. We suggest you use a program like
"CHARMM"_charmm or "AMBER"_amber or other molecular builders to setup
such problems and dump its information to a file. You can then
reformat the file as LAMMPS input. Some of the tools in "this
section"_Section_tools.html can assist in this process.
Similarly, LAMMPS creates output files in a simple format. Most users
post-process these files with their own analysis tools or re-format
them for input into other programs, including visualization packages.
If you are convinced you need to compute something on-the-fly as
LAMMPS runs, see "this section"_Section_modify.html for a discussion
of how you can use the "dump"_dump.html and "compute"_compute.html and
"fix"_fix.html commands to print out data of your choosing. Keep in
mind that complicated computations can slow down the molecular
dynamics timestepping, particularly if the computations are not
parallel, so it is often better to leave such analysis to
post-processing codes.
A very simple (yet fast) visualizer is provided with the LAMMPS
package - see the "xmovie"_Section_tools.html#xmovie tool in "this
section"_Section_tools.html. It creates xyz projection views of
atomic coordinates and animates them. We find it very useful for
debugging purposes. For high-quality visualization we recommend the
following packages:
"VMD"_http://www.ks.uiuc.edu/Research/vmd
"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A
"PyMol"_http://pymol.sourceforge.net
"Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html
"RasMol"_http://www.openrasmol.org :ul
Other features that LAMMPS does not yet (and may never) support are
discussed in "this section"_Section_history.html.
Finally, these are freely-available molecular dynamics codes, most of
them parallel, which may be well-suited to the problems you want to
model. They can also be used in conjunction with LAMMPS to perform
complementary modeling tasks.
"CHARMM"_charmm
"AMBER"_amber
"NAMD"_namd
"NWCHEM"_nwchem
"DL_POLY"_dlpoly
"Tinker"_tinker :ul
:link(charmm,http://www.scripps.edu/brooks)
:link(amber,http://amber.scripps.edu)
:link(namd,http://www.ks.uiuc.edu/Research/namd/)
:link(nwchem,http://www.emsl.pnl.gov/docs/nwchem/nwchem.html)
:link(dlpoly,http://www.cse.clrc.ac.uk/msi/software/DL_POLY)
:link(tinker,http://dasher.wustl.edu/tinker)
CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for
modeling biological molecules. CHARMM and AMBER use
atom-decomposition (replicated-data) strategies for parallelism; NAMD
and NWCHEM use spatial-decomposition approaches, similar to LAMMPS.
Tinker is a serial code. DL_POLY includes potentials for a variety of
biological and non-biological materials; both a replicated-data and
spatial-decomposition version exist.
:line
1.4 Open source distribution :link(intro_4),h4
LAMMPS comes with no warranty of any kind. As each source file states
in its header, it is a copyrighted code that is distributed free-of-
charge, under the terms of the "GNU Public License"_gnu (GPL). This
is often referred to as open-source distribution - see
"www.gnu.org"_gnuorg or "www.opensource.org"_opensource for more
details. The legal text of the GPL is in the LICENSE file that is
included in the LAMMPS distribution.
:link(gnuorg,http://www.gnu.org)
:link(opensource,http://www.opensource.org)
Here is a summary of what the GPL means for LAMMPS users:
(1) Anyone is free to use, modify, or extend LAMMPS in any way they
choose, including for commercial purposes.
(2) If you distribute a modified version of LAMMPS, it must remain
open-source, meaning you distribute it under the terms of the GPL.
You should clearly annotate such a code as a derivative version of
LAMMPS.
(3) If you release any code that includes LAMMPS source code, then it
must also be open-sourced, meaning you distribute it under the terms
of the GPL.
(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
source file headers (including the copyright and GPL notices) should
remain part of the code.
In the spirit of an open-source code, these are various ways you can
contribute to making LAMMPS better. You can send email to the
"developers"_http://lammps.sandia.gov/authors.html on any of these
items.
Point prospective users to the "LAMMPS WWW Site"_lws. Mention it in
talks or link to it from your WWW site. :ulb,l
If you find an error or omission in this manual or on the "LAMMPS WWW
Site"_lws, or have a suggestion for something to clarify or include,
send an email to the
"developers"_http://lammps.sandia.gov/authors.html. :l
If you find a bug, "this section"_Section_errors.html#err_2 describes
how to report it. :l
If you publish a paper using LAMMPS results, send the citation (and
any cool pictures or movies if you like) to add to the Publications,
Pictures, and Movies pages of the "LAMMPS WWW Site"_lws, with links
and attributions back to you. :l
Create a new Makefile.machine that can be added to the src/MAKE
directory. :l
The tools sub-directory of the LAMMPS distribution has various
stand-alone codes for pre- and post-processing of LAMMPS data. More
details are given in "this section"_Section_tools.html. If you write
a new tool that users will find useful, it can be added to the LAMMPS
distribution. :l
LAMMPS is designed to be easy to extend with new code for features
like potentials, boundary conditions, diagnostic computations, etc.
"This section"_Section_modify.html gives details. If you add a
feature of general interest, it can be added to the LAMMPS
distribution. :l
The Benchmark page of the "LAMMPS WWW Site"_lws lists LAMMPS
performance on various platforms. The files needed to run the
benchmarks are part of the LAMMPS distribution. If your machine is
sufficiently different from those listed, your timing data can be
added to the page. :l
You can send feedback for the User Comments page of the "LAMMPS WWW
Site"_lws. It might be added to the page. No promises. :l
Cash. Small denominations, unmarked bills preferred. Paper sack OK.
Leave on desk. VISA also accepted. Chocolate chip cookies
encouraged. :ule,l
:line
1.5 Acknowledgments and citations :h4,link(intro_5)
LAMMPS development has been funded by the "US Department of
Energy"_doe (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
programs and its "OASCR"_oascr and "OBER"_ober offices.
Specifically, work on the latest version was funded in part by the US
Department of Energy's Genomics:GTL program
("www.doegenomestolife.org"_gtl) under the "project"_ourgtl, "Carbon
Sequestration in Synechococcus Sp.: From Molecular Machines to
Hierarchical Modeling".
:link(doe,http://www.doe.gov)
:link(gtl,http://www.doegenomestolife.org)
:link(ourgtl,http://www.genomes2life.org)
:link(oascr,http://www.sc.doe.gov/ascr/home.html)
:link(ober,http://www.er.doe.gov/production/ober/ober_top.html)
The following papers describe the parallel algorithms used in LAMMPS.
S. J. Plimpton, [Fast Parallel Algorithms for Short-Range Molecular
Dynamics], J Comp Phys, 117, 1-19 (1995).
S. J. Plimpton, R. Pollock, M. Stevens, [Particle-Mesh Ewald and
rRESPA for Parallel Molecular Dynamics Simulations], in Proc of the
Eighth SIAM Conference on Parallel Processing for Scientific
Computing, Minneapolis, MN (March 1997).
If you use LAMMPS results in your published work, please cite the J
Comp Phys reference and include a pointer to the "LAMMPS WWW Site"_lws
(http://lammps.sandia.gov).
If you send is information about your publication, we'll be pleased to
add it to the Publications page of the "LAMMPS WWW Site"_lws. Ditto
for a picture or movie for the Pictures or Movies pages.
The core group of LAMMPS developers is at Sandia National Labs. They
include "Steve Plimpton"_sjp, Paul Crozier, and Aidan Thompson and can
be contacted via email: sjplimp, pscrozi, athomps at sandia.gov.
Here are various folks who have made significant contributions to
features in LAMMPS. The most recent contributions are at the top of
the list.
:link(sjp,http://www.sandia.gov/~sjplimp)
pppm GPU single and double : Mike Brown (ORNL)
pair_style lj/cut/expand : Inderaj Bains (NVIDIA)
temperature accelerated dynamics (TAD) : Aidan Thompson (Sandia)
pair reax/c and fix qeq/reax : Metin Aktulga (Purdue, now LBNL)
DREIDING force field, pair_style hbond/dreiding, etc : Tod Pascal (CalTech)
fix adapt and compute ti for thermodynamic integreation for free energies : Sai Jayaraman (Sandia)
pair born and pair gauss : Sai Jayaraman (Sandia)
stochastic rotation dynamics (SRD) via fix srd : Jemery Lechman (Sandia) and Pieter in 't Veld (BASF)
ipp Perl script tool : Reese Jones (Sandia)
eam_database and createatoms tools : Xiaowang Zhou (Sandia)
electron force field (eFF) : Andres Jaramillo-Botero and Julius Su (Caltech)
embedded ion method (EIM) potential : Xiaowang Zhou (Sandia)
COMB potential with charge equilibration : Tzu-Ray Shan (U Florida)
fix ave/correlate : Benoit Leblanc, Dave Rigby, Paul Saxe (Materials Design) and Reese Jones (Sandia)
pair_style peri/lps : Mike Parks (Sandia)
fix msst : Lawrence Fried (LLNL), Evan Reed (LLNL, Stanford)
thermo_style custom tpcpu & spcpu keywords : Axel Kohlmeyer (Temple U)
fix rigid/nve, fix rigid/nvt : Tony Sheh and Trung Dac Nguyen (U Michigan)
public SVN & Git repositories for LAMMPS : Axel Kohlmeyer (Temple U) and Bill Goldman (Sandia)
fix nvt, fix nph, fix npt, Parinello/Rahman dynamics, fix box/relax : Aidan Thompson (Sandia)
compute heat/flux : German Samolyuk (ORNL) and Mario Pinto (Computational Research Lab, Pune, India)
pair yukawa/colloid : Randy Schunk (Sandia)
fix wall/colloid : Jeremy Lechman (Sandia)
pair_style dsmc for Direct Simulation Monte Carlo (DSMC) modeling : Paul Crozier (Sandia)
fix imd for real-time viz and interactive MD : Axel Kohlmeyer (Temple Univ)
concentration-dependent EAM potential : Alexander Stukowski (Technical University of Darmstadt)
parallel replica dymamics (PRD) : Mike Brown (Sandia)
min_style hftn : Todd Plantenga (Sandia)
fix atc : Reese Jones, Jon Zimmerman, Jeremy Templeton (Sandia)
dump cfg : Liang Wan (Chinese Academy of Sciences)
fix nvt with Nose/Hoover chains : Andy Ballard (U Maryland)
pair_style lj/cut/gpu, pair_style gayberne/gpu : Mike Brown (Sandia)
pair_style lj96/cut, bond_style table, angle_style table : Chuanfu Luo
fix langevin tally : Carolyn Phillips (U Michigan)
compute heat/flux for Green-Kubo : Reese Jones (Sandia), Philip Howell (Siemens), Vikas Varsney (AFRL)
region cone : Pim Schravendijk
fix reax/bonds : Aidan Thompson (Sandia)
pair born/coul/long : Ahmed Ismail (Sandia)
fix ttm : Paul Crozier (Sandia) and Carolyn Phillips (U Michigan)
fix box/relax : Aidan Thompson and David Olmsted (Sandia)
ReaxFF potential : Aidan Thompson (Sandia) and Hansohl Cho (MIT)
compute cna/atom : Wan Liang (Chinese Academy of Sciences)
Tersoff/ZBL potential : Dave Farrell (Northwestern U)
peridynamics : Mike Parks (Sandia)
fix smd for steered MD : Axel Kohlmeyer (U Penn)
GROMACS pair potentials : Mark Stevens (Sandia)
lmp2vmd tool : Axel Kohlmeyer (U Penn)
compute group/group : Naveen Michaud-Agrawal (Johns Hopkins U)
-CG-CMM user package for coarse-graining : Axel Kohlmeyer (U Penn)
+USER-CG-CMM package for coarse-graining : Axel Kohlmeyer (U Penn)
cosine/delta angle potential : Axel Kohlmeyer (U Penn)
VIM editor add-ons for LAMMPS input scripts : Gerolf Ziegenhain
pair lubricate : Randy Schunk (Sandia)
compute ackland/atom : Gerolf Zeigenhain
kspace_style ewald/n, pair_style lj/coul, pair_style buck/coul : \
Pieter in 't Veld (Sandia)
AIREBO bond-order potential : Ase Henry (MIT)
making LAMMPS a true "object" that can be instantiated multiple times, \
e.g. as a library : Ben FrantzDale (RPI)
pymol_asphere viz tool : Mike Brown (Sandia)
NEMD SLLOD integration : Pieter in 't Veld (Sandia)
tensile and shear deformations : Pieter in 't Veld (Sandia)
GayBerne potential : Mike Brown (Sandia)
ellipsoidal particles : Mike Brown (Sandia)
colloid potentials : Pieter in 't Veld (Sandia)
fix heat : Paul Crozier and Ed Webb (Sandia)
neighbor multi and communicate multi : Pieter in 't Veld (Sandia)
MATLAB post-processing scripts : Arun Subramaniyan (Purdue)
triclinic (non-orthogonal) simulation domains : Pieter in 't Veld (Sandia)
thermo_extract tool: Vikas Varshney (Wright Patterson AFB)
fix ave/time and fix ave/spatial : Pieter in 't Veld (Sandia)
MEAM potential : Greg Wagner (Sandia)
optimized pair potentials for lj/cut, charmm/long, eam, morse : \
James Fischer (High Performance Technologies), \
David Richie and Vincent Natoli (Stone Ridge Technologies)
fix wall/lj126 : Mark Stevens (Sandia)
Stillinger-Weber and Tersoff potentials : Aidan Thompson and Xiaowang Zhou (Sandia)
region prism : Pieter in 't Veld (Sandia)
LJ tail corrections for energy/pressure : Paul Crozier (Sandia)
fix momentum and recenter : Naveen Michaud-Agrawal (Johns Hopkins U)
multi-letter variable names : Naveen Michaud-Agrawal (Johns Hopkins U)
OPLS dihedral potential: Mark Stevens (Sandia)
POEMS coupled rigid body integrator: Rudranarayan Mukherjee (RPI)
faster pair hybrid potential: James Fischer \
(High Performance Technologies, Inc), Vincent Natoli and \
David Richie (Stone Ridge Technology)
breakable bond quartic potential: Chris Lorenz and Mark Stevens (Sandia)
DCD and XTC dump styles: Naveen Michaud-Agrawal (Johns Hopkins U)
grain boundary orientation fix : Koenraad Janssens and David Olmsted (Sandia)
lj/smooth pair potential : Craig Maloney (UCSB)
radius-of-gyration spring fix : Naveen Michaud-Agrawal (Johns Hopkins U) and \
Paul Crozier (Sandia)
self spring fix : Naveen Michaud-Agrawal (Johns Hopkins U)
EAM CoAl and AlCu potentials : Kwang-Reoul Lee (KIST, Korea)
cosine/squared angle potential : Naveen Michaud-Agrawal (Johns Hopkins U)
helix dihedral potential : Naveen Michaud-Agrawal (Johns Hopkins U) and \
Mark Stevens (Sandia)
Finnis/Sinclair EAM: Tim Lau (MIT)
dissipative particle dynamics (DPD) potentials: Kurt Smith (U Pitt) and \
Frank van Swol (Sandia)
TIP4P potential (4-site water): Ahmed Ismail and Amalie Frischknecht (Sandia)
uniaxial strain fix: Carsten Svaneborg (Max Planck Institute)
thermodynamics enhanced by fix quantities: Aidan Thompson (Sandia)
compressed dump files: Erik Luijten (U Illinois)
cylindrical indenter fix: Ravi Agrawal (Northwestern U)
electric field fix: Christina Payne (Vanderbilt U)
AMBER <-> LAMMPS tool: Keir Novik (Univ College London) and \
Vikas Varshney (U Akron)
CHARMM <-> LAMMPS tool: Pieter in 't Veld and Paul Crozier (Sandia)
Morse bond potential: Jeff Greathouse (Sandia)
radial distribution functions: Paul Crozier & Jeff Greathouse (Sandia)
force tables for long-range Coulombics: Paul Crozier (Sandia)
targeted molecular dynamics (TMD): Paul Crozier (Sandia) and \
Christian Burisch (Bochum University, Germany)
FFT support for SGI SCSL (Altix): Jim Shepherd (Ga Tech)
lmp2cfg and lmp2traj tools: Ara Kooser, Jeff Greathouse, \
Andrey Kalinichev (Sandia)
parallel tempering: Mark Sears (Sandia)
embedded atom method (EAM) potential: Stephen Foiles (Sandia)
multi-harmonic dihedral potential: Mathias Puetz (Sandia)
granular force fields and BC: Leo Silbert & Gary Grest (Sandia)
2d Ewald/PPPM: Paul Crozier (Sandia)
CHARMM force fields: Paul Crozier (Sandia)
msi2lmp tool: Steve Lustig (Dupont), Mike Peachey & John Carpenter (Cray)
HTFN energy minimizer: Todd Plantenga (Sandia)
class 2 force fields: Eric Simon (Cray)
NVT/NPT integrators: Mark Stevens (Sandia)
rRESPA: Mark Stevens & Paul Crozier (Sandia)
Ewald and PPPM solvers: Roy Pollock (LLNL) : :tb(s=:)
Other CRADA partners involved in the design and testing of LAMMPS were
John Carpenter (Mayo Clinic, formerly at Cray Research)
Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
Steve Lustig (Dupont)
Jim Belak (LLNL) :ul
diff --git a/doc/Section_packages.html b/doc/Section_packages.html
new file mode 100644
index 000000000..64de534fa
--- /dev/null
+++ b/doc/Section_packages.html
@@ -0,0 +1,388 @@
+<HTML>
+<CENTER><A HREF = "Section_commands.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
+<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_accelerate.html">Next
+Section</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>4. Packages
+</H3>
+<P>LAMMPS includes many optional packages, which are groups of files that
+enable a specific set of features. For example, force fields for
+molecular systems or granular systems are in packages. You can see
+the list of all packages by typing "make package" from within the src
+directory of the LAMMPS distribution.
+</P>
+<P>See <A HREF = "Section_start.html#start_3">this section</A> of the manual for
+details on how to include/exclude specific packages as part of the
+LAMMPS build process, and for more details about the differences
+between standard packages and user packages in LAMMPS.
+</P>
+<P>Below, the packages currently availabe in LAMMPS are listed. For
+standard packages, just a one-line description is given. For user
+packages, more details are provided.
+</P>
+4.1 <A HREF = "#pkg_1">Standard packages</A><BR>
+4.2 <A HREF = "#pkg_2">User packages</A> <BR>
+
+<HR>
+
+<HR>
+
+<H4><A NAME = "pkg_1"></A>4.1 Standard packages
+</H4>
+<P>The current list of standard packages is as follows:
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD >Package</TD><TD > Description</TD><TD > Author(s)</TD><TD > Doc page</TD><TD > Example</TD><TD > Library</TD></TR>
+<TR ALIGN="center"><TD >ASPHERE</TD><TD > aspherical particles</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_14">howto</A></TD><TD > ellipse</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >CLASS2</TD><TD > class 2 force fields</TD><TD > -</TD><TD > <A HREF = "pair_class2.html">pair_style lj/class2</A></TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >COLLOID</TD><TD > colloidal particles</TD><TD > -</TD><TD > <A HREF = "atom_style.html">atom_style colloid</A></TD><TD > colloid</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >DIPOLE</TD><TD > point dipole particles</TD><TD > -</TD><TD > <A HREF = "pair_dipole.html">pair_style dipole/cut</A></TD><TD > dipole</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >GPU</TD><TD > GPU-enabled potentials</TD><TD > Mike Brown (ORNL)</TD><TD > <A HREF = "Section_accelerate.html#acc_3">accelerate</A></TD><TD > gpu</TD><TD > lib/gpu</TD></TR>
+<TR ALIGN="center"><TD >GRANULAR</TD><TD > granular systems</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_6">howto</A></TD><TD > pour</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >KSPACE</TD><TD > long-range Coulombic solvers</TD><TD > -</TD><TD > <A HREF = "kspace_style.html">kspace_style</A></TD><TD > peptide</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >MANYBODY</TD><TD > many-body potentials</TD><TD > -</TD><TD > <A HREF = "pair_tersoff.html">pair_style tersoff</A></TD><TD > shear</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >MEAM</TD><TD > modified EAM potential</TD><TD > Greg Wagner (Sandia)</TD><TD > <A HREF = "pair_meam.html">pair_style meam</A></TD><TD > meam</TD><TD > lib/meam</TD></TR>
+<TR ALIGN="center"><TD >MC</TD><TD > Monte Carlo options</TD><TD > -</TD><TD > <A HREF = "fix_gcmc.html">fix gcmc</A></TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >MOLECULE</TD><TD > molecular system force fields</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_3">howto</A></TD><TD > peptide</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >OPT</TD><TD > optimized pair potentials</TD><TD > Fischer & Richie & Natoli (1)</TD><TD > <A HREF = "Section_accelerate.html#acc_1">howto</A></TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >PERI</TD><TD > Peridynamics models</TD><TD > Mike Parks (Sandia)</TD><TD > <A HREF = "pair_peri.html">pair_style peri</A></TD><TD > peri</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >POEMS</TD><TD > coupled rigid body motion</TD><TD > Rudra Mukherjee (JPL)</TD><TD > <A HREF = "fix_poems.html">fix poems</A></TD><TD > rigid</TD><TD > lib/poems</TD></TR>
+<TR ALIGN="center"><TD >REAX</TD><TD > ReaxFF potential</TD><TD > Aidan Thompson (Sandia)</TD><TD > <A HREF = "pair_reax.html">pair_style reax</A></TD><TD > reax</TD><TD > lib/reax</TD></TR>
+<TR ALIGN="center"><TD >REPLICA</TD><TD > multi-replica methods</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_5">howto</A></TD><TD > tad</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >SHOCK</TD><TD > shock loading methods</TD><TD > -</TD><TD > <A HREF = "fix_msst.html">fix msst</A></TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >SRD</TD><TD > stochastic rotation dynamics</TD><TD > -</TD><TD > <A HREF = "fix_srd.html">fix srd</A></TD><TD > srd</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >XTC</TD><TD > dumps in XTC format</TD><TD > -</TD><TD > <A HREF = "dump.html">dump</A></TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >
+</TD></TR></TABLE></DIV>
+
+<P>The "Authors" column lists a name(s) if a specific person is
+responible for creating and maintaining the package.
+</P>
+<P>(1) The OPT package was created by James Fischer (High Performance
+Technologies), David Richie, and Vincent Natoli (Stone Ridge
+Technolgy).
+</P>
+<P>The "Doc page" column links to either a portion of the
+<A HREF = "Section_howto.html">Section_howto</A> of the manual, or an input script
+command implemented as part of the package.
+</P>
+<P>The "Example" column is a sub-directory in the examples directory of
+the distribution which has an input script that uses the package.
+E.g. "peptide" refers to the examples/peptide directory.
+</P>
+<P>The "Library" column lists an external library which must be built first and which LAMMPS links to when it is built. These are in the lib directory of the distribution. <A HREF = "Section_start.html#start_3_3">This section</A> of the manual gives details on the 2-step build process with external libraries.
+</P>
+<HR>
+
+<HR>
+
+<H4><A NAME = "pkg_2"></A>4.2 User packages
+</H4>
+<P>The current list of user-contributed packages is as follows:
+</P>
+<DIV ALIGN=center><TABLE BORDER=1 >
+<TR ALIGN="center"><TD >Package</TD><TD > Description</TD><TD > Author(s)</TD><TD > Doc page</TD><TD > Example</TD><TD > Pic/movie</TD><TD > Library</TD></TR>
+<TR ALIGN="center"><TD >USER-MISC</TD><TD > single-file contributions</TD><TD > USER-MISC/README</TD><TD > -</TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >USER-ATC</TD><TD > atom-to-continuum coupling</TD><TD > Jones & Templeton & Zimmerman (2)</TD><TD > <A HREF = "fix_atc.html">fix atc</A></TD><TD > USER/atc</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#atc">atc</A></TD><TD > lib/atc</TD></TR>
+<TR ALIGN="center"><TD >USER-AWPMD</TD><TD > wave-packet MD</TD><TD > Ilya Valuev (JIHT)</TD><TD > <A HREF = "pair_awpmd.html">pair_style awpmd/cut</A></TD><TD > USER/awpmd</TD><TD > -</TD><TD > lib/awpmd</TD></TR>
+<TR ALIGN="center"><TD >USER-CG-CMM</TD><TD > coarse-graining model</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "pair_cmm.html">pair_style cg/cmm</A></TD><TD > USER/cg-cmm</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#cg">cg</A></TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >USER-CUDA</TD><TD > NVIDIA GPU styles</TD><TD > Christian Trott (U Tech Ilmenau)</TD><TD > <A HREF = "Section_accelerate.html#acc_4">accelerate</A></TD><TD > USER/cuda</TD><TD > -</TD><TD > lib/cuda</TD></TR>
+<TR ALIGN="center"><TD >USER-EFF</TD><TD > electron force field</TD><TD > Andres Jaramillo-Botero (Caltech)</TD><TD > <A HREF = "pair_eff.html">pair_style eff/cut</A></TD><TD > USER/eff</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#eff">eff</A></TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >USER-EWALDN</TD><TD > Ewald for 1/R^n</TD><TD > Pieter in' t Veld (BASF)</TD><TD > <A HREF = "kspace_style.html">kspace_style</A></TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >USER-REAXC</TD><TD > C version of ReaxFF</TD><TD > Metin Aktulga (LBNL)</TD><TD > <A HREF = "pair_reax_c.html">pair_style reaxc</A></TD><TD > reax</TD><TD > -</TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >USER-SPH</TD><TD > smoothed particle hydrodynamics</TD><TD > Georg Ganzenmuller (EMI)</TD><TD > <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">SPH_LAMMPS_userguide.pdf</A></TD><TD > USER/sph</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#sph">sph</A></TD><TD > -</TD></TR>
+<TR ALIGN="center"><TD >
+</TD></TR></TABLE></DIV>
+
+
+
+
+
+
+
+
+
+<P>The "Authors" column lists a name(s) if a specific person is
+responible for creating and maintaining the package.
+</P>
+<P>(2) The ATC package was created by Reese Jones, Jeremy Templeton, and Jon Zimmerman (Sandia).
+</P>
+<P>The "Doc page" column links to either a portion of the
+<A HREF = "Section_howto.html">Section_howto</A> of the manual, or an input script
+command implemented as part of the package, or to additional
+documentation provided witht he package.
+</P>
+<P>The "Example" column is a sub-directory in the examples directory of
+the distribution which has an input script that uses the package.
+E.g. "peptide" refers to the examples/peptide directory. USER/cuda
+refers to the examples/USER/cuda directory.
+</P>
+<P>The "Library" column lists an external library which must be built
+first and which LAMMPS links to when it is built. These are in the
+lib directory of the distribution. <A HREF = "Section_start.html#start_3_3">This
+section</A> of the manual gives details on
+the 2-step build process with external libraries.
+</P>
+<P>More details on each package, from the USER-blah/README file
+is given below.
+</P>
+<HR>
+
+<H4>USER-MISC package
+</H4>
+<P>The files in this package are a potpourri of (mostly) unrelated
+features contributed to LAMMPS by users. Each feature is a single
+pair of files (*.cpp and *.h).
+</P>
+<P>More information about each feature can be found by reading its doc
+page in the LAMMPS doc directory. The doc page which lists all LAMMPS
+input script commands is as follows:
+</P>
+<P><A HREF = "Section_commands.html#cmd_5">Section_commands</A>
+</P>
+<P>User-contributed features are listed at the bottom of the fix,
+compute, pair, etc sections.
+</P>
+<P>The list of features and author of each is given in the
+src/USER-MISC/README file.
+</P>
+<P>You should contact the author directly if you have specific questions
+about the feature or its coding.
+</P>
+<HR>
+
+<H4>USER-ATC package
+</H4>
+<P>This package implements a "fix atc" command which can be used in a
+LAMMPS input script. This fix can be employed to either do concurrent
+coupling of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.
+</P>
+<P>See the doc page for the fix atc command to get started. At the
+bottom of the doc page are many links to additional documentation
+contained in the doc/USER/atc directory.
+</P>
+<P>There are example scripts for using this package in examples/USER/atc.
+</P>
+<P>This package uses an external library in lib/atc which must be
+compiled before making LAMMPS. See the lib/atc/README file and the
+LAMMPS manual for information on building LAMMPS with external
+libraries.
+</P>
+<P>The primary people who created this package are Reese Jones (rjones at
+sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon
+Zimmerman (jzimmer at sandia.gov) at Sandia. Contact them directly if
+you have questions.
+</P>
+<HR>
+
+<H4>USER-AWPMD package
+</H4>
+<P>This package contains a LAMMPS implementation of the Antisymmetrized
+Wave Packet Molecular Dynamics (AWPMD) method.
+</P>
+<P>See the doc page for the pair_style awpmd/cut command to get started.
+</P>
+<P>There are example scripts for using this package in examples/USER/awpmd.
+</P>
+<P>This package uses an external library in lib/awpmd which must be
+compiled before making LAMMPS. See the lib/awpmd/README file and the
+LAMMPS manual for information on building LAMMPS with external
+libraries.
+</P>
+<P>The person who created this package is Ilya Valuev at the JIHT in
+Russia (valuev at physik.hu-berlin.de). Contact him directly if you
+have questions.
+</P>
+<HR>
+
+<H4>USER-CG-CMM package
+</H4>
+<P>This package implements 4 commands which can be used in a LAMMPS input
+script:
+</P>
+<UL><LI>pair_style cg/cmm
+<LI>pair_style cg/cmm/coul/cut
+<LI>pair_style cg/cmm/coul/long
+<LI>angle_style cg/cmm
+</UL>
+<P>These styles allow coarse grained MD simulations with the
+parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
+(cg/cmm), with extensions to simulate ionic liquids, electrolytes,
+lipids and charged amino acids (to be published soon).
+</P>
+<P>See the doc pages for these commands for details.
+</P>
+<P>There are example scripts for using this package in
+examples/USER/cg-cmm.
+</P>
+<P>The current version of this package should be considered beta
+quality. The CG potentials work correctly and well, but there will be
+optimizations, cleanups and additional tools to aid in setting up and
+analyzing simulations with this package added in the next months.
+</P>
+<P>The person who created this package is Axel Kohlmeyer at Temple U
+(akohlmey at gmail.com). Contact him directly if you have questions.
+</P>
+<HR>
+
+<H4>USER-CUDA package
+</H4>
+<P>This package provides acceleration of various LAMMPS pair styles, fix
+styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
+GPUs.
+</P>
+<P>See this section of the manual to get started:
+</P>
+<P><A HREF = "Section_accelerate.html#acc_4">Section_accelerate</A>
+</P>
+<P>There are example scripts for using this package in
+examples/USER/cuda.
+</P>
+<P>This package uses an external library in lib/cuda which must be
+compiled before making LAMMPS. See the lib/cuda/README file and the
+LAMMPS manual for information on building LAMMPS with external
+libraries.
+</P>
+<P>The person who created this package is Christian Trott at the
+University of Technology Ilmenau, Germany (christian.trott at
+tu-ilmenau.de). Contact him directly if you have questions.
+</P>
+<HR>
+
+<H4>USER-EFF package
+</H4>
+<P>This package contains a LAMMPS implementation of the electron Force
+Field (eFF) currently under development at Caltech, as described in
+A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
+2010. The eFF potential was first introduced by Su and Goddard, in
+2007.
+</P>
+<P>eFF can be viewed as an approximation to QM wave packet dynamics and
+Fermionic molecular dynamics, combining the ability of electronic
+structure methods to describe atomic structure, bonding, and chemistry
+in materials, and of plasma methods to describe nonequilibrium
+dynamics of large systems with a large number of highly excited
+electrons. We classify it as a mixed QM-classical approach rather than
+a conventional force field method, which introduces QM-based terms (a
+spin-dependent repulsion term to account for the Pauli exclusion
+principle and the electron wavefunction kinetic energy associated with
+the Heisenberg principle) that reduce, along with classical
+electrostatic terms between nuclei and electrons, to the sum of a set
+of effective pairwise potentials. This makes eFF uniquely suited to
+simulate materials over a wide range of temperatures and pressures
+where electronically excited and ionized states of matter can occur
+and coexist.
+</P>
+<P>The necessary customizations to the LAMMPS core are in place to
+enable the correct handling of explicit electron properties during
+minimization and dynamics.
+</P>
+<P>See the doc page for the pair_style eff/cut command to get started.
+</P>
+<P>There are example scripts for using this package in
+examples/USER/eff.
+</P>
+<P>There are auxiliary tools for using this package in tools/eff.
+</P>
+<P>The person who created this package is Andres Jaramillo-Botero at
+CalTech (ajaramil at wag.caltech.edu). Contact him directly if you
+have questions.
+</P>
+<HR>
+
+<H4>USER-EWALDN package
+</H4>
+<P>This package implements 3 commands which can be used in a LAMMPS input
+script: pair_style lj/coul, pair_style buck/coul, and kspace_style
+ewald/n.
+</P>
+<P>The "kspace_style ewald/n" command is similar to standard Ewald for
+charges, but also enables the Lennard-Jones interaction, or any 1/r^N
+interaction to be of infinite extent, instead of being cutoff. LAMMPS
+pair potentials for long-range Coulombic interactions, such as
+lj/cut/coul/long can be used with ewald/n. The two new pair_style
+commands provide the modifications for the short-range LJ and
+Buckingham interactions that can also be used with ewald/n.
+</P>
+<P>Another advantage of kspace_style ewald/n is that it can be used with
+non-orthogonal (triclinic symmetry) simulation boxes, either for just
+long-range Coulombic interactions, or for both Coulombic and 1/r^N LJ
+or Buckingham, which is not currently possible for other kspace styles
+such as PPPM and ewald.
+</P>
+<P>See the doc pages for these commands for details.
+</P>
+<P>The person who created these files is Pieter in' t Veld while at
+Sandia. He is now at BASF (pieter.intveld at basf.com). Contact him
+directly if you have questions.
+</P>
+<HR>
+
+<H4>USER-REAXC package
+</H4>
+<P>This package contains a implementation for LAMMPS of the ReaxFF force
+field. ReaxFF uses distance-dependent bond-order functions to
+represent the contributions of chemical bonding to the potential
+energy. It was originally developed by Adri van Duin and the Goddard
+group at CalTech.
+</P>
+<P>The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in
+C, should give identical or very similar results to pair_style reax,
+which is a ReaxFF implementation on top of a Fortran library, a
+version of which library was originally authored by Adri van Duin.
+</P>
+<P>The reax/c version should be somewhat faster and more scalable,
+particularly with respect to the charge equilibration calculation. It
+should also be easier to build and use since there are no complicating
+issues with Fortran memory allocation or linking to a Fortran library.
+</P>
+<P>For technical details about this implemention of ReaxFF, see
+this paper:
+</P>
+<P>Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods
+and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty,
+S. A. Pandit, A. Y. Grama, Parallel Computing, to appear (2011).
+</P>
+<P>See the doc page for the pair_style reax/c command for details
+of how to use it in LAMMPS.
+</P>
+<P>The person who created this package is Hasan Metin Aktulga (hmaktulga
+at lbl.gov), while at Purdue University. Contact him directly, or
+Aidan Thompson at Sandia (athomps at sandia.gov), if you have
+questions.
+</P>
+<HR>
+
+<H4>USER-SPH package
+</H4>
+<P>This package implements smoothed particle hydrodynamics (SPH) in
+LAMMPS. Currently, the package has the following features:
+</P>
+<P>* Tait, ideal gas, Lennard-Jones equation of states, full support for
+ complete (i.e. internal-energy dependent) equations of state
+* plain or Monaghans XSPH integration of the equations of motion
+* density continuity or density summation to propagate the density field
+* commands to set internal energy and density of particles from the
+ input script
+* output commands to access internal energy and density for dumping and
+ thermo output
+</P>
+<P>See the file doc/USER/sph/SPH_LAMMPS_userguide.pdf to get started.
+</P>
+<P>There are example scripts for using this package in examples/USER/sph.
+</P>
+<P>The person who created this package is Georg Ganzenmuller at the
+Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
+Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
+you have questions.
+</P>
+</HTML>
diff --git a/doc/Section_packages.txt b/doc/Section_packages.txt
new file mode 100644
index 000000000..356611af9
--- /dev/null
+++ b/doc/Section_packages.txt
@@ -0,0 +1,374 @@
+"Previous Section"_Section_commands.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Section_accelerate.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+4. Packages :h3
+
+LAMMPS includes many optional packages, which are groups of files that
+enable a specific set of features. For example, force fields for
+molecular systems or granular systems are in packages. You can see
+the list of all packages by typing "make package" from within the src
+directory of the LAMMPS distribution.
+
+See "this section"_Section_start.html#start_3 of the manual for
+details on how to include/exclude specific packages as part of the
+LAMMPS build process, and for more details about the differences
+between standard packages and user packages in LAMMPS.
+
+Below, the packages currently availabe in LAMMPS are listed. For
+standard packages, just a one-line description is given. For user
+packages, more details are provided.
+
+4.1 "Standard packages"_#pkg_1
+4.2 "User packages"_#pkg_2 :all(b)
+
+:line
+:line
+
+4.1 Standard packages :h4,link(pkg_1)
+
+The current list of standard packages is as follows:
+
+Package, Description, Author(s), Doc page, Example, Library
+ASPHERE, aspherical particles, -, "howto"_Section_howto.html#howto_14, ellipse, -
+CLASS2, class 2 force fields, -, "pair_style lj/class2"_pair_class2.html, -, -
+COLLOID, colloidal particles, -, "atom_style colloid"_atom_style.html, colloid, -
+DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dipole, -
+GPU, GPU-enabled potentials, Mike Brown (ORNL), "accelerate"_Section_accelerate.html#acc_3, gpu, lib/gpu
+GRANULAR, granular systems, -, "howto"_Section_howto.html#howto_6, pour, -
+KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, -
+MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, -
+MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam
+MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, -
+MOLECULE, molecular system force fields, -, "howto"_Section_howto.html#howto_3, peptide, -
+OPT, optimized pair potentials, Fischer & Richie & Natoli (1), "howto"_Section_accelerate.html#acc_1, -, -
+PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
+POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
+REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax, lib/reax
+REPLICA, multi-replica methods, -, "howto"_Section_howto.html#howto_5, tad, -
+SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -
+SRD, stochastic rotation dynamics, -, "fix srd"_fix_srd.html, srd, -
+XTC, dumps in XTC format, -, "dump"_dump.html, -, -
+:tb(ea=c)
+
+The "Authors" column lists a name(s) if a specific person is
+responible for creating and maintaining the package.
+
+(1) The OPT package was created by James Fischer (High Performance
+Technologies), David Richie, and Vincent Natoli (Stone Ridge
+Technolgy).
+
+The "Doc page" column links to either a portion of the
+"Section_howto"_Section_howto.html of the manual, or an input script
+command implemented as part of the package.
+
+The "Example" column is a sub-directory in the examples directory of
+the distribution which has an input script that uses the package.
+E.g. "peptide" refers to the examples/peptide directory.
+
+The "Library" column lists an external library which must be built first and which LAMMPS links to when it is built. These are in the lib directory of the distribution. "This section"_Section_start.html#start_3_3 of the manual gives details on the 2-step build process with external libraries.
+
+:line
+:line
+
+4.2 User packages :h4,link(pkg_2)
+
+The current list of user-contributed packages is as follows:
+
+Package, Description, Author(s), Doc page, Example, Pic/movie, Library
+USER-MISC, single-file contributions, USER-MISC/README, -, -, -, -
+USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (2), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
+USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
+USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style cg/cmm"_pair_cmm.html, USER/cg-cmm, "cg"_cg, -
+USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "accelerate"_Section_accelerate.html#acc_4, USER/cuda, -, lib/cuda
+USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
+USER-EWALDN, Ewald for 1/R^n, Pieter in' t Veld (BASF), "kspace_style"_kspace_style.html, -, -, -
+USER-REAXC, C version of ReaxFF, Metin Aktulga (LBNL), "pair_style reaxc"_pair_reax_c.html, reax, -, -
+USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "SPH_LAMMPS_userguide.pdf"_USER/sph/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, -
+:tb(ea=c)
+
+:link(atc,http://lammps.sandia.gov/pictures.html#atc)
+:link(cg,http://lammps.sandia.gov/pictures.html#cg)
+:link(eff,http://lammps.sandia.gov/movies.html#eff)
+:link(sph,http://lammps.sandia.gov/movies.html#sph)
+
+The "Authors" column lists a name(s) if a specific person is
+responible for creating and maintaining the package.
+
+(2) The ATC package was created by Reese Jones, Jeremy Templeton, and Jon Zimmerman (Sandia).
+
+The "Doc page" column links to either a portion of the
+"Section_howto"_Section_howto.html of the manual, or an input script
+command implemented as part of the package, or to additional
+documentation provided witht he package.
+
+The "Example" column is a sub-directory in the examples directory of
+the distribution which has an input script that uses the package.
+E.g. "peptide" refers to the examples/peptide directory. USER/cuda
+refers to the examples/USER/cuda directory.
+
+The "Library" column lists an external library which must be built
+first and which LAMMPS links to when it is built. These are in the
+lib directory of the distribution. "This
+section"_Section_start.html#start_3_3 of the manual gives details on
+the 2-step build process with external libraries.
+
+More details on each package, from the USER-blah/README file
+is given below.
+
+:line
+
+USER-MISC package :h4
+
+The files in this package are a potpourri of (mostly) unrelated
+features contributed to LAMMPS by users. Each feature is a single
+pair of files (*.cpp and *.h).
+
+More information about each feature can be found by reading its doc
+page in the LAMMPS doc directory. The doc page which lists all LAMMPS
+input script commands is as follows:
+
+"Section_commands"_Section_commands.html#cmd_5
+
+User-contributed features are listed at the bottom of the fix,
+compute, pair, etc sections.
+
+The list of features and author of each is given in the
+src/USER-MISC/README file.
+
+You should contact the author directly if you have specific questions
+about the feature or its coding.
+
+:line
+
+USER-ATC package :h4
+
+This package implements a "fix atc" command which can be used in a
+LAMMPS input script. This fix can be employed to either do concurrent
+coupling of MD with FE-based physics surrogates or on-the-fly
+post-processing of atomic information to continuum fields.
+
+See the doc page for the fix atc command to get started. At the
+bottom of the doc page are many links to additional documentation
+contained in the doc/USER/atc directory.
+
+There are example scripts for using this package in examples/USER/atc.
+
+This package uses an external library in lib/atc which must be
+compiled before making LAMMPS. See the lib/atc/README file and the
+LAMMPS manual for information on building LAMMPS with external
+libraries.
+
+The primary people who created this package are Reese Jones (rjones at
+sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon
+Zimmerman (jzimmer at sandia.gov) at Sandia. Contact them directly if
+you have questions.
+
+:line
+
+USER-AWPMD package :h4
+
+This package contains a LAMMPS implementation of the Antisymmetrized
+Wave Packet Molecular Dynamics (AWPMD) method.
+
+See the doc page for the pair_style awpmd/cut command to get started.
+
+There are example scripts for using this package in examples/USER/awpmd.
+
+This package uses an external library in lib/awpmd which must be
+compiled before making LAMMPS. See the lib/awpmd/README file and the
+LAMMPS manual for information on building LAMMPS with external
+libraries.
+
+The person who created this package is Ilya Valuev at the JIHT in
+Russia (valuev at physik.hu-berlin.de). Contact him directly if you
+have questions.
+
+:line
+
+USER-CG-CMM package :h4
+
+This package implements 4 commands which can be used in a LAMMPS input
+script:
+
+pair_style cg/cmm
+pair_style cg/cmm/coul/cut
+pair_style cg/cmm/coul/long
+angle_style cg/cmm :ul
+
+These styles allow coarse grained MD simulations with the
+parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
+(cg/cmm), with extensions to simulate ionic liquids, electrolytes,
+lipids and charged amino acids (to be published soon).
+
+See the doc pages for these commands for details.
+
+There are example scripts for using this package in
+examples/USER/cg-cmm.
+
+The current version of this package should be considered beta
+quality. The CG potentials work correctly and well, but there will be
+optimizations, cleanups and additional tools to aid in setting up and
+analyzing simulations with this package added in the next months.
+
+The person who created this package is Axel Kohlmeyer at Temple U
+(akohlmey at gmail.com). Contact him directly if you have questions.
+
+:line
+
+USER-CUDA package :h4
+
+This package provides acceleration of various LAMMPS pair styles, fix
+styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
+GPUs.
+
+See this section of the manual to get started:
+
+"Section_accelerate"_Section_accelerate.html#acc_4
+
+There are example scripts for using this package in
+examples/USER/cuda.
+
+This package uses an external library in lib/cuda which must be
+compiled before making LAMMPS. See the lib/cuda/README file and the
+LAMMPS manual for information on building LAMMPS with external
+libraries.
+
+The person who created this package is Christian Trott at the
+University of Technology Ilmenau, Germany (christian.trott at
+tu-ilmenau.de). Contact him directly if you have questions.
+
+:line
+
+USER-EFF package :h4
+
+This package contains a LAMMPS implementation of the electron Force
+Field (eFF) currently under development at Caltech, as described in
+A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
+2010. The eFF potential was first introduced by Su and Goddard, in
+2007.
+
+eFF can be viewed as an approximation to QM wave packet dynamics and
+Fermionic molecular dynamics, combining the ability of electronic
+structure methods to describe atomic structure, bonding, and chemistry
+in materials, and of plasma methods to describe nonequilibrium
+dynamics of large systems with a large number of highly excited
+electrons. We classify it as a mixed QM-classical approach rather than
+a conventional force field method, which introduces QM-based terms (a
+spin-dependent repulsion term to account for the Pauli exclusion
+principle and the electron wavefunction kinetic energy associated with
+the Heisenberg principle) that reduce, along with classical
+electrostatic terms between nuclei and electrons, to the sum of a set
+of effective pairwise potentials. This makes eFF uniquely suited to
+simulate materials over a wide range of temperatures and pressures
+where electronically excited and ionized states of matter can occur
+and coexist.
+
+The necessary customizations to the LAMMPS core are in place to
+enable the correct handling of explicit electron properties during
+minimization and dynamics.
+
+See the doc page for the pair_style eff/cut command to get started.
+
+There are example scripts for using this package in
+examples/USER/eff.
+
+There are auxiliary tools for using this package in tools/eff.
+
+The person who created this package is Andres Jaramillo-Botero at
+CalTech (ajaramil at wag.caltech.edu). Contact him directly if you
+have questions.
+
+:line
+
+USER-EWALDN package :h4
+
+This package implements 3 commands which can be used in a LAMMPS input
+script: pair_style lj/coul, pair_style buck/coul, and kspace_style
+ewald/n.
+
+The "kspace_style ewald/n" command is similar to standard Ewald for
+charges, but also enables the Lennard-Jones interaction, or any 1/r^N
+interaction to be of infinite extent, instead of being cutoff. LAMMPS
+pair potentials for long-range Coulombic interactions, such as
+lj/cut/coul/long can be used with ewald/n. The two new pair_style
+commands provide the modifications for the short-range LJ and
+Buckingham interactions that can also be used with ewald/n.
+
+Another advantage of kspace_style ewald/n is that it can be used with
+non-orthogonal (triclinic symmetry) simulation boxes, either for just
+long-range Coulombic interactions, or for both Coulombic and 1/r^N LJ
+or Buckingham, which is not currently possible for other kspace styles
+such as PPPM and ewald.
+
+See the doc pages for these commands for details.
+
+The person who created these files is Pieter in' t Veld while at
+Sandia. He is now at BASF (pieter.intveld at basf.com). Contact him
+directly if you have questions.
+
+:line
+
+USER-REAXC package :h4
+
+This package contains a implementation for LAMMPS of the ReaxFF force
+field. ReaxFF uses distance-dependent bond-order functions to
+represent the contributions of chemical bonding to the potential
+energy. It was originally developed by Adri van Duin and the Goddard
+group at CalTech.
+
+The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in
+C, should give identical or very similar results to pair_style reax,
+which is a ReaxFF implementation on top of a Fortran library, a
+version of which library was originally authored by Adri van Duin.
+
+The reax/c version should be somewhat faster and more scalable,
+particularly with respect to the charge equilibration calculation. It
+should also be easier to build and use since there are no complicating
+issues with Fortran memory allocation or linking to a Fortran library.
+
+For technical details about this implemention of ReaxFF, see
+this paper:
+
+Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods
+and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty,
+S. A. Pandit, A. Y. Grama, Parallel Computing, to appear (2011).
+
+See the doc page for the pair_style reax/c command for details
+of how to use it in LAMMPS.
+
+The person who created this package is Hasan Metin Aktulga (hmaktulga
+at lbl.gov), while at Purdue University. Contact him directly, or
+Aidan Thompson at Sandia (athomps at sandia.gov), if you have
+questions.
+
+:line
+
+USER-SPH package :h4
+
+This package implements smoothed particle hydrodynamics (SPH) in
+LAMMPS. Currently, the package has the following features:
+
+* Tait, ideal gas, Lennard-Jones equation of states, full support for
+ complete (i.e. internal-energy dependent) equations of state
+* plain or Monaghans XSPH integration of the equations of motion
+* density continuity or density summation to propagate the density field
+* commands to set internal energy and density of particles from the
+ input script
+* output commands to access internal energy and density for dumping and
+ thermo output
+
+See the file doc/USER/sph/SPH_LAMMPS_userguide.pdf to get started.
+
+There are example scripts for using this package in examples/USER/sph.
+
+The person who created this package is Georg Ganzenmuller at the
+Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
+Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
+you have questions.
diff --git a/doc/Section_start.html b/doc/Section_start.html
index 09c0fb8fa..ef2720530 100644
--- a/doc/Section_start.html
+++ b/doc/Section_start.html
@@ -1,1151 +1,1154 @@
<HTML>
<CENTER><A HREF = "Section_intro.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_commands.html">Next Section</A>
</CENTER>
<HR>
<H3>2. Getting Started
</H3>
<P>This section describes how to build and run LAMMPS, for both new and
experienced users.
</P>
2.1 <A HREF = "#start_1">What's in the LAMMPS distribution</A><BR>
2.2 <A HREF = "#start_2">Making LAMMPS</A><BR>
2.3 <A HREF = "#start_3">Making LAMMPS with optional packages</A><BR>
2.4 <A HREF = "#start_4">Building LAMMPS as a library</A><BR>
2.5 <A HREF = "#start_5">Running LAMMPS</A><BR>
2.6 <A HREF = "#start_6">Command-line options</A><BR>
2.7 <A HREF = "#start_7">Screen output</A><BR>
2.8 <A HREF = "#start_8">Tips for users of previous versions</A> <BR>
<HR>
<H4><A NAME = "start_1"></A>2.1 What's in the LAMMPS distribution
</H4>
<P>When you download LAMMPS you will need to unzip and untar the
downloaded file with the following commands, after placing the file in
an appropriate directory.
</P>
<PRE>gunzip lammps*.tar.gz
tar xvf lammps*.tar
</PRE>
<P>This will create a LAMMPS directory containing two files and several
sub-directories:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >README</TD><TD > text file</TD></TR>
<TR><TD >LICENSE</TD><TD > the GNU General Public License (GPL)</TD></TR>
<TR><TD >bench</TD><TD > benchmark problems</TD></TR>
<TR><TD >couple</TD><TD > code coupling examples, using LAMMPS as a library</TD></TR>
<TR><TD >doc</TD><TD > documentation</TD></TR>
<TR><TD >examples</TD><TD > simple test problems</TD></TR>
<TR><TD >potentials</TD><TD > embedded atom method (EAM) potential files</TD></TR>
<TR><TD >src</TD><TD > source files</TD></TR>
<TR><TD >tools</TD><TD > pre- and post-processing tools
</TD></TR></TABLE></DIV>
<P>If you download one of the Windows executables from the download page,
then you just get a single file:
</P>
<PRE>lmp_windows.exe
</PRE>
<P>Skip to the <A HREF = "#start_5">Running LAMMPS</A> sections for info on how to
launch these executables on a Windows box.
</P>
<P>The Windows executables for serial or parallel only include certain
packages and bug-fixes/upgrades listed on <A HREF = "http://lammps.sandia.gov/bug.html">this
page</A> up to a certain date, as
stated on the download page. If you want something with more packages
or that is more current, you'll have to download the source tarball
and build it yourself from source code using Microsoft Visual Studio,
as described in the next section.
</P>
<HR>
<H4><A NAME = "start_2"></A>2.2 Making LAMMPS
</H4>
<P>This section has the following sub-sections:
</P>
<UL><LI><A HREF = "#start_2_1">Read this first</A>
<LI><A HREF = "#start_2_2">Steps to build a LAMMPS executable</A>
<LI><A HREF = "#start_2_3">Common errors that can occur when making LAMMPS</A>
<LI><A HREF = "#start_2_4">Additional build tips</A>
<LI><A HREF = "#start_2_5">Building for a Mac</A>
<LI><A HREF = "#start_2_6">Building for Windows</A>
</UL>
<HR>
<A NAME = "start_2_1"></A><B><I>Read this first:</I></B>
<P>Building LAMMPS can be non-trivial. You may need to edit a makefile,
there are compiler options to consider, additional libraries can be
used (MPI, FFT, JPEG), LAMMPS packages may be included or excluded,
some of these packages use auxiliary libraries which need to be
pre-built, etc.
</P>
<P>Please read this section carefully. If you are not comfortable with
makefiles, or building codes on a Unix platform, or running an MPI job
on your machine, please find a local expert to help you. Many
compiling, linking, and run problems that users have are not really
LAMMPS issues - they are peculiar to the user's system, compilers,
libraries, etc. Such questions are better answered by a local expert.
</P>
<P>If you have a build problem that you are convinced is a LAMMPS issue
(e.g. the compiler complains about a line of LAMMPS source code), then
please send an email to the
<A HREF = "http://lammps.sandia.gov/authors.html">developers</A>.
</P>
<P>If you succeed in building LAMMPS on a new kind of machine, for which
there isn't a similar Makefile for in the src/MAKE directory, send it
to the developers and we'll include it in future LAMMPS releases.
</P>
<HR>
<A NAME = "start_2_2"></A><B><I>Steps to build a LAMMPS executable:</I></B>
<P><B>Step 0</B>
</P>
<P>The src directory contains the C++ source and header files for LAMMPS.
It also contains a top-level Makefile and a MAKE sub-directory with
low-level Makefile.* files for many machines. From within the src
directory, type "make" or "gmake". You should see a list of available
choices. If one of those is the machine and options you want, you can
type a command like:
</P>
<PRE>make linux
or
gmake mac
</PRE>
<P>Note that on a multi-processor or multi-core platform you can launch a
parallel make, by using the "-j" switch with the make command, which
will build LAMMPS more quickly.
</P>
<P>If you get no errors and an executable like lmp_linux or lmp_mac is
produced, you're done; it's your lucky day.
</P>
<P>Note that by default only a few of LAMMPS optional pacakges are
installed. To build LAMMPS with optional packages, see <A HREF = "#start_3">this
section</A> below.
</P>
<P><B>Step 1</B>
</P>
<P>If Step 0 did not work, you will need to create a low-level Makefile
for your machine, like Makefile.foo. You should make a copy of an
existing src/MAKE/Makefile.* as a starting point. The only portions
of the file you need to edit are the first line, the "compiler/linker
settings" section, and the "LAMMPS-specific settings" section.
</P>
<P><B>Step 2</B>
</P>
<P>Change the first line of src/MAKE/Makefile.foo to list the word "foo"
after the "#", and whatever other options it will set. This is the
line you will see if you just type "make".
</P>
<P><B>Step 3</B>
</P>
<P>The "compiler/linker settings" section lists compiler and linker
settings for your C++ compiler, including optimization flags. You can
use g++, the open-source GNU compiler, which is available on all Unix
systems. You can also use mpicc which will typically be available if
MPI is installed on your system, though you should check which actual
compiler it wraps. Vendor compilers often produce faster code. On
boxes with Intel CPUs, we suggest using the commercial Intel icc
compiler, which can be downloaded from <A HREF = "http://www.intel.com/software/products/noncom">Intel's compiler site</A>.
</P>
<P>If building a C++ code on your machine requires additional libraries,
then you should list them as part of the LIB variable.
</P>
<P>The DEPFLAGS setting is what triggers the C++ compiler to create a
dependency list for a source file. This speeds re-compilation when
source (*.cpp) or header (*.h) files are edited. Some compilers do
not support dependency file creation, or may use a different switch
than -D. GNU g++ works with -D. If your compiler can't create
dependency files, then you'll need to create a Makefile.foo patterned
after Makefile.storm, which uses different rules that do not involve
dependency files. Note that when you build LAMMPS for the first time
on a new platform, a long list of *.d files will be printed out
rapidly. This is not an error; it is the Makefile doing its normal
creation of dependencies.
</P>
<P><B>Step 4</B>
</P>
<P>The "system-specific settings" section has several parts. Note that
if you change any -D setting in this section, you should do a full
re-compile, after typing "make clean" (which will describe different
clean options).
</P>
<P>The LMP_INC variable is used to include options that turn on ifdefs
within the LAMMPS code. The options that are currently recogized are:
</P>
<UL><LI>-DLAMMPS_GZIP
<LI>-DLAMMPS_JPEG
<LI>-DLAMMPS_XDR
<LI>-DLAMMPS_SMALLBIG
<LI>-DLAMMPS_BIGBIG
<LI>-DLAMMPS_SMALLSMALL
<LI>-DLAMMPS_LONGLONG_TO_LONG
<LI>-DPACK_ARRAY
<LI>-DPACK_POINTER
<LI>-DPACK_MEMCPY
</UL>
<P>The read_data and dump commands will read/write gzipped files if you
compile with -DLAMMPS_GZIP. It requires that your Unix support the
"popen" command.
</P>
<P>If you use -DLAMMPS_JPEG, the <A HREF = "dump.html">dump image</A> command will be
able to write out JPEG image files. If not, it will only be able to
write out text-based PPM image files. For JPEG files, you must also
link LAMMPS with a JPEG library, as described below.
</P>
<P>If you use -DLAMMPS_XDR, the build will include XDR compatibility
files for doing particle dumps in XTC format. This is only necessary
if your platform does have its own XDR files available. See the
Restrictions section of the <A HREF = "dump.html">dump</A> command for details.
</P>
<P>Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG,
-D-DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG.
These refer to use of 4-byte (small) vs 8-byte (big) integers within
LAMMPS, as described in src/lmptype.h. The only reason to use the
BIGBIG setting is to enable simulation of huge molecular systems with
more than 2 billion atoms. The only reason to use the SMALLSMALL
setting is if your machine does not support 64-bit integers.
</P>
<P>The -DLAMMPS_LONGLONG_TO_LONG setting may be needed if your system or
MPI version does not recognize "long long" data types. In this case a
"long" data type is likely already 64-bits, in which case this setting
will convert to that data type.
</P>
<P>Using one of the -DPACK_ARRAY, -DPACK_POINTER, and -DPACK_MEMCPY
options can make for faster parallel FFTs (in the PPPM solver) on some
platforms. The -DPACK_ARRAY setting is the default. See the
<A HREF = "kspace_style.html">kspace_style</A> command for info about PPPM. See
Step 6 below for info about building LAMMPS with an FFT library.
</P>
<P><B>Step 5</B>
</P>
<P>The 3 MPI variables are used to specify an MPI library to build LAMMPS
with.
</P>
<P>If you want LAMMPS to run in parallel, you must have an MPI library
installed on your platform. If you use an MPI-wrapped compiler, such
as "mpicc" to build LAMMPS, you should be able to leave these 3
variables blank; the MPI wrapper knows where to find the needed files.
If not, and MPI is installed on your system in the usual place (under
/usr/local), you also may not need to specify these 3 variables. On
some large parallel machines which use "modules" for their
compile/link environements, you may simply need to include the correct
module in your build environment. Or the parallel machine may have a
vendor-provided MPI which the compiler has no trouble finding.
</P>
<P>Failing this, with these 3 variables you can specify where the mpi.h
file (MPI_INC) and the MPI library file (MPI_PATH) are found and the
name of the library file (MPI_LIB).
</P>
<P>If you are installing MPI yourself, we recommend Argonne's MPICH 1.2
or 2.0 or OpenMPI. MPICH can be downloaded from the <A HREF = "http://www-unix.mcs.anl.gov/mpi">Argonne MPI
site</A>. OpenMPI can be downloaded the
<A HREF = "http://www.open-mpi.org">OpenMPI site</A>. LAM MPI should also work. If
you are running on a big parallel platform, your system people or the
vendor should have already installed a version of MPI, which will be
faster than MPICH or OpenMPI or LAM, so find out how to build and link
with it. If you use MPICH or OpenMPI or LAM, you will have to
configure and build it for your platform. The MPI configure script
should have compiler options to enable you to use the same compiler
you are using for the LAMMPS build, which can avoid problems that can
arise when linking LAMMPS to the MPI library.
</P>
<P>If you just want to run LAMMPS on a single processor, you can use the
dummy MPI library provided in src/STUBS, since you don't need a true
MPI library installed on your system. See the
src/MAKE/Makefile.serial file for how to specify the 3 MPI variables
in this case. You will also need to build the STUBS library for your
platform before making LAMMPS itself. From the src directory, type
"make stubs", or from the STUBS dir, type "make" and it should create
a libmpi.a suitable for linking to LAMMPS. If this build fails, you
will need to edit the STUBS/Makefile for your platform.
</P>
<P>The file STUBS/mpi.cpp provides a CPU timer function called
MPI_Wtime() that calls gettimeofday() . If your system doesn't
support gettimeofday() , you'll need to insert code to call another
timer. Note that the ANSI-standard function clock() rolls over after
an hour or so, and is therefore insufficient for timing long LAMMPS
simulations.
</P>
<P><B>Step 6</B>
</P>
<P>The 3 FFT variables allow you to specify an FFT library which LAMMPS
uses (for performing 1d FFTs) when running the particle-particle
particle-mesh (PPPM) option for long-range Coulombics via the
<A HREF = "kspace_style.html">kspace_style</A> command.
</P>
<P>LAMMPS supports various open-source or vendor-supplied FFT libraries
for this purpose. If you leave these 3 variables blank, LAMMPS will
use the open-source <A HREF = "http://kissfft.sf.net">KISS FFT library</A>, which is
included in the LAMMPS distribution. This library is portable to all
platforms and for typical LAMMPS simulations is almost as fast as FFTW
or vendor optimized libraries. If you are not including the KSPACE
package in your build, you can also leave the 3 variables blank.
</P>
<P>Otherwise, select which kinds of FFTs to use as part of the FFT_INC
setting by a switch of the form -DFFT_XXX. Recommended values for XXX
are: MKL, SCSL, FFTW2, and FFTW3. Legacy options are: INTEL, SGI,
ACML, and T3E. For backward compatability, using -DFFT_FFTW will use
the FFTW2 library. Using -DFFT_NONE will use the KISS library
described above.
</P>
<P>You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables,
so the compiler and linker can find the needed FFT header and library
files. Note that on some large parallel machines which use "modules"
for their compile/link environements, you may simply need to include
the correct module in your build environment. Or the parallel machine
may have a vendor-provided FFT library which the compiler has no
trouble finding.
</P>
<P>FFTW is a fast, portable library that should also work on any
platform. You can download it from
<A HREF = "http://www.fftw.org">www.fftw.org</A>. Both the legacy version 2.1.X and
the newer 3.X versions are supported as -DFFT_FFTW2 or -DFFT_FFTW3.
Building FFTW for your box should be as simple as ./configure; make.
Note that on some platforms FFTW2 has been pre-installed, and uses
renamed files indicating the precision it was compiled with,
e.g. sfftw.h, or dfftw.h instead of fftw.h. In this case, you can
specify an additional define variable for FFT_INC called -DFFTW2_SIZE,
which will select the correct include file. In this case, for FFT_LIB
you must also manually specify the correct library, namely -lsfftw or
-ldfftw.
</P>
<P>The FFT_INC variable also allows for a -DFFT_SINGLE setting that will
use single-precision FFTs with PPPM, which can speed-up long-range
calulations, particularly in parallel or on GPUs. Fourier transform
and related PPPM operations are somewhat insensitive to floating point
truncation errors and thus do not always need to be performed in
double precision. Using the -DFFT_SINGLE setting trades off a little
accuracy for reduced memory use and parallel communication costs for
transposing 3d FFT data. Note that single precision FFTs have only
been tested with the FFTW3, FFTW2, MKL, and KISS FFT options.
</P>
<P><B>Step 7</B>
</P>
<P>The 3 JPG variables allow you to specify a JPEG library which LAMMPS
uses when writing out JPEG files via the <A HREF = "dump_image.html">dump image</A>
command. These can be left blank if you do not use the -DLAMMPS_JPEG
switch discussed above in Step 4, since in that case JPEG output will
be disabled.
</P>
<P>A standard JPEG library usually goes by the name libjpeg.a and has an
associated header file jpeglib.h. Whichever JPEG library you have on
your platform, you'll need to set the appropriate JPG_INC, JPG_PATH,
and JPG_LIB variables, so that the compiler and linker can find it.
</P>
<P>As before, if these header and library files are in the usual place on
your machine, you may not need to set these variables.
</P>
<P><B>Step 8</B>
</P>
<P>Note that by default only a few of LAMMPS optional pacakges are
installed. To build LAMMPS with optional packages, see <A HREF = "#start_3">this
section</A> below, before proceeding to Step 9.
</P>
<P><B>Step 9</B>
</P>
<P>That's it. Once you have a correct Makefile.foo, you have installed
the optional LAMMPS packages you want to include in your build, and
you have pre-built any other needed libraries (e.g. MPI, FFT, package
libraries), all you need to do from the src directory is type
something like this:
</P>
<PRE>make foo
or
gmake foo
</PRE>
<P>You should get the executable lmp_foo when the build is complete.
</P>
<HR>
<A NAME = "start_2_3"></A><B><I>Errors that can occur when making LAMMPS:</I></B>
<P>IMPORTANT NOTE: If an error occurs when building LAMMPS, the compiler
or linker will state very explicitly what the problem is. The error
message should give you a hint as to which of the steps above has
failed, and what you need to do in order to fix it. Building a code
with a Makefile is a very logical process. The compiler and linker
need to find the appropriate files and those files need to be
compatible with LAMMPS source files. When a make fails, there is
usually a very simple reason, which you or a local expert will need to
fix.
</P>
<P>Here are two non-obvious errors that can occur:
</P>
<P>(1) If the make command breaks immediately with errors that indicate
it can't find files with a "*" in their names, this can be because
your machine's native make doesn't support wildcard expansion in a
makefile. Try gmake instead of make. If that doesn't work, try using
a -f switch with your make command to use a pre-generated
Makefile.list which explicitly lists all the needed files, e.g.
</P>
<PRE>make makelist
make -f Makefile.list linux
gmake -f Makefile.list mac
</PRE>
<P>The first "make" command will create a current Makefile.list with all
the file names in your src dir. The 2nd "make" command (make or
gmake) will use it to build LAMMPS. Note that you should
include/exclude any desired optional packages before using the "make
makelist" command.
</P>
<P>(2) If you get an error that says something like 'identifier "atoll"
is undefined', then your machine does not support "long long"
integers. Try using the -DLAMMPS_LONGLONG_TO_LONG setting described
above in Step 4.
</P>
<HR>
<A NAME = "start_2_4"></A><B><I>Additional build tips:</I></B>
<P>(1) Building LAMMPS for multiple platforms.
</P>
<P>You can make LAMMPS for multiple platforms from the same src
directory. Each target creates its own object sub-directory called
Obj_name where it stores the system-specific *.o files.
</P>
<P>(2) Cleaning up.
</P>
<P>Typing "make clean-all" or "make clean-foo" will delete *.o object
files created when LAMMPS is built, for either all builds or for a
particular machine.
</P>
<P>(3) Changing the size limits in src/lmptype.h
</P>
<P>If you are running a very large problem (billions of atoms or more)
and get a run-time error about the system being too big, either on a
per-processor basis or in total size, then you may need to change one
or more settings in src/lmptype.h and re-compile LAMMPS.
</P>
<P>As the documentation in that file explains, you have basically
two choices to make:
</P>
<UL><LI>set the data type size of integer atom IDs to 4 or 8 bytes
<LI>set the data type size of integers that store the total system size to 4 or 8 bytes
</UL>
<P>The default for atom IDs is 4-byte integers since there is a memory
and communication cost for 8-byte integers. Non-molecular problems do
not need atom IDs so this does not restrict their size. Molecular
problems (which use IDs to define molecular topology), are limited to
about 2 billion atoms (2^31) with 4-byte IDs. With 8-byte IDs they
are effectively unlimited in size (2^63).
</P>
<P>The default for total system size quantities (like the number of atoms
or timesteps) is 8-byte integers by default which is effectively
unlimited in size (2^63). If your system or MPI implementation does
not support 8-byte integers, an error will be generated, and you will
need to set "bigint" to 4-byte integers. This restricts your total
system size to about 2 billion atoms or timesteps (2^31).
</P>
<P>Note that in src/lmptype.h there are also settings for the MPI data
types associated with the integers that store atom IDs and total
system sizes, which need to be set consistent with the associated C
data types.
</P>
<P>In all cases, the size of problem that can be run on a per-processor
basis is limited by 4-byte integer storage to about 2 billion atoms
per processor (2^31), which should not normally be a restriction since
such a problem would have a huge per-processor memory footprint due to
neighbor lists and would run very slowly in terms of CPU
secs/timestep.
</P>
<HR>
<A NAME = "start_2_5"></A><B><I>Building for a Mac:</I></B>
<P>OS X is BSD Unix, so it should just work. See the Makefile.mac file.
</P>
<HR>
<A NAME = "start_2_6"></A><B><I>Building for Windows:</I></B>
<P>The LAMMPS download page has an option to download both a serial and
parallel pre-built Windows exeutable. See the <A HREF = "#start_5">Running
LAMMPS</A> section for instructions for running these
executables on a Windows box.
</P>
<P>If the pre-built executable doesn't have the options you want, then
you can build LAMMPS from its source files on a Windows box. One way
to do this is install and use cygwin to build LAMMPS with a standard
Linus make, just as you would on any Linux box; see
src/MAKE/Makefile.cygwin.
</P>
<P>There is a also a src/WINDOWS directory that contains project files
for Microsoft Visual Studio 2005, which should also work with later
versions of VS. That directory contains a README.txt file which
provides instructions for building LAMMPS from source code using
Visual Studio that are hopefully easy to follow for Windows and VS
users.
</P>
<P>Four VS project options are provided. The first includes the default
packages (MANYBODY, MOLECULE, and KSPACE). The second includes all
standard packages (except GPU, MEAM, and REAX which are not yet
included because they require NVIDIA or Fortran compilation). The
third includes all standard packages (with the exceptions) and some
user packages. The included user packages are USER-EFF, USER-CG-CMM,
and USER-REAXC. The fourth project includes the USER-AWPMD package.
</P>
<HR>
<H4><A NAME = "start_3"></A>2.3 Making LAMMPS with optional packages
</H4>
<P>This section has the following sub-sections:
</P>
<UL><LI><A HREF = "#start_3_1">Package basics</A>
<LI><A HREF = "#start_3_2">Including/excluding packages</A>
<LI><A HREF = "#start_3_3">Packages that require extra libraries</A>
<LI><A HREF = "#start_3_4">Additional Makefile settings for extra libraries</A>
</UL>
<HR>
<A NAME = "start_3_1"></A><B><I>Package basics:</I></B>
<P>The source code for LAMMPS is structured as a set of core files which
are always included, plus optional packages. Packages are groups of
files that enable a specific set of features. For example, force
fields for molecular systems or granular systems are in packages. You
can see the list of all packages by typing "make package" from within
the src directory of the LAMMPS distribution.
</P>
<P>If you use a command in a LAMMPS input script that is specific to a
particular package, you must have built LAMMPS with that package, else
you will get an error that the style is invalid or the command is
unknown. Every command's doc page specfies if it is part of a
package. You can also type
</P>
<PRE>lmp_machine -h
</PRE>
<P>to run your executable with the optional <A HREF = "#start_6">-h command-line
switch</A> for "help", which will list the styles and commands
known to your executable.
</P>
<P>There are two kinds of packages in LAMMPS, standard and user packages.
More information about the contents of standard and user packages is
given in <A HREF = "Section_packages.html">this section</A> of the manual. The
difference between standard and user packages is as follows:
</P>
<P>Standard packages are supported by the LAMMPS developers and are
written in a syntax and style consistent with the rest of LAMMPS.
This means we will answer questions about them, debug and fix them if
necessary, and keep them compatible with future changes to LAMMPS.
</P>
<P>User packages have been contributed by users, and always begin with
the user prefix. If they are a single command (single file), they are
typically in the user-misc package. Otherwise, they are a a set of
files grouped together which add a specific functionality to the code.
</P>
<P>User packages don't necessarily meet the requirements of the standard
packages. If you have problems using a feature provided in a user
package, you will likely need to contact the contributor directly to
get help. Information on how to submit additions you make to LAMMPS
as a user-contributed package is given in <A HREF = "Section_modify.html#mod_14">this
section</A> of the documentation.
</P>
<HR>
<A NAME = "start_3_2"></A><B><I>Including/excluding packages:</I></B>
<P>To use or not use a package you must include or exclude it before
building LAMMPS. From the src directory, this is typically as simple
as:
</P>
<PRE>make yes-colloid
make g++
</PRE>
<P>or
</P>
<PRE>make no-manybody
make g++
</PRE>
<P>Some packages have individual files that depend on other packages
being included. LAMMPS checks for this and does the right thing.
I.e. individual files are only included if their dependencies are
already included. Likewise, if a package is excluded, other files
dependent on that package are also excluded.
</P>
<P>The reason to exclude packages is if you will never run certain kinds
of simulations. For some packages, this will keep you from having to
build auxiliary libraries (see below), and will also produce a smaller
executable which may run a bit faster.
</P>
-<P>By default, LAMMPS includes only the "kspace", "manybody", and
-"molecule" packages.
+<P>When you download a LAMMPS tarball, these packages are pre-installed
+in the src directory: KSPACE, MANYBODY,MOLECULE. When you download
+LAMMPS source files from the SVN or Git repositories, no packages are
+pre-installed.
</P>
<P>Packages are included or excluded by typing "make yes-name" or "make
-no-name", where "name" is the name of the package. You can also type
-"make yes-standard", "make no-standard", "make yes-user", "make
-no-user", "make yes-all" or "make no-all" to include/exclude various
-sets of packages. Type "make package" to see the all of the
-package-related make options.
+no-name", where "name" is the name of the package in lower-case, e.g.
+name = kspace for the KSPACE package or name = user-atc for the
+USER-ATC package. You can also type "make yes-standard", "make
+no-standard", "make yes-user", "make no-user", "make yes-all" or "make
+no-all" to include/exclude various sets of packages. Type "make
+package" to see the all of the package-related make options.
</P>
<P>IMPORTANT NOTE: Inclusion/exclusion of a package works by simply
moving files back and forth between the main src directory and
sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
so that the files are seen or not seen when LAMMPS is built. After
you have included or excluded a package, you must re-build LAMMPS.
</P>
<P>Additional package-related make options exist to help manage LAMMPS
files that exist in both the src directory and in package
sub-directories. You do not normally need to use these commands
unless you are editing LAMMPS files or have downloaded a patch from
the LAMMPS WWW site.
</P>
<P>Typing "make package-update" will overwrite src files with files from
the package sub-directories if the package has been included. It
should be used after a patch is installed, since patches only update
the files in the package sub-directory, but not the src files. Typing
"make package-overwrite" will overwrite files in the package
sub-directories with src files.
</P>
<P>Typing "make package-status" will show which packages are currently
included. Of those that are included, it will list files that are
different in the src directory and package sub-directory. Typing
"make package-diff" lists all differences between these files. Again,
type "make package" to see all of the package-related make options.
</P>
<HR>
<A NAME = "start_3_3"></A><B><I>Packages that require extra libraries:</I></B>
<P>A few of the standard and user packages require additional auxiliary
libraries to be compiled first. If you get a LAMMPS build error about
a missing library, this is likely the reason. The source code for
these libraries is included in the LAMMPS distribution under the "lib"
directory. Look at the lib/README file for a list of these or see
<A HREF = "Section_packages.html">this section</A> of the doc pages.
</P>
<P>Each lib directory has a README file (e.g. lib/reax/README) with
instructions on how to build that library. Typically this is done
in this manner:
</P>
<PRE>make -f Makefile.g++
</PRE>
<P>in the appropriate directory, e.g. in lib/reax. Some of the libraries
do not build this way. Again, see the libary README file for details.
</P>
<P>In any event, you will need to use a Makefile that is a match for your
system. If one of the provided Makefiles is not appropriate for your
system you will need to edit or add one. For example, in the case of
Fortran-based libraries, your system must have a Fortran compiler, the
settings for which will need to be listed in the Makefile.
</P>
<P>When you have built one of these libraries, there are 2 things to
check:
</P>
<P>(1) The file libname.a should now exist in lib/name.
E.g. lib/reax/libreax.a. This is the library file LAMMPS will link
against. One exception is the lib/cuda library which produces the
file liblammpscuda.a, because there is already a system library
libcuda.a.
</P>
<P>(2) The file Makefile.lammps should exist in lib/name. E.g.
lib/cuda/Makefile.lammps. This file may be auto-generated by the
build of the library, or you may need to make a copy of the
appropriate provided file (e.g. lib/meam/Makefile.lammps.gfortran).
Either way you should insure that the settings in this file are
appropriate for your system.
</P>
<P>There are typically 3 settings in the Makefile.lammps file (unless
some are blank or not needed): a SYSINC, SYSPATH, and SYSLIB setting,
specific to this package. These are settings the LAMMPS build will
import when compiling the LAMMPS package files (not the library
files), and linking to the auxiliary library. They typically list any
other system libraries needed to support the package and where to find
them. An example is the BLAS and LAPACK libraries needed by the
USER-ATC package. Or the system libraries that support calling
Fortran from C++, as the MEAM and REAX packages do.
</P>
<P>Note that if these settings are not correct for your box, the LAMMPS
build will likely fail.
</P>
<HR>
<H4><A NAME = "start_4"></A>2.4 Building LAMMPS as a library
</H4>
<P>LAMMPS itself can be built as a library, which can then be called from
another application or a scripting language. See <A HREF = "Section_howto.html#howto_10">this
section</A> for more info on coupling LAMMPS
to other codes. Building LAMMPS as a library is done by typing
</P>
<PRE>make makelib
make -f Makefile.lib foo
</PRE>
<P>where foo is the machine name. Note that inclusion or exclusion of
any desired optional packages should be done before typing "make
makelib". The first "make" command will create a current Makefile.lib
with all the file names in your src dir. The 2nd "make" command will
use it to build LAMMPS as a library. This requires that Makefile.foo
have a library target (lib) and system-specific settings for ARCHIVE
and ARFLAGS. See Makefile.linux for an example. The build will
create the file liblmp_foo.a which another application can link to.
</P>
<P>When used from a C++ program, the library allows one or more LAMMPS
objects to be instantiated. All of LAMMPS is wrapped in a LAMMPS_NS
namespace; you can safely use any of its classes and methods from
within your application code, as needed.
</P>
<P>When used from a C or Fortran program or a scripting language, the
library has a simple function-style interface, provided in
src/library.cpp and src/library.h.
</P>
<P>See the sample codes couple/simple/simple.cpp and simple.c as examples
of C++ and C codes that invoke LAMMPS thru its library interface.
There are other examples as well in the couple directory which are
discussed in <A HREF = "Section_howto.html#howto_10">this section</A> of the manual.
See <A HREF = "Section_python.html">this section</A> of the manual for a description
of the Python wrapper provided with LAMMPS that operates through the
LAMMPS library interface.
</P>
<P>The files src/library.cpp and library.h contain the C-style interface
to LAMMPS. See <A HREF = "Section_howto.html#howto_19">this section</A> of the
manual for a description of the interface and how to extend it for
your needs.
</P>
<HR>
<H4><A NAME = "start_5"></A>2.5 Running LAMMPS
</H4>
<P>By default, LAMMPS runs by reading commands from stdin; e.g. lmp_linux
< in.file. This means you first create an input script (e.g. in.file)
containing the desired commands. <A HREF = "Section_commands.html">This section</A>
describes how input scripts are structured and what commands they
contain.
</P>
<P>You can test LAMMPS on any of the sample inputs provided in the
examples or bench directory. Input scripts are named in.* and sample
outputs are named log.*.name.P where name is a machine and P is the
number of processors it was run on.
</P>
<P>Here is how you might run a standard Lennard-Jones benchmark on a
Linux box, using mpirun to launch a parallel job:
</P>
<PRE>cd src
make linux
cp lmp_linux ../bench
cd ../bench
mpirun -np 4 lmp_linux < in.lj
</PRE>
<P>See <A HREF = "http://lammps.sandia.gov/bench.html">this page</A> for timings for this and the other benchmarks
on various platforms.
</P>
<HR>
<P>On a Windows box, you can skip making LAMMPS and simply download an
executable, as described above, though the pre-packaged executables
include only certain packages.
</P>
<P>To run a LAMMPS executable on a Windows machine, first decide whether
you want to download the non-MPI (serial) or the MPI (parallel)
version of the executable. Download and save the version you have
chosen.
</P>
<P>For the non-MPI version, follow these steps:
</P>
<UL><LI>Get a command prompt by going to Start->Run... ,
then typing "cmd".
<LI>Move to the directory where you have saved lmp_win_no-mpi.exe
(e.g. by typing: cd "Documents").
<LI>At the command prompt, type "lmp_win_no-mpi -in in.lj", replacing in.lj
with the name of your LAMMPS input script.
</UL>
<P>For the MPI version, which allows you to run LAMMPS under Windows on
multiple processors, follow these steps:
</P>
<UL><LI>Download and install
<A HREF = "http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downloads">MPICH2</A>
for Windows.
<LI>You'll need to use the mpiexec.exe and smpd.exe files from the MPICH2 package. Put them in
same directory (or path) as the LAMMPS Windows executable.
<LI>Get a command prompt by going to Start->Run... ,
then typing "cmd".
<LI>Move to the directory where you have saved lmp_win_mpi.exe
(e.g. by typing: cd "Documents").
<LI>Then type something like this: "mpiexec -np 4 -localonly lmp_win_mpi -in in.lj",
replacing in.lj with the name of your LAMMPS input script.
<LI>Note that you may need to provide smpd with a passphrase --- it doesn't matter what you
type.
<LI>In this mode, output may not immediately show up on the screen, so
if your input script takes a long time to execute, you may need to be
patient before the output shows up.
<LI>Alternatively, you can still use this executable to run on a single processor by
typing something like: "lmp_win_mpi -in in.lj".
</UL>
<HR>
<P>The screen output from LAMMPS is described in the next section. As it
runs, LAMMPS also writes a log.lammps file with the same information.
</P>
<P>Note that this sequence of commands copies the LAMMPS executable
(lmp_linux) to the directory with the input files. This may not be
necessary, but some versions of MPI reset the working directory to
where the executable is, rather than leave it as the directory where
you launch mpirun from (if you launch lmp_linux on its own and not
under mpirun). If that happens, LAMMPS will look for additional input
files and write its output files to the executable directory, rather
than your working directory, which is probably not what you want.
</P>
<P>If LAMMPS encounters errors in the input script or while running a
simulation it will print an ERROR message and stop or a WARNING
message and continue. See <A HREF = "Section_errors.html">this section</A> for a
discussion of the various kinds of errors LAMMPS can or can't detect,
a list of all ERROR and WARNING messages, and what to do about them.
</P>
<P>LAMMPS can run a problem on any number of processors, including a
single processor. In theory you should get identical answers on any
number of processors and on any machine. In practice, numerical
round-off can cause slight differences and eventual divergence of
molecular dynamics phase space trajectories.
</P>
<P>LAMMPS can run as large a problem as will fit in the physical memory
of one or more processors. If you run out of memory, you must run on
more processors or setup a smaller problem.
</P>
<HR>
<H4><A NAME = "start_6"></A>2.6 Command-line options
</H4>
<P>At run time, LAMMPS recognizes several optional command-line switches
which may be used in any order. Either the full word or a one-or-two
letter abbreviation can be used:
</P>
<UL><LI>-c or -cuda
<LI>-e or -echo
<LI>-i or -in
<LI>-h or -help
<LI>-l or -log
<LI>-p or -partition
<LI>-pl or -plog
<LI>-ps or -pscreen
<LI>-sc or -screen
<LI>-sf or -suffix
<LI>-v or -var
</UL>
<P>For example, lmp_ibm might be launched as follows:
</P>
<PRE>mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none < in.alloy
mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none < in.alloy
</PRE>
<P>Here are the details on the options:
</P>
<PRE>-cuda on/off
</PRE>
<P>Explicitly enable or disable CUDA support, as provided by the
USER-CUDA package. If LAMMPS is built with this package, as described
above in <A HREF = "#start_3">Section 2.3</A>, then by default LAMMPS will run in
CUDA mode. If this switch is set to "off", then it will not, even if
it was built with the USER-CUDA package, which means you can run
standard LAMMPS or with the GPU package for testing or benchmarking
purposes. The only reason to set the switch to "on", is to check if
LAMMPS was built with the USER-CUDA package, since an error will be
generated if it was not.
</P>
<PRE>-echo style
</PRE>
<P>Set the style of command echoing. The style can be <I>none</I> or <I>screen</I>
or <I>log</I> or <I>both</I>. Depending on the style, each command read from
the input script will be echoed to the screen and/or logfile. This
can be useful to figure out which line of your script is causing an
input error. The default value is <I>log</I>. The echo style can also be
set by using the <A HREF = "echo.html">echo</A> command in the input script itself.
</P>
<PRE>-in file
</PRE>
<P>Specify a file to use as an input script. This is an optional switch
when running LAMMPS in one-partition mode. If it is not specified,
LAMMPS reads its input script from stdin - e.g. lmp_linux < in.run.
This is a required switch when running LAMMPS in multi-partition mode,
since multiple processors cannot all read from stdin.
</P>
<PRE>-help
</PRE>
<P>Print a list of options compiled into this executable for each LAMMPS
style (atom_style, fix, compute, pair_style, bond_style, etc). This
can help you know if the command you want to use was included via the
appropriate package. LAMMPS will print the info and immediately exit
if this switch is used.
</P>
<PRE>-log file
</PRE>
<P>Specify a log file for LAMMPS to write status information to. In
one-partition mode, if the switch is not used, LAMMPS writes to the
file log.lammps. If this switch is used, LAMMPS writes to the
specified file. In multi-partition mode, if the switch is not used, a
log.lammps file is created with hi-level status information. Each
partition also writes to a log.lammps.N file where N is the partition
ID. If the switch is specified in multi-partition mode, the hi-level
logfile is named "file" and each partition also logs information to a
file.N. For both one-partition and multi-partition mode, if the
specified file is "none", then no log files are created. Using a
<A HREF = "log.html">log</A> command in the input script will override this setting.
Option -plog will override the name of the partition log files file.N.
</P>
<PRE>-partition 8x2 4 5 ...
</PRE>
<P>Invoke LAMMPS in multi-partition mode. When LAMMPS is run on P
processors and this switch is not used, LAMMPS runs in one partition,
i.e. all P processors run a single simulation. If this switch is
used, the P processors are split into separate partitions and each
partition runs its own simulation. The arguments to the switch
specify the number of processors in each partition. Arguments of the
form MxN mean M partitions, each with N processors. Arguments of the
form N mean a single partition with N processors. The sum of
processors in all partitions must equal P. Thus the command
"-partition 8x2 4 5" has 10 partitions and runs on a total of 25
processors.
</P>
<P>Note that with MPI installed on a machine (e.g. your desktop), you can
run on more (virtual) processors than you have physical processors.
This can be useful for running <A HREF = "Section_howto.html#howto_5">multi-replica
simulations</A>, on one or a few processors.
</P>
<P>The input script specifies what simulation is run on which partition;
see the <A HREF = "variable.html">variable</A> and <A HREF = "next.html">next</A> commands. This
<A HREF = "Section_howto.html#howto_4">howto section</A> gives examples of how to
use these commands in this way. Simulations running on different
partitions can also communicate with each other; see the
<A HREF = "temper.html">temper</A> command.
</P>
<PRE>-plog file
</PRE>
<P>Specify the base name for the partition log files,
so partition N writes log information to file.N. If file is
none, then no partition log files are created.
This overrides the
filename specified in the -log command-line option.
This option is useful when working with large numbers of partitions,
allowing the partition log files to be suppressed (-plog none) or
placed in a sub-directory (-plog replica_files/log.lammps)
If this option is not used
the log file for partition N is log.lammps.N or whatever is specified by
the -log command-line option.
</P>
<PRE>-pscreen file
</PRE>
<P>Specify the base name for the
partition screen file, so partition N writes
screen information to file.N. If file is
none, then no partition screen files are created.
This overrides the
filename specified in the -screen command-line option.
This option is useful when working with large numbers of partitions,
allowing the partition screen files to be suppressed (-pscreen none) or
placed in a sub-directory (-pscreen replica_files/screen)
If this option is not used
the screen file for partition N is screen.N or whatever is specified by
the -screen command-line option.
</P>
<PRE>-screen file
</PRE>
<P>Specify a file for LAMMPS to write its screen information to. In
one-partition mode, if the switch is not used, LAMMPS writes to the
screen. If this switch is used, LAMMPS writes to the specified file
instead and you will see no screen output. In multi-partition mode,
if the switch is not used, hi-level status information is written to
the screen. Each partition also writes to a screen.N file where N is
the partition ID. If the switch is specified in multi-partition mode,
the hi-level screen dump is named "file" and each partition also
writes screen information to a file.N. For both one-partition and
multi-partition mode, if the specified file is "none", then no screen
output is performed. Option -pscreen will override the name of the
partition screen files file.N.
</P>
<PRE>-suffix style
</PRE>
<P>Use variants of various styles if they exist. The specified style can
be <I>opt</I> or <I>gpu</I> or <I>cuda</I>. These refer to optional packages that
LAMMPS can be built with, as described above in <A HREF = "#start_3">Section
2.3</A>. The "opt" style corrsponds to the OPT package, the
"gpu" style to the GPU package, and the "cuda" style to the USER-CUDA
package.
</P>
<P>As an example, all of the packages provide a <A HREF = "pair_lj.html">pair_style
lj/cut</A> variant, with style names lj/cut/opt or
lj/cut/gpu or lj/cut/cuda. A variant styles can be specified
explicitly in your input script, e.g. pair_style lj/cut/gpu. If the
-suffix switch is used, you do not need to modify your input script.
The specified suffix (opt,gpu,cuda) is automatically appended whenever
your input script command creates a new <A HREF = "atom_style.html">atom</A>,
<A HREF = "pair_style.html">pair</A>, <A HREF = "fix.html">fix</A>, <A HREF = "compute.html">compute</A>, or
<A HREF = "run_style.html">run</A> style. atom, pair, fix, compute, or integrate
style. If the variant version does not exist, the standard version is
created.
</P>
<P>The <A HREF = "suffix.html">suffix</A> command can also set a suffix and it can also
turn off/on any suffix setting made via the command line.
</P>
<PRE>-var name value1 value2 ...
</PRE>
<P>Specify a variable that will be defined for substitution purposes when
the input script is read. "Name" is the variable name which can be a
single character (referenced as $x in the input script) or a full
string (referenced as ${abc}). An <A HREF = "variable.html">index-style
variable</A> will be created and populated with the
subsequent values, e.g. a set of filenames. Using this command-line
option is equivalent to putting the line "variable name index value1
value2 ..." at the beginning of the input script. Defining an index
variable as a command-line argument overrides any setting for the same
index variable in the input script, since index variables cannot be
re-defined. See the <A HREF = "variable.html">variable</A> command for more info on
defining index and other kinds of variables and <A HREF = "Section_commands.html#cmd_2">this
section</A> for more info on using variables
in input scripts.
</P>
<HR>
<H4><A NAME = "start_7"></A>2.7 LAMMPS screen output
</H4>
<P>As LAMMPS reads an input script, it prints information to both the
screen and a log file about significant actions it takes to setup a
simulation. When the simulation is ready to begin, LAMMPS performs
various initializations and prints the amount of memory (in MBytes per
processor) that the simulation requires. It also prints details of
the initial thermodynamic state of the system. During the run itself,
thermodynamic information is printed periodically, every few
timesteps. When the run concludes, LAMMPS prints the final
thermodynamic state and a total run time for the simulation. It then
appends statistics about the CPU time and storage requirements for the
simulation. An example set of statistics is shown here:
</P>
<PRE>Loop time of 49.002 on 2 procs for 2004 atoms
</PRE>
<PRE>Pair time (%) = 35.0495 (71.5267)
Bond time (%) = 0.092046 (0.187841)
Kspce time (%) = 6.42073 (13.103)
Neigh time (%) = 2.73485 (5.5811)
Comm time (%) = 1.50291 (3.06703)
Outpt time (%) = 0.013799 (0.0281601)
Other time (%) = 2.13669 (4.36041)
</PRE>
<PRE>Nlocal: 1002 ave, 1015 max, 989 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8720 ave, 8724 max, 8716 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 354141 ave, 361422 max, 346860 min
Histogram: 1 0 0 0 0 0 0 0 0 1
</PRE>
<PRE>Total # of neighbors = 708282
Ave neighs/atom = 353.434
Ave special neighs/atom = 2.34032
Number of reneighborings = 42
Dangerous reneighborings = 2
</PRE>
<P>The first section gives the breakdown of the CPU run time (in seconds)
into major categories. The second section lists the number of owned
atoms (Nlocal), ghost atoms (Nghost), and pair-wise neighbors stored
per processor. The max and min values give the spread of these values
across processors with a 10-bin histogram showing the distribution.
The total number of histogram counts is equal to the number of
processors.
</P>
<P>The last section gives aggregate statistics for pair-wise neighbors
and special neighbors that LAMMPS keeps track of (see the
<A HREF = "special_bonds.html">special_bonds</A> command). The number of times
neighbor lists were rebuilt during the run is given as well as the
number of potentially "dangerous" rebuilds. If atom movement
triggered neighbor list rebuilding (see the
<A HREF = "neigh_modify.html">neigh_modify</A> command), then dangerous
reneighborings are those that were triggered on the first timestep
atom movement was checked for. If this count is non-zero you may wish
to reduce the delay factor to insure no force interactions are missed
by atoms moving beyond the neighbor skin distance before a rebuild
takes place.
</P>
<P>If an energy minimization was performed via the
<A HREF = "minimize.html">minimize</A> command, additional information is printed,
e.g.
</P>
<PRE>Minimization stats:
E initial, next-to-last, final = -0.895962 -2.94193 -2.94342
Gradient 2-norm init/final= 1920.78 20.9992
Gradient inf-norm init/final= 304.283 9.61216
Iterations = 36
Force evaluations = 177
</PRE>
<P>The first line lists the initial and final energy, as well as the
energy on the next-to-last iteration. The next 2 lines give a measure
of the gradient of the energy (force on all atoms). The 2-norm is the
"length" of this force vector; the inf-norm is the largest component.
The last 2 lines are statistics on how many iterations and
force-evaluations the minimizer required. Multiple force evaluations
are typically done at each iteration to perform a 1d line minimization
in the search direction.
</P>
<P>If a <A HREF = "kspace_style.html">kspace_style</A> long-range Coulombics solve was
performed during the run (PPPM, Ewald), then additional information is
printed, e.g.
</P>
<PRE>FFT time (% of Kspce) = 0.200313 (8.34477)
FFT Gflps 3d 1d-only = 2.31074 9.19989
</PRE>
<P>The first line gives the time spent doing 3d FFTs (4 per timestep) and
the fraction it represents of the total KSpace time (listed above).
Each 3d FFT requires computation (3 sets of 1d FFTs) and communication
(transposes). The total flops performed is 5Nlog_2(N), where N is the
number of points in the 3d grid. The FFTs are timed with and without
the communication and a Gflop rate is computed. The 3d rate is with
communication; the 1d rate is without (just the 1d FFTs). Thus you
can estimate what fraction of your FFT time was spent in
communication, roughly 75% in the example above.
</P>
<HR>
<H4><A NAME = "start_8"></A>2.8 Tips for users of previous LAMMPS versions
</H4>
<P>The current C++ began with a complete rewrite of LAMMPS 2001, which
was written in F90. Features of earlier versions of LAMMPS are listed
in <A HREF = "Section_history.html">this section</A>. The F90 and F77 versions
(2001 and 99) are also freely distributed as open-source codes; check
the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> for distribution information if you prefer
those versions. The 99 and 2001 versions are no longer under active
development; they do not have all the features of C++ LAMMPS.
</P>
<P>If you are a previous user of LAMMPS 2001, these are the most
significant changes you will notice in C++ LAMMPS:
</P>
<P>(1) The names and arguments of many input script commands have
changed. All commands are now a single word (e.g. read_data instead
of read data).
</P>
<P>(2) All the functionality of LAMMPS 2001 is included in C++ LAMMPS,
but you may need to specify the relevant commands in different ways.
</P>
<P>(3) The format of the data file can be streamlined for some problems.
See the <A HREF = "read_data.html">read_data</A> command for details. The data file
section "Nonbond Coeff" has been renamed to "Pair Coeff" in C++ LAMMPS.
</P>
<P>(4) Binary restart files written by LAMMPS 2001 cannot be read by C++
LAMMPS with a <A HREF = "read_restart.html">read_restart</A> command. This is
because they were output by F90 which writes in a different binary
format than C or C++ writes or reads. Use the <I>restart2data</I> tool
provided with LAMMPS 2001 to convert the 2001 restart file to a text
data file. Then edit the data file as necessary before using the C++
LAMMPS <A HREF = "read_data.html">read_data</A> command to read it in.
</P>
<P>(5) There are numerous small numerical changes in C++ LAMMPS that mean
you will not get identical answers when comparing to a 2001 run.
However, your initial thermodynamic energy and MD trajectory should be
close if you have setup the problem for both codes the same.
</P>
</HTML>
diff --git a/doc/Section_start.txt b/doc/Section_start.txt
index 7435bd204..5b8e08286 100644
--- a/doc/Section_start.txt
+++ b/doc/Section_start.txt
@@ -1,1141 +1,1144 @@
"Previous Section"_Section_intro.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_commands.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
2. Getting Started :h3
This section describes how to build and run LAMMPS, for both new and
experienced users.
2.1 "What's in the LAMMPS distribution"_#start_1
2.2 "Making LAMMPS"_#start_2
2.3 "Making LAMMPS with optional packages"_#start_3
2.4 "Building LAMMPS as a library"_#start_4
2.5 "Running LAMMPS"_#start_5
2.6 "Command-line options"_#start_6
2.7 "Screen output"_#start_7
2.8 "Tips for users of previous versions"_#start_8 :all(b)
:line
2.1 What's in the LAMMPS distribution :h4,link(start_1)
When you download LAMMPS you will need to unzip and untar the
downloaded file with the following commands, after placing the file in
an appropriate directory.
gunzip lammps*.tar.gz
tar xvf lammps*.tar :pre
This will create a LAMMPS directory containing two files and several
sub-directories:
README: text file
LICENSE: the GNU General Public License (GPL)
bench: benchmark problems
couple: code coupling examples, using LAMMPS as a library
doc: documentation
examples: simple test problems
potentials: embedded atom method (EAM) potential files
src: source files
tools: pre- and post-processing tools :tb(s=:)
If you download one of the Windows executables from the download page,
then you just get a single file:
lmp_windows.exe :pre
Skip to the "Running LAMMPS"_#start_5 sections for info on how to
launch these executables on a Windows box.
The Windows executables for serial or parallel only include certain
packages and bug-fixes/upgrades listed on "this
page"_http://lammps.sandia.gov/bug.html up to a certain date, as
stated on the download page. If you want something with more packages
or that is more current, you'll have to download the source tarball
and build it yourself from source code using Microsoft Visual Studio,
as described in the next section.
:line
2.2 Making LAMMPS :h4,link(start_2)
This section has the following sub-sections:
"Read this first"_#start_2_1
"Steps to build a LAMMPS executable"_#start_2_2
"Common errors that can occur when making LAMMPS"_#start_2_3
"Additional build tips"_#start_2_4
"Building for a Mac"_#start_2_5
"Building for Windows"_#start_2_6 :ul
:line
[{Read this first:}] :link(start_2_1)
Building LAMMPS can be non-trivial. You may need to edit a makefile,
there are compiler options to consider, additional libraries can be
used (MPI, FFT, JPEG), LAMMPS packages may be included or excluded,
some of these packages use auxiliary libraries which need to be
pre-built, etc.
Please read this section carefully. If you are not comfortable with
makefiles, or building codes on a Unix platform, or running an MPI job
on your machine, please find a local expert to help you. Many
compiling, linking, and run problems that users have are not really
LAMMPS issues - they are peculiar to the user's system, compilers,
libraries, etc. Such questions are better answered by a local expert.
If you have a build problem that you are convinced is a LAMMPS issue
(e.g. the compiler complains about a line of LAMMPS source code), then
please send an email to the
"developers"_http://lammps.sandia.gov/authors.html.
If you succeed in building LAMMPS on a new kind of machine, for which
there isn't a similar Makefile for in the src/MAKE directory, send it
to the developers and we'll include it in future LAMMPS releases.
:line
[{Steps to build a LAMMPS executable:}] :link(start_2_2)
[Step 0]
The src directory contains the C++ source and header files for LAMMPS.
It also contains a top-level Makefile and a MAKE sub-directory with
low-level Makefile.* files for many machines. From within the src
directory, type "make" or "gmake". You should see a list of available
choices. If one of those is the machine and options you want, you can
type a command like:
make linux
or
gmake mac :pre
Note that on a multi-processor or multi-core platform you can launch a
parallel make, by using the "-j" switch with the make command, which
will build LAMMPS more quickly.
If you get no errors and an executable like lmp_linux or lmp_mac is
produced, you're done; it's your lucky day.
Note that by default only a few of LAMMPS optional pacakges are
installed. To build LAMMPS with optional packages, see "this
section"_#start_3 below.
[Step 1]
If Step 0 did not work, you will need to create a low-level Makefile
for your machine, like Makefile.foo. You should make a copy of an
existing src/MAKE/Makefile.* as a starting point. The only portions
of the file you need to edit are the first line, the "compiler/linker
settings" section, and the "LAMMPS-specific settings" section.
[Step 2]
Change the first line of src/MAKE/Makefile.foo to list the word "foo"
after the "#", and whatever other options it will set. This is the
line you will see if you just type "make".
[Step 3]
The "compiler/linker settings" section lists compiler and linker
settings for your C++ compiler, including optimization flags. You can
use g++, the open-source GNU compiler, which is available on all Unix
systems. You can also use mpicc which will typically be available if
MPI is installed on your system, though you should check which actual
compiler it wraps. Vendor compilers often produce faster code. On
boxes with Intel CPUs, we suggest using the commercial Intel icc
compiler, which can be downloaded from "Intel's compiler site"_intel.
:link(intel,http://www.intel.com/software/products/noncom)
If building a C++ code on your machine requires additional libraries,
then you should list them as part of the LIB variable.
The DEPFLAGS setting is what triggers the C++ compiler to create a
dependency list for a source file. This speeds re-compilation when
source (*.cpp) or header (*.h) files are edited. Some compilers do
not support dependency file creation, or may use a different switch
than -D. GNU g++ works with -D. If your compiler can't create
dependency files, then you'll need to create a Makefile.foo patterned
after Makefile.storm, which uses different rules that do not involve
dependency files. Note that when you build LAMMPS for the first time
on a new platform, a long list of *.d files will be printed out
rapidly. This is not an error; it is the Makefile doing its normal
creation of dependencies.
[Step 4]
The "system-specific settings" section has several parts. Note that
if you change any -D setting in this section, you should do a full
re-compile, after typing "make clean" (which will describe different
clean options).
The LMP_INC variable is used to include options that turn on ifdefs
within the LAMMPS code. The options that are currently recogized are:
-DLAMMPS_GZIP
-DLAMMPS_JPEG
-DLAMMPS_XDR
-DLAMMPS_SMALLBIG
-DLAMMPS_BIGBIG
-DLAMMPS_SMALLSMALL
-DLAMMPS_LONGLONG_TO_LONG
-DPACK_ARRAY
-DPACK_POINTER
-DPACK_MEMCPY :ul
The read_data and dump commands will read/write gzipped files if you
compile with -DLAMMPS_GZIP. It requires that your Unix support the
"popen" command.
If you use -DLAMMPS_JPEG, the "dump image"_dump.html command will be
able to write out JPEG image files. If not, it will only be able to
write out text-based PPM image files. For JPEG files, you must also
link LAMMPS with a JPEG library, as described below.
If you use -DLAMMPS_XDR, the build will include XDR compatibility
files for doing particle dumps in XTC format. This is only necessary
if your platform does have its own XDR files available. See the
Restrictions section of the "dump"_dump.html command for details.
Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG,
-D-DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG.
These refer to use of 4-byte (small) vs 8-byte (big) integers within
LAMMPS, as described in src/lmptype.h. The only reason to use the
BIGBIG setting is to enable simulation of huge molecular systems with
more than 2 billion atoms. The only reason to use the SMALLSMALL
setting is if your machine does not support 64-bit integers.
The -DLAMMPS_LONGLONG_TO_LONG setting may be needed if your system or
MPI version does not recognize "long long" data types. In this case a
"long" data type is likely already 64-bits, in which case this setting
will convert to that data type.
Using one of the -DPACK_ARRAY, -DPACK_POINTER, and -DPACK_MEMCPY
options can make for faster parallel FFTs (in the PPPM solver) on some
platforms. The -DPACK_ARRAY setting is the default. See the
"kspace_style"_kspace_style.html command for info about PPPM. See
Step 6 below for info about building LAMMPS with an FFT library.
[Step 5]
The 3 MPI variables are used to specify an MPI library to build LAMMPS
with.
If you want LAMMPS to run in parallel, you must have an MPI library
installed on your platform. If you use an MPI-wrapped compiler, such
as "mpicc" to build LAMMPS, you should be able to leave these 3
variables blank; the MPI wrapper knows where to find the needed files.
If not, and MPI is installed on your system in the usual place (under
/usr/local), you also may not need to specify these 3 variables. On
some large parallel machines which use "modules" for their
compile/link environements, you may simply need to include the correct
module in your build environment. Or the parallel machine may have a
vendor-provided MPI which the compiler has no trouble finding.
Failing this, with these 3 variables you can specify where the mpi.h
file (MPI_INC) and the MPI library file (MPI_PATH) are found and the
name of the library file (MPI_LIB).
If you are installing MPI yourself, we recommend Argonne's MPICH 1.2
or 2.0 or OpenMPI. MPICH can be downloaded from the "Argonne MPI
site"_http://www-unix.mcs.anl.gov/mpi. OpenMPI can be downloaded the
"OpenMPI site"_http://www.open-mpi.org. LAM MPI should also work. If
you are running on a big parallel platform, your system people or the
vendor should have already installed a version of MPI, which will be
faster than MPICH or OpenMPI or LAM, so find out how to build and link
with it. If you use MPICH or OpenMPI or LAM, you will have to
configure and build it for your platform. The MPI configure script
should have compiler options to enable you to use the same compiler
you are using for the LAMMPS build, which can avoid problems that can
arise when linking LAMMPS to the MPI library.
If you just want to run LAMMPS on a single processor, you can use the
dummy MPI library provided in src/STUBS, since you don't need a true
MPI library installed on your system. See the
src/MAKE/Makefile.serial file for how to specify the 3 MPI variables
in this case. You will also need to build the STUBS library for your
platform before making LAMMPS itself. From the src directory, type
"make stubs", or from the STUBS dir, type "make" and it should create
a libmpi.a suitable for linking to LAMMPS. If this build fails, you
will need to edit the STUBS/Makefile for your platform.
The file STUBS/mpi.cpp provides a CPU timer function called
MPI_Wtime() that calls gettimeofday() . If your system doesn't
support gettimeofday() , you'll need to insert code to call another
timer. Note that the ANSI-standard function clock() rolls over after
an hour or so, and is therefore insufficient for timing long LAMMPS
simulations.
[Step 6]
The 3 FFT variables allow you to specify an FFT library which LAMMPS
uses (for performing 1d FFTs) when running the particle-particle
particle-mesh (PPPM) option for long-range Coulombics via the
"kspace_style"_kspace_style.html command.
LAMMPS supports various open-source or vendor-supplied FFT libraries
for this purpose. If you leave these 3 variables blank, LAMMPS will
use the open-source "KISS FFT library"_http://kissfft.sf.net, which is
included in the LAMMPS distribution. This library is portable to all
platforms and for typical LAMMPS simulations is almost as fast as FFTW
or vendor optimized libraries. If you are not including the KSPACE
package in your build, you can also leave the 3 variables blank.
Otherwise, select which kinds of FFTs to use as part of the FFT_INC
setting by a switch of the form -DFFT_XXX. Recommended values for XXX
are: MKL, SCSL, FFTW2, and FFTW3. Legacy options are: INTEL, SGI,
ACML, and T3E. For backward compatability, using -DFFT_FFTW will use
the FFTW2 library. Using -DFFT_NONE will use the KISS library
described above.
You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables,
so the compiler and linker can find the needed FFT header and library
files. Note that on some large parallel machines which use "modules"
for their compile/link environements, you may simply need to include
the correct module in your build environment. Or the parallel machine
may have a vendor-provided FFT library which the compiler has no
trouble finding.
FFTW is a fast, portable library that should also work on any
platform. You can download it from
"www.fftw.org"_http://www.fftw.org. Both the legacy version 2.1.X and
the newer 3.X versions are supported as -DFFT_FFTW2 or -DFFT_FFTW3.
Building FFTW for your box should be as simple as ./configure; make.
Note that on some platforms FFTW2 has been pre-installed, and uses
renamed files indicating the precision it was compiled with,
e.g. sfftw.h, or dfftw.h instead of fftw.h. In this case, you can
specify an additional define variable for FFT_INC called -DFFTW2_SIZE,
which will select the correct include file. In this case, for FFT_LIB
you must also manually specify the correct library, namely -lsfftw or
-ldfftw.
The FFT_INC variable also allows for a -DFFT_SINGLE setting that will
use single-precision FFTs with PPPM, which can speed-up long-range
calulations, particularly in parallel or on GPUs. Fourier transform
and related PPPM operations are somewhat insensitive to floating point
truncation errors and thus do not always need to be performed in
double precision. Using the -DFFT_SINGLE setting trades off a little
accuracy for reduced memory use and parallel communication costs for
transposing 3d FFT data. Note that single precision FFTs have only
been tested with the FFTW3, FFTW2, MKL, and KISS FFT options.
[Step 7]
The 3 JPG variables allow you to specify a JPEG library which LAMMPS
uses when writing out JPEG files via the "dump image"_dump_image.html
command. These can be left blank if you do not use the -DLAMMPS_JPEG
switch discussed above in Step 4, since in that case JPEG output will
be disabled.
A standard JPEG library usually goes by the name libjpeg.a and has an
associated header file jpeglib.h. Whichever JPEG library you have on
your platform, you'll need to set the appropriate JPG_INC, JPG_PATH,
and JPG_LIB variables, so that the compiler and linker can find it.
As before, if these header and library files are in the usual place on
your machine, you may not need to set these variables.
[Step 8]
Note that by default only a few of LAMMPS optional pacakges are
installed. To build LAMMPS with optional packages, see "this
section"_#start_3 below, before proceeding to Step 9.
[Step 9]
That's it. Once you have a correct Makefile.foo, you have installed
the optional LAMMPS packages you want to include in your build, and
you have pre-built any other needed libraries (e.g. MPI, FFT, package
libraries), all you need to do from the src directory is type
something like this:
make foo
or
gmake foo :pre
You should get the executable lmp_foo when the build is complete.
:line
[{Errors that can occur when making LAMMPS:}] :link(start_2_3)
IMPORTANT NOTE: If an error occurs when building LAMMPS, the compiler
or linker will state very explicitly what the problem is. The error
message should give you a hint as to which of the steps above has
failed, and what you need to do in order to fix it. Building a code
with a Makefile is a very logical process. The compiler and linker
need to find the appropriate files and those files need to be
compatible with LAMMPS source files. When a make fails, there is
usually a very simple reason, which you or a local expert will need to
fix.
Here are two non-obvious errors that can occur:
(1) If the make command breaks immediately with errors that indicate
it can't find files with a "*" in their names, this can be because
your machine's native make doesn't support wildcard expansion in a
makefile. Try gmake instead of make. If that doesn't work, try using
a -f switch with your make command to use a pre-generated
Makefile.list which explicitly lists all the needed files, e.g.
make makelist
make -f Makefile.list linux
gmake -f Makefile.list mac :pre
The first "make" command will create a current Makefile.list with all
the file names in your src dir. The 2nd "make" command (make or
gmake) will use it to build LAMMPS. Note that you should
include/exclude any desired optional packages before using the "make
makelist" command.
(2) If you get an error that says something like 'identifier "atoll"
is undefined', then your machine does not support "long long"
integers. Try using the -DLAMMPS_LONGLONG_TO_LONG setting described
above in Step 4.
:line
[{Additional build tips:}] :link(start_2_4)
(1) Building LAMMPS for multiple platforms.
You can make LAMMPS for multiple platforms from the same src
directory. Each target creates its own object sub-directory called
Obj_name where it stores the system-specific *.o files.
(2) Cleaning up.
Typing "make clean-all" or "make clean-foo" will delete *.o object
files created when LAMMPS is built, for either all builds or for a
particular machine.
(3) Changing the size limits in src/lmptype.h
If you are running a very large problem (billions of atoms or more)
and get a run-time error about the system being too big, either on a
per-processor basis or in total size, then you may need to change one
or more settings in src/lmptype.h and re-compile LAMMPS.
As the documentation in that file explains, you have basically
two choices to make:
set the data type size of integer atom IDs to 4 or 8 bytes
set the data type size of integers that store the total system size to 4 or 8 bytes :ul
The default for atom IDs is 4-byte integers since there is a memory
and communication cost for 8-byte integers. Non-molecular problems do
not need atom IDs so this does not restrict their size. Molecular
problems (which use IDs to define molecular topology), are limited to
about 2 billion atoms (2^31) with 4-byte IDs. With 8-byte IDs they
are effectively unlimited in size (2^63).
The default for total system size quantities (like the number of atoms
or timesteps) is 8-byte integers by default which is effectively
unlimited in size (2^63). If your system or MPI implementation does
not support 8-byte integers, an error will be generated, and you will
need to set "bigint" to 4-byte integers. This restricts your total
system size to about 2 billion atoms or timesteps (2^31).
Note that in src/lmptype.h there are also settings for the MPI data
types associated with the integers that store atom IDs and total
system sizes, which need to be set consistent with the associated C
data types.
In all cases, the size of problem that can be run on a per-processor
basis is limited by 4-byte integer storage to about 2 billion atoms
per processor (2^31), which should not normally be a restriction since
such a problem would have a huge per-processor memory footprint due to
neighbor lists and would run very slowly in terms of CPU
secs/timestep.
:line
[{Building for a Mac:}] :link(start_2_5)
OS X is BSD Unix, so it should just work. See the Makefile.mac file.
:line
[{Building for Windows:}] :link(start_2_6)
The LAMMPS download page has an option to download both a serial and
parallel pre-built Windows exeutable. See the "Running
LAMMPS"_#start_5 section for instructions for running these
executables on a Windows box.
If the pre-built executable doesn't have the options you want, then
you can build LAMMPS from its source files on a Windows box. One way
to do this is install and use cygwin to build LAMMPS with a standard
Linus make, just as you would on any Linux box; see
src/MAKE/Makefile.cygwin.
There is a also a src/WINDOWS directory that contains project files
for Microsoft Visual Studio 2005, which should also work with later
versions of VS. That directory contains a README.txt file which
provides instructions for building LAMMPS from source code using
Visual Studio that are hopefully easy to follow for Windows and VS
users.
Four VS project options are provided. The first includes the default
packages (MANYBODY, MOLECULE, and KSPACE). The second includes all
standard packages (except GPU, MEAM, and REAX which are not yet
included because they require NVIDIA or Fortran compilation). The
third includes all standard packages (with the exceptions) and some
user packages. The included user packages are USER-EFF, USER-CG-CMM,
and USER-REAXC. The fourth project includes the USER-AWPMD package.
:line
2.3 Making LAMMPS with optional packages :h4,link(start_3)
This section has the following sub-sections:
"Package basics"_#start_3_1
"Including/excluding packages"_#start_3_2
"Packages that require extra libraries"_#start_3_3
"Additional Makefile settings for extra libraries"_#start_3_4 :ul
:line
[{Package basics:}] :link(start_3_1)
The source code for LAMMPS is structured as a set of core files which
are always included, plus optional packages. Packages are groups of
files that enable a specific set of features. For example, force
fields for molecular systems or granular systems are in packages. You
can see the list of all packages by typing "make package" from within
the src directory of the LAMMPS distribution.
If you use a command in a LAMMPS input script that is specific to a
particular package, you must have built LAMMPS with that package, else
you will get an error that the style is invalid or the command is
unknown. Every command's doc page specfies if it is part of a
package. You can also type
lmp_machine -h :pre
to run your executable with the optional "-h command-line
switch"_#start_6 for "help", which will list the styles and commands
known to your executable.
There are two kinds of packages in LAMMPS, standard and user packages.
More information about the contents of standard and user packages is
given in "this section"_Section_packages.html of the manual. The
difference between standard and user packages is as follows:
Standard packages are supported by the LAMMPS developers and are
written in a syntax and style consistent with the rest of LAMMPS.
This means we will answer questions about them, debug and fix them if
necessary, and keep them compatible with future changes to LAMMPS.
User packages have been contributed by users, and always begin with
the user prefix. If they are a single command (single file), they are
typically in the user-misc package. Otherwise, they are a a set of
files grouped together which add a specific functionality to the code.
User packages don't necessarily meet the requirements of the standard
packages. If you have problems using a feature provided in a user
package, you will likely need to contact the contributor directly to
get help. Information on how to submit additions you make to LAMMPS
as a user-contributed package is given in "this
section"_Section_modify.html#mod_14 of the documentation.
:line
[{Including/excluding packages:}] :link(start_3_2)
To use or not use a package you must include or exclude it before
building LAMMPS. From the src directory, this is typically as simple
as:
make yes-colloid
make g++ :pre
or
make no-manybody
make g++ :pre
Some packages have individual files that depend on other packages
being included. LAMMPS checks for this and does the right thing.
I.e. individual files are only included if their dependencies are
already included. Likewise, if a package is excluded, other files
dependent on that package are also excluded.
The reason to exclude packages is if you will never run certain kinds
of simulations. For some packages, this will keep you from having to
build auxiliary libraries (see below), and will also produce a smaller
executable which may run a bit faster.
-By default, LAMMPS includes only the "kspace", "manybody", and
-"molecule" packages.
+When you download a LAMMPS tarball, these packages are pre-installed
+in the src directory: KSPACE, MANYBODY,MOLECULE. When you download
+LAMMPS source files from the SVN or Git repositories, no packages are
+pre-installed.
Packages are included or excluded by typing "make yes-name" or "make
-no-name", where "name" is the name of the package. You can also type
-"make yes-standard", "make no-standard", "make yes-user", "make
-no-user", "make yes-all" or "make no-all" to include/exclude various
-sets of packages. Type "make package" to see the all of the
-package-related make options.
+no-name", where "name" is the name of the package in lower-case, e.g.
+name = kspace for the KSPACE package or name = user-atc for the
+USER-ATC package. You can also type "make yes-standard", "make
+no-standard", "make yes-user", "make no-user", "make yes-all" or "make
+no-all" to include/exclude various sets of packages. Type "make
+package" to see the all of the package-related make options.
IMPORTANT NOTE: Inclusion/exclusion of a package works by simply
moving files back and forth between the main src directory and
sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
so that the files are seen or not seen when LAMMPS is built. After
you have included or excluded a package, you must re-build LAMMPS.
Additional package-related make options exist to help manage LAMMPS
files that exist in both the src directory and in package
sub-directories. You do not normally need to use these commands
unless you are editing LAMMPS files or have downloaded a patch from
the LAMMPS WWW site.
Typing "make package-update" will overwrite src files with files from
the package sub-directories if the package has been included. It
should be used after a patch is installed, since patches only update
the files in the package sub-directory, but not the src files. Typing
"make package-overwrite" will overwrite files in the package
sub-directories with src files.
Typing "make package-status" will show which packages are currently
included. Of those that are included, it will list files that are
different in the src directory and package sub-directory. Typing
"make package-diff" lists all differences between these files. Again,
type "make package" to see all of the package-related make options.
:line
[{Packages that require extra libraries:}] :link(start_3_3)
A few of the standard and user packages require additional auxiliary
libraries to be compiled first. If you get a LAMMPS build error about
a missing library, this is likely the reason. The source code for
these libraries is included in the LAMMPS distribution under the "lib"
directory. Look at the lib/README file for a list of these or see
"this section"_Section_packages.html of the doc pages.
Each lib directory has a README file (e.g. lib/reax/README) with
instructions on how to build that library. Typically this is done
in this manner:
make -f Makefile.g++ :pre
in the appropriate directory, e.g. in lib/reax. Some of the libraries
do not build this way. Again, see the libary README file for details.
In any event, you will need to use a Makefile that is a match for your
system. If one of the provided Makefiles is not appropriate for your
system you will need to edit or add one. For example, in the case of
Fortran-based libraries, your system must have a Fortran compiler, the
settings for which will need to be listed in the Makefile.
When you have built one of these libraries, there are 2 things to
check:
(1) The file libname.a should now exist in lib/name.
E.g. lib/reax/libreax.a. This is the library file LAMMPS will link
against. One exception is the lib/cuda library which produces the
file liblammpscuda.a, because there is already a system library
libcuda.a.
(2) The file Makefile.lammps should exist in lib/name. E.g.
lib/cuda/Makefile.lammps. This file may be auto-generated by the
build of the library, or you may need to make a copy of the
appropriate provided file (e.g. lib/meam/Makefile.lammps.gfortran).
Either way you should insure that the settings in this file are
appropriate for your system.
There are typically 3 settings in the Makefile.lammps file (unless
some are blank or not needed): a SYSINC, SYSPATH, and SYSLIB setting,
specific to this package. These are settings the LAMMPS build will
import when compiling the LAMMPS package files (not the library
files), and linking to the auxiliary library. They typically list any
other system libraries needed to support the package and where to find
them. An example is the BLAS and LAPACK libraries needed by the
USER-ATC package. Or the system libraries that support calling
Fortran from C++, as the MEAM and REAX packages do.
Note that if these settings are not correct for your box, the LAMMPS
build will likely fail.
:line
2.4 Building LAMMPS as a library :h4,link(start_4)
LAMMPS itself can be built as a library, which can then be called from
another application or a scripting language. See "this
section"_Section_howto.html#howto_10 for more info on coupling LAMMPS
to other codes. Building LAMMPS as a library is done by typing
make makelib
make -f Makefile.lib foo :pre
where foo is the machine name. Note that inclusion or exclusion of
any desired optional packages should be done before typing "make
makelib". The first "make" command will create a current Makefile.lib
with all the file names in your src dir. The 2nd "make" command will
use it to build LAMMPS as a library. This requires that Makefile.foo
have a library target (lib) and system-specific settings for ARCHIVE
and ARFLAGS. See Makefile.linux for an example. The build will
create the file liblmp_foo.a which another application can link to.
When used from a C++ program, the library allows one or more LAMMPS
objects to be instantiated. All of LAMMPS is wrapped in a LAMMPS_NS
namespace; you can safely use any of its classes and methods from
within your application code, as needed.
When used from a C or Fortran program or a scripting language, the
library has a simple function-style interface, provided in
src/library.cpp and src/library.h.
See the sample codes couple/simple/simple.cpp and simple.c as examples
of C++ and C codes that invoke LAMMPS thru its library interface.
There are other examples as well in the couple directory which are
discussed in "this section"_Section_howto.html#howto_10 of the manual.
See "this section"_Section_python.html of the manual for a description
of the Python wrapper provided with LAMMPS that operates through the
LAMMPS library interface.
The files src/library.cpp and library.h contain the C-style interface
to LAMMPS. See "this section"_Section_howto.html#howto_19 of the
manual for a description of the interface and how to extend it for
your needs.
:line
2.5 Running LAMMPS :h4,link(start_5)
By default, LAMMPS runs by reading commands from stdin; e.g. lmp_linux
< in.file. This means you first create an input script (e.g. in.file)
containing the desired commands. "This section"_Section_commands.html
describes how input scripts are structured and what commands they
contain.
You can test LAMMPS on any of the sample inputs provided in the
examples or bench directory. Input scripts are named in.* and sample
outputs are named log.*.name.P where name is a machine and P is the
number of processors it was run on.
Here is how you might run a standard Lennard-Jones benchmark on a
Linux box, using mpirun to launch a parallel job:
cd src
make linux
cp lmp_linux ../bench
cd ../bench
mpirun -np 4 lmp_linux < in.lj :pre
See "this page"_bench for timings for this and the other benchmarks
on various platforms.
:link(bench,http://lammps.sandia.gov/bench.html)
:line
On a Windows box, you can skip making LAMMPS and simply download an
executable, as described above, though the pre-packaged executables
include only certain packages.
To run a LAMMPS executable on a Windows machine, first decide whether
you want to download the non-MPI (serial) or the MPI (parallel)
version of the executable. Download and save the version you have
chosen.
For the non-MPI version, follow these steps:
Get a command prompt by going to Start->Run... ,
then typing "cmd". :ulb,l
Move to the directory where you have saved lmp_win_no-mpi.exe
(e.g. by typing: cd "Documents"). :l
At the command prompt, type "lmp_win_no-mpi -in in.lj", replacing in.lj
with the name of your LAMMPS input script. :l,ule
For the MPI version, which allows you to run LAMMPS under Windows on
multiple processors, follow these steps:
Download and install
"MPICH2"_http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downloads
for Windows. :ulb,l
You'll need to use the mpiexec.exe and smpd.exe files from the MPICH2 package. Put them in
same directory (or path) as the LAMMPS Windows executable. :l
Get a command prompt by going to Start->Run... ,
then typing "cmd". :l
Move to the directory where you have saved lmp_win_mpi.exe
(e.g. by typing: cd "Documents"). :l
Then type something like this: "mpiexec -np 4 -localonly lmp_win_mpi -in in.lj",
replacing in.lj with the name of your LAMMPS input script. :l
Note that you may need to provide smpd with a passphrase --- it doesn't matter what you
type. :l
In this mode, output may not immediately show up on the screen, so
if your input script takes a long time to execute, you may need to be
patient before the output shows up. :l
Alternatively, you can still use this executable to run on a single processor by
typing something like: "lmp_win_mpi -in in.lj". :l,ule
:line
The screen output from LAMMPS is described in the next section. As it
runs, LAMMPS also writes a log.lammps file with the same information.
Note that this sequence of commands copies the LAMMPS executable
(lmp_linux) to the directory with the input files. This may not be
necessary, but some versions of MPI reset the working directory to
where the executable is, rather than leave it as the directory where
you launch mpirun from (if you launch lmp_linux on its own and not
under mpirun). If that happens, LAMMPS will look for additional input
files and write its output files to the executable directory, rather
than your working directory, which is probably not what you want.
If LAMMPS encounters errors in the input script or while running a
simulation it will print an ERROR message and stop or a WARNING
message and continue. See "this section"_Section_errors.html for a
discussion of the various kinds of errors LAMMPS can or can't detect,
a list of all ERROR and WARNING messages, and what to do about them.
LAMMPS can run a problem on any number of processors, including a
single processor. In theory you should get identical answers on any
number of processors and on any machine. In practice, numerical
round-off can cause slight differences and eventual divergence of
molecular dynamics phase space trajectories.
LAMMPS can run as large a problem as will fit in the physical memory
of one or more processors. If you run out of memory, you must run on
more processors or setup a smaller problem.
:line
2.6 Command-line options :h4,link(start_6)
At run time, LAMMPS recognizes several optional command-line switches
which may be used in any order. Either the full word or a one-or-two
letter abbreviation can be used:
-c or -cuda
-e or -echo
-i or -in
-h or -help
-l or -log
-p or -partition
-pl or -plog
-ps or -pscreen
-sc or -screen
-sf or -suffix
-v or -var :ul
For example, lmp_ibm might be launched as follows:
mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none < in.alloy
mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none < in.alloy :pre
Here are the details on the options:
-cuda on/off :pre
Explicitly enable or disable CUDA support, as provided by the
USER-CUDA package. If LAMMPS is built with this package, as described
above in "Section 2.3"_#start_3, then by default LAMMPS will run in
CUDA mode. If this switch is set to "off", then it will not, even if
it was built with the USER-CUDA package, which means you can run
standard LAMMPS or with the GPU package for testing or benchmarking
purposes. The only reason to set the switch to "on", is to check if
LAMMPS was built with the USER-CUDA package, since an error will be
generated if it was not.
-echo style :pre
Set the style of command echoing. The style can be {none} or {screen}
or {log} or {both}. Depending on the style, each command read from
the input script will be echoed to the screen and/or logfile. This
can be useful to figure out which line of your script is causing an
input error. The default value is {log}. The echo style can also be
set by using the "echo"_echo.html command in the input script itself.
-in file :pre
Specify a file to use as an input script. This is an optional switch
when running LAMMPS in one-partition mode. If it is not specified,
LAMMPS reads its input script from stdin - e.g. lmp_linux < in.run.
This is a required switch when running LAMMPS in multi-partition mode,
since multiple processors cannot all read from stdin.
-help :pre
Print a list of options compiled into this executable for each LAMMPS
style (atom_style, fix, compute, pair_style, bond_style, etc). This
can help you know if the command you want to use was included via the
appropriate package. LAMMPS will print the info and immediately exit
if this switch is used.
-log file :pre
Specify a log file for LAMMPS to write status information to. In
one-partition mode, if the switch is not used, LAMMPS writes to the
file log.lammps. If this switch is used, LAMMPS writes to the
specified file. In multi-partition mode, if the switch is not used, a
log.lammps file is created with hi-level status information. Each
partition also writes to a log.lammps.N file where N is the partition
ID. If the switch is specified in multi-partition mode, the hi-level
logfile is named "file" and each partition also logs information to a
file.N. For both one-partition and multi-partition mode, if the
specified file is "none", then no log files are created. Using a
"log"_log.html command in the input script will override this setting.
Option -plog will override the name of the partition log files file.N.
-partition 8x2 4 5 ... :pre
Invoke LAMMPS in multi-partition mode. When LAMMPS is run on P
processors and this switch is not used, LAMMPS runs in one partition,
i.e. all P processors run a single simulation. If this switch is
used, the P processors are split into separate partitions and each
partition runs its own simulation. The arguments to the switch
specify the number of processors in each partition. Arguments of the
form MxN mean M partitions, each with N processors. Arguments of the
form N mean a single partition with N processors. The sum of
processors in all partitions must equal P. Thus the command
"-partition 8x2 4 5" has 10 partitions and runs on a total of 25
processors.
Note that with MPI installed on a machine (e.g. your desktop), you can
run on more (virtual) processors than you have physical processors.
This can be useful for running "multi-replica
simulations"_Section_howto.html#howto_5, on one or a few processors.
The input script specifies what simulation is run on which partition;
see the "variable"_variable.html and "next"_next.html commands. This
"howto section"_Section_howto.html#howto_4 gives examples of how to
use these commands in this way. Simulations running on different
partitions can also communicate with each other; see the
"temper"_temper.html command.
-plog file :pre
Specify the base name for the partition log files,
so partition N writes log information to file.N. If file is
none, then no partition log files are created.
This overrides the
filename specified in the -log command-line option.
This option is useful when working with large numbers of partitions,
allowing the partition log files to be suppressed (-plog none) or
placed in a sub-directory (-plog replica_files/log.lammps)
If this option is not used
the log file for partition N is log.lammps.N or whatever is specified by
the -log command-line option.
-pscreen file :pre
Specify the base name for the
partition screen file, so partition N writes
screen information to file.N. If file is
none, then no partition screen files are created.
This overrides the
filename specified in the -screen command-line option.
This option is useful when working with large numbers of partitions,
allowing the partition screen files to be suppressed (-pscreen none) or
placed in a sub-directory (-pscreen replica_files/screen)
If this option is not used
the screen file for partition N is screen.N or whatever is specified by
the -screen command-line option.
-screen file :pre
Specify a file for LAMMPS to write its screen information to. In
one-partition mode, if the switch is not used, LAMMPS writes to the
screen. If this switch is used, LAMMPS writes to the specified file
instead and you will see no screen output. In multi-partition mode,
if the switch is not used, hi-level status information is written to
the screen. Each partition also writes to a screen.N file where N is
the partition ID. If the switch is specified in multi-partition mode,
the hi-level screen dump is named "file" and each partition also
writes screen information to a file.N. For both one-partition and
multi-partition mode, if the specified file is "none", then no screen
output is performed. Option -pscreen will override the name of the
partition screen files file.N.
-suffix style :pre
Use variants of various styles if they exist. The specified style can
be {opt} or {gpu} or {cuda}. These refer to optional packages that
LAMMPS can be built with, as described above in "Section
2.3"_#start_3. The "opt" style corrsponds to the OPT package, the
"gpu" style to the GPU package, and the "cuda" style to the USER-CUDA
package.
As an example, all of the packages provide a "pair_style
lj/cut"_pair_lj.html variant, with style names lj/cut/opt or
lj/cut/gpu or lj/cut/cuda. A variant styles can be specified
explicitly in your input script, e.g. pair_style lj/cut/gpu. If the
-suffix switch is used, you do not need to modify your input script.
The specified suffix (opt,gpu,cuda) is automatically appended whenever
your input script command creates a new "atom"_atom_style.html,
"pair"_pair_style.html, "fix"_fix.html, "compute"_compute.html, or
"run"_run_style.html style. atom, pair, fix, compute, or integrate
style. If the variant version does not exist, the standard version is
created.
The "suffix"_suffix.html command can also set a suffix and it can also
turn off/on any suffix setting made via the command line.
-var name value1 value2 ... :pre
Specify a variable that will be defined for substitution purposes when
the input script is read. "Name" is the variable name which can be a
single character (referenced as $x in the input script) or a full
string (referenced as $\{abc\}). An "index-style
variable"_variable.html will be created and populated with the
subsequent values, e.g. a set of filenames. Using this command-line
option is equivalent to putting the line "variable name index value1
value2 ..." at the beginning of the input script. Defining an index
variable as a command-line argument overrides any setting for the same
index variable in the input script, since index variables cannot be
re-defined. See the "variable"_variable.html command for more info on
defining index and other kinds of variables and "this
section"_Section_commands.html#cmd_2 for more info on using variables
in input scripts.
:line
2.7 LAMMPS screen output :h4,link(start_7)
As LAMMPS reads an input script, it prints information to both the
screen and a log file about significant actions it takes to setup a
simulation. When the simulation is ready to begin, LAMMPS performs
various initializations and prints the amount of memory (in MBytes per
processor) that the simulation requires. It also prints details of
the initial thermodynamic state of the system. During the run itself,
thermodynamic information is printed periodically, every few
timesteps. When the run concludes, LAMMPS prints the final
thermodynamic state and a total run time for the simulation. It then
appends statistics about the CPU time and storage requirements for the
simulation. An example set of statistics is shown here:
Loop time of 49.002 on 2 procs for 2004 atoms :pre
Pair time (%) = 35.0495 (71.5267)
Bond time (%) = 0.092046 (0.187841)
Kspce time (%) = 6.42073 (13.103)
Neigh time (%) = 2.73485 (5.5811)
Comm time (%) = 1.50291 (3.06703)
Outpt time (%) = 0.013799 (0.0281601)
Other time (%) = 2.13669 (4.36041) :pre
Nlocal: 1002 ave, 1015 max, 989 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8720 ave, 8724 max, 8716 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 354141 ave, 361422 max, 346860 min
Histogram: 1 0 0 0 0 0 0 0 0 1 :pre
Total # of neighbors = 708282
Ave neighs/atom = 353.434
Ave special neighs/atom = 2.34032
Number of reneighborings = 42
Dangerous reneighborings = 2 :pre
The first section gives the breakdown of the CPU run time (in seconds)
into major categories. The second section lists the number of owned
atoms (Nlocal), ghost atoms (Nghost), and pair-wise neighbors stored
per processor. The max and min values give the spread of these values
across processors with a 10-bin histogram showing the distribution.
The total number of histogram counts is equal to the number of
processors.
The last section gives aggregate statistics for pair-wise neighbors
and special neighbors that LAMMPS keeps track of (see the
"special_bonds"_special_bonds.html command). The number of times
neighbor lists were rebuilt during the run is given as well as the
number of potentially "dangerous" rebuilds. If atom movement
triggered neighbor list rebuilding (see the
"neigh_modify"_neigh_modify.html command), then dangerous
reneighborings are those that were triggered on the first timestep
atom movement was checked for. If this count is non-zero you may wish
to reduce the delay factor to insure no force interactions are missed
by atoms moving beyond the neighbor skin distance before a rebuild
takes place.
If an energy minimization was performed via the
"minimize"_minimize.html command, additional information is printed,
e.g.
Minimization stats:
E initial, next-to-last, final = -0.895962 -2.94193 -2.94342
Gradient 2-norm init/final= 1920.78 20.9992
Gradient inf-norm init/final= 304.283 9.61216
Iterations = 36
Force evaluations = 177 :pre
The first line lists the initial and final energy, as well as the
energy on the next-to-last iteration. The next 2 lines give a measure
of the gradient of the energy (force on all atoms). The 2-norm is the
"length" of this force vector; the inf-norm is the largest component.
The last 2 lines are statistics on how many iterations and
force-evaluations the minimizer required. Multiple force evaluations
are typically done at each iteration to perform a 1d line minimization
in the search direction.
If a "kspace_style"_kspace_style.html long-range Coulombics solve was
performed during the run (PPPM, Ewald), then additional information is
printed, e.g.
FFT time (% of Kspce) = 0.200313 (8.34477)
FFT Gflps 3d 1d-only = 2.31074 9.19989 :pre
The first line gives the time spent doing 3d FFTs (4 per timestep) and
the fraction it represents of the total KSpace time (listed above).
Each 3d FFT requires computation (3 sets of 1d FFTs) and communication
(transposes). The total flops performed is 5Nlog_2(N), where N is the
number of points in the 3d grid. The FFTs are timed with and without
the communication and a Gflop rate is computed. The 3d rate is with
communication; the 1d rate is without (just the 1d FFTs). Thus you
can estimate what fraction of your FFT time was spent in
communication, roughly 75% in the example above.
:line
2.8 Tips for users of previous LAMMPS versions :h4,link(start_8)
The current C++ began with a complete rewrite of LAMMPS 2001, which
was written in F90. Features of earlier versions of LAMMPS are listed
in "this section"_Section_history.html. The F90 and F77 versions
(2001 and 99) are also freely distributed as open-source codes; check
the "LAMMPS WWW Site"_lws for distribution information if you prefer
those versions. The 99 and 2001 versions are no longer under active
development; they do not have all the features of C++ LAMMPS.
If you are a previous user of LAMMPS 2001, these are the most
significant changes you will notice in C++ LAMMPS:
(1) The names and arguments of many input script commands have
changed. All commands are now a single word (e.g. read_data instead
of read data).
(2) All the functionality of LAMMPS 2001 is included in C++ LAMMPS,
but you may need to specify the relevant commands in different ways.
(3) The format of the data file can be streamlined for some problems.
See the "read_data"_read_data.html command for details. The data file
section "Nonbond Coeff" has been renamed to "Pair Coeff" in C++ LAMMPS.
(4) Binary restart files written by LAMMPS 2001 cannot be read by C++
LAMMPS with a "read_restart"_read_restart.html command. This is
because they were output by F90 which writes in a different binary
format than C or C++ writes or reads. Use the {restart2data} tool
provided with LAMMPS 2001 to convert the 2001 restart file to a text
data file. Then edit the data file as necessary before using the C++
LAMMPS "read_data"_read_data.html command to read it in.
(5) There are numerous small numerical changes in C++ LAMMPS that mean
you will not get identical answers when comparing to a 2001 run.
However, your initial thermodynamic energy and MD trajectory should be
close if you have setup the problem for both codes the same.
diff --git a/doc/USER/sph/SPH_LAMMPS_userguide.pdf b/doc/USER/sph/SPH_LAMMPS_userguide.pdf
new file mode 100755
index 000000000..7ca4a7291
Binary files /dev/null and b/doc/USER/sph/SPH_LAMMPS_userguide.pdf differ
diff --git a/doc/angle_charmm.html b/doc/angle_charmm.html
index 2b3dddbfe..94c0e3bcf 100644
--- a/doc/angle_charmm.html
+++ b/doc/angle_charmm.html
@@ -1,68 +1,68 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>angle_style charmm command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style charmm
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style charmm
angle_coeff 1 300.0 107.0 50.0 3.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>charmm</I> angle style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/angle_charmm.jpg">
</CENTER>
<P>with an additional Urey_Bradley term based on the distance <I>r</I> between
the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are
coefficients defined for each angle type.
</P>
<P>See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
field.
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy/radian^2)
<LI>theta0 (degrees)
<LI>K_ub (energy/distance^2)
<LI>r_ub (distance)
</UL>
<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
</P>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "MacKerell"></A>
<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
</P>
</HTML>
diff --git a/doc/angle_charmm.txt b/doc/angle_charmm.txt
index a3e06ffd6..13cdc03f8 100644
--- a/doc/angle_charmm.txt
+++ b/doc/angle_charmm.txt
@@ -1,62 +1,62 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
angle_style charmm command :h3
[Syntax:]
angle_style charmm :pre
[Examples:]
angle_style charmm
angle_coeff 1 300.0 107.0 50.0 3.0 :pre
[Description:]
The {charmm} angle style uses the potential
:c,image(Eqs/angle_charmm.jpg)
with an additional Urey_Bradley term based on the distance {r} between
the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are
coefficients defined for each angle type.
See "(MacKerell)"_#MacKerell for a description of the CHARMM force
field.
The following coefficients must be defined for each angle type via the
"angle_coeff"_angle_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy/radian^2)
theta0 (degrees)
K_ub (energy/distance^2)
r_ub (distance) :ul
Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"angle_coeff"_angle_coeff.html
[Default:] none
:line
:link(MacKerell)
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
diff --git a/doc/angle_class2.html b/doc/angle_class2.html
index 65e552342..c2aea849a 100644
--- a/doc/angle_class2.html
+++ b/doc/angle_class2.html
@@ -1,99 +1,99 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>angle_style class2 command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style class2
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style class2
angle_coeff * 75.0
angle_coeff 1 bb 10.5872 1.0119 1.5228
angle_coeff * ba 3.6551 24.895 1.0119 1.5228
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>class2</I> angle style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/angle_class2.jpg">
</CENTER>
<P>where Ea is the angle term, Ebb is a bond-bond term, and Eba is a
bond-angle term. Theta0 is the equilibrium angle and r1 and r2 are
the equilibrium bond lengths.
</P>
<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
</P>
<P>Coefficients for the Ea, Ebb, and Eba formulas must be defined for
each angle type via the <A HREF = "bond_coeff.html">bond_coeff</A> command as in the
example above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands.
</P>
<P>These are the 4 coefficients for the Ea formula:
</P>
<UL><LI>theta0 (degrees)
<LI>K2 (energy/radian^2)
<LI>K3 (energy/radian^3)
<LI>K4 (energy/radian^4)
</UL>
<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of the various K are in per-radian.
</P>
<P>For the Ebb formula, each line in a <A HREF = "bond_coeff.html">bond_coeff</A>
command in the input script lists 4 coefficients, the first of which
is "bb" to indicate they are BondBond coefficients. In a data file,
these coefficients should be listed under a "BondBond Coeffs" heading
and you must leave out the "bb", i.e. only list 3 coefficients after
the angle type.
</P>
<UL><LI>bb
<LI>M (energy/distance^2)
<LI>r1 (distance)
<LI>r2 (distance)
</UL>
<P>For the Eba formula, each line in a <A HREF = "bond_coeff.html">bond_coeff</A>
command in the input script lists 5 coefficients, the first of which
is "ba" to indicate they are BondAngle coefficients. In a data file,
these coefficients should be listed under a "BondAngle Coeffs" heading
and you must leave out the "ba", i.e. only list 4 coefficients after
the angle type.
</P>
<UL><LI>ba
<LI>N1 (energy/distance^2)
<LI>N2 (energy/distance^2)
<LI>r1 (distance)
<LI>r2 (distance)
</UL>
<P>The theta0 value in the Eba formula is not specified, since it is the
same value from the Ea formula.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This angle style can only be used if LAMMPS was built with the
-"class2" package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
-section for more info on packages.
+<P>This angle style can only be used if LAMMPS was built with the CLASS2
+package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
+for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Sun"></A>
<P><B>(Sun)</B> Sun, J Phys Chem B 102, 7338-7364 (1998).
</P>
</HTML>
diff --git a/doc/angle_class2.txt b/doc/angle_class2.txt
index b63ea798b..93e2ea25e 100644
--- a/doc/angle_class2.txt
+++ b/doc/angle_class2.txt
@@ -1,93 +1,93 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
angle_style class2 command :h3
[Syntax:]
angle_style class2 :pre
[Examples:]
angle_style class2
angle_coeff * 75.0
angle_coeff 1 bb 10.5872 1.0119 1.5228
angle_coeff * ba 3.6551 24.895 1.0119 1.5228 :pre
[Description:]
The {class2} angle style uses the potential
:c,image(Eqs/angle_class2.jpg)
where Ea is the angle term, Ebb is a bond-bond term, and Eba is a
bond-angle term. Theta0 is the equilibrium angle and r1 and r2 are
the equilibrium bond lengths.
See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
Coefficients for the Ea, Ebb, and Eba formulas must be defined for
each angle type via the "bond_coeff"_bond_coeff.html command as in the
example above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands.
These are the 4 coefficients for the Ea formula:
theta0 (degrees)
K2 (energy/radian^2)
K3 (energy/radian^3)
K4 (energy/radian^4) :ul
Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of the various K are in per-radian.
For the Ebb formula, each line in a "bond_coeff"_bond_coeff.html
command in the input script lists 4 coefficients, the first of which
is "bb" to indicate they are BondBond coefficients. In a data file,
these coefficients should be listed under a "BondBond Coeffs" heading
and you must leave out the "bb", i.e. only list 3 coefficients after
the angle type.
bb
M (energy/distance^2)
r1 (distance)
r2 (distance) :ul
For the Eba formula, each line in a "bond_coeff"_bond_coeff.html
command in the input script lists 5 coefficients, the first of which
is "ba" to indicate they are BondAngle coefficients. In a data file,
these coefficients should be listed under a "BondAngle Coeffs" heading
and you must leave out the "ba", i.e. only list 4 coefficients after
the angle type.
ba
N1 (energy/distance^2)
N2 (energy/distance^2)
r1 (distance)
r2 (distance) :ul
The theta0 value in the Eba formula is not specified, since it is the
same value from the Ea formula.
[Restrictions:]
-This angle style can only be used if LAMMPS was built with the
-"class2" package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+This angle style can only be used if LAMMPS was built with the CLASS2
+package. See the "Making LAMMPS"_Section_start.html#start_3 section
+for more info on packages.
[Related commands:]
"angle_coeff"_angle_coeff.html
[Default:] none
:line
:link(Sun)
[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998).
diff --git a/doc/angle_cmm.html b/doc/angle_cmm.html
index cdb93122f..bfd2507f6 100644
--- a/doc/angle_cmm.html
+++ b/doc/angle_cmm.html
@@ -1,65 +1,65 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>angle_style cg/cmm command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style cg/cmm
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style cg/cmm
angle_coeff 1 300.0 107.0 lj9_6 0.4491 3.7130
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>cg/cmm</I> angle style is a combination of the harmonic angle potential,
</P>
<CENTER><IMG SRC = "Eqs/angle_harmonic.jpg">
</CENTER>
<P>where theta0 is the equilibrium value of the angle and K a prefactor,
with the <I>repulsive</I> part of the non-bonded <I>cg/cmm</I> pair style
between the atoms 1 and 3. This angle potential is intended for
coarse grained MD simulations with the CMM parametrization using the
<A HREF = "pair_cmm.html">pair_style cg/cmm</A>. Relative to the pair_style
<I>cg/cmm</I>, however, the energy is shifted by <I>epsilon</I>, to avoid sudden
jumps. Note that the usual 1/2 factor is included in K.
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above. As
with other CMM coarse grained parameters, they cannot be set in the
data file, but can be restored from restarts via the
<A HREF = "read_restart.html">read_restart</A> command:
</P>
<UL><LI>K (energy/radian^2)
<LI>theta0 (degrees)
<LI>cg_type (string, one of lj9_6, lj12_4, lj12_6)
<LI>epsilon (energy units)
<LI>sigma (distance units)
</UL>
<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
</P>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
-"user-cg-cmm" package. See the <A HREF = "Section_start.html#start_3">Making
+USER-CG-CMM package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>, <A HREF = "angle_harmonic.html">angle_style
harmonic</A>, <A HREF = "pair_cmm.html">pair_style cg/cmm</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/angle_cmm.txt b/doc/angle_cmm.txt
index bbedf8b0e..bbc5033ad 100644
--- a/doc/angle_cmm.txt
+++ b/doc/angle_cmm.txt
@@ -1,60 +1,60 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
angle_style cg/cmm command :h3
[Syntax:]
angle_style cg/cmm :pre
[Examples:]
angle_style cg/cmm
angle_coeff 1 300.0 107.0 lj9_6 0.4491 3.7130 :pre
[Description:]
The {cg/cmm} angle style is a combination of the harmonic angle potential,
:c,image(Eqs/angle_harmonic.jpg)
where theta0 is the equilibrium value of the angle and K a prefactor,
with the {repulsive} part of the non-bonded {cg/cmm} pair style
between the atoms 1 and 3. This angle potential is intended for
coarse grained MD simulations with the CMM parametrization using the
"pair_style cg/cmm"_pair_cmm.html. Relative to the pair_style
{cg/cmm}, however, the energy is shifted by {epsilon}, to avoid sudden
jumps. Note that the usual 1/2 factor is included in K.
The following coefficients must be defined for each angle type via the
"angle_coeff"_angle_coeff.html command as in the example above. As
with other CMM coarse grained parameters, they cannot be set in the
data file, but can be restored from restarts via the
"read_restart"_read_restart.html command:
K (energy/radian^2)
theta0 (degrees)
cg_type (string, one of lj9_6, lj12_4, lj12_6)
epsilon (energy units)
sigma (distance units) :ul
Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-"user-cg-cmm" package. See the "Making
+USER-CG-CMM package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"angle_coeff"_angle_coeff.html, "angle_style
harmonic"_angle_harmonic.html, "pair_style cg/cmm"_pair_cmm.html
[Default:] none
diff --git a/doc/angle_cosine.html b/doc/angle_cosine.html
index c4075bd91..3321405fb 100644
--- a/doc/angle_cosine.html
+++ b/doc/angle_cosine.html
@@ -1,50 +1,50 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>angle_style cosine command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style cosine
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style cosine
angle_coeff * 75.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>cosine</I> angle style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/angle_cosine.jpg">
</CENTER>
<P>where K is defined for each angle type.
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy)
</UL>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/angle_cosine.txt b/doc/angle_cosine.txt
index 19d4fedd8..a2fbabf98 100644
--- a/doc/angle_cosine.txt
+++ b/doc/angle_cosine.txt
@@ -1,45 +1,45 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
angle_style cosine command :h3
[Syntax:]
angle_style cosine :pre
[Examples:]
angle_style cosine
angle_coeff * 75.0 :pre
[Description:]
The {cosine} angle style uses the potential
:c,image(Eqs/angle_cosine.jpg)
where K is defined for each angle type.
The following coefficients must be defined for each angle type via the
"angle_coeff"_angle_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy) :ul
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"angle_coeff"_angle_coeff.html
[Default:] none
diff --git a/doc/angle_cosine_delta.html b/doc/angle_cosine_delta.html
index 22927d7a9..9bfd85ea0 100644
--- a/doc/angle_cosine_delta.html
+++ b/doc/angle_cosine_delta.html
@@ -1,56 +1,56 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>angle_style cosine/delta command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style cosine/delta
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style cosine/delta
angle_coeff 2*4 75.0 100.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>cosine/delta</I> angle style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/angle_cosine_delta.jpg">
</CENTER>
<P>where theta0 is the equilibrium value of the angle, and K is a
prefactor. Note that the usual 1/2 factor is included in K.
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy)
<LI>theta0 (degrees)
</UL>
<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally.
</P>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>, <A HREF = "angle_cosine_squared.html">angle_style
cosine/squared</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/angle_cosine_delta.txt b/doc/angle_cosine_delta.txt
index 95c7da3a8..57de081f8 100644
--- a/doc/angle_cosine_delta.txt
+++ b/doc/angle_cosine_delta.txt
@@ -1,51 +1,51 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
angle_style cosine/delta command :h3
[Syntax:]
angle_style cosine/delta :pre
[Examples:]
angle_style cosine/delta
angle_coeff 2*4 75.0 100.0 :pre
[Description:]
The {cosine/delta} angle style uses the potential
:c,image(Eqs/angle_cosine_delta.jpg)
where theta0 is the equilibrium value of the angle, and K is a
prefactor. Note that the usual 1/2 factor is included in K.
The following coefficients must be defined for each angle type via the
"angle_coeff"_angle_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy)
theta0 (degrees) :ul
Theta0 is specified in degrees, but LAMMPS converts it to radians
internally.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"angle_coeff"_angle_coeff.html, "angle_style
cosine/squared"_angle_cosine_squared.html
[Default:] none
diff --git a/doc/angle_cosine_periodic.html b/doc/angle_cosine_periodic.html
index b5d316fc2..5e409b025 100644
--- a/doc/angle_cosine_periodic.html
+++ b/doc/angle_cosine_periodic.html
@@ -1,70 +1,70 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>angle_style cosine/periodic command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style cosine/periodic
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style cosine/periodic
angle_coeff * 75.0 1 6
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>cosine/periodic</I> angle style uses the following potential, which
is commonly used in the <A HREF = "Section_howto.html#howto_4">DREIDING</A> force
field, particularly for organometallic systems where <I>n</I> = 4 might be
used for an octahedral complex and <I>n</I> = 3 might be used for a
trigonal center:
</P>
<CENTER><IMG SRC = "Eqs/angle_cosine_periodic.jpg">
</CENTER>
<P>where C, B and n are coefficients defined for each angle type.
</P>
<P>See <A HREF = "#Mayo">(Mayo)</A> for a description of the DREIDING force field
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>C (energy)
<LI>B = 1 or -1
<LI>n = 1, 2, 3, 4, 5 or 6 for periodicity
</UL>
<P>Note that the prefactor C is specified and not the overall force
constant K = C / n^2. When B = 1, it leads to a minimum for the
linear geometry. When B = -1, it leads to a maximum for the linear
geometry.
</P>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Mayo"></A>
<P><B>(Mayo)</B> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).
</P>
</HTML>
diff --git a/doc/angle_cosine_periodic.txt b/doc/angle_cosine_periodic.txt
index 024c914ad..a5fb88fdb 100644
--- a/doc/angle_cosine_periodic.txt
+++ b/doc/angle_cosine_periodic.txt
@@ -1,64 +1,64 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
angle_style cosine/periodic command :h3
[Syntax:]
angle_style cosine/periodic :pre
[Examples:]
angle_style cosine/periodic
angle_coeff * 75.0 1 6 :pre
[Description:]
The {cosine/periodic} angle style uses the following potential, which
is commonly used in the "DREIDING"_Section_howto.html#howto_4 force
field, particularly for organometallic systems where {n} = 4 might be
used for an octahedral complex and {n} = 3 might be used for a
trigonal center:
:c,image(Eqs/angle_cosine_periodic.jpg)
where C, B and n are coefficients defined for each angle type.
See "(Mayo)"_#Mayo for a description of the DREIDING force field
The following coefficients must be defined for each angle type via the
"angle_coeff"_angle_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
C (energy)
B = 1 or -1
n = 1, 2, 3, 4, 5 or 6 for periodicity :ul
Note that the prefactor C is specified and not the overall force
constant K = C / n^2. When B = 1, it leads to a minimum for the
linear geometry. When B = -1, it leads to a maximum for the linear
geometry.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"angle_coeff"_angle_coeff.html
[Default:] none
:line
:link(Mayo)
[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).
diff --git a/doc/angle_cosine_shift.html b/doc/angle_cosine_shift.html
index 7ddfdd924..8f97069f7 100644
--- a/doc/angle_cosine_shift.html
+++ b/doc/angle_cosine_shift.html
@@ -1,54 +1,54 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>angle_style cosine/shift command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style cosine/shift
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style cosine/shift
angle_coeff * 10.0 45.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>cosine/shift</I> angle style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/angle_cosine_shift.jpg">
</CENTER>
<P>where theta0 is the equilibrium angle. The potential is bounded
between -Umin and zero. In the neighborhood of the minimum E=- Umin +
Umin/4(theta-theta0)^2 hence the spring constant is umin/2.
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>umin (energy)
<LI>theta (angle)
</UL>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
-"user-misc" package. See the <A HREF = "Section_start.html#start_3">Making
-LAMMPS</A> section for more info on packages.
+USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>,
<A HREF = "angle_cosineshiftexp.html">angle_cosineshiftexp</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/angle_cosine_shift.txt b/doc/angle_cosine_shift.txt
index e17813bc2..e7c641718 100644
--- a/doc/angle_cosine_shift.txt
+++ b/doc/angle_cosine_shift.txt
@@ -1,49 +1,49 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
angle_style cosine/shift command :h3
[Syntax:]
angle_style cosine/shift :pre
[Examples:]
angle_style cosine/shift
angle_coeff * 10.0 45.0 :pre
[Description:]
The {cosine/shift} angle style uses the potential
:c,image(Eqs/angle_cosine_shift.jpg)
where theta0 is the equilibrium angle. The potential is bounded
between -Umin and zero. In the neighborhood of the minimum E=- Umin +
Umin/4(theta-theta0)^2 hence the spring constant is umin/2.
The following coefficients must be defined for each angle type via the
"angle_coeff"_angle_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
umin (energy)
theta (angle) :ul
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-"user-misc" package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
+section for more info on packages.
[Related commands:]
"angle_coeff"_angle_coeff.html,
"angle_cosineshiftexp"_angle_cosineshiftexp.html
[Default:] none
diff --git a/doc/angle_cosine_shift_exp.html b/doc/angle_cosine_shift_exp.html
index cd4dea4ce..ceccb16b8 100644
--- a/doc/angle_cosine_shift_exp.html
+++ b/doc/angle_cosine_shift_exp.html
@@ -1,67 +1,67 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>angle_style cosine/shift/exp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style cosine/shift/exp
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style cosine/shift/exp
angle_coeff * 10.0 45.0 2.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>cosine/shift/exp</I> angle style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/angle_cosine_shift_exp.jpg">
</CENTER>
<P>where Umin, theta, and a are defined for each angle type.
</P>
<P>The potential is bounded between [-Umin:0] and the minimum is
located at the angle theta0. The a parameter can be both positive or
negative and is used to control the spring constant at the
equilibrium.
</P>
<P>The spring constant is given by k = A exp(A) Umin / [2 (Exp(a)-1)].
For a > 3, k/Umin = a/2 to better than 5% relative error. For negative
values of the a parameter, the spring constant is essentially zero,
and anharmonic terms takes over. The potential is furthermore well
behaved in the limit a -> 0, where it has been implemented to linear
order in a for a < 0.001. In this limit the potential reduces to the
cosineshifted potential.
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>umin (energy)
<LI>theta (angle)
<LI>A (real number)
</UL>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
-"user-misc" package. See the <A HREF = "Section_start.html#start_3">Making
-LAMMPS</A> section for more info on packages.
+USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>,
<A HREF = "angle_cosineshift.html">angle_cosineshift</A>,
<A HREF = "dihedral_cosineshift.html">dihedral_cosineshift</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/angle_cosine_shift_exp.txt b/doc/angle_cosine_shift_exp.txt
index 9e52466d6..12612a533 100644
--- a/doc/angle_cosine_shift_exp.txt
+++ b/doc/angle_cosine_shift_exp.txt
@@ -1,62 +1,62 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
angle_style cosine/shift/exp command :h3
[Syntax:]
angle_style cosine/shift/exp :pre
[Examples:]
angle_style cosine/shift/exp
angle_coeff * 10.0 45.0 2.0 :pre
[Description:]
The {cosine/shift/exp} angle style uses the potential
:c,image(Eqs/angle_cosine_shift_exp.jpg)
where Umin, theta, and a are defined for each angle type.
The potential is bounded between \[-Umin:0\] and the minimum is
located at the angle theta0. The a parameter can be both positive or
negative and is used to control the spring constant at the
equilibrium.
The spring constant is given by k = A exp(A) Umin / \[2 (Exp(a)-1)\].
For a > 3, k/Umin = a/2 to better than 5% relative error. For negative
values of the a parameter, the spring constant is essentially zero,
and anharmonic terms takes over. The potential is furthermore well
behaved in the limit a -> 0, where it has been implemented to linear
order in a for a < 0.001. In this limit the potential reduces to the
cosineshifted potential.
The following coefficients must be defined for each angle type via the
"angle_coeff"_angle_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
umin (energy)
theta (angle)
A (real number) :ul
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-"user-misc" package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
+section for more info on packages.
[Related commands:]
"angle_coeff"_angle_coeff.html,
"angle_cosineshift"_angle_cosineshift.html,
"dihedral_cosineshift"_dihedral_cosineshift.html
[Default:] none
diff --git a/doc/angle_cosine_squared.html b/doc/angle_cosine_squared.html
index 01b669567..2b888d40e 100644
--- a/doc/angle_cosine_squared.html
+++ b/doc/angle_cosine_squared.html
@@ -1,55 +1,55 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>angle_style cosine/squared command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style cosine/squared
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style cosine/squared
angle_coeff 2*4 75.0 100.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>cosine/squared</I> angle style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/angle_cosine_squared.jpg">
</CENTER>
<P>where theta0 is the equilibrium value of the angle, and K is a
prefactor. Note that the usual 1/2 factor is included in K.
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy)
<LI>theta0 (degrees)
</UL>
<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally.
</P>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/angle_cosine_squared.txt b/doc/angle_cosine_squared.txt
index edfbfb87c..383c0b302 100644
--- a/doc/angle_cosine_squared.txt
+++ b/doc/angle_cosine_squared.txt
@@ -1,50 +1,50 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
angle_style cosine/squared command :h3
[Syntax:]
angle_style cosine/squared :pre
[Examples:]
angle_style cosine/squared
angle_coeff 2*4 75.0 100.0 :pre
[Description:]
The {cosine/squared} angle style uses the potential
:c,image(Eqs/angle_cosine_squared.jpg)
where theta0 is the equilibrium value of the angle, and K is a
prefactor. Note that the usual 1/2 factor is included in K.
The following coefficients must be defined for each angle type via the
"angle_coeff"_angle_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy)
theta0 (degrees) :ul
Theta0 is specified in degrees, but LAMMPS converts it to radians
internally.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"angle_coeff"_angle_coeff.html
[Default:] none
diff --git a/doc/angle_harmonic.html b/doc/angle_harmonic.html
index c346de08e..2094fb2cc 100644
--- a/doc/angle_harmonic.html
+++ b/doc/angle_harmonic.html
@@ -1,55 +1,55 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>angle_style harmonic command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style harmonic
</PRE>
<P><B>Examples:</B>
</P>
<PRE>angle_style harmonic
angle_coeff 1 300.0 107.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>harmonic</I> angle style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/angle_harmonic.jpg">
</CENTER>
<P>where theta0 is the equilibrium value of the angle, and K is a
prefactor. Note that the usual 1/2 factor is included in K.
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy/radian^2)
<LI>theta0 (degrees)
</UL>
<P>Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
</P>
<P><B>Restrictions:</B> none
</P>
<P>This angle style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/angle_harmonic.txt b/doc/angle_harmonic.txt
index 99c3065c4..92c318dc2 100644
--- a/doc/angle_harmonic.txt
+++ b/doc/angle_harmonic.txt
@@ -1,50 +1,50 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
angle_style harmonic command :h3
[Syntax:]
angle_style harmonic :pre
[Examples:]
angle_style harmonic
angle_coeff 1 300.0 107.0 :pre
[Description:]
The {harmonic} angle style uses the potential
:c,image(Eqs/angle_harmonic.jpg)
where theta0 is the equilibrium value of the angle, and K is a
prefactor. Note that the usual 1/2 factor is included in K.
The following coefficients must be defined for each angle type via the
"angle_coeff"_angle_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy/radian^2)
theta0 (degrees) :ul
Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
[Restrictions:] none
This angle style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"angle_coeff"_angle_coeff.html
[Default:] none
diff --git a/doc/angle_hybrid.html b/doc/angle_hybrid.html
index 5e0bd97c1..bd7ff2db0 100644
--- a/doc/angle_hybrid.html
+++ b/doc/angle_hybrid.html
@@ -1,94 +1,94 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>angle_style hybrid command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style hybrid style1 style2 ...
</PRE>
<UL><LI>style1,style2 = list of one or more angle styles
</UL>
<P><B>Examples:</B>
</P>
<PRE>angle_style hybrid harmonic cosine
angle_coeff 1 harmonic 80.0 30.0
angle_coeff 2* cosine 50.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>hybrid</I> style enables the use of multiple angle styles in one
simulation. An angle style is assigned to each angle type. For
example, angles in a polymer flow (of angle type 1) could be computed
with a <I>harmonic</I> potential and angles in the wall boundary (of angle
type 2) could be computed with a <I>cosine</I> potential. The assignment
of angle type to style is made via the <A HREF = "angle_coeff.html">angle_coeff</A>
command or in the data file.
</P>
<P>In the angle_coeff commands, the name of an angle style must be added
after the angle type, with the remaining coefficients being those
appropriate to that style. In the example above, the 2 angle_coeff
commands set angles of angle type 1 to be computed with a <I>harmonic</I>
potential with coefficients 80.0, 30.0 for K, theta0. All other angle
types (2-N) are computed with a <I>cosine</I> potential with coefficient
50.0 for K.
</P>
<P>If angle coefficients are specified in the data file read via the
<A HREF = "read_data.html">read_data</A> command, then the same rule applies.
E.g. "harmonic" or "cosine", must be added after the angle type, for each
line in the "Angle Coeffs" section, e.g.
</P>
<PRE>Angle Coeffs
</PRE>
<PRE>1 harmonic 80.0 30.0
2 cosine 50.0
...
</PRE>
<P>If <I>class2</I> is one of the angle hybrid styles, the same rule holds for
specifying additional BondBond (and BondAngle) coefficients either via
the input script or in the data file. I.e. <I>class2</I> must be added to
each line after the angle type. For lines in the BondBond (or
BondAngle) section of the data file for angle types that are not
<I>class2</I>, you must use an angle style of <I>skip</I> as a placeholder, e.g.
</P>
<PRE>BondBond Coeffs
</PRE>
<PRE>1 skip
2 class2 3.6512 1.0119 1.0119
...
</PRE>
<P>Note that it is not necessary to use the angle style <I>skip</I> in the
input script, since BondBond (or BondAngle) coefficients need not be
specified at all for angle types that are not <I>class2</I>.
</P>
<P>An angle style of <I>none</I> with no additional coefficients can be used
in place of an angle style, either in a input script angle_coeff
command or in the data file, if you desire to turn off interactions
for specific angle types.
</P>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P>Unlike other angle styles, the hybrid angle style does not store angle
coefficient info for individual sub-styles in a <A HREF = "restart.html">binary restart
files</A>. Thus when retarting a simulation from a restart
file, you need to re-specify angle_coeff commands.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/angle_hybrid.txt b/doc/angle_hybrid.txt
index 79c776ba6..2996d3ddb 100644
--- a/doc/angle_hybrid.txt
+++ b/doc/angle_hybrid.txt
@@ -1,89 +1,89 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
angle_style hybrid command :h3
[Syntax:]
angle_style hybrid style1 style2 ... :pre
style1,style2 = list of one or more angle styles :ul
[Examples:]
angle_style hybrid harmonic cosine
angle_coeff 1 harmonic 80.0 30.0
angle_coeff 2* cosine 50.0 :pre
[Description:]
The {hybrid} style enables the use of multiple angle styles in one
simulation. An angle style is assigned to each angle type. For
example, angles in a polymer flow (of angle type 1) could be computed
with a {harmonic} potential and angles in the wall boundary (of angle
type 2) could be computed with a {cosine} potential. The assignment
of angle type to style is made via the "angle_coeff"_angle_coeff.html
command or in the data file.
In the angle_coeff commands, the name of an angle style must be added
after the angle type, with the remaining coefficients being those
appropriate to that style. In the example above, the 2 angle_coeff
commands set angles of angle type 1 to be computed with a {harmonic}
potential with coefficients 80.0, 30.0 for K, theta0. All other angle
types (2-N) are computed with a {cosine} potential with coefficient
50.0 for K.
If angle coefficients are specified in the data file read via the
"read_data"_read_data.html command, then the same rule applies.
E.g. "harmonic" or "cosine", must be added after the angle type, for each
line in the "Angle Coeffs" section, e.g.
Angle Coeffs :pre
1 harmonic 80.0 30.0
2 cosine 50.0
... :pre
If {class2} is one of the angle hybrid styles, the same rule holds for
specifying additional BondBond (and BondAngle) coefficients either via
the input script or in the data file. I.e. {class2} must be added to
each line after the angle type. For lines in the BondBond (or
BondAngle) section of the data file for angle types that are not
{class2}, you must use an angle style of {skip} as a placeholder, e.g.
BondBond Coeffs :pre
1 skip
2 class2 3.6512 1.0119 1.0119
... :pre
Note that it is not necessary to use the angle style {skip} in the
input script, since BondBond (or BondAngle) coefficients need not be
specified at all for angle types that are not {class2}.
An angle style of {none} with no additional coefficients can be used
in place of an angle style, either in a input script angle_coeff
command or in the data file, if you desire to turn off interactions
for specific angle types.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
Unlike other angle styles, the hybrid angle style does not store angle
coefficient info for individual sub-styles in a "binary restart
files"_restart.html. Thus when retarting a simulation from a restart
file, you need to re-specify angle_coeff commands.
[Related commands:]
"angle_coeff"_angle_coeff.html
[Default:] none
diff --git a/doc/angle_style.html b/doc/angle_style.html
index 3edbe63e2..73e016b00 100644
--- a/doc/angle_style.html
+++ b/doc/angle_style.html
@@ -1,100 +1,100 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>angle_style command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style style
</PRE>
<UL><LI>style = <I>none</I> or <I>hybrid</I> or <I>charmm</I> or <I>class2</I> or <I>cosine</I> or <I>cosine/squared</I> or <I>harmonic</I>
</UL>
<P><B>Examples:</B>
</P>
<PRE>angle_style harmonic
angle_style charmm
angle_style hybrid harmonic cosine
</PRE>
<P><B>Description:</B>
</P>
<P>Set the formula(s) LAMMPS uses to compute angle interactions between
triplets of atoms, which remain in force for the duration of the
simulation. The list of angle triplets is read in by a
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A> command
from a data or restart file.
</P>
<P>Hybrid models where angles are computed using different angle
potentials can be setup using the <I>hybrid</I> angle style.
</P>
<P>The coefficients associated with a angle style can be specified in a
data or restart file or via the <A HREF = "angle_coeff.html">angle_coeff</A> command.
</P>
<P>All angle potentials store their coefficient data in binary restart
files which means angle_style and <A HREF = "angle_coeff.html">angle_coeff</A>
commands do not need to be re-specified in an input script that
restarts a simulation. See the <A HREF = "read_restart.html">read_restart</A>
command for details on how to do this. The one exception is that
angle_style <I>hybrid</I> only stores the list of sub-styles in the restart
file; angle coefficients need to be re-specified.
</P>
<P>IMPORTANT NOTE: When both an angle and pair style is defined, the
<A HREF = "special_bonds.html">special_bonds</A> command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
exist between 3 bonded atoms.
</P>
<P>In the formulas listed for each angle style, <I>theta</I> is the angle
between the 3 atoms in the angle.
</P>
<HR>
<P>Here is an alphabetic list of angle styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated <A HREF = "angle_coeff.html">angle_coeff</A> command:
</P>
<UL><LI><A HREF = "angle_none.html">angle_style none</A> - turn off angle interactions
<LI><A HREF = "angle_hybrid.html">angle_style hybrid</A> - define multiple styles of angle interactions
</UL>
<UL><LI><A HREF = "angle_charmm.html">angle_style charmm</A> - CHARMM angle
<LI><A HREF = "angle_class2.html">angle_style class2</A> - COMPASS (class 2) angle
<LI><A HREF = "angle_cosine.html">angle_style cosine</A> - cosine angle potential
<LI><A HREF = "angle_cosine_delta.html">angle_style cosine/delta</A> - difference of cosines angle potential
<LI><A HREF = "angle_cosine_periodic.html">angle_style cosine/periodic</A> - DREIDING angle
<LI><A HREF = "angle_cosine_squared.html">angle_style cosine/squared</A> - cosine squared angle potential
<LI><A HREF = "angle_harmonic.html">angle_style harmonic</A> - harmonic angle
<LI><A HREF = "angle_table.html">angle_style table</A> - tabulated by angle
</UL>
<P>There are also additional angle styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the angle section of <A HREF = "Section_commands.html#cmd_5">this
page</A>.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>Angle styles can only be set for atom_styles that allow angles to be
defined.
</P>
-<P>Most angle styles are part of the "molecular" package. They are only
+<P>Most angle styles are part of the MOLECULAR package. They are only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
The doc pages for individual bond potentials tell if it is part of a
package.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B>
</P>
<PRE>angle_style none
</PRE>
</HTML>
diff --git a/doc/angle_style.txt b/doc/angle_style.txt
index e5faffa66..ec4f92307 100644
--- a/doc/angle_style.txt
+++ b/doc/angle_style.txt
@@ -1,96 +1,96 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
angle_style command :h3
[Syntax:]
angle_style style :pre
style = {none} or {hybrid} or {charmm} or {class2} or {cosine} or \
{cosine/squared} or {harmonic} :ul
[Examples:]
angle_style harmonic
angle_style charmm
angle_style hybrid harmonic cosine :pre
[Description:]
Set the formula(s) LAMMPS uses to compute angle interactions between
triplets of atoms, which remain in force for the duration of the
simulation. The list of angle triplets is read in by a
"read_data"_read_data.html or "read_restart"_read_restart.html command
from a data or restart file.
Hybrid models where angles are computed using different angle
potentials can be setup using the {hybrid} angle style.
The coefficients associated with a angle style can be specified in a
data or restart file or via the "angle_coeff"_angle_coeff.html command.
All angle potentials store their coefficient data in binary restart
files which means angle_style and "angle_coeff"_angle_coeff.html
commands do not need to be re-specified in an input script that
restarts a simulation. See the "read_restart"_read_restart.html
command for details on how to do this. The one exception is that
angle_style {hybrid} only stores the list of sub-styles in the restart
file; angle coefficients need to be re-specified.
IMPORTANT NOTE: When both an angle and pair style is defined, the
"special_bonds"_special_bonds.html command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
exist between 3 bonded atoms.
In the formulas listed for each angle style, {theta} is the angle
between the 3 atoms in the angle.
:line
Here is an alphabetic list of angle styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "angle_coeff"_angle_coeff.html command:
"angle_style none"_angle_none.html - turn off angle interactions
"angle_style hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul
"angle_style charmm"_angle_charmm.html - CHARMM angle
"angle_style class2"_angle_class2.html - COMPASS (class 2) angle
"angle_style cosine"_angle_cosine.html - cosine angle potential
"angle_style cosine/delta"_angle_cosine_delta.html - difference of cosines angle potential
"angle_style cosine/periodic"_angle_cosine_periodic.html - DREIDING angle
"angle_style cosine/squared"_angle_cosine_squared.html - cosine squared angle potential
"angle_style harmonic"_angle_harmonic.html - harmonic angle
"angle_style table"_angle_table.html - tabulated by angle :ul
There are also additional angle styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the angle section of "this
page"_Section_commands.html#cmd_5.
:line
[Restrictions:]
Angle styles can only be set for atom_styles that allow angles to be
defined.
-Most angle styles are part of the "molecular" package. They are only
+Most angle styles are part of the MOLECULAR package. They are only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
The doc pages for individual bond potentials tell if it is part of a
package.
[Related commands:]
"angle_coeff"_angle_coeff.html
[Default:]
angle_style none :pre
diff --git a/doc/angle_table.html b/doc/angle_table.html
index 5592e6cad..2b1bfb165 100644
--- a/doc/angle_table.html
+++ b/doc/angle_table.html
@@ -1,136 +1,136 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>angle_style table command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>angle_style table style N
</PRE>
<UL><LI>style = <I>linear</I> or <I>spline</I> = method of interpolation
<LI>N = use N values in table
</UL>
<P><B>Examples:</B>
</P>
<PRE>angle_style table linear 1000
angle_coeff 3 file.table ENTRY1
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>table</I> creates interpolation tables of length <I>N</I> from angle
potential and derivative values listed in a file(s) as a function of
angle The files are read by the <A HREF = "angle_coeff.html">angle_coeff</A>
command.
</P>
<P>The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and derivative values at each of
<I>N</I> angles. During a simulation, these tables are used to interpolate
energy and force values on individual atoms as needed. The
interpolation is done in one of 2 styles: <I>linear</I> or <I>spline</I>.
</P>
<P>For the <I>linear</I> style, the angle is used to find 2 surrounding table
values from which an energy or its derivative is computed by linear
interpolation.
</P>
<P>For the <I>spline</I> style, a cubic spline coefficients are computed and
stored at each of the <I>N</I> values in the table. The angle is used to
find the appropriate set of coefficients which are used to evaluate a
cubic polynomial which computes the energy or derivative.
</P>
<P>The following coefficients must be defined for each angle type via the
<A HREF = "angle_coeff.html">angle_coeff</A> command as in the example above.
</P>
<UL><LI>filename
<LI>keyword
</UL>
<P>The filename specifies a file containing tabulated energy and
derivative values. The keyword specifies a section of the file. The
format of this file is described below.
</P>
<HR>
<P>The format of a tabulated file is as follows (without the
parenthesized comments):
</P>
<PRE># Angle potential for harmonic (one or more comment or blank lines)
</PRE>
<PRE>HAM (keyword is the first text on line)
N 181 FP 0 0 EQ 90.0 (N, FP, EQ parameters)
(blank line)
N 181 FP 0 0 (N, FP parameters)
1 0.0 200.5 2.5 (index, angle, energy, derivative)
2 1.0 198.0 2.5
...
181 180.0 0.0 0.0
</PRE>
<P>A section begins with a non-blank line whose 1st character is not a
"#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
initial text must match the argument specified in the
<A HREF = "angle_coeff.html">angle_coeff</A> command. The next line lists (in any
order) one or more parameters for the table. Each parameter is a
keyword followed by one or more numeric values.
</P>
<P>The parameter "N" is required and its value is the number of table
entries that follow. Note that this may be different than the <I>N</I>
specified in the <A HREF = "angle_style.html">angle_style table</A> command. Let
Ntable = <I>N</I> in the angle_style command, and Nfile = "N" in the
tabulated file. What LAMMPS does is a preliminary interpolation by
creating splines using the Nfile tabulated values as nodal points. It
uses these to interpolate as needed to generate energy and derivative
values at Ntable different points. The resulting tables of length
Ntable are then used as described above, when computing energy and
force for individual angles and their atoms. This means that if you
want the interpolation tables of length Ntable to match exactly what
is in the tabulated file (with effectively no preliminary
interpolation), you should set Ntable = Nfile.
</P>
<P>The "FP" parameter is optional. If used, it is followed by two values
fplo and fphi, which are the 2nd derivatives at the innermost and
outermost angle settings. These values are needed by the spline
construction routines. If not specified by the "FP" parameter, they
are estimated (less accurately) by the first two and last two
derivative values in the table.
</P>
<P>The "EQ" parameter is also optional. If used, it is followed by a the
equilibrium angle value, which is used, for example, by the <A HREF = "fix_shake.html">fix
shake</A> command. If not used, the equilibrium angle is
set to 180.0.
</P>
<P>Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is
the angle value (in degrees), the 3rd value is the energy (in energy
units), and the 4th is -dE/d(theta) (also in energy units). The 3rd
term is the energy of the 3-atom configuration for the specified
angle. The last term is the derivative of the energy with respect to
the angle (in degrees, not radians). Thus the units of the last term
are still energy, not force. The angle values must increase from one
line to the next. The angle values must also begin with 0.0 and end
with 180.0, i.e. span the full range of possible angles.
</P>
<P>Note that one file can contain many sections, each with a tabulated
potential. LAMMPS reads the file section by section until it finds
one that matches the specified keyword.
</P>
<P><B>Restrictions:</B>
</P>
<P>This angle style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/angle_table.txt b/doc/angle_table.txt
index 2c7c2d747..eaee17968 100644
--- a/doc/angle_table.txt
+++ b/doc/angle_table.txt
@@ -1,131 +1,131 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
angle_style table command :h3
[Syntax:]
angle_style table style N :pre
style = {linear} or {spline} = method of interpolation
N = use N values in table :ul
[Examples:]
angle_style table linear 1000
angle_coeff 3 file.table ENTRY1 :pre
[Description:]
Style {table} creates interpolation tables of length {N} from angle
potential and derivative values listed in a file(s) as a function of
angle The files are read by the "angle_coeff"_angle_coeff.html
command.
The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and derivative values at each of
{N} angles. During a simulation, these tables are used to interpolate
energy and force values on individual atoms as needed. The
interpolation is done in one of 2 styles: {linear} or {spline}.
For the {linear} style, the angle is used to find 2 surrounding table
values from which an energy or its derivative is computed by linear
interpolation.
For the {spline} style, a cubic spline coefficients are computed and
stored at each of the {N} values in the table. The angle is used to
find the appropriate set of coefficients which are used to evaluate a
cubic polynomial which computes the energy or derivative.
The following coefficients must be defined for each angle type via the
"angle_coeff"_angle_coeff.html command as in the example above.
filename
keyword :ul
The filename specifies a file containing tabulated energy and
derivative values. The keyword specifies a section of the file. The
format of this file is described below.
:line
The format of a tabulated file is as follows (without the
parenthesized comments):
# Angle potential for harmonic (one or more comment or blank lines) :pre
HAM (keyword is the first text on line)
N 181 FP 0 0 EQ 90.0 (N, FP, EQ parameters)
(blank line)
N 181 FP 0 0 (N, FP parameters)
1 0.0 200.5 2.5 (index, angle, energy, derivative)
2 1.0 198.0 2.5
...
181 180.0 0.0 0.0 :pre
A section begins with a non-blank line whose 1st character is not a
"#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
initial text must match the argument specified in the
"angle_coeff"_angle_coeff.html command. The next line lists (in any
order) one or more parameters for the table. Each parameter is a
keyword followed by one or more numeric values.
The parameter "N" is required and its value is the number of table
entries that follow. Note that this may be different than the {N}
specified in the "angle_style table"_angle_style.html command. Let
Ntable = {N} in the angle_style command, and Nfile = "N" in the
tabulated file. What LAMMPS does is a preliminary interpolation by
creating splines using the Nfile tabulated values as nodal points. It
uses these to interpolate as needed to generate energy and derivative
values at Ntable different points. The resulting tables of length
Ntable are then used as described above, when computing energy and
force for individual angles and their atoms. This means that if you
want the interpolation tables of length Ntable to match exactly what
is in the tabulated file (with effectively no preliminary
interpolation), you should set Ntable = Nfile.
The "FP" parameter is optional. If used, it is followed by two values
fplo and fphi, which are the 2nd derivatives at the innermost and
outermost angle settings. These values are needed by the spline
construction routines. If not specified by the "FP" parameter, they
are estimated (less accurately) by the first two and last two
derivative values in the table.
The "EQ" parameter is also optional. If used, it is followed by a the
equilibrium angle value, which is used, for example, by the "fix
shake"_fix_shake.html command. If not used, the equilibrium angle is
set to 180.0.
Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is
the angle value (in degrees), the 3rd value is the energy (in energy
units), and the 4th is -dE/d(theta) (also in energy units). The 3rd
term is the energy of the 3-atom configuration for the specified
angle. The last term is the derivative of the energy with respect to
the angle (in degrees, not radians). Thus the units of the last term
are still energy, not force. The angle values must increase from one
line to the next. The angle values must also begin with 0.0 and end
with 180.0, i.e. span the full range of possible angles.
Note that one file can contain many sections, each with a tabulated
potential. LAMMPS reads the file section by section until it finds
one that matches the specified keyword.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"angle_coeff"_angle_coeff.html
[Default:] none
diff --git a/doc/atom_style.html b/doc/atom_style.html
index f32112188..8356e44df 100644
--- a/doc/atom_style.html
+++ b/doc/atom_style.html
@@ -1,145 +1,152 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>atom_style command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>atom_style style args
</PRE>
-<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>bond</I> or <I>charge</I> or <I>dipole</I> or <I>electron</I> or <I>ellipsoid</I> or <I>full</I> or <I>molecular</I> or <I>peri</I> or <I>sphere</I> or <I>hybrid</I>
+<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>bond</I> or <I>charge</I> or <I>dipole</I> or <I>electron</I> or <I>ellipsoid</I> or <I>full</I> or <I>meso</I> or <I>molecular</I> or <I>peri</I> or <I>sphere</I> or <I>hybrid</I>
</UL>
<PRE> args = none for any style except <I>hybrid</I>
<I>hybrid</I> args = list of one or more sub-styles
</PRE>
<P><B>Examples:</B>
</P>
<PRE>atom_style atomic
atom_style bond
atom_style full
atom_style hybrid charge bond
</PRE>
<P><B>Description:</B>
</P>
<P>Define what style of atoms to use in a simulation. This determines
what attributes are associated with the atoms. This command must be
used before a simulation is setup via a <A HREF = "read_data.html">read_data</A>,
<A HREF = "read_restart.html">read_restart</A>, or <A HREF = "create_box.html">create_box</A>
command.
</P>
<P>Once a style is assigned, it cannot be changed, so use a style general
enough to encompass all attributes. E.g. with style <I>bond</I>, angular
terms cannot be used or added later to the model. It is OK to use a
style more general than needed, though it may be slightly inefficient.
</P>
<P>The choice of style affects what quantities are stored by each atom,
what quantities are communicated between processors to enable forces
to be computed, and what quantities are listed in the data file read
by the <A HREF = "read_data.html">read_data</A> command.
</P>
<P>These are the additional attributes of each style and the typical
kinds of physical systems they are used to model. All styles store
coordinates, velocities, atom IDs and types. See the
<A HREF = "read_data.html">read_data</A>, <A HREF = "create_atoms.html">create_atoms</A>, and
<A HREF = "set.html">set</A> commands for info on how to set these various
quantities.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD ><I>angle</I> </TD><TD > bonds and angles </TD><TD > bead-spring polymers with stiffness </TD></TR>
<TR><TD ><I>atomic</I> </TD><TD > only the default values </TD><TD > coarse-grain liquids, solids, metals </TD></TR>
<TR><TD ><I>bond</I> </TD><TD > bonds </TD><TD > bead-spring polymers </TD></TR>
<TR><TD ><I>charge</I> </TD><TD > charge </TD><TD > atomic system with charges </TD></TR>
<TR><TD ><I>dipole</I> </TD><TD > charge and dipole moment </TD><TD > system with dipolar particles </TD></TR>
<TR><TD ><I>electron</I> </TD><TD > charge and spin and eradius </TD><TD > electronic force field </TD></TR>
<TR><TD ><I>ellipsoid</I> </TD><TD > shape, quaternion for particle orientation, angular momentum </TD><TD > extended aspherical particles </TD></TR>
<TR><TD ><I>full</I> </TD><TD > molecular + charge </TD><TD > bio-molecules </TD></TR>
+<TR><TD ><I>meso</I> </TD><TD > rho, e, cv </TD><TD > SPH particles </TD></TR>
<TR><TD ><I>molecular</I> </TD><TD > bonds, angles, dihedrals, impropers </TD><TD > uncharged molecules </TD></TR>
<TR><TD ><I>peri</I> </TD><TD > mass, volume </TD><TD > mesocopic Peridynamic models </TD></TR>
<TR><TD ><I>sphere</I> </TD><TD > diameter, mass, angular velocity </TD><TD > granular models </TD></TR>
<TR><TD ><I>wavepacket</I> </TD><TD > charge, spin, eradius, etag, cs_re, cs_im </TD><TD > AWPMD
</TD></TR></TABLE></DIV>
<P>All of the styles assign mass to particles on a per-type basis, using
the <A HREF = "mass.html">mass</A> command, except for the finite-size particle
styles discussed below. They assign mass on a per-atom basis.
</P>
<P>All of the styles define point particles, except the <I>sphere</I>,
<I>ellipsoid</I>, <I>electron</I>, <I>peri</I>, and <I>wavepacket</I> styles, which define
finite-size particles.
</P>
<P>For the <I>sphere</I> style, the particles are spheres and each stores a
per-particle diameter and mass. If the diameter > 0.0, the particle
is a finite-size sphere. If the diameter = 0.0, it is a point
particle.
</P>
<P>For the <I>ellipsoid</I> style, the particles are ellipsoids and each
stores a flag which indicates whether it is a finite-size ellipsoid or
a point particle. If it is an ellipsoid, it also stores a shape
vector with the 3 diamters of the ellipsoid and a quaternion 4-vector
with its orientation.
</P>
<P>For the <I>electron</I> style, the particles representing electrons are 3d
Gaussians with a specified position and bandwidth or uncertainty in
position, which is represented by the eradius = electron size.
</P>
<P>For the <I>peri</I> style, the particles are spherical and each stores a
per-particle mass and volume.
</P>
+<P>The <I>meso</I> style is for smoothed particle hydrodynamics (SPH)
+particles which store a density (rho), energy (e), and heat capacity
+(cv).
+</P>
<P>The <I>wavepacket</I> style is similar to <I>electron</I>, but the electrons may
consist of several Gaussian wave packets, summed up with coefficients
cs= (cs_re,cs_im). Each of the wave packets is treated as a separate
particle in LAMMPS, wave packets belonging to the same electron must
have identical <I>etag</I> values.
</P>
<HR>
<P>Typically, simulations require only a single (non-hybrid) atom style.
If some atoms in the simulation do not have all the properties defined
by a particular style, use the simplest style that defines all the
needed properties by any atom. For example, if some atoms in a
simulation are charged, but others are not, use the <I>charge</I> style.
If some atoms have bonds, but others do not, use the <I>bond</I> style.
</P>
<P>The only scenario where the <I>hybrid</I> style is needed is if there is no
single style which defines all needed properties of all atoms. For
example, if you want dipolar particles which will be torqued and
rotate, you would need to use "atom_style hybrid sphere dipole". When
a hybrid style is used, atoms store and communicate the union of all
quantities implied by the individual styles.
</P>
<P>LAMMPS can be extended with new atom styles; see <A HREF = "Section_modify.html">this
section</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This command cannot be used after the simulation box is defined by a
<A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command.
</P>
<P>The <I>angle</I>, <I>bond</I>, <I>full</I>, and <I>molecular</I> styles are part of the
-"molecular" package. The <I>dipole</I> style is part of the "dipole"
+MOLECULAR package. The <I>dipole</I> style is part of the "dipole"
package. The <I>ellipsoid</I> style is part of the "asphere" package. The
-<I>peri</I> style is part of the "peri" package for Peridynamics. The
-<I>electron</I> style is part of the "user-eff" package for <A HREF = "pair_eff.html">electronic
-force fields</A>. The <I>wavepacket</I> style is part of the
-"user-awpmd" package for the <A HREF = "pair_awpmd.html">antisymmetrized wave packet MD
-method</A>. They are only enabled if LAMMPS was built
-with that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
-section for more info.
+<I>peri</I> style is part of the PERI package for Peridynamics. The
+<I>electron</I> style is part of the USER-EFF package for <A HREF = "pair_eff.html">electronic force
+fields</A>. The <I>meso</I> style is part of the USER-SPH
+package for smoothed particle hydrodyanmics (SPH). See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF
+guide</A> to using SPH in LAMMPS. The
+<I>wavepacket</I> style is part of the USER-AWPMD package for the
+<A HREF = "pair_awpmd.html">antisymmetrized wave packet MD method</A>. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "read_data.html">read_data</A>, <A HREF = "pair_style.html">pair_style</A>
</P>
<P><B>Default:</B>
</P>
<P>atom_style atomic
</P>
</HTML>
diff --git a/doc/atom_style.txt b/doc/atom_style.txt
index 0dcf1e8e5..8925291bc 100644
--- a/doc/atom_style.txt
+++ b/doc/atom_style.txt
@@ -1,139 +1,146 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
atom_style command :h3
[Syntax:]
atom_style style args :pre
style = {angle} or {atomic} or {bond} or {charge} or {dipole} or \
- {electron} or {ellipsoid} or {full} or {molecular} or \
+ {electron} or {ellipsoid} or {full} or {meso} or {molecular} or \
{peri} or {sphere} or {hybrid} :ul
args = none for any style except {hybrid}
{hybrid} args = list of one or more sub-styles :pre
[Examples:]
atom_style atomic
atom_style bond
atom_style full
atom_style hybrid charge bond :pre
[Description:]
Define what style of atoms to use in a simulation. This determines
what attributes are associated with the atoms. This command must be
used before a simulation is setup via a "read_data"_read_data.html,
"read_restart"_read_restart.html, or "create_box"_create_box.html
command.
Once a style is assigned, it cannot be changed, so use a style general
enough to encompass all attributes. E.g. with style {bond}, angular
terms cannot be used or added later to the model. It is OK to use a
style more general than needed, though it may be slightly inefficient.
The choice of style affects what quantities are stored by each atom,
what quantities are communicated between processors to enable forces
to be computed, and what quantities are listed in the data file read
by the "read_data"_read_data.html command.
These are the additional attributes of each style and the typical
kinds of physical systems they are used to model. All styles store
coordinates, velocities, atom IDs and types. See the
"read_data"_read_data.html, "create_atoms"_create_atoms.html, and
"set"_set.html commands for info on how to set these various
quantities.
{angle} | bonds and angles | bead-spring polymers with stiffness |
{atomic} | only the default values | coarse-grain liquids, solids, metals |
{bond} | bonds | bead-spring polymers |
{charge} | charge | atomic system with charges |
{dipole} | charge and dipole moment | system with dipolar particles |
{electron} | charge and spin and eradius | electronic force field |
{ellipsoid} | shape, quaternion for particle orientation, angular momentum | extended aspherical particles |
{full} | molecular + charge | bio-molecules |
+{meso} | rho, e, cv | SPH particles |
{molecular} | bonds, angles, dihedrals, impropers | uncharged molecules |
{peri} | mass, volume | mesocopic Peridynamic models |
{sphere} | diameter, mass, angular velocity | granular models |
{wavepacket} | charge, spin, eradius, etag, cs_re, cs_im | AWPMD :tb(c=3,s=|)
All of the styles assign mass to particles on a per-type basis, using
the "mass"_mass.html command, except for the finite-size particle
styles discussed below. They assign mass on a per-atom basis.
All of the styles define point particles, except the {sphere},
{ellipsoid}, {electron}, {peri}, and {wavepacket} styles, which define
finite-size particles.
For the {sphere} style, the particles are spheres and each stores a
per-particle diameter and mass. If the diameter > 0.0, the particle
is a finite-size sphere. If the diameter = 0.0, it is a point
particle.
For the {ellipsoid} style, the particles are ellipsoids and each
stores a flag which indicates whether it is a finite-size ellipsoid or
a point particle. If it is an ellipsoid, it also stores a shape
vector with the 3 diamters of the ellipsoid and a quaternion 4-vector
with its orientation.
For the {electron} style, the particles representing electrons are 3d
Gaussians with a specified position and bandwidth or uncertainty in
position, which is represented by the eradius = electron size.
For the {peri} style, the particles are spherical and each stores a
per-particle mass and volume.
+The {meso} style is for smoothed particle hydrodynamics (SPH)
+particles which store a density (rho), energy (e), and heat capacity
+(cv).
+
The {wavepacket} style is similar to {electron}, but the electrons may
consist of several Gaussian wave packets, summed up with coefficients
cs= (cs_re,cs_im). Each of the wave packets is treated as a separate
particle in LAMMPS, wave packets belonging to the same electron must
have identical {etag} values.
:line
Typically, simulations require only a single (non-hybrid) atom style.
If some atoms in the simulation do not have all the properties defined
by a particular style, use the simplest style that defines all the
needed properties by any atom. For example, if some atoms in a
simulation are charged, but others are not, use the {charge} style.
If some atoms have bonds, but others do not, use the {bond} style.
The only scenario where the {hybrid} style is needed is if there is no
single style which defines all needed properties of all atoms. For
example, if you want dipolar particles which will be torqued and
rotate, you would need to use "atom_style hybrid sphere dipole". When
a hybrid style is used, atoms store and communicate the union of all
quantities implied by the individual styles.
LAMMPS can be extended with new atom styles; see "this
section"_Section_modify.html.
[Restrictions:]
This command cannot be used after the simulation box is defined by a
"read_data"_read_data.html or "create_box"_create_box.html command.
The {angle}, {bond}, {full}, and {molecular} styles are part of the
-"molecular" package. The {dipole} style is part of the "dipole"
+MOLECULAR package. The {dipole} style is part of the "dipole"
package. The {ellipsoid} style is part of the "asphere" package. The
-{peri} style is part of the "peri" package for Peridynamics. The
-{electron} style is part of the "user-eff" package for "electronic
-force fields"_pair_eff.html. The {wavepacket} style is part of the
-"user-awpmd" package for the "antisymmetrized wave packet MD
-method"_pair_awpmd.html. They are only enabled if LAMMPS was built
-with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+{peri} style is part of the PERI package for Peridynamics. The
+{electron} style is part of the USER-EFF package for "electronic force
+fields"_pair_eff.html. The {meso} style is part of the USER-SPH
+package for smoothed particle hydrodyanmics (SPH). See "this PDF
+guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. The
+{wavepacket} style is part of the USER-AWPMD package for the
+"antisymmetrized wave packet MD method"_pair_awpmd.html. They are
+only enabled if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"read_data"_read_data.html, "pair_style"_pair_style.html
[Default:]
atom_style atomic
diff --git a/doc/bond_class2.html b/doc/bond_class2.html
index 2de46dc2f..b560a514d 100644
--- a/doc/bond_class2.html
+++ b/doc/bond_class2.html
@@ -1,61 +1,61 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>bond_style class2 command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style class2
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style class2
bond_coeff 1 1.0 100.0 80.0 80.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>class2</I> bond style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/bond_class2.jpg">
</CENTER>
<P>where r0 is the equilibrium bond distance.
</P>
<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>R0 (distance)
<LI>K2 (energy/distance^2)
<LI>K3 (energy/distance^3)
<LI>K4 (energy/distance^4)
</UL>
<P><B>Restrictions:</B>
</P>
-<P>This bond style can only be used if LAMMPS was built with the "class2"
+<P>This bond style can only be used if LAMMPS was built with the CLASS2
package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Sun"></A>
<P><B>(Sun)</B> Sun, J Phys Chem B 102, 7338-7364 (1998).
</P>
</HTML>
diff --git a/doc/bond_class2.txt b/doc/bond_class2.txt
index 2e596a083..855be7b91 100644
--- a/doc/bond_class2.txt
+++ b/doc/bond_class2.txt
@@ -1,55 +1,55 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
bond_style class2 command :h3
[Syntax:]
bond_style class2 :pre
[Examples:]
bond_style class2
bond_coeff 1 1.0 100.0 80.0 80.0 :pre
[Description:]
The {class2} bond style uses the potential
:c,image(Eqs/bond_class2.jpg)
where r0 is the equilibrium bond distance.
See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
R0 (distance)
K2 (energy/distance^2)
K3 (energy/distance^3)
K4 (energy/distance^4) :ul
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the "class2"
+This bond style can only be used if LAMMPS was built with the CLASS2
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info on packages.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none
:line
:link(Sun)
[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998).
diff --git a/doc/bond_fene.html b/doc/bond_fene.html
index fce83ddff..6076d3cdb 100644
--- a/doc/bond_fene.html
+++ b/doc/bond_fene.html
@@ -1,67 +1,67 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>bond_style fene command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style fene
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>fene</I> bond style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/bond_fene.jpg">
</CENTER>
<P>to define a finite extensible nonlinear elastic (FENE) potential
<A HREF = "#Kremer">(Kremer)</A>, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive. The
first term extends to R0, the maximum extent of the bond. The 2nd
term is cutoff at 2^(1/6) sigma, the minimum of the LJ potential.
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy/distance^2)
<LI>R0 (distance)
<LI>epsilon (energy)
<LI>sigma (distance)
</UL>
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P>You typically should specify <A HREF = "special_bonds.html"">special_bonds fene</A>
or <A HREF = "special_bonds.html">special_bonds lj/coul 0 1 1</A> to use this bond
style. LAMMPS will issue a warning it that's not the case.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Kremer"></A>
<P><B>(Kremer)</B> Kremer, Grest, J Chem Phys, 92, 5057 (1990).
</P>
</HTML>
diff --git a/doc/bond_fene.txt b/doc/bond_fene.txt
index 1c15f24ae..6a6a40acd 100644
--- a/doc/bond_fene.txt
+++ b/doc/bond_fene.txt
@@ -1,61 +1,61 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
bond_style fene command :h3
[Syntax:]
bond_style fene :pre
[Examples:]
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0 :pre
[Description:]
The {fene} bond style uses the potential
:c,image(Eqs/bond_fene.jpg)
to define a finite extensible nonlinear elastic (FENE) potential
"(Kremer)"_#Kremer, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive. The
first term extends to R0, the maximum extent of the bond. The 2nd
term is cutoff at 2^(1/6) sigma, the minimum of the LJ potential.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy/distance^2)
R0 (distance)
epsilon (energy)
sigma (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
You typically should specify "special_bonds fene"_special_bonds.html"
or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
style. LAMMPS will issue a warning it that's not the case.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none
:line
:link(Kremer)
[(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990).
diff --git a/doc/bond_fene_expand.html b/doc/bond_fene_expand.html
index e8f6f2522..da9b2e2da 100644
--- a/doc/bond_fene_expand.html
+++ b/doc/bond_fene_expand.html
@@ -1,72 +1,72 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>bond_style fene/expand command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style fene/expand
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style fene/expand
bond_coeff 1 30.0 1.5 1.0 1.0 0.5
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>fene/expand</I> bond style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/bond_fene_expand.jpg">
</CENTER>
<P>to define a finite extensible nonlinear elastic (FENE) potential
<A HREF = "#Kremer">(Kremer)</A>, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive.
</P>
<P>The <I>fene/expand</I> bond style is similar to <I>fene</I> except that an extra
shift factor of delta (positive or negative) is added to <I>r</I> to
effectively change the bead size of the bonded atoms. The first term
now extends to R0 + delta and the 2nd term is cutoff at 2^(1/6) sigma
+ delta.
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy/distance^2)
<LI>R0 (distance)
<LI>epsilon (energy)
<LI>sigma (distance)
<LI>delta (distance)
</UL>
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P>You typically should specify <A HREF = "special_bonds.html"">special_bonds fene</A>
or <A HREF = "special_bonds.html">special_bonds lj/coul 0 1 1</A> to use this bond
style. LAMMPS will issue a warning it that's not the case.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Kremer"></A>
<P><B>(Kremer)</B> Kremer, Grest, J Chem Phys, 92, 5057 (1990).
</P>
</HTML>
diff --git a/doc/bond_fene_expand.txt b/doc/bond_fene_expand.txt
index c4a535dc8..011d6321a 100644
--- a/doc/bond_fene_expand.txt
+++ b/doc/bond_fene_expand.txt
@@ -1,66 +1,66 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
bond_style fene/expand command :h3
[Syntax:]
bond_style fene/expand :pre
[Examples:]
bond_style fene/expand
bond_coeff 1 30.0 1.5 1.0 1.0 0.5 :pre
[Description:]
The {fene/expand} bond style uses the potential
:c,image(Eqs/bond_fene_expand.jpg)
to define a finite extensible nonlinear elastic (FENE) potential
"(Kremer)"_#Kremer, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive.
The {fene/expand} bond style is similar to {fene} except that an extra
shift factor of delta (positive or negative) is added to {r} to
effectively change the bead size of the bonded atoms. The first term
now extends to R0 + delta and the 2nd term is cutoff at 2^(1/6) sigma
+ delta.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy/distance^2)
R0 (distance)
epsilon (energy)
sigma (distance)
delta (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
You typically should specify "special_bonds fene"_special_bonds.html"
or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
style. LAMMPS will issue a warning it that's not the case.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none
:line
:link(Kremer)
[(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990).
diff --git a/doc/bond_harmonic.html b/doc/bond_harmonic.html
index bc1176af6..efb2d26ab 100644
--- a/doc/bond_harmonic.html
+++ b/doc/bond_harmonic.html
@@ -1,52 +1,52 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>bond_style harmonic command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style harmonic
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style harmonic
bond_coeff 5 80.0 1.2
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>harmonic</I> bond style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/bond_harmonic.jpg">
</CENTER>
<P>where r0 is the equilibrium bond distance. Note that the usual 1/2
factor is included in K.
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy/distance^2)
<LI>r0 (distance)
</UL>
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/bond_harmonic.txt b/doc/bond_harmonic.txt
index 5dc87e5d2..658c87378 100644
--- a/doc/bond_harmonic.txt
+++ b/doc/bond_harmonic.txt
@@ -1,47 +1,47 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
bond_style harmonic command :h3
[Syntax:]
bond_style harmonic :pre
[Examples:]
bond_style harmonic
bond_coeff 5 80.0 1.2 :pre
[Description:]
The {harmonic} bond style uses the potential
:c,image(Eqs/bond_harmonic.jpg)
where r0 is the equilibrium bond distance. Note that the usual 1/2
factor is included in K.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy/distance^2)
r0 (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none
diff --git a/doc/bond_harmonic_shift.html b/doc/bond_harmonic_shift.html
index 08e7a2d53..8394ebf85 100644
--- a/doc/bond_harmonic_shift.html
+++ b/doc/bond_harmonic_shift.html
@@ -1,58 +1,58 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>bond_style harmonic/shift command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style harmonic/shift
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style harmonic/shift
bond_coeff 5 10.0 0.5 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>harmonic/shift</I> bond style is a shifted harmonic bond that uses
the potential
</P>
<CENTER><IMG SRC = "Eqs/bond_harmonic_shift.jpg">
</CENTER>
<P>where r0 is the equilibrium bond distance, and rc the critical distance.
The potential is -Umin at r0 and zero at rc. The spring constant is
k = Umin / [ 2 (r0-rc)^2].
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>Umin (energy)
</UL>
<UL><LI>r0 (distance)
</UL>
<UL><LI>rc (distance)
</UL>
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
-"user-misc" package. See the <A HREF = "Section_start.html#start_3">Making
-LAMMPS</A> section for more info on packages.
+USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>,
<A HREF = "bond_harmonic.html">bond_harmonic</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/bond_harmonic_shift.txt b/doc/bond_harmonic_shift.txt
index ca0d33ba3..4bef45dd1 100644
--- a/doc/bond_harmonic_shift.txt
+++ b/doc/bond_harmonic_shift.txt
@@ -1,51 +1,51 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
bond_style harmonic/shift command :h3
[Syntax:]
bond_style harmonic/shift :pre
[Examples:]
bond_style harmonic/shift
bond_coeff 5 10.0 0.5 1.0 :pre
[Description:]
The {harmonic/shift} bond style is a shifted harmonic bond that uses
the potential
:c,image(Eqs/bond_harmonic_shift.jpg)
where r0 is the equilibrium bond distance, and rc the critical distance.
The potential is -Umin at r0 and zero at rc. The spring constant is
k = Umin / \[ 2 (r0-rc)^2\].
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
Umin (energy) :ul
r0 (distance) :ul
rc (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
-"user-misc" package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
+section for more info on packages.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html,
"bond_harmonic"_bond_harmonic.html
[Default:] none
diff --git a/doc/bond_harmonic_shift_cut.html b/doc/bond_harmonic_shift_cut.html
index 83d6ff154..2142fc5f8 100644
--- a/doc/bond_harmonic_shift_cut.html
+++ b/doc/bond_harmonic_shift_cut.html
@@ -1,57 +1,57 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>bond_style harmonic/shift/cut command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style harmonic/shift/cut
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style harmonic/shift/cut
bond_coeff 5 10.0 0.5 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>harmonic/shift/cut</I> bond style is a shifted harmonic bond that
uses the potential
</P>
<CENTER><IMG SRC = "Eqs/bond_harmonic_shift_cut.jpg">
</CENTER>
<P>where r0 is the equilibrium bond distance, and rc the critical distance.
The bond potential is zero for distances r > rc. The potential is -Umin
at r0 and zero at rc. The spring constant is k = Umin / [ 2 (r0-rc)^2].
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>Umin (energy)
<LI>r0 (distance)
<LI>rc (distance)
</UL>
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
-"user-misc" package. See the <A HREF = "Section_start.html#start_3">Making
-LAMMPS</A> section for more info on packages.
+USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>,
<A HREF = "bond_harmonic.html">bond_harmonic</A>,
<A HREF = "bond_harmonicshift.html">bond_harmonicshift</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/bond_harmonic_shift_cut.txt b/doc/bond_harmonic_shift_cut.txt
index f5a8d3488..ea9de8e93 100644
--- a/doc/bond_harmonic_shift_cut.txt
+++ b/doc/bond_harmonic_shift_cut.txt
@@ -1,52 +1,52 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
bond_style harmonic/shift/cut command :h3
[Syntax:]
bond_style harmonic/shift/cut :pre
[Examples:]
bond_style harmonic/shift/cut
bond_coeff 5 10.0 0.5 1.0 :pre
[Description:]
The {harmonic/shift/cut} bond style is a shifted harmonic bond that
uses the potential
:c,image(Eqs/bond_harmonic_shift_cut.jpg)
where r0 is the equilibrium bond distance, and rc the critical distance.
The bond potential is zero for distances r > rc. The potential is -Umin
at r0 and zero at rc. The spring constant is k = Umin / \[ 2 (r0-rc)^2\].
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
Umin (energy)
r0 (distance)
rc (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
-"user-misc" package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
+section for more info on packages.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html,
"bond_harmonic"_bond_harmonic.html,
"bond_harmonicshift"_bond_harmonicshift.html
[Default:] none
diff --git a/doc/bond_hybrid.html b/doc/bond_hybrid.html
index 4dd3b380f..b9073bd9d 100644
--- a/doc/bond_hybrid.html
+++ b/doc/bond_hybrid.html
@@ -1,77 +1,77 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>bond_style hybrid command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style hybrid style1 style2 ...
</PRE>
<UL><LI>style1,style2 = list of one or more bond styles
</UL>
<P><B>Examples:</B>
</P>
<PRE>bond_style hybrid harmonic fene
bond_coeff 1 harmonic 80.0 1.2
bond_coeff 2* fene 30.0 1.5 1.0 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>hybrid</I> style enables the use of multiple bond styles in one
simulation. A bond style is assigned to each bond type. For example,
bonds in a polymer flow (of bond type 1) could be computed with a
<I>fene</I> potential and bonds in the wall boundary (of bond type 2) could
be computed with a <I>harmonic</I> potential. The assignment of bond type
to style is made via the <A HREF = "bond_coeff.html">bond_coeff</A> command or in
the data file.
</P>
<P>In the bond_coeff commands, the name of a bond style must be added
after the bond type, with the remaining coefficients being those
appropriate to that style. In the example above, the 2 bond_coeff
commands set bonds of bond type 1 to be computed with a <I>harmonic</I>
potential with coefficients 80.0, 1.2 for K, r0. All other bond types
(2-N) are computed with a <I>fene</I> potential with coefficients 30.0,
1.5, 1.0, 1.0 for K, R0, epsilon, sigma.
</P>
<P>If bond coefficients are specified in the data file read via the
<A HREF = "read_data.html">read_data</A> command, then the same rule applies.
E.g. "harmonic" or "fene" must be added after the bond type, for each
line in the "Bond Coeffs" section, e.g.
</P>
<PRE>Bond Coeffs
</PRE>
<PRE>1 harmonic 80.0 1.2
2 fene 30.0 1.5 1.0 1.0
...
</PRE>
<P>A bond style of <I>none</I> with no additional coefficients can be used in
place of a bond style, either in a input script bond_coeff command or
in the data file, if you desire to turn off interactions for specific
bond types.
</P>
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P>Unlike other bond styles, the hybrid bond style does not store bond
coefficient info for individual sub-styles in a <A HREF = "restart.html">binary restart
files</A>. Thus when retarting a simulation from a restart
file, you need to re-specify bond_coeff commands.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/bond_hybrid.txt b/doc/bond_hybrid.txt
index 11d77f494..f4a995922 100644
--- a/doc/bond_hybrid.txt
+++ b/doc/bond_hybrid.txt
@@ -1,72 +1,72 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
bond_style hybrid command :h3
[Syntax:]
bond_style hybrid style1 style2 ... :pre
style1,style2 = list of one or more bond styles :ul
[Examples:]
bond_style hybrid harmonic fene
bond_coeff 1 harmonic 80.0 1.2
bond_coeff 2* fene 30.0 1.5 1.0 1.0 :pre
[Description:]
The {hybrid} style enables the use of multiple bond styles in one
simulation. A bond style is assigned to each bond type. For example,
bonds in a polymer flow (of bond type 1) could be computed with a
{fene} potential and bonds in the wall boundary (of bond type 2) could
be computed with a {harmonic} potential. The assignment of bond type
to style is made via the "bond_coeff"_bond_coeff.html command or in
the data file.
In the bond_coeff commands, the name of a bond style must be added
after the bond type, with the remaining coefficients being those
appropriate to that style. In the example above, the 2 bond_coeff
commands set bonds of bond type 1 to be computed with a {harmonic}
potential with coefficients 80.0, 1.2 for K, r0. All other bond types
(2-N) are computed with a {fene} potential with coefficients 30.0,
1.5, 1.0, 1.0 for K, R0, epsilon, sigma.
If bond coefficients are specified in the data file read via the
"read_data"_read_data.html command, then the same rule applies.
E.g. "harmonic" or "fene" must be added after the bond type, for each
line in the "Bond Coeffs" section, e.g.
Bond Coeffs :pre
1 harmonic 80.0 1.2
2 fene 30.0 1.5 1.0 1.0
... :pre
A bond style of {none} with no additional coefficients can be used in
place of a bond style, either in a input script bond_coeff command or
in the data file, if you desire to turn off interactions for specific
bond types.
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
Unlike other bond styles, the hybrid bond style does not store bond
coefficient info for individual sub-styles in a "binary restart
files"_restart.html. Thus when retarting a simulation from a restart
file, you need to re-specify bond_coeff commands.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none
diff --git a/doc/bond_morse.html b/doc/bond_morse.html
index 6cd8d70bc..e82692404 100644
--- a/doc/bond_morse.html
+++ b/doc/bond_morse.html
@@ -1,53 +1,53 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>bond_style morse command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style morse
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style morse
bond_coeff 5 1.0 2.0 1.2
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>morse</I> bond style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/bond_morse.jpg">
</CENTER>
<P>where r0 is the equilibrium bond distance, alpha is a stiffness
parameter, and D determines the depth of the potential well.
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>D (energy)
<LI>alpha (inverse distance)
<LI>r0 (distance)
</UL>
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/bond_morse.txt b/doc/bond_morse.txt
index 22a075c7f..be9c00665 100644
--- a/doc/bond_morse.txt
+++ b/doc/bond_morse.txt
@@ -1,48 +1,48 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
bond_style morse command :h3
[Syntax:]
bond_style morse :pre
[Examples:]
bond_style morse
bond_coeff 5 1.0 2.0 1.2 :pre
[Description:]
The {morse} bond style uses the potential
:c,image(Eqs/bond_morse.jpg)
where r0 is the equilibrium bond distance, alpha is a stiffness
parameter, and D determines the depth of the potential well.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
D (energy)
alpha (inverse distance)
r0 (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none
diff --git a/doc/bond_nonlinear.html b/doc/bond_nonlinear.html
index be0cdc097..06fd7cb45 100644
--- a/doc/bond_nonlinear.html
+++ b/doc/bond_nonlinear.html
@@ -1,59 +1,59 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>bond_style nonlinear command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style nonlinear
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style nonlinear
bond_coeff 2 100.0 1.1 1.4
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>nonlinear</I> bond style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/bond_nonlinear.jpg">
</CENTER>
<P>to define an anharmonic spring <A HREF = "#Rector">(Rector)</A> of equilibrium
length r0 and maximum extension lamda.
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>epsilon (energy)
<LI>r0 (distance)
<LI>lamda (distance)
</UL>
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Rector"></A>
<P><B>(Rector)</B> Rector, Van Swol, Henderson, Molecular Physics, 82, 1009 (1994).
</P>
</HTML>
diff --git a/doc/bond_nonlinear.txt b/doc/bond_nonlinear.txt
index 8f4437303..2cd41962e 100644
--- a/doc/bond_nonlinear.txt
+++ b/doc/bond_nonlinear.txt
@@ -1,53 +1,53 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
bond_style nonlinear command :h3
[Syntax:]
bond_style nonlinear :pre
[Examples:]
bond_style nonlinear
bond_coeff 2 100.0 1.1 1.4 :pre
[Description:]
The {nonlinear} bond style uses the potential
:c,image(Eqs/bond_nonlinear.jpg)
to define an anharmonic spring "(Rector)"_#Rector of equilibrium
length r0 and maximum extension lamda.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
epsilon (energy)
r0 (distance)
lamda (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none
:line
:link(Rector)
[(Rector)] Rector, Van Swol, Henderson, Molecular Physics, 82, 1009 (1994).
diff --git a/doc/bond_quartic.html b/doc/bond_quartic.html
index 5bbffc032..824c46716 100644
--- a/doc/bond_quartic.html
+++ b/doc/bond_quartic.html
@@ -1,92 +1,92 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>bond_style quartic command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style quartic
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style quartic
bond_coeff 2 1200 -0.55 0.25 1.3 34.6878
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>quartic</I> bond style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/bond_quartic.jpg">
</CENTER>
<P>to define a bond that can be broken as the simulation proceeds (e.g.
due to a polymer being stretched). The sigma and epsilon used in the
LJ portion of the formula are both set equal to 1.0 by LAMMPS.
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy/distance^2)
<LI>B1 (distance)
<LI>B2 (distance)
<LI>Rc (distance)
<LI>U0 (energy)
</UL>
<P>This potential was constructed to mimic the FENE bond potential for
coarse-grained polymer chains. When monomers with sigma = epsilon =
1.0 are used, the following choice of parameters gives a quartic
potential that looks nearly like the FENE potential: K = 1200, B1 =
-0.55, B2 = 0.25, Rc = 1.3, and U0 = 34.6878. Different parameters
can be specified using the <A HREF = "bond_coeff.html">bond_coeff</A> command, but
you will need to choose them carefully so they form a suitable bond
potential.
</P>
<P>Rc is the cutoff length at which the bond potential goes smoothly to a
local maximum. If a bond length ever becomes > Rc, LAMMPS "breaks"
the bond, which means two things. First, the bond potential is turned
off by setting its type to 0, and is no longer computed. Second, a
pairwise interaction between the two atoms is turned on, since they
are no longer bonded.
</P>
<P>LAMMPS does the second task via a computational sleight-of-hand. It
subtracts the pairwise interaction as part of the bond computation.
When the bond breaks, the subtraction stops. For this to work, the
pairwise interaction must always be computed by the
<A HREF = "pair_style.html">pair_style</A> command, whether the bond is broken or
not. This means that <A HREF = "special_bonds.html">special_bonds</A> must be set
to 1,1,1, as indicated as a restriction below.
</P>
<P>Note that when bonds are dumped to a file via the <A HREF = "dump.html">dump
local</A> command, bonds with type 0 are not included. The
<A HREF = "delete_bonds.html">delete_bonds</A> command can also be used to query the
status of broken bonds or permanently delete them, e.g.:
</P>
<PRE>delete_bonds all stats
delete_bonds all bond 0 remove
</PRE>
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P>The <I>quartic</I> style requires that <A HREF = "special_bonds.html">special_bonds</A>
parameters be set to 1,1,1. Three- and four-body interactions (angle,
dihedral, etc) cannot be used with <I>quartic</I> bonds.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/bond_quartic.txt b/doc/bond_quartic.txt
index 5cb2639b3..068defb54 100644
--- a/doc/bond_quartic.txt
+++ b/doc/bond_quartic.txt
@@ -1,87 +1,87 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
bond_style quartic command :h3
[Syntax:]
bond_style quartic :pre
[Examples:]
bond_style quartic
bond_coeff 2 1200 -0.55 0.25 1.3 34.6878 :pre
[Description:]
The {quartic} bond style uses the potential
:c,image(Eqs/bond_quartic.jpg)
to define a bond that can be broken as the simulation proceeds (e.g.
due to a polymer being stretched). The sigma and epsilon used in the
LJ portion of the formula are both set equal to 1.0 by LAMMPS.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy/distance^2)
B1 (distance)
B2 (distance)
Rc (distance)
U0 (energy) :ul
This potential was constructed to mimic the FENE bond potential for
coarse-grained polymer chains. When monomers with sigma = epsilon =
1.0 are used, the following choice of parameters gives a quartic
potential that looks nearly like the FENE potential: K = 1200, B1 =
-0.55, B2 = 0.25, Rc = 1.3, and U0 = 34.6878. Different parameters
can be specified using the "bond_coeff"_bond_coeff.html command, but
you will need to choose them carefully so they form a suitable bond
potential.
Rc is the cutoff length at which the bond potential goes smoothly to a
local maximum. If a bond length ever becomes > Rc, LAMMPS "breaks"
the bond, which means two things. First, the bond potential is turned
off by setting its type to 0, and is no longer computed. Second, a
pairwise interaction between the two atoms is turned on, since they
are no longer bonded.
LAMMPS does the second task via a computational sleight-of-hand. It
subtracts the pairwise interaction as part of the bond computation.
When the bond breaks, the subtraction stops. For this to work, the
pairwise interaction must always be computed by the
"pair_style"_pair_style.html command, whether the bond is broken or
not. This means that "special_bonds"_special_bonds.html must be set
to 1,1,1, as indicated as a restriction below.
Note that when bonds are dumped to a file via the "dump
local"_dump.html command, bonds with type 0 are not included. The
"delete_bonds"_delete_bonds.html command can also be used to query the
status of broken bonds or permanently delete them, e.g.:
delete_bonds all stats
delete_bonds all bond 0 remove :pre
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
The {quartic} style requires that "special_bonds"_special_bonds.html
parameters be set to 1,1,1. Three- and four-body interactions (angle,
dihedral, etc) cannot be used with {quartic} bonds.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none
diff --git a/doc/bond_style.html b/doc/bond_style.html
index 5be22aa83..22021efc5 100644
--- a/doc/bond_style.html
+++ b/doc/bond_style.html
@@ -1,109 +1,109 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>bond_style command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style style args
</PRE>
<UL><LI>style = <I>none</I> or <I>hybrid</I> or <I>class2</I> or <I>fene</I> or <I>fene/expand</I> or <I>harmonic</I> or <I>morse</I> or <I>nonlinear</I> or <I>quartic</I>
</UL>
<PRE> args = none for any style except <I>hybrid</I>
<I>hybrid</I> args = list of one or more styles
</PRE>
<P><B>Examples:</B>
</P>
<PRE>bond_style harmonic
bond_style fene
bond_style hybrid harmonic fene
</PRE>
<P><B>Description:</B>
</P>
<P>Set the formula(s) LAMMPS uses to compute bond interactions between
pairs of atoms. In LAMMPS, a bond differs from a pairwise
interaction, which are set via the <A HREF = "pair_style.html">pair_style</A>
command. Bonds are defined between specified pairs of atoms and
remain in force for the duration of the simulation (unless the bond
breaks which is possible in some bond potentials). The list of bonded
atoms is read in by a <A HREF = "read_data.html">read_data</A> or
<A HREF = "read_restart.html">read_restart</A> command from a data or restart file.
By contrast, pair potentials are typically defined between all pairs
of atoms within a cutoff distance and the set of active interactions
changes over time.
</P>
<P>Hybrid models where bonds are computed using different bond potentials
can be setup using the <I>hybrid</I> bond style.
</P>
<P>The coefficients associated with a bond style can be specified in a
data or restart file or via the <A HREF = "bond_coeff.html">bond_coeff</A> command.
</P>
<P>All bond potentials store their coefficient data in binary restart
files which means bond_style and <A HREF = "bond_coeff.html">bond_coeff</A> commands
do not need to be re-specified in an input script that restarts a
simulation. See the <A HREF = "read_restart.html">read_restart</A> command for
details on how to do this. The one exception is that bond_style
<I>hybrid</I> only stores the list of sub-styles in the restart file; bond
coefficients need to be re-specified.
</P>
<P>IMPORTANT NOTE: When both a bond and pair style is defined, the
<A HREF = "special_bonds.html">special_bonds</A> command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
exist between 2 bonded atoms.
</P>
<P>In the formulas listed for each bond style, <I>r</I> is the distance
between the 2 atoms in the bond.
</P>
<HR>
<P>Here is an alphabetic list of bond styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated <A HREF = "bond_coeff.html">bond_coeff</A> command:
</P>
<UL><LI><A HREF = "bond_none.html">bond_style none</A> - turn off bonded interactions
<LI><A HREF = "bond_hybrid.html">bond_style hybrid</A> - define multiple styles of bond interactions
</UL>
<UL><LI><A HREF = "bond_class2.html">bond_style class2</A> - COMPASS (class 2) bond
<LI><A HREF = "bond_fene.html">bond_style fene</A> - FENE (finite-extensible non-linear elastic) bond
<LI><A HREF = "bond_fene_expand.html">bond_style fene/expand</A> - FENE bonds with variable size particles
<LI><A HREF = "bond_harmonic.html">bond_style harmonic</A> - harmonic bond
<LI><A HREF = "bond_morse.html">bond_style morse</A> - Morse bond
<LI><A HREF = "bond_nonlinear.html">bond_style nonlinear</A> - nonlinear bond
<LI><A HREF = "bond_quartic.html">bond_style quartic</A> - breakable quartic bond
<LI><A HREF = "bond_table.html">bond_style table</A> - tabulated by bond length
</UL>
<P>There are also additional bond styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the bond section of <A HREF = "Section_commands.html#cmd_5">this
page</A>.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>Bond styles can only be set for atom styles that allow bonds to be
defined.
</P>
-<P>Most bond styles are part of the "molecular" package. They are only
+<P>Most bond styles are part of the MOLECULAR package. They are only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
The doc pages for individual bond potentials tell if it is part of a
package.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
</P>
<P><B>Default:</B>
</P>
<P>bond_style none
</P>
</HTML>
diff --git a/doc/bond_style.txt b/doc/bond_style.txt
index 953a764ce..f89edc296 100644
--- a/doc/bond_style.txt
+++ b/doc/bond_style.txt
@@ -1,104 +1,104 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
bond_style command :h3
[Syntax:]
bond_style style args :pre
style = {none} or {hybrid} or {class2} or {fene} or {fene/expand} or \
{harmonic} or {morse} or {nonlinear} or {quartic} :ul
args = none for any style except {hybrid}
{hybrid} args = list of one or more styles :pre
[Examples:]
bond_style harmonic
bond_style fene
bond_style hybrid harmonic fene :pre
[Description:]
Set the formula(s) LAMMPS uses to compute bond interactions between
pairs of atoms. In LAMMPS, a bond differs from a pairwise
interaction, which are set via the "pair_style"_pair_style.html
command. Bonds are defined between specified pairs of atoms and
remain in force for the duration of the simulation (unless the bond
breaks which is possible in some bond potentials). The list of bonded
atoms is read in by a "read_data"_read_data.html or
"read_restart"_read_restart.html command from a data or restart file.
By contrast, pair potentials are typically defined between all pairs
of atoms within a cutoff distance and the set of active interactions
changes over time.
Hybrid models where bonds are computed using different bond potentials
can be setup using the {hybrid} bond style.
The coefficients associated with a bond style can be specified in a
data or restart file or via the "bond_coeff"_bond_coeff.html command.
All bond potentials store their coefficient data in binary restart
files which means bond_style and "bond_coeff"_bond_coeff.html commands
do not need to be re-specified in an input script that restarts a
simulation. See the "read_restart"_read_restart.html command for
details on how to do this. The one exception is that bond_style
{hybrid} only stores the list of sub-styles in the restart file; bond
coefficients need to be re-specified.
IMPORTANT NOTE: When both a bond and pair style is defined, the
"special_bonds"_special_bonds.html command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
exist between 2 bonded atoms.
In the formulas listed for each bond style, {r} is the distance
between the 2 atoms in the bond.
:line
Here is an alphabetic list of bond styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "bond_coeff"_bond_coeff.html command:
"bond_style none"_bond_none.html - turn off bonded interactions
"bond_style hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul
"bond_style class2"_bond_class2.html - COMPASS (class 2) bond
"bond_style fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond
"bond_style fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles
"bond_style harmonic"_bond_harmonic.html - harmonic bond
"bond_style morse"_bond_morse.html - Morse bond
"bond_style nonlinear"_bond_nonlinear.html - nonlinear bond
"bond_style quartic"_bond_quartic.html - breakable quartic bond
"bond_style table"_bond_table.html - tabulated by bond length :ul
There are also additional bond styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the bond section of "this
page"_Section_commands.html#cmd_5.
:line
[Restrictions:]
Bond styles can only be set for atom styles that allow bonds to be
defined.
-Most bond styles are part of the "molecular" package. They are only
+Most bond styles are part of the MOLECULAR package. They are only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
The doc pages for individual bond potentials tell if it is part of a
package.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:]
bond_style none
diff --git a/doc/bond_table.html b/doc/bond_table.html
index 319bcbba7..29ec7bc94 100644
--- a/doc/bond_table.html
+++ b/doc/bond_table.html
@@ -1,133 +1,133 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>bond_style table command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>bond_style table style N
</PRE>
<UL><LI>style = <I>linear</I> or <I>spline</I> = method of interpolation
<LI>N = use N values in table
</UL>
<P><B>Examples:</B>
</P>
<PRE>bond_style table linear 1000
bond_coeff 1 file.table ENTRY1
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>table</I> creates interpolation tables of length <I>N</I> from bond
potential and force values listed in a file(s) as a function of bond
length. The files are read by the <A HREF = "bond_coeff.html">bond_coeff</A>
command.
</P>
<P>The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and force values at each of <I>N</I>
distances. During a simulation, these tables are used to interpolate
energy and force values as needed. The interpolation is done in one
of 2 styles: <I>linear</I> or <I>spline</I>.
</P>
<P>For the <I>linear</I> style, the bond length is used to find 2 surrounding
table values from which an energy or force is computed by linear
interpolation.
</P>
<P>For the <I>spline</I> style, a cubic spline coefficients are computed and
stored at each of the <I>N</I> values in the table. The bond length is
used to find the appropriate set of coefficients which are used to
evaluate a cubic polynomial which computes the energy or force.
</P>
<P>The following coefficients must be defined for each bond type via the
<A HREF = "bond_coeff.html">bond_coeff</A> command as in the example above.
</P>
<UL><LI>filename
<LI>keyword
</UL>
<P>The filename specifies a file containing tabulated energy and force
values. The keyword specifies a section of the file. The format of
this file is described below.
</P>
<HR>
<P>The format of a tabulated file is as follows (without the
parenthesized comments):
</P>
<PRE># Bond potential for harmonic (one or more comment or blank lines)
</PRE>
<PRE>HAM (keyword is the first text on line)
N 101 FP 0 0 EQ 0.5 (N, FP, EQ parameters)
(blank line)
1 0.00 338.0000 1352.0000 (index, bond-length, energy, force)
2 0.01 324.6152 1324.9600
...
101 1.00 338.0000 -1352.0000
</PRE>
<P>A section begins with a non-blank line whose 1st character is not a
"#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
initial text must match the argument specified in the
<A HREF = "bond_coeff.html">bond_coeff</A> command. The next line lists (in any
order) one or more parameters for the table. Each parameter is a
keyword followed by one or more numeric values.
</P>
<P>The parameter "N" is required and its value is the number of table
entries that follow. Note that this may be different than the <I>N</I>
specified in the <A HREF = "bond_style.html">bond_style table</A> command. Let
Ntable = <I>N</I> in the bond_style command, and Nfile = "N" in the
tabulated file. What LAMMPS does is a preliminary interpolation by
creating splines using the Nfile tabulated values as nodal points. It
uses these to interpolate as needed to generate energy and force
values at Ntable different points. The resulting tables of length
Ntable are then used as described above, when computing energy and
force for individual bond lengths. This means that if you want the
interpolation tables of length Ntable to match exactly what is in the
tabulated file (with effectively no preliminary interpolation), you
should set Ntable = Nfile.
</P>
<P>The "FP" parameter is optional. If used, it is followed by two values
fplo and fphi, which are the derivatives of the force at the innermost
and outermost bond lengths. These values are needed by the spline
construction routines. If not specified by the "FP" parameter, they
are estimated (less accurately) by the first two and last two force
values in the table.
</P>
<P>The "EQ" parameter is also optional. If used, it is followed by a the
equilibrium bond length, which is used, for example, by the <A HREF = "fix_shake.html">fix
shake</A> command. If not used, the equilibrium bond
length is set to 0.0.
</P>
<P>Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is
the bond length r (in distance units), the 3rd value is the energy (in
energy units), and the 4th is the force (in force units). The bond
lengths must range from a LO value to a HI value, and increase from
one line to the next. If the actual bond length is ever smaller than
the LO value or larger than the HI value, then the bond energy and
force is evaluated as if the bond were the LO or HI length.
</P>
<P>Note that one file can contain many sections, each with a tabulated
potential. LAMMPS reads the file section by section until it finds
one that matches the specified keyword.
</P>
<P><B>Restrictions:</B>
</P>
<P>This bond style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/bond_table.txt b/doc/bond_table.txt
index 9dd243c46..c02b71e86 100644
--- a/doc/bond_table.txt
+++ b/doc/bond_table.txt
@@ -1,128 +1,128 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
bond_style table command :h3
[Syntax:]
bond_style table style N :pre
style = {linear} or {spline} = method of interpolation
N = use N values in table :ul
[Examples:]
bond_style table linear 1000
bond_coeff 1 file.table ENTRY1 :pre
[Description:]
Style {table} creates interpolation tables of length {N} from bond
potential and force values listed in a file(s) as a function of bond
length. The files are read by the "bond_coeff"_bond_coeff.html
command.
The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and force values at each of {N}
distances. During a simulation, these tables are used to interpolate
energy and force values as needed. The interpolation is done in one
of 2 styles: {linear} or {spline}.
For the {linear} style, the bond length is used to find 2 surrounding
table values from which an energy or force is computed by linear
interpolation.
For the {spline} style, a cubic spline coefficients are computed and
stored at each of the {N} values in the table. The bond length is
used to find the appropriate set of coefficients which are used to
evaluate a cubic polynomial which computes the energy or force.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above.
filename
keyword :ul
The filename specifies a file containing tabulated energy and force
values. The keyword specifies a section of the file. The format of
this file is described below.
:line
The format of a tabulated file is as follows (without the
parenthesized comments):
# Bond potential for harmonic (one or more comment or blank lines) :pre
HAM (keyword is the first text on line)
N 101 FP 0 0 EQ 0.5 (N, FP, EQ parameters)
(blank line)
1 0.00 338.0000 1352.0000 (index, bond-length, energy, force)
2 0.01 324.6152 1324.9600
...
101 1.00 338.0000 -1352.0000 :pre
A section begins with a non-blank line whose 1st character is not a
"#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
initial text must match the argument specified in the
"bond_coeff"_bond_coeff.html command. The next line lists (in any
order) one or more parameters for the table. Each parameter is a
keyword followed by one or more numeric values.
The parameter "N" is required and its value is the number of table
entries that follow. Note that this may be different than the {N}
specified in the "bond_style table"_bond_style.html command. Let
Ntable = {N} in the bond_style command, and Nfile = "N" in the
tabulated file. What LAMMPS does is a preliminary interpolation by
creating splines using the Nfile tabulated values as nodal points. It
uses these to interpolate as needed to generate energy and force
values at Ntable different points. The resulting tables of length
Ntable are then used as described above, when computing energy and
force for individual bond lengths. This means that if you want the
interpolation tables of length Ntable to match exactly what is in the
tabulated file (with effectively no preliminary interpolation), you
should set Ntable = Nfile.
The "FP" parameter is optional. If used, it is followed by two values
fplo and fphi, which are the derivatives of the force at the innermost
and outermost bond lengths. These values are needed by the spline
construction routines. If not specified by the "FP" parameter, they
are estimated (less accurately) by the first two and last two force
values in the table.
The "EQ" parameter is also optional. If used, it is followed by a the
equilibrium bond length, which is used, for example, by the "fix
shake"_fix_shake.html command. If not used, the equilibrium bond
length is set to 0.0.
Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is
the bond length r (in distance units), the 3rd value is the energy (in
energy units), and the 4th is the force (in force units). The bond
lengths must range from a LO value to a HI value, and increase from
one line to the next. If the actual bond length is ever smaller than
the LO value or larger than the HI value, then the bond energy and
force is evaluated as if the bond were the LO or HI length.
Note that one file can contain many sections, each with a tabulated
potential. LAMMPS reads the file section by section until it finds
one that matches the specified keyword.
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none
diff --git a/doc/compute_ackland_atom.html b/doc/compute_ackland_atom.html
index 31abcf1f9..16ad975e8 100644
--- a/doc/compute_ackland_atom.html
+++ b/doc/compute_ackland_atom.html
@@ -1,77 +1,80 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute ackland/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID ackland/atom
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>ackland/atom = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all ackland/atom
</PRE>
<P><B>Description:</B>
</P>
<P>Defines a computation that calculates the local lattice structure
according to the formulation given in <A HREF = "#Ackland">(Ackland)</A>.
</P>
<P>In contrast to the <A HREF = "compute_centro_atom.html">centro-symmetry
parameter</A> this method is stable against
temperature boost, because it is based not on the distance between
particles but the angles. Therefore statistical fluctuations are
averaged out a little more. A comparison with the Common Neighbor
Analysis metric is made in the paper.
</P>
<P>The result is a number which is mapped to the following different
lattice structures:
</P>
<UL><LI>0 = UNKNOWN
<LI>1 = BCC
<LI>2 = FCC
<LI>3 = HCP
<LI>4 = ICO
</UL>
<P>The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each of
which computes this quantity.-
</P>
<P><B>Output info:</B>
</P>
-<P>This compute calculates a scalar quantity for each atom, which can be
-accessed by any command that uses per-atom values from a compute as
-input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
-of LAMMPS output options.
+<P>This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
+output options.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This compute is part of the "user-misc" package. It is only enabled
-if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+<P>This compute is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
+<P>The per-atom vector values will be unitless since they are the
+integers defined above.
+</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_centro_atom.html">compute centro/atom</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Ackland"></A>
<P><B>(Ackland)</B> Ackland, Jones, Phys Rev B, 73, 054104 (2006).
</P>
</HTML>
diff --git a/doc/compute_ackland_atom.txt b/doc/compute_ackland_atom.txt
index 99991c798..5a9dcebba 100644
--- a/doc/compute_ackland_atom.txt
+++ b/doc/compute_ackland_atom.txt
@@ -1,71 +1,74 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute ackland/atom command :h3
[Syntax:]
compute ID group-ID ackland/atom :pre
ID, group-ID are documented in "compute"_compute.html command
ackland/atom = style name of this compute command :ul
[Examples:]
compute 1 all ackland/atom :pre
[Description:]
Defines a computation that calculates the local lattice structure
according to the formulation given in "(Ackland)"_#Ackland.
In contrast to the "centro-symmetry
parameter"_compute_centro_atom.html this method is stable against
temperature boost, because it is based not on the distance between
particles but the angles. Therefore statistical fluctuations are
averaged out a little more. A comparison with the Common Neighbor
Analysis metric is made in the paper.
The result is a number which is mapped to the following different
lattice structures:
0 = UNKNOWN
1 = BCC
2 = FCC
3 = HCP
4 = ICO :ul
The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each of
which computes this quantity.-
[Output info:]
-This compute calculates a scalar quantity for each atom, which can be
-accessed by any command that uses per-atom values from a compute as
-input. See "this section"_Section_howto.html#howto_15 for an overview
-of LAMMPS output options.
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
+output options.
[Restrictions:]
-This compute is part of the "user-misc" package. It is only enabled
-if LAMMPS was built with that package. See the "Making
+This compute is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
+The per-atom vector values will be unitless since they are the
+integers defined above.
+
[Related commands:]
"compute centro/atom"_compute_centro_atom.html
[Default:] none
:line
:link(Ackland)
[(Ackland)] Ackland, Jones, Phys Rev B, 73, 054104 (2006).
diff --git a/doc/compute_damage_atom.html b/doc/compute_damage_atom.html
index b15291a14..b5e0d03d8 100644
--- a/doc/compute_damage_atom.html
+++ b/doc/compute_damage_atom.html
@@ -1,58 +1,58 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute damage/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID damage/atom
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>damage/atom = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all damage/atom
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the per-atom damage for each atom
in a group. Please see the <A HREF = "http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf">PDLAMMPS user
guide</A> for a formal
definition of "damage" and more details about Peridynamics as it is
implemented in LAMMPS.
</P>
<P>The value of the damage will be 0.0 for atoms not in the specified
compute group.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
output options.
</P>
<P>The per-atom vector values will be a number >= 0.0, as explained
above.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This compute is part of the "peri" package. It is only enabled if
+<P>This compute is part of the PERI package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dump.html">dump custom</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/compute_damage_atom.txt b/doc/compute_damage_atom.txt
index 830caa933..104cf22b5 100644
--- a/doc/compute_damage_atom.txt
+++ b/doc/compute_damage_atom.txt
@@ -1,53 +1,53 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute damage/atom command :h3
[Syntax:]
compute ID group-ID damage/atom :pre
ID, group-ID are documented in "compute"_compute.html command
damage/atom = style name of this compute command :ul
[Examples:]
compute 1 all damage/atom :pre
[Description:]
Define a computation that calculates the per-atom damage for each atom
in a group. Please see the "PDLAMMPS user
guide"_http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf for a formal
definition of "damage" and more details about Peridynamics as it is
implemented in LAMMPS.
The value of the damage will be 0.0 for atoms not in the specified
compute group.
[Output info:]
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
output options.
The per-atom vector values will be a number >= 0.0, as explained
above.
[Restrictions:]
-This compute is part of the "peri" package. It is only enabled if
+This compute is part of the PERI package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"dump custom"_dump.html
[Default:] none
diff --git a/doc/compute_event_displace.html b/doc/compute_event_displace.html
index 66a3d841c..ae63a96bb 100644
--- a/doc/compute_event_displace.html
+++ b/doc/compute_event_displace.html
@@ -1,67 +1,67 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute event/displace command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID event/displace threshold
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>event/displace = style name of this compute command
<LI>threshold = minimum distance anyparticle must move to trigger an event (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all event/displace 0.5
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that flags an "event" if any particle in the
group has moved a distance greater than the specified threshold
distance when compared to a previously stored reference state
(i.e. the previous event). This compute is typically used in
conjunction with the <A HREF = "prd.html">prd</A> and <A HREF = "tad.html">tad</A> commands,
to detect if a transition
to a new minimum energy basin has occurred.
</P>
<P>This value calculated by the compute is equal to 0 if no particle has
moved far enough, and equal to 1 if one or more particles have moved
further than the threshold distance.
</P>
<P>NOTE: If the system is undergoing significant center-of-mass motion,
due to thermal motion, an external force, or an initial net momentum,
then this compute will not be able to distinguish that motion from
local atom displacements and may generate "false postives."
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the flag). This value can be
used by any command that uses a global scalar value from a compute as
input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
of LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "intensive". The
scalar value will be a 0 or 1 as explained above.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This command can only be used if LAMMPS was built with the "replica"
+<P>This command can only be used if LAMMPS was built with the REPLICA
package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "prd.html">prd</A>, <A HREF = "tad.html">tad</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/compute_event_displace.txt b/doc/compute_event_displace.txt
index 2b84eafab..7b26d3120 100644
--- a/doc/compute_event_displace.txt
+++ b/doc/compute_event_displace.txt
@@ -1,62 +1,62 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute event/displace command :h3
[Syntax:]
compute ID group-ID event/displace threshold :pre
ID, group-ID are documented in "compute"_compute.html command
event/displace = style name of this compute command
threshold = minimum distance anyparticle must move to trigger an event (distance units) :ul
[Examples:]
compute 1 all event/displace 0.5 :pre
[Description:]
Define a computation that flags an "event" if any particle in the
group has moved a distance greater than the specified threshold
distance when compared to a previously stored reference state
(i.e. the previous event). This compute is typically used in
conjunction with the "prd"_prd.html and "tad"_tad.html commands,
to detect if a transition
to a new minimum energy basin has occurred.
This value calculated by the compute is equal to 0 if no particle has
moved far enough, and equal to 1 if one or more particles have moved
further than the threshold distance.
NOTE: If the system is undergoing significant center-of-mass motion,
due to thermal motion, an external force, or an initial net momentum,
then this compute will not be able to distinguish that motion from
local atom displacements and may generate "false postives."
[Output info:]
This compute calculates a global scalar (the flag). This value can be
used by any command that uses a global scalar value from a compute as
input. See "this section"_Section_howto.html#howto_15 for an overview
of LAMMPS output options.
The scalar value calculated by this compute is "intensive". The
scalar value will be a 0 or 1 as explained above.
[Restrictions:]
-This command can only be used if LAMMPS was built with the "replica"
+This command can only be used if LAMMPS was built with the REPLICA
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info on packages.
[Related commands:]
"prd"_prd.html, "tad"_tad.html
[Default:] none
diff --git a/doc/compute_ke_atom_eff.html b/doc/compute_ke_atom_eff.html
index 4bd6b6f95..19ffb3f77 100644
--- a/doc/compute_ke_atom_eff.html
+++ b/doc/compute_ke_atom_eff.html
@@ -1,82 +1,82 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute ke/atom/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID ke/atom/eff
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>ke/atom/eff = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all ke/atom/eff
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the per-atom translational
(nuclei and electrons) and radial kinetic energy (electron only) in a
group. The particles are assumed to be nuclei and electrons modeled
with the <A HREF = "pair_eff.html">electronic force field</A>.
</P>
<P>The kinetic energy for each nucleus is computed as 1/2 m v^2, where m
corresponds to the corresponding nuclear mass, and the kinetic energy
for each electron is computed as 1/2 (me v^2 + 3/4 me s^2), where me
and v correspond to the mass and translational velocity of each
electron, and s to its radial velocity, respectively.
</P>
<P>There is a subtle difference between the quantity calculated by this
compute and the kinetic energy calculated by the <I>ke</I> or <I>etotal</I>
keyword used in thermodynamic output, as specified by the
<A HREF = "thermo_style.html">thermo_style</A> command. For this compute, kinetic
energy is "translational" plus electronic "radial" kinetic energy,
calculated by the simple formula above. For thermodynamic output, the
<I>ke</I> keyword infers kinetic energy from the temperature of the system
with 1/2 Kb T of energy for each (nuclear-only) degree of freedom in
eFF.
</P>
<P>IMPORTANT NOTE: The temperature in eFF should be monitored via the
<A HREF = "compute_temp_eff.html">compute temp/eff</A> command, which can be printed
with thermodynamic output by using the
<A HREF = "thermo_modify.html">thermo_modify</A> command, as shown in the following
example:
</P>
<PRE>compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp
</PRE>
<P>The value of the kinetic energy will be 0.0 for atoms (nuclei or
electrons) not in the specified compute group.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom computes as input. See
<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
output options.
</P>
<P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This compute is part of the "user-eff" package. It is only enabled if
+<P>This compute is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dump.html">dump custom</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/compute_ke_atom_eff.txt b/doc/compute_ke_atom_eff.txt
index cb69fc5a8..00c32be62 100644
--- a/doc/compute_ke_atom_eff.txt
+++ b/doc/compute_ke_atom_eff.txt
@@ -1,77 +1,77 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute ke/atom/eff command :h3
[Syntax:]
compute ID group-ID ke/atom/eff :pre
ID, group-ID are documented in "compute"_compute.html command
ke/atom/eff = style name of this compute command :ul
[Examples:]
compute 1 all ke/atom/eff :pre
[Description:]
Define a computation that calculates the per-atom translational
(nuclei and electrons) and radial kinetic energy (electron only) in a
group. The particles are assumed to be nuclei and electrons modeled
with the "electronic force field"_pair_eff.html.
The kinetic energy for each nucleus is computed as 1/2 m v^2, where m
corresponds to the corresponding nuclear mass, and the kinetic energy
for each electron is computed as 1/2 (me v^2 + 3/4 me s^2), where me
and v correspond to the mass and translational velocity of each
electron, and s to its radial velocity, respectively.
There is a subtle difference between the quantity calculated by this
compute and the kinetic energy calculated by the {ke} or {etotal}
keyword used in thermodynamic output, as specified by the
"thermo_style"_thermo_style.html command. For this compute, kinetic
energy is "translational" plus electronic "radial" kinetic energy,
calculated by the simple formula above. For thermodynamic output, the
{ke} keyword infers kinetic energy from the temperature of the system
with 1/2 Kb T of energy for each (nuclear-only) degree of freedom in
eFF.
IMPORTANT NOTE: The temperature in eFF should be monitored via the
"compute temp/eff"_compute_temp_eff.html command, which can be printed
with thermodynamic output by using the
"thermo_modify"_thermo_modify.html command, as shown in the following
example:
compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp :pre
The value of the kinetic energy will be 0.0 for atoms (nuclei or
electrons) not in the specified compute group.
[Output info:]
This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom computes as input. See
"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
output options.
The per-atom vector values will be in energy "units"_units.html.
[Restrictions:]
-This compute is part of the "user-eff" package. It is only enabled if
+This compute is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"dump custom"_dump.html
[Default:] none
diff --git a/doc/compute_ke_eff.html b/doc/compute_ke_eff.html
index 3b0d55b2d..2fa318f8a 100644
--- a/doc/compute_ke_eff.html
+++ b/doc/compute_ke_eff.html
@@ -1,83 +1,83 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute ke/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID ke/eff
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>ke/eff = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all ke/eff
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the kinetic energy of motion of a
group of eFF particles (nuclei and electrons), as modeled with the
<A HREF = "pair_eff.html">electronic force field</A>.
</P>
<P>The kinetic energy for each nucleus is computed as 1/2 m v^2 and the
kinetic energy for each electron is computed as 1/2(me v^2 + 3/4 me
s^2), where m corresponds to the nuclear mass, me to the electron
mass, v to the translational velocity of each particle, and s to the
radial velocity of the electron, respectively.
</P>
<P>There is a subtle difference between the quantity calculated by this
compute and the kinetic energy calculated by the <I>ke</I> or <I>etotal</I>
keyword used in thermodynamic output, as specified by the
<A HREF = "thermo_style.html">thermo_style</A> command. For this compute, kinetic
energy is "translational" and "radial" (only for electrons) kinetic
energy, calculated by the simple formula above. For thermodynamic
output, the <I>ke</I> keyword infers kinetic energy from the temperature of
the system with 1/2 Kb T of energy for each degree of freedom. For
the eFF temperature computation via the <A HREF = "compute_temp_eff.html">compute
temp_eff</A> command, these are the same. But
different computes that calculate temperature can subtract out
different non-thermal components of velocity and/or include other
degrees of freedom.
</P>
<P>IMPRORTANT NOTE: The temperature in eFF models should be monitored via
the <A HREF = "compute_temp_eff.html">compute temp/eff</A> command, which can be
printed with thermodynamic output by using the
<A HREF = "thermo_modify.html">thermo_modify</A> command, as shown in the following
example:
</P>
<PRE>compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp
</PRE>
<P>See <A HREF = "compute_temp_eff.html">compute temp/eff</A>.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
of LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "extensive". The
scalar value will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This compute is part of the "user-eff" package. It is only enabled if
+<P>This compute is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/compute_ke_eff.txt b/doc/compute_ke_eff.txt
index e5c0216db..2ebe435df 100644
--- a/doc/compute_ke_eff.txt
+++ b/doc/compute_ke_eff.txt
@@ -1,78 +1,78 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute ke/eff command :h3
[Syntax:]
compute ID group-ID ke/eff :pre
ID, group-ID are documented in "compute"_compute.html command
ke/eff = style name of this compute command :ul
[Examples:]
compute 1 all ke/eff :pre
[Description:]
Define a computation that calculates the kinetic energy of motion of a
group of eFF particles (nuclei and electrons), as modeled with the
"electronic force field"_pair_eff.html.
The kinetic energy for each nucleus is computed as 1/2 m v^2 and the
kinetic energy for each electron is computed as 1/2(me v^2 + 3/4 me
s^2), where m corresponds to the nuclear mass, me to the electron
mass, v to the translational velocity of each particle, and s to the
radial velocity of the electron, respectively.
There is a subtle difference between the quantity calculated by this
compute and the kinetic energy calculated by the {ke} or {etotal}
keyword used in thermodynamic output, as specified by the
"thermo_style"_thermo_style.html command. For this compute, kinetic
energy is "translational" and "radial" (only for electrons) kinetic
energy, calculated by the simple formula above. For thermodynamic
output, the {ke} keyword infers kinetic energy from the temperature of
the system with 1/2 Kb T of energy for each degree of freedom. For
the eFF temperature computation via the "compute
temp_eff"_compute_temp_eff.html command, these are the same. But
different computes that calculate temperature can subtract out
different non-thermal components of velocity and/or include other
degrees of freedom.
IMPRORTANT NOTE: The temperature in eFF models should be monitored via
the "compute temp/eff"_compute_temp_eff.html command, which can be
printed with thermodynamic output by using the
"thermo_modify"_thermo_modify.html command, as shown in the following
example:
compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp :pre
See "compute temp/eff"_compute_temp_eff.html.
[Output info:]
This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See "this section"_Section_howto.html#howto_15 for an overview
of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy "units"_units.html.
[Restrictions:]
-This compute is part of the "user-eff" package. It is only enabled if
+This compute is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:] none
[Default:] none
diff --git a/doc/compute_damage_atom.html b/doc/compute_meso_e_atom.html
similarity index 50%
copy from doc/compute_damage_atom.html
copy to doc/compute_meso_e_atom.html
index b15291a14..69d903799 100644
--- a/doc/compute_damage_atom.html
+++ b/doc/compute_meso_e_atom.html
@@ -1,58 +1,61 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
-<H3>compute damage/atom command
+<H3>compute meso_e/atom command
</H3>
<P><B>Syntax:</B>
</P>
-<PRE>compute ID group-ID damage/atom
+<PRE>compute ID group-ID meso_e/atom
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
-<LI>damage/atom = style name of this compute command
+<LI>meso_e/atom = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
-<PRE>compute 1 all damage/atom
+<PRE>compute 1 all meso_e/atom
</PRE>
<P><B>Description:</B>
</P>
-<P>Define a computation that calculates the per-atom damage for each atom
-in a group. Please see the <A HREF = "http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf">PDLAMMPS user
-guide</A> for a formal
-definition of "damage" and more details about Peridynamics as it is
-implemented in LAMMPS.
+<P>Define a computation that calculates the per-atom internal energy
+for each atom in a group.
</P>
-<P>The value of the damage will be 0.0 for atoms not in the specified
-compute group.
+<P>The internal energy is the energy associated with the internal degrees
+of freedom of a mesoscopic particles, e.g. a Smooth-Particle
+Hydrodynamics particle.
+</P>
+<P>See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+LAMMPS.
+</P>
+<P>The value of the internal energy will be 0.0 for atoms not in the
+specified compute group.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
+<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
output options.
</P>
-<P>The per-atom vector values will be a number >= 0.0, as explained
-above.
+<P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This compute is part of the "peri" package. It is only enabled if
+<P>This compute is part of the USER-SPH package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dump.html">dump custom</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/compute_meso_e_atom.txt b/doc/compute_meso_e_atom.txt
new file mode 100644
index 000000000..b85115da4
--- /dev/null
+++ b/doc/compute_meso_e_atom.txt
@@ -0,0 +1,56 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute meso_e/atom command :h3
+
+[Syntax:]
+
+compute ID group-ID meso_e/atom :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+meso_e/atom = style name of this compute command :ul
+
+[Examples:]
+
+compute 1 all meso_e/atom :pre
+
+[Description:]
+
+Define a computation that calculates the per-atom internal energy
+for each atom in a group.
+
+The internal energy is the energy associated with the internal degrees
+of freedom of a mesoscopic particles, e.g. a Smooth-Particle
+Hydrodynamics particle.
+
+See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in
+LAMMPS.
+
+The value of the internal energy will be 0.0 for atoms not in the
+specified compute group.
+
+[Output info:]
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+"this section"_Section_howto.html#4_15 for an overview of LAMMPS
+output options.
+
+The per-atom vector values will be in energy "units"_units.html.
+
+[Restrictions:]
+
+This compute is part of the USER-SPH package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"dump custom"_dump.html
+
+[Default:] none
diff --git a/doc/compute_damage_atom.html b/doc/compute_meso_rho_atom.html
similarity index 50%
copy from doc/compute_damage_atom.html
copy to doc/compute_meso_rho_atom.html
index b15291a14..202be3573 100644
--- a/doc/compute_damage_atom.html
+++ b/doc/compute_meso_rho_atom.html
@@ -1,58 +1,61 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
-<H3>compute damage/atom command
+<H3>compute meso_rho/atom command
</H3>
<P><B>Syntax:</B>
</P>
-<PRE>compute ID group-ID damage/atom
+<PRE>compute ID group-ID meso_rho/atom
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
-<LI>damage/atom = style name of this compute command
+<LI>meso_rho/atom = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
-<PRE>compute 1 all damage/atom
+<PRE>compute 1 all meso_rho/atom
</PRE>
<P><B>Description:</B>
</P>
-<P>Define a computation that calculates the per-atom damage for each atom
-in a group. Please see the <A HREF = "http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf">PDLAMMPS user
-guide</A> for a formal
-definition of "damage" and more details about Peridynamics as it is
-implemented in LAMMPS.
+<P>Define a computation that calculates the per-atom mesoscopic density
+for each atom in a group.
</P>
-<P>The value of the damage will be 0.0 for atoms not in the specified
-compute group.
+<P>The mesoscopic density is the mass density of a mesoscopic particle,
+calculated by kernel function interpolation using "pair style
+sph/rhosum".
+</P>
+<P>See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+LAMMPS.
+</P>
+<P>The value of the mesoscopic density will be 0.0 for atoms not in the
+specified compute group.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
-<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
+<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
output options.
</P>
-<P>The per-atom vector values will be a number >= 0.0, as explained
-above.
+<P>The per-atom vector values will be in mass/volume <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This compute is part of the "peri" package. It is only enabled if
+<P>This compute is part of the USER-SPH package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dump.html">dump custom</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/compute_meso_rho_atom.txt b/doc/compute_meso_rho_atom.txt
new file mode 100644
index 000000000..c09581864
--- /dev/null
+++ b/doc/compute_meso_rho_atom.txt
@@ -0,0 +1,56 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute meso_rho/atom command :h3
+
+[Syntax:]
+
+compute ID group-ID meso_rho/atom :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+meso_rho/atom = style name of this compute command :ul
+
+[Examples:]
+
+compute 1 all meso_rho/atom :pre
+
+[Description:]
+
+Define a computation that calculates the per-atom mesoscopic density
+for each atom in a group.
+
+The mesoscopic density is the mass density of a mesoscopic particle,
+calculated by kernel function interpolation using "pair style
+sph/rhosum".
+
+See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in
+LAMMPS.
+
+The value of the mesoscopic density will be 0.0 for atoms not in the
+specified compute group.
+
+[Output info:]
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+"this section"_Section_howto.html#4_15 for an overview of LAMMPS
+output options.
+
+The per-atom vector values will be in mass/volume "units"_units.html.
+
+[Restrictions:]
+
+This compute is part of the USER-SPH package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"dump custom"_dump.html
+
+[Default:] none
diff --git a/doc/compute_meso_t_atom.html b/doc/compute_meso_t_atom.html
new file mode 100644
index 000000000..dc41ea8d3
--- /dev/null
+++ b/doc/compute_meso_t_atom.html
@@ -0,0 +1,63 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute meso_t/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID meso_t/atom
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
+<LI>meso_t/atom = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all meso_t/atom
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the per-atom internal temperature
+for each atom in a group.
+</P>
+<P>The internal temperature is the ratio of internal energy over the heat
+capacity associated with the internal degrees of freedom of a mesoscopic
+particles, e.g. a Smooth-Particle Hydrodynamics particle.
+</P>
+<P>T_<I>int</I> = E_<I>int</I> / C_<I>V, int</I>
+</P>
+<P>See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+LAMMPS.
+</P>
+<P>The value of the internal energy will be 0.0 for atoms not in the
+specified compute group.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
+output options.
+</P>
+<P>The per-atom vector values will be in temperature <A HREF = "units.html">units</A>.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the USER-SPH package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "dump.html">dump custom</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/compute_meso_t_atom.txt b/doc/compute_meso_t_atom.txt
new file mode 100644
index 000000000..1d1a3a12a
--- /dev/null
+++ b/doc/compute_meso_t_atom.txt
@@ -0,0 +1,58 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute meso_t/atom command :h3
+
+[Syntax:]
+
+compute ID group-ID meso_t/atom :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+meso_t/atom = style name of this compute command :ul
+
+[Examples:]
+
+compute 1 all meso_t/atom :pre
+
+[Description:]
+
+Define a computation that calculates the per-atom internal temperature
+for each atom in a group.
+
+The internal temperature is the ratio of internal energy over the heat
+capacity associated with the internal degrees of freedom of a mesoscopic
+particles, e.g. a Smooth-Particle Hydrodynamics particle.
+
+T_{int} = E_{int} / C_{V, int}
+
+See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in
+LAMMPS.
+
+The value of the internal energy will be 0.0 for atoms not in the
+specified compute group.
+
+[Output info:]
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+"this section"_Section_howto.html#4_15 for an overview of LAMMPS
+output options.
+
+The per-atom vector values will be in temperature "units"_units.html.
+
+[Restrictions:]
+
+This compute is part of the USER-SPH package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"dump custom"_dump.html
+
+[Default:] none
diff --git a/doc/compute_pe.html b/doc/compute_pe.html
index f86c8d8bd..96a25eb42 100644
--- a/doc/compute_pe.html
+++ b/doc/compute_pe.html
@@ -1,100 +1,100 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute pe command
</H3>
<H3>compute pe/cuda command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID pe keyword ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>pe = style name of this compute command
<LI>zero or more keywords may be appended
<LI>keyword = <I>pair</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or <I>kspace</I>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all pe
compute molPE all pe bond angle dihedral improper
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the potential energy of the
entire system of atoms. The specified group must be "all". See the
<A HREF = "compute_pe_atom.html">compute pe/atom</A> command if you want per-atom
energies. These per-atom values could be summed for a group of atoms
via the <A HREF = "compute_reduce.html">compute reduce</A> command.
</P>
<P>The energy is calculated by the various pair, bond, etc potentials
defined for the simulation. If no extra keywords are listed, then the
potential energy is the sum of pair, bond, angle, dihedral, improper,
and kspace (long-range) energy. If any extra keywords are listed,
then only those components are summed to compute the potential energy.
</P>
<P>Various fixes can contribute to the total potential energy of the
system. See the doc pages for <A HREF = "fix.html">individual fixes</A> for
details. The <I>thermo</I> option of the
<A HREF = "compute_modify.html">compute_modify</A> command determines whether these
contributions are added into the computed potential energy. If no
keywords are specified the default is <I>yes</I>. If any keywords are
specified, the default is <I>no</I>.
</P>
<P>A compute of this style with the ID of "thermo_pe" is created when
LAMMPS starts up, as if this command were in the input script:
</P>
<PRE>compute thermo_pe all pe
</PRE>
<P>See the "thermo_style" command for more details.
</P>
<HR>
<P>Styles with a <I>cuda</I> suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
<A HREF = "Section_accelerate.html">this section</A> of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the potential energy). This
value can be used by any command that uses a global scalar value from
a compute as input. See <A HREF = "Section_howto.html#howto_15">this section</A>
for an overview of LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "extensive". The
scalar value will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_pe_atom.html">compute pe/atom</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/compute_pe.txt b/doc/compute_pe.txt
index 17d0cc0e2..46d54268e 100644
--- a/doc/compute_pe.txt
+++ b/doc/compute_pe.txt
@@ -1,94 +1,94 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute pe command :h3
compute pe/cuda command :h3
[Syntax:]
compute ID group-ID pe keyword ... :pre
ID, group-ID are documented in "compute"_compute.html command
pe = style name of this compute command
zero or more keywords may be appended
keyword = {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} :ul
[Examples:]
compute 1 all pe
compute molPE all pe bond angle dihedral improper :pre
[Description:]
Define a computation that calculates the potential energy of the
entire system of atoms. The specified group must be "all". See the
"compute pe/atom"_compute_pe_atom.html command if you want per-atom
energies. These per-atom values could be summed for a group of atoms
via the "compute reduce"_compute_reduce.html command.
The energy is calculated by the various pair, bond, etc potentials
defined for the simulation. If no extra keywords are listed, then the
potential energy is the sum of pair, bond, angle, dihedral, improper,
and kspace (long-range) energy. If any extra keywords are listed,
then only those components are summed to compute the potential energy.
Various fixes can contribute to the total potential energy of the
system. See the doc pages for "individual fixes"_fix.html for
details. The {thermo} option of the
"compute_modify"_compute_modify.html command determines whether these
contributions are added into the computed potential energy. If no
keywords are specified the default is {yes}. If any keywords are
specified, the default is {no}.
A compute of this style with the ID of "thermo_pe" is created when
LAMMPS starts up, as if this command were in the input script:
compute thermo_pe all pe :pre
See the "thermo_style" command for more details.
:line
Styles with a {cuda} suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
"this section"_Section_accelerate.html of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Output info:]
This compute calculates a global scalar (the potential energy). This
value can be used by any command that uses a global scalar value from
a compute as input. See "this section"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy "units"_units.html.
[Restrictions:] none
[Related commands:]
"compute pe/atom"_compute_pe_atom.html
[Default:] none
diff --git a/doc/compute_pressure.html b/doc/compute_pressure.html
index 95f7eeebc..53cc3132c 100644
--- a/doc/compute_pressure.html
+++ b/doc/compute_pressure.html
@@ -1,135 +1,135 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute pressure command
</H3>
<H3>compute pressure/cuda command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID pressure temp-ID keyword ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>pressure = style name of this compute command
<LI>temp-ID = ID of compute that calculates temperature
<LI>zero or more keywords may be appended
<LI>keyword = <I>ke</I> or <I>pair</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or <I>kspace</I> or <I>fix</I> or <I>virial</I>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all pressure myTemp
compute 1 all pressure thermo_temp pair bond
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the pressure of the entire system
of atoms. The specified group must be "all". See the <A HREF = "compute_stress_atom.html">compute
stress/atom</A> command if you want per-atom
pressure (stress). These per-atom values could be summed for a group
of atoms via the <A HREF = "compute_reduce.html">compute reduce</A> command.
</P>
<P>The pressure is computed by the formula
</P>
<CENTER><IMG SRC = "Eqs/pressure.jpg">
</CENTER>
<P>where N is the number of atoms in the system (see discussion of DOF
below), Kb is the Boltzmann constant, T is the temperature, d is the
dimensionality of the system (2 or 3 for 2d/3d), V is the system
volume (or area in 2d), and the second term is the virial, computed
within LAMMPS for all pairwise as well as 2-body, 3-body, and 4-body,
and long-range interactions. <A HREF = "fix.html">Fixes</A> that impose constraints
(e.g. the <A HREF = "fix_shake.html">fix shake</A> command) also contribute to the
virial term.
</P>
<P>A symmetric pressure tensor, stored as a 6-element vector, is also
calculated by this compute. The 6 components of the vector are
ordered xx, yy, zz, xy, xz, yz. The equation for the I,J components
(where I and J = x,y,z) is similar to the above formula, except that
the first term uses components of the kinetic energy tensor and the
second term uses components of the virial tensor:
</P>
<CENTER><IMG SRC = "Eqs/pressure_tensor.jpg">
</CENTER>
<P>If no extra keywords are listed, the entire equations above are
calculated which include a kinetic energy (temperature) term and the
virial as the sum of pair, bond, angle, dihedral, improper, kspace
(long-range), and fix contributions to the force on each atom. If any
extra keywords are listed, then only those components are summed to
compute temperature or ke and/or the virial. The <I>virial</I> keyword
means include all terms except the kinetic energy <I>ke</I>.
</P>
<P>The temperature and kinetic energy tensor is not calculated by this
compute, but rather by the temperature compute specified with the
command. Normally this compute should calculate the temperature of
all atoms for consistency with the virial term, but any compute style
that calculates temperature can be used, e.g. one that excludes frozen
atoms or other degrees of freedom.
</P>
<P>Note that the N in the first formula above is really
degrees-of-freedom divided by d = dimensionality, where the DOF value
is calcluated by the temperature compute. See the various <A HREF = "compute.html">compute
temperature</A> styles for details.
</P>
<P>A compute of this style with the ID of "thermo_press" is created when
LAMMPS starts up, as if this command were in the input script:
</P>
<PRE>compute thermo_press all pressure thermo_temp
</PRE>
<P>where "thermo_temp" is the ID of a similarly defined compute of style
"temp". See the "thermo_style" command for more details.
</P>
<HR>
<P>Styles with a <I>cuda</I> suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
<A HREF = "Section_accelerate.html">this section</A> of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the pressure) and a global
vector of length 6 (pressure tensor), which can be accessed by indices
1-6. These values can be used by any command that uses global scalar
or vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The scalar and vector values calculated by this compute are
"intensive". The scalar and vector values will be in pressure
<A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_stress_atom.html">compute
stress/atom</A>,
<A HREF = "thermo_style.html">thermo_style</A>,
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/compute_pressure.txt b/doc/compute_pressure.txt
index c8dafd229..28d77dd17 100644
--- a/doc/compute_pressure.txt
+++ b/doc/compute_pressure.txt
@@ -1,129 +1,129 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute pressure command :h3
compute pressure/cuda command :h3
[Syntax:]
compute ID group-ID pressure temp-ID keyword ... :pre
ID, group-ID are documented in "compute"_compute.html command
pressure = style name of this compute command
temp-ID = ID of compute that calculates temperature
zero or more keywords may be appended
keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} :ul
[Examples:]
compute 1 all pressure myTemp
compute 1 all pressure thermo_temp pair bond :pre
[Description:]
Define a computation that calculates the pressure of the entire system
of atoms. The specified group must be "all". See the "compute
stress/atom"_compute_stress_atom.html command if you want per-atom
pressure (stress). These per-atom values could be summed for a group
of atoms via the "compute reduce"_compute_reduce.html command.
The pressure is computed by the formula
:c,image(Eqs/pressure.jpg)
where N is the number of atoms in the system (see discussion of DOF
below), Kb is the Boltzmann constant, T is the temperature, d is the
dimensionality of the system (2 or 3 for 2d/3d), V is the system
volume (or area in 2d), and the second term is the virial, computed
within LAMMPS for all pairwise as well as 2-body, 3-body, and 4-body,
and long-range interactions. "Fixes"_fix.html that impose constraints
(e.g. the "fix shake"_fix_shake.html command) also contribute to the
virial term.
A symmetric pressure tensor, stored as a 6-element vector, is also
calculated by this compute. The 6 components of the vector are
ordered xx, yy, zz, xy, xz, yz. The equation for the I,J components
(where I and J = x,y,z) is similar to the above formula, except that
the first term uses components of the kinetic energy tensor and the
second term uses components of the virial tensor:
:c,image(Eqs/pressure_tensor.jpg)
If no extra keywords are listed, the entire equations above are
calculated which include a kinetic energy (temperature) term and the
virial as the sum of pair, bond, angle, dihedral, improper, kspace
(long-range), and fix contributions to the force on each atom. If any
extra keywords are listed, then only those components are summed to
compute temperature or ke and/or the virial. The {virial} keyword
means include all terms except the kinetic energy {ke}.
The temperature and kinetic energy tensor is not calculated by this
compute, but rather by the temperature compute specified with the
command. Normally this compute should calculate the temperature of
all atoms for consistency with the virial term, but any compute style
that calculates temperature can be used, e.g. one that excludes frozen
atoms or other degrees of freedom.
Note that the N in the first formula above is really
degrees-of-freedom divided by d = dimensionality, where the DOF value
is calcluated by the temperature compute. See the various "compute
temperature"_compute.html styles for details.
A compute of this style with the ID of "thermo_press" is created when
LAMMPS starts up, as if this command were in the input script:
compute thermo_press all pressure thermo_temp :pre
where "thermo_temp" is the ID of a similarly defined compute of style
"temp". See the "thermo_style" command for more details.
:line
Styles with a {cuda} suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
"this section"_Section_accelerate.html of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Output info:]
This compute calculates a global scalar (the pressure) and a global
vector of length 6 (pressure tensor), which can be accessed by indices
1-6. These values can be used by any command that uses global scalar
or vector values from a compute as input. See "this
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The scalar and vector values calculated by this compute are
"intensive". The scalar and vector values will be in pressure
"units"_units.html.
[Restrictions:] none
[Related commands:]
"compute temp"_compute_temp.html, "compute
stress/atom"_compute_stress_atom.html,
"thermo_style"_thermo_style.html,
[Default:] none
diff --git a/doc/compute_temp.html b/doc/compute_temp.html
index d93a945e1..6005da58d 100644
--- a/doc/compute_temp.html
+++ b/doc/compute_temp.html
@@ -1,117 +1,117 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute temp command
</H3>
<H3>compute temp/cuda command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID temp
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>temp = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all temp
compute myTemp mobile temp
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the temperature of a group of
atoms. A compute of this style can be used by any command that
computes a temperature, e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, <A HREF = "fix_nh.html">fix npt</A>, etc.
</P>
<P>The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
in the group, k = Boltzmann constant, and T = temperature.
</P>
<P>A kinetic energy tensor, stored as a 6-element vector, is also
calculated by this compute for use in the computation of a pressure
tensor. The formula for the components of the tensor is the same as
the above formula, except that v^2 is replaced by vx*vy for the xy
component, etc. The 6 components of the vector are ordered xx, yy,
zz, xy, xz, yz.
</P>
<P>The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the <I>dynamic</I> option of the
<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
</P>
<P>This compute subtracts out degrees-of-freedom due to fixes that
constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
<A HREF = "fix_rigid.html">fix rigid</A>. This means the temperature of groups of
atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
</P>
<P>A compute of this style with the ID of "thermo_temp" is created when
LAMMPS starts up, as if this command were in the input script:
</P>
<PRE>compute thermo_temp all temp
</PRE>
<P>See the "thermo_style" command for more details.
</P>
<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
a discussion of different ways to compute temperature and perform
thermostatting.
</P>
<HR>
<P>Styles with a <I>cuda</I> suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
<A HREF = "Section_accelerate.html">this section</A> of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The scalar value calculated by this compute is "intensive". The
vector are "extensive".
</P>
<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
vector values will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_temp_partial.html">compute temp/partial</A>, <A HREF = "compute_temp_region.html">compute
temp/region</A>, <A HREF = "compute_pressure.html">compute
pressure</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/compute_temp.txt b/doc/compute_temp.txt
index 3ead16aca..7915e8683 100644
--- a/doc/compute_temp.txt
+++ b/doc/compute_temp.txt
@@ -1,111 +1,111 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute temp command :h3
compute temp/cuda command :h3
[Syntax:]
compute ID group-ID temp :pre
ID, group-ID are documented in "compute"_compute.html command
temp = style name of this compute command :ul
[Examples:]
compute 1 all temp
compute myTemp mobile temp :pre
[Description:]
Define a computation that calculates the temperature of a group of
atoms. A compute of this style can be used by any command that
computes a temperature, e.g. "thermo_modify"_thermo_modify.html, "fix
temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_nh.html, etc.
The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
in the group, k = Boltzmann constant, and T = temperature.
A kinetic energy tensor, stored as a 6-element vector, is also
calculated by this compute for use in the computation of a pressure
tensor. The formula for the components of the tensor is the same as
the above formula, except that v^2 is replaced by vx*vy for the xy
component, etc. The 6 components of the vector are ordered xx, yy,
zz, xy, xz, yz.
The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the {dynamic} option of the
"compute_modify"_compute_modify.html command if this is not the case.
This compute subtracts out degrees-of-freedom due to fixes that
constrain molecular motion, such as "fix shake"_fix_shake.html and
"fix rigid"_fix_rigid.html. This means the temperature of groups of
atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
{extra} option of the "compute_modify"_compute_modify.html command.
A compute of this style with the ID of "thermo_temp" is created when
LAMMPS starts up, as if this command were in the input script:
compute thermo_temp all temp :pre
See the "thermo_style" command for more details.
See "this howto section"_Section_howto.html#howto_16 of the manual for
a discussion of different ways to compute temperature and perform
thermostatting.
:line
Styles with a {cuda} suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
"this section"_Section_accelerate.html of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Output info:]
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See "this
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
vector are "extensive".
The scalar value will be in temperature "units"_units.html. The
vector values will be in energy "units"_units.html.
[Restrictions:] none
[Related commands:]
"compute temp/partial"_compute_temp_partial.html, "compute
temp/region"_compute_temp_region.html, "compute
pressure"_compute_pressure.html
[Default:] none
diff --git a/doc/compute_temp_asphere.html b/doc/compute_temp_asphere.html
index 64815209b..59b32f695 100644
--- a/doc/compute_temp_asphere.html
+++ b/doc/compute_temp_asphere.html
@@ -1,158 +1,158 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute temp/asphere command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID temp/asphere keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>temp/asphere = style name of this compute command
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>bias</I> or <I>dof</I>
<PRE> <I>bias</I> value = bias-ID<I>uniform</I> or <I>gaussian</I>
bias-ID = ID of a temperature compute that removes a velocity bias
<I>dof</I> value = <I>all</I> or <I>rotate</I>
all = compute temperature of translational and rotational degrees of freedom
rotate = compute temperature of just rotational degrees of freedom
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all temp/asphere
compute myTemp mobile temp/asphere bias tempCOM
compute myTemp mobile temp/asphere dof rotate
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the temperature of a group of
aspherical particles, including a contribution from both their
translational and rotational kinetic energy. This differs from the
usual <A HREF = "compute_temp.html">compute temp</A> command, which assumes point
particles with only translational kinetic energy.
</P>
<P>Only finite-size particles (aspherical or spherical) can be included
in the group. For 3d finite-size particles, each has 6 degrees of
freedom (3 translational, 3 rotational). For 2d finite-size
particles, each has 3 degrees of freedom (2 translational, 1
rotational).
</P>
<P>IMPORTANT NOTE: This choice for degrees of freedom (dof) assumes that
all finite-size aspherical or spherical particles in your model will
freely rotate, sampling all their rotational dof. It is possible to
use a combination of interaction potentials and fixes that induce no
torque or otherwise constrain some of all of your particles so that
this is not the case. Then there are less dof and you should use the
<A HREF = "compute_modify.html">compute_modify extra</A> command to adjust the dof
accordingly.
</P>
<P>For example, an aspherical particle with all three of its shape
parameters the same is a sphere. If it does not rotate, then it
should have 3 dof instead of 6 in 3d (or 2 instead of 3 in 2d). A
uniaxial aspherical particle has two of its three shape parameters the
same. If it does not rotate around the axis perpendicular to its
circular cross section, then it should have 5 dof instead of 6 in 3d.
</P>
<P>The translational kinetic energy is computed the same as is described
by the <A HREF = "compute_temp.html">compute temp</A> command. The rotational
kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor
for the aspherical particle and w is its angular velocity, which is
computed from its angular momentum.
</P>
<P>IMPORTANT NOTE: For <A HREF = "dimension.html">2d models</A>, particles are treated
as ellipsoids, not ellipses, meaning their moments of inertia will be
the same as in 3d.
</P>
<P>A kinetic energy tensor, stored as a 6-element vector, is also
calculated by this compute. The formula for the components of the
tensor is the same as the above formula, except that v^2 and w^2 are
replaced by vx*vy and wx*wy for the xy component, and the appropriate
elements of the inertia tensor are used. The 6 components of the
vector are ordered xx, yy, zz, xy, xz, yz.
</P>
<P>The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the <I>dynamic</I> option of the
<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
</P>
<P>This compute subtracts out translational degrees-of-freedom due to
fixes that constrain molecular motion, such as <A HREF = "fix_shake.html">fix
shake</A> and <A HREF = "fix_rigid.html">fix rigid</A>. This means the
temperature of groups of atoms that include these constraints will be
computed correctly. If needed, the subtracted degrees-of-freedom can
be altered using the <I>extra</I> option of the
<A HREF = "compute_modify.html">compute_modify</A> command.
</P>
<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
a discussion of different ways to compute temperature and perform
thermostatting.
</P>
<HR>
<P>The keyword/value option pairs are used in the following ways.
</P>
<P>For the <I>bias</I> keyword, <I>bias-ID</I> refers to the ID of a temperature
compute that removes a "bias" velocity from each atom. This allows
compute temp/sphere to compute its thermal temperature after the
translational kinetic energy components have been altered in a
prescribed way, e.g. to remove a velocity profile. Thermostats that
use this compute will work with this bias term. See the doc pages for
individual computes that calculate a temperature and the doc pages for
fixes that perform thermostatting for more details.
</P>
<P>For the <I>dof</I> keyword, a setting of <I>all</I> calculates a temperature
that includes both translational and rotational degrees of freedom. A
setting of <I>rotate</I> calculates a temperature that includes only
rotational degrees of freedom.
</P>
<HR>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
</P>
<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
vector values will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This compute is part of the "asphere" package. It is only enabled if
+<P>This compute is part of the ASPHERE package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>This compute requires that atoms store angular momementum and a
quaternion as defined by the <A HREF = "atom_style.html">atom_style ellipsoid</A>
command.
</P>
<P>All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical as defined by their
shape attribute.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_temp.html">compute temp</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/compute_temp_asphere.txt b/doc/compute_temp_asphere.txt
index 3be406ffb..019c1f72c 100755
--- a/doc/compute_temp_asphere.txt
+++ b/doc/compute_temp_asphere.txt
@@ -1,148 +1,148 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute temp/asphere command :h3
[Syntax:]
compute ID group-ID temp/asphere keyword value ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
temp/asphere = style name of this compute command :l
zero or more keyword/value pairs may be appended :l
keyword = {bias} or {dof} :l
{bias} value = bias-ID{uniform} or {gaussian}
bias-ID = ID of a temperature compute that removes a velocity bias
{dof} value = {all} or {rotate}
all = compute temperature of translational and rotational degrees of freedom
rotate = compute temperature of just rotational degrees of freedom :pre
:ule
[Examples:]
compute 1 all temp/asphere
compute myTemp mobile temp/asphere bias tempCOM
compute myTemp mobile temp/asphere dof rotate :pre
[Description:]
Define a computation that calculates the temperature of a group of
aspherical particles, including a contribution from both their
translational and rotational kinetic energy. This differs from the
usual "compute temp"_compute_temp.html command, which assumes point
particles with only translational kinetic energy.
Only finite-size particles (aspherical or spherical) can be included
in the group. For 3d finite-size particles, each has 6 degrees of
freedom (3 translational, 3 rotational). For 2d finite-size
particles, each has 3 degrees of freedom (2 translational, 1
rotational).
IMPORTANT NOTE: This choice for degrees of freedom (dof) assumes that
all finite-size aspherical or spherical particles in your model will
freely rotate, sampling all their rotational dof. It is possible to
use a combination of interaction potentials and fixes that induce no
torque or otherwise constrain some of all of your particles so that
this is not the case. Then there are less dof and you should use the
"compute_modify extra"_compute_modify.html command to adjust the dof
accordingly.
For example, an aspherical particle with all three of its shape
parameters the same is a sphere. If it does not rotate, then it
should have 3 dof instead of 6 in 3d (or 2 instead of 3 in 2d). A
uniaxial aspherical particle has two of its three shape parameters the
same. If it does not rotate around the axis perpendicular to its
circular cross section, then it should have 5 dof instead of 6 in 3d.
The translational kinetic energy is computed the same as is described
by the "compute temp"_compute_temp.html command. The rotational
kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor
for the aspherical particle and w is its angular velocity, which is
computed from its angular momentum.
IMPORTANT NOTE: For "2d models"_dimension.html, particles are treated
as ellipsoids, not ellipses, meaning their moments of inertia will be
the same as in 3d.
A kinetic energy tensor, stored as a 6-element vector, is also
calculated by this compute. The formula for the components of the
tensor is the same as the above formula, except that v^2 and w^2 are
replaced by vx*vy and wx*wy for the xy component, and the appropriate
elements of the inertia tensor are used. The 6 components of the
vector are ordered xx, yy, zz, xy, xz, yz.
The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the {dynamic} option of the
"compute_modify"_compute_modify.html command if this is not the case.
This compute subtracts out translational degrees-of-freedom due to
fixes that constrain molecular motion, such as "fix
shake"_fix_shake.html and "fix rigid"_fix_rigid.html. This means the
temperature of groups of atoms that include these constraints will be
computed correctly. If needed, the subtracted degrees-of-freedom can
be altered using the {extra} option of the
"compute_modify"_compute_modify.html command.
See "this howto section"_Section_howto.html#howto_16 of the manual for
a discussion of different ways to compute temperature and perform
thermostatting.
:line
The keyword/value option pairs are used in the following ways.
For the {bias} keyword, {bias-ID} refers to the ID of a temperature
compute that removes a "bias" velocity from each atom. This allows
compute temp/sphere to compute its thermal temperature after the
translational kinetic energy components have been altered in a
prescribed way, e.g. to remove a velocity profile. Thermostats that
use this compute will work with this bias term. See the doc pages for
individual computes that calculate a temperature and the doc pages for
fixes that perform thermostatting for more details.
For the {dof} keyword, a setting of {all} calculates a temperature
that includes both translational and rotational degrees of freedom. A
setting of {rotate} calculates a temperature that includes only
rotational degrees of freedom.
:line
[Output info:]
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See "this
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature "units"_units.html. The
vector values will be in energy "units"_units.html.
[Restrictions:]
-This compute is part of the "asphere" package. It is only enabled if
+This compute is part of the ASPHERE package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
This compute requires that atoms store angular momementum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
command.
All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical as defined by their
shape attribute.
[Related commands:]
"compute temp"_compute_temp.html
[Default:] none
diff --git a/doc/compute_temp_deform_eff.html b/doc/compute_temp_deform_eff.html
index d36649219..6331c8e91 100644
--- a/doc/compute_temp_deform_eff.html
+++ b/doc/compute_temp_deform_eff.html
@@ -1,78 +1,78 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute temp/deform/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID temp/deform/eff
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>temp/deform/eff = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute myTemp all temp/deform/eff
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the temperature of a group of
nuclei and electrons in the <A HREF = "pair_eff.html">electron force field</A>
model, after subtracting out a streaming velocity induced by the
simulation box changing size and/or shape, for example in a
non-equilibrium MD (NEMD) simulation. The size/shape change is
induced by use of the <A HREF = "fix_deform_eff.html">fix deform/eff</A> command. A
compute of this style is created by the <A HREF = "fix_nvt_sllod_eff.html">fix
nvt/sllod/eff</A> command to compute the thermal
temperature of atoms for thermostatting purposes. A compute of this
style can also be used by any command that computes a temperature,
e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_nh.html">fix npt/eff</A>,
etc.
</P>
<P>The calculation performed by this compute is exactly like that
described by the <A HREF = "compute_temp_deform.html">compute temp/deform</A>
command, except that the formula for the temperature includes the
radial electron velocity contributions, as discussed by the <A HREF = "compute_temp_eff.html">compute
temp/eff</A> command. Note that only the
translational degrees of freedom for each nuclei or electron are
affected by the streaming velocity adjustment. The radial velocity
component of the electrons is not affected.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
</P>
<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
vector values will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This compute is part of the "user-eff" package. It is only enabled if
+<P>This compute is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_temp_ramp.html">compute temp/ramp</A>, <A HREF = "fix_deform_eff.html">fix
deform/eff</A>, <A HREF = "fix_nvt_sllod_eff.html">fix
nvt/sllod/eff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/compute_temp_deform_eff.txt b/doc/compute_temp_deform_eff.txt
index 3a0497e5b..199fa5fdc 100644
--- a/doc/compute_temp_deform_eff.txt
+++ b/doc/compute_temp_deform_eff.txt
@@ -1,73 +1,73 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute temp/deform/eff command :h3
[Syntax:]
compute ID group-ID temp/deform/eff :pre
ID, group-ID are documented in "compute"_compute.html command
temp/deform/eff = style name of this compute command :ul
[Examples:]
compute myTemp all temp/deform/eff :pre
[Description:]
Define a computation that calculates the temperature of a group of
nuclei and electrons in the "electron force field"_pair_eff.html
model, after subtracting out a streaming velocity induced by the
simulation box changing size and/or shape, for example in a
non-equilibrium MD (NEMD) simulation. The size/shape change is
induced by use of the "fix deform/eff"_fix_deform_eff.html command. A
compute of this style is created by the "fix
nvt/sllod/eff"_fix_nvt_sllod_eff.html command to compute the thermal
temperature of atoms for thermostatting purposes. A compute of this
style can also be used by any command that computes a temperature,
e.g. "thermo_modify"_thermo_modify.html, "fix npt/eff"_fix_nh.html,
etc.
The calculation performed by this compute is exactly like that
described by the "compute temp/deform"_compute_temp_deform.html
command, except that the formula for the temperature includes the
radial electron velocity contributions, as discussed by the "compute
temp/eff"_compute_temp_eff.html command. Note that only the
translational degrees of freedom for each nuclei or electron are
affected by the streaming velocity adjustment. The radial velocity
component of the electrons is not affected.
[Output info:]
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See "this
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature "units"_units.html. The
vector values will be in energy "units"_units.html.
[Restrictions:]
-This compute is part of the "user-eff" package. It is only enabled if
+This compute is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"compute temp/ramp"_compute_temp_ramp.html, "fix
deform/eff"_fix_deform_eff.html, "fix
nvt/sllod/eff"_fix_nvt_sllod_eff.html
[Default:] none
diff --git a/doc/compute_temp_eff.html b/doc/compute_temp_eff.html
index bdb8a4ee7..3cc20e9db 100644
--- a/doc/compute_temp_eff.html
+++ b/doc/compute_temp_eff.html
@@ -1,100 +1,100 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute temp/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID temp/eff
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>temp/eff = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all temp/eff
compute myTemp mobile temp/eff
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the temperature of a group of
nuclei and electrons in the <A HREF = "pair_eff.html">electron force field</A>
model. A compute of this style can be used by commands that compute a
temperature, e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_npt_eff.html">fix
npt/eff</A>, etc.
</P>
<P>The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2 for
nuclei and sum of 1/2 (m v^2 + 3/4 m s^2) for electrons, where s
includes the radial electron velocity contributions), dim = 2 or 3 =
dimensionality of the simulation, N = number of atoms (only total
number of nuclei in the eFF (see the <A HREF = "pair_style.html">pair_eff</A>
command) in the group, k = Boltzmann constant, and T = temperature.
This expression is summed over all nuclear and electronic degrees of
freedom, essentially by setting the kinetic contribution to the heat
capacity to 3/2k (where only nuclei contribute). This subtlety is
valid for temperatures well below the Fermi temperature, which for
densities two to five times the density of liquid H2 ranges from
86,000 to 170,000 K.
</P>
<P>IMPORTANT NOTE: For eFF models, in order to override the default
temperature reported by LAMMPS in the thermodynamic quantities
reported via the <A HREF = "thermo.html">thermo</A> command, the user should apply a
<A HREF = "thermo_modify.html">thermo_modify</A> command, as shown in the following
example:
</P>
<PRE>compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp
</PRE>
<P>A 6-component kinetic energy tensor is also calculated by this compute
for use in the computation of a pressure tensor. The formula for the
components of the tensor is the same as the above formula, except that
v^2 is replaced by vx * vy for the xy component, etc. For the eFF,
again, the radial electronic velocities are also considered.
</P>
<P>The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the <I>dynamic</I> option of the
<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
</P>
<P>This compute subtracts out degrees-of-freedom due to fixes that
constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
<A HREF = "fix_rigid.html">fix rigid</A>. This means the temperature of groups of
atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
</P>
<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
a discussion of different ways to compute temperature and perform
thermostatting.
</P>
<P><B>Output info:</B>
</P>
<P>The scalar value calculated by this compute is "intensive", meaning it
is independent of the number of atoms in the simulation. The vector
values are "extensive", meaning they scale with the number of atoms in
the simulation.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This compute is part of the "user-eff" package. It is only enabled if
+<P>This compute is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_temp_partial.html">compute temp/partial</A>, <A HREF = "compute_temp_region.html">compute
temp/region</A>, <A HREF = "compute_pressure.html">compute
pressure</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/compute_temp_eff.txt b/doc/compute_temp_eff.txt
index a83ee8b61..194aaa3c7 100644
--- a/doc/compute_temp_eff.txt
+++ b/doc/compute_temp_eff.txt
@@ -1,95 +1,95 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute temp/eff command :h3
[Syntax:]
compute ID group-ID temp/eff :pre
ID, group-ID are documented in "compute"_compute.html command
temp/eff = style name of this compute command :ul
[Examples:]
compute 1 all temp/eff
compute myTemp mobile temp/eff :pre
[Description:]
Define a computation that calculates the temperature of a group of
nuclei and electrons in the "electron force field"_pair_eff.html
model. A compute of this style can be used by commands that compute a
temperature, e.g. "thermo_modify"_thermo_modify.html, "fix
npt/eff"_fix_npt_eff.html, etc.
The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2 for
nuclei and sum of 1/2 (m v^2 + 3/4 m s^2) for electrons, where s
includes the radial electron velocity contributions), dim = 2 or 3 =
dimensionality of the simulation, N = number of atoms (only total
number of nuclei in the eFF (see the "pair_eff"_pair_style.html
command) in the group, k = Boltzmann constant, and T = temperature.
This expression is summed over all nuclear and electronic degrees of
freedom, essentially by setting the kinetic contribution to the heat
capacity to 3/2k (where only nuclei contribute). This subtlety is
valid for temperatures well below the Fermi temperature, which for
densities two to five times the density of liquid H2 ranges from
86,000 to 170,000 K.
IMPORTANT NOTE: For eFF models, in order to override the default
temperature reported by LAMMPS in the thermodynamic quantities
reported via the "thermo"_thermo.html command, the user should apply a
"thermo_modify"_thermo_modify.html command, as shown in the following
example:
compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp :pre
A 6-component kinetic energy tensor is also calculated by this compute
for use in the computation of a pressure tensor. The formula for the
components of the tensor is the same as the above formula, except that
v^2 is replaced by vx * vy for the xy component, etc. For the eFF,
again, the radial electronic velocities are also considered.
The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the {dynamic} option of the
"compute_modify"_compute_modify.html command if this is not the case.
This compute subtracts out degrees-of-freedom due to fixes that
constrain molecular motion, such as "fix shake"_fix_shake.html and
"fix rigid"_fix_rigid.html. This means the temperature of groups of
atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
{extra} option of the "compute_modify"_compute_modify.html command.
See "this howto section"_Section_howto.html#howto_16 of the manual for
a discussion of different ways to compute temperature and perform
thermostatting.
[Output info:]
The scalar value calculated by this compute is "intensive", meaning it
is independent of the number of atoms in the simulation. The vector
values are "extensive", meaning they scale with the number of atoms in
the simulation.
[Restrictions:]
-This compute is part of the "user-eff" package. It is only enabled if
+This compute is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"compute temp/partial"_compute_temp_partial.html, "compute
temp/region"_compute_temp_region.html, "compute
pressure"_compute_pressure.html
[Default:] none
diff --git a/doc/compute_temp_partial.html b/doc/compute_temp_partial.html
index 62529fcfb..c076a2be5 100644
--- a/doc/compute_temp_partial.html
+++ b/doc/compute_temp_partial.html
@@ -1,125 +1,125 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute temp/partial command
</H3>
<H3>compute temp/partial/cuda command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID temp/partial xflag yflag zflag
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>temp/partial = style name of this compute command
<LI>xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute newT flow temp/partial 1 1 0
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the temperature of a group of
atoms, after excluding one or more velocity components. A compute of
this style can be used by any command that computes a temperature,
e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, <A HREF = "fix_nh.html">fix npt</A>, etc.
</P>
<P>The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
dim = dimensionality of the simulation, N = number of atoms in the
group, k = Boltzmann constant, and T = temperature. The calculation
of KE excludes the x, y, or z dimensions if xflag, yflag, or zflag =
0. The dim parameter is adjusted to give the correct number of
degrees of freedom.
</P>
<P>A kinetic energy tensor, stored as a 6-element vector, is also
calculated by this compute for use in the calculation of a pressure
tensor. The formula for the components of the tensor is the same as
the above formula, except that v^2 is replaced by vx*vy for the xy
component, etc. The 6 components of the vector are ordered xx, yy,
zz, xy, xz, yz.
</P>
<P>The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the <I>dynamic</I> option of the
<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
</P>
<P>The removal of velocity components by this fix is essentially
computing the temperature after a "bias" has been removed from the
velocity of the atoms. If this compute is used with a fix command
that performs thermostatting then this bias will be subtracted from
each atom, thermostatting of the remaining thermal velocity will be
performed, and the bias will be added back in. Thermostatting fixes
that work in this way include <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
langevin</A>.
</P>
<P>This compute subtracts out degrees-of-freedom due to fixes that
constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
<A HREF = "fix_rigid.html">fix rigid</A>. This means the temperature of groups of
atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
</P>
<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
a discussion of different ways to compute temperature and perform
thermostatting.
</P>
<HR>
<P>Styles with a <I>cuda</I> suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
<A HREF = "Section_accelerate.html">this section</A> of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
</P>
<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
vector values will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_temp_region.html">compute
temp/region</A>, <A HREF = "compute_pressure.html">compute
pressure</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/compute_temp_partial.txt b/doc/compute_temp_partial.txt
index 1d81bd29c..ab5d42f9d 100644
--- a/doc/compute_temp_partial.txt
+++ b/doc/compute_temp_partial.txt
@@ -1,119 +1,119 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute temp/partial command :h3
compute temp/partial/cuda command :h3
[Syntax:]
compute ID group-ID temp/partial xflag yflag zflag :pre
ID, group-ID are documented in "compute"_compute.html command
temp/partial = style name of this compute command
xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension :ul
[Examples:]
compute newT flow temp/partial 1 1 0 :pre
[Description:]
Define a computation that calculates the temperature of a group of
atoms, after excluding one or more velocity components. A compute of
this style can be used by any command that computes a temperature,
e.g. "thermo_modify"_thermo_modify.html, "fix
temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_nh.html, etc.
The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
dim = dimensionality of the simulation, N = number of atoms in the
group, k = Boltzmann constant, and T = temperature. The calculation
of KE excludes the x, y, or z dimensions if xflag, yflag, or zflag =
0. The dim parameter is adjusted to give the correct number of
degrees of freedom.
A kinetic energy tensor, stored as a 6-element vector, is also
calculated by this compute for use in the calculation of a pressure
tensor. The formula for the components of the tensor is the same as
the above formula, except that v^2 is replaced by vx*vy for the xy
component, etc. The 6 components of the vector are ordered xx, yy,
zz, xy, xz, yz.
The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the {dynamic} option of the
"compute_modify"_compute_modify.html command if this is not the case.
The removal of velocity components by this fix is essentially
computing the temperature after a "bias" has been removed from the
velocity of the atoms. If this compute is used with a fix command
that performs thermostatting then this bias will be subtracted from
each atom, thermostatting of the remaining thermal velocity will be
performed, and the bias will be added back in. Thermostatting fixes
that work in this way include "fix nvt"_fix_nh.html, "fix
temp/rescale"_fix_temp_rescale.html, "fix
temp/berendsen"_fix_temp_berendsen.html, and "fix
langevin"_fix_langevin.html.
This compute subtracts out degrees-of-freedom due to fixes that
constrain molecular motion, such as "fix shake"_fix_shake.html and
"fix rigid"_fix_rigid.html. This means the temperature of groups of
atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
{extra} option of the "compute_modify"_compute_modify.html command.
See "this howto section"_Section_howto.html#howto_16 of the manual for
a discussion of different ways to compute temperature and perform
thermostatting.
:line
Styles with a {cuda} suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
"this section"_Section_accelerate.html of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Output info:]
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See "this
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature "units"_units.html. The
vector values will be in energy "units"_units.html.
[Restrictions:] none
[Related commands:]
"compute temp"_compute_temp.html, "compute
temp/region"_compute_temp_region.html, "compute
pressure"_compute_pressure.html
[Default:] none
diff --git a/doc/compute_temp_region_eff.html b/doc/compute_temp_region_eff.html
index 6bb12a428..e4e84b9e8 100644
--- a/doc/compute_temp_region_eff.html
+++ b/doc/compute_temp_region_eff.html
@@ -1,69 +1,69 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute temp/region/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID temp/region/eff region-ID
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>temp/region/eff = style name of this compute command
<LI>region-ID = ID of region to use for choosing atoms
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute mine flow temp/region/eff boundary
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the temperature of a group of
nuclei and electrons in the <A HREF = "pair_eff.html">electron force field</A>
model, within a geometric region using the electron force field. A
compute of this style can be used by commands that compute a
temperature, e.g. <A HREF = "thermo_modify.html">thermo_modify</A>.
</P>
<P>The operation of this compute is exactly like that described by the
<A HREF = "compute_temp_region.html">compute temp/region</A> command, except that
the formula for the temperature itself includes the radial electron
velocity contributions, as discussed by the <A HREF = "compute_temp_eff.html">compute
temp/eff</A> command.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
</P>
<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
vector values will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This compute is part of the "user-eff" package. It is only enabled if
+<P>This compute is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_temp_region.html">compute temp/region</A>, <A HREF = "compute_temp_eff.html">compute
temp/eff</A>, <A HREF = "compute_pressure.html">compute
pressure</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/compute_temp_region_eff.txt b/doc/compute_temp_region_eff.txt
index 7231f9862..8baf2dd46 100644
--- a/doc/compute_temp_region_eff.txt
+++ b/doc/compute_temp_region_eff.txt
@@ -1,64 +1,64 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute temp/region/eff command :h3
[Syntax:]
compute ID group-ID temp/region/eff region-ID :pre
ID, group-ID are documented in "compute"_compute.html command
temp/region/eff = style name of this compute command
region-ID = ID of region to use for choosing atoms :ul
[Examples:]
compute mine flow temp/region/eff boundary :pre
[Description:]
Define a computation that calculates the temperature of a group of
nuclei and electrons in the "electron force field"_pair_eff.html
model, within a geometric region using the electron force field. A
compute of this style can be used by commands that compute a
temperature, e.g. "thermo_modify"_thermo_modify.html.
The operation of this compute is exactly like that described by the
"compute temp/region"_compute_temp_region.html command, except that
the formula for the temperature itself includes the radial electron
velocity contributions, as discussed by the "compute
temp/eff"_compute_temp_eff.html command.
[Output info:]
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See "this
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature "units"_units.html. The
vector values will be in energy "units"_units.html.
[Restrictions:]
-This compute is part of the "user-eff" package. It is only enabled if
+This compute is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"compute temp/region"_compute_temp_region.html, "compute
temp/eff"_compute_temp_eff.html, "compute
pressure"_compute_pressure.html
[Default:] none
diff --git a/doc/compute_temp_rotate.html b/doc/compute_temp_rotate.html
index 389fa20ce..cbd3a3104 100644
--- a/doc/compute_temp_rotate.html
+++ b/doc/compute_temp_rotate.html
@@ -1,101 +1,101 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute temp/rotate command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID temp/rotate
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>temp/rotate = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute Tbead bead temp/rotate
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the temperature of a group of
atoms, after subtracting out the center-of-mass velocity and angular velocity of the group.
This is useful if the group is expected to have a non-zero net
velocity and/or global rotation motion for some reason. A compute of this style can be used by any
command that computes a temperature,
e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, <A HREF = "fix_nh.html">fix npt</A>, etc.
</P>
<P>After the center-of-mass velocity and angular velocity has been subtracted from each atom,
the temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
in the group, k = Boltzmann constant, and T = temperature.
</P>
<P>A kinetic energy tensor, stored as a 6-element vector, is also
calculated by this compute for use in the computation of a pressure
tensor. The formula for the components of the tensor is the same as
the above formula, except that v^2 is replaced by vx*vy for the xy
component, etc. The 6 components of the vector are ordered xx, yy,
zz, xy, xz, yz.
</P>
<P>The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the <I>dynamic</I> option of the
<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
</P>
<P>The removal of the center-of-mass velocity and angular velocity by this fix is essentially
computing the temperature after a "bias" has been removed from the
velocity of the atoms. If this compute is used with a fix command
that performs thermostatting then this bias will be subtracted from
each atom, thermostatting of the remaining thermal velocity will be
performed, and the bias will be added back in. Thermostatting fixes
that work in this way include <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
langevin</A>.
</P>
<P>This compute subtracts out degrees-of-freedom due to fixes that
constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
<A HREF = "fix_rigid.html">fix rigid</A>. This means the temperature of groups of
atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
</P>
<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
a discussion of different ways to compute temperature and perform
thermostatting.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
</P>
<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
vector values will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This compute is part of the "user-misc" package. It is only enabled
-if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+<P>This compute is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_temp.html">compute temp</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/compute_temp_rotate.txt b/doc/compute_temp_rotate.txt
index 13acc2a97..34feca7b6 100644
--- a/doc/compute_temp_rotate.txt
+++ b/doc/compute_temp_rotate.txt
@@ -1,96 +1,96 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute temp/rotate command :h3
[Syntax:]
compute ID group-ID temp/rotate :pre
ID, group-ID are documented in "compute"_compute.html command
temp/rotate = style name of this compute command :ul
[Examples:]
compute Tbead bead temp/rotate :pre
[Description:]
Define a computation that calculates the temperature of a group of
atoms, after subtracting out the center-of-mass velocity and angular velocity of the group.
This is useful if the group is expected to have a non-zero net
velocity and/or global rotation motion for some reason. A compute of this style can be used by any
command that computes a temperature,
e.g. "thermo_modify"_thermo_modify.html, "fix
temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_nh.html, etc.
After the center-of-mass velocity and angular velocity has been subtracted from each atom,
the temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
in the group, k = Boltzmann constant, and T = temperature.
A kinetic energy tensor, stored as a 6-element vector, is also
calculated by this compute for use in the computation of a pressure
tensor. The formula for the components of the tensor is the same as
the above formula, except that v^2 is replaced by vx*vy for the xy
component, etc. The 6 components of the vector are ordered xx, yy,
zz, xy, xz, yz.
The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the {dynamic} option of the
"compute_modify"_compute_modify.html command if this is not the case.
The removal of the center-of-mass velocity and angular velocity by this fix is essentially
computing the temperature after a "bias" has been removed from the
velocity of the atoms. If this compute is used with a fix command
that performs thermostatting then this bias will be subtracted from
each atom, thermostatting of the remaining thermal velocity will be
performed, and the bias will be added back in. Thermostatting fixes
that work in this way include "fix nvt"_fix_nh.html, "fix
temp/rescale"_fix_temp_rescale.html, "fix
temp/berendsen"_fix_temp_berendsen.html, and "fix
langevin"_fix_langevin.html.
This compute subtracts out degrees-of-freedom due to fixes that
constrain molecular motion, such as "fix shake"_fix_shake.html and
"fix rigid"_fix_rigid.html. This means the temperature of groups of
atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
{extra} option of the "compute_modify"_compute_modify.html command.
See "this howto section"_Section_howto.html#howto_16 of the manual for
a discussion of different ways to compute temperature and perform
thermostatting.
[Output info:]
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See "this
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature "units"_units.html. The
vector values will be in energy "units"_units.html.
[Restrictions:]
-This compute is part of the "user-misc" package. It is only enabled
-if LAMMPS was built with that package. See the "Making
+This compute is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"compute temp"_compute_temp.html
[Default:] none
diff --git a/doc/dihedral_charmm.html b/doc/dihedral_charmm.html
index e8b8ca58a..5a30dd7a4 100644
--- a/doc/dihedral_charmm.html
+++ b/doc/dihedral_charmm.html
@@ -1,94 +1,94 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>dihedral_style charmm command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>dihedral_style charmm
</PRE>
<P><B>Examples:</B>
</P>
<PRE>dihedral_style charmm
dihedral_coeff 1 120.0 1 60 0.5
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>charmm</I> dihedral style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/dihedral_charmm.jpg">
</CENTER>
<P>See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
field. This dihedral style can also be used for the AMBER force field
(see comment on weighting factors below). See <A HREF = "#Cornell">(Cornell)</A>
for a description of the AMBER force field.
</P>
<P>The following coefficients must be defined for each dihedral type via the
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy)
<LI>n (integer >= 0)
<LI>d (integer value of degrees)
<LI>weighting factor (0.0 to 1.0)
</UL>
<P>The weighting factor is applied to pairwise interaction between the
1st and 4th atoms in the dihedral, which are computed by a CHARMM
<A HREF = "pair_charmm.html">pair_style</A> with epsilon and sigma values specified
with a <A HREF = "pair_charmm.html">pair_coeff</A> command. Note that this
weighting factor is unrelated to the weighting factor specified by the
<A HREF = "special_bonds.html">special bonds</A> command which applies to all 1-4
interactions in the system.
</P>
<P>For CHARMM force fields, the special_bonds 1-4 weighting factor should
be set to 0.0. This is because the pair styles that contain "charmm"
(e.g. <A HREF = "pair_charmm.html">pair_style lj/charmm/coul/long</A>) define extra
1-4 interaction coefficients that are used by this dihedral style to
compute those interactions explicitly. This means that if any of the
weighting factors defined as dihedral coefficients (4th coeff above)
are non-zero, then you must use a charmm pair style. Note that if you
do not set the special_bonds 1-4 weighting factor to 0.0 (which is the
default) then 1-4 interactions in dihedrals will be computed twice,
once by the pair routine and once by the dihedral routine, which is
probably not what you want.
</P>
<P>For AMBER force fields, the special_bonds 1-4 weighting factor should
be set to the AMBER defaults (1/2 and 5/6) and all the dihedral
weighting factors (4th coeff above) should be set to 0.0. In this
case, you can use any pair style you wish, since the dihedral does not
need any 1-4 information.
</P>
<P><B>Restrictions:</B>
</P>
<P>This dihedral style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Cornell"></A>
<P><B>(Cornell)</B> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
</P>
<A NAME = "MacKerell"></A>
<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998).
</P>
</HTML>
diff --git a/doc/dihedral_charmm.txt b/doc/dihedral_charmm.txt
index e28adab34..410557345 100644
--- a/doc/dihedral_charmm.txt
+++ b/doc/dihedral_charmm.txt
@@ -1,87 +1,87 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
dihedral_style charmm command :h3
[Syntax:]
dihedral_style charmm :pre
[Examples:]
dihedral_style charmm
dihedral_coeff 1 120.0 1 60 0.5 :pre
[Description:]
The {charmm} dihedral style uses the potential
:c,image(Eqs/dihedral_charmm.jpg)
See "(MacKerell)"_#MacKerell for a description of the CHARMM force
field. This dihedral style can also be used for the AMBER force field
(see comment on weighting factors below). See "(Cornell)"_#Cornell
for a description of the AMBER force field.
The following coefficients must be defined for each dihedral type via the
"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy)
n (integer >= 0)
d (integer value of degrees)
weighting factor (0.0 to 1.0) :ul
The weighting factor is applied to pairwise interaction between the
1st and 4th atoms in the dihedral, which are computed by a CHARMM
"pair_style"_pair_charmm.html with epsilon and sigma values specified
with a "pair_coeff"_pair_charmm.html command. Note that this
weighting factor is unrelated to the weighting factor specified by the
"special bonds"_special_bonds.html command which applies to all 1-4
interactions in the system.
For CHARMM force fields, the special_bonds 1-4 weighting factor should
be set to 0.0. This is because the pair styles that contain "charmm"
(e.g. "pair_style lj/charmm/coul/long"_pair_charmm.html) define extra
1-4 interaction coefficients that are used by this dihedral style to
compute those interactions explicitly. This means that if any of the
weighting factors defined as dihedral coefficients (4th coeff above)
are non-zero, then you must use a charmm pair style. Note that if you
do not set the special_bonds 1-4 weighting factor to 0.0 (which is the
default) then 1-4 interactions in dihedrals will be computed twice,
once by the pair routine and once by the dihedral routine, which is
probably not what you want.
For AMBER force fields, the special_bonds 1-4 weighting factor should
be set to the AMBER defaults (1/2 and 5/6) and all the dihedral
weighting factors (4th coeff above) should be set to 0.0. In this
case, you can use any pair style you wish, since the dihedral does not
need any 1-4 information.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"dihedral_coeff"_dihedral_coeff.html
[Default:] none
:line
:link(Cornell)
[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
:link(MacKerell)
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998).
diff --git a/doc/dihedral_class2.html b/doc/dihedral_class2.html
index 5b55f4e39..471ccdd17 100644
--- a/doc/dihedral_class2.html
+++ b/doc/dihedral_class2.html
@@ -1,158 +1,158 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>dihedral_style class2 command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>dihedral_style class2
</PRE>
<P><B>Examples:</B>
</P>
<PRE>dihedral_style class2
dihedral_coeff 1 100 75 100 70 80 60
dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228
dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010
dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270
dihedral_coeff * aat -13.5271 110.2453 105.1270
dihedral_coeff * bb13 0.0 1.0119 1.1010
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>class2</I> dihedral style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/dihedral_class2.jpg">
</CENTER>
<P>where Ed is the dihedral term, Embt is a middle-bond-torsion term,
Eebt is an end-bond-torsion term, Eat is an angle-torsion term, Eaat
is an angle-angle-torsion term, and Ebb13 is a bond-bond-13 term.
</P>
<P>Theta1 and theta2 are equilibrium angles and r1 r2 r3 are equilibrium
bond lengths.
</P>
<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
</P>
<P>Coefficients for the Ed, Embt, Eebt, Eat, Eaat, and Ebb13 formulas
must be defined for each dihedral type via the
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example above,
or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands.
</P>
<P>These are the 6 coefficients for the Ed formula:
</P>
<UL><LI>K1 (energy)
<LI>phi1 (degrees)
<LI>K2 (energy)
<LI>phi2 (degrees)
<LI>K3 (energy)
<LI>phi3 (degrees)
</UL>
<P>For the Embt formula, each line in a
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script lists
5 coefficients, the first of which is "mbt" to indicate they are
MiddleBondTorsion coefficients. In a data file, these coefficients
should be listed under a "MiddleBondTorsion Coeffs" heading and you
must leave out the "mbt", i.e. only list 4 coefficients after the
dihedral type.
</P>
<UL><LI>mbt
<LI>A1 (energy/distance)
<LI>A2 (energy/distance)
<LI>A3 (energy/distance)
<LI>r2 (distance)
</UL>
<P>For the Eebt formula, each line in a
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script lists
9 coefficients, the first of which is "ebt" to indicate they are
EndBondTorsion coefficients. In a data file, these coefficients
should be listed under a "EndBondTorsion Coeffs" heading and you must
leave out the "ebt", i.e. only list 8 coefficients after the dihedral
type.
</P>
<UL><LI>ebt
<LI>B1 (energy/distance)
<LI>B2 (energy/distance)
<LI>B3 (energy/distance)
<LI>C1 (energy/distance)
<LI>C2 (energy/distance)
<LI>C3 (energy/distance)
<LI>r1 (distance)
<LI>r3 (distance)
</UL>
<P>For the Eat formula, each line in a
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script lists
9 coefficients, the first of which is "at" to indicate they are
AngleTorsion coefficients. In a data file, these coefficients should
be listed under a "AngleTorsion Coeffs" heading and you must leave out
the "at", i.e. only list 8 coefficients after the dihedral type.
</P>
<UL><LI>at
<LI>D1 (energy/radian)
<LI>D2 (energy/radian)
<LI>D3 (energy/radian)
<LI>E1 (energy/radian)
<LI>E2 (energy/radian)
<LI>E3 (energy/radian)
<LI>theta1 (degrees)
<LI>theta2 (degrees)
</UL>
<P>Theta1 and theta2 are specified in degrees, but LAMMPS converts them
to radians internally; hence the units of D and E are in
energy/radian.
</P>
<P>For the Eaat formula, each line in a
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script lists
4 coefficients, the first of which is "aat" to indicate they are
AngleAngleTorsion coefficients. In a data file, these coefficients
should be listed under a "AngleAngleTorsion Coeffs" heading and you
must leave out the "aat", i.e. only list 3 coefficients after the
dihedral type.
</P>
<UL><LI>aat
<LI>M (energy/radian^2)
<LI>theta1 (degrees)
<LI>theta2 (degrees)
</UL>
<P>Theta1 and theta2 are specified in degrees, but LAMMPS converts them
to radians internally; hence the units of M are in energy/radian^2.
</P>
<P>For the Ebb13 formula, each line in a
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script lists
4 coefficients, the first of which is "bb13" to indicate they are
BondBond13 coefficients. In a data file, these coefficients should be
listed under a "BondBond13 Coeffs" heading and you must leave out the
"bb13", i.e. only list 3 coefficients after the dihedral type.
</P>
<UL><LI>bb13
<LI>N (energy/distance^2)
<LI>r1 (distance)
<LI>r3 (distance)
</UL>
<P><B>Restrictions:</B>
</P>
<P>This dihedral style can only be used if LAMMPS was built with the
-"class2" package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+CLASS2 package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Sun"></A>
<P><B>(Sun)</B> Sun, J Phys Chem B 102, 7338-7364 (1998).
</P>
</HTML>
diff --git a/doc/dihedral_class2.txt b/doc/dihedral_class2.txt
index ea9fa52cf..21e37cb12 100644
--- a/doc/dihedral_class2.txt
+++ b/doc/dihedral_class2.txt
@@ -1,152 +1,152 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
dihedral_style class2 command :h3
[Syntax:]
dihedral_style class2 :pre
[Examples:]
dihedral_style class2
dihedral_coeff 1 100 75 100 70 80 60
dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228
dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010
dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270
dihedral_coeff * aat -13.5271 110.2453 105.1270
dihedral_coeff * bb13 0.0 1.0119 1.1010 :pre
[Description:]
The {class2} dihedral style uses the potential
:c,image(Eqs/dihedral_class2.jpg)
where Ed is the dihedral term, Embt is a middle-bond-torsion term,
Eebt is an end-bond-torsion term, Eat is an angle-torsion term, Eaat
is an angle-angle-torsion term, and Ebb13 is a bond-bond-13 term.
Theta1 and theta2 are equilibrium angles and r1 r2 r3 are equilibrium
bond lengths.
See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
Coefficients for the Ed, Embt, Eebt, Eat, Eaat, and Ebb13 formulas
must be defined for each dihedral type via the
"dihedral_coeff"_dihedral_coeff.html command as in the example above,
or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands.
These are the 6 coefficients for the Ed formula:
K1 (energy)
phi1 (degrees)
K2 (energy)
phi2 (degrees)
K3 (energy)
phi3 (degrees) :ul
For the Embt formula, each line in a
"dihedral_coeff"_dihedral_coeff.html command in the input script lists
5 coefficients, the first of which is "mbt" to indicate they are
MiddleBondTorsion coefficients. In a data file, these coefficients
should be listed under a "MiddleBondTorsion Coeffs" heading and you
must leave out the "mbt", i.e. only list 4 coefficients after the
dihedral type.
mbt
A1 (energy/distance)
A2 (energy/distance)
A3 (energy/distance)
r2 (distance) :ul
For the Eebt formula, each line in a
"dihedral_coeff"_dihedral_coeff.html command in the input script lists
9 coefficients, the first of which is "ebt" to indicate they are
EndBondTorsion coefficients. In a data file, these coefficients
should be listed under a "EndBondTorsion Coeffs" heading and you must
leave out the "ebt", i.e. only list 8 coefficients after the dihedral
type.
ebt
B1 (energy/distance)
B2 (energy/distance)
B3 (energy/distance)
C1 (energy/distance)
C2 (energy/distance)
C3 (energy/distance)
r1 (distance)
r3 (distance) :ul
For the Eat formula, each line in a
"dihedral_coeff"_dihedral_coeff.html command in the input script lists
9 coefficients, the first of which is "at" to indicate they are
AngleTorsion coefficients. In a data file, these coefficients should
be listed under a "AngleTorsion Coeffs" heading and you must leave out
the "at", i.e. only list 8 coefficients after the dihedral type.
at
D1 (energy/radian)
D2 (energy/radian)
D3 (energy/radian)
E1 (energy/radian)
E2 (energy/radian)
E3 (energy/radian)
theta1 (degrees)
theta2 (degrees) :ul
Theta1 and theta2 are specified in degrees, but LAMMPS converts them
to radians internally; hence the units of D and E are in
energy/radian.
For the Eaat formula, each line in a
"dihedral_coeff"_dihedral_coeff.html command in the input script lists
4 coefficients, the first of which is "aat" to indicate they are
AngleAngleTorsion coefficients. In a data file, these coefficients
should be listed under a "AngleAngleTorsion Coeffs" heading and you
must leave out the "aat", i.e. only list 3 coefficients after the
dihedral type.
aat
M (energy/radian^2)
theta1 (degrees)
theta2 (degrees) :ul
Theta1 and theta2 are specified in degrees, but LAMMPS converts them
to radians internally; hence the units of M are in energy/radian^2.
For the Ebb13 formula, each line in a
"dihedral_coeff"_dihedral_coeff.html command in the input script lists
4 coefficients, the first of which is "bb13" to indicate they are
BondBond13 coefficients. In a data file, these coefficients should be
listed under a "BondBond13 Coeffs" heading and you must leave out the
"bb13", i.e. only list 3 coefficients after the dihedral type.
bb13
N (energy/distance^2)
r1 (distance)
r3 (distance) :ul
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-"class2" package. See the "Making LAMMPS"_Section_start.html#start_3
+CLASS2 package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info on packages.
[Related commands:]
"dihedral_coeff"_dihedral_coeff.html
[Default:] none
:line
:link(Sun)
[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998).
diff --git a/doc/dihedral_cosine_shift_exp.html b/doc/dihedral_cosine_shift_exp.html
index 5062bb6f2..a4927685d 100644
--- a/doc/dihedral_cosine_shift_exp.html
+++ b/doc/dihedral_cosine_shift_exp.html
@@ -1,65 +1,65 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>dihedral_style cosine/shift/exp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>dihedral_style cosine/shift/exp
</PRE>
<P><B>Examples:</B>
</P>
<PRE>dihedral_style cosine/shift/exp
dihedral_coeff 1 10.0 45.0 2.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>cosine/shift/exp</I> dihedral style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/dihedral_cosine_shift_exp.jpg">
</CENTER>
<P>where Umin, theta, and a are defined for each dihedral type.
</P>
<P>The potential is bounded between [-Umin:0] and the minimum is located
at the angle theta0. The a parameter can be both positive or negative
and is used to control the spring constant at the equilibrium.
</P>
<P>The spring constant is given by k=a exp(a) Umin/ [2 (Exp(a)-1)].
For a>3 k/Umin = a/2 to better than 5% relative error. For negative
values of the a parameter, the spring constant is essentially zero,
and anharmonic terms takes over. The potential is furthermore well
behaved in the limit a->0, where it has been implemented to linear
order in a for a < 0.001.
</P>
<P>The following coefficients must be defined for each dihedral type via
the <A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands:
</P>
<UL><LI>umin (energy)
<LI>theta (angle)
<LI>A (real number)
</UL>
<P><B>Restrictions:</B>
</P>
<P>This dihedral style can only be used if LAMMPS was built with the
-"user-misc" package. See the <A HREF = "Section_start.html#start_3">Making
-LAMMPS</A> section for more info on packages.
+USER-MISC package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>,
<A HREF = "angle_cosineshiftexp.html">angle_cosineshiftexp</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/dihedral_cosine_shift_exp.txt b/doc/dihedral_cosine_shift_exp.txt
index f4e94263f..dd49b2759 100644
--- a/doc/dihedral_cosine_shift_exp.txt
+++ b/doc/dihedral_cosine_shift_exp.txt
@@ -1,60 +1,60 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
dihedral_style cosine/shift/exp command :h3
[Syntax:]
dihedral_style cosine/shift/exp :pre
[Examples:]
dihedral_style cosine/shift/exp
dihedral_coeff 1 10.0 45.0 2.0 :pre
[Description:]
The {cosine/shift/exp} dihedral style uses the potential
:c,image(Eqs/dihedral_cosine_shift_exp.jpg)
where Umin, theta, and a are defined for each dihedral type.
The potential is bounded between \[-Umin:0\] and the minimum is located
at the angle theta0. The a parameter can be both positive or negative
and is used to control the spring constant at the equilibrium.
The spring constant is given by k=a exp(a) Umin/ \[2 (Exp(a)-1)\].
For a>3 k/Umin = a/2 to better than 5% relative error. For negative
values of the a parameter, the spring constant is essentially zero,
and anharmonic terms takes over. The potential is furthermore well
behaved in the limit a->0, where it has been implemented to linear
order in a for a < 0.001.
The following coefficients must be defined for each dihedral type via
the "dihedral_coeff"_dihedral_coeff.html command as in the example
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands:
umin (energy)
theta (angle)
A (real number) :ul
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-"user-misc" package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
+section for more info on packages.
[Related commands:]
"dihedral_coeff"_dihedral_coeff.html,
"angle_cosineshiftexp"_angle_cosineshiftexp.html
[Default:] none
diff --git a/doc/dihedral_harmonic.html b/doc/dihedral_harmonic.html
index eb1b760ee..68a8a6bbc 100644
--- a/doc/dihedral_harmonic.html
+++ b/doc/dihedral_harmonic.html
@@ -1,50 +1,50 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>dihedral_style harmonic command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>dihedral_style harmonic
</PRE>
<P><B>Examples:</B>
</P>
<PRE>dihedral_style harmonic
dihedral_coeff 1 80.0 1 2
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>harmonic</I> dihedral style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/dihedral_harmonic.jpg">
</CENTER>
<P>The following coefficients must be defined for each dihedral type via the
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K (energy)
<LI>d (+1 or -1)
<LI>n (integer >= 0)
</UL>
<P><B>Restrictions:</B>
</P>
<P>This dihedral style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/dihedral_harmonic.txt b/doc/dihedral_harmonic.txt
index 99452498a..bb4192f81 100644
--- a/doc/dihedral_harmonic.txt
+++ b/doc/dihedral_harmonic.txt
@@ -1,45 +1,45 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
dihedral_style harmonic command :h3
[Syntax:]
dihedral_style harmonic :pre
[Examples:]
dihedral_style harmonic
dihedral_coeff 1 80.0 1 2 :pre
[Description:]
The {harmonic} dihedral style uses the potential
:c,image(Eqs/dihedral_harmonic.jpg)
The following coefficients must be defined for each dihedral type via the
"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy)
d (+1 or -1)
n (integer >= 0) :ul
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"dihedral_coeff"_dihedral_coeff.html
[Default:] none
diff --git a/doc/dihedral_helix.html b/doc/dihedral_helix.html
index 403625c6c..93dd55216 100644
--- a/doc/dihedral_helix.html
+++ b/doc/dihedral_helix.html
@@ -1,64 +1,64 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>dihedral_style helix command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>dihedral_style helix
</PRE>
<P><B>Examples:</B>
</P>
<PRE>dihedral_style helix
dihedral_coeff 1 80.0 100.0 40.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>helix</I> dihedral style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/dihedral_helix.jpg">
</CENTER>
<P>This coarse-grain dihedral potential is described in <A HREF = "#Guo">(Guo)</A>.
For dihedral angles in the helical region, the energy function is
represented by a standard potential consisting of three minima, one
corresponding to the trans (t) state and the other to gauche states
(g+ and g-). The paper describes how the A,B,C parameters are chosen
so as to balance secondary (largely driven by local interactions) and
tertiary structure (driven by long-range interactions).
</P>
<P>The following coefficients must be defined for each dihedral type via the
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>A (energy)
<LI>B (energy)
<LI>C (energy)
</UL>
<P><B>Restrictions:</B>
</P>
<P>This dihedral style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Guo"></A>
<P><B>(Guo)</B> Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).
</P>
</HTML>
diff --git a/doc/dihedral_helix.txt b/doc/dihedral_helix.txt
index 122092498..3ff9b5389 100644
--- a/doc/dihedral_helix.txt
+++ b/doc/dihedral_helix.txt
@@ -1,58 +1,58 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
dihedral_style helix command :h3
[Syntax:]
dihedral_style helix :pre
[Examples:]
dihedral_style helix
dihedral_coeff 1 80.0 100.0 40.0 :pre
[Description:]
The {helix} dihedral style uses the potential
:c,image(Eqs/dihedral_helix.jpg)
This coarse-grain dihedral potential is described in "(Guo)"_#Guo.
For dihedral angles in the helical region, the energy function is
represented by a standard potential consisting of three minima, one
corresponding to the trans (t) state and the other to gauche states
(g+ and g-). The paper describes how the A,B,C parameters are chosen
so as to balance secondary (largely driven by local interactions) and
tertiary structure (driven by long-range interactions).
The following coefficients must be defined for each dihedral type via the
"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
A (energy)
B (energy)
C (energy) :ul
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"dihedral_coeff"_dihedral_coeff.html
[Default:] none
:line
:link(Guo)
[(Guo)] Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).
diff --git a/doc/dihedral_hybrid.html b/doc/dihedral_hybrid.html
index 673240052..07e9f6ee4 100644
--- a/doc/dihedral_hybrid.html
+++ b/doc/dihedral_hybrid.html
@@ -1,95 +1,95 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>dihedral_style hybrid command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>dihedral_style hybrid style1 style2 ...
</PRE>
<UL><LI>style1,style2 = list of one or more dihedral styles
</UL>
<P><B>Examples:</B>
</P>
<PRE>dihedral_style hybrid harmonic helix
dihedral_coeff 1 harmonic 6.0 1 3
dihedral_coeff 2* helix 10 10 10
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>hybrid</I> style enables the use of multiple dihedral styles in one
simulation. An dihedral style is assigned to each dihedral type. For
example, dihedrals in a polymer flow (of dihedral type 1) could be
computed with a <I>harmonic</I> potential and dihedrals in the wall
boundary (of dihedral type 2) could be computed with a <I>helix</I>
potential. The assignment of dihedral type to style is made via the
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command or in the data file.
</P>
<P>In the dihedral_coeff commands, the name of a dihedral style must be
added after the dihedral type, with the remaining coefficients being
those appropriate to that style. In the example above, the 2
dihedral_coeff commands set dihedrals of dihedral type 1 to be
computed with a <I>harmonic</I> potential with coefficients 6.0, 1, 3 for
K, d, n. All other dihedral types (2-N) are computed with a <I>helix</I>
potential with coefficients 10, 10, 10 for A, B, C.
</P>
<P>If dihedral coefficients are specified in the data file read via the
<A HREF = "read_data.html">read_data</A> command, then the same rule applies.
E.g. "harmonic" or "helix", must be added after the dihedral type, for
each line in the "Dihedral Coeffs" section, e.g.
</P>
<PRE>Dihedral Coeffs
</PRE>
<PRE>1 harmonic 6.0 1 3
2 helix 10 10 10
...
</PRE>
<P>If <I>class2</I> is one of the dihedral hybrid styles, the same rule holds
for specifying additional AngleTorsion (and EndBondTorsion, etc)
coefficients either via the input script or in the data file.
I.e. <I>class2</I> must be added to each line after the dihedral type. For
lines in the AngleTorsion (or EndBondTorsion, etc) section of the data
file for dihedral types that are not <I>class2</I>, you must use an
dihedral style of <I>skip</I> as a placeholder, e.g.
</P>
<PRE>AngleTorsion Coeffs
</PRE>
<PRE>1 skip
2 class2 1.0 1.0 1.0 3.0 3.0 3.0 30.0 50.0
...
</PRE>
<P>Note that it is not necessary to use the dihedral style <I>skip</I> in the
input script, since AngleTorsion (or EndBondTorsion, etc) coefficients
need not be specified at all for dihedral types that are not <I>class2</I>.
</P>
<P>A dihedral style of <I>none</I> with no additional coefficients can be used
in place of a dihedral style, either in a input script dihedral_coeff
command or in the data file, if you desire to turn off interactions
for specific dihedral types.
</P>
<P><B>Restrictions:</B>
</P>
<P>This dihedral style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P>Unlike other dihedral styles, the hybrid dihedral style does not store
dihedral coefficient info for individual sub-styles in a <A HREF = "restart.html">binary
restart files</A>. Thus when retarting a simulation from a
restart file, you need to re-specify dihedral_coeff commands.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/dihedral_hybrid.txt b/doc/dihedral_hybrid.txt
index 74a2ef1b9..4ccf8ef05 100644
--- a/doc/dihedral_hybrid.txt
+++ b/doc/dihedral_hybrid.txt
@@ -1,90 +1,90 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
dihedral_style hybrid command :h3
[Syntax:]
dihedral_style hybrid style1 style2 ... :pre
style1,style2 = list of one or more dihedral styles :ul
[Examples:]
dihedral_style hybrid harmonic helix
dihedral_coeff 1 harmonic 6.0 1 3
dihedral_coeff 2* helix 10 10 10 :pre
[Description:]
The {hybrid} style enables the use of multiple dihedral styles in one
simulation. An dihedral style is assigned to each dihedral type. For
example, dihedrals in a polymer flow (of dihedral type 1) could be
computed with a {harmonic} potential and dihedrals in the wall
boundary (of dihedral type 2) could be computed with a {helix}
potential. The assignment of dihedral type to style is made via the
"dihedral_coeff"_dihedral_coeff.html command or in the data file.
In the dihedral_coeff commands, the name of a dihedral style must be
added after the dihedral type, with the remaining coefficients being
those appropriate to that style. In the example above, the 2
dihedral_coeff commands set dihedrals of dihedral type 1 to be
computed with a {harmonic} potential with coefficients 6.0, 1, 3 for
K, d, n. All other dihedral types (2-N) are computed with a {helix}
potential with coefficients 10, 10, 10 for A, B, C.
If dihedral coefficients are specified in the data file read via the
"read_data"_read_data.html command, then the same rule applies.
E.g. "harmonic" or "helix", must be added after the dihedral type, for
each line in the "Dihedral Coeffs" section, e.g.
Dihedral Coeffs :pre
1 harmonic 6.0 1 3
2 helix 10 10 10
... :pre
If {class2} is one of the dihedral hybrid styles, the same rule holds
for specifying additional AngleTorsion (and EndBondTorsion, etc)
coefficients either via the input script or in the data file.
I.e. {class2} must be added to each line after the dihedral type. For
lines in the AngleTorsion (or EndBondTorsion, etc) section of the data
file for dihedral types that are not {class2}, you must use an
dihedral style of {skip} as a placeholder, e.g.
AngleTorsion Coeffs :pre
1 skip
2 class2 1.0 1.0 1.0 3.0 3.0 3.0 30.0 50.0
... :pre
Note that it is not necessary to use the dihedral style {skip} in the
input script, since AngleTorsion (or EndBondTorsion, etc) coefficients
need not be specified at all for dihedral types that are not {class2}.
A dihedral style of {none} with no additional coefficients can be used
in place of a dihedral style, either in a input script dihedral_coeff
command or in the data file, if you desire to turn off interactions
for specific dihedral types.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
Unlike other dihedral styles, the hybrid dihedral style does not store
dihedral coefficient info for individual sub-styles in a "binary
restart files"_restart.html. Thus when retarting a simulation from a
restart file, you need to re-specify dihedral_coeff commands.
[Related commands:]
"dihedral_coeff"_dihedral_coeff.html
[Default:] none
diff --git a/doc/dihedral_multi_harmonic.html b/doc/dihedral_multi_harmonic.html
index 0cff3cab2..f63c22fc2 100644
--- a/doc/dihedral_multi_harmonic.html
+++ b/doc/dihedral_multi_harmonic.html
@@ -1,52 +1,52 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>dihedral_style multi/harmonic command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>dihedral_style multi/harmonic
</PRE>
<P><B>Examples:</B>
</P>
<PRE>dihedral_style multi/harmonic
dihedral_coeff 1 20 20 20 20 20
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>multi/harmonic</I> dihedral style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/dihedral_multi_harmonic.jpg">
</CENTER>
<P>The following coefficients must be defined for each dihedral type via the
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>A1 (energy)
<LI>A2 (energy)
<LI>A3 (energy)
<LI>A4 (energy)
<LI>A5 (energy)
</UL>
<P><B>Restrictions:</B>
</P>
<P>This dihedral style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/dihedral_multi_harmonic.txt b/doc/dihedral_multi_harmonic.txt
index e5c9c2939..d0196279b 100644
--- a/doc/dihedral_multi_harmonic.txt
+++ b/doc/dihedral_multi_harmonic.txt
@@ -1,47 +1,47 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
dihedral_style multi/harmonic command :h3
[Syntax:]
dihedral_style multi/harmonic :pre
[Examples:]
dihedral_style multi/harmonic
dihedral_coeff 1 20 20 20 20 20 :pre
[Description:]
The {multi/harmonic} dihedral style uses the potential
:c,image(Eqs/dihedral_multi_harmonic.jpg)
The following coefficients must be defined for each dihedral type via the
"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
A1 (energy)
A2 (energy)
A3 (energy)
A4 (energy)
A5 (energy) :ul
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"dihedral_coeff"_dihedral_coeff.html
[Default:] none
diff --git a/doc/dihedral_opls.html b/doc/dihedral_opls.html
index 098a8fed8..39cd3f6b9 100644
--- a/doc/dihedral_opls.html
+++ b/doc/dihedral_opls.html
@@ -1,62 +1,62 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>dihedral_style opls command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>dihedral_style opls
</PRE>
<P><B>Examples:</B>
</P>
<PRE>dihedral_style opls
dihedral_coeff 1 90.0 90.0 90.0 70.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>opls</I> dihedral style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/dihedral_opls.jpg">
</CENTER>
<P>Note that the usual 1/2 factor is not included in the K values.
</P>
<P>This dihedral potential is used in the OPLS force field and is
described in <A HREF = "#Watkins">(Watkins)</A>.
</P>
<P>The following coefficients must be defined for each dihedral type via the
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands:
</P>
<UL><LI>K1 (energy)
<LI>K2 (energy)
<LI>K3 (energy)
<LI>K4 (energy)
</UL>
<P><B>Restrictions:</B>
</P>
<P>This dihedral style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Watkins"></A>
<P><B>(Watkins)</B> Watkins and Jorgensen, J Phys Chem A, 105, 4118-4125 (2001).
</P>
</HTML>
diff --git a/doc/dihedral_opls.txt b/doc/dihedral_opls.txt
index 048e1f363..530201899 100644
--- a/doc/dihedral_opls.txt
+++ b/doc/dihedral_opls.txt
@@ -1,56 +1,56 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
dihedral_style opls command :h3
[Syntax:]
dihedral_style opls :pre
[Examples:]
dihedral_style opls
dihedral_coeff 1 90.0 90.0 90.0 70.0 :pre
[Description:]
The {opls} dihedral style uses the potential
:c,image(Eqs/dihedral_opls.jpg)
Note that the usual 1/2 factor is not included in the K values.
This dihedral potential is used in the OPLS force field and is
described in "(Watkins)"_#Watkins.
The following coefficients must be defined for each dihedral type via the
"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K1 (energy)
K2 (energy)
K3 (energy)
K4 (energy) :ul
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"dihedral_coeff"_dihedral_coeff.html
[Default:] none
:line
:link(Watkins)
[(Watkins)] Watkins and Jorgensen, J Phys Chem A, 105, 4118-4125 (2001).
diff --git a/doc/dihedral_style.html b/doc/dihedral_style.html
index 654f0f81e..e2f6ea532 100644
--- a/doc/dihedral_style.html
+++ b/doc/dihedral_style.html
@@ -1,115 +1,115 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>dihedral_style command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>dihedral_style style
</PRE>
<UL><LI>style = <I>none</I> or <I>hybrid</I> or <I>charmm</I> or <I>class2</I> or <I>harmonic</I> or <I>helix</I> or <I>multi/harmonic</I> or <I>opls</I>
</UL>
<P><B>Examples:</B>
</P>
<PRE>dihedral_style harmonic
dihedral_style multi/harmonic
dihedral_style hybrid harmonic charmm
</PRE>
<P><B>Description:</B>
</P>
<P>Set the formula(s) LAMMPS uses to compute dihedral interactions
between quadruplets of atoms, which remain in force for the duration
of the simulation. The list of dihedral quadruplets is read in by a
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A> command
from a data or restart file.
</P>
<P>Hybrid models where dihedrals are computed using different dihedral
potentials can be setup using the <I>hybrid</I> dihedral style.
</P>
<P>The coefficients associated with a dihedral style can be specified in
a data or restart file or via the <A HREF = "dihedral_coeff.html">dihedral_coeff</A>
command.
</P>
<P>All dihedral potentials store their coefficient data in binary restart
files which means dihedral_style and
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> commands do not need to be
re-specified in an input script that restarts a simulation. See the
<A HREF = "read_restart.html">read_restart</A> command for details on how to do
this. The one exception is that dihedral_style <I>hybrid</I> only stores
the list of sub-styles in the restart file; dihedral coefficients need
to be re-specified.
</P>
<P>IMPORTANT NOTE: When both a dihedral and pair style is defined, the
<A HREF = "special_bonds.html">special_bonds</A> command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
exist between 4 bonded atoms.
</P>
<P>In the formulas listed for each dihedral style, <I>phi</I> is the torsional
angle defined by the quadruplet of atoms.
</P>
<P>Here are some important points to take note of when defining the
LAMMPS dihedral coefficients in the formulas that follow so that they
are compatible with other force fields:
</P>
<UL><LI>The LAMMPS convention is that the trans position = 180 degrees, while
in some force fields trans = 0 degrees.
<LI>Some force fields reverse the sign convention on <I>d</I>.
<LI>Some force fields divide/multiply <I>K</I> by the number of multiple
torsions that contain the j-k bond in an i-j-k-l torsion.
<LI>Some force fields let <I>n</I> be positive or negative which corresponds to
<I>d</I> = 1 or -1 for the harmonic style.
</UL>
<HR>
<P>Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated <A HREF = "dihedral_coeff.html">dihedral_coeff</A> command:
</P>
<UL><LI><A HREF = "dihedral_none.html">dihedral_style none</A> - turn off dihedral interactions
<LI><A HREF = "dihedral_hybrid.html">dihedral_style hybrid</A> - define multiple styles of dihedral interactions
</UL>
<UL><LI><A HREF = "dihedral_charmm.html">dihedral_style charmm</A> - CHARMM dihedral
<LI><A HREF = "dihedral_class2.html">dihedral_style class2</A> - COMPASS (class 2) dihedral
<LI><A HREF = "dihedral_harmonic.html">dihedral_style harmonic</A> - harmonic dihedral
<LI><A HREF = "dihedral_helix.html">dihedral_style helix</A> - helix dihedral
<LI><A HREF = "dihedral_multi_harmonic.html">dihedral_style multi/harmonic</A> - multi-harmonic dihedral
<LI><A HREF = "dihedral_opls.html">dihedral_style opls</A> - OPLS dihedral
</UL>
<P>There are also additional dihedral styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the dihedral section of <A HREF = "Section_commands.html#cmd_5">this
page</A>.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>Dihedral styles can only be set for atom styles that allow dihedrals
to be defined.
</P>
-<P>Most dihedral styles are part of the "molecular" package. They are
-only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+<P>Most dihedral styles are part of the MOLECULAR package. They are only
+enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
The doc pages for individual dihedral potentials tell if it is part of
a package.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
</P>
<P><B>Default:</B>
</P>
<P>dihedral_style none
</P>
</HTML>
diff --git a/doc/dihedral_style.txt b/doc/dihedral_style.txt
index 82c2123de..788215a6e 100644
--- a/doc/dihedral_style.txt
+++ b/doc/dihedral_style.txt
@@ -1,111 +1,111 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
dihedral_style command :h3
[Syntax:]
dihedral_style style :pre
style = {none} or {hybrid} or {charmm} or {class2} or {harmonic} or {helix} or \
{multi/harmonic} or {opls} :ul
[Examples:]
dihedral_style harmonic
dihedral_style multi/harmonic
dihedral_style hybrid harmonic charmm :pre
[Description:]
Set the formula(s) LAMMPS uses to compute dihedral interactions
between quadruplets of atoms, which remain in force for the duration
of the simulation. The list of dihedral quadruplets is read in by a
"read_data"_read_data.html or "read_restart"_read_restart.html command
from a data or restart file.
Hybrid models where dihedrals are computed using different dihedral
potentials can be setup using the {hybrid} dihedral style.
The coefficients associated with a dihedral style can be specified in
a data or restart file or via the "dihedral_coeff"_dihedral_coeff.html
command.
All dihedral potentials store their coefficient data in binary restart
files which means dihedral_style and
"dihedral_coeff"_dihedral_coeff.html commands do not need to be
re-specified in an input script that restarts a simulation. See the
"read_restart"_read_restart.html command for details on how to do
this. The one exception is that dihedral_style {hybrid} only stores
the list of sub-styles in the restart file; dihedral coefficients need
to be re-specified.
IMPORTANT NOTE: When both a dihedral and pair style is defined, the
"special_bonds"_special_bonds.html command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
exist between 4 bonded atoms.
In the formulas listed for each dihedral style, {phi} is the torsional
angle defined by the quadruplet of atoms.
Here are some important points to take note of when defining the
LAMMPS dihedral coefficients in the formulas that follow so that they
are compatible with other force fields:
The LAMMPS convention is that the trans position = 180 degrees, while
in some force fields trans = 0 degrees. :ulb,l
Some force fields reverse the sign convention on {d}. :l
Some force fields divide/multiply {K} by the number of multiple
torsions that contain the j-k bond in an i-j-k-l torsion. :l
Some force fields let {n} be positive or negative which corresponds to
{d} = 1 or -1 for the harmonic style. :ule,l
:line
Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "dihedral_coeff"_dihedral_coeff.html command:
"dihedral_style none"_dihedral_none.html - turn off dihedral interactions
"dihedral_style hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul
"dihedral_style charmm"_dihedral_charmm.html - CHARMM dihedral
"dihedral_style class2"_dihedral_class2.html - COMPASS (class 2) dihedral
"dihedral_style harmonic"_dihedral_harmonic.html - harmonic dihedral
"dihedral_style helix"_dihedral_helix.html - helix dihedral
"dihedral_style multi/harmonic"_dihedral_multi_harmonic.html - multi-harmonic dihedral
"dihedral_style opls"_dihedral_opls.html - OPLS dihedral :ul
There are also additional dihedral styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the dihedral section of "this
page"_Section_commands.html#cmd_5.
:line
[Restrictions:]
Dihedral styles can only be set for atom styles that allow dihedrals
to be defined.
-Most dihedral styles are part of the "molecular" package. They are
-only enabled if LAMMPS was built with that package. See the "Making
+Most dihedral styles are part of the MOLECULAR package. They are only
+enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
The doc pages for individual dihedral potentials tell if it is part of
a package.
[Related commands:]
"dihedral_coeff"_dihedral_coeff.html
[Default:]
dihedral_style none
diff --git a/doc/dump.html b/doc/dump.html
index 7e599ea3c..23bd26c17 100644
--- a/doc/dump.html
+++ b/doc/dump.html
@@ -1,540 +1,540 @@
<HTML>
<CENTER> <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>dump command
</H3>
<H3><A HREF = "dump_image.html">dump image</A> command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>dump ID group-ID style N file args
</PRE>
<UL><LI>ID = user-assigned name for the dump
<LI>group-ID = ID of the group of atoms to be dumped
<LI>style = <I>atom</I> or <I>cfg</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>image</I> or <I>local</I> or <I>custom</I>
<LI>N = dump every this many timesteps
<LI>file = name of file to write dump info to
<LI>args = list of arguments for a particular style
<PRE> <I>atom</I> args = none
<I>cfg</I> args = same as <I>custom</I> args, see below
<I>dcd</I> args = none
<I>xtc</I> args = none
<I>xyz</I> args = none
</PRE>
<PRE> <I>image</I> args = discussed on <A HREF = "dump_image.html">dump image</A> doc page
</PRE>
<PRE> <I>local</I> args = list of local attributes
possible attributes = index, c_ID, c_ID[N], f_ID, f_ID[N]
index = enumeration of local values
c_ID = local vector calculated by a compute with ID
c_ID[N] = Nth column of local array calculated by a compute with ID
f_ID = local vector calculated by a fix with ID
f_ID[N] = Nth column of local array calculated by a fix with ID
</PRE>
<PRE> <I>custom</I> args = list of atom attributes
possible attributes = id, mol, type, element, mass,
x, y, z, xs, ys, zs, xu, yu, zu,
xsu, ysu, zsu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu,
radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, tqx, tqy, tqz,
spin, eradius, ervel, erforce,
c_ID, c_ID[N], f_ID, f_ID[N], v_name
</PRE>
<PRE> id = atom ID
mol = molecule ID
type = atom type
element = name of atom element, as defined by <A HREF = "dump_modify.html">dump_modify</A> command
mass = atom mass
x,y,z = unscaled atom coordinates
xs,ys,zs = scaled atom coordinates
xu,yu,zu = unwrapped atom coordinates
xsu,ysu,zsu = scaled unwrapped atom coordinates
ix,iy,iz = box image that the atom is in
vx,vy,vz = atom velocities
fx,fy,fz = forces on atoms
q = atom charge
mux,muy,muz = orientation of dipole moment of atom
mu = magnitude of dipole moment of atom
radius,diameter = radius,diameter of spherical particle
omegax,omegay,omegaz = angular velocity of extended particle
angmomx,angmomy,angmomz = angular momentum of extended particle
tqx,tqy,tqz = torque on extended particles
spin = electron spin
eradius = electron radius
ervel = electron radial velocity
erforce = electron radial force
c_ID = per-atom vector calculated by a compute with ID
c_ID[N] = Nth column of per-atom array calculated by a compute with ID
f_ID = per-atom vector calculated by a fix with ID
f_ID[N] = Nth column of per-atom array calculated by a fix with ID
v_name = per-atom vector calculated by an atom-style variable with name
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>dump myDump all atom 100 dump.atom
dump 2 subgroup atom 50 dump.run.bin
dump 4a all custom 100 dump.myforce.* id type x y vx fx
dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
dump 2 inner cfg 10 dump.snap.*.cfg id type xs ys zs vx vy vz
dump snap all cfg 100 dump.config.*.cfg id type xs ys zs id type c_Stress<B>2</B>
dump 1 all xtc 1000 file.xtc
dump e_data all custom 100 dump.eff id type x y z spin eradius fx fy fz eforce
</PRE>
<P><B>Description:</B>
</P>
<P>Dump a snapshot of atom quantities to one or more files every N
timesteps in one of several styles. The <I>image</I> style is the
exception; it creates a JPG or PPM image file of the atom
configuration every N timesteps, as discussed on the <A HREF = "dump_image.html">dump
image</A> doc page.
</P>
<P>Only information for atoms in the specified group is dumped. The
<A HREF = "dump_modify.html">dump_modify thresh and region</A> commands can also
alter what atoms are included. Not all styles support all these
options; see details below.
</P>
<P>As described below, the filename determines the kind of output (text
or binary or gzipped, one big file or one per timestep, one big file
or one per processor).
</P>
<P>IMPORTANT NOTE: Because periodic boundary conditions are enforced only
on timesteps when neighbor lists are rebuilt, the coordinates of an
atom written to a dump file may be slightly outside the simulation
box.
</P>
<P>IMPORTANT NOTE: Unless the <A HREF = "dump_modify.html">dump_modify sort</A> option
is invoked, the lines of atom information written to dump files
(typically one line per atom) will be in an indeterminate order for
each snapshot. This is even true when running on a single processor,
if the <A HREF = "atom_modify.html">atom_modify sort</A> option is on, which it is
by default. In this case atoms are re-ordered periodically during a
simulation, due to spatial sorting. It is also true when running in
parallel, because data for a single snapshot is collected from
multiple processors.
</P>
<P>For the <I>atom</I>, <I>custom</I>, <I>cfg</I>, and <I>local</I> styles, sorting is off by
default. For the <I>dcd</I>, <I>xtc</I>, and <I>xyz</I> styles, sorting by atom ID
is on by default. See the <A HREF = "dump_modify.html">dump_modify</A> doc page for
details.
</P>
<HR>
<P>The <I>style</I> keyword determines what atom quantities are written to the
file and in what format. Settings made via the
<A HREF = "dump_modify.html">dump_modify</A> command can also alter the format of
individual values and the file itself.
</P>
<P>The <I>atom</I>, <I>local</I>, and <I>custom</I> styles create files in a simple text
format that is self-explanatory when viewing a dump file. Many of the
LAMMPS <A HREF = "Section_tools.html">post-processing tools</A>, including
<A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A>, work with
this format.
</P>
<P>For post-processing purposes the <I>atom</I> and <I>custom</I> text files are
self-describing in the following sense.
</P>
<P>The dimensions of the simulation box are included in each snapshot.
For an orthogonal simulation box this information is is formatted as:
</P>
<PRE>ITEM: BOX BOUNDS xx yy zz
xlo xhi
ylo yhi
zlo zhi
</PRE>
<P>where xlo,xhi are the maximum extents of the simulation box in the
x-dimension, and similarly for y and z. The "xx yy zz" represent 6
characters that encode the style of boundary for each of the 6
simulation box boundaries (xlo,xhi and ylo,yhi and zlo,zhi). Each of
the 6 characters is either p = periodic, f = fixed, s = shrink wrap,
or m = shrink wrapped with a minimum value. See the
<A HREF = "doc/boundary.html">boundary</A> command for details.
</P>
<P>For triclinic simulation boxes (non-orthogonal), an orthogonal
bounding box which encloses the triclinic simulation box is output,
along with the 3 tilt factors (xy, xz, yz) of the triclinic box,
formatted as follows:
</P>
<PRE>ITEM: BOX BOUNDS xy xz yz xx yy zz
xlo_bound xhi_bound xy
ylo_bound yhi_bound xz
zlo_bound zhi_bound yz
</PRE>
<P>The presence of the text "xy xz yz" in the ITEM line indicates that
the 3 tilt factors will be included on each of the 3 following lines.
This bounding box is convenient for many visualization programs. The
meaning of the 6 character flags for "xx yy zz" is the same as above.
</P>
<P>Note that the first two numbers on each line are now xlo_bound instead
of xlo, etc, since they repesent a bounding box. See <A HREF = "Section_howto.html#howto_12">this
section</A> of the doc pages for a geometric
description of triclinic boxes, as defined by LAMMPS, simple formulas
for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are
calculated from the triclinic parameters, and how to transform those
parameters to and from other commonly used triclinic representations.
</P>
<P>The "ITEM: ATOMS" line in each snapshot lists column descriptors for
the per-atom lines that follow. For example, the descriptors would be
"id type xs ys zs" for the default <I>atom</I> style, and would be the atom
attributes you specify in the dump command for the <I>custom</I> style.
</P>
<P>For style <I>atom</I>, atom coordinates are written to the file, along with
the atom ID and atom type. By default, atom coords are written in a
scaled format (from 0 to 1). I.e. an x value of 0.25 means the atom
is at a location 1/4 of the distance from xlo to xhi of the box
boundaries. The format can be changed to unscaled coords via the
<A HREF = "dump_modify.html">dump_modify</A> settings. Image flags can also be
added for each atom via dump_modify.
</P>
<P>Style <I>custom</I> allows you to specify a list of atom attributes to be
written to the dump file for each atom. Possible attributes are
listed above and will appear in the order specified. You cannot
specify a quantity that is not defined for a particular simulation -
such as <I>q</I> for atom style <I>bond</I>, since that atom style doesn't
assign charges. Dumps occur at the very end of a timestep, so atom
attributes will include effects due to fixes that are applied during
the timestep. An explanation of the possible dump custom attributes
is given below.
</P>
<P>For style <I>local</I>, local output generated by <A HREF = "compute.html">computes</A>
and <A HREF = "fix.html">fixes</A> is used to gnerate lines of output that is
written to the dump file. This local data is typically calculated by
each processor based on the atoms it owns, but there may be zero or
more entities per atom, e.g. a list of bond distances. An explanation
of the possible dump local attributes is given below. Note that by
using input from the <A HREF = "compute_property_local.html">compute
property/local</A> command with dump local,
it is possible to generate information on bonds, angles, etc that can
be cut and pasted directly into a data file read by the
<A HREF = "read_data.html">read_data</A> command.
</P>
<P>Style <I>cfg</I> has the same command syntax as style <I>custom</I> and writes
extended CFG format files, as used by the
<A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualization
package. Since the extended CFG format uses a single snapshot of the
system per file, a wildcard "*" must be included in the filename, as
discussed below. The list of atom attributes for style <I>cfg</I> must
begin with either "id type xs ys zs" or "id type xsu ysu zsu" or
since these quantities are needed to
write the CFG files in the appropriate format (though the "id" and
"type" fields do not appear explicitly in the file). Any remaining
attributes will be stored as "auxiliary properties" in the CFG files.
Note that you will typically want to use the <A HREF = "dump_modify.html">dump_modify
element</A> command with CFG-formatted files, to
associate element names with atom types, so that AtomEye can render
atoms appropriately. When unwrapped coordinates <I>xsu</I>, <I>ysu</I>, and <I>zsu</I>
are requested, the nominal AtomEye periodic cell dimensions are expanded
by a large factor UNWRAPEXPAND = 10.0, which ensures atoms that are
displayed correctly for up to UNWRAPEXPAND/2 periodic boundary crossings
in any direction.
Beyond this, AtomEye will rewrap the unwrapped coordinates.
The expansion causes the atoms to be drawn farther
away from the viewer, but it is easy to zoom the atoms closer, and
the interatomic distances are unaffected.
</P>
<P>The <I>dcd</I> style writes DCD files, a standard atomic trajectory format
used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD
files are binary and thus may not be portable to different machines.
The number of atoms per snapshot cannot change with the <I>dcd</I> style.
The <I>unwrap</I> option of the <A HREF = "dump_modify.html">dump_modify</A> command
allows DCD coordinates to be written "unwrapped" by the image flags
for each atom. Unwrapped means that if the atom has passed through
a periodic boundary one or more times, the value is printed for what
the coordinate would be if it had not been wrapped back into the
periodic box. Note that these coordinates may thus be far outside
the box size stored with the snapshot.
</P>
<P>The <I>xtc</I> style writes XTC files, a compressed trajectory format used
by the GROMACS molecular dynamics package, and described
<A HREF = "http://manual.gromacs.org/current/online/xtc.html">here</A>.
The precision used in XTC files can be adjusted via the
<A HREF = "dump_modify.html">dump_modify</A> command. The default value of 1000
means that coordinates are stored to 1/1000 nanometer accuracy. XTC
files are portable binary files written in the NFS XDR data format,
so that any machine which supports XDR should be able to read them.
The number of atoms per snapshot cannot change with the <I>xtc</I> style.
The <I>unwrap</I> option of the <A HREF = "dump_modify.html">dump_modify</A> command allows
XTC coordinates to be written "unwrapped" by the image flags for each
atom. Unwrapped means that if the atom has passed thru a periodic
boundary one or more times, the value is printed for what the
coordinate would be if it had not been wrapped back into the periodic
box. Note that these coordinates may thus be far outside the box size
stored with the snapshot.
</P>
<P>The <I>xyz</I> style writes XYZ files, which is a simple text-based
coordinate format that many codes can read.
</P>
<P>Note that DCD, XTC, and XYZ formatted files can be read directly by
<A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> (a popular molecular viewing
program). See <A HREF = "Section_tools.html#vmd">this section</A> of the manual and
the tools/lmp2vmd/README.txt file for more information about support
in VMD for reading and visualizing LAMMPS dump files.
</P>
<HR>
<P>Dumps are performed on timesteps that are a multiple of N (including
timestep 0) and on the last timestep of a minimization if the
minimization converges. Note that this means a dump will not be
performed on the initial timestep after the dump command is invoked,
if the current timestep is not a multiple of N. This behavior can be
changed via the <A HREF = "dump_modify.html">dump_modify first</A> command, which
can be useful if the dump command is invoked after a minimization
ended on an arbitrary timestep. N can be changed between runs by
using the <A HREF = "dump_modify.html">dump_modify every</A> command (not allowed
for <I>dcd</I> style).
</P>
<P>The specified filename determines how the dump file(s) is written.
The default is to write one large text file, which is opened when the
dump command is invoked and closed when an <A HREF = "undump.html">undump</A>
command is used or when LAMMPS exits. For the <I>dcd</I> and <I>xtc</I> styles,
this is a single large binary file.
</P>
<P>Dump filenames can contain two wildcard characters. If a "*"
character appears in the filename, then one file per snapshot is
written and the "*" character is replaced with the timestep value.
For example, tmp.dump.* becomes tmp.dump.0, tmp.dump.10000,
tmp.dump.20000, etc. This option is not available for the <I>dcd</I> and
<I>xtc</I> styles. Note that the <A HREF = "dump_modify.html">dump_modify pad</A>
command can be used to insure all timestep numbers are the same length
(e.g. 00010), which can make it easier to read a series of dump files
in order by some post-processing tools.
</P>
<P>If a "%" character appears in the filename, then one file is written
for each processor and the "%" character is replaced with the
processor ID from 0 to P-1. For example, tmp.dump.% becomes
tmp.dump.0, tmp.dump.1, ... tmp.dump.P-1, etc. This creates smaller
files and can be a fast mode of output on parallel machines that
support parallel I/O for output. This option is not available for the
<I>dcd</I>, <I>xtc</I>, and <I>xyz</I> styles.
</P>
<P>Note that the "*" and "%" characters can be used together to produce a
large number of small dump files!
</P>
<P>If the filename ends with ".bin", the dump file (or files, if "*" or
"%" is also used) is written in binary format. A binary dump file
will be about the same size as a text version, but will typically
write out much faster. Of course, when post-processing, you will need
to convert it back to text format (see the <A HREF = "Section_tools.html#binary">binary2txt
tool</A>) or write your own code to read the
binary file. The format of the binary file can be understood by
looking at the tools/binary2txt.cpp file. This option is only
available for the <I>atom</I> and <I>custom</I> styles.
</P>
<P>If the filename ends with ".gz", the dump file (or files, if "*" or "%"
is also used) is written in gzipped format. A gzipped dump file will
be about 3x smaller than the text version, but will also take longer
to write. This option is not available for the <I>dcd</I> and <I>xtc</I>
styles.
</P>
<HR>
<P>This section explains the local attributes that can be specified as
part of the <I>local</I> style.
</P>
<P>The <I>index</I> attribute can be used to generate an index number from 1
to N for each line written into the dump file, where N is the total
number of local datums from all processors, or lines of output that
will appear in the snapshot. Note that because data from different
processors depend on what atoms they currently own, and atoms migrate
between processor, there is no guarantee that the same index will be
used for the same info (e.g. a particular bond) in successive
snapshots.
</P>
<P>The <I>c_ID</I> and <I>c_ID[N]</I> attributes allow local vectors or arrays
calculated by a <A HREF = "compute.html">compute</A> to be output. The ID in the
attribute should be replaced by the actual ID of the compute that has
been defined previously in the input script. See the
<A HREF = "compute.html">compute</A> command for details. There are computes for
calculating local information such as indices, types, and energies for
bonds and angles.
</P>
<P>Note that computes which calculate global or per-atom quantities, as
opposed to local quantities, cannot be output in a dump local command.
Instead, global quantities can be output by the <A HREF = "thermo_style.html">thermo_style
custom</A> command, and per-atom quantities can be
output by the dump custom command.
</P>
<P>If <I>c_ID</I> is used as a attribute, then the local vector calculated by
the compute is printed. If <I>c_ID[N]</I> is used, then N must be in the
range from 1-M, which will print the Nth column of the M-length local
array calculated by the compute.
</P>
<P>The <I>f_ID</I> and <I>f_ID[N]</I> attributes allow local vectors or arrays
calculated by a <A HREF = "fix.html">fix</A> to be output. The ID in the attribute
should be replaced by the actual ID of the fix that has been defined
previously in the input script.
</P>
<P>If <I>f_ID</I> is used as a attribute, then the local vector calculated by
the fix is printed. If <I>f_ID[N]</I> is used, then N must be in the
range from 1-M, which will print the Nth column of the M-length local
array calculated by the fix.
</P>
<HR>
<P>This section explains the atom attributes that can be specified as
part of the <I>custom</I> and <I>cfg</I> styles.
</P>
<P>The <I>id</I>, <I>mol</I>, <I>type</I>, <I>element</I>, <I>mass</I>, <I>vx</I>, <I>vy</I>, <I>vz</I>, <I>fx</I>, <I>fy</I>,
<I>fz</I>, <I>q</I> attributes are self-explanatory.
</P>
<P><I>Id</I> is the atom ID. <I>Mol</I> is the molecule ID, included in the data
file for molecular systems. <I>Type</I> is the atom type. <I>Element</I> is
typically the chemical name of an element, which you must assign to
each type via the <A HREF = "dump_modify.html">dump_modify element</A> command.
More generally, it can be any string you wish to associated with an
atom type. <I>Mass</I> is the atom mass. <I>Vx</I>, <I>vy</I>, <I>vz</I>, <I>fx</I>, <I>fy</I>,
<I>fz</I>, and <I>q</I> are components of atom velocity and force and atomic
charge.
</P>
<P>There are several options for outputting atom coordinates. The <I>x</I>,
<I>y</I>, <I>z</I> attributes write atom coordinates "unscaled", in the
appropriate distance <A HREF = "units.html">units</A> (Angstroms, sigma, etc). Use
<I>xs</I>, <I>ys</I>, <I>zs</I> if you want the coordinates "scaled" to the box size,
so that each value is 0.0 to 1.0. If the simulation box is triclinic
(tilted), then all atom coords will still be between 0.0 and 1.0. Use
<I>xu</I>, <I>yu</I>, <I>zu</I> if you want the coordinates "unwrapped" by the image
flags for each atom. Unwrapped means that if the atom has passed thru
a periodic boundary one or more times, the value is printed for what
the coordinate would be if it had not been wrapped back into the
periodic box. Note that using <I>xu</I>, <I>yu</I>, <I>zu</I> means that the
coordinate values may be far outside the box bounds printed with the
snapshot. Using <I>xsu</I>, <I>ysu</I>, <I>zsu</I> is similar to using <I>xu</I>, <I>yu</I>, <I>zu</I>,
except that the unwrapped coordinates are scaled by the box size. Atoms
that have passed through a periodic boundary will have the corresponding
cooordinate increased or decreased by 1.0.
</P>
<P>The image flags can be printed directly using the <I>ix</I>,
<I>iy</I>, <I>iz</I> attributes. The <A HREF = "dump_modify.html">dump_modify</A> command
describes in more detail what is meant by scaled vs unscaled
coordinates and the image flags.
</P>
<P>The <I>mux</I>, <I>muy</I>, <I>muz</I> attributes are specific to dipolar systems
defined with an atom style of <I>dipole</I>. They give the orientation of
the atom's point dipole moment. The <I>mu</I> attribute gives the
magnitude of the atom's dipole moment.
</P>
<P>The <I>radius</I> and <I>diameter</I> attributes are specific to extended
spherical particles that have a finite size, such as those defined
with an atom style of <I>sphere</I>.
</P>
<P>The <I>omegax</I>, <I>omegay</I>, and <I>omegaz</I> attributes are specific to
extended spherical or aspherical particles that have an angular
velocity. Only certain atom styles, such as <I>sphere</I> define this
quantity.
</P>
<P>The <I>angmomx</I>, <I>angmomy</I>, and <I>angmomz</I> attributes are specific to
extended aspherical particles that have an angular momentum. Only
the <I>ellipsoid</I> atom style defines this quantity.
</P>
<P>The <I>tqx</I>, <I>tqy</I>, <I>tqz</I> attributes are for extended spherical or
aspherical particles that can sustain a rotational torque due
to interactions with other particles.
</P>
<P>The <I>spin</I>, <I>eradius</I>, <I>ervel</I>, and <I>erforce</I> attributes are for
particles that represent nuclei and electrons modeled with the
electronic force field (EFF). See <A HREF = "atom_style.html">atom_style
electron</A> and <A HREF = "pair_eff.html">pair_style eff</A> for more
details.
</P>
<P>The <I>c_ID</I> and <I>c_ID[N]</I> attributes allow per-atom vectors or arrays
calculated by a <A HREF = "compute.html">compute</A> to be output. The ID in the
attribute should be replaced by the actual ID of the compute that has
been defined previously in the input script. See the
<A HREF = "compute.html">compute</A> command for details. There are computes for
calculating the per-atom energy, stress, centro-symmetry parameter,
and coordination number of individual atoms.
</P>
<P>Note that computes which calculate global or local quantities, as
opposed to per-atom quantities, cannot be output in a dump custom
command. Instead, global quantities can be output by the
<A HREF = "thermo_style.html">thermo_style custom</A> command, and local quantities
can be output by the dump local command.
</P>
<P>If <I>c_ID</I> is used as a attribute, then the per-atom vector calculated
by the compute is printed. If <I>c_ID[N]</I> is used, then N must be in
the range from 1-M, which will print the Nth column of the M-length
per-atom array calculated by the compute.
</P>
<P>The <I>f_ID</I> and <I>f_ID[N]</I> attributes allow vector or array per-atom
quantities calculated by a <A HREF = "fix.html">fix</A> to be output. The ID in the
attribute should be replaced by the actual ID of the fix that has been
defined previously in the input script. The <A HREF = "fix_ave_atom.html">fix
ave/atom</A> command is one that calculates per-atom
quantities. Since it can time-average per-atom quantities produced by
any <A HREF = "compute.html">compute</A>, <A HREF = "fix.html">fix</A>, or atom-style
<A HREF = "variable.html">variable</A>, this allows those time-averaged results to
be written to a dump file.
</P>
<P>If <I>f_ID</I> is used as a attribute, then the per-atom vector calculated
by the fix is printed. If <I>f_ID[N]</I> is used, then N must be in the
range from 1-M, which will print the Nth column of the M-length
per-atom array calculated by the fix.
</P>
<P>The <I>v_name</I> attribute allows per-atom vectors calculated by a
<A HREF = "variable.html">variable</A> to be output. The name in the attribute
should be replaced by the actual name of the variable that has been
defined previously in the input script. Only an atom-style variable
can be referenced, since it is the only style that generates per-atom
values. Variables of style <I>atom</I> can reference individual atom
attributes, per-atom atom attributes, thermodynamic keywords, or
invoke other computes, fixes, or variables when they are evaluated, so
this is a very general means of creating quantities to output to a
dump file.
</P>
<P>See <A HREF = "Section_modify.html">this section</A> of the manual for information
on how to add new compute and fix styles to LAMMPS to calculate
per-atom quantities which could then be output into dump files.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>To write gzipped dump files, you must compile LAMMPS with the
-DLAMMPS_GZIP option - see the <A HREF = "Section_start.html#start_2">Making
LAMMPS</A> section of the documentation.
</P>
-<P>The <I>xtc</I> style is part of the "xtc" package. It is only enabled if
+<P>The <I>xtc</I> style is part of the XTC package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info. This is
because some machines may not support the low-level XDR data format
that XTC files are written with, which will result in a compile-time
error when a low-level include file is not found. Putting this style
in a package makes it easy to exclude from a LAMMPS build for those
machines. However, the XTC package also includes two compatibility
header files and associated functions, which should be a suitable
substitute on machines that do not have the appropriate native header
files. This option can be invoked at build time by adding
-DLAMMPS_XDR to the CCFLAGS variable in the appropriate low-level
Makefile, e.g. src/MAKE/Makefile.foo. This compatibility mode has
been tested successfully on Cray XT3/XT4/XT5 and IBM BlueGene/L
machines and should also work on IBM BG/P, and Windows XP/Vista/7
machines.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dump_image.html">dump image</A>, <A HREF = "dump_modify.html">dump_modify</A>,
<A HREF = "undump.html">undump</A>
</P>
<P><B>Default:</B>
</P>
<P>The defaults for the image style are listed on the <A HREF = "dump_image.html">dump
image</A> doc page.
</P>
</HTML>
diff --git a/doc/dump.txt b/doc/dump.txt
index 96b3126b4..56df5f44a 100644
--- a/doc/dump.txt
+++ b/doc/dump.txt
@@ -1,527 +1,527 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
dump command :h3
"dump image"_dump_image.html command :h3
[Syntax:]
dump ID group-ID style N file args :pre
ID = user-assigned name for the dump :ulb,l
group-ID = ID of the group of atoms to be dumped :l
style = {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {image} or {local} or {custom} :l
N = dump every this many timesteps :l
file = name of file to write dump info to :l
args = list of arguments for a particular style :l
{atom} args = none
{cfg} args = same as {custom} args, see below
{dcd} args = none
{xtc} args = none
{xyz} args = none :pre
{image} args = discussed on "dump image"_dump_image.html doc page :pre
{local} args = list of local attributes
possible attributes = index, c_ID, c_ID\[N\], f_ID, f_ID\[N\]
index = enumeration of local values
c_ID = local vector calculated by a compute with ID
c_ID\[N\] = Nth column of local array calculated by a compute with ID
f_ID = local vector calculated by a fix with ID
f_ID\[N\] = Nth column of local array calculated by a fix with ID :pre
{custom} args = list of atom attributes
possible attributes = id, mol, type, element, mass,
x, y, z, xs, ys, zs, xu, yu, zu,
xsu, ysu, zsu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu,
radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, tqx, tqy, tqz,
spin, eradius, ervel, erforce,
c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
id = atom ID
mol = molecule ID
type = atom type
element = name of atom element, as defined by "dump_modify"_dump_modify.html command
mass = atom mass
x,y,z = unscaled atom coordinates
xs,ys,zs = scaled atom coordinates
xu,yu,zu = unwrapped atom coordinates
xsu,ysu,zsu = scaled unwrapped atom coordinates
ix,iy,iz = box image that the atom is in
vx,vy,vz = atom velocities
fx,fy,fz = forces on atoms
q = atom charge
mux,muy,muz = orientation of dipole moment of atom
mu = magnitude of dipole moment of atom
radius,diameter = radius,diameter of spherical particle
omegax,omegay,omegaz = angular velocity of extended particle
angmomx,angmomy,angmomz = angular momentum of extended particle
tqx,tqy,tqz = torque on extended particles
spin = electron spin
eradius = electron radius
ervel = electron radial velocity
erforce = electron radial force
c_ID = per-atom vector calculated by a compute with ID
c_ID\[N\] = Nth column of per-atom array calculated by a compute with ID
f_ID = per-atom vector calculated by a fix with ID
f_ID\[N\] = Nth column of per-atom array calculated by a fix with ID
v_name = per-atom vector calculated by an atom-style variable with name :pre
:ule
[Examples:]
dump myDump all atom 100 dump.atom
dump 2 subgroup atom 50 dump.run.bin
dump 4a all custom 100 dump.myforce.* id type x y vx fx
dump 4b flow custom 100 dump.%.myforce id type c_myF\[3\] v_ke
dump 2 inner cfg 10 dump.snap.*.cfg id type xs ys zs vx vy vz
dump snap all cfg 100 dump.config.*.cfg id type xs ys zs id type c_Stress[2]
dump 1 all xtc 1000 file.xtc
dump e_data all custom 100 dump.eff id type x y z spin eradius fx fy fz eforce :pre
[Description:]
Dump a snapshot of atom quantities to one or more files every N
timesteps in one of several styles. The {image} style is the
exception; it creates a JPG or PPM image file of the atom
configuration every N timesteps, as discussed on the "dump
image"_dump_image.html doc page.
Only information for atoms in the specified group is dumped. The
"dump_modify thresh and region"_dump_modify.html commands can also
alter what atoms are included. Not all styles support all these
options; see details below.
As described below, the filename determines the kind of output (text
or binary or gzipped, one big file or one per timestep, one big file
or one per processor).
IMPORTANT NOTE: Because periodic boundary conditions are enforced only
on timesteps when neighbor lists are rebuilt, the coordinates of an
atom written to a dump file may be slightly outside the simulation
box.
IMPORTANT NOTE: Unless the "dump_modify sort"_dump_modify.html option
is invoked, the lines of atom information written to dump files
(typically one line per atom) will be in an indeterminate order for
each snapshot. This is even true when running on a single processor,
if the "atom_modify sort"_atom_modify.html option is on, which it is
by default. In this case atoms are re-ordered periodically during a
simulation, due to spatial sorting. It is also true when running in
parallel, because data for a single snapshot is collected from
multiple processors.
For the {atom}, {custom}, {cfg}, and {local} styles, sorting is off by
default. For the {dcd}, {xtc}, and {xyz} styles, sorting by atom ID
is on by default. See the "dump_modify"_dump_modify.html doc page for
details.
:line
The {style} keyword determines what atom quantities are written to the
file and in what format. Settings made via the
"dump_modify"_dump_modify.html command can also alter the format of
individual values and the file itself.
The {atom}, {local}, and {custom} styles create files in a simple text
format that is self-explanatory when viewing a dump file. Many of the
LAMMPS "post-processing tools"_Section_tools.html, including
"Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html, work with
this format.
For post-processing purposes the {atom} and {custom} text files are
self-describing in the following sense.
The dimensions of the simulation box are included in each snapshot.
For an orthogonal simulation box this information is is formatted as:
ITEM: BOX BOUNDS xx yy zz
xlo xhi
ylo yhi
zlo zhi :pre
where xlo,xhi are the maximum extents of the simulation box in the
x-dimension, and similarly for y and z. The "xx yy zz" represent 6
characters that encode the style of boundary for each of the 6
simulation box boundaries (xlo,xhi and ylo,yhi and zlo,zhi). Each of
the 6 characters is either p = periodic, f = fixed, s = shrink wrap,
or m = shrink wrapped with a minimum value. See the
"boundary"_doc/boundary.html command for details.
For triclinic simulation boxes (non-orthogonal), an orthogonal
bounding box which encloses the triclinic simulation box is output,
along with the 3 tilt factors (xy, xz, yz) of the triclinic box,
formatted as follows:
ITEM: BOX BOUNDS xy xz yz xx yy zz
xlo_bound xhi_bound xy
ylo_bound yhi_bound xz
zlo_bound zhi_bound yz :pre
The presence of the text "xy xz yz" in the ITEM line indicates that
the 3 tilt factors will be included on each of the 3 following lines.
This bounding box is convenient for many visualization programs. The
meaning of the 6 character flags for "xx yy zz" is the same as above.
Note that the first two numbers on each line are now xlo_bound instead
of xlo, etc, since they repesent a bounding box. See "this
section"_Section_howto.html#howto_12 of the doc pages for a geometric
description of triclinic boxes, as defined by LAMMPS, simple formulas
for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are
calculated from the triclinic parameters, and how to transform those
parameters to and from other commonly used triclinic representations.
The "ITEM: ATOMS" line in each snapshot lists column descriptors for
the per-atom lines that follow. For example, the descriptors would be
"id type xs ys zs" for the default {atom} style, and would be the atom
attributes you specify in the dump command for the {custom} style.
For style {atom}, atom coordinates are written to the file, along with
the atom ID and atom type. By default, atom coords are written in a
scaled format (from 0 to 1). I.e. an x value of 0.25 means the atom
is at a location 1/4 of the distance from xlo to xhi of the box
boundaries. The format can be changed to unscaled coords via the
"dump_modify"_dump_modify.html settings. Image flags can also be
added for each atom via dump_modify.
Style {custom} allows you to specify a list of atom attributes to be
written to the dump file for each atom. Possible attributes are
listed above and will appear in the order specified. You cannot
specify a quantity that is not defined for a particular simulation -
such as {q} for atom style {bond}, since that atom style doesn't
assign charges. Dumps occur at the very end of a timestep, so atom
attributes will include effects due to fixes that are applied during
the timestep. An explanation of the possible dump custom attributes
is given below.
For style {local}, local output generated by "computes"_compute.html
and "fixes"_fix.html is used to gnerate lines of output that is
written to the dump file. This local data is typically calculated by
each processor based on the atoms it owns, but there may be zero or
more entities per atom, e.g. a list of bond distances. An explanation
of the possible dump local attributes is given below. Note that by
using input from the "compute
property/local"_compute_property_local.html command with dump local,
it is possible to generate information on bonds, angles, etc that can
be cut and pasted directly into a data file read by the
"read_data"_read_data.html command.
Style {cfg} has the same command syntax as style {custom} and writes
extended CFG format files, as used by the
"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A visualization
package. Since the extended CFG format uses a single snapshot of the
system per file, a wildcard "*" must be included in the filename, as
discussed below. The list of atom attributes for style {cfg} must
begin with either "id type xs ys zs" or "id type xsu ysu zsu" or
since these quantities are needed to
write the CFG files in the appropriate format (though the "id" and
"type" fields do not appear explicitly in the file). Any remaining
attributes will be stored as "auxiliary properties" in the CFG files.
Note that you will typically want to use the "dump_modify
element"_dump_modify.html command with CFG-formatted files, to
associate element names with atom types, so that AtomEye can render
atoms appropriately. When unwrapped coordinates {xsu}, {ysu}, and {zsu}
are requested, the nominal AtomEye periodic cell dimensions are expanded
by a large factor UNWRAPEXPAND = 10.0, which ensures atoms that are
displayed correctly for up to UNWRAPEXPAND/2 periodic boundary crossings
in any direction.
Beyond this, AtomEye will rewrap the unwrapped coordinates.
The expansion causes the atoms to be drawn farther
away from the viewer, but it is easy to zoom the atoms closer, and
the interatomic distances are unaffected.
The {dcd} style writes DCD files, a standard atomic trajectory format
used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD
files are binary and thus may not be portable to different machines.
The number of atoms per snapshot cannot change with the {dcd} style.
The {unwrap} option of the "dump_modify"_dump_modify.html command
allows DCD coordinates to be written "unwrapped" by the image flags
for each atom. Unwrapped means that if the atom has passed through
a periodic boundary one or more times, the value is printed for what
the coordinate would be if it had not been wrapped back into the
periodic box. Note that these coordinates may thus be far outside
the box size stored with the snapshot.
The {xtc} style writes XTC files, a compressed trajectory format used
by the GROMACS molecular dynamics package, and described
"here"_http://manual.gromacs.org/current/online/xtc.html.
The precision used in XTC files can be adjusted via the
"dump_modify"_dump_modify.html command. The default value of 1000
means that coordinates are stored to 1/1000 nanometer accuracy. XTC
files are portable binary files written in the NFS XDR data format,
so that any machine which supports XDR should be able to read them.
The number of atoms per snapshot cannot change with the {xtc} style.
The {unwrap} option of the "dump_modify"_dump_modify.html command allows
XTC coordinates to be written "unwrapped" by the image flags for each
atom. Unwrapped means that if the atom has passed thru a periodic
boundary one or more times, the value is printed for what the
coordinate would be if it had not been wrapped back into the periodic
box. Note that these coordinates may thus be far outside the box size
stored with the snapshot.
The {xyz} style writes XYZ files, which is a simple text-based
coordinate format that many codes can read.
Note that DCD, XTC, and XYZ formatted files can be read directly by
"VMD"_http://www.ks.uiuc.edu/Research/vmd (a popular molecular viewing
program). See "this section"_Section_tools.html#vmd of the manual and
the tools/lmp2vmd/README.txt file for more information about support
in VMD for reading and visualizing LAMMPS dump files.
:line
Dumps are performed on timesteps that are a multiple of N (including
timestep 0) and on the last timestep of a minimization if the
minimization converges. Note that this means a dump will not be
performed on the initial timestep after the dump command is invoked,
if the current timestep is not a multiple of N. This behavior can be
changed via the "dump_modify first"_dump_modify.html command, which
can be useful if the dump command is invoked after a minimization
ended on an arbitrary timestep. N can be changed between runs by
using the "dump_modify every"_dump_modify.html command (not allowed
for {dcd} style).
The specified filename determines how the dump file(s) is written.
The default is to write one large text file, which is opened when the
dump command is invoked and closed when an "undump"_undump.html
command is used or when LAMMPS exits. For the {dcd} and {xtc} styles,
this is a single large binary file.
Dump filenames can contain two wildcard characters. If a "*"
character appears in the filename, then one file per snapshot is
written and the "*" character is replaced with the timestep value.
For example, tmp.dump.* becomes tmp.dump.0, tmp.dump.10000,
tmp.dump.20000, etc. This option is not available for the {dcd} and
{xtc} styles. Note that the "dump_modify pad"_dump_modify.html
command can be used to insure all timestep numbers are the same length
(e.g. 00010), which can make it easier to read a series of dump files
in order by some post-processing tools.
If a "%" character appears in the filename, then one file is written
for each processor and the "%" character is replaced with the
processor ID from 0 to P-1. For example, tmp.dump.% becomes
tmp.dump.0, tmp.dump.1, ... tmp.dump.P-1, etc. This creates smaller
files and can be a fast mode of output on parallel machines that
support parallel I/O for output. This option is not available for the
{dcd}, {xtc}, and {xyz} styles.
Note that the "*" and "%" characters can be used together to produce a
large number of small dump files!
If the filename ends with ".bin", the dump file (or files, if "*" or
"%" is also used) is written in binary format. A binary dump file
will be about the same size as a text version, but will typically
write out much faster. Of course, when post-processing, you will need
to convert it back to text format (see the "binary2txt
tool"_Section_tools.html#binary) or write your own code to read the
binary file. The format of the binary file can be understood by
looking at the tools/binary2txt.cpp file. This option is only
available for the {atom} and {custom} styles.
If the filename ends with ".gz", the dump file (or files, if "*" or "%"
is also used) is written in gzipped format. A gzipped dump file will
be about 3x smaller than the text version, but will also take longer
to write. This option is not available for the {dcd} and {xtc}
styles.
:line
This section explains the local attributes that can be specified as
part of the {local} style.
The {index} attribute can be used to generate an index number from 1
to N for each line written into the dump file, where N is the total
number of local datums from all processors, or lines of output that
will appear in the snapshot. Note that because data from different
processors depend on what atoms they currently own, and atoms migrate
between processor, there is no guarantee that the same index will be
used for the same info (e.g. a particular bond) in successive
snapshots.
The {c_ID} and {c_ID\[N\]} attributes allow local vectors or arrays
calculated by a "compute"_compute.html to be output. The ID in the
attribute should be replaced by the actual ID of the compute that has
been defined previously in the input script. See the
"compute"_compute.html command for details. There are computes for
calculating local information such as indices, types, and energies for
bonds and angles.
Note that computes which calculate global or per-atom quantities, as
opposed to local quantities, cannot be output in a dump local command.
Instead, global quantities can be output by the "thermo_style
custom"_thermo_style.html command, and per-atom quantities can be
output by the dump custom command.
If {c_ID} is used as a attribute, then the local vector calculated by
the compute is printed. If {c_ID\[N\]} is used, then N must be in the
range from 1-M, which will print the Nth column of the M-length local
array calculated by the compute.
The {f_ID} and {f_ID\[N\]} attributes allow local vectors or arrays
calculated by a "fix"_fix.html to be output. The ID in the attribute
should be replaced by the actual ID of the fix that has been defined
previously in the input script.
If {f_ID} is used as a attribute, then the local vector calculated by
the fix is printed. If {f_ID\[N\]} is used, then N must be in the
range from 1-M, which will print the Nth column of the M-length local
array calculated by the fix.
:line
This section explains the atom attributes that can be specified as
part of the {custom} and {cfg} styles.
The {id}, {mol}, {type}, {element}, {mass}, {vx}, {vy}, {vz}, {fx}, {fy},
{fz}, {q} attributes are self-explanatory.
{Id} is the atom ID. {Mol} is the molecule ID, included in the data
file for molecular systems. {Type} is the atom type. {Element} is
typically the chemical name of an element, which you must assign to
each type via the "dump_modify element"_dump_modify.html command.
More generally, it can be any string you wish to associated with an
atom type. {Mass} is the atom mass. {Vx}, {vy}, {vz}, {fx}, {fy},
{fz}, and {q} are components of atom velocity and force and atomic
charge.
There are several options for outputting atom coordinates. The {x},
{y}, {z} attributes write atom coordinates "unscaled", in the
appropriate distance "units"_units.html (Angstroms, sigma, etc). Use
{xs}, {ys}, {zs} if you want the coordinates "scaled" to the box size,
so that each value is 0.0 to 1.0. If the simulation box is triclinic
(tilted), then all atom coords will still be between 0.0 and 1.0. Use
{xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the image
flags for each atom. Unwrapped means that if the atom has passed thru
a periodic boundary one or more times, the value is printed for what
the coordinate would be if it had not been wrapped back into the
periodic box. Note that using {xu}, {yu}, {zu} means that the
coordinate values may be far outside the box bounds printed with the
snapshot. Using {xsu}, {ysu}, {zsu} is similar to using {xu}, {yu}, {zu},
except that the unwrapped coordinates are scaled by the box size. Atoms
that have passed through a periodic boundary will have the corresponding
cooordinate increased or decreased by 1.0.
The image flags can be printed directly using the {ix},
{iy}, {iz} attributes. The "dump_modify"_dump_modify.html command
describes in more detail what is meant by scaled vs unscaled
coordinates and the image flags.
The {mux}, {muy}, {muz} attributes are specific to dipolar systems
defined with an atom style of {dipole}. They give the orientation of
the atom's point dipole moment. The {mu} attribute gives the
magnitude of the atom's dipole moment.
The {radius} and {diameter} attributes are specific to extended
spherical particles that have a finite size, such as those defined
with an atom style of {sphere}.
The {omegax}, {omegay}, and {omegaz} attributes are specific to
extended spherical or aspherical particles that have an angular
velocity. Only certain atom styles, such as {sphere} define this
quantity.
The {angmomx}, {angmomy}, and {angmomz} attributes are specific to
extended aspherical particles that have an angular momentum. Only
the {ellipsoid} atom style defines this quantity.
The {tqx}, {tqy}, {tqz} attributes are for extended spherical or
aspherical particles that can sustain a rotational torque due
to interactions with other particles.
The {spin}, {eradius}, {ervel}, and {erforce} attributes are for
particles that represent nuclei and electrons modeled with the
electronic force field (EFF). See "atom_style
electron"_atom_style.html and "pair_style eff"_pair_eff.html for more
details.
The {c_ID} and {c_ID\[N\]} attributes allow per-atom vectors or arrays
calculated by a "compute"_compute.html to be output. The ID in the
attribute should be replaced by the actual ID of the compute that has
been defined previously in the input script. See the
"compute"_compute.html command for details. There are computes for
calculating the per-atom energy, stress, centro-symmetry parameter,
and coordination number of individual atoms.
Note that computes which calculate global or local quantities, as
opposed to per-atom quantities, cannot be output in a dump custom
command. Instead, global quantities can be output by the
"thermo_style custom"_thermo_style.html command, and local quantities
can be output by the dump local command.
If {c_ID} is used as a attribute, then the per-atom vector calculated
by the compute is printed. If {c_ID\[N\]} is used, then N must be in
the range from 1-M, which will print the Nth column of the M-length
per-atom array calculated by the compute.
The {f_ID} and {f_ID\[N\]} attributes allow vector or array per-atom
quantities calculated by a "fix"_fix.html to be output. The ID in the
attribute should be replaced by the actual ID of the fix that has been
defined previously in the input script. The "fix
ave/atom"_fix_ave_atom.html command is one that calculates per-atom
quantities. Since it can time-average per-atom quantities produced by
any "compute"_compute.html, "fix"_fix.html, or atom-style
"variable"_variable.html, this allows those time-averaged results to
be written to a dump file.
If {f_ID} is used as a attribute, then the per-atom vector calculated
by the fix is printed. If {f_ID\[N\]} is used, then N must be in the
range from 1-M, which will print the Nth column of the M-length
per-atom array calculated by the fix.
The {v_name} attribute allows per-atom vectors calculated by a
"variable"_variable.html to be output. The name in the attribute
should be replaced by the actual name of the variable that has been
defined previously in the input script. Only an atom-style variable
can be referenced, since it is the only style that generates per-atom
values. Variables of style {atom} can reference individual atom
attributes, per-atom atom attributes, thermodynamic keywords, or
invoke other computes, fixes, or variables when they are evaluated, so
this is a very general means of creating quantities to output to a
dump file.
See "this section"_Section_modify.html of the manual for information
on how to add new compute and fix styles to LAMMPS to calculate
per-atom quantities which could then be output into dump files.
:line
[Restrictions:]
To write gzipped dump files, you must compile LAMMPS with the
-DLAMMPS_GZIP option - see the "Making
LAMMPS"_Section_start.html#start_2 section of the documentation.
-The {xtc} style is part of the "xtc" package. It is only enabled if
+The {xtc} style is part of the XTC package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info. This is
because some machines may not support the low-level XDR data format
that XTC files are written with, which will result in a compile-time
error when a low-level include file is not found. Putting this style
in a package makes it easy to exclude from a LAMMPS build for those
machines. However, the XTC package also includes two compatibility
header files and associated functions, which should be a suitable
substitute on machines that do not have the appropriate native header
files. This option can be invoked at build time by adding
-DLAMMPS_XDR to the CCFLAGS variable in the appropriate low-level
Makefile, e.g. src/MAKE/Makefile.foo. This compatibility mode has
been tested successfully on Cray XT3/XT4/XT5 and IBM BlueGene/L
machines and should also work on IBM BG/P, and Windows XP/Vista/7
machines.
[Related commands:]
"dump image"_dump_image.html, "dump_modify"_dump_modify.html,
"undump"_undump.html
[Default:]
The defaults for the image style are listed on the "dump
image"_dump_image.html doc page.
diff --git a/doc/fix_addforce.html b/doc/fix_addforce.html
index 2e5455418..4fe72468f 100644
--- a/doc/fix_addforce.html
+++ b/doc/fix_addforce.html
@@ -1,176 +1,176 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix addforce command
</H3>
<H3>fix addforce/cuda command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID addforce fx fy fz keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>addforce = style name of this fix command
<LI>fx,fy,fz = force component values (force units)
<LI>any of fx,fy,fz can be a variable (see below)
<LI>zero or more keyword/value pairs may be appended to args
<LI>keyword = <I>region</I> or <I>energy</I>
<PRE> <I>region</I> value = region-ID
region-ID = ID of region atoms must be in to have added force
<I>energy</I> value = v_name
v_name = variable with name that calculates the potential energy of each atom in the added force field
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix kick flow addforce 1.0 0.0 0.0
fix kick flow addforce 1.0 0.0 v_oscillate
fix ff boundary addforce 0.0 0.0 v_push energy v_espace
</PRE>
<P><B>Description:</B>
</P>
<P>Add fx,fy,fz to the corresponding component of force for each atom in
the group. This command can be used to give an additional push to
atoms in a simulation, such as for a simulation of Poiseuille flow in
a channel.
</P>
<P>Any of the 3 quantities defining the force components can be specified
as an equal-style or atom-style <A HREF = "variable.html">variable</A>, namely <I>fx</I>,
<I>fy</I>, <I>fz</I>. If the value is a variable, it should be specified as
v_name, where name is the variable name. In this case, the variable
will be evaluated each timestep, and its value used to determine the
force component.
</P>
<P>Equal-style variables can specify formulas with various mathematical
functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent force field.
</P>
<P>Atom-style variables can specify the same formulas as equal-style
variables but can also include per-atom values, such as atom
coordinates. Thus it is easy to specify a spatially-dependent force
field with optional time-dependence as well.
</P>
<P>If the <I>region</I> keyword is used, the atom must also be in the
specified geometric <A HREF = "region.html">region</A> in order to have force added
to it.
</P>
<HR>
<P>Adding a force to atoms implies a change in their potential energy as
they move due to the applied force field. For dynamics via the "run"
command, this energy can be optionally added to the system's potential
energy for thermodynamic output (see below). For energy minimization
via the "minimize" command, this energy must be added to the system's
potential energy to formulate a self-consistent minimization problem
(see below).
</P>
<P>The <I>energy</I> keyword is not allowed if the added force is a constant
vector F = (fx,fy,fz), with all components defined as numeric
constants and not as variables. This is because LAMMPS can compute
the energy for each atom directly as E = -x dot F = -(x*fx + y*fy +
z*fz), so that -Grad(E) = F.
</P>
<P>The <I>energy</I> keyword is optional if the added force is defined with
one or more variables, and if you are performing dynamics via the
<A HREF = "run.html">run</A> command. If the keyword is not used, LAMMPS will set
the energy to 0.0, which is typically fine for dynamics.
</P>
<P>The <I>energy</I> keyword is required if the added force is defined with
one or more variables, and you are performing energy minimization via
the "minimize" command. The keyword specifies the name of an
atom-style <A HREF = "variable.html">variable</A> which is used to compute the
energy of each atom as function of its position. Like variables used
for <I>fx</I>, <I>fy</I>, <I>fz</I>, the energy variable is specified as v_name,
where name is the variable name.
</P>
<P>Note that when the <I>energy</I> keyword is used during an energy
minimization, you must insure that the formula defined for the
atom-style <A HREF = "variable.html">variable</A> is consistent with the force
variable formulas, i.e. that -Grad(E) = F. For example, if the force
were a spring-like F = kx, then the energy formula should be E =
-0.5kx^2. If you don't do this correctly, the minimization will not
converge properly.
</P>
<HR>
<P>Styles with a <I>cuda</I> suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
<A HREF = "Section_accelerate.html">this section</A> of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the potential "energy" inferred by the added force to the
system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>. This is a fictitious quantity but is
needed so that the <A HREF = "minimize.html">minimize</A> command can include the
forces added by this fix in a consistent manner. I.e. there is a
decrease in potential energy when atoms move in the direction of the
added force.
</P>
<P>This fix computes a global scalar and a global 3-vector of forces,
which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. The scalar is the potential
energy discussed above. The vector is the total force on the group of
atoms before the forces on individual atoms are changed by the fix.
The scalar and vector values calculated by this fix are "extensive".
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command.
</P>
<P>The forces due to this fix are imposed during an energy minimization,
invoked by the <A HREF = "minimize.html">minimize</A> command. You should not
specify force components with a variable that has time-dependence for
use with a minimizer, since the minimizer increments the timestep as
the iteration count during the minimization.
</P>
<P>IMPORTANT NOTE: If you want the fictitious potential energy associated
with the added forces to be included in the total potential energy of
the system (the quantity being minimized), you MUST enable the
<A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for this fix.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_setforce.html">fix setforce</A>, <A HREF = "fix_aveforce.html">fix aveforce</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/fix_addforce.txt b/doc/fix_addforce.txt
index 3dc0b740b..e2c6e2e1f 100644
--- a/doc/fix_addforce.txt
+++ b/doc/fix_addforce.txt
@@ -1,163 +1,163 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix addforce command :h3
fix addforce/cuda command :h3
[Syntax:]
fix ID group-ID addforce fx fy fz keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
addforce = style name of this fix command :l
fx,fy,fz = force component values (force units) :l
any of fx,fy,fz can be a variable (see below) :l
zero or more keyword/value pairs may be appended to args :l
keyword = {region} or {energy} :l
{region} value = region-ID
region-ID = ID of region atoms must be in to have added force
{energy} value = v_name
v_name = variable with name that calculates the potential energy of each atom in the added force field :pre
:ule
[Examples:]
fix kick flow addforce 1.0 0.0 0.0
fix kick flow addforce 1.0 0.0 v_oscillate
fix ff boundary addforce 0.0 0.0 v_push energy v_espace :pre
[Description:]
Add fx,fy,fz to the corresponding component of force for each atom in
the group. This command can be used to give an additional push to
atoms in a simulation, such as for a simulation of Poiseuille flow in
a channel.
Any of the 3 quantities defining the force components can be specified
as an equal-style or atom-style "variable"_variable.html, namely {fx},
{fy}, {fz}. If the value is a variable, it should be specified as
v_name, where name is the variable name. In this case, the variable
will be evaluated each timestep, and its value used to determine the
force component.
Equal-style variables can specify formulas with various mathematical
functions, and include "thermo_style"_thermo_style.html command
keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent force field.
Atom-style variables can specify the same formulas as equal-style
variables but can also include per-atom values, such as atom
coordinates. Thus it is easy to specify a spatially-dependent force
field with optional time-dependence as well.
If the {region} keyword is used, the atom must also be in the
specified geometric "region"_region.html in order to have force added
to it.
:line
Adding a force to atoms implies a change in their potential energy as
they move due to the applied force field. For dynamics via the "run"
command, this energy can be optionally added to the system's potential
energy for thermodynamic output (see below). For energy minimization
via the "minimize" command, this energy must be added to the system's
potential energy to formulate a self-consistent minimization problem
(see below).
The {energy} keyword is not allowed if the added force is a constant
vector F = (fx,fy,fz), with all components defined as numeric
constants and not as variables. This is because LAMMPS can compute
the energy for each atom directly as E = -x dot F = -(x*fx + y*fy +
z*fz), so that -Grad(E) = F.
The {energy} keyword is optional if the added force is defined with
one or more variables, and if you are performing dynamics via the
"run"_run.html command. If the keyword is not used, LAMMPS will set
the energy to 0.0, which is typically fine for dynamics.
The {energy} keyword is required if the added force is defined with
one or more variables, and you are performing energy minimization via
the "minimize" command. The keyword specifies the name of an
atom-style "variable"_variable.html which is used to compute the
energy of each atom as function of its position. Like variables used
for {fx}, {fy}, {fz}, the energy variable is specified as v_name,
where name is the variable name.
Note that when the {energy} keyword is used during an energy
minimization, you must insure that the formula defined for the
atom-style "variable"_variable.html is consistent with the force
variable formulas, i.e. that -Grad(E) = F. For example, if the force
were a spring-like F = kx, then the energy formula should be E =
-0.5kx^2. If you don't do this correctly, the minimization will not
converge properly.
:line
Styles with a {cuda} suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
"this section"_Section_accelerate.html of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the potential "energy" inferred by the added force to the
system's potential energy as part of "thermodynamic
output"_thermo_style.html. This is a fictitious quantity but is
needed so that the "minimize"_minimize.html command can include the
forces added by this fix in a consistent manner. I.e. there is a
decrease in potential energy when atoms move in the direction of the
added force.
This fix computes a global scalar and a global 3-vector of forces,
which can be accessed by various "output
commands"_Section_howto.html#howto_15. The scalar is the potential
energy discussed above. The vector is the total force on the group of
atoms before the forces on individual atoms are changed by the fix.
The scalar and vector values calculated by this fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command. You should not
specify force components with a variable that has time-dependence for
use with a minimizer, since the minimizer increments the timestep as
the iteration count during the minimization.
IMPORTANT NOTE: If you want the fictitious potential energy associated
with the added forces to be included in the total potential energy of
the system (the quantity being minimized), you MUST enable the
"fix_modify"_fix_modify.html {energy} option for this fix.
[Restrictions:] none
[Related commands:]
"fix setforce"_fix_setforce.html, "fix aveforce"_fix_aveforce.html
[Default:] none
diff --git a/doc/fix_addtorque.html b/doc/fix_addtorque.html
index 5db501ff5..a9a521e3b 100644
--- a/doc/fix_addtorque.html
+++ b/doc/fix_addtorque.html
@@ -1,102 +1,102 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix addtorque command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID addtorque Tx Ty Tz
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>addtorque = style name of this fix command
<LI>Tx,Ty,Tz = torque component values (torque units)
<LI>any of Tx,Ty,Tz can be a variable (see below)
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix kick bead addtorque 2.0 3.0 5.0
fix kick bead addtorque 0.0 0.0 v_oscillate
</PRE>
<P><B>Description:</B>
</P>
<P>Add a set of forces to each atom in
the group such that:
</P>
<UL><LI>the components of the total torque applied on the group (around its
center of mass) are Tx,Ty,Tz
<LI>the group would move as a rigid body in the absence of other
forces.
</UL>
<P>This command can be used to drive a group of atoms into rotation.
</P>
<P>Any of the 3 quantities defining the torque components can be specified
as an equal-style <A HREF = "variable.html">variable</A>, namely <I>Tx</I>,
<I>Ty</I>, <I>Tz</I>. If the value is a variable, it should be specified as
v_name, where name is the variable name. In this case, the variable
will be evaluated each timestep, and its value used to determine the
torque component.
</P>
<P>Equal-style variables can specify formulas with various mathematical
functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent torque.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the potential "energy" inferred by the added forces to the
system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>. This is a fictitious quantity but is
needed so that the <A HREF = "minimize.html">minimize</A> command can include the
forces added by this fix in a consistent manner. I.e. there is a
decrease in potential energy when atoms move in the direction of the
added forces.
</P>
<P>This fix computes a global scalar and a global 3-vector, which can be
accessed by various <A HREF = "Section_howto.html#howto_15">output commands</A>.
The scalar is the potential energy discussed above. The vector is the
total torque on the group of atoms before the forces on individual
atoms are changed by the fix. The scalar and vector values calculated
by this fix are "extensive".
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command.
</P>
<P>The forces due to this fix are imposed during an energy minimization,
invoked by the <A HREF = "minimize.html">minimize</A> command. You should not
specify force components with a variable that has time-dependence for
use with a minimizer, since the minimizer increments the timestep as
the iteration count during the minimization.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "user-misc" package. It is only enabled if
+<P>This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_addforce.html">fix addforce</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/fix_addtorque.txt b/doc/fix_addtorque.txt
index 9e8b82f73..3cda16af6 100644
--- a/doc/fix_addtorque.txt
+++ b/doc/fix_addtorque.txt
@@ -1,93 +1,93 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix addtorque command :h3
[Syntax:]
fix ID group-ID addtorque Tx Ty Tz :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
addtorque = style name of this fix command :l
Tx,Ty,Tz = torque component values (torque units) :l
any of Tx,Ty,Tz can be a variable (see below) :l
:ule
[Examples:]
fix kick bead addtorque 2.0 3.0 5.0
fix kick bead addtorque 0.0 0.0 v_oscillate :pre
[Description:]
Add a set of forces to each atom in
the group such that:
the components of the total torque applied on the group (around its
center of mass) are Tx,Ty,Tz :ulb,l
the group would move as a rigid body in the absence of other
forces. :l,ule
This command can be used to drive a group of atoms into rotation.
Any of the 3 quantities defining the torque components can be specified
as an equal-style "variable"_variable.html, namely {Tx},
{Ty}, {Tz}. If the value is a variable, it should be specified as
v_name, where name is the variable name. In this case, the variable
will be evaluated each timestep, and its value used to determine the
torque component.
Equal-style variables can specify formulas with various mathematical
functions, and include "thermo_style"_thermo_style.html command
keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent torque.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the potential "energy" inferred by the added forces to the
system's potential energy as part of "thermodynamic
output"_thermo_style.html. This is a fictitious quantity but is
needed so that the "minimize"_minimize.html command can include the
forces added by this fix in a consistent manner. I.e. there is a
decrease in potential energy when atoms move in the direction of the
added forces.
This fix computes a global scalar and a global 3-vector, which can be
accessed by various "output commands"_Section_howto.html#howto_15.
The scalar is the potential energy discussed above. The vector is the
total torque on the group of atoms before the forces on individual
atoms are changed by the fix. The scalar and vector values calculated
by this fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command. You should not
specify force components with a variable that has time-dependence for
use with a minimizer, since the minimizer increments the timestep as
the iteration count during the minimization.
[Restrictions:]
-This fix is part of the "user-misc" package. It is only enabled if
+This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"fix addforce"_fix_addforce.html
[Default:] none
diff --git a/doc/fix_atc.html b/doc/fix_atc.html
index 7e37dd198..18063dd10 100644
--- a/doc/fix_atc.html
+++ b/doc/fix_atc.html
@@ -1,239 +1,239 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix atc command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID groupID atc type paramfile
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>atc = style name of this fix command
<LI>type = <I>thermal</I> or <I>two_temperature</I> or <I>hardy</I>
<PRE> <I>thermal</I> = thermal coupling with field: temperature
<I>two_temperature</I> = electron-phonon coupling with field, temperature and electron_temperature
<I>hardy</I> = Hardy on-the-fly post-processing
</PRE>
<LI>paramfile = file with material parameters (not specified for <I>hardy</I> type)
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix AtC atc_atoms atc thermal Ar_thermal.dat
fix AtC atc_atoms atc transfer hardy
</PRE>
<P><B>Description:</B>
</P>
<P>This fix creates a coupled finite element (FE) and molecular dynamics
(MD) simulation and/or an on-the-fly estimation of continuum fields,
where a FE mesh is specified and overlaps the particles, something
like this:
</P>
<CENTER><IMG SRC = "JPG/atc_nanotube.jpg">
</CENTER>
<P>Interscale operators are defined that construct continuum fields from
atomic data. Coupled simulations use FE projection approximated on a
discrete field. Currently, coupling is restricted to thermal physics.
The Hardy module can use either FE projection or integration Kernels
evaluated at mesh points.
</P>
<P>Coupling methods enable appropriate corrections to the atomic data to
be made based on the FE field. For example, a Gaussian isokinetic
thermostat can apply heat sources to the atoms that varies in space on
the same scale as the FE element size. Meshes are not created
automatically and must be specified on LAMMPS regions with prescribed
element sizes.
</P>
<P>Coupling and post-processing can be combined in the same simulations
using separate fix atc commands.
</P>
<P>Note that mesh computations and storage run in serial (not
parallelized) so performance will degrade when large element counts
are used.
</P>
<P>For detailed exposition of the theory and algorithms implemented in
this fix, please see the papers <A HREF = "#Wagner">here</A> and <A HREF = "#Zimmerman">here</A>.
Please refer to the standard finite element (FE) texts, such as <A HREF = "#Hughes">this
book</A>, for the basics of FE simulation.
</P>
<HR>
<P><I>Thermal</I> and <I>two_temperature</I> (coupling) types use a Verlet
time-integration algorithm. The <I>hardy</I> type does not contain its own
time-integrator and must be used with a separate fix that does contain
one, e.g. <A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nh.html">fix nvt</A>, etc.
</P>
<P>A set of example input files with the attendant material files are
included in the examples/USER/atc directory of the LAMMPS
distribution.
</P>
<P>An extensive set of additional documentation pages for the options
turned on via the <A HREF = "fix_modify.html">fix_modify</A> command for this fix
are inlcluded in the doc/USER/atc directory of the LAMMPS
distribution. Individual doc pages are listed and linked to below.
</P>
<P>The following commands are typical of a coupling problem:
</P>
<PRE> # ... commands to create and initialize the MD system
</PRE>
<PRE> # initial fix to designate coupling type and group to apply it to
# tag group physics material_file
fix AtC internal atc thermal Ar_thermal.mat
</PRE>
<PRE> # create a uniform 12 x 2 x 2 mesh that covers region contain the group
# nx ny nz region periodicity
fix_modify AtC fem create mesh 12 2 2 mdRegion f p p
</PRE>
<PRE> # specify the control method for the type of coupling
# physics control_type
fix_modify AtC transfer thermal control flux
</PRE>
<PRE> # specify the initial values for the empirical field "temperature"
# field node_group value
fix_modify AtC transfer initial temperature all 30.0
</PRE>
<PRE> # create an output stream for nodal fields
# filename output_frequency
fix_modify AtC transfer output atc_fe_output 100
</PRE>
<PRE> run 1000
</PRE>
<P>The following commands are typical of a post-processing (Hardy) problem:
</P>
<PRE> # ... commands to create and initialize the MD system
</PRE>
<PRE> # initial fix to designate post-processing and the group to apply it to
# no material file is allowed nor required
fix AtC internal atc hardy
</PRE>
<PRE> # create a uniform 1 x 1 x 1 mesh that covers region contain the group
# with periodicity this effectively creats a system average
fix_modify AtC fem create mesh 1 1 1 box p p p
</PRE>
<PRE> # change from default lagrangian map to eulerian
# refreshed every 100 steps
fix_modify AtC atom_element_map eulerian 100
</PRE>
<PRE> # start with no field defined
fix_modify AtC transfer fields none
</PRE>
<PRE> # add mass density, potential energy density, stress and temperature
fix_modify AtC transfer fields add density energy stress temperature
</PRE>
<PRE> # create an output stream for nodal fields
# filename output_frequency
fix_modify AtC transfer output nvtFE 100 text
</PRE>
<PRE> run 1000
</PRE>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. The <A HREF = "fix_modify.html">fix_modify</A> options
relevant to this fix are listed below. No global scalar or vector or
per-atom quantities are stored by this fix for access by various
<A HREF = "Section_howto.html#howto_15">output commands</A>. No parameter of this
fix can be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A>
command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "user-atc" package. It is only enabled if
+<P>This fix is part of the USER-ATC package. It is only enabled if
LAMMPS was built with that package, which also requires the ATC
library be built and linked with LAMMPS. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P>After specifying this fix in your input script, several other
<A HREF = "fix_modify.html">fix_modify</A> commands are used to setup the problem,
e.g. define the finite element mesh and prescribe initial and boundary
conditions.
</P>
<P>fix_modify commands for setup:
</P>
<UL><LI><A HREF = "USER/atc/man_fem_mesh.html">fix_modify AtC fem create mesh</A>
<LI><A HREF = "USER/atc/man_mesh_nodeset.html">fix_modify AtC mesh create_nodeset</A>
<LI><A HREF = "USER/atc/man_mesh_faceset.html">fix_modify AtC mesh create_faceset</A>
<LI><A HREF = "USER/atc/man_mesh_elemset.html">fix_modify AtC mesh create_elementset</A>
<LI><A HREF = "USER/atc/man_transfer_internal.html">fix_modify AtC transfer internal</A>
<LI><A HREF = "USER/atc/man_transfer_boundary.html">fix_modify AtC transfer boundary</A>
<LI><A HREF = "USER/atc/man_internal_quadrature.html">fix_modify AtC transfer internal_quadrature</A>
<LI><A HREF = "USER/atc/man_time_integration.html">fix_modify AtC transfer pmfc</A>
<LI><A HREF = "USER/atc/man_electron_integration.html">fix_modify AtC extrinsic electron_integration</A>
</UL>
<P>fix_modify commands for boundary and initial conditions:
</P>
<UL><LI><A HREF = "USER/atc/man_initial.html">fix_modify AtC transfer initial</A>
<LI><A HREF = "USER/atc/man_fix_nodes.html">fix_modify AtC transfer fix</A>
<LI><A HREF = "USER/atc/man_unfix_nodes.html">fix_modify AtC transfer unfix</A>
<LI><A HREF = "USER/atc/man_fix_flux.html">fix_modify AtC transfer fix_flux</A>
<LI><A HREF = "USER/atc/man_unfix_flux.html">fix_modify AtC transferunfix_flux</A>
<LI><A HREF = "USER/atc/man_source.html">fix_modify AtC transfer source</A>
<LI><A HREF = "USER/atc/man_remove_source.html">fix_modify AtC transfer remove_source</A>
</UL>
<P>fix_modify commands for control and filtering:
</P>
<UL><LI><A HREF = "USER/atc/man_thermal_control.html">fix_modify AtC transfer thermal control</A>
<LI><A HREF = "USER/atc/man_time_filter.html">fix_modify AtC transfer filter</A>
<LI><A HREF = "USER/atc/man_filter_scale.html">fix_modify AtC transfer filter scale</A>
<LI><A HREF = "USER/atc/man_equilibrium_start.html">fix_modify AtC transfer equilibrium_start</A>
<LI><A HREF = "USER/atc/man_extrinsic_exchange.html">fix_modify AtC extrinsic exchange</A>
</UL>
<P>fix_modify commands for output:
</P>
<UL><LI><A HREF = "USER/atc/man_transfer_output.html">fix_modify AtC transfer output</A>
<LI><A HREF = "USER/atc/man_transfer_atomic_output.html">fix_modify AtC transfer atomic_output</A>
<LI><A HREF = "USER/atc/man_mesh_output.html">fix_modify AtC mesh output</A>
<LI><A HREF = "USER/atc/man_write_restart.html">fix_modify AtC transfer write_restart</A>
<LI><A HREF = "USER/atc/man_read_restart.html">fix_modify AtC transfer read_restart</A>
</UL>
<P>fix_modify commands for post-processing:
</P>
<UL><LI><A HREF = "USER/atc/man_hardy_fields.html">fix_modify AtC transfer fields</A>
<LI><A HREF = "USER/atc/man_hardy_gradients.html">fix_modify AtC transfer gradients</A>
<LI><A HREF = "USER/atc/man_hardy_rates.html">fix_modify AtC transfer rates</A>
<LI><A HREF = "USER/atc/man_hardy_computes.html">fix_modify AtC transfer computes</A>
<LI><A HREF = "USER/atc/man_hardy_set.html">fix_modify AtC set</A>
<LI><A HREF = "USER/atc/man_hardy_on_the_fly.html">fix_modify AtC transfer on_the_fly</A>
<LI><A HREF = "USER/atc/man_boundary_integral.html">fix_modify AtC boundary_integral</A>
<LI><A HREF = "USER/atc/man_contour_integral.html">fix_modify AtC contour_integral</A>
</UL>
<P>miscellaneous fix_modify commands:
</P>
<UL><LI><A HREF = "USER/atc/man_atom_element_map.html">fix_modify AtC transfer atom_element_map</A>
<LI><A HREF = "USER/atc/man_neighbor_reset_frequency.html">fix_modify AtC transfer neighbor_reset_frequency</A>
</UL>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Wagner"></A>
<P><B>(Wagner)</B> Wagner, Jones, Templeton, Parks, Special Issue of
Computer Methods and Applied Mechanics, 197, 3351-3365 (2008).
</P>
<A NAME = "Zimmerman"></A>
<P><B>(Zimmerman)</B> Zimmerman, Webb, Hoyt, Jones, Klein, Bammann, Special
Issue of Modelling and Simulation in Materials Science and
Engineering, 12, S319 (2004).
</P>
<A NAME = "Hughes"></A>
<P><B>(Hughes)</B> T.J.R Hughes, "The Finite Element Method," Dover (2003).
</P>
</HTML>
diff --git a/doc/fix_atc.txt b/doc/fix_atc.txt
index d7ad329dd..551265b9e 100644
--- a/doc/fix_atc.txt
+++ b/doc/fix_atc.txt
@@ -1,227 +1,227 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix atc command :h3
[Syntax:]
fix ID groupID atc type paramfile :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
atc = style name of this fix command :l
type = {thermal} or {two_temperature} or {hardy} :l
{thermal} = thermal coupling with field: temperature
{two_temperature} = electron-phonon coupling with field, temperature and electron_temperature
{hardy} = Hardy on-the-fly post-processing :pre
paramfile = file with material parameters (not specified for {hardy} type) :l,ule
[Examples:]
fix AtC atc_atoms atc thermal Ar_thermal.dat
fix AtC atc_atoms atc transfer hardy :pre
[Description:]
This fix creates a coupled finite element (FE) and molecular dynamics
(MD) simulation and/or an on-the-fly estimation of continuum fields,
where a FE mesh is specified and overlaps the particles, something
like this:
:c,image(JPG/atc_nanotube.jpg)
Interscale operators are defined that construct continuum fields from
atomic data. Coupled simulations use FE projection approximated on a
discrete field. Currently, coupling is restricted to thermal physics.
The Hardy module can use either FE projection or integration Kernels
evaluated at mesh points.
Coupling methods enable appropriate corrections to the atomic data to
be made based on the FE field. For example, a Gaussian isokinetic
thermostat can apply heat sources to the atoms that varies in space on
the same scale as the FE element size. Meshes are not created
automatically and must be specified on LAMMPS regions with prescribed
element sizes.
Coupling and post-processing can be combined in the same simulations
using separate fix atc commands.
Note that mesh computations and storage run in serial (not
parallelized) so performance will degrade when large element counts
are used.
For detailed exposition of the theory and algorithms implemented in
this fix, please see the papers "here"_#Wagner and "here"_#Zimmerman.
Please refer to the standard finite element (FE) texts, such as "this
book"_#Hughes, for the basics of FE simulation.
:line
{Thermal} and {two_temperature} (coupling) types use a Verlet
time-integration algorithm. The {hardy} type does not contain its own
time-integrator and must be used with a separate fix that does contain
one, e.g. "fix nve"_fix_nve.html, "fix nvt"_fix_nh.html, etc.
A set of example input files with the attendant material files are
included in the examples/USER/atc directory of the LAMMPS
distribution.
An extensive set of additional documentation pages for the options
turned on via the "fix_modify"_fix_modify.html command for this fix
are inlcluded in the doc/USER/atc directory of the LAMMPS
distribution. Individual doc pages are listed and linked to below.
The following commands are typical of a coupling problem:
# ... commands to create and initialize the MD system :pre
# initial fix to designate coupling type and group to apply it to
# tag group physics material_file
fix AtC internal atc thermal Ar_thermal.mat :pre
# create a uniform 12 x 2 x 2 mesh that covers region contain the group
# nx ny nz region periodicity
fix_modify AtC fem create mesh 12 2 2 mdRegion f p p :pre
# specify the control method for the type of coupling
# physics control_type
fix_modify AtC transfer thermal control flux :pre
# specify the initial values for the empirical field "temperature"
# field node_group value
fix_modify AtC transfer initial temperature all 30.0 :pre
# create an output stream for nodal fields
# filename output_frequency
fix_modify AtC transfer output atc_fe_output 100 :pre
run 1000 :pre
The following commands are typical of a post-processing (Hardy) problem:
# ... commands to create and initialize the MD system :pre
# initial fix to designate post-processing and the group to apply it to
# no material file is allowed nor required
fix AtC internal atc hardy :pre
# create a uniform 1 x 1 x 1 mesh that covers region contain the group
# with periodicity this effectively creats a system average
fix_modify AtC fem create mesh 1 1 1 box p p p :pre
# change from default lagrangian map to eulerian
# refreshed every 100 steps
fix_modify AtC atom_element_map eulerian 100 :pre
# start with no field defined
fix_modify AtC transfer fields none :pre
# add mass density, potential energy density, stress and temperature
fix_modify AtC transfer fields add density energy stress temperature :pre
# create an output stream for nodal fields
# filename output_frequency
fix_modify AtC transfer output nvtFE 100 text :pre
run 1000 :pre
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. The "fix_modify"_fix_modify.html options
relevant to this fix are listed below. No global scalar or vector or
per-atom quantities are stored by this fix for access by various
"output commands"_Section_howto.html#howto_15. No parameter of this
fix can be used with the {start/stop} keywords of the "run"_run.html
command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
-This fix is part of the "user-atc" package. It is only enabled if
+This fix is part of the USER-ATC package. It is only enabled if
LAMMPS was built with that package, which also requires the ATC
library be built and linked with LAMMPS. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
After specifying this fix in your input script, several other
"fix_modify"_fix_modify.html commands are used to setup the problem,
e.g. define the finite element mesh and prescribe initial and boundary
conditions.
fix_modify commands for setup:
"fix_modify AtC fem create mesh"_USER/atc/man_fem_mesh.html
"fix_modify AtC mesh create_nodeset"_USER/atc/man_mesh_nodeset.html
"fix_modify AtC mesh create_faceset"_USER/atc/man_mesh_faceset.html
"fix_modify AtC mesh create_elementset"_USER/atc/man_mesh_elemset.html
"fix_modify AtC transfer internal"_USER/atc/man_transfer_internal.html
"fix_modify AtC transfer boundary"_USER/atc/man_transfer_boundary.html
"fix_modify AtC transfer internal_quadrature"_USER/atc/man_internal_quadrature.html
"fix_modify AtC transfer pmfc"_USER/atc/man_time_integration.html
"fix_modify AtC extrinsic electron_integration"_USER/atc/man_electron_integration.html :ul
fix_modify commands for boundary and initial conditions:
"fix_modify AtC transfer initial"_USER/atc/man_initial.html
"fix_modify AtC transfer fix"_USER/atc/man_fix_nodes.html
"fix_modify AtC transfer unfix"_USER/atc/man_unfix_nodes.html
"fix_modify AtC transfer fix_flux"_USER/atc/man_fix_flux.html
"fix_modify AtC transferunfix_flux"_USER/atc/man_unfix_flux.html
"fix_modify AtC transfer source"_USER/atc/man_source.html
"fix_modify AtC transfer remove_source"_USER/atc/man_remove_source.html :ul
fix_modify commands for control and filtering:
"fix_modify AtC transfer thermal control"_USER/atc/man_thermal_control.html
"fix_modify AtC transfer filter"_USER/atc/man_time_filter.html
"fix_modify AtC transfer filter scale"_USER/atc/man_filter_scale.html
"fix_modify AtC transfer equilibrium_start"_USER/atc/man_equilibrium_start.html
"fix_modify AtC extrinsic exchange"_USER/atc/man_extrinsic_exchange.html :ul
fix_modify commands for output:
"fix_modify AtC transfer output"_USER/atc/man_transfer_output.html
"fix_modify AtC transfer atomic_output"_USER/atc/man_transfer_atomic_output.html
"fix_modify AtC mesh output"_USER/atc/man_mesh_output.html
"fix_modify AtC transfer write_restart"_USER/atc/man_write_restart.html
"fix_modify AtC transfer read_restart"_USER/atc/man_read_restart.html :ul
fix_modify commands for post-processing:
"fix_modify AtC transfer fields"_USER/atc/man_hardy_fields.html
"fix_modify AtC transfer gradients"_USER/atc/man_hardy_gradients.html
"fix_modify AtC transfer rates"_USER/atc/man_hardy_rates.html
"fix_modify AtC transfer computes"_USER/atc/man_hardy_computes.html
"fix_modify AtC set"_USER/atc/man_hardy_set.html
"fix_modify AtC transfer on_the_fly"_USER/atc/man_hardy_on_the_fly.html
"fix_modify AtC boundary_integral"_USER/atc/man_boundary_integral.html
"fix_modify AtC contour_integral"_USER/atc/man_contour_integral.html :ul
miscellaneous fix_modify commands:
"fix_modify AtC transfer atom_element_map"_USER/atc/man_atom_element_map.html
"fix_modify AtC transfer neighbor_reset_frequency"_USER/atc/man_neighbor_reset_frequency.html :ul
[Default:] none
:line
:link(Wagner)
[(Wagner)] Wagner, Jones, Templeton, Parks, Special Issue of
Computer Methods and Applied Mechanics, 197, 3351-3365 (2008).
:link(Zimmerman)
[(Zimmerman)] Zimmerman, Webb, Hoyt, Jones, Klein, Bammann, Special
Issue of Modelling and Simulation in Materials Science and
Engineering, 12, S319 (2004).
:link(Hughes)
[(Hughes)] T.J.R Hughes, "The Finite Element Method," Dover (2003).
diff --git a/doc/fix_aveforce.html b/doc/fix_aveforce.html
index 27a17ec49..d2f935509 100644
--- a/doc/fix_aveforce.html
+++ b/doc/fix_aveforce.html
@@ -1,128 +1,128 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix aveforce command
</H3>
<H3>fix aveforce/cuda command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID aveforce fx fy fz keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>aveforce = style name of this fix command
<LI>fx,fy,fz = force component values (force units)
<LI>any of fx,fy,fz can be a variable (see below)
<LI>zero or more keyword/value pairs may be appended to args
<LI>keyword = <I>region</I>
<PRE> <I>region</I> value = region-ID
region-ID = ID of region atoms must be in to have added force
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix pressdown topwall aveforce 0.0 -1.0 0.0
fix 2 bottomwall aveforce NULL -1.0 0.0 region top
fix 2 bottomwall aveforce NULL -1.0 v_oscillate region top
</PRE>
<P><B>Description:</B>
</P>
<P>Apply an additional external force to a group of atoms in such a way
that every atom experiences the same force. This is useful for
pushing on wall or boundary atoms so that the structure of the wall
does not change over time.
</P>
<P>The existing force is averaged for the group of atoms, component by
component. The actual force on each atom is then set to the average
value plus the component specified in this command. This means each
atom in the group receives the same force.
</P>
<P>Any of the fx,fy,fz values can be specified as NULL which means the
force in that dimension is not changed. Note that this is not the
same as specifying a 0.0 value, since that sets all forces to the same
average value without adding in any additional force.
</P>
<P>Any of the 3 quantities defining the force components can be specified
as an equal-style <A HREF = "variable.html">variable</A>, namely <I>fx</I>, <I>fy</I>, <I>fz</I>.
If the value is a variable, it should be specified as v_name, where
name is the variable name. In this case, the variable will be
evaluated each timestep, and its value used to determine the average
force.
</P>
<P>Equal-style variables can specify formulas with various mathematical
functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent average force.
</P>
<P>If the <I>region</I> keyword is used, the atom must also be in the
specified geometric <A HREF = "region.html">region</A> in order to have force added
to it.
</P>
<HR>
<P>Styles with a <I>cuda</I> suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
<A HREF = "Section_accelerate.html">this section</A> of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix.
</P>
<P>This fix computes a global 3-vector of forces, which can be accessed
by various <A HREF = "Section_howto.html#howto_15">output commands</A>. This is the
total force on the group of atoms before the forces on individual
atoms are changed by the fix. The vector values calculated by this
fix are "extensive".
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command.
</P>
<P>The forces due to this fix are imposed during an energy minimization,
invoked by the <A HREF = "minimize.html">minimize</A> command. You should not
specify force components with a variable that has time-dependence for
use with a minimizer, since the minimizer increments the timestep as
the iteration count during the minimization.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_setforce.html">fix setforce</A>, <A HREF = "fix_addforce.html">fix addforce</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/fix_aveforce.txt b/doc/fix_aveforce.txt
index af83f5212..b8db603c5 100644
--- a/doc/fix_aveforce.txt
+++ b/doc/fix_aveforce.txt
@@ -1,115 +1,115 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix aveforce command :h3
fix aveforce/cuda command :h3
[Syntax:]
fix ID group-ID aveforce fx fy fz keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
aveforce = style name of this fix command :l
fx,fy,fz = force component values (force units) :l
any of fx,fy,fz can be a variable (see below) :l
zero or more keyword/value pairs may be appended to args :l
keyword = {region} :l
{region} value = region-ID
region-ID = ID of region atoms must be in to have added force :pre
:ule
[Examples:]
fix pressdown topwall aveforce 0.0 -1.0 0.0
fix 2 bottomwall aveforce NULL -1.0 0.0 region top
fix 2 bottomwall aveforce NULL -1.0 v_oscillate region top :pre
[Description:]
Apply an additional external force to a group of atoms in such a way
that every atom experiences the same force. This is useful for
pushing on wall or boundary atoms so that the structure of the wall
does not change over time.
The existing force is averaged for the group of atoms, component by
component. The actual force on each atom is then set to the average
value plus the component specified in this command. This means each
atom in the group receives the same force.
Any of the fx,fy,fz values can be specified as NULL which means the
force in that dimension is not changed. Note that this is not the
same as specifying a 0.0 value, since that sets all forces to the same
average value without adding in any additional force.
Any of the 3 quantities defining the force components can be specified
as an equal-style "variable"_variable.html, namely {fx}, {fy}, {fz}.
If the value is a variable, it should be specified as v_name, where
name is the variable name. In this case, the variable will be
evaluated each timestep, and its value used to determine the average
force.
Equal-style variables can specify formulas with various mathematical
functions, and include "thermo_style"_thermo_style.html command
keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent average force.
If the {region} keyword is used, the atom must also be in the
specified geometric "region"_region.html in order to have force added
to it.
:line
Styles with a {cuda} suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
"this section"_Section_accelerate.html of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global 3-vector of forces, which can be accessed
by various "output commands"_Section_howto.html#howto_15. This is the
total force on the group of atoms before the forces on individual
atoms are changed by the fix. The vector values calculated by this
fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command. You should not
specify force components with a variable that has time-dependence for
use with a minimizer, since the minimizer increments the timestep as
the iteration count during the minimization.
[Restrictions:] none
[Related commands:]
"fix setforce"_fix_setforce.html, "fix addforce"_fix_addforce.html
[Default:] none
diff --git a/doc/fix_bond_break.html b/doc/fix_bond_break.html
index 497df4775..55e786263 100644
--- a/doc/fix_bond_break.html
+++ b/doc/fix_bond_break.html
@@ -1,163 +1,163 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix bond/break command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID bond/break Nevery bondtype Rmax keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>bond/break = style name of this fix command
<LI>Nevery = attempt bond breaking every this many steps
<LI>bondtype = type of bonds to break
<LI>Rmax = bond longer than Rmax can break (distance units)
<LI>zero or more keyword/value pairs may be appended to args
<LI>keyword = <I>prob</I>
<PRE> <I>prob</I> values = fraction seed
fraction = break a bond with this probability if otherwise eligible
seed = random number seed (positive integer)
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 5 all bond/break 10 2 1.2
fix 5 polymer bond/break 1 1 2.0 prob 0.5 49829
</PRE>
<P><B>Description:</B>
</P>
<P>Break bonds between pairs of atoms as a simulation runs according to
specified criteria. This can be used to model the dissolution of a
polymer network due to stretching of the simulation box or other
deformations. In this context, a bond means an interaction between a
pair of atoms computed by the <A HREF = "bond_style.html">bond_style</A> command.
Once the bond is broken it will be permanently deleted. This is
different than a <A HREF = "pair_style.html">pairwise</A> bond-order potential such
as Tersoff or AIREBO which infers bonds and many-body interactions
based on the current geometry of a small cluster of atoms and
effectively creates and destroys bonds from timestep to timestep as
atoms move.
</P>
<P>A check for possible bond breakage is performed every <I>Nevery</I>
timesteps. If two bonded atoms I,J are further than a distance <I>Rmax</I>
of each other, if the bond is of type <I>bondtype</I>, and if both I and J
are in the specified fix group, then I,J is labeled as a "possible"
bond to break.
</P>
<P>If several bonds involving an atom are stretched, it may have multiple
possible bonds to break. Every atom checks its list of possible bonds
to break and labels the longest such bond as its "sole" bond to break.
After this is done, if atom I is bonded to atom J in its sole bond,
and atom J is bonded to atom I in its sole bond, then the I,J bond is
"eligible" to be broken.
</P>
<P>Note that these rules mean an atom will only be part of at most one
broken bond on a given timestep. It also means that if atom I chooses
atom J as its sole partner, but atom J chooses atom K is its sole
partner (due to Rjk > Rij), then this means atom I will not be part of
a broken bond on this timestep, even if it has other possible bond
partners.
</P>
<P>The <I>prob</I> keyword can effect whether an eligible bond is actually
broken. The <I>fraction</I> setting must be a value between 0.0 and 1.0.
A uniform random number between 0.0 and 1.0 is generated and the
eligible bond is only broken if the random number < fraction.
</P>
<P>When a bond is broken, data structures within LAMMPS that store bond
topology are updated to reflect the breakage. This can also affect
subsequent computation of pairwise interactions involving the atoms in
the bond. See the Restriction section below for additional
information.
</P>
<P>Computationally, each timestep this fix operates, it loops over bond
lists and computes distances between pairs of bonded atoms in the
list. It also communicates between neighboring processors to
coordinate which bonds are broken. Thus it will increase the cost of
a timestep. Thus you should be cautious about invoking this fix too
frequently.
</P>
<P>You can dump out snapshots of the current bond topology via the <A HREF = "dump.html">dump
local</A> command.
</P>
<P>IMPORTANT NOTE: Breaking a bond typically alters the energy of a
system. You should be careful not to choose bond breaking criteria
that induce a dramatic change in energy. For example, if you define a
very stiff harmonic bond and break it when 2 atoms are separated by a
distance far from the equilibribum bond length, then the 2 atoms will
be dramatically released when the bond is broken. More generally, you
may need to thermostat your system to compensate for energy changes
resulting from broken bonds.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix.
</P>
<P>This fix computes two statistics which it stores in a global vector of
length 2, which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. The vector values calculated
by this fix are "intensive".
</P>
<P>These are the 2 quantities:
</P>
<UL><LI>(1) # of bonds broken on the most recent breakage timestep
<LI>(2) cummulative # of bonds broken
</UL>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "mc" package. It is only enabled if LAMMPS
-was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+<P>This fix is part of the MC package. It is only enabled if LAMMPS was
+built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>Currently, there are 2 restrictions for using this fix. We may relax
these in the future if there are new models that would be enabled by
it.
</P>
<P>When a bond is broken, you might wish to turn off angle and dihedral
interactions that include that bond. However, LAMMPS does not check
for these angles and dihedrals, even if your simulation defines an
<A HREF = "angle_style.html">angle_style</A> or
<A HREF = "dihedral_style.html">dihedral_style</A>.
</P>
<P>This fix requires that the pairwise weightings defined by the
<A HREF = "special_bonds.html">special_bonds</A> command be 0,1,1 for 1-2, 1-3, and
1-4 neighbors within the bond topology. This effectively means that
the pairwise interaction between atoms I and J is turned off when a
bond between them exists and will be turned on when the bond is
broken. It also means that the pairwise interaction of I with J's
other bond partners is unaffected by the existence of the bond.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_bond_create.html">fix bond/create</A>, <A HREF = "fix_bond_swap.html">fix
bond/swap</A>, <A HREF = "dump.html">dump local</A>,
<A HREF = "special_bonds.html">special_bonds</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are prob = 1.0.
</P>
</HTML>
diff --git a/doc/fix_bond_break.txt b/doc/fix_bond_break.txt
index 97cb2fa59..d6ee6bec0 100755
--- a/doc/fix_bond_break.txt
+++ b/doc/fix_bond_break.txt
@@ -1,150 +1,150 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix bond/break command :h3
[Syntax:]
fix ID group-ID bond/break Nevery bondtype Rmax keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
bond/break = style name of this fix command :l
Nevery = attempt bond breaking every this many steps :l
bondtype = type of bonds to break :l
Rmax = bond longer than Rmax can break (distance units) :l
zero or more keyword/value pairs may be appended to args :l
keyword = {prob} :l
{prob} values = fraction seed
fraction = break a bond with this probability if otherwise eligible
seed = random number seed (positive integer) :pre
:ule
[Examples:]
fix 5 all bond/break 10 2 1.2
fix 5 polymer bond/break 1 1 2.0 prob 0.5 49829 :pre
[Description:]
Break bonds between pairs of atoms as a simulation runs according to
specified criteria. This can be used to model the dissolution of a
polymer network due to stretching of the simulation box or other
deformations. In this context, a bond means an interaction between a
pair of atoms computed by the "bond_style"_bond_style.html command.
Once the bond is broken it will be permanently deleted. This is
different than a "pairwise"_pair_style.html bond-order potential such
as Tersoff or AIREBO which infers bonds and many-body interactions
based on the current geometry of a small cluster of atoms and
effectively creates and destroys bonds from timestep to timestep as
atoms move.
A check for possible bond breakage is performed every {Nevery}
timesteps. If two bonded atoms I,J are further than a distance {Rmax}
of each other, if the bond is of type {bondtype}, and if both I and J
are in the specified fix group, then I,J is labeled as a "possible"
bond to break.
If several bonds involving an atom are stretched, it may have multiple
possible bonds to break. Every atom checks its list of possible bonds
to break and labels the longest such bond as its "sole" bond to break.
After this is done, if atom I is bonded to atom J in its sole bond,
and atom J is bonded to atom I in its sole bond, then the I,J bond is
"eligible" to be broken.
Note that these rules mean an atom will only be part of at most one
broken bond on a given timestep. It also means that if atom I chooses
atom J as its sole partner, but atom J chooses atom K is its sole
partner (due to Rjk > Rij), then this means atom I will not be part of
a broken bond on this timestep, even if it has other possible bond
partners.
The {prob} keyword can effect whether an eligible bond is actually
broken. The {fraction} setting must be a value between 0.0 and 1.0.
A uniform random number between 0.0 and 1.0 is generated and the
eligible bond is only broken if the random number < fraction.
When a bond is broken, data structures within LAMMPS that store bond
topology are updated to reflect the breakage. This can also affect
subsequent computation of pairwise interactions involving the atoms in
the bond. See the Restriction section below for additional
information.
Computationally, each timestep this fix operates, it loops over bond
lists and computes distances between pairs of bonded atoms in the
list. It also communicates between neighboring processors to
coordinate which bonds are broken. Thus it will increase the cost of
a timestep. Thus you should be cautious about invoking this fix too
frequently.
You can dump out snapshots of the current bond topology via the "dump
local"_dump.html command.
IMPORTANT NOTE: Breaking a bond typically alters the energy of a
system. You should be careful not to choose bond breaking criteria
that induce a dramatic change in energy. For example, if you define a
very stiff harmonic bond and break it when 2 atoms are separated by a
distance far from the equilibribum bond length, then the 2 atoms will
be dramatically released when the bond is broken. More generally, you
may need to thermostat your system to compensate for energy changes
resulting from broken bonds.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes two statistics which it stores in a global vector of
length 2, which can be accessed by various "output
commands"_Section_howto.html#howto_15. The vector values calculated
by this fix are "intensive".
These are the 2 quantities:
(1) # of bonds broken on the most recent breakage timestep
(2) cummulative # of bonds broken :ul
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
-This fix is part of the "mc" package. It is only enabled if LAMMPS
-was built with that package. See the "Making
+This fix is part of the MC package. It is only enabled if LAMMPS was
+built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
Currently, there are 2 restrictions for using this fix. We may relax
these in the future if there are new models that would be enabled by
it.
When a bond is broken, you might wish to turn off angle and dihedral
interactions that include that bond. However, LAMMPS does not check
for these angles and dihedrals, even if your simulation defines an
"angle_style"_angle_style.html or
"dihedral_style"_dihedral_style.html.
This fix requires that the pairwise weightings defined by the
"special_bonds"_special_bonds.html command be 0,1,1 for 1-2, 1-3, and
1-4 neighbors within the bond topology. This effectively means that
the pairwise interaction between atoms I and J is turned off when a
bond between them exists and will be turned on when the bond is
broken. It also means that the pairwise interaction of I with J's
other bond partners is unaffected by the existence of the bond.
[Related commands:]
"fix bond/create"_fix_bond_create.html, "fix
bond/swap"_fix_bond_swap.html, "dump local"_dump.html,
"special_bonds"_special_bonds.html
[Default:]
The option defaults are prob = 1.0.
diff --git a/doc/fix_bond_create.html b/doc/fix_bond_create.html
index 80090cbee..a521d0191 100644
--- a/doc/fix_bond_create.html
+++ b/doc/fix_bond_create.html
@@ -1,221 +1,221 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix bond/create command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID bond/create Nevery itype jtype Rmin bondtype keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>bond/create = style name of this fix command
<LI>Nevery = attempt bond creation every this many steps
<LI>itype,jtype = atoms of itype can bond to atoms of jtype
<LI>Rmin = 2 atoms separated by less than Rmin can bond (distance units)
<LI>bondtype = type of created bonds
<LI>zero or more keyword/value pairs may be appended to args
<LI>keyword = <I>iparam</I> or <I>jparam</I> or <I>prob</I>
<PRE> <I>iparam</I> values = maxbond, newtype
maxbond = max # of bonds of bondtype the itype atom can have
newtype = change the itype atom to this type when maxbonds exist
<I>jparam</I> values = maxbond, newtype
maxbond = max # of bonds of bondtype the jtype atom can have
newtype = change the jtype atom to this type when maxbonds exist
<I>prob</I> values = fraction seed
fraction = create a bond with this probability if otherwise eligible
seed = random number seed (positive integer)
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 5 all bond/create 10 1 2 0.8 1
fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3
</PRE>
<P><B>Description:</B>
</P>
<P>Create bonds between pairs of atoms as a simulation runs according to
specified criteria. This can be used to model cross-linking of
polymers, the formation of a percolation network, etc. In this
context, a bond means an interaction between a pair of atoms computed
by the <A HREF = "bond_style.html">bond_style</A> command. Once the bond is created
it will be permanently in place. This is different than a
<A HREF = "pair_style.html">pairwise</A> bond-order potential such as Tersoff or
AIREBO which infers bonds and many-body interactions based on the
current geometry of a small cluster of atoms and effectively creates
and destroys bonds from timestep to timestep as atoms move.
</P>
<P>A check for possible new bonds is performed every <I>Nevery</I> timesteps.
If two atoms I,J are within a distance <I>Rmin</I> of each other, if I is
of atom type <I>itype</I>, if J is of atom type <I>jtype</I>, if both I and J
are in the specified fix group, if a bond does not already exist
between I and J, and if both I and J meet their respective <I>maxbond</I>
requirement (explained below), then I,J is labeled as a "possible"
bond pair.
</P>
<P>If several atoms are close to an atom, it may have multiple possible
bond partners. Every atom checks its list of possible bond partners
and labels the closest such partner as its "sole" bond partner. After
this is done, if atom I has atom J as its sole partner, and atom J has
atom I as its sole partner, then the I,J bond is "eligible" to be
formed.
</P>
<P>Note that these rules mean an atom will only be part of at most one
created bond on a given timestep. It also means that if atom I
chooses atom J as its sole partner, but atom J chooses atom K is its
sole partner (due to Rjk < Rij), then this means atom I will not form
a bond on this timestep, even if it has other possible bond partners.
</P>
<P>It is permissible to have <I>itype</I> = <I>jtype</I>. <I>Rmin</I> must be <= the
pairwise cutoff distance between <I>itype</I> and <I>jtype</I> atoms, as defined
by the <A HREF = "pair_style.html">pair_style</A> command.
</P>
<P>The <I>iparam</I> and <I>jparam</I> keywords can be used to limit the bonding
functionality of the participating atoms. Each atom keeps track of
how many bonds of <I>bondtype</I> it already has. If atom I of
itype already has <I>maxbond</I> bonds (as set by the <I>iparam</I>
keyword), then it will not form any more. Likewise for atom J. If
<I>maxbond</I> is set to 0, then there is no limit on the number of bonds
that can be formed with that atom.
</P>
<P>The <I>newtype</I> value for <I>iparam</I> and <I>jparam</I> can be used to change
the atom type of atom I or J when it reaches <I>maxbond</I> number of bonds
of type <I>bondtype</I>. This means it can now interact in a pairwise
fashion with other atoms in a different way by specifying different
<A HREF = "pair_coeff.html">pair_coeff</A> coefficients. If you do not wish the
atom type to change, simply specify <I>newtype</I> as <I>itype</I> or <I>jtype</I>.
</P>
<P>The <I>prob</I> keyword can also effect whether an eligible bond is
actually created. The <I>fraction</I> setting must be a value between 0.0
and 1.0. A uniform random number between 0.0 and 1.0 is generated and
the eligible bond is only created if the random number < fraction.
</P>
<P>Any bond that is created is assigned a bond type of <I>bondtype</I>. Data
structures within LAMMPS that store bond topology are updated to
reflect the new bond. This can also affect subsequent computation of
pairwise interactions involving the atoms in the bond. See the
Restriction section below for additional information.
</P>
<P>IMPORTANT NOTE: To create a new bond, the internal LAMMPS data
structures that store this information must have space for it. When
LAMMPS is initialized from a data file, the list of bonds is scanned
and the maximum number of bonds per atom is tallied. If some atom
will acquire more bonds than this limit as this fix operates, then the
"extra bonds per atom" parameter in the data file header must be set
to allow for it. See the <A HREF = "read_data.html">read_data</A> command for more
details. Note that if this parameter needs to be set, it means a data
file must be used to initialize the system, even if it initially has
no bonds. A data file with no atoms can be used if you wish to add
unbonded atoms via the <A HREF = "create_atoms.html">create atoms</A> command,
e.g. for a percolation simulation.
</P>
<P>IMPORTANT NOTE: LAMMPS also maintains a data structure that stores a
list of 1st, 2nd, and 3rd neighbors of each atom (in the bond topology
of the system) for use in weighting pairwise interactions for bonded
atoms. Adding a bond adds a single entry to this list. The "extra"
keyword of the <A HREF = "special_bonds.html">special_bonds</A> command should be
used to leave space for new bonds if the maximum number of entries for
any atom will be exceeded as this fix operates. See the
<A HREF = "special_bonds.html">special_bonds</A> command for details.
</P>
<P>Note that even if your simulation starts with no bonds, you must
define a <A HREF = "bond_style.html">bond_style</A> and use the
<A HREF = "bond_coeff.html">bond_coeff</A> command to specify coefficients for the
<I>bondtype</I>. Similarly, if new atom types are specified by the
<I>iparam</I> or <I>jparam</I> keywords, they must be within the range of atom
types allowed by the simulation and pairwise coefficients must be
specified for the new types.
</P>
<P>Computationally, each timestep this fix operates, it loops over
neighbor lists and computes distances between pairs of atoms in the
list. It also communicates between neighboring processors to
coordinate which bonds are created. Thus it roughly doubles the cost
of a timestep. Thus you should be cautious about invoking this fix
too frequently.
</P>
<P>You can dump out snapshots of the current bond topology via the <A HREF = "dump.html">dump
local</A> command.
</P>
<P>IMPORTANT NOTE: Creating a bond typically alters the energy of a
system. You should be careful not to choose bond creation criteria
that induce a dramatic change in energy. For example, if you define a
very stiff harmonic bond and create it when 2 atoms are separated by a
distance far from the equilibribum bond length, then the 2 atoms will
oscillate dramatically when the bond is formed. More generally, you
may need to thermostat your system to compensate for energy changes
resulting from created bonds.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix.
</P>
<P>This fix computes two statistics which it stores in a global vector of
length 2, which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. The vector values calculated
by this fix are "intensive".
</P>
<P>These are the 2 quantities:
</P>
<UL><LI>(1) # of bonds created on the most recent creation timestep
<LI>(2) cummulative # of bonds created
</UL>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "mc" package. It is only enabled if LAMMPS
-was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+<P>This fix is part of the MC package. It is only enabled if LAMMPS was
+built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>Currently, there are 2 restrictions for using this fix. We may relax
these in the future if there are new models that would be enabled by
it.
</P>
<P>When a bond is created, you might wish to induce new angle and
dihedral interactions that include that bond. However, LAMMPS does
not create these angles and dihedrals, even if your simulation defines
an <A HREF = "angle_style.html">angle_style</A> or
<A HREF = "dihedral_style.html">dihedral_style</A>.
</P>
<P>This fix requires that the pairwise weightings defined by the
<A HREF = "special_bonds.html">special_bonds</A> command be 0,1,1 for 1-2, 1-3, and
1-4 neighbors within the bond topology. This effectively means that
the pairwise interaction between atoms I and J will be turned off when
a bond between them is created. It also means that the pairwise
interaction of I with J's other bond partners will be unaffected by
the new bond.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_bond_break.html">fix bond/break</A>, <A HREF = "fix_bond_swap.html">fix
bond/swap</A>, <A HREF = "dump.html">dump local</A>,
<A HREF = "special_bonds.html">special_bonds</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are iparam = (0,itype), jparam = (0,jtype), and
prob = 1.0.
</P>
</HTML>
diff --git a/doc/fix_bond_create.txt b/doc/fix_bond_create.txt
index d373e6066..17fbb77ed 100755
--- a/doc/fix_bond_create.txt
+++ b/doc/fix_bond_create.txt
@@ -1,207 +1,207 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix bond/create command :h3
[Syntax:]
fix ID group-ID bond/create Nevery itype jtype Rmin bondtype keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
bond/create = style name of this fix command :l
Nevery = attempt bond creation every this many steps :l
itype,jtype = atoms of itype can bond to atoms of jtype :l
Rmin = 2 atoms separated by less than Rmin can bond (distance units) :l
bondtype = type of created bonds :l
zero or more keyword/value pairs may be appended to args :l
keyword = {iparam} or {jparam} or {prob} :l
{iparam} values = maxbond, newtype
maxbond = max # of bonds of bondtype the itype atom can have
newtype = change the itype atom to this type when maxbonds exist
{jparam} values = maxbond, newtype
maxbond = max # of bonds of bondtype the jtype atom can have
newtype = change the jtype atom to this type when maxbonds exist
{prob} values = fraction seed
fraction = create a bond with this probability if otherwise eligible
seed = random number seed (positive integer) :pre
:ule
[Examples:]
fix 5 all bond/create 10 1 2 0.8 1
fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3 :pre
[Description:]
Create bonds between pairs of atoms as a simulation runs according to
specified criteria. This can be used to model cross-linking of
polymers, the formation of a percolation network, etc. In this
context, a bond means an interaction between a pair of atoms computed
by the "bond_style"_bond_style.html command. Once the bond is created
it will be permanently in place. This is different than a
"pairwise"_pair_style.html bond-order potential such as Tersoff or
AIREBO which infers bonds and many-body interactions based on the
current geometry of a small cluster of atoms and effectively creates
and destroys bonds from timestep to timestep as atoms move.
A check for possible new bonds is performed every {Nevery} timesteps.
If two atoms I,J are within a distance {Rmin} of each other, if I is
of atom type {itype}, if J is of atom type {jtype}, if both I and J
are in the specified fix group, if a bond does not already exist
between I and J, and if both I and J meet their respective {maxbond}
requirement (explained below), then I,J is labeled as a "possible"
bond pair.
If several atoms are close to an atom, it may have multiple possible
bond partners. Every atom checks its list of possible bond partners
and labels the closest such partner as its "sole" bond partner. After
this is done, if atom I has atom J as its sole partner, and atom J has
atom I as its sole partner, then the I,J bond is "eligible" to be
formed.
Note that these rules mean an atom will only be part of at most one
created bond on a given timestep. It also means that if atom I
chooses atom J as its sole partner, but atom J chooses atom K is its
sole partner (due to Rjk < Rij), then this means atom I will not form
a bond on this timestep, even if it has other possible bond partners.
It is permissible to have {itype} = {jtype}. {Rmin} must be <= the
pairwise cutoff distance between {itype} and {jtype} atoms, as defined
by the "pair_style"_pair_style.html command.
The {iparam} and {jparam} keywords can be used to limit the bonding
functionality of the participating atoms. Each atom keeps track of
how many bonds of {bondtype} it already has. If atom I of
itype already has {maxbond} bonds (as set by the {iparam}
keyword), then it will not form any more. Likewise for atom J. If
{maxbond} is set to 0, then there is no limit on the number of bonds
that can be formed with that atom.
The {newtype} value for {iparam} and {jparam} can be used to change
the atom type of atom I or J when it reaches {maxbond} number of bonds
of type {bondtype}. This means it can now interact in a pairwise
fashion with other atoms in a different way by specifying different
"pair_coeff"_pair_coeff.html coefficients. If you do not wish the
atom type to change, simply specify {newtype} as {itype} or {jtype}.
The {prob} keyword can also effect whether an eligible bond is
actually created. The {fraction} setting must be a value between 0.0
and 1.0. A uniform random number between 0.0 and 1.0 is generated and
the eligible bond is only created if the random number < fraction.
Any bond that is created is assigned a bond type of {bondtype}. Data
structures within LAMMPS that store bond topology are updated to
reflect the new bond. This can also affect subsequent computation of
pairwise interactions involving the atoms in the bond. See the
Restriction section below for additional information.
IMPORTANT NOTE: To create a new bond, the internal LAMMPS data
structures that store this information must have space for it. When
LAMMPS is initialized from a data file, the list of bonds is scanned
and the maximum number of bonds per atom is tallied. If some atom
will acquire more bonds than this limit as this fix operates, then the
"extra bonds per atom" parameter in the data file header must be set
to allow for it. See the "read_data"_read_data.html command for more
details. Note that if this parameter needs to be set, it means a data
file must be used to initialize the system, even if it initially has
no bonds. A data file with no atoms can be used if you wish to add
unbonded atoms via the "create atoms"_create_atoms.html command,
e.g. for a percolation simulation.
IMPORTANT NOTE: LAMMPS also maintains a data structure that stores a
list of 1st, 2nd, and 3rd neighbors of each atom (in the bond topology
of the system) for use in weighting pairwise interactions for bonded
atoms. Adding a bond adds a single entry to this list. The "extra"
keyword of the "special_bonds"_special_bonds.html command should be
used to leave space for new bonds if the maximum number of entries for
any atom will be exceeded as this fix operates. See the
"special_bonds"_special_bonds.html command for details.
Note that even if your simulation starts with no bonds, you must
define a "bond_style"_bond_style.html and use the
"bond_coeff"_bond_coeff.html command to specify coefficients for the
{bondtype}. Similarly, if new atom types are specified by the
{iparam} or {jparam} keywords, they must be within the range of atom
types allowed by the simulation and pairwise coefficients must be
specified for the new types.
Computationally, each timestep this fix operates, it loops over
neighbor lists and computes distances between pairs of atoms in the
list. It also communicates between neighboring processors to
coordinate which bonds are created. Thus it roughly doubles the cost
of a timestep. Thus you should be cautious about invoking this fix
too frequently.
You can dump out snapshots of the current bond topology via the "dump
local"_dump.html command.
IMPORTANT NOTE: Creating a bond typically alters the energy of a
system. You should be careful not to choose bond creation criteria
that induce a dramatic change in energy. For example, if you define a
very stiff harmonic bond and create it when 2 atoms are separated by a
distance far from the equilibribum bond length, then the 2 atoms will
oscillate dramatically when the bond is formed. More generally, you
may need to thermostat your system to compensate for energy changes
resulting from created bonds.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes two statistics which it stores in a global vector of
length 2, which can be accessed by various "output
commands"_Section_howto.html#howto_15. The vector values calculated
by this fix are "intensive".
These are the 2 quantities:
(1) # of bonds created on the most recent creation timestep
(2) cummulative # of bonds created :ul
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
-This fix is part of the "mc" package. It is only enabled if LAMMPS
-was built with that package. See the "Making
+This fix is part of the MC package. It is only enabled if LAMMPS was
+built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
Currently, there are 2 restrictions for using this fix. We may relax
these in the future if there are new models that would be enabled by
it.
When a bond is created, you might wish to induce new angle and
dihedral interactions that include that bond. However, LAMMPS does
not create these angles and dihedrals, even if your simulation defines
an "angle_style"_angle_style.html or
"dihedral_style"_dihedral_style.html.
This fix requires that the pairwise weightings defined by the
"special_bonds"_special_bonds.html command be 0,1,1 for 1-2, 1-3, and
1-4 neighbors within the bond topology. This effectively means that
the pairwise interaction between atoms I and J will be turned off when
a bond between them is created. It also means that the pairwise
interaction of I with J's other bond partners will be unaffected by
the new bond.
[Related commands:]
"fix bond/break"_fix_bond_break.html, "fix
bond/swap"_fix_bond_swap.html, "dump local"_dump.html,
"special_bonds"_special_bonds.html
[Default:]
The option defaults are iparam = (0,itype), jparam = (0,jtype), and
prob = 1.0.
diff --git a/doc/fix_bond_swap.html b/doc/fix_bond_swap.html
index 493339409..4a6e5b736 100644
--- a/doc/fix_bond_swap.html
+++ b/doc/fix_bond_swap.html
@@ -1,188 +1,188 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix bond/swap command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID bond/swap fraction cutoff seed
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>bond/swap = style name of this fix command
<LI>fraction = fraction of group atoms to consider for swapping
<LI>cutoff = distance at which swapping will be considered (distance units)
<LI>seed = random # seed (positive integer)
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all bond/swap 0.5 1.3 598934
</PRE>
<P><B>Description:</B>
</P>
<P>In a simulation of polymer chains, this command attempts to swap bonds
between two different chains, effectively grafting the end of one
chain onto another chain and vice versa. This is done via Monte Carlo
rules using the Boltzmann acceptance criterion. The purpose is to
equilibrate the polymer chain conformations more rapidly than dynamics
alone would do it, by enabling instantaneous large conformational
changes in a dense polymer melt. The polymer chains should thus more
rapidly converge to the proper end-to-end distances and radii of
gyration. It is designed for use with systems of
<A HREF = "bond_fene.html">FENE</A> or <A HREF = "bond_harmonic.html">harmonic</A> bead-spring
polymer chains where each polymer is a linear chain of monomers, but
LAMMPS does not enforce this requirement, i.e. any
<A HREF = "bond_style.html">bond_style</A> can be used.
</P>
<P>A schematic of the kinds of bond swaps that can occur is shown here:
</P>
<CENTER><IMG SRC = "JPG/bondswap.jpg">
</CENTER>
<P>On the left, the red and blue chains have two monomers A1 and B1 close
to each other, which are currently bonded to monomers A2 and B2
respectively within their own chains. The bond swap operation will
attempt to delete the A1-A2 and B1-B2 bonds and replace them with
A1-B2 and B1-A2 bonds. If the swap is energetically favorable, the
two chains on the right are the result and each polymer chain has
undergone a dramatic conformational change. This reference provides
more details on how the algorithm works and its application:
<A HREF = "#Sides">(Sides)</A>.
</P>
<P>The bond swapping operation is invoked each time neighbor lists are
built during a simulation, since it potentially alters the list of
which neighbors are considered for pairwise interaction. At each
reneighboring step, each processor considers a random specified
<I>fraction</I> of its atoms as potential swapping monomers for this
timestep. Choosing a small <I>fraction</I> value can reduce the likelihood
of a reverse swap occurring soon after an initial swap.
</P>
<P>For each monomer A1, its neighbors are examined to find a possible B1
monomer. Both A1 and B1 must be in the fix group, their separation
must be less than the specified <I>cutoff</I>, and the molecule IDs of A1
and B1 must be the same (see below). If a suitable partner is found,
the energy change due to swapping the 2 bonds is computed. This
includes changes in pairwise, bond, and angle energies due to the
altered connectivity of the 2 chains. Dihedral and improper
interactions are not allowed to be defined when this fix is used.
</P>
<P>If the energy decreases due to the swap operation, the bond swap is
accepted. If the energy increases it is accepted with probability
exp(-delta/kT) where delta is the increase in energy, k is the
Boltzmann constant, and T is the current temperature of the system.
Whether the swap is accepted or rejected, no other swaps are attempted
by this processor on this timestep.
</P>
<P>The criterion for matching molecule IDs is how bond swaps performed by
this fix conserve chain length. To use this features you must setup
the molecule IDs for your polymer chains in a certain way, typically
in the data file, read by the <A HREF = "read_data.html">read_data</A> comand.
Consider a system of 6-mer chains. You have 3 choices. If the
molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then
swaps will conserve length. For a particular momoner there will be
only one other monomer on another chain which is a potential swap
partner. If the molecule IDs for monomers on each chain are set to
1,2,3,3,2,1 then swaps will conserve length but swaps will be able to
occur at either end of a chain. Thus for a particular monomer there
will be 2 possible swap partners on another chain. In this scenario,
swaps can also occur within a single chain, i.e. the two ends of a
chain swap with each other. The third choice is to give all monomers
on all chains the same molecule ID, e.g. 0. This will allow a wide
variety of swaps to occur, but will NOT conserve chain lengths.
</P>
<P>IMPORTANT NOTE: If your simulation uses molecule IDs in the usual way,
where all monomers on a single chain are assigned the same ID
(different for each chain), then swaps will only occur within the same
chain and will NOT conserve chain length. This is probably not what
you want for this fix.
</P>
<HR>
<P>This fix computes a temperature each time it is invoked for use by the
Boltzmann criterion. To do this, the fix creates its own compute of
style <I>temp</I>, as if this command had been issued:
</P>
<PRE>compute fix-ID_temp all temp
</PRE>
<P>See the <A HREF = "compute_temp.html">compute temp</A> command for details. Note
that the ID of the new compute is the fix-ID with underscore + "temp"
appended and the group for the new compute is "all", so that the
temperature of the entire system is used.
</P>
<P>Note that this is NOT the compute used by thermodynamic output (see
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> will have no
effect on this fix.
</P>
<HR>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. Because the state of the random number generator
is not saved in restart files, this means you cannot do "exact"
restarts with this fix, where the simulation continues on the same as
if no restart had taken place. However, in a statistical sense, a
restarted simulation should produce the same behavior. Also note that
each processor generates possible swaps independently of other
processors. Thus if you repeat the same simulation on a different number
of processors, the specific swaps performed will be different.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
fix. You can use it to assign a <A HREF = "compute.html">compute</A> you have
defined to this fix which will be used to compute the temperature for
the Boltzmann criterion.
</P>
<P>This fix computes two statistical quantities as a global 2-vector of
output, which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. The first component of the
vector is the cummulative number of swaps performed by all processors.
The second component of the vector is the cummulative number of swaps
attempted (whether accepted or rejected). Note that a swap "attempt"
only occurs when swap partners meeting the criteria described above
are found on a particular timestep. The vector values calculated by
this fix are "intensive".
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "mc" package. It is only enabled if LAMMPS
-was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+<P>This fix is part of the MC package. It is only enabled if LAMMPS was
+built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>The setings of the "special_bond" command must be 0,1,1 in order to
use this fix, which is typical of bead-spring chains with FENE or
harmonic bonds. This means that pairwise interactions between bonded
atoms are turned off, but are turned on between atoms two or three
hops away along the chain backbone.
</P>
<P>Currently, energy changes in dihedral and improper interactions due to
a bond swap are not considered. Thus a simulation that uses this fix
cannot use a dihedral or improper potential.
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Sides"></A>
<P><B>(Sides)</B> Sides, Grest, Stevens, Plimpton, J Polymer Science B, 42,
199-208 (2004).
</P>
</HTML>
diff --git a/doc/fix_bond_swap.txt b/doc/fix_bond_swap.txt
index f5cb81f8f..e1e1aeba5 100755
--- a/doc/fix_bond_swap.txt
+++ b/doc/fix_bond_swap.txt
@@ -1,182 +1,182 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix bond/swap command :h3
[Syntax:]
fix ID group-ID bond/swap fraction cutoff seed :pre
ID, group-ID are documented in "fix"_fix.html command
bond/swap = style name of this fix command
fraction = fraction of group atoms to consider for swapping
cutoff = distance at which swapping will be considered (distance units)
seed = random # seed (positive integer) :ul
[Examples:]
fix 1 all bond/swap 0.5 1.3 598934 :pre
[Description:]
In a simulation of polymer chains, this command attempts to swap bonds
between two different chains, effectively grafting the end of one
chain onto another chain and vice versa. This is done via Monte Carlo
rules using the Boltzmann acceptance criterion. The purpose is to
equilibrate the polymer chain conformations more rapidly than dynamics
alone would do it, by enabling instantaneous large conformational
changes in a dense polymer melt. The polymer chains should thus more
rapidly converge to the proper end-to-end distances and radii of
gyration. It is designed for use with systems of
"FENE"_bond_fene.html or "harmonic"_bond_harmonic.html bead-spring
polymer chains where each polymer is a linear chain of monomers, but
LAMMPS does not enforce this requirement, i.e. any
"bond_style"_bond_style.html can be used.
A schematic of the kinds of bond swaps that can occur is shown here:
:c,image(JPG/bondswap.jpg)
On the left, the red and blue chains have two monomers A1 and B1 close
to each other, which are currently bonded to monomers A2 and B2
respectively within their own chains. The bond swap operation will
attempt to delete the A1-A2 and B1-B2 bonds and replace them with
A1-B2 and B1-A2 bonds. If the swap is energetically favorable, the
two chains on the right are the result and each polymer chain has
undergone a dramatic conformational change. This reference provides
more details on how the algorithm works and its application:
"(Sides)"_#Sides.
The bond swapping operation is invoked each time neighbor lists are
built during a simulation, since it potentially alters the list of
which neighbors are considered for pairwise interaction. At each
reneighboring step, each processor considers a random specified
{fraction} of its atoms as potential swapping monomers for this
timestep. Choosing a small {fraction} value can reduce the likelihood
of a reverse swap occurring soon after an initial swap.
For each monomer A1, its neighbors are examined to find a possible B1
monomer. Both A1 and B1 must be in the fix group, their separation
must be less than the specified {cutoff}, and the molecule IDs of A1
and B1 must be the same (see below). If a suitable partner is found,
the energy change due to swapping the 2 bonds is computed. This
includes changes in pairwise, bond, and angle energies due to the
altered connectivity of the 2 chains. Dihedral and improper
interactions are not allowed to be defined when this fix is used.
If the energy decreases due to the swap operation, the bond swap is
accepted. If the energy increases it is accepted with probability
exp(-delta/kT) where delta is the increase in energy, k is the
Boltzmann constant, and T is the current temperature of the system.
Whether the swap is accepted or rejected, no other swaps are attempted
by this processor on this timestep.
The criterion for matching molecule IDs is how bond swaps performed by
this fix conserve chain length. To use this features you must setup
the molecule IDs for your polymer chains in a certain way, typically
in the data file, read by the "read_data"_read_data.html comand.
Consider a system of 6-mer chains. You have 3 choices. If the
molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then
swaps will conserve length. For a particular momoner there will be
only one other monomer on another chain which is a potential swap
partner. If the molecule IDs for monomers on each chain are set to
1,2,3,3,2,1 then swaps will conserve length but swaps will be able to
occur at either end of a chain. Thus for a particular monomer there
will be 2 possible swap partners on another chain. In this scenario,
swaps can also occur within a single chain, i.e. the two ends of a
chain swap with each other. The third choice is to give all monomers
on all chains the same molecule ID, e.g. 0. This will allow a wide
variety of swaps to occur, but will NOT conserve chain lengths.
IMPORTANT NOTE: If your simulation uses molecule IDs in the usual way,
where all monomers on a single chain are assigned the same ID
(different for each chain), then swaps will only occur within the same
chain and will NOT conserve chain length. This is probably not what
you want for this fix.
:line
This fix computes a temperature each time it is invoked for use by the
Boltzmann criterion. To do this, the fix creates its own compute of
style {temp}, as if this command had been issued:
compute fix-ID_temp all temp :pre
See the "compute temp"_compute_temp.html command for details. Note
that the ID of the new compute is the fix-ID with underscore + "temp"
appended and the group for the new compute is "all", so that the
temperature of the entire system is used.
Note that this is NOT the compute used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
"compute_modify"_compute_modify.html command or print this temperature
during thermodyanmic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} will have no
effect on this fix.
:line
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. Because the state of the random number generator
is not saved in restart files, this means you cannot do "exact"
restarts with this fix, where the simulation continues on the same as
if no restart had taken place. However, in a statistical sense, a
restarted simulation should produce the same behavior. Also note that
each processor generates possible swaps independently of other
processors. Thus if you repeat the same simulation on a different number
of processors, the specific swaps performed will be different.
The "fix_modify"_fix_modify.html {temp} option is supported by this
fix. You can use it to assign a "compute"_compute.html you have
defined to this fix which will be used to compute the temperature for
the Boltzmann criterion.
This fix computes two statistical quantities as a global 2-vector of
output, which can be accessed by various "output
commands"_Section_howto.html#howto_15. The first component of the
vector is the cummulative number of swaps performed by all processors.
The second component of the vector is the cummulative number of swaps
attempted (whether accepted or rejected). Note that a swap "attempt"
only occurs when swap partners meeting the criteria described above
are found on a particular timestep. The vector values calculated by
this fix are "intensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
-This fix is part of the "mc" package. It is only enabled if LAMMPS
-was built with that package. See the "Making
+This fix is part of the MC package. It is only enabled if LAMMPS was
+built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
The setings of the "special_bond" command must be 0,1,1 in order to
use this fix, which is typical of bead-spring chains with FENE or
harmonic bonds. This means that pairwise interactions between bonded
atoms are turned off, but are turned on between atoms two or three
hops away along the chain backbone.
Currently, energy changes in dihedral and improper interactions due to
a bond swap are not considered. Thus a simulation that uses this fix
cannot use a dihedral or improper potential.
[Related commands:] none
[Default:] none
:line
:link(Sides)
[(Sides)] Sides, Grest, Stevens, Plimpton, J Polymer Science B, 42,
199-208 (2004).
diff --git a/doc/fix_enforce2d.html b/doc/fix_enforce2d.html
index 67cfe4da1..cad153683 100644
--- a/doc/fix_enforce2d.html
+++ b/doc/fix_enforce2d.html
@@ -1,74 +1,74 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix enforce2d command
</H3>
<H3>fix enforce2d/cuda command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID enforce2d
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>enforce2d = style name of this fix command
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 5 all enforce2d
</PRE>
<P><B>Description:</B>
</P>
<P>Zero out the z-dimension velocity and force on each atom in the group.
This is useful when running a 2d simulation to insure that atoms do
not move from their initial z coordinate.
</P>
<HR>
<P>Styles with a <I>cuda</I> suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
<A HREF = "Section_accelerate.html">this section</A> of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. No parameter of this fix can
be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
</P>
<P>The forces due to this fix are imposed during an energy minimization,
invoked by the <A HREF = "minimize.html">minimize</A> command.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/fix_enforce2d.txt b/doc/fix_enforce2d.txt
index 578b31179..20bcf8f3c 100644
--- a/doc/fix_enforce2d.txt
+++ b/doc/fix_enforce2d.txt
@@ -1,68 +1,68 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix enforce2d command :h3
fix enforce2d/cuda command :h3
[Syntax:]
fix ID group-ID enforce2d :pre
ID, group-ID are documented in "fix"_fix.html command
enforce2d = style name of this fix command :ul
[Examples:]
fix 5 all enforce2d :pre
[Description:]
Zero out the z-dimension velocity and force on each atom in the group.
This is useful when running a 2d simulation to insure that atoms do
not move from their initial z coordinate.
:line
Styles with a {cuda} suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
"this section"_Section_accelerate.html of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command.
[Restrictions:] none
[Related commands:] none
[Default:] none
diff --git a/doc/fix_freeze.html b/doc/fix_freeze.html
index 8cf86af53..762460f39 100644
--- a/doc/fix_freeze.html
+++ b/doc/fix_freeze.html
@@ -1,91 +1,91 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix freeze command
</H3>
<H3>fix freeze/cuda command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID freeze
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>freeze = style name of this fix command
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 2 bottom freeze
</PRE>
<P><B>Description:</B>
</P>
<P>Zero out the force and torque on a granular particle. This is useful
for preventing certain particles from moving in a simulation. The
<A HREF = "pair_gran.html">granular pair styles</A> also detect if this fix has been
defined and compute interactions between frozen and non-frozen
particles appropriately, as if the frozen particle has infinite mass.
</P>
<HR>
<P>Styles with a <I>cuda</I> suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
<A HREF = "Section_accelerate.html">this section</A> of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix.
</P>
<P>This fix computes a global 3-vector of forces, which can be accessed
by various <A HREF = "Section_howto.html#howto_15">output commands</A>. This is the
total force on the group of atoms before the forces on individual
atoms are changed by the fix. The vector values calculated by this
fix are "extensive".
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "granular" package. It is only enabled if
+<P>This fix is part of the GRANULAR package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>There can only be a single freeze fix defined. This is because other
the <A HREF = "pair_gran.html">granular pair styles</A> treat frozen particles
differently and need to be able to reference a single group to which
this fix is applied.
</P>
<P><B>Related commands:</B> none
</P>
<P><A HREF = "atom_style.html">atom_style sphere</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/fix_freeze.txt b/doc/fix_freeze.txt
index 52c069877..ac89b1819 100644
--- a/doc/fix_freeze.txt
+++ b/doc/fix_freeze.txt
@@ -1,85 +1,85 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix freeze command :h3
fix freeze/cuda command :h3
[Syntax:]
fix ID group-ID freeze :pre
ID, group-ID are documented in "fix"_fix.html command
freeze = style name of this fix command :ul
[Examples:]
fix 2 bottom freeze :pre
[Description:]
Zero out the force and torque on a granular particle. This is useful
for preventing certain particles from moving in a simulation. The
"granular pair styles"_pair_gran.html also detect if this fix has been
defined and compute interactions between frozen and non-frozen
particles appropriately, as if the frozen particle has infinite mass.
:line
Styles with a {cuda} suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
"this section"_Section_accelerate.html of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global 3-vector of forces, which can be accessed
by various "output commands"_Section_howto.html#howto_15. This is the
total force on the group of atoms before the forces on individual
atoms are changed by the fix. The vector values calculated by this
fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
-This fix is part of the "granular" package. It is only enabled if
+This fix is part of the GRANULAR package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
There can only be a single freeze fix defined. This is because other
the "granular pair styles"_pair_gran.html treat frozen particles
differently and need to be able to reference a single group to which
this fix is applied.
[Related commands:] none
"atom_style sphere"_atom_style.html
[Default:] none
diff --git a/doc/fix_gcmc.html b/doc/fix_gcmc.html
index c2a5db81a..2832f4f12 100644
--- a/doc/fix_gcmc.html
+++ b/doc/fix_gcmc.html
@@ -1,187 +1,187 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix gcmc command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID gcmc N X M type seed T mu displace keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>gcmc = style name of this fix command
<LI>N = invoke this fix every N steps
<LI>X = number of exchanges to attempt every N steps
<LI>M = number of MC displacements to attempt every N steps
<LI>type = atom type of exchanged particles
<LI>seed = random # seed (positive integer)
<LI>T = temperature of the ideal gas reservoir (temperature units)
<LI>mu = chemical potential of the ideal gas reservoir (energy units)
<LI>displace = maximum Monte Carlo displacement distance (length units)
<LI>zero or more keyword/value pairs may be appended to args
<PRE>keyword = <I>molecule</I>
<I>molecule</I> value = <I>no</I> or <I>yes</I>
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 2 all gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
fix 3 all gcmc 10 100 100 1 3456543 3.0 -2.5 0.1 molecule yes
</PRE>
<P><B>Description:</B>
</P>
<P>This fix performs grand canonical Monte Carlo (GCMC) exchanges of
particles of the given type with an imaginary ideal gas reservoir at
the specified T and chemical potential (mu) as discussed in
<A HREF = "#Frenkel">(Frenkel)</A>. If used with the <A HREF = "fix_nh.html">fix nvt</A> command,
simulations in the grand canonical enemble (muVT, constant chemical
potential, constant volume, and constant temperature) can be
performed. Specific uses include computing isotherms in microporous
materials, or computing vapor-liquid coexistence curves.
</P>
<P>Perform up to X exchanges of particles of the given type between the
simulation domain and the imaginary reservoir every N timesteps. Also
perform M Monte Carlo displacements of particles of the given type
within the simulation domain. M should typically be chosen to be
approximately equal to the expected number of particles of the given
type within the domain, which will result in roughly one MC
translation per particle per MC cycle.
</P>
<P>This fix cannot be used to perform MC displacements of particles other
than the exchanged type. All particles in the simulation domain can be
moved using regular time integration displacements, e.g. via
<A HREF = "fix_nvt.html">fix_nvt</A>, resulting in a hybrid GCMC+MD simulation.
</P>
<P>If used with <A HREF = "fix_nvt.html">fix_nvt</A>, the temperature of the imaginary
reservoir, T, should be set to be equivalent to the target temperature
used in <A HREF = "fix_nvt.html">fix_nvt</A>. Otherwise, the imaginary reservoir
will not be in thermal equilibrium with the simulation domain.
</P>
<P>Note that neighbor lists are re-built every timestep that this fix is
invoked, so you should not set N to be too small. However, periodic
rebuilds are necessary in order to avoid dangerous rebuilds and missed
interactions. Specifically, avoid performing so many MC displacements
per timestep that a particle can move beyond the neighbor list skin
distance. See the <A HREF = "neighbor.html">neighbor</A> command for details.
</P>
<P>When a particle is to be inserted, its coordinates are chosen as a
random position within the current simulation domain, and its velocity
is randomly chosen from the specified temperature distribution given
by T.
</P>
<P>Exchanged particles have the specified atom type and are assigned to
two groups: the default group "all" and the group specified in the fix
gcmc command (which can also be "all").
</P>
<P>If the setting for the <I>molecule</I> keyword is <I>no</I>, then only single
atoms are exchanged. In this case, you should ensure you do not
delete only a portion of a molecule (only some of its atoms), or
LAMMPS will soon generate an error when it tries to find those atoms.
LAMMPS will warn you if any of the atoms eligible for deletion have a
non-zero molecule ID, but does not check for this at the time of
deletion.
</P>
<P>If the setting for the <I>molecule</I> keyword is <I>yes</I>, entire molecules
are exchanged. This feature is not yet supported.
</P>
<P>Use of this fix typically will cause the number of atoms to fluctuate,
therefore, you will want to use the
<A HREF = "compute_modify.html">compute_modify</A> command to insure that the
current number of atoms is used as a normalizing factor each time
temperature is computed. Here is the necessary command:
</P>
<PRE>compute_modify thermo_temp dynamic yes
</PRE>
<P>If LJ units are used, note that a value of 0.18292026 is used by this
fix as the reduced value for Planck's constant. This value was
derived from LJ paramters for argon, where h* = h/sqrt(sigma^2 *
epsilon * mass), sigma = 3.429 angstroms, epsilon/k = 121.85 K, and
mass = 39.948 amu.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the deposition to <A HREF = "restart.html">binary restart
files</A>. This includes information about the random
number generator seed, the next timestep for MC exchanges, etc. See
the <A HREF = "read_restart.html">read_restart</A> command for info on how to
re-specify a fix in an input script that reads a restart file, so that
the operation of the fix continues in an uninterrupted fashion.
</P>
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
fix.
</P>
<P>This fix computes a global vector of length 6, which can be accessed
by various <A HREF = "Section_howto.html#howto_15">output commands</A>. The vector
values are the following global cummulative quantities:
</P>
<UL><LI>1 = displacement attempts
<LI>2 = displacement successes
<LI>3 = deletion attempts
<LI>4 = deletion successes
<LI>5 = insertion attempts
<LI>6 = insertion successes
</UL>
<P>The vector values calculated by this fix are "extensive".
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "mc" package. It is only enabled if LAMMPS
-was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+<P>This fix is part of the MC package. It is only enabled if LAMMPS was
+built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>Do not set "neigh_modify once yes" or else this fix will never be
called. Reneighboring is required.
</P>
<P>You cannot currently exchange charged particles or molecules with a
net charge.
</P>
<P>Only pairwise interactions, as defined by the
<A HREF = "pair_style.html">pair_style</A> command, are included in this
calculation. Long-range interactions due to a
<A HREF = "kspace_style.html">kspace_style</A> command are not included. Not all
pair potentials can be evaluated in a pairwise mode as required by
this fix. For example, 3-body potentials, such as
<A HREF = "pair_tersoff.html">Tersoff</A> and <A HREF = "pair_sw.html">Stillinger-Weber</A> cannot
be used. <A HREF = "pair_eam.html">EAM</A> potentials for metals only include the
pair potential portion of the EAM interaction, not the embedding term.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nvt.html">fix_nvt</A>, <A HREF = "neighbor.html">neighbor</A>,
<A HREF = "fix_deposit.html">fix_deposit</A>, <A HREF = "fix_evaporate.html">fix_evaporate</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are molecule = no.
</P>
<HR>
<A NAME = "Frenkel"></A>
<P><B>(Frenkel)</B> Frenkel and Smit, Understanding Molecular Simulation,
Academic Press, London, 2002.
</P>
</HTML>
diff --git a/doc/fix_gcmc.txt b/doc/fix_gcmc.txt
index ecf56d1de..e428e5c6a 100644
--- a/doc/fix_gcmc.txt
+++ b/doc/fix_gcmc.txt
@@ -1,169 +1,169 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix gcmc command :h3
[Syntax:]
fix ID group-ID gcmc N X M type seed T mu displace keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
gcmc = style name of this fix command :l
N = invoke this fix every N steps :l
X = number of exchanges to attempt every N steps :l
M = number of MC displacements to attempt every N steps :l
type = atom type of exchanged particles :l
seed = random # seed (positive integer) :l
T = temperature of the ideal gas reservoir (temperature units) :l
mu = chemical potential of the ideal gas reservoir (energy units) :l
displace = maximum Monte Carlo displacement distance (length units) :l
zero or more keyword/value pairs may be appended to args :l
keyword = {molecule}
{molecule} value = {no} or {yes} :pre
:ule
[Examples:]
fix 2 all gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
fix 3 all gcmc 10 100 100 1 3456543 3.0 -2.5 0.1 molecule yes :pre
[Description:]
This fix performs grand canonical Monte Carlo (GCMC) exchanges of
particles of the given type with an imaginary ideal gas reservoir at
the specified T and chemical potential (mu) as discussed in
"(Frenkel)"_#Frenkel. If used with the "fix nvt"_fix_nh.html command,
simulations in the grand canonical enemble (muVT, constant chemical
potential, constant volume, and constant temperature) can be
performed. Specific uses include computing isotherms in microporous
materials, or computing vapor-liquid coexistence curves.
Perform up to X exchanges of particles of the given type between the
simulation domain and the imaginary reservoir every N timesteps. Also
perform M Monte Carlo displacements of particles of the given type
within the simulation domain. M should typically be chosen to be
approximately equal to the expected number of particles of the given
type within the domain, which will result in roughly one MC
translation per particle per MC cycle.
This fix cannot be used to perform MC displacements of particles other
than the exchanged type. All particles in the simulation domain can be
moved using regular time integration displacements, e.g. via
"fix_nvt"_fix_nvt.html, resulting in a hybrid GCMC+MD simulation.
If used with "fix_nvt"_fix_nvt.html, the temperature of the imaginary
reservoir, T, should be set to be equivalent to the target temperature
used in "fix_nvt"_fix_nvt.html. Otherwise, the imaginary reservoir
will not be in thermal equilibrium with the simulation domain.
Note that neighbor lists are re-built every timestep that this fix is
invoked, so you should not set N to be too small. However, periodic
rebuilds are necessary in order to avoid dangerous rebuilds and missed
interactions. Specifically, avoid performing so many MC displacements
per timestep that a particle can move beyond the neighbor list skin
distance. See the "neighbor"_neighbor.html command for details.
When a particle is to be inserted, its coordinates are chosen as a
random position within the current simulation domain, and its velocity
is randomly chosen from the specified temperature distribution given
by T.
Exchanged particles have the specified atom type and are assigned to
two groups: the default group "all" and the group specified in the fix
gcmc command (which can also be "all").
If the setting for the {molecule} keyword is {no}, then only single
atoms are exchanged. In this case, you should ensure you do not
delete only a portion of a molecule (only some of its atoms), or
LAMMPS will soon generate an error when it tries to find those atoms.
LAMMPS will warn you if any of the atoms eligible for deletion have a
non-zero molecule ID, but does not check for this at the time of
deletion.
If the setting for the {molecule} keyword is {yes}, entire molecules
are exchanged. This feature is not yet supported.
Use of this fix typically will cause the number of atoms to fluctuate,
therefore, you will want to use the
"compute_modify"_compute_modify.html command to insure that the
current number of atoms is used as a normalizing factor each time
temperature is computed. Here is the necessary command:
compute_modify thermo_temp dynamic yes :pre
If LJ units are used, note that a value of 0.18292026 is used by this
fix as the reduced value for Planck's constant. This value was
derived from LJ paramters for argon, where h* = h/sqrt(sigma^2 *
epsilon * mass), sigma = 3.429 angstroms, epsilon/k = 121.85 K, and
mass = 39.948 amu.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the state of the deposition to "binary restart
files"_restart.html. This includes information about the random
number generator seed, the next timestep for MC exchanges, etc. See
the "read_restart"_read_restart.html command for info on how to
re-specify a fix in an input script that reads a restart file, so that
the operation of the fix continues in an uninterrupted fashion.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix.
This fix computes a global vector of length 6, which can be accessed
by various "output commands"_Section_howto.html#howto_15. The vector
values are the following global cummulative quantities:
1 = displacement attempts
2 = displacement successes
3 = deletion attempts
4 = deletion successes
5 = insertion attempts
6 = insertion successes :ul
The vector values calculated by this fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
-This fix is part of the "mc" package. It is only enabled if LAMMPS
-was built with that package. See the "Making
+This fix is part of the MC package. It is only enabled if LAMMPS was
+built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
Do not set "neigh_modify once yes" or else this fix will never be
called. Reneighboring is required.
You cannot currently exchange charged particles or molecules with a
net charge.
Only pairwise interactions, as defined by the
"pair_style"_pair_style.html command, are included in this
calculation. Long-range interactions due to a
"kspace_style"_kspace_style.html command are not included. Not all
pair potentials can be evaluated in a pairwise mode as required by
this fix. For example, 3-body potentials, such as
"Tersoff"_pair_tersoff.html and "Stillinger-Weber"_pair_sw.html cannot
be used. "EAM"_pair_eam.html potentials for metals only include the
pair potential portion of the EAM interaction, not the embedding term.
[Related commands:]
"fix_nvt"_fix_nvt.html, "neighbor"_neighbor.html,
"fix_deposit"_fix_deposit.html, "fix_evaporate"_fix_evaporate.html
[Default:]
The option defaults are molecule = no.
:line
:link(Frenkel)
[(Frenkel)] Frenkel and Smit, Understanding Molecular Simulation,
Academic Press, London, 2002.
diff --git a/doc/fix_gravity.html b/doc/fix_gravity.html
index 3446d9b08..782338366 100644
--- a/doc/fix_gravity.html
+++ b/doc/fix_gravity.html
@@ -1,131 +1,142 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix gravity command
</H3>
<H3>fix gravity/cuda command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group gravity style magnitude args
</PRE>
<UL><LI>ID, group are documented in <A HREF = "fix.html">fix</A> command
<LI>gravity = style name of this fix command
<LI>magnitude = size of acceleration (force/mass units)
<LI>style = <I>chute</I> or <I>spherical</I> or <I>gradient</I> or <I>vector</I>
<PRE> <I>chute</I> args = angle
angle = angle in +x away from -z or -y axis in 3d/2d (in degrees)
<I>spherical</I> args = phi theta
phi = azimuthal angle from +x axis (in degrees)
theta = angle from +z or +y axis in 3d/2d (in degrees)
<I>gradient</I> args = phi theta phi_grad theta_grad
phi = azimuthal angle from +x axis (in degrees)
theta = angle from +z or +y axis in 3d/2d (in degrees)
phi_grad = rate of change of angle phi (full rotations per time unit)
theta_grad = rate of change of angle theta (full rotations per time unit)
<I>vector</I> args = x y z
x y z = vector direction to apply the acceleration
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all gravity 1.0 chute 24.0
fix 1 all gravity 1.0 spherical 0.0 -180.0
fix 1 all gravity 1.0 gradient 0.0 -180.0 0.0 0.1
fix 1 all gravity 100.0 vector 1 1 0
</PRE>
<P><B>Description:</B>
</P>
<P>Impose an additional acceleration on each particle in the group. This
fix is typically used with granular systems to include a "gravity"
term acting on the macroscopic particles. More generally, it can
represent any kind of driving field, e.g. a pressure gradient inducing
a Poiseuille flow in a fluid. Note that this fix operates differently
than the <A HREF = "fix_addforce.html">fix addforce</A> command. The addforce fix
adds the same force to each atom, independent of its mass. This
command imparts the same acceleration to each atom (force/mass).
</P>
<P>The <I>magnitude</I> of the acceleration is specified in force/mass units.
For granular systems (LJ units) this is typically 1.0. See the
<A HREF = "units.html">units</A> command for details.
</P>
<P>Style <I>chute</I> is typically used for simulations of chute flow where
the specified angle is the chute angle, with flow occurring in the +x
direction. For 3d systems, the tilt is away from the z axis; for 2d
systems, the tilt is away from the y axis.
</P>
<P>Style <I>spherical</I> allows an arbitrary 3d direction to be specified for
the acceleration vector. Phi and theta are defined in the usual
spherical coordinates. Thus for acceleration acting in the -z
direction, theta would be 180.0 (or -180.0). Theta = 90.0 and phi =
-90.0 would mean acceleration acts in the -y direction. For 2d
systems, <I>phi</I> is ignored and <I>theta</I> is an angle in the xy plane
where theta = 0.0 is the y-axis.
</P>
<P>Style <I>gradient</I> is the same as style <I>spherical</I> except that the
direction of the acceleration vector is time dependent. The units of
the gradient arguments are in full rotations per time unit. E.g. a
timestep of 0.001 and a gradient of 0.1 means the acceleration vector
would rotate thru 360 degrees every 10,000 timesteps. For the
time-dependent case, the initial direction of the acceleration vector
is set to phi,theta when the fix is specified and evolves thereafter.
For 2d systems, <I>phi</I> and <I>phi_grad</I> are ignored.
</P>
<P>Style <I>vector</I> imposes an acceleration in the vector direction given
by (x,y,z). For 2d systems, the z component is ignored.
</P>
<HR>
<P>Styles with a <I>cuda</I> suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
<A HREF = "Section_accelerate.html">this section</A> of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
-files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
-are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
-commands</A>. No parameter of this fix can
-be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
-This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+files</A>.
+</P>
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
+fix to add the gravitational potential energy of the system to the
+system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
+output</A>.
+</P>
+<P>This fix computes a global scalar which can be accessed by various
+<A HREF = "Section_howto.html#howto_15">output commands</A>. This scalar is the
+gravitational potential energy of the particles in the defined field,
+namely mass * (g dot x) for each particles, where x and mass are the
+particles position and mass, and g is the gravitational field. The
+scalar value calculated by this fix is "extensive".
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "atom_style.html">atom_style sphere</A>, <A HREF = "fix_addforce.html">fix addforce</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/fix_gravity.txt b/doc/fix_gravity.txt
index 1ee4b5ce3..f383755ac 100644
--- a/doc/fix_gravity.txt
+++ b/doc/fix_gravity.txt
@@ -1,120 +1,131 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix gravity command :h3
fix gravity/cuda command :h3
[Syntax:]
fix ID group gravity style magnitude args :pre
ID, group are documented in "fix"_fix.html command :ulb,l
gravity = style name of this fix command :l
magnitude = size of acceleration (force/mass units) :l
style = {chute} or {spherical} or {gradient} or {vector} :l
{chute} args = angle
angle = angle in +x away from -z or -y axis in 3d/2d (in degrees)
{spherical} args = phi theta
phi = azimuthal angle from +x axis (in degrees)
theta = angle from +z or +y axis in 3d/2d (in degrees)
{gradient} args = phi theta phi_grad theta_grad
phi = azimuthal angle from +x axis (in degrees)
theta = angle from +z or +y axis in 3d/2d (in degrees)
phi_grad = rate of change of angle phi (full rotations per time unit)
theta_grad = rate of change of angle theta (full rotations per time unit)
{vector} args = x y z
x y z = vector direction to apply the acceleration :pre
:ule
[Examples:]
fix 1 all gravity 1.0 chute 24.0
fix 1 all gravity 1.0 spherical 0.0 -180.0
fix 1 all gravity 1.0 gradient 0.0 -180.0 0.0 0.1
fix 1 all gravity 100.0 vector 1 1 0 :pre
[Description:]
Impose an additional acceleration on each particle in the group. This
fix is typically used with granular systems to include a "gravity"
term acting on the macroscopic particles. More generally, it can
represent any kind of driving field, e.g. a pressure gradient inducing
a Poiseuille flow in a fluid. Note that this fix operates differently
than the "fix addforce"_fix_addforce.html command. The addforce fix
adds the same force to each atom, independent of its mass. This
command imparts the same acceleration to each atom (force/mass).
The {magnitude} of the acceleration is specified in force/mass units.
For granular systems (LJ units) this is typically 1.0. See the
"units"_units.html command for details.
Style {chute} is typically used for simulations of chute flow where
the specified angle is the chute angle, with flow occurring in the +x
direction. For 3d systems, the tilt is away from the z axis; for 2d
systems, the tilt is away from the y axis.
Style {spherical} allows an arbitrary 3d direction to be specified for
the acceleration vector. Phi and theta are defined in the usual
spherical coordinates. Thus for acceleration acting in the -z
direction, theta would be 180.0 (or -180.0). Theta = 90.0 and phi =
-90.0 would mean acceleration acts in the -y direction. For 2d
systems, {phi} is ignored and {theta} is an angle in the xy plane
where theta = 0.0 is the y-axis.
Style {gradient} is the same as style {spherical} except that the
direction of the acceleration vector is time dependent. The units of
the gradient arguments are in full rotations per time unit. E.g. a
timestep of 0.001 and a gradient of 0.1 means the acceleration vector
would rotate thru 360 degrees every 10,000 timesteps. For the
time-dependent case, the initial direction of the acceleration vector
is set to phi,theta when the fix is specified and evolves thereafter.
For 2d systems, {phi} and {phi_grad} are ignored.
Style {vector} imposes an acceleration in the vector direction given
by (x,y,z). For 2d systems, the z component is ignored.
:line
Styles with a {cuda} suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
"this section"_Section_accelerate.html of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
-files"_restart.html. None of the "fix_modify"_fix_modify.html options
-are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+files"_restart.html.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the gravitational potential energy of the system to the
+system's potential energy as part of "thermodynamic
+output"_thermo_style.html.
+
+This fix computes a global scalar which can be accessed by various
+"output commands"_Section_howto.html#howto_15. This scalar is the
+gravitational potential energy of the particles in the defined field,
+namely mass * (g dot x) for each particles, where x and mass are the
+particles position and mass, and g is the gravitational field. The
+scalar value calculated by this fix is "extensive".
+
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:] none
[Related commands:]
"atom_style sphere"_atom_style.html, "fix addforce"_fix_addforce.html
[Default:] none
diff --git a/doc/fix_imd.html b/doc/fix_imd.html
index d800f16b1..529fa9686 100644
--- a/doc/fix_imd.html
+++ b/doc/fix_imd.html
@@ -1,178 +1,178 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix imd command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID imd trate port keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>imd = style name of this fix command
<LI>port = port number on which the fix listens for an IMD client
<LI>keyword = <I>unwrap</I> or <I>fscale</I> or <I>trate</I>
<PRE> <I>unwrap</I> arg = <I>on</I> or <I>off</I>
off = coordinates are wrapped back into the principal unit cell (default)
on = "unwrapped" coordinates using the image flags used
<I>fscale</I> arg = factor
factor = floating point number to scale IMD forces (default: 1.0)
<I>trate</I> arg = transmission rate of coordinate data sets (default: 1)
<I>nowait</I> arg = <I>on</I> or <I>off</I>
off = LAMMPS waits to be connected to an IMD client before continuing (default)
on = LAMMPS listens for an IMD client, but continues with the run
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix vmd all imd 5678
fix comm all imd 8888 trate 5 unwrap on fscale 10.0
</PRE>
<P><B>Description:</B>
</P>
<P>This fix implements the "Interactive MD" (IMD) protocol which allows
realtime visualization and manipulation of MD simulations through the
IMD protocol, as initially implemented in VMD and NAMD. Specifically
it allows LAMMPS to connect an IMD client, for example the <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD
visualization program</A>, so that it can monitor the progress of the
simulation and interactively apply forces to selected atoms.
</P>
<P>If LAMMPS is compiled with the preprocessor flag -DLAMMPS_ASYNC_IMD
then fix imd will use posix threads to spawn a thread on MPI rank 0 in
order to offload data reading and writing from the main execution
thread and potentiall lower the inferred latencies for slow
communication links. This feature has only been tested under linux.
</P>
<P>There are example scripts for using this package with LAMMPS in
examples/USER/imd. Additional examples and a driver for use with the
Novint Falcon game controller as haptic device can be found at:
http://sites.google.com/site/akohlmey/software/vrpn-icms.
</P>
<P>The source code for this fix includes code developed by the
Theoretical and Computational Biophysics Group in the Beckman
Institute for Advanced Science and Technology at the University of
Illinois at Urbana-Champaign. We thank them for providing a software
interface that allows codes like LAMMPS to hook to <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>.
</P>
<P>Upon initialization of the fix, it will open a communication port on
the node with MPI task 0 and wait for an incoming connection. As soon
as an IMD client is connected, the simulation will continue and the
fix will send the current coordinates of the fix's group to the IMD
client at every trate MD step. When using r-RESPA, trate applies to
the steps of the outmost RESPA level. During a run with an active IMD
connection also the IMD client can request to apply forces to selected
atoms of the fix group.
</P>
<P>The port number selected must be an available network port number. On
many machines, port numbers < 1024 are reserved for accounts with
system manager privilege and specific applications. If multiple imd
fixes would be active at the same time, each needs to use a different
port number.
</P>
<P>The <I>nowait</I> keyword controls the behavior of the fix when no IMD
client is connected. With the default setting of <I>off</I>, LAMMPS will
wait until a connection is made before continuing with the
execution. Setting <I>nowait</I> to <I>on</I> will have the LAMMPS code be ready
to connect to a client, but continue with the simulation. This can for
example be used to monitor the progress of an ongoing calculation
without the need to be permanently connected or having to download a
trajectory file.
</P>
<P>The <I>trate</I> keyword allows to select how often the coordinate data is
sent to the IMD client. It can also be changed on request of the IMD
client through an IMD protocol message. The <I>unwrap</I> keyword allows
to send "unwrapped" coordinates to the IMD client that undo the
wrapping back of coordinates into the principle unit cell, as done by
default in LAMMPS. The <I>fscale</I> keyword allows to apply a scaling
factor to forces transmitted by the IMD client. The IMD protocols
stipulates that forces are transferred in kcal/mol/angstrom under the
assumption that coordinates are given in angstrom. For LAMMPS runs
with different units or as a measure to tweak the forces generated by
the manipulation of the IMD client, this option allows to make
adjustments.
</P>
<P>To connect VMD to a listening LAMMPS simulation on the same machine
with fix imd enabled, one needs to start VMD and load a coordinate or
topology file that matches the fix group. When the VMD command
prompts appears, one types the command line:
</P>
<PRE>imd connect localhost 5678
</PRE>
<P>This assumes that <I>fix imd</I> was started with 5678 as a port
number for the IMD protocol.
</P>
<P>The steps to do interactive manipulation of a running simulation in
VMD are the following:
</P>
<P>In the Mouse menu of the VMD Main window, select "Mouse -> Force ->
Atom". You may alternately select "Residue", or "Fragment" to apply
forces to whole residues or fragments. Your mouse can now be used to
apply forces to your simulation. Click on an atom, residue, or
fragment and drag to apply a force. Click quickly without moving the
mouse to turn the force off. You can also use a variety of 3D position
trackers to apply forces to your simulation. Game controllers or haptic
devices with force-feedback such as the Novint Falcon or Sensable
PHANTOM allow you to feel the resistance due to inertia or interactions
with neighbors that the atoms experience you are trying to move, as if
they were real objects. See the <A HREF = "http://www.ks.uiuc.edu/Research/vmd/imd/">VMD IMD Homepage</A> and the
<A HREF = "http://sites.google.com/site/akohlmey/software/vrpn-icms">VRPN-ICMS Homepage</A> for more details.
</P>
<P>If IMD control messages are received, a line of text describing the
message and its effect will be printed to the LAMMPS output screen, if
screen output is active.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global scalar or vector or per-atom
quantities are stored by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. No parameter of this fix can
be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "user-misc" package. It is only enabled if
+<P>This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>On platforms that support multi-threading, this fix can be compiled in
a way that the coordinate transfers to the IMD client can be handled
from a separate thread, when LAMMPS is compiled with the
-DLAMMPS_ASYNC_IMD preprocessor flag. This should to keep MD loop
times low and transfer rates high, especially for systems with many
atoms and for slow connections.
</P>
<P>When used in combination with VMD, a topology or coordinate file has
to be loaded, which matches (in number and ordering of atoms) the
group the fix is applied to. The fix internally sorts atom IDs by
ascending integer value; in VMD (and thus the IMD protocol) those will
be assigned 0-based consecutive index numbers.
</P>
<P>When using multiple active IMD connections at the same time, each
needs to use a different port number.
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/fix_imd.txt b/doc/fix_imd.txt
index 66ea5676d..246cb36e0 100644
--- a/doc/fix_imd.txt
+++ b/doc/fix_imd.txt
@@ -1,166 +1,166 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix imd command :h3
[Syntax:]
fix ID group-ID imd trate port keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
imd = style name of this fix command :l
port = port number on which the fix listens for an IMD client :l
keyword = {unwrap} or {fscale} or {trate} :l
{unwrap} arg = {on} or {off}
off = coordinates are wrapped back into the principal unit cell (default)
on = "unwrapped" coordinates using the image flags used
{fscale} arg = factor
factor = floating point number to scale IMD forces (default: 1.0)
{trate} arg = transmission rate of coordinate data sets (default: 1)
{nowait} arg = {on} or {off}
off = LAMMPS waits to be connected to an IMD client before continuing (default)
on = LAMMPS listens for an IMD client, but continues with the run :pre
:ule
[Examples:]
fix vmd all imd 5678
fix comm all imd 8888 trate 5 unwrap on fscale 10.0 :pre
[Description:]
This fix implements the "Interactive MD" (IMD) protocol which allows
realtime visualization and manipulation of MD simulations through the
IMD protocol, as initially implemented in VMD and NAMD. Specifically
it allows LAMMPS to connect an IMD client, for example the "VMD
visualization program"_VMD, so that it can monitor the progress of the
simulation and interactively apply forces to selected atoms.
If LAMMPS is compiled with the preprocessor flag -DLAMMPS_ASYNC_IMD
then fix imd will use posix threads to spawn a thread on MPI rank 0 in
order to offload data reading and writing from the main execution
thread and potentiall lower the inferred latencies for slow
communication links. This feature has only been tested under linux.
There are example scripts for using this package with LAMMPS in
examples/USER/imd. Additional examples and a driver for use with the
Novint Falcon game controller as haptic device can be found at:
http://sites.google.com/site/akohlmey/software/vrpn-icms.
The source code for this fix includes code developed by the
Theoretical and Computational Biophysics Group in the Beckman
Institute for Advanced Science and Technology at the University of
Illinois at Urbana-Champaign. We thank them for providing a software
interface that allows codes like LAMMPS to hook to "VMD"_VMD.
Upon initialization of the fix, it will open a communication port on
the node with MPI task 0 and wait for an incoming connection. As soon
as an IMD client is connected, the simulation will continue and the
fix will send the current coordinates of the fix's group to the IMD
client at every trate MD step. When using r-RESPA, trate applies to
the steps of the outmost RESPA level. During a run with an active IMD
connection also the IMD client can request to apply forces to selected
atoms of the fix group.
The port number selected must be an available network port number. On
many machines, port numbers < 1024 are reserved for accounts with
system manager privilege and specific applications. If multiple imd
fixes would be active at the same time, each needs to use a different
port number.
The {nowait} keyword controls the behavior of the fix when no IMD
client is connected. With the default setting of {off}, LAMMPS will
wait until a connection is made before continuing with the
execution. Setting {nowait} to {on} will have the LAMMPS code be ready
to connect to a client, but continue with the simulation. This can for
example be used to monitor the progress of an ongoing calculation
without the need to be permanently connected or having to download a
trajectory file.
The {trate} keyword allows to select how often the coordinate data is
sent to the IMD client. It can also be changed on request of the IMD
client through an IMD protocol message. The {unwrap} keyword allows
to send "unwrapped" coordinates to the IMD client that undo the
wrapping back of coordinates into the principle unit cell, as done by
default in LAMMPS. The {fscale} keyword allows to apply a scaling
factor to forces transmitted by the IMD client. The IMD protocols
stipulates that forces are transferred in kcal/mol/angstrom under the
assumption that coordinates are given in angstrom. For LAMMPS runs
with different units or as a measure to tweak the forces generated by
the manipulation of the IMD client, this option allows to make
adjustments.
To connect VMD to a listening LAMMPS simulation on the same machine
with fix imd enabled, one needs to start VMD and load a coordinate or
topology file that matches the fix group. When the VMD command
prompts appears, one types the command line:
imd connect localhost 5678 :pre
This assumes that {fix imd} was started with 5678 as a port
number for the IMD protocol.
The steps to do interactive manipulation of a running simulation in
VMD are the following:
In the Mouse menu of the VMD Main window, select "Mouse -> Force ->
Atom". You may alternately select "Residue", or "Fragment" to apply
forces to whole residues or fragments. Your mouse can now be used to
apply forces to your simulation. Click on an atom, residue, or
fragment and drag to apply a force. Click quickly without moving the
mouse to turn the force off. You can also use a variety of 3D position
trackers to apply forces to your simulation. Game controllers or haptic
devices with force-feedback such as the Novint Falcon or Sensable
PHANTOM allow you to feel the resistance due to inertia or interactions
with neighbors that the atoms experience you are trying to move, as if
they were real objects. See the "VMD IMD Homepage"_imdvmd and the
"VRPN-ICMS Homepage"_vrpnicms for more details.
If IMD control messages are received, a line of text describing the
message and its effect will be printed to the LAMMPS output screen, if
screen output is active.
:link(VMD,http://www.ks.uiuc.edu/Research/vmd)x
:link(imdvmd,http://www.ks.uiuc.edu/Research/vmd/imd/)
:link(vrpnicms,http://sites.google.com/site/akohlmey/software/vrpn-icms)
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global scalar or vector or per-atom
quantities are stored by this fix for access by various "output
commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
-This fix is part of the "user-misc" package. It is only enabled if
+This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
On platforms that support multi-threading, this fix can be compiled in
a way that the coordinate transfers to the IMD client can be handled
from a separate thread, when LAMMPS is compiled with the
-DLAMMPS_ASYNC_IMD preprocessor flag. This should to keep MD loop
times low and transfer rates high, especially for systems with many
atoms and for slow connections.
When used in combination with VMD, a topology or coordinate file has
to be loaded, which matches (in number and ordering of atoms) the
group the fix is applied to. The fix internally sorts atom IDs by
ascending integer value; in VMD (and thus the IMD protocol) those will
be assigned 0-based consecutive index numbers.
When using multiple active IMD connections at the same time, each
needs to use a different port number.
[Related commands:] none
[Default:] none
diff --git a/doc/fix_langevin_eff.html b/doc/fix_langevin_eff.html
index 60ad5d1e7..db8601092 100644
--- a/doc/fix_langevin_eff.html
+++ b/doc/fix_langevin_eff.html
@@ -1,124 +1,124 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix langevin/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID langevin/eff Tstart Tstop damp seed keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>langevin/eff = style name of this fix command
<LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
<LI>damp = damping parameter (time units)
<LI>seed = random number seed to use for white noise (positive integer)
<LI>zero or more keyword/value pairs may be appended
<PRE>keyword = <I>scale</I> or <I>tally</I>
<I>scale</I> values = type ratio
type = atom type (1-N)
ratio = factor by which to scale the damping coefficient
<I>tally</I> values = <I>no</I> or <I>yes</I>
<I>no</I> = do not tally the energy added/subtracted to atoms
<I>yes</I> = do tally the energy added/subtracted to atoms
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 3 boundary langevin/eff 1.0 1.0 10.0 699483
fix 1 all langevin/eff 1.0 1.1 10.0 48279 scale 3 1.5
</PRE>
<P><B>Description:</B>
</P>
<P>Apply a Langevin thermostat as described in <A HREF = "#Schneider">(Schneider)</A>
to a group of nuclei and electrons in the <A HREF = "pair_eff.html">electron force
field</A> model. Used with <A HREF = "fix_nve_eff.html">fix nve/eff</A>,
this command performs Brownian dynamics (BD), since the total force on
each atom will have the form:
</P>
<PRE>F = Fc + Ff + Fr
Ff = - (m / damp) v
Fr is proportional to sqrt(Kb T m / (dt damp))
</PRE>
<P>Fc is the conservative force computed via the usual inter-particle
interactions (<A HREF = "pair_style.html">pair_style</A>).
</P>
<P>The Ff and Fr terms are added by this fix on a per-particle basis.
</P>
<P>The operation of this fix is exactly like that described by the <A HREF = "fix_langevin.html">fix
langevin</A> command, except that the thermostatting
is also applied to the radial electron velocity for electron
particles.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. Because the state of the random number generator
is not saved in restart files, this means you cannot do "exact"
restarts with this fix, where the simulation continues on the same as
if no restart had taken place. However, in a statistical sense, a
restarted simulation should produce the same behavior.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
fix. You can use it to assign a temperature <A HREF = "compute.html">compute</A>
you have defined to this fix which will be used in its thermostatting
procedure, as described above. For consistency, the group used by
this fix and by the compute should be the same.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change induced by Langevin thermostatting to the
system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>. Note that use of this option requires
setting the <I>tally</I> keyword to <I>yes</I>.
</P>
<P>This fix computes a global scalar which can be accessed by various
<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
cummulative energy change due to this fix. The scalar value
calculated by this fix is "extensive". Note that calculation of this
quantity requires setting the <I>tally</I> keyword to <I>yes</I>.
</P>
<P>This fix can ramp its target temperature over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
<A HREF = "run.html">run</A> command for details of how to do this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
-<P>This fix is part of the "user-eff" package. It is only enabled if
+<P>This fix is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_langevin.html">fix langevin</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are scale = 1.0 for all types and tally = no.
</P>
<HR>
<A NAME = "Dunweg"></A>
<P><B>(Dunweg)</B> Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).
</P>
<A NAME = "Schneider"></A>
<P><B>(Schneider)</B> Schneider and Stoll, Phys Rev B, 17, 1302 (1978).
</P>
</HTML>
diff --git a/doc/fix_langevin_eff.txt b/doc/fix_langevin_eff.txt
index 1ee877bd6..a6806a39c 100644
--- a/doc/fix_langevin_eff.txt
+++ b/doc/fix_langevin_eff.txt
@@ -1,110 +1,110 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix langevin/eff command :h3
[Syntax:]
fix ID group-ID langevin/eff Tstart Tstop damp seed keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
langevin/eff = style name of this fix command :l
Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
damp = damping parameter (time units) :l
seed = random number seed to use for white noise (positive integer) :l
zero or more keyword/value pairs may be appended :l
keyword = {scale} or {tally}
{scale} values = type ratio
type = atom type (1-N)
ratio = factor by which to scale the damping coefficient
{tally} values = {no} or {yes}
{no} = do not tally the energy added/subtracted to atoms
{yes} = do tally the energy added/subtracted to atoms :pre
:ule
[Examples:]
fix 3 boundary langevin/eff 1.0 1.0 10.0 699483
fix 1 all langevin/eff 1.0 1.1 10.0 48279 scale 3 1.5 :pre
[Description:]
Apply a Langevin thermostat as described in "(Schneider)"_#Schneider
to a group of nuclei and electrons in the "electron force
field"_pair_eff.html model. Used with "fix nve/eff"_fix_nve_eff.html,
this command performs Brownian dynamics (BD), since the total force on
each atom will have the form:
F = Fc + Ff + Fr
Ff = - (m / damp) v
Fr is proportional to sqrt(Kb T m / (dt damp)) :pre
Fc is the conservative force computed via the usual inter-particle
interactions ("pair_style"_pair_style.html).
The Ff and Fr terms are added by this fix on a per-particle basis.
The operation of this fix is exactly like that described by the "fix
langevin"_fix_langevin.html command, except that the thermostatting
is also applied to the radial electron velocity for electron
particles.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. Because the state of the random number generator
is not saved in restart files, this means you cannot do "exact"
restarts with this fix, where the simulation continues on the same as
if no restart had taken place. However, in a statistical sense, a
restarted simulation should produce the same behavior.
The "fix_modify"_fix_modify.html {temp} option is supported by this
fix. You can use it to assign a temperature "compute"_compute.html
you have defined to this fix which will be used in its thermostatting
procedure, as described above. For consistency, the group used by
this fix and by the compute should be the same.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change induced by Langevin thermostatting to the
system's potential energy as part of "thermodynamic
output"_thermo_style.html. Note that use of this option requires
setting the {tally} keyword to {yes}.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
cummulative energy change due to this fix. The scalar value
calculated by this fix is "extensive". Note that calculation of this
quantity requires setting the {tally} keyword to {yes}.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
"run"_run.html command for details of how to do this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] none
-This fix is part of the "user-eff" package. It is only enabled if
+This fix is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"fix langevin"_fix_langevin.html
[Default:]
The option defaults are scale = 1.0 for all types and tally = no.
:line
:link(Dunweg)
[(Dunweg)] Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).
:link(Schneider)
[(Schneider)] Schneider and Stoll, Phys Rev B, 17, 1302 (1978).
diff --git a/doc/fix_nve_eff.html b/doc/fix_meso.html
similarity index 53%
copy from doc/fix_nve_eff.html
copy to doc/fix_meso.html
index dcc053450..b3684d872 100644
--- a/doc/fix_nve_eff.html
+++ b/doc/fix_meso.html
@@ -1,59 +1,57 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
-<H3>fix nve/eff command
+<H3>fix meso command
</H3>
<P><B>Syntax:</B>
</P>
-<PRE>fix ID group-ID nve/eff
+<PRE>fix ID group-ID meso
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
-<LI>nve/eff = style name of this fix command
+<LI>meso = style name of this fix command
</UL>
<P><B>Examples:</B>
</P>
-<PRE>fix 1 all nve/eff
+<PRE>fix 1 all meso
</PRE>
<P><B>Description:</B>
</P>
-<P>Perform constant NVE integration to update position and velocity for
-nuclei and electrons in the group for the <A HREF = "pair_eff.html">electron force
-field</A> model. V is volume; E is energy. This creates a
-system trajectory consistent with the microcanonical ensemble.
+<P>Perform time integration to update position, velocity, internal energy
+and local density for atoms in the group each timestep. This fix is
+needed to time-integrate mesoscopic systems where particles carry
+internal variables such as SPH or DPDE.
</P>
-<P>The operation of this fix is exactly like that described by the <A HREF = "fix_nve.html">fix
-nve</A> command, except that the radius and radial velocity
-of electrons are also updated.
+<P>See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+LAMMPS.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
-commands</A>. No parameter of this fix can
-be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+by this fix for access by various <A HREF = "Section_howto.html#4_15">output
+commands</A>. No parameter of this fix can be
+used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "user-eff" package. It is only enabled if
+<P>This fix is part of the USER-SPH package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
-<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nh_eff.html">fix nvt/eff</A>, <A HREF = "fix_nh_eff.html">fix
-npt/eff</A>
+<P>"fix meso/stationary"
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/fix_meso.txt b/doc/fix_meso.txt
new file mode 100644
index 000000000..7c6a5cfc4
--- /dev/null
+++ b/doc/fix_meso.txt
@@ -0,0 +1,52 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix meso command :h3
+
+[Syntax:]
+
+fix ID group-ID meso :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+meso = style name of this fix command :ul
+
+[Examples:]
+
+fix 1 all meso :pre
+
+[Description:]
+
+Perform time integration to update position, velocity, internal energy
+and local density for atoms in the group each timestep. This fix is
+needed to time-integrate mesoscopic systems where particles carry
+internal variables such as SPH or DPDE.
+
+See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in
+LAMMPS.
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html. None of the "fix_modify"_fix_modify.html options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various "output
+commands"_Section_howto.html#4_15. No parameter of this fix can be
+used with the {start/stop} keywords of the "run"_run.html command.
+This fix is not invoked during "energy minimization"_minimize.html.
+
+[Restrictions:]
+
+This fix is part of the USER-SPH package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"fix meso/stationary"
+
+[Default:] none
diff --git a/doc/fix_nve_eff.html b/doc/fix_meso_stationary.html
similarity index 53%
copy from doc/fix_nve_eff.html
copy to doc/fix_meso_stationary.html
index dcc053450..67a9a6a20 100644
--- a/doc/fix_nve_eff.html
+++ b/doc/fix_meso_stationary.html
@@ -1,59 +1,58 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
-<H3>fix nve/eff command
+<H3>fix meso/stationary command
</H3>
<P><B>Syntax:</B>
</P>
-<PRE>fix ID group-ID nve/eff
+<PRE>fix ID group-ID meso/stationary
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
-<LI>nve/eff = style name of this fix command
+<LI>meso = style name of this fix command
</UL>
<P><B>Examples:</B>
</P>
-<PRE>fix 1 all nve/eff
+<PRE>fix 1 boundary meso/stationary
</PRE>
<P><B>Description:</B>
</P>
-<P>Perform constant NVE integration to update position and velocity for
-nuclei and electrons in the group for the <A HREF = "pair_eff.html">electron force
-field</A> model. V is volume; E is energy. This creates a
-system trajectory consistent with the microcanonical ensemble.
+<P>Perform time integration to update internal energy and local density,
+but not position or velocity for atoms in the group each timestep.
+This fix is needed for SPH simulations to correctly time-integrate
+fixed boundary particles which constrain a fluid to a given region in
+space.
</P>
-<P>The operation of this fix is exactly like that described by the <A HREF = "fix_nve.html">fix
-nve</A> command, except that the radius and radial velocity
-of electrons are also updated.
+<P>See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+LAMMPS.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
-commands</A>. No parameter of this fix can
-be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
+by this fix for access by various <A HREF = "Section_howto.html#4_15">output
+commands</A>. No parameter of this fix can be
+used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "user-eff" package. It is only enabled if
+<P>This fix is part of the USER-SPH package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
-<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nh_eff.html">fix nvt/eff</A>, <A HREF = "fix_nh_eff.html">fix
-npt/eff</A>
+<P>"fix meso"
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/fix_meso_stationary.txt b/doc/fix_meso_stationary.txt
new file mode 100644
index 000000000..31bdb4b1f
--- /dev/null
+++ b/doc/fix_meso_stationary.txt
@@ -0,0 +1,53 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix meso/stationary command :h3
+
+[Syntax:]
+
+fix ID group-ID meso/stationary :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+meso = style name of this fix command :ul
+
+[Examples:]
+
+fix 1 boundary meso/stationary :pre
+
+[Description:]
+
+Perform time integration to update internal energy and local density,
+but not position or velocity for atoms in the group each timestep.
+This fix is needed for SPH simulations to correctly time-integrate
+fixed boundary particles which constrain a fluid to a given region in
+space.
+
+See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in
+LAMMPS.
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html. None of the "fix_modify"_fix_modify.html options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various "output
+commands"_Section_howto.html#4_15. No parameter of this fix can be
+used with the {start/stop} keywords of the "run"_run.html command.
+This fix is not invoked during "energy minimization"_minimize.html.
+
+[Restrictions:]
+
+This fix is part of the USER-SPH package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"fix meso"
+
+[Default:] none
diff --git a/doc/fix_msst.html b/doc/fix_msst.html
index 3368fea2b..8be90641a 100644
--- a/doc/fix_msst.html
+++ b/doc/fix_msst.html
@@ -1,171 +1,171 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3> fix msst command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID msst dir shockvel keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>msst = style name of this fix
<LI>dir = <I>x</I> or <I>y</I> or <I>z</I>
<LI>shockvel = shock velocity (strictly positive, distance/time units)
<LI>zero or more keyword value pairs may be appended
<LI>keyword = <I>q</I> or <I>mu</I> or <I>p0</I> or <I>v0</I> or <I>e0</I> or <I>tscale</I>
<PRE> <I>q</I> value = cell mass-like parameter (mass^2/distance^4 units)
<I>mu</I> value = artificial viscosity (mass/length/time units)
<I>p0</I> value = initial pressure in the shock equations (pressure units)
<I>v0</I> value = initial simulation cell volume in the shock equations (distance^3 units)
<I>e0</I> value = initial total energy (energy units)
<I>tscale</I> value = reduction in initial temperature (unitless fraction between 0.0 and 1.0)
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all msst y 100.0 q 1.0e5 mu 1.0e5
fix 2 all msst z 50.0 q 1.0e4 mu 1.0e4 v0 4.3419e+03 p0 3.7797e+03 e0 -9.72360e+02 tscale 0.01
</PRE>
<P><B>Description:</B>
</P>
<P>This command performs the Multi-Scale Shock Technique (MSST)
integration to update positions and velocities each timestep to mimic
a compressive shock wave passing over the system. See <A HREF = "#Reed">(Reed)</A>
for a detailed description of this method. The MSST varies the cell
volume and temperature in such a way as to restrain the system to the
shock Hugoniot and the Rayleigh line. These restraints correspond to
the macroscopic conservation laws dictated by a shock
front. <I>shockvel</I> determines the steady shock velocity that will be
simulated.
</P>
<P>To perform a simulation, choose a value of <I>q</I> that provides volume
compression on the timescale of 100 fs to 1 ps. If the volume is not
compressing, either the shock speed is chosen to be below the material
sound speed or <I>p0</I> has been chosen inaccurately. Volume compression
at the start can be sped up by using a non-zero value of <I>tscale</I>. Use
the smallest value of <I>tscale</I> that results in compression.
</P>
<P>Under some special high-symmetry conditions, the pressure (volume)
and/or temperature of the system may oscillate for many cycles even
with an appropriate choice of mass-like parameter <I>q</I>. Such
oscillations have physical significance in some cases. The optional
<I>mu</I> keyword adds an artificial viscosity that helps break the system
symmetry to equilibrate to the shock Hugoniot and Rayleigh line more
rapidly in such cases.
</P>
<P><I>tscale</I> is a factor between 0 and 1 that determines what fraction of
thermal kinetic energy is converted to compressive strain kinetic
energy at the start of the simulation. Setting this parameter to a
non-zero value may assist in compression at the start of simulations
where it is slow to occur.
</P>
<P>If keywords <I>e0</I>, <I>p0</I>,or <I>v0</I> are not supplied, these quantities will
be calculated on the first step, after the energy specified by
<I>tscale</I> is removed. The value of <I>e0</I> is not used in the dynamical
equations, but is used in calculating the deviation from the Hugoniot.
</P>
<P>Values of shockvel less than a critical value determined by the
material response will not have compressive solutions. This will be
reflected in lack of significant change of the volume in the MSST.
</P>
<P>For all pressure styles, the simulation box stays orthogonal in shape.
Parrinello-Rahman boundary conditions (tilted box) are supported by
LAMMPS, but are not implemented for MSST.
</P>
<P>This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp" and "pressure",
as if these commands had been issued:
</P>
<PRE>compute fix-ID_temp group-ID temp
compute fix-ID_press group-ID pressure fix-ID_temp
</PRE>
<P>See the <A HREF = "compute_temp.html">compute temp</A> and <A HREF = "compute_pressure.html">compute
pressure</A> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
+ underscore + "press". The group for the new computes is "all".
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of all internal variables to <A HREF = "restart.html">binary restart
files</A>. See the <A HREF = "read_restart.html">read_restart</A> command
for info on how to re-specify a fix in an input script that reads a
restart file, so that the operation of the fix continues in an
uninterrupted fashion.
</P>
<P>The progress of the MSST can be monitored by printing the global
scalar and global vector quantities computed by the fix.
</P>
<P>The scalar is the cumulative energy change due to the fix. This is
also the energy added to the potential energy by the
<A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> command. With this command, the
thermo keyword <I>etotal</I> prints the conserved quantity of the MSST
dynamic equations. This can be used to test if the MD timestep is
sufficiently small for accurate integration of the dynamic
equations. See also <A HREF = "thermo_style.html">thermo_style</A> command.
</P>
<P>The global vector contains four values in this order:
</P>
<P>[<I>dhugoniot</I>, <I>drayleigh</I>, <I>lagrangian_speed</I>, <I>lagrangian_position</I>]
</P>
<OL><LI><I>dhugoniot</I> is the departure from the Hugoniot (temperature units).
<LI><I>drayleigh</I> is the departure from the Rayleigh line (pressure units).
<LI><I>lagrangian_speed</I> is the laboratory-frame Lagrangian speed (particle velocity) of the computational cell (velocity units).
<LI><I>lagrangian_position</I> is the computational cell position in the reference frame moving at the shock speed. This is usually a good estimate of distance of the computational cell behind the shock front.
</OL>
<P>To print these quantities to the log file with descriptive column
headers, the following LAMMPS commands are suggested:
</P>
<PRE>fix msst all msst z
fix_modify msst energy yes
variable dhug equal f_msst[1]
variable dray equal f_msst[2]
variable lgr_vel equal f_msst[3]
variable lgr_pos equal f_msst[4]
thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
</PRE>
<P>These fixes compute a global scalar and a global vector of 4
quantities, which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. The scalar values calculated
by this fix are "extensive"; the vector values are "intensive".
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix style is part of the "shock" package. It is only enabled if
+<P>This fix style is part of the SHOCK package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>All cell dimensions must be periodic. This fix can not be used with a
triclinic cell. The MSST fix has been tested only for the group-ID
all.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_deform.html">fix deform</A>
</P>
<P><B>Default:</B>
</P>
<P>The keyword defaults are q = 10, mu = 0, tscale = 0.01. p0, v0, and e0
are calculated on the first step.
</P>
<HR>
<A NAME = "Reed"></A>
<P><B>(Reed)</B> Reed, Fried, and Joannopoulos, Phys. Rev. Lett., 90, 235503 (2003).
</P>
</HTML>
diff --git a/doc/fix_msst.txt b/doc/fix_msst.txt
index 1e7707796..0a606bf81 100644
--- a/doc/fix_msst.txt
+++ b/doc/fix_msst.txt
@@ -1,158 +1,158 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix msst command :h3
[Syntax:]
fix ID group-ID msst dir shockvel keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
msst = style name of this fix :l
dir = {x} or {y} or {z} :l
shockvel = shock velocity (strictly positive, distance/time units) :l
zero or more keyword value pairs may be appended :l
keyword = {q} or {mu} or {p0} or {v0} or {e0} or {tscale} :l
{q} value = cell mass-like parameter (mass^2/distance^4 units)
{mu} value = artificial viscosity (mass/length/time units)
{p0} value = initial pressure in the shock equations (pressure units)
{v0} value = initial simulation cell volume in the shock equations (distance^3 units)
{e0} value = initial total energy (energy units)
{tscale} value = reduction in initial temperature (unitless fraction between 0.0 and 1.0) :pre
:ule
[Examples:]
fix 1 all msst y 100.0 q 1.0e5 mu 1.0e5
fix 2 all msst z 50.0 q 1.0e4 mu 1.0e4 v0 4.3419e+03 p0 3.7797e+03 e0 -9.72360e+02 tscale 0.01 :pre
[Description:]
This command performs the Multi-Scale Shock Technique (MSST)
integration to update positions and velocities each timestep to mimic
a compressive shock wave passing over the system. See "(Reed)"_#Reed
for a detailed description of this method. The MSST varies the cell
volume and temperature in such a way as to restrain the system to the
shock Hugoniot and the Rayleigh line. These restraints correspond to
the macroscopic conservation laws dictated by a shock
front. {shockvel} determines the steady shock velocity that will be
simulated.
To perform a simulation, choose a value of {q} that provides volume
compression on the timescale of 100 fs to 1 ps. If the volume is not
compressing, either the shock speed is chosen to be below the material
sound speed or {p0} has been chosen inaccurately. Volume compression
at the start can be sped up by using a non-zero value of {tscale}. Use
the smallest value of {tscale} that results in compression.
Under some special high-symmetry conditions, the pressure (volume)
and/or temperature of the system may oscillate for many cycles even
with an appropriate choice of mass-like parameter {q}. Such
oscillations have physical significance in some cases. The optional
{mu} keyword adds an artificial viscosity that helps break the system
symmetry to equilibrate to the shock Hugoniot and Rayleigh line more
rapidly in such cases.
{tscale} is a factor between 0 and 1 that determines what fraction of
thermal kinetic energy is converted to compressive strain kinetic
energy at the start of the simulation. Setting this parameter to a
non-zero value may assist in compression at the start of simulations
where it is slow to occur.
If keywords {e0}, {p0},or {v0} are not supplied, these quantities will
be calculated on the first step, after the energy specified by
{tscale} is removed. The value of {e0} is not used in the dynamical
equations, but is used in calculating the deviation from the Hugoniot.
Values of shockvel less than a critical value determined by the
material response will not have compressive solutions. This will be
reflected in lack of significant change of the volume in the MSST.
For all pressure styles, the simulation box stays orthogonal in shape.
Parrinello-Rahman boundary conditions (tilted box) are supported by
LAMMPS, but are not implemented for MSST.
This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp" and "pressure",
as if these commands had been issued:
compute fix-ID_temp group-ID temp
compute fix-ID_press group-ID pressure fix-ID_temp :pre
See the "compute temp"_compute_temp.html and "compute
pressure"_compute_pressure.html commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
+ underscore + "press". The group for the new computes is "all".
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the state of all internal variables to "binary restart
files"_restart.html. See the "read_restart"_read_restart.html command
for info on how to re-specify a fix in an input script that reads a
restart file, so that the operation of the fix continues in an
uninterrupted fashion.
The progress of the MSST can be monitored by printing the global
scalar and global vector quantities computed by the fix.
The scalar is the cumulative energy change due to the fix. This is
also the energy added to the potential energy by the
"fix_modify"_fix_modify.html {energy} command. With this command, the
thermo keyword {etotal} prints the conserved quantity of the MSST
dynamic equations. This can be used to test if the MD timestep is
sufficiently small for accurate integration of the dynamic
equations. See also "thermo_style"_thermo_style.html command.
The global vector contains four values in this order:
\[{dhugoniot}, {drayleigh}, {lagrangian_speed}, {lagrangian_position}\]
{dhugoniot} is the departure from the Hugoniot (temperature units).
{drayleigh} is the departure from the Rayleigh line (pressure units).
{lagrangian_speed} is the laboratory-frame Lagrangian speed (particle velocity) of the computational cell (velocity units).
{lagrangian_position} is the computational cell position in the reference frame moving at the shock speed. This is usually a good estimate of distance of the computational cell behind the shock front. :ol
To print these quantities to the log file with descriptive column
headers, the following LAMMPS commands are suggested:
fix msst all msst z
fix_modify msst energy yes
variable dhug equal f_msst\[1\]
variable dray equal f_msst\[2\]
variable lgr_vel equal f_msst\[3\]
variable lgr_pos equal f_msst\[4\]
thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst :pre
These fixes compute a global scalar and a global vector of 4
quantities, which can be accessed by various "output
commands"_Section_howto.html#howto_15. The scalar values calculated
by this fix are "extensive"; the vector values are "intensive".
[Restrictions:]
-This fix style is part of the "shock" package. It is only enabled if
+This fix style is part of the SHOCK package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
All cell dimensions must be periodic. This fix can not be used with a
triclinic cell. The MSST fix has been tested only for the group-ID
all.
[Related commands:]
"fix deform"_fix_deform.html
[Default:]
The keyword defaults are q = 10, mu = 0, tscale = 0.01. p0, v0, and e0
are calculated on the first step.
:line
:link(Reed)
[(Reed)] Reed, Fried, and Joannopoulos, Phys. Rev. Lett., 90, 235503 (2003).
diff --git a/doc/fix_neb.html b/doc/fix_neb.html
index 0b41163b2..79390f9b3 100644
--- a/doc/fix_neb.html
+++ b/doc/fix_neb.html
@@ -1,113 +1,113 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix neb command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID neb Kspring
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>neb = style name of this fix command
<LI>Kspring = inter-replica spring constant (force/distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 active neb 10.0
</PRE>
<P><B>Description:</B>
</P>
<P>Add inter-replica forces to atoms in the group for a multi-replica
simulation run via the <A HREF = "neb.html">neb</A> command to perform a nudged
elastic band (NEB) calculation for transition state finding. Hi-level
explanations of NEB are given with the <A HREF = "neb.html">neb</A> command and in
<A HREF = "Section_howto.html#howto_5">this section</A> of the manual. The fix neb
command must be used with the "neb" command to define how
inter-replica forces are computed.
</P>
<P>Only the N atoms in the fix group experience inter-replica forces.
Atoms in the two end-point replicas do not experience these forces,
but those in intermediate replicas do. During the initial stage of
NEB, the 3N-length vector of interatomic forces Fi = -Grad(V) acting
on the atoms of each intermediate replica I is altered, as described
in the <A HREF = "#Henkelman1">(Henkelman1)</A> paper, to become:
</P>
<PRE>Fi = -Grad(V) + (Grad(V) dot That) That + Kspring (|Ri+i - Ri| - |Ri - Ri-1|) That
</PRE>
<P>Ri are the atomic coordinates of replica I; Ri-1 and Ri+1 are the
coordinates of its neighbor replicas. That (t with a hat over it) is
the unit "tangent" vector for replica I which is a function of Ri,
Ri-1, Ri+1, and the potential energy of the 3 replicas; it points
roughly in the direction of (Ri+i - Ri-1); see the
<A HREF = "#Henkelman1">(Henkelman1)</A> paper for details.
</P>
<P>The first two terms in the above equation are the component of the
interatomic forces perpendicular to the tangent vector. The last term
is a spring force between replica I and its neighbors, parallel to the
tangent vector direction with the specified spring constant <I>Kspring</I>.
</P>
<P>The effect of the first two terms is to push the atoms of each replica
toward the minimum energy path (MEP) of conformational states that
transition over the energy barrier. The MEP for an energy barrier is
defined as a sequence of 3N-dimensional states which cross the barrier
at its saddle point, each of which has a potential energy gradient
parallel to the MEP itself.
</P>
<P>The effect of the last term is to push each replica away from its two
neighbors in a direction along the MEP, so that the final set of
states are equidistant from each other.
</P>
<P>During the second stage of NEB, the forces on the N atoms in the
replica nearest the top of the energy barrier are altered so that it
climbs to the top of the barrier and finds the saddle point. The
forces on atoms in this replica are described in the
<A HREF = "#Henkelman2">(Henkelman2)</A> paper, and become:
</P>
<PRE>Fi = -Grad(V) + 2 (Grad(V) dot That) That
</PRE>
<P>The inter-replica forces for the other replicas are unchanged from the
first equation.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. No parameter of this fix can
be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
</P>
<P>The forces due to this fix are imposed during an energy minimization,
as invoked by the <A HREF = "minimize.html">minimize</A> command via the
<A HREF = "neb.html">neb</A> command.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This command can only be used if LAMMPS was built with the "replica"
+<P>This command can only be used if LAMMPS was built with the REPLICA
package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "neb.html">neb</A>
</P>
<P><B>Default:</B> none
</P>
<A NAME = "Henkelman"></A>
<P><B>(Henkelman1)</B> Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
</P>
<A NAME = "Henkelman"></A>
<P><B>(Henkelman2)</B> Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
9901-9904 (2000).
</P>
</HTML>
diff --git a/doc/fix_neb.txt b/doc/fix_neb.txt
index fa8cb1b71..397a259c4 100644
--- a/doc/fix_neb.txt
+++ b/doc/fix_neb.txt
@@ -1,106 +1,106 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix neb command :h3
[Syntax:]
fix ID group-ID neb Kspring :pre
ID, group-ID are documented in "fix"_fix.html command
neb = style name of this fix command
Kspring = inter-replica spring constant (force/distance units) :ul
[Examples:]
fix 1 active neb 10.0 :pre
[Description:]
Add inter-replica forces to atoms in the group for a multi-replica
simulation run via the "neb"_neb.html command to perform a nudged
elastic band (NEB) calculation for transition state finding. Hi-level
explanations of NEB are given with the "neb"_neb.html command and in
"this section"_Section_howto.html#howto_5 of the manual. The fix neb
command must be used with the "neb" command to define how
inter-replica forces are computed.
Only the N atoms in the fix group experience inter-replica forces.
Atoms in the two end-point replicas do not experience these forces,
but those in intermediate replicas do. During the initial stage of
NEB, the 3N-length vector of interatomic forces Fi = -Grad(V) acting
on the atoms of each intermediate replica I is altered, as described
in the "(Henkelman1)"_#Henkelman1 paper, to become:
Fi = -Grad(V) + (Grad(V) dot That) That + Kspring (|Ri+i - Ri| - |Ri - Ri-1|) That :pre
Ri are the atomic coordinates of replica I; Ri-1 and Ri+1 are the
coordinates of its neighbor replicas. That (t with a hat over it) is
the unit "tangent" vector for replica I which is a function of Ri,
Ri-1, Ri+1, and the potential energy of the 3 replicas; it points
roughly in the direction of (Ri+i - Ri-1); see the
"(Henkelman1)"_#Henkelman1 paper for details.
The first two terms in the above equation are the component of the
interatomic forces perpendicular to the tangent vector. The last term
is a spring force between replica I and its neighbors, parallel to the
tangent vector direction with the specified spring constant {Kspring}.
The effect of the first two terms is to push the atoms of each replica
toward the minimum energy path (MEP) of conformational states that
transition over the energy barrier. The MEP for an energy barrier is
defined as a sequence of 3N-dimensional states which cross the barrier
at its saddle point, each of which has a potential energy gradient
parallel to the MEP itself.
The effect of the last term is to push each replica away from its two
neighbors in a direction along the MEP, so that the final set of
states are equidistant from each other.
During the second stage of NEB, the forces on the N atoms in the
replica nearest the top of the energy barrier are altered so that it
climbs to the top of the barrier and finds the saddle point. The
forces on atoms in this replica are described in the
"(Henkelman2)"_#Henkelman2 paper, and become:
Fi = -Grad(V) + 2 (Grad(V) dot That) That :pre
The inter-replica forces for the other replicas are unchanged from the
first equation.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
as invoked by the "minimize"_minimize.html command via the
"neb"_neb.html command.
[Restrictions:]
-This command can only be used if LAMMPS was built with the "replica"
+This command can only be used if LAMMPS was built with the REPLICA
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info on packages.
[Related commands:]
"neb"_neb.html
[Default:] none
:link(Henkelman)
[(Henkelman1)] Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
:link(Henkelman)
[(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
9901-9904 (2000).
diff --git a/doc/fix_nh.html b/doc/fix_nh.html
index 526c9075f..49165c16c 100644
--- a/doc/fix_nh.html
+++ b/doc/fix_nh.html
@@ -1,545 +1,545 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix nvt command
</H3>
<H3>fix nvt/cuda command
</H3>
<H3>fix npt command
</H3>
<H3>fix npt/cuda command
</H3>
<H3>fix nph command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID style_name keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>style_name = <I>nvt</I> or <I>npt</I> or <I>nph</I>
<PRE>one or more keyword value pairs may be appended
keyword = <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>tri</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>couple</I> or <I>tchain</I> or <I>pchain</I> or <I>mtk</I> or <I>tloop</I> or <I>ploop</I> or <I>nreset</I> or <I>drag</I> or <I>dilate</I>
<I>temp</I> values = Tstart Tstop Tdamp
Tstart,Tstop = external temperature at start/end of run
Tdamp = temperature damping parameter (time units)
<I>iso</I> or <I>aniso</I> or <I>tri</I> values = Pstart Pstop Pdamp
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
<I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> values = Pstart Pstop Pdamp
Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
Pdamp = stress damping parameter (time units)
<I>couple</I> = <I>none</I> or <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I>
<I>tchain</I> value = length of thermostat chain (1 = single thermostat)
<I>pchain</I> values = length of thermostat chain on barostat (0 = no thermostat)
<I>mtk</I> value = <I>yes</I> or <I>no</I> = add in MTK adjustment term or not
<I>tloop</I> value = number of sub-cycles to perform on thermostat
<I>ploop</I> value = number of sub-cycles to perform on barostat thermostat
<I>nreset</I> value = reset reference cell every this many timesteps
<I>drag</I> value = drag factor added to barostat/thermostat (0.0 = no drag)
<I>dilate</I> value = <I>all</I> or <I>partial</I>
<I>scaleyz</I> value = <I>yes</I> or <I>no</I> = scale yz with lz
<I>scalexz</I> value = <I>yes</I> or <I>no</I> = scale xz with lz
<I>scalexy</I> value = <I>yes</I> or <I>no</I> = scale xy with ly
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all nvt temp 300.0 300.0 100.0
fix 1 water npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
fix 2 jello npt temp 300.0 300.0 100.0 tri 5.0 5.0 1000.0
fix 2 ice nph x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000
</PRE>
<P><B>Description:</B>
</P>
<P>These commands perform time integration on Nose-Hoover style
non-Hamiltonian equations of motion which are designed to generate
positions and velocities sampled from the canonical (nvt),
isothermal-isobaric (npt), and isenthalpic (nph) ensembles. This is
achieved by adding some dynamic variables which are coupled to the
particle velocities (thermostatting) and simulation domain dimensions
(barostatting). In addition to basic thermostatting and barostatting,
these fixes can also create a chain of thermostats coupled to the
particle thermostat, and another chain of thermostats coupled to the
barostat variables. The barostat can be coupled to the overall box
volume, or to individual dimensions, including the <I>xy</I>, <I>xz</I> and <I>yz</I>
tilt dimensions. The external pressure of the barostat can be
specified as either a scalar pressure (isobaric ensemble) or as
components of a symmetric stress tensor (constant stress ensemble).
When used correctly, the time-averaged temperature and stress tensor
of the particles will match the target values specified by
Tstart/Tstop and Pstart/Pstop.
</P>
<P>The equations of motion used are those of Shinoda et al. in
<A HREF = "#Shinoda">(Shinoda)</A>, which combine the hydrostatic equations of
Martyna, Tobias and Klein in <A HREF = "#Martyna">(Martyna)</A> with the strain
energy proposed by Parrinello and Rahman in
<A HREF = "#Parrinello">(Parrinello)</A>. The time integration schemes closely
follow the time-reversible measure-preserving Verlet and
rRESPA integrators derived by Tuckerman et al. in <A HREF = "#Tuckerman">(Tuckerman)</A>.
</P>
<HR>
<P>The thermostat for fix styles <I>nvt</I> and <I>npt</I> is specified using the
<I>temp</I> keyword. Other thermostat-related keywords are <I>tchain</I>,
<I>tloop</I> and <I>drag</I>, which are discussed below.
</P>
<P>The thermostat is applied to only the translational degrees of freedom
for the particles. The translational degrees of freedom can also have
a bias velocity removed before thermostatting takes place; see the
description below. The desired temperature at each timestep is a
ramped value during the run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I>
parameter is specified in time units and determines how rapidly the
temperature is relaxed. For example, a value of 10.0 means to relax
the temperature in a timespan of (roughly) 10 time units (e.g. tau or
fmsec or psec - see the <A HREF = "units.html">units</A> command). The atoms in the
fix group are the only ones whose velocities and positions are updated
by the velocity/position update portion of the integration.
</P>
<P>IMPORTANT NOTE: A Nose-Hoover thermostat will not work well for
arbitrary values of <I>Tdamp</I>. If <I>Tdamp</I> is too small, the temperature
can fluctuate wildly; if it is too large, the temperature will take a
very long time to equilibrate. A good choice for many models is a
<I>Tdamp</I> of around 100 timesteps. Note that this is NOT the same as
100 time units for most <A HREF = "units.html">units</A> settings.
</P>
<HR>
<P>The barostat for fix styles <I>npt</I> and <I>nph</I> is specified using one or
more of the <I>iso</I>, <I>aniso</I>, <I>tri</I>, <I>x</I>, <I>y</I>, <I>z</I>, <I>xy</I>, <I>xz</I>, <I>yz</I>,
and <I>couple</I> keywords. These keywords give you the ability to specify
all 6 components of an external stress tensor, and to couple various
of these components together so that the dimensions they represent are
varied together during a constant-pressure simulation.
</P>
<P>Other barostat-related keywords are <I>pchain</I>, <I>mtk</I>, <I>ploop</I>,
<I>nreset</I>, <I>drag</I>, and <I>dilate</I>, which are discussed below.
</P>
<P>Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z).
Triclinic (non-orthogonal) simulation boxes have 6 adjustable
dimensions (x,y,z,xy,xz,yz). The <A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read
data</A>, and <A HREF = "read_restart.html">read_restart</A> commands
specify whether the simulation box is orthogonal or non-orthogonal
(triclinic) and explain the meaning of the xy,xz,yz tilt factors.
</P>
<P>The target pressures for each of the 6 components of the stress tensor
can be specified independently via the <I>x</I>, <I>y</I>, <I>z</I>, <I>xy</I>, <I>xz</I>, <I>yz</I>
keywords, which correspond to the 6 simulation box dimensions. For
each component, the external pressure or tensor component at each
timestep is a ramped value during the run from <I>Pstart</I> to <I>Pstop</I>.
If a target pressure is specified for a component, then the
corresponding box dimension will change during a simulation. For
example, if the <I>y</I> keyword is used, the y-box length will change. If
the <I>xy</I> keyword is used, the xy tilt factor will change. A box
dimension will not change if that component is not specified, although
you have the option to change that dimension via the <A HREF = "fix_deform.html">fix
deform</A> command.
</P>
<P>Note that in order to use the <I>xy</I>, <I>xz</I>, or <I>yz</I> keywords, the
simulation box must be triclinic, even if its initial tilt factors are
0.0.
</P>
<P>For all barostat keywords, the <I>Pdamp</I> parameter operates like the
<I>Tdamp</I> parameter, determining the time scale on which pressure is
relaxed. For example, a value of 10.0 means to relax the pressure in
a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see
the <A HREF = "units.html">units</A> command).
</P>
<P>IMPORTANT NOTE: A Nose-Hoover barostat will not work well for
arbitrary values of <I>Pdamp</I>. If <I>Pdamp</I> is too small, the pressure
and volume can fluctuate wildly; if it is too large, the pressure will
take a very long time to equilibrate. A good choice for many models
is a <I>Pdamp</I> of around 1000 timesteps. Note that this is NOT the same
as 1000 time units for most <A HREF = "units.html">units</A> settings.
</P>
<P>Regardless of what atoms are in the fix group, a global pressure or
stress tensor is computed for all atoms. Similarly, when the size of
the simulation box is changed, all atoms are re-scaled to new
positions, unless the keyword <I>dilate</I> is specified with a value of
<I>partial</I>, in which case only the atoms in the fix group are
re-scaled. The latter can be useful for leaving the coordinates of
atoms in a solid substrate unchanged and controlling the pressure of a
surrounding fluid.
</P>
<HR>
<P>The <I>couple</I> keyword allows two or three of the diagonal components of
the pressure tensor to be "coupled" together. The value specified
with the keyword determines which are coupled. For example, <I>xz</I>
means the <I>Pxx</I> and <I>Pzz</I> components of the stress tensor are coupled.
<I>Xyz</I> means all 3 diagonal components are coupled. Coupling means two
things: the instantaneous stress will be computed as an average of the
corresponding diagonal components, and the coupled box dimensions will
be changed together in lockstep, meaning coupled dimensions will be
dilated or contracted by the same percentage every timestep. The
<I>Pstart</I>, <I>Pstop</I>, <I>Pdamp</I> parameters for any coupled dimensions must
be identical. <I>Couple xyz</I> can be used for a 2d simulation; the <I>z</I>
dimension is simply ignored.
</P>
<HR>
<P>The <I>iso</I>, <I>aniso</I>, and <I>tri</I> keywords are simply shortcuts that are
equivalent to specifying several other keywords together.
</P>
<P>The keyword <I>iso</I> means couple all 3 diagonal components together when
pressure is computed (hydrostatic pressure), and dilate/contract the
dimensions together. Using "iso Pstart Pstop Pdamp" is the same as
specifying these 4 keywords:
</P>
<PRE>x Pstart Pstop Pdamp
y Pstart Pstop Pdamp
z Pstart Pstop Pdamp
couple xyz
</PRE>
<P>The keyword <I>aniso</I> means <I>x</I>, <I>y</I>, and <I>z</I> dimensions are controlled
independently using the <I>Pxx</I>, <I>Pyy</I>, and <I>Pzz</I> components of the
stress tensor as the driving forces, and the specified scalar external
pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying
these 4 keywords:
</P>
<PRE>x Pstart Pstop Pdamp
y Pstart Pstop Pdamp
z Pstart Pstop Pdamp
couple none
</PRE>
<P>The keyword <I>tri</I> means <I>x</I>, <I>y</I>, <I>z</I>, <I>xy</I>, <I>xz</I>, and <I>yz</I> dimensions
are controlled independently using their individual stress components
as the driving forces, and the specified scalar pressure as the
external normal stress. Using "tri Pstart Pstop Pdamp" is the same as
specifying these 7 keywords:
</P>
<PRE>x Pstart Pstop Pdamp
y Pstart Pstop Pdamp
z Pstart Pstop Pdamp
xy 0.0 0.0 Pdamp
yz 0.0 0.0 Pdamp
xz 0.0 0.0 Pdamp
couple none
</PRE>
<HR>
<P>In some cases (e.g. for solids) the pressure (volume) and/or
temperature of the system can oscillate undesirably when a Nose/Hoover
barostat and thermostat is applied. The optional <I>drag</I> keyword will
damp these oscillations, although it alters the Nose/Hoover equations.
A value of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged.
A non-zero value adds a drag term; the larger the value specified, the
greater the damping effect. Performing a short run and monitoring the
pressure and temperature is the best way to determine if the drag term
is working. Typically a value between 0.2 to 2.0 is sufficient to
damp oscillations after a few periods. Note that use of the drag
keyword will interfere with energy conservation and will also change
the distribution of positions and velocities so that they do not
correspond to the nominal NVT, NPT, or NPH ensembles.
</P>
<P>An alternative way to control initial oscillations is to use chain
thermostats. The keyword <I>tchain</I> determines the number of thermostats
in the particle thermostat. A value of 1 corresponds to the original
Nose-Hoover thermostat. The keyword <I>pchain</I> specifies the number of
thermostats in the chain thermostatting the barostat degrees of
freedom. A value of 0 corresponds to no thermostatting of the
barostat variables.
</P>
<P>The <I>mtk</I> keyword controls whether or not the correction terms due to
Martyna, Tuckerman, and Klein are included in the equations of motion
<A HREF = "#Martyna">(Martyna)</A>. Specifying <I>no</I> reproduces the original
Hoover barostat, whose volume probability distribution function
differs from the true NPT and NPH ensembles by a factor of 1/V. Hence
using <I>yes</I> is more correct, but in many cases the difference is
negligible.
</P>
<P>The keyword <I>tloop</I> can be used to improve the accuracy of integration
scheme at little extra cost. The initial and final updates of the
thermostat variables are broken up into <I>tloop</I> substeps, each of
length <I>dt</I>/<I>tloop</I>. This corresponds to using a first-order
Suzuki-Yoshida scheme <A HREF = "#Tuckerman2006">(Tuckerman2006)</A>. The keyword
<I>ploop</I> does the same thing for the barostat thermostat.
</P>
<P>The keyword <I>nreset</I> controls how often the reference dimensions used
to define the strain energy are reset. If this keyword is not used,
or is given a value of zero, then the reference dimensions are set to
those of the initial simulation domain and are never changed. If the
simulation domain changes significantly during the simulation, then
the final average pressure tensor will differ significantly from the
specified values of the external stress tensor. A value of <I>nstep</I>
means that every <I>nstep</I> timesteps, the reference dimensions are set
to those of the current simulation domain.
</P>
<P>The <I>scaleyz</I>, <I>scalexz</I>, and <I>scalexy</I> keywords control whether or
not the corresponding tilt factors are scaled with the
associated box dimensions
when barostatting triclinic periodic cells.
The default values <I>yes</I> will turn on scaling, which corresponds to
adjusting the linear dimensions of the cell while preserving its shape.
Choosing <I>no</I> ensures that the tilt factors are not scaled with the
box dimensions. See below for restrictions and default values in different
situations. In older versions of LAMMPS, scaling of tilt factors was not
performed. The old behavior can be recovered by setting all three
scale keywords to <I>no</I>.
</P>
<HR>
<P>IMPORTANT NOTE: Using a barostat coupled to tilt dimensions <I>xy</I>,
<I>xz</I>, <I>yz</I> can sometimes result in arbitrarily large values of the
tilt dimensions, i.e. a dramatically deformed simulation box. LAMMPS
allows the tilt factors to grow a little beyond the normal limit
of half the box length (0.6 times the box length), and then performs
flipping or re-shaping to an equivalent periodic cell. The re-shaping
operation is described in more detail in the doc page for
<A HREF = "fix_deform.html">fix deform</A>. Both the barostat dynamics and
the atom trajectories are unaffected by this operation. However,
if a tilt factor is incremented by a large amount (1.5 times the
box length) on a single timestep, LAMMPS can not accomodate
this event and will terminate the simulation
with an error. This error typically
indicates that there is something badly wrong with how the simulation
was constructed, such as specifying values of <I>Pstart</I> that are
too far from the current stress value, or specifying a timestep that
is too large. Triclinic barostatting should be used with
care. This also is true for other barostat styles, although they tend
to be more forgiving of insults. In particular, it is important to
recognize that equilibrium liquids can not support a shear stress and
that equilibrium solids can not support shear stresses that exceed the yield stress.
</P>
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_temp_berendsen.html">fix
temp/berendsen</A> command which performs
thermostatting but NO time integration, these fixes perform
thermostatting/barostatting AND time integration. Thus you should not
use any other time integration fix, such as <A HREF = "fix_nve.html">fix nve</A> on
atoms to which this fix is applied. Likewise, the <I>temp</I> options for
fix nvt and fix npt should not normally be used on atoms that also
have their temperature controlled by another fix - e.g. by <A HREF = "fix_nh.html">fix
langevin</A> or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>
commands.
</P>
<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
a discussion of different ways to compute temperature and perform
thermostatting and barostatting.
</P>
<HR>
<P>These fixes compute a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp" and "pressure",
as if one of these two sets of commands had been issued:
</P>
<PRE>compute fix-ID_temp group-ID temp
compute fix-ID_press group-ID pressure fix-ID_temp
</PRE>
<PRE>compute fix-ID_temp all temp
compute fix-ID_press all pressure fix-ID_temp
</PRE>
<P>See the <A HREF = "compute_temp.html">compute temp</A> and <A HREF = "compute_pressure.html">compute
pressure</A> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
+ underscore + "press". For fix nvt, the group for the new computes
is the same as the fix group. For fix nph and fix npt, the group for
the new computes is "all" since pressure is computed for the entire
system.
</P>
<P>Note that these are NOT the computes used by thermodynamic output (see
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
and <I>thermo_press</I>. This means you can change the attributes of this
fix's temperature or pressure via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> or
<I>thermo_press</I> will have no effect on this fix.
</P>
<P>Like other fixes that perform thermostatting, fix nvt and fix npt can
be used with <A HREF = "compute.html">compute commands</A> that calculate a
temperature after removing a "bias" from the atom velocities.
E.g. removing the center-of-mass velocity from a group of atoms or
only calculating temperature on the x-component of velocity or only
calculating temperature for atoms in a geometric region. This is not
done by default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command
is used to assign a temperature compute to this fix that includes such
a bias term. See the doc pages for individual <A HREF = "compute.html">compute
commands</A> to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
</P>
<HR>
<P>Styles with a <I>cuda</I> suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
<A HREF = "Section_accelerate.html">this section</A> of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>These fixes writes the state of all the thermostat and barostat
variables to <A HREF = "restart.html">binary restart files</A>. See the
<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
supported by these fixes. You can use them to assign a
<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
in its thermostatting or barostatting procedure, as described above.
If you do this, note that the kinetic energy derived from the compute
temperature should be consistent with the virial term computed using
all atoms for the pressure. LAMMPS will warn you if you choose to
compute temperature on a subset of atoms.
</P>
<P>IMPORTANT NOTE: If both the <I>temp</I> and <I>press</I> keywords are used in a
single thermo_modify command (or in two separate commands), then the
order in which the keywords are specified is important. Note that a
<A HREF = "compute_pressure.html">pressure compute</A> defines its own temperature
compute as an argument when it is specified. The <I>temp</I> keyword will
override this (for the pressure compute being used by fix npt), but
only if the <I>temp</I> keyword comes after the <I>press</I> keyword. If the
<I>temp</I> keyword comes before the <I>press</I> keyword, then the new pressure
compute specified by the <I>press</I> keyword will be unaffected by the
<I>temp</I> setting.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by these
fixes to add the energy change induced by Nose/Hoover thermostatting
and barostatting to the system's potential energy as part of
<A HREF = "thermo_style.html">thermodynamic output</A>.
</P>
<P>These fixes compute a global scalar and a global vector of quantities,
which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. The scalar value calculated by
these fixes is "extensive"; the vector values are "intensive".
</P>
<P>The scalar is the cumulative energy change due to the fix.
</P>
<P>The vector stores internal Nose/Hoover thermostat and barostat
variables. The number and meaning of the vector values depends on
which fix is used and the settings for keywords <I>tchain</I> and <I>pchain</I>,
which specify the number of Nose/Hoover chains for the thermostat and
barostat. If no thermostatting is done, then <I>tchain</I> is 0. If no
barostatting is done, then <I>pchain</I> is 0. In the following list,
"ndof" is 0, 1, 3, or 6, and is the number of degrees of freedom in
the barostat. Its value is 0 if no barostat is used, else its value
is 6 if any off-diagonal stress tensor component is barostatted, else
its value is 1 if <I>couple xyz</I> is used or <I>couple xy</I> for a 2d
simulation, otherwise its value is 3.
</P>
<P>The order of values in the global vector and their meaning is as
follows. The notation means there are tchain values for eta, followed
by tchain for eta_dot, followed by ndof for omega, etc:
</P>
<UL><LI>eta[tchain] = particle thermostat displacements (unitless)
<LI>eta_dot[tchain] = particle thermostat velocities (1/time units)
<LI>omega[ndof] = barostat displacements (unitless)
<LI>omega_dot[ndof] = barostat velocities (1/time units)
<LI>etap[pchain] = barostat thermostat displacements (unitless)
<LI>etap_dot[pchain] = barostat thermostat velocities (1/time units)
<LI>PE_eta[tchain] = potential energy of each particle thermostat displacement (energy units)
<LI>KE_eta_dot[tchain] = kinetic energy of each particle thermostat velocity (energy units)
<LI>PE_omega[ndof] = potential energy of each barostat displacement (energy units)
<LI>KE_omega_dot[ndof] = kinetic energy of each barostat velocity (energy units)
<LI>PE_etap[pchain] = potential energy of each barostat thermostat displacement (energy units)
<LI>KE_etap_dot[pchain] = kinetic energy of each barostat thermostat velocity (energy units)
<LI>PE_strain[1] = scalar strain energy (energy units)
</UL>
<P>These fixes can ramp their external temperature and pressure over
multiple runs, using the <I>start</I> and <I>stop</I> keywords of the
<A HREF = "run.html">run</A> command. See the <A HREF = "run.html">run</A> command for details of
how to do this.
</P>
<P>These fixes are not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P>These fixes can be used with either the <I>verlet</I> or <I>respa</I>
<A HREF = "run_style.html">integrators</A>. When using one of the barostat fixes
with <I>respa</I>, LAMMPS uses an integrator constructed
according to the following factorization of the Liouville propagator
(for two rRESPA levels):
</P>
<CENTER><IMG SRC = "Eqs/fix_nh1.jpg">
</CENTER>
<P>This factorization differs somewhat from that of Tuckerman et al., in that
the barostat is only updated at the outermost rRESPA level, whereas
Tuckerman's factorization requires splitting the pressure into pieces
corresponding to the forces computed at each rRESPA level. In theory, the
latter method will exhibit better numerical stability. In practice,
because Pdamp is normally chosen to be a large multiple of the
outermost rRESPA timestep, the barostat dynamics are not the
limiting factor for numerical stability. Both
factorizations are time-reversible and can be shown to preserve the phase
space measure of the underlying non-Hamiltonian equations of motion.
</P>
<P><B>Restrictions:</B>
</P>
<P>Non-periodic dimensions cannot be barostatted. <I>Z</I>, <I>xz</I>, and <I>yz</I>,
cannot be barostatted 2D simulations. <I>Xy</I>, <I>xz</I>, and <I>yz</I> can only
be barostatted if the simulation domain is triclinic and the 2nd
dimension in the keyword (<I>y</I> dimension in <I>xy</I>) is periodic. The
<A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read data</A>, and
<A HREF = "read_restart.html">read_restart</A> commands specify whether the
simulation box is orthogonal or non-orthogonal (triclinic) and explain
the meaning of the xy,xz,yz tilt factors.
</P>
<P>For the <I>temp</I> keyword, the final Tstop cannot be 0.0 since it would
make the external T = 0.0 at some timestep during the simulation which
is not allowed in the Nose/Hoover formulation.
</P>
<P>The <I>scaleyz yes</I> and <I>scalexz yes</I> keyword/value pairs can not be used
for 2D simulations. <I>scaleyz yes</I>, <I>scalexz yes</I>, and <I>scalexy yes</I> options
can only be used if the 2nd dimension in the keyword is periodic,
and if the tilt factor is not coupled to the barostat via keywords
<I>tri</I>, <I>yz</I>, <I>xz</I>, and <I>xy</I>.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "run_style.html">run_style</A>
</P>
<P><B>Default:</B>
</P>
<P>The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and
not coupled to barostat, otherwise no.
</P>
<HR>
<A NAME = "Martyna"></A>
<P><B>(Martyna)</B> Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
</P>
<A NAME = "Parrinello"></A>
<P><B>(Parrinello)</B> Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
</P>
<A NAME = "Tuckerman"></A>
<P><B>(Tuckerman)</B> Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
Martyna, J Phys A: Math Gen, 39, 5629 (2006).
</P>
<A NAME = "Shinoda"></A>
<P><B>(Shinoda)</B> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
</P>
</HTML>
diff --git a/doc/fix_nh.txt b/doc/fix_nh.txt
index 6c6ca6072..4b4ea236e 100644
--- a/doc/fix_nh.txt
+++ b/doc/fix_nh.txt
@@ -1,529 +1,529 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix nvt command :h3
fix nvt/cuda command :h3
fix npt command :h3
fix npt/cuda command :h3
fix nph command :h3
[Syntax:]
fix ID group-ID style_name keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
style_name = {nvt} or {npt} or {nph} :l
one or more keyword value pairs may be appended
keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {tchain} or {pchain} or {mtk} or {tloop} or {ploop} or {nreset} or {drag} or {dilate}
{temp} values = Tstart Tstop Tdamp
Tstart,Tstop = external temperature at start/end of run
Tdamp = temperature damping parameter (time units)
{iso} or {aniso} or {tri} values = Pstart Pstop Pdamp
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
{x} or {y} or {z} or {xy} or {yz} or {xz} values = Pstart Pstop Pdamp
Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
Pdamp = stress damping parameter (time units)
{couple} = {none} or {xyz} or {xy} or {yz} or {xz}
{tchain} value = length of thermostat chain (1 = single thermostat)
{pchain} values = length of thermostat chain on barostat (0 = no thermostat)
{mtk} value = {yes} or {no} = add in MTK adjustment term or not
{tloop} value = number of sub-cycles to perform on thermostat
{ploop} value = number of sub-cycles to perform on barostat thermostat
{nreset} value = reset reference cell every this many timesteps
{drag} value = drag factor added to barostat/thermostat (0.0 = no drag)
{dilate} value = {all} or {partial}
{scaleyz} value = {yes} or {no} = scale yz with lz
{scalexz} value = {yes} or {no} = scale xz with lz
{scalexy} value = {yes} or {no} = scale xy with ly :pre
:ule
[Examples:]
fix 1 all nvt temp 300.0 300.0 100.0
fix 1 water npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
fix 2 jello npt temp 300.0 300.0 100.0 tri 5.0 5.0 1000.0
fix 2 ice nph x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000 :pre
[Description:]
These commands perform time integration on Nose-Hoover style
non-Hamiltonian equations of motion which are designed to generate
positions and velocities sampled from the canonical (nvt),
isothermal-isobaric (npt), and isenthalpic (nph) ensembles. This is
achieved by adding some dynamic variables which are coupled to the
particle velocities (thermostatting) and simulation domain dimensions
(barostatting). In addition to basic thermostatting and barostatting,
these fixes can also create a chain of thermostats coupled to the
particle thermostat, and another chain of thermostats coupled to the
barostat variables. The barostat can be coupled to the overall box
volume, or to individual dimensions, including the {xy}, {xz} and {yz}
tilt dimensions. The external pressure of the barostat can be
specified as either a scalar pressure (isobaric ensemble) or as
components of a symmetric stress tensor (constant stress ensemble).
When used correctly, the time-averaged temperature and stress tensor
of the particles will match the target values specified by
Tstart/Tstop and Pstart/Pstop.
The equations of motion used are those of Shinoda et al. in
"(Shinoda)"_#Shinoda, which combine the hydrostatic equations of
Martyna, Tobias and Klein in "(Martyna)"_#Martyna with the strain
energy proposed by Parrinello and Rahman in
"(Parrinello)"_#Parrinello. The time integration schemes closely
follow the time-reversible measure-preserving Verlet and
rRESPA integrators derived by Tuckerman et al. in "(Tuckerman)"_#Tuckerman.
:line
The thermostat for fix styles {nvt} and {npt} is specified using the
{temp} keyword. Other thermostat-related keywords are {tchain},
{tloop} and {drag}, which are discussed below.
The thermostat is applied to only the translational degrees of freedom
for the particles. The translational degrees of freedom can also have
a bias velocity removed before thermostatting takes place; see the
description below. The desired temperature at each timestep is a
ramped value during the run from {Tstart} to {Tstop}. The {Tdamp}
parameter is specified in time units and determines how rapidly the
temperature is relaxed. For example, a value of 10.0 means to relax
the temperature in a timespan of (roughly) 10 time units (e.g. tau or
fmsec or psec - see the "units"_units.html command). The atoms in the
fix group are the only ones whose velocities and positions are updated
by the velocity/position update portion of the integration.
IMPORTANT NOTE: A Nose-Hoover thermostat will not work well for
arbitrary values of {Tdamp}. If {Tdamp} is too small, the temperature
can fluctuate wildly; if it is too large, the temperature will take a
very long time to equilibrate. A good choice for many models is a
{Tdamp} of around 100 timesteps. Note that this is NOT the same as
100 time units for most "units"_units.html settings.
:line
The barostat for fix styles {npt} and {nph} is specified using one or
more of the {iso}, {aniso}, {tri}, {x}, {y}, {z}, {xy}, {xz}, {yz},
and {couple} keywords. These keywords give you the ability to specify
all 6 components of an external stress tensor, and to couple various
of these components together so that the dimensions they represent are
varied together during a constant-pressure simulation.
Other barostat-related keywords are {pchain}, {mtk}, {ploop},
{nreset}, {drag}, and {dilate}, which are discussed below.
Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z).
Triclinic (non-orthogonal) simulation boxes have 6 adjustable
dimensions (x,y,z,xy,xz,yz). The "create_box"_create_box.html, "read
data"_read_data.html, and "read_restart"_read_restart.html commands
specify whether the simulation box is orthogonal or non-orthogonal
(triclinic) and explain the meaning of the xy,xz,yz tilt factors.
The target pressures for each of the 6 components of the stress tensor
can be specified independently via the {x}, {y}, {z}, {xy}, {xz}, {yz}
keywords, which correspond to the 6 simulation box dimensions. For
each component, the external pressure or tensor component at each
timestep is a ramped value during the run from {Pstart} to {Pstop}.
If a target pressure is specified for a component, then the
corresponding box dimension will change during a simulation. For
example, if the {y} keyword is used, the y-box length will change. If
the {xy} keyword is used, the xy tilt factor will change. A box
dimension will not change if that component is not specified, although
you have the option to change that dimension via the "fix
deform"_fix_deform.html command.
Note that in order to use the {xy}, {xz}, or {yz} keywords, the
simulation box must be triclinic, even if its initial tilt factors are
0.0.
For all barostat keywords, the {Pdamp} parameter operates like the
{Tdamp} parameter, determining the time scale on which pressure is
relaxed. For example, a value of 10.0 means to relax the pressure in
a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see
the "units"_units.html command).
IMPORTANT NOTE: A Nose-Hoover barostat will not work well for
arbitrary values of {Pdamp}. If {Pdamp} is too small, the pressure
and volume can fluctuate wildly; if it is too large, the pressure will
take a very long time to equilibrate. A good choice for many models
is a {Pdamp} of around 1000 timesteps. Note that this is NOT the same
as 1000 time units for most "units"_units.html settings.
Regardless of what atoms are in the fix group, a global pressure or
stress tensor is computed for all atoms. Similarly, when the size of
the simulation box is changed, all atoms are re-scaled to new
positions, unless the keyword {dilate} is specified with a value of
{partial}, in which case only the atoms in the fix group are
re-scaled. The latter can be useful for leaving the coordinates of
atoms in a solid substrate unchanged and controlling the pressure of a
surrounding fluid.
:line
The {couple} keyword allows two or three of the diagonal components of
the pressure tensor to be "coupled" together. The value specified
with the keyword determines which are coupled. For example, {xz}
means the {Pxx} and {Pzz} components of the stress tensor are coupled.
{Xyz} means all 3 diagonal components are coupled. Coupling means two
things: the instantaneous stress will be computed as an average of the
corresponding diagonal components, and the coupled box dimensions will
be changed together in lockstep, meaning coupled dimensions will be
dilated or contracted by the same percentage every timestep. The
{Pstart}, {Pstop}, {Pdamp} parameters for any coupled dimensions must
be identical. {Couple xyz} can be used for a 2d simulation; the {z}
dimension is simply ignored.
:line
The {iso}, {aniso}, and {tri} keywords are simply shortcuts that are
equivalent to specifying several other keywords together.
The keyword {iso} means couple all 3 diagonal components together when
pressure is computed (hydrostatic pressure), and dilate/contract the
dimensions together. Using "iso Pstart Pstop Pdamp" is the same as
specifying these 4 keywords:
x Pstart Pstop Pdamp
y Pstart Pstop Pdamp
z Pstart Pstop Pdamp
couple xyz :pre
The keyword {aniso} means {x}, {y}, and {z} dimensions are controlled
independently using the {Pxx}, {Pyy}, and {Pzz} components of the
stress tensor as the driving forces, and the specified scalar external
pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying
these 4 keywords:
x Pstart Pstop Pdamp
y Pstart Pstop Pdamp
z Pstart Pstop Pdamp
couple none :pre
The keyword {tri} means {x}, {y}, {z}, {xy}, {xz}, and {yz} dimensions
are controlled independently using their individual stress components
as the driving forces, and the specified scalar pressure as the
external normal stress. Using "tri Pstart Pstop Pdamp" is the same as
specifying these 7 keywords:
x Pstart Pstop Pdamp
y Pstart Pstop Pdamp
z Pstart Pstop Pdamp
xy 0.0 0.0 Pdamp
yz 0.0 0.0 Pdamp
xz 0.0 0.0 Pdamp
couple none :pre
:line
In some cases (e.g. for solids) the pressure (volume) and/or
temperature of the system can oscillate undesirably when a Nose/Hoover
barostat and thermostat is applied. The optional {drag} keyword will
damp these oscillations, although it alters the Nose/Hoover equations.
A value of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged.
A non-zero value adds a drag term; the larger the value specified, the
greater the damping effect. Performing a short run and monitoring the
pressure and temperature is the best way to determine if the drag term
is working. Typically a value between 0.2 to 2.0 is sufficient to
damp oscillations after a few periods. Note that use of the drag
keyword will interfere with energy conservation and will also change
the distribution of positions and velocities so that they do not
correspond to the nominal NVT, NPT, or NPH ensembles.
An alternative way to control initial oscillations is to use chain
thermostats. The keyword {tchain} determines the number of thermostats
in the particle thermostat. A value of 1 corresponds to the original
Nose-Hoover thermostat. The keyword {pchain} specifies the number of
thermostats in the chain thermostatting the barostat degrees of
freedom. A value of 0 corresponds to no thermostatting of the
barostat variables.
The {mtk} keyword controls whether or not the correction terms due to
Martyna, Tuckerman, and Klein are included in the equations of motion
"(Martyna)"_#Martyna. Specifying {no} reproduces the original
Hoover barostat, whose volume probability distribution function
differs from the true NPT and NPH ensembles by a factor of 1/V. Hence
using {yes} is more correct, but in many cases the difference is
negligible.
The keyword {tloop} can be used to improve the accuracy of integration
scheme at little extra cost. The initial and final updates of the
thermostat variables are broken up into {tloop} substeps, each of
length {dt}/{tloop}. This corresponds to using a first-order
Suzuki-Yoshida scheme "(Tuckerman2006)"_#Tuckerman2006. The keyword
{ploop} does the same thing for the barostat thermostat.
The keyword {nreset} controls how often the reference dimensions used
to define the strain energy are reset. If this keyword is not used,
or is given a value of zero, then the reference dimensions are set to
those of the initial simulation domain and are never changed. If the
simulation domain changes significantly during the simulation, then
the final average pressure tensor will differ significantly from the
specified values of the external stress tensor. A value of {nstep}
means that every {nstep} timesteps, the reference dimensions are set
to those of the current simulation domain.
The {scaleyz}, {scalexz}, and {scalexy} keywords control whether or
not the corresponding tilt factors are scaled with the
associated box dimensions
when barostatting triclinic periodic cells.
The default values {yes} will turn on scaling, which corresponds to
adjusting the linear dimensions of the cell while preserving its shape.
Choosing {no} ensures that the tilt factors are not scaled with the
box dimensions. See below for restrictions and default values in different
situations. In older versions of LAMMPS, scaling of tilt factors was not
performed. The old behavior can be recovered by setting all three
scale keywords to {no}.
:line
IMPORTANT NOTE: Using a barostat coupled to tilt dimensions {xy},
{xz}, {yz} can sometimes result in arbitrarily large values of the
tilt dimensions, i.e. a dramatically deformed simulation box. LAMMPS
allows the tilt factors to grow a little beyond the normal limit
of half the box length (0.6 times the box length), and then performs
flipping or re-shaping to an equivalent periodic cell. The re-shaping
operation is described in more detail in the doc page for
"fix deform"_fix_deform.html. Both the barostat dynamics and
the atom trajectories are unaffected by this operation. However,
if a tilt factor is incremented by a large amount (1.5 times the
box length) on a single timestep, LAMMPS can not accomodate
this event and will terminate the simulation
with an error. This error typically
indicates that there is something badly wrong with how the simulation
was constructed, such as specifying values of {Pstart} that are
too far from the current stress value, or specifying a timestep that
is too large. Triclinic barostatting should be used with
care. This also is true for other barostat styles, although they tend
to be more forgiving of insults. In particular, it is important to
recognize that equilibrium liquids can not support a shear stress and
that equilibrium solids can not support shear stresses that exceed the yield stress.
IMPORTANT NOTE: Unlike the "fix
temp/berendsen"_fix_temp_berendsen.html command which performs
thermostatting but NO time integration, these fixes perform
thermostatting/barostatting AND time integration. Thus you should not
use any other time integration fix, such as "fix nve"_fix_nve.html on
atoms to which this fix is applied. Likewise, the {temp} options for
fix nvt and fix npt should not normally be used on atoms that also
have their temperature controlled by another fix - e.g. by "fix
langevin"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html
commands.
See "this howto section"_Section_howto.html#howto_16 of the manual for
a discussion of different ways to compute temperature and perform
thermostatting and barostatting.
:line
These fixes compute a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp" and "pressure",
as if one of these two sets of commands had been issued:
compute fix-ID_temp group-ID temp
compute fix-ID_press group-ID pressure fix-ID_temp :pre
compute fix-ID_temp all temp
compute fix-ID_press all pressure fix-ID_temp :pre
See the "compute temp"_compute_temp.html and "compute
pressure"_compute_pressure.html commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
+ underscore + "press". For fix nvt, the group for the new computes
is the same as the fix group. For fix nph and fix npt, the group for
the new computes is "all" since pressure is computed for the entire
system.
Note that these are NOT the computes used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
and {thermo_press}. This means you can change the attributes of this
fix's temperature or pressure via the
"compute_modify"_compute_modify.html command or print this temperature
or pressure during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} or
{thermo_press} will have no effect on this fix.
Like other fixes that perform thermostatting, fix nvt and fix npt can
be used with "compute commands"_compute.html that calculate a
temperature after removing a "bias" from the atom velocities.
E.g. removing the center-of-mass velocity from a group of atoms or
only calculating temperature on the x-component of velocity or only
calculating temperature for atoms in a geometric region. This is not
done by default, but only if the "fix_modify"_fix_modify.html command
is used to assign a temperature compute to this fix that includes such
a bias term. See the doc pages for individual "compute
commands"_compute.html to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
:line
Styles with a {cuda} suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
"this section"_Section_accelerate.html of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
These fixes writes the state of all the thermostat and barostat
variables to "binary restart files"_restart.html. See the
"read_restart"_read_restart.html command for info on how to re-specify
a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.
The "fix_modify"_fix_modify.html {temp} and {press} options are
supported by these fixes. You can use them to assign a
"compute"_compute.html you have defined to this fix which will be used
in its thermostatting or barostatting procedure, as described above.
If you do this, note that the kinetic energy derived from the compute
temperature should be consistent with the virial term computed using
all atoms for the pressure. LAMMPS will warn you if you choose to
compute temperature on a subset of atoms.
IMPORTANT NOTE: If both the {temp} and {press} keywords are used in a
single thermo_modify command (or in two separate commands), then the
order in which the keywords are specified is important. Note that a
"pressure compute"_compute_pressure.html defines its own temperature
compute as an argument when it is specified. The {temp} keyword will
override this (for the pressure compute being used by fix npt), but
only if the {temp} keyword comes after the {press} keyword. If the
{temp} keyword comes before the {press} keyword, then the new pressure
compute specified by the {press} keyword will be unaffected by the
{temp} setting.
The "fix_modify"_fix_modify.html {energy} option is supported by these
fixes to add the energy change induced by Nose/Hoover thermostatting
and barostatting to the system's potential energy as part of
"thermodynamic output"_thermo_style.html.
These fixes compute a global scalar and a global vector of quantities,
which can be accessed by various "output
commands"_Section_howto.html#howto_15. The scalar value calculated by
these fixes is "extensive"; the vector values are "intensive".
The scalar is the cumulative energy change due to the fix.
The vector stores internal Nose/Hoover thermostat and barostat
variables. The number and meaning of the vector values depends on
which fix is used and the settings for keywords {tchain} and {pchain},
which specify the number of Nose/Hoover chains for the thermostat and
barostat. If no thermostatting is done, then {tchain} is 0. If no
barostatting is done, then {pchain} is 0. In the following list,
"ndof" is 0, 1, 3, or 6, and is the number of degrees of freedom in
the barostat. Its value is 0 if no barostat is used, else its value
is 6 if any off-diagonal stress tensor component is barostatted, else
its value is 1 if {couple xyz} is used or {couple xy} for a 2d
simulation, otherwise its value is 3.
The order of values in the global vector and their meaning is as
follows. The notation means there are tchain values for eta, followed
by tchain for eta_dot, followed by ndof for omega, etc:
eta\[tchain\] = particle thermostat displacements (unitless)
eta_dot\[tchain\] = particle thermostat velocities (1/time units)
omega\[ndof\] = barostat displacements (unitless)
omega_dot\[ndof\] = barostat velocities (1/time units)
etap\[pchain\] = barostat thermostat displacements (unitless)
etap_dot\[pchain\] = barostat thermostat velocities (1/time units)
PE_eta\[tchain\] = potential energy of each particle thermostat displacement (energy units)
KE_eta_dot\[tchain\] = kinetic energy of each particle thermostat velocity (energy units)
PE_omega\[ndof\] = potential energy of each barostat displacement (energy units)
KE_omega_dot\[ndof\] = kinetic energy of each barostat velocity (energy units)
PE_etap\[pchain\] = potential energy of each barostat thermostat displacement (energy units)
KE_etap_dot\[pchain\] = kinetic energy of each barostat thermostat velocity (energy units)
PE_strain\[1\] = scalar strain energy (energy units) :ul
These fixes can ramp their external temperature and pressure over
multiple runs, using the {start} and {stop} keywords of the
"run"_run.html command. See the "run"_run.html command for details of
how to do this.
These fixes are not invoked during "energy
minimization"_minimize.html.
These fixes can be used with either the {verlet} or {respa}
"integrators"_run_style.html. When using one of the barostat fixes
with {respa}, LAMMPS uses an integrator constructed
according to the following factorization of the Liouville propagator
(for two rRESPA levels):
:c,image(Eqs/fix_nh1.jpg)
This factorization differs somewhat from that of Tuckerman et al., in that
the barostat is only updated at the outermost rRESPA level, whereas
Tuckerman's factorization requires splitting the pressure into pieces
corresponding to the forces computed at each rRESPA level. In theory, the
latter method will exhibit better numerical stability. In practice,
because Pdamp is normally chosen to be a large multiple of the
outermost rRESPA timestep, the barostat dynamics are not the
limiting factor for numerical stability. Both
factorizations are time-reversible and can be shown to preserve the phase
space measure of the underlying non-Hamiltonian equations of motion.
[Restrictions:]
Non-periodic dimensions cannot be barostatted. {Z}, {xz}, and {yz},
cannot be barostatted 2D simulations. {Xy}, {xz}, and {yz} can only
be barostatted if the simulation domain is triclinic and the 2nd
dimension in the keyword ({y} dimension in {xy}) is periodic. The
"create_box"_create_box.html, "read data"_read_data.html, and
"read_restart"_read_restart.html commands specify whether the
simulation box is orthogonal or non-orthogonal (triclinic) and explain
the meaning of the xy,xz,yz tilt factors.
For the {temp} keyword, the final Tstop cannot be 0.0 since it would
make the external T = 0.0 at some timestep during the simulation which
is not allowed in the Nose/Hoover formulation.
The {scaleyz yes} and {scalexz yes} keyword/value pairs can not be used
for 2D simulations. {scaleyz yes}, {scalexz yes}, and {scalexy yes} options
can only be used if the 2nd dimension in the keyword is periodic,
and if the tilt factor is not coupled to the barostat via keywords
{tri}, {yz}, {xz}, and {xy}.
[Related commands:]
"fix nve"_fix_nve.html, "fix_modify"_fix_modify.html, "run_style"_run_style.html
[Default:]
The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and
not coupled to barostat, otherwise no.
:line
:link(Martyna)
[(Martyna)] Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
:link(Parrinello)
[(Parrinello)] Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
:link(Tuckerman)
[(Tuckerman)] Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
Martyna, J Phys A: Math Gen, 39, 5629 (2006).
:link(Shinoda)
[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
diff --git a/doc/fix_nh_eff.html b/doc/fix_nh_eff.html
index 2b798928d..7d159b4bd 100644
--- a/doc/fix_nh_eff.html
+++ b/doc/fix_nh_eff.html
@@ -1,158 +1,158 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix nvt/eff command
</H3>
<H3>fix npt/eff command
</H3>
<H3>fix nph/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID style_name keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>style_name = <I>nvt/eff</I> or <I>npt/eff</I> or <I>nph/eff</I>
<PRE>one or more keyword value pairs may be appended
keyword = <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>tri</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>couple</I> or <I>tchain</I> or <I>pchain</I> or <I>mtk</I> or <I>tloop</I> or <I>ploop</I> or <I>nreset</I> or <I>drag</I> or <I>dilate</I>
<I>temp</I> values = Tstart Tstop Tdamp
Tstart,Tstop = external temperature at start/end of run
Tdamp = temperature damping parameter (time units)
<I>iso</I> or <I>aniso</I> or <I>tri</I> values = Pstart Pstop Pdamp
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
<I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> values = Pstart Pstop Pdamp
Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
Pdamp = stress damping parameter (time units)
<I>couple</I> = <I>none</I> or <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I>
<I>tchain</I> value = length of thermostat chain (1 = single thermostat)
<I>pchain</I> values = length of thermostat chain on barostat (0 = no thermostat)
<I>mtk</I> value = <I>yes</I> or <I>no</I> = add in MTK adjustment term or not
<I>tloop</I> value = number of sub-cycles to perform on thermostat
<I>ploop</I> value = number of sub-cycles to perform on barostat thermostat
<I>nreset</I> value = reset reference cell every this many timesteps
<I>drag</I> value = drag factor added to barostat/thermostat (0.0 = no drag)
<I>dilate</I> value = <I>all</I> or <I>partial</I>
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all nvt/eff temp 300.0 300.0 0.1
fix 1 part npt/eff temp 300.0 300.0 0.1 iso 0.0 0.0 1.0
fix 2 part npt/eff temp 300.0 300.0 0.1 tri 5.0 5.0 1.0
fix 2 ice nph/eff x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000
</PRE>
<P><B>Description:</B>
</P>
<P>These commands perform time integration on Nose-Hoover style
non-Hamiltonian equations of motion for nuclei and electrons in the
group for the <A HREF = "pair_eff.html">electron force field</A> model. The fixes
are designed to generate positions and velocities sampled from the
canonical (nvt), isothermal-isobaric (npt), and isenthalpic (nph)
ensembles. This is achieved by adding some dynamic variables which
are coupled to the particle velocities (thermostatting) and simulation
domain dimensions (barostatting). In addition to basic thermostatting
and barostatting, these fixes can also create a chain of thermostats
coupled to the particle thermostat, and another chain of thermostats
coupled to the barostat variables. The barostat can be coupled to the
overall box volume, or to individual dimensions, including the <I>xy</I>,
<I>xz</I> and <I>yz</I> tilt dimensions. The external pressure of the barostat
can be specified as either a scalar pressure (isobaric ensemble) or as
components of a symmetric stress tensor (constant stress ensemble).
When used correctly, the time-averaged temperature and stress tensor
of the particles will match the target values specified by
Tstart/Tstop and Pstart/Pstop.
</P>
<P>The operation of these fixes is exactly like that described by the
<A HREF = "fix_nh.html">fix nvt, npt, and nph</A> commands, except that the radius
and radial velocity of electrons are also updated. Likewise the
temperature and pressure calculated by the fix, using the computes it
creates (as discussed in the <A HREF = "fix_nh.html">fix nvt, npt, and nph</A>
doc page), are performed with computes that include the eFF contribution
to the temperature or kinetic energy from the electron radial velocity.
</P>
<P>IMPORTANT NOTE: there are two different pressures that can be reported
for eFF when defining the pair_style (see <A HREF = "pair_eff_cut.html">pair
eff/cut</A> to understand these settings), one
(default) that considers electrons do not contribute radial virial
components (i.e. electrons treated as incompressible 'rigid' spheres)
and one that does. The radial electronic contributions to the virials
are only tallied if the flexible pressure option is set, and this will
affect both global and per-atom quantities. In principle, the true
pressure of a system is somewhere in between the rigid and the
flexible eFF pressures, but, for most cases, the difference between
these two pressures will not be significant over long-term averaged
runs (i.e. even though the energy partitioning changes, the total
energy remains similar).
</P>
<P>IMPORTANT NOTE: currently, there is no available option for the user
to set or create temperature distributions that include the radial
electronic degrees of freedom with the <A HREF = "velocity.html">velocity</A>
command, so the the user must allow for these degrees of freedom to
equilibrate (i.e. equi-partitioning of energy) through time
integration.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>See the doc page for the <A HREF = "fix_nh.html">fix nvt, npt, and nph</A> commands
for details.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "user-eff" package. It is only enabled if
+<P>This fix is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>Other restriction discussed on the doc page for the <A HREF = "fix_nh.html">fix nvt, npt, and
nph</A> commands also apply.
</P>
<P>IMPORTANT NOTE: The temperature for systems (regions or groups) with
only electrons and no nuclei is 0.0 (i.e. not defined) in the current
temperature calculations, a practical example would be a uniform
electron gas or a very hot plasma, where electrons remain delocalized
from the nuclei. This is because, even though electron virials are
included in the temperature calculation, these are averaged over the
nuclear degrees of freedom only. In such cases a corrective term must
be added to the pressure to get the correct kinetic contribution.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_nh.html">fix nph</A>, <A HREF = "fix_nh.html">fix npt</A>,
<A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "run_style.html">run_style</A>
</P>
<P><B>Default:</B>
</P>
<P>The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
ploop = 1, nreset = 0, drag = 0.0, dilate = all, and couple = none.
</P>
<HR>
<A NAME = "Martyna"></A>
<P><B>(Martyna)</B> Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
</P>
<A NAME = "Parrinello"></A>
<P><B>(Parrinello)</B> Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
</P>
<A NAME = "Tuckerman"></A>
<P><B>(Tuckerman)</B> Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
Martyna, J Phys A: Math Gen, 39, 5629 (2006).
</P>
<A NAME = "Shinoda"></A>
<P><B>(Shinoda)</B> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
</P>
</HTML>
diff --git a/doc/fix_nh_eff.txt b/doc/fix_nh_eff.txt
index 9c7a9db43..84ef87d6f 100644
--- a/doc/fix_nh_eff.txt
+++ b/doc/fix_nh_eff.txt
@@ -1,144 +1,144 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix nvt/eff command :h3
fix npt/eff command :h3
fix nph/eff command :h3
[Syntax:]
fix ID group-ID style_name keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
style_name = {nvt/eff} or {npt/eff} or {nph/eff} :l
one or more keyword value pairs may be appended
keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {tchain} or {pchain} or {mtk} or {tloop} or {ploop} or {nreset} or {drag} or {dilate}
{temp} values = Tstart Tstop Tdamp
Tstart,Tstop = external temperature at start/end of run
Tdamp = temperature damping parameter (time units)
{iso} or {aniso} or {tri} values = Pstart Pstop Pdamp
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
{x} or {y} or {z} or {xy} or {yz} or {xz} values = Pstart Pstop Pdamp
Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
Pdamp = stress damping parameter (time units)
{couple} = {none} or {xyz} or {xy} or {yz} or {xz}
{tchain} value = length of thermostat chain (1 = single thermostat)
{pchain} values = length of thermostat chain on barostat (0 = no thermostat)
{mtk} value = {yes} or {no} = add in MTK adjustment term or not
{tloop} value = number of sub-cycles to perform on thermostat
{ploop} value = number of sub-cycles to perform on barostat thermostat
{nreset} value = reset reference cell every this many timesteps
{drag} value = drag factor added to barostat/thermostat (0.0 = no drag)
{dilate} value = {all} or {partial} :pre
:ule
[Examples:]
fix 1 all nvt/eff temp 300.0 300.0 0.1
fix 1 part npt/eff temp 300.0 300.0 0.1 iso 0.0 0.0 1.0
fix 2 part npt/eff temp 300.0 300.0 0.1 tri 5.0 5.0 1.0
fix 2 ice nph/eff x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000 :pre
[Description:]
These commands perform time integration on Nose-Hoover style
non-Hamiltonian equations of motion for nuclei and electrons in the
group for the "electron force field"_pair_eff.html model. The fixes
are designed to generate positions and velocities sampled from the
canonical (nvt), isothermal-isobaric (npt), and isenthalpic (nph)
ensembles. This is achieved by adding some dynamic variables which
are coupled to the particle velocities (thermostatting) and simulation
domain dimensions (barostatting). In addition to basic thermostatting
and barostatting, these fixes can also create a chain of thermostats
coupled to the particle thermostat, and another chain of thermostats
coupled to the barostat variables. The barostat can be coupled to the
overall box volume, or to individual dimensions, including the {xy},
{xz} and {yz} tilt dimensions. The external pressure of the barostat
can be specified as either a scalar pressure (isobaric ensemble) or as
components of a symmetric stress tensor (constant stress ensemble).
When used correctly, the time-averaged temperature and stress tensor
of the particles will match the target values specified by
Tstart/Tstop and Pstart/Pstop.
The operation of these fixes is exactly like that described by the
"fix nvt, npt, and nph"_fix_nh.html commands, except that the radius
and radial velocity of electrons are also updated. Likewise the
temperature and pressure calculated by the fix, using the computes it
creates (as discussed in the "fix nvt, npt, and nph"_fix_nh.html
doc page), are performed with computes that include the eFF contribution
to the temperature or kinetic energy from the electron radial velocity.
IMPORTANT NOTE: there are two different pressures that can be reported
for eFF when defining the pair_style (see "pair
eff/cut"_pair_eff_cut.html to understand these settings), one
(default) that considers electrons do not contribute radial virial
components (i.e. electrons treated as incompressible 'rigid' spheres)
and one that does. The radial electronic contributions to the virials
are only tallied if the flexible pressure option is set, and this will
affect both global and per-atom quantities. In principle, the true
pressure of a system is somewhere in between the rigid and the
flexible eFF pressures, but, for most cases, the difference between
these two pressures will not be significant over long-term averaged
runs (i.e. even though the energy partitioning changes, the total
energy remains similar).
IMPORTANT NOTE: currently, there is no available option for the user
to set or create temperature distributions that include the radial
electronic degrees of freedom with the "velocity"_velocity.html
command, so the the user must allow for these degrees of freedom to
equilibrate (i.e. equi-partitioning of energy) through time
integration.
[Restart, fix_modify, output, run start/stop, minimize info:]
See the doc page for the "fix nvt, npt, and nph"_fix_nh.html commands
for details.
[Restrictions:]
-This fix is part of the "user-eff" package. It is only enabled if
+This fix is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
Other restriction discussed on the doc page for the "fix nvt, npt, and
nph"_fix_nh.html commands also apply.
IMPORTANT NOTE: The temperature for systems (regions or groups) with
only electrons and no nuclei is 0.0 (i.e. not defined) in the current
temperature calculations, a practical example would be a uniform
electron gas or a very hot plasma, where electrons remain delocalized
from the nuclei. This is because, even though electron virials are
included in the temperature calculation, these are averaged over the
nuclear degrees of freedom only. In such cases a corrective term must
be added to the pressure to get the correct kinetic contribution.
[Related commands:]
"fix nvt"_fix_nh.html, "fix nph"_fix_nh.html, "fix npt"_fix_nh.html,
"fix_modify"_fix_modify.html, "run_style"_run_style.html
[Default:]
The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
ploop = 1, nreset = 0, drag = 0.0, dilate = all, and couple = none.
:line
:link(Martyna)
[(Martyna)] Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
:link(Parrinello)
[(Parrinello)] Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
:link(Tuckerman)
[(Tuckerman)] Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
Martyna, J Phys A: Math Gen, 39, 5629 (2006).
:link(Shinoda)
[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
diff --git a/doc/fix_nph_asphere.html b/doc/fix_nph_asphere.html
index 060e17ec9..43e2383ab 100644
--- a/doc/fix_nph_asphere.html
+++ b/doc/fix_nph_asphere.html
@@ -1,134 +1,134 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix nph/asphere command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID nph/asphere args keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>nph/asphere = style name of this fix command
<LI>additional barostat related keyword/value pairs from the <A HREF = "fix_nh.html">fix nph</A> command can be appended
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all nph/asphere iso 0.0 0.0 1000.0
fix 2 all nph/asphere x 5.0 5.0 1000.0
fix 2 all nph/asphere x 5.0 5.0 1000.0 drag 0.2
fix 2 water nph/asphere aniso 0.0 0.0 1000.0 dilate partial
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NPH integration to update position, velocity,
orientation, and angular velocity each timestep for aspherical or
ellipsoidal particles in the group using a Nose/Hoover pressure
barostat. P is pressure; H is enthalpy. This creates a system
trajectory consistent with the isenthalpic ensemble.
</P>
<P>This fix differs from the <A HREF = "fix_nh.html">fix nph</A> command, which assumes
point particles and only updates their position and velocity.
</P>
<P>Additional parameters affecting the barostat are specified by keywords
and values documented with the <A HREF = "fix_nh.html">fix nph</A> command. See,
for example, discussion of the <I>aniso</I>, and <I>dilate</I> keywords.
</P>
<P>The particles in the fix group are the only ones whose velocities and
positions are updated by the velocity/position update portion of the
NPH integration.
</P>
<P>Regardless of what particles are in the fix group, a global pressure is
computed for all particles. Similarly, when the size of the simulation
box is changed, all particles are re-scaled to new positions, unless the
keyword <I>dilate</I> is specified with a value of <I>partial</I>, in which case
only the particles in the fix group are re-scaled. The latter can be
useful for leaving the coordinates of particles in a solid substrate
unchanged and controlling the pressure of a surrounding fluid.
</P>
<HR>
<P>This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp/asphere" and
"pressure", as if these commands had been issued:
</P>
<PRE>compute fix-ID_temp all temp/asphere
compute fix-ID_press all pressure fix-ID_temp
</PRE>
<P>See the <A HREF = "compute_temp_asphere.html">compute temp/asphere</A> and <A HREF = "compute_pressure.html">compute
pressure</A> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
+ underscore + "press", and the group for the new computes is "all"
since pressure is computed for the entire system.
</P>
<P>Note that these are NOT the computes used by thermodynamic output (see
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
and <I>thermo_press</I>. This means you can change the attributes of this
fix's temperature or pressure via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> or
<I>thermo_press</I> will have no effect on this fix.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the Nose/Hoover barostat to <A HREF = "restart.html">binary
restart files</A>. See the <A HREF = "read_restart.html">read_restart</A>
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
supported by this fix. You can use them to assign a
<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
in its thermostatting or barostatting procedure. If you do this, note
that the kinetic energy derived from the compute temperature should be
consistent with the virial term computed using all atoms for the
pressure. LAMMPS will warn you if you choose to compute temperature
on a subset of atoms.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change induced by Nose/Hoover barostatting to
the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
<P>This fix computes the same global scalar and global vector of
quantities as does the <A HREF = "fix_nh.html">fix nph</A> command.
</P>
<P>This fix can ramp its target pressure over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
<A HREF = "run.html">run</A> command for details of how to do this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "asphere" package. It is only enabled if
-LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+<P>This fix is part of the ASPHERE package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>This fix requires that atoms store torque and angular momementum and a
quaternion as defined by the <A HREF = "atom_style.html">atom_style ellipsoid</A>
command.
</P>
<P>All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical as defined by their
shape attribute.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nh.html">fix nph</A>, <A HREF = "fix_nve_asphere.html">fix nve_asphere</A>, <A HREF = "fix_nvt_asphere.html">fix
nvt_asphere</A>, <A HREF = "fix_npt_asphere.html">fix
npt_asphere</A>, <A HREF = "fix_modify.html">fix_modify</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/fix_nph_asphere.txt b/doc/fix_nph_asphere.txt
index 99954fc68..857ff9fd8 100755
--- a/doc/fix_nph_asphere.txt
+++ b/doc/fix_nph_asphere.txt
@@ -1,129 +1,129 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix nph/asphere command :h3
[Syntax:]
fix ID group-ID nph/asphere args keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command
nph/asphere = style name of this fix command
additional barostat related keyword/value pairs from the "fix nph"_fix_nh.html command can be appended :ul
[Examples:]
fix 1 all nph/asphere iso 0.0 0.0 1000.0
fix 2 all nph/asphere x 5.0 5.0 1000.0
fix 2 all nph/asphere x 5.0 5.0 1000.0 drag 0.2
fix 2 water nph/asphere aniso 0.0 0.0 1000.0 dilate partial :pre
[Description:]
Perform constant NPH integration to update position, velocity,
orientation, and angular velocity each timestep for aspherical or
ellipsoidal particles in the group using a Nose/Hoover pressure
barostat. P is pressure; H is enthalpy. This creates a system
trajectory consistent with the isenthalpic ensemble.
This fix differs from the "fix nph"_fix_nh.html command, which assumes
point particles and only updates their position and velocity.
Additional parameters affecting the barostat are specified by keywords
and values documented with the "fix nph"_fix_nh.html command. See,
for example, discussion of the {aniso}, and {dilate} keywords.
The particles in the fix group are the only ones whose velocities and
positions are updated by the velocity/position update portion of the
NPH integration.
Regardless of what particles are in the fix group, a global pressure is
computed for all particles. Similarly, when the size of the simulation
box is changed, all particles are re-scaled to new positions, unless the
keyword {dilate} is specified with a value of {partial}, in which case
only the particles in the fix group are re-scaled. The latter can be
useful for leaving the coordinates of particles in a solid substrate
unchanged and controlling the pressure of a surrounding fluid.
:line
This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp/asphere" and
"pressure", as if these commands had been issued:
compute fix-ID_temp all temp/asphere
compute fix-ID_press all pressure fix-ID_temp :pre
See the "compute temp/asphere"_compute_temp_asphere.html and "compute
pressure"_compute_pressure.html commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
+ underscore + "press", and the group for the new computes is "all"
since pressure is computed for the entire system.
Note that these are NOT the computes used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
and {thermo_press}. This means you can change the attributes of this
fix's temperature or pressure via the
"compute_modify"_compute_modify.html command or print this temperature
or pressure during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} or
{thermo_press} will have no effect on this fix.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the state of the Nose/Hoover barostat to "binary
restart files"_restart.html. See the "read_restart"_read_restart.html
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
The "fix_modify"_fix_modify.html {temp} and {press} options are
supported by this fix. You can use them to assign a
"compute"_compute.html you have defined to this fix which will be used
in its thermostatting or barostatting procedure. If you do this, note
that the kinetic energy derived from the compute temperature should be
consistent with the virial term computed using all atoms for the
pressure. LAMMPS will warn you if you choose to compute temperature
on a subset of atoms.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change induced by Nose/Hoover barostatting to
the system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes the same global scalar and global vector of
quantities as does the "fix nph"_fix_nh.html command.
This fix can ramp its target pressure over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
"run"_run.html command for details of how to do this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
-This fix is part of the "asphere" package. It is only enabled if
-LAMMPS was built with that package. See the "Making
+This fix is part of the ASPHERE package. It is only enabled if LAMMPS
+was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
This fix requires that atoms store torque and angular momementum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
command.
All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical as defined by their
shape attribute.
[Related commands:]
"fix nph"_fix_nh.html, "fix nve_asphere"_fix_nve_asphere.html, "fix
nvt_asphere"_fix_nvt_asphere.html, "fix
npt_asphere"_fix_npt_asphere.html, "fix_modify"_fix_modify.html
[Default:] none
diff --git a/doc/fix_npt_asphere.html b/doc/fix_npt_asphere.html
index dcfc1ae0c..7eb9df9ab 100644
--- a/doc/fix_npt_asphere.html
+++ b/doc/fix_npt_asphere.html
@@ -1,158 +1,158 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix npt/asphere command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID npt/asphere keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>npt/asphere = style name of this fix command
<LI>additional thermostat and barostat related keyword/value pairs from the <A HREF = "fix_nh.html">fix npt</A> command can be appended
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all npt/asphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
fix 2 all npt/asphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
fix 2 all npt/asphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2
fix 2 water npt/asphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NPT integration to update position, velocity,
orientation, and angular velocity each timestep for aspherical or
ellipsoidal particles in the group using a Nose/Hoover temperature
thermostat and Nose/Hoover pressure barostat. P is pressure; T is
temperature. This creates a system trajectory consistent with the
isothermal-isobaric ensemble.
</P>
<P>This fix differs from the <A HREF = "fix_nh.html">fix npt</A> command, which
assumes point particles and only updates their position and velocity.
</P>
<P>The thermostat is applied to both the translational and rotational
degrees of freedom for the aspherical particles, assuming a compute is
used which calculates a temperature that includes the rotational
degrees of freedom (see below). The translational degrees of freedom
can also have a bias velocity removed from them before thermostatting
takes place; see the description below.
</P>
<P>Additional parameters affecting the thermostat and barostat are
specified by keywords and values documented with the <A HREF = "fix_nh.html">fix
npt</A> command. See, for example, discussion of the <I>temp</I>,
<I>iso</I>, <I>aniso</I>, and <I>dilate</I> keywords.
</P>
<P>The particles in the fix group are the only ones whose velocities and
positions are updated by the velocity/position update portion of the
NPT integration.
</P>
<P>Regardless of what particles are in the fix group, a global pressure is
computed for all particles. Similarly, when the size of the simulation
box is changed, all particles are re-scaled to new positions, unless the
keyword <I>dilate</I> is specified with a value of <I>partial</I>, in which case
only the particles in the fix group are re-scaled. The latter can be
useful for leaving the coordinates of particles in a solid substrate
unchanged and controlling the pressure of a surrounding fluid.
</P>
<HR>
<P>This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp/asphere" and
"pressure", as if these commands had been issued:
</P>
<PRE>compute fix-ID_temp all temp/asphere
compute fix-ID_press all pressure fix-ID_temp
</PRE>
<P>See the <A HREF = "compute_temp_asphere.html">compute temp/asphere</A> and <A HREF = "compute_pressure.html">compute
pressure</A> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
+ underscore + "press", and the group for the new computes is "all"
since pressure is computed for the entire system.
</P>
<P>Note that these are NOT the computes used by thermodynamic output (see
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
and <I>thermo_press</I>. This means you can change the attributes of this
fix's temperature or pressure via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> or
<I>thermo_press</I> will have no effect on this fix.
</P>
<P>Like other fixes that perform thermostatting, this fix can be used
with <A HREF = "compute.html">compute commands</A> that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual <A HREF = "compute.html">compute
commands</A> to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the Nose/Hoover thermostat and barostat
to <A HREF = "restart.html">binary restart files</A>. See the
<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
supported by this fix. You can use them to assign a
<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
in its thermostatting or barostatting procedure. If you do this, note
that the kinetic energy derived from the compute temperature should be
consistent with the virial term computed using all atoms for the
pressure. LAMMPS will warn you if you choose to compute temperature
on a subset of atoms.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting and
barostatting to the system's potential energy as part of
<A HREF = "thermo_style.html">thermodynamic output</A>.
</P>
<P>This fix computes the same global scalar and global vector of
quantities as does the <A HREF = "fix_nh.html">fix npt</A> command.
</P>
<P>This fix can ramp its target temperature and pressure over multiple
runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A>
command. See the <A HREF = "run.html">run</A> command for details of how to do
this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "asphere" package. It is only enabled if
-LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+<P>This fix is part of the ASPHERE package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>This fix requires that atoms store torque and angular momementum and a
quaternion as defined by the <A HREF = "atom_style.html">atom_style ellipsoid</A>
command.
</P>
<P>All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical as defined by their
shape attribute.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nh.html">fix npt</A>, <A HREF = "fix_nve_asphere.html">fix nve_asphere</A>, <A HREF = "fix_nvt_asphere.html">fix
nvt_asphere</A>, <A HREF = "fix_modify.html">fix_modify</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/fix_npt_asphere.txt b/doc/fix_npt_asphere.txt
index a3b61b539..e11ef0eb7 100755
--- a/doc/fix_npt_asphere.txt
+++ b/doc/fix_npt_asphere.txt
@@ -1,153 +1,153 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix npt/asphere command :h3
[Syntax:]
fix ID group-ID npt/asphere keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command
npt/asphere = style name of this fix command
additional thermostat and barostat related keyword/value pairs from the "fix npt"_fix_nh.html command can be appended :ul
[Examples:]
fix 1 all npt/asphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
fix 2 all npt/asphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
fix 2 all npt/asphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2
fix 2 water npt/asphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial :pre
[Description:]
Perform constant NPT integration to update position, velocity,
orientation, and angular velocity each timestep for aspherical or
ellipsoidal particles in the group using a Nose/Hoover temperature
thermostat and Nose/Hoover pressure barostat. P is pressure; T is
temperature. This creates a system trajectory consistent with the
isothermal-isobaric ensemble.
This fix differs from the "fix npt"_fix_nh.html command, which
assumes point particles and only updates their position and velocity.
The thermostat is applied to both the translational and rotational
degrees of freedom for the aspherical particles, assuming a compute is
used which calculates a temperature that includes the rotational
degrees of freedom (see below). The translational degrees of freedom
can also have a bias velocity removed from them before thermostatting
takes place; see the description below.
Additional parameters affecting the thermostat and barostat are
specified by keywords and values documented with the "fix
npt"_fix_nh.html command. See, for example, discussion of the {temp},
{iso}, {aniso}, and {dilate} keywords.
The particles in the fix group are the only ones whose velocities and
positions are updated by the velocity/position update portion of the
NPT integration.
Regardless of what particles are in the fix group, a global pressure is
computed for all particles. Similarly, when the size of the simulation
box is changed, all particles are re-scaled to new positions, unless the
keyword {dilate} is specified with a value of {partial}, in which case
only the particles in the fix group are re-scaled. The latter can be
useful for leaving the coordinates of particles in a solid substrate
unchanged and controlling the pressure of a surrounding fluid.
:line
This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style "temp/asphere" and
"pressure", as if these commands had been issued:
compute fix-ID_temp all temp/asphere
compute fix-ID_press all pressure fix-ID_temp :pre
See the "compute temp/asphere"_compute_temp_asphere.html and "compute
pressure"_compute_pressure.html commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
+ underscore + "press", and the group for the new computes is "all"
since pressure is computed for the entire system.
Note that these are NOT the computes used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
and {thermo_press}. This means you can change the attributes of this
fix's temperature or pressure via the
"compute_modify"_compute_modify.html command or print this temperature
or pressure during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} or
{thermo_press} will have no effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with "compute commands"_compute.html that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the "fix_modify"_fix_modify.html command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual "compute
commands"_compute.html to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the state of the Nose/Hoover thermostat and barostat
to "binary restart files"_restart.html. See the
"read_restart"_read_restart.html command for info on how to re-specify
a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.
The "fix_modify"_fix_modify.html {temp} and {press} options are
supported by this fix. You can use them to assign a
"compute"_compute.html you have defined to this fix which will be used
in its thermostatting or barostatting procedure. If you do this, note
that the kinetic energy derived from the compute temperature should be
consistent with the virial term computed using all atoms for the
pressure. LAMMPS will warn you if you choose to compute temperature
on a subset of atoms.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting and
barostatting to the system's potential energy as part of
"thermodynamic output"_thermo_style.html.
This fix computes the same global scalar and global vector of
quantities as does the "fix npt"_fix_nh.html command.
This fix can ramp its target temperature and pressure over multiple
runs, using the {start} and {stop} keywords of the "run"_run.html
command. See the "run"_run.html command for details of how to do
this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
-This fix is part of the "asphere" package. It is only enabled if
-LAMMPS was built with that package. See the "Making
+This fix is part of the ASPHERE package. It is only enabled if LAMMPS
+was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
This fix requires that atoms store torque and angular momementum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
command.
All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical as defined by their
shape attribute.
[Related commands:]
"fix npt"_fix_nh.html, "fix nve_asphere"_fix_nve_asphere.html, "fix
nvt_asphere"_fix_nvt_asphere.html, "fix_modify"_fix_modify.html
[Default:] none
diff --git a/doc/fix_nve.html b/doc/fix_nve.html
index 14f94a659..e08b86dcd 100644
--- a/doc/fix_nve.html
+++ b/doc/fix_nve.html
@@ -1,75 +1,75 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix nve command
</H3>
<H3>fix nve/cuda command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID nve
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>nve = style name of this fix command
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all nve
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NVE integration to update position and velocity for
atoms in the group each timestep. V is volume; E is energy. This
creates a system trajectory consistent with the microcanonical
ensemble.
</P>
<HR>
<P>Styles with a <I>cuda</I> suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
<A HREF = "Section_accelerate.html">this section</A> of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. No parameter of this fix can
be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_nh.html">fix npt</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/fix_nve.txt b/doc/fix_nve.txt
index b6aa2fc0d..fbc23c25e 100644
--- a/doc/fix_nve.txt
+++ b/doc/fix_nve.txt
@@ -1,69 +1,69 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix nve command :h3
fix nve/cuda command :h3
[Syntax:]
fix ID group-ID nve :pre
ID, group-ID are documented in "fix"_fix.html command
nve = style name of this fix command :ul
[Examples:]
fix 1 all nve :pre
[Description:]
Perform constant NVE integration to update position and velocity for
atoms in the group each timestep. V is volume; E is energy. This
creates a system trajectory consistent with the microcanonical
ensemble.
:line
Styles with a {cuda} suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
"this section"_Section_accelerate.html of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] none
[Related commands:]
"fix nvt"_fix_nh.html, "fix npt"_fix_nh.html
[Default:] none
diff --git a/doc/fix_nve_asphere.html b/doc/fix_nve_asphere.html
index 03bafd876..8b5ea4a3f 100644
--- a/doc/fix_nve_asphere.html
+++ b/doc/fix_nve_asphere.html
@@ -1,65 +1,65 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix nve/asphere command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID nve/asphere
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>nve/asphere = style name of this fix command
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all nve/asphere
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NVE integration to update position, velocity,
orientation, and angular velocity for aspherical particles in the
group each timestep. V is volume; E is energy. This creates a system
trajectory consistent with the microcanonical ensemble.
</P>
<P>This fix differs from the <A HREF = "fix_nve.html">fix nve</A> command, which
assumes point particles and only updates their position and velocity.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. No parameter of this fix can
be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "asphere" package. It is only enabled if
-LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+<P>This fix is part of the ASPHERE package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>This fix requires that atoms store torque and angular momementum and a
quaternion as defined by the <A HREF = "atom_style.html">atom_style ellipsoid</A>
command.
</P>
<P>All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical as defined by their
shape attribute.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/fix_nve_asphere.txt b/doc/fix_nve_asphere.txt
index 29902973f..d7b70f41e 100755
--- a/doc/fix_nve_asphere.txt
+++ b/doc/fix_nve_asphere.txt
@@ -1,60 +1,60 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix nve/asphere command :h3
[Syntax:]
fix ID group-ID nve/asphere :pre
ID, group-ID are documented in "fix"_fix.html command
nve/asphere = style name of this fix command :ul
[Examples:]
fix 1 all nve/asphere :pre
[Description:]
Perform constant NVE integration to update position, velocity,
orientation, and angular velocity for aspherical particles in the
group each timestep. V is volume; E is energy. This creates a system
trajectory consistent with the microcanonical ensemble.
This fix differs from the "fix nve"_fix_nve.html command, which
assumes point particles and only updates their position and velocity.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
-This fix is part of the "asphere" package. It is only enabled if
-LAMMPS was built with that package. See the "Making
+This fix is part of the ASPHERE package. It is only enabled if LAMMPS
+was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
This fix requires that atoms store torque and angular momementum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
command.
All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical as defined by their
shape attribute.
[Related commands:]
"fix nve"_fix_nve.html, "fix nve/sphere"_fix_nve_sphere.html
[Default:] none
diff --git a/doc/fix_nve_eff.html b/doc/fix_nve_eff.html
index dcc053450..80b150924 100644
--- a/doc/fix_nve_eff.html
+++ b/doc/fix_nve_eff.html
@@ -1,59 +1,59 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix nve/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID nve/eff
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>nve/eff = style name of this fix command
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all nve/eff
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NVE integration to update position and velocity for
nuclei and electrons in the group for the <A HREF = "pair_eff.html">electron force
field</A> model. V is volume; E is energy. This creates a
system trajectory consistent with the microcanonical ensemble.
</P>
<P>The operation of this fix is exactly like that described by the <A HREF = "fix_nve.html">fix
nve</A> command, except that the radius and radial velocity
of electrons are also updated.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. No parameter of this fix can
be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "user-eff" package. It is only enabled if
+<P>This fix is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nh_eff.html">fix nvt/eff</A>, <A HREF = "fix_nh_eff.html">fix
npt/eff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/fix_nve_eff.txt b/doc/fix_nve_eff.txt
index f500bc198..156f184da 100644
--- a/doc/fix_nve_eff.txt
+++ b/doc/fix_nve_eff.txt
@@ -1,54 +1,54 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix nve/eff command :h3
[Syntax:]
fix ID group-ID nve/eff :pre
ID, group-ID are documented in "fix"_fix.html command
nve/eff = style name of this fix command :ul
[Examples:]
fix 1 all nve/eff :pre
[Description:]
Perform constant NVE integration to update position and velocity for
nuclei and electrons in the group for the "electron force
field"_pair_eff.html model. V is volume; E is energy. This creates a
system trajectory consistent with the microcanonical ensemble.
The operation of this fix is exactly like that described by the "fix
nve"_fix_nve.html command, except that the radius and radial velocity
of electrons are also updated.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
-This fix is part of the "user-eff" package. It is only enabled if
+This fix is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"fix nve"_fix_nve.html, "fix nvt/eff"_fix_nh_eff.html, "fix
npt/eff"_fix_nh_eff.html
[Default:] none
diff --git a/doc/fix_nvt_asphere.html b/doc/fix_nvt_asphere.html
index dd3a8e7e7..903d3bccb 100644
--- a/doc/fix_nvt_asphere.html
+++ b/doc/fix_nvt_asphere.html
@@ -1,134 +1,134 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix nvt/asphere command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID nvt/asphere keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>nvt/asphere = style name of this fix command
<LI>additional thermostat related keyword/value pairs from the <A HREF = "fix_nh.html">fix nvt</A> command can be appended
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all nvt/asphere temp 300.0 300.0 100.0
fix 1 all nvt/asphere temp 300.0 300.0 100.0 drag 0.2
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NVT integration to update position, velocity,
orientation, and angular velocity each timestep for aspherical or
ellipsoidal particles in the group using a Nose/Hoover temperature
thermostat. V is volume; T is temperature. This creates a system
trajectory consistent with the canonical ensemble.
</P>
<P>This fix differs from the <A HREF = "fix_nh.html">fix nvt</A> command, which
assumes point particles and only updates their position and velocity.
</P>
<P>The thermostat is applied to both the translational and rotational
degrees of freedom for the aspherical particles, assuming a compute is
used which calculates a temperature that includes the rotational
degrees of freedom (see below). The translational degrees of freedom
can also have a bias velocity removed from them before thermostatting
takes place; see the description below.
</P>
<P>Additional parameters affecting the thermostat are specified by
keywords and values documented with the <A HREF = "fix_nh.html">fix nvt</A>
command. See, for example, discussion of the <I>temp</I> and <I>drag</I>
keywords.
</P>
<P>This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp/asphere", as if this command
had been issued:
</P>
<PRE>compute fix-ID_temp group-ID temp/asphere
</PRE>
<P>See the <A HREF = "compute_temp_asphere.html">compute temp/asphere</A> command for
details. Note that the ID of the new compute is the fix-ID +
underscore + "temp", and the group for the new compute is the same as
the fix group.
</P>
<P>Note that this is NOT the compute used by thermodynamic output (see
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> will have no
effect on this fix.
</P>
<P>Like other fixes that perform thermostatting, this fix can be used
with <A HREF = "compute.html">compute commands</A> that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual <A HREF = "compute.html">compute
commands</A> to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the Nose/Hoover thermostat to <A HREF = "restart.html">binary
restart files</A>. See the <A HREF = "read_restart.html">read_restart</A>
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
fix. You can use it to assign a <A HREF = "compute.html">compute</A> you have
defined to this fix which will be used in its thermostatting
procedure.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
<P>This fix computes the same global scalar and global vector of
quantities as does the <A HREF = "fix_nh.html">fix nvt</A> command.
</P>
<P>This fix can ramp its target temperature over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
<A HREF = "run.html">run</A> command for details of how to do this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "asphere" package. It is only enabled if
-LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+<P>This fix is part of the ASPHERE package. It is only enabled if LAMMPS
+was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>This fix requires that atoms store torque and angular momementum and a
quaternion as defined by the <A HREF = "atom_style.html">atom_style ellipsoid</A>
command.
</P>
<P>All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical as defined by their
shape attribute.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_nve_asphere.html">fix nve_asphere</A>, <A HREF = "fix_npt_asphere.html">fix
npt_asphere</A>, <A HREF = "fix_modify.html">fix_modify</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/fix_nvt_asphere.txt b/doc/fix_nvt_asphere.txt
index 1b910fd38..8af5be128 100755
--- a/doc/fix_nvt_asphere.txt
+++ b/doc/fix_nvt_asphere.txt
@@ -1,129 +1,129 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix nvt/asphere command :h3
[Syntax:]
fix ID group-ID nvt/asphere keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command
nvt/asphere = style name of this fix command
additional thermostat related keyword/value pairs from the "fix nvt"_fix_nh.html command can be appended :ul
[Examples:]
fix 1 all nvt/asphere temp 300.0 300.0 100.0
fix 1 all nvt/asphere temp 300.0 300.0 100.0 drag 0.2 :pre
[Description:]
Perform constant NVT integration to update position, velocity,
orientation, and angular velocity each timestep for aspherical or
ellipsoidal particles in the group using a Nose/Hoover temperature
thermostat. V is volume; T is temperature. This creates a system
trajectory consistent with the canonical ensemble.
This fix differs from the "fix nvt"_fix_nh.html command, which
assumes point particles and only updates their position and velocity.
The thermostat is applied to both the translational and rotational
degrees of freedom for the aspherical particles, assuming a compute is
used which calculates a temperature that includes the rotational
degrees of freedom (see below). The translational degrees of freedom
can also have a bias velocity removed from them before thermostatting
takes place; see the description below.
Additional parameters affecting the thermostat are specified by
keywords and values documented with the "fix nvt"_fix_nh.html
command. See, for example, discussion of the {temp} and {drag}
keywords.
This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp/asphere", as if this command
had been issued:
compute fix-ID_temp group-ID temp/asphere :pre
See the "compute temp/asphere"_compute_temp_asphere.html command for
details. Note that the ID of the new compute is the fix-ID +
underscore + "temp", and the group for the new compute is the same as
the fix group.
Note that this is NOT the compute used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
"compute_modify"_compute_modify.html command or print this temperature
during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} will have no
effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with "compute commands"_compute.html that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the "fix_modify"_fix_modify.html command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual "compute
commands"_compute.html to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the state of the Nose/Hoover thermostat to "binary
restart files"_restart.html. See the "read_restart"_read_restart.html
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
The "fix_modify"_fix_modify.html {temp} option is supported by this
fix. You can use it to assign a "compute"_compute.html you have
defined to this fix which will be used in its thermostatting
procedure.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes the same global scalar and global vector of
quantities as does the "fix nvt"_fix_nh.html command.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
"run"_run.html command for details of how to do this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
-This fix is part of the "asphere" package. It is only enabled if
-LAMMPS was built with that package. See the "Making
+This fix is part of the ASPHERE package. It is only enabled if LAMMPS
+was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
This fix requires that atoms store torque and angular momementum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
command.
All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical as defined by their
shape attribute.
[Related commands:]
"fix nvt"_fix_nh.html, "fix nve_asphere"_fix_nve_asphere.html, "fix
npt_asphere"_fix_npt_asphere.html, "fix_modify"_fix_modify.html
[Default:] none
diff --git a/doc/fix_nvt_sllod_eff.html b/doc/fix_nvt_sllod_eff.html
index 947c19051..072b12435 100644
--- a/doc/fix_nvt_sllod_eff.html
+++ b/doc/fix_nvt_sllod_eff.html
@@ -1,100 +1,100 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix nvt/sllod/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID nvt/sllod/eff keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>nvt/sllod/eff = style name of this fix command
<LI>additional thermostat related keyword/value pairs from the <A HREF = "fix_nh_eff.html">fix nvt/eff</A> command can be appended
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1
fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1 drag 0.2
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NVT integration to update positions and velocities
each timestep for nuclei and electrons in the group for the <A HREF = "pair_eff.html">electron
force field</A> model, using a Nose/Hoover temperature
thermostat. V is volume; T is temperature. This creates a system
trajectory consistent with the canonical ensemble.
</P>
<P>The operation of this fix is exactly like that described by the <A HREF = "fix_nvt_sllod.html">fix
nvt/sllod</A> command, except that the radius and
radial velocity of electrons are also updated and thermostatted.
Likewise the temperature calculated by the fix, using the compute it
creates (as discussed in the <A HREF = "fix_nh.html">fix nvt, npt, and nph</A> doc
page), is performed with a <A HREF = "compute_temp_deform_eff.html">compute
temp/deform/eff</A> commmand that includes
the eFF contribution to the temperature from the electron radial
velocity.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the Nose/Hoover thermostat to <A HREF = "restart.html">binary
restart files</A>. See the <A HREF = "read_restart.html">read_restart</A>
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
fix. You can use it to assign a <A HREF = "compute.html">compute</A> you have
defined to this fix which will be used in its thermostatting
procedure.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
<P>This fix computes the same global scalar and global vector of
quantities as does the <A HREF = "fix_nh_eff.html">fix nvt/eff</A> command.
</P>
<P>This fix can ramp its target temperature over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
<A HREF = "run.html">run</A> command for details of how to do this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "user-eff" package. It is only enabled if
+<P>This fix is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>This fix works best without Nose-Hoover chain thermostats, i.e. using
tchain = 1. Setting tchain to larger values can result in poor
equilibration.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nve_eff.html">fix nve/eff</A>, <A HREF = "fix_nh_eff.html">fix nvt/eff</A>, <A HREF = "fix_langevin_eff.html">fix
langevin/eff</A>, <A HREF = "fix_nvt_sllod.html">fix
nvt/sllod</A>, <A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "compute_temp_deform_eff.html">compute
temp/deform/eff</A>
</P>
<P><B>Default:</B>
</P>
<P>Same as <A HREF = "fix_nh_eff.html">fix nvt/eff</A>, except tchain = 1.
</P>
<HR>
<A NAME = "Tuckerman"></A>
<P><B>(Tuckerman)</B> Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys,
106, 5615 (1997).
</P>
</HTML>
diff --git a/doc/fix_nvt_sllod_eff.txt b/doc/fix_nvt_sllod_eff.txt
index 23ed2ba73..c2d397097 100644
--- a/doc/fix_nvt_sllod_eff.txt
+++ b/doc/fix_nvt_sllod_eff.txt
@@ -1,94 +1,94 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix nvt/sllod/eff command :h3
[Syntax:]
fix ID group-ID nvt/sllod/eff keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command
nvt/sllod/eff = style name of this fix command
additional thermostat related keyword/value pairs from the "fix nvt/eff"_fix_nh_eff.html command can be appended :ul
[Examples:]
fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1
fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1 drag 0.2 :pre
[Description:]
Perform constant NVT integration to update positions and velocities
each timestep for nuclei and electrons in the group for the "electron
force field"_pair_eff.html model, using a Nose/Hoover temperature
thermostat. V is volume; T is temperature. This creates a system
trajectory consistent with the canonical ensemble.
The operation of this fix is exactly like that described by the "fix
nvt/sllod"_fix_nvt_sllod.html command, except that the radius and
radial velocity of electrons are also updated and thermostatted.
Likewise the temperature calculated by the fix, using the compute it
creates (as discussed in the "fix nvt, npt, and nph"_fix_nh.html doc
page), is performed with a "compute
temp/deform/eff"_compute_temp_deform_eff.html commmand that includes
the eFF contribution to the temperature from the electron radial
velocity.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the state of the Nose/Hoover thermostat to "binary
restart files"_restart.html. See the "read_restart"_read_restart.html
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
The "fix_modify"_fix_modify.html {temp} option is supported by this
fix. You can use it to assign a "compute"_compute.html you have
defined to this fix which will be used in its thermostatting
procedure.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes the same global scalar and global vector of
quantities as does the "fix nvt/eff"_fix_nh_eff.html command.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
"run"_run.html command for details of how to do this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
-This fix is part of the "user-eff" package. It is only enabled if
+This fix is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
This fix works best without Nose-Hoover chain thermostats, i.e. using
tchain = 1. Setting tchain to larger values can result in poor
equilibration.
[Related commands:]
"fix nve/eff"_fix_nve_eff.html, "fix nvt/eff"_fix_nh_eff.html, "fix
langevin/eff"_fix_langevin_eff.html, "fix
nvt/sllod"_fix_nvt_sllod.html, "fix_modify"_fix_modify.html, "compute
temp/deform/eff"_compute_temp_deform_eff.html
[Default:]
Same as "fix nvt/eff"_fix_nh_eff.html, except tchain = 1.
:line
:link(Tuckerman)
[(Tuckerman)] Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys,
106, 5615 (1997).
diff --git a/doc/fix_poems.html b/doc/fix_poems.html
index 3a6e47ff0..0bc381f4e 100644
--- a/doc/fix_poems.html
+++ b/doc/fix_poems.html
@@ -1,146 +1,146 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix poems
</H3>
<P>Syntax:
</P>
<PRE>fix ID group-ID poems keyword values
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>poems = style name of this fix command
<LI>keyword = <I>group</I> or <I>file</I> or <I>molecule</I>
<PRE> <I>group</I> values = list of group IDs
<I>molecule</I> values = none
<I>file</I> values = filename
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 3 fluid poems group clump1 clump2 clump3
fix 3 fluid poems file cluster.list
</PRE>
<P><B>Description:</B>
</P>
<P>Treats one or more sets of atoms as coupled rigid bodies. This means
that each timestep the total force and torque on each rigid body is
computed and the coordinates and velocities of the atoms are updated
so that the collection of bodies move as a coupled set. This can be
useful for treating a large biomolecule as a collection of connected,
coarse-grained particles.
</P>
<P>The coupling, associated motion constraints, and time integration is
performed by the software package <A HREF = "http://www.rpi.edu/~anderk5/lab">Parallelizable Open source
Efficient Multibody Software (POEMS)</A> which computes the
constrained rigid-body motion of articulated (jointed) multibody
systems <A HREF = "#Anderson">(Anderson)</A>. POEMS was written and is distributed
by Prof Kurt Anderson, his graduate student Rudranarayan Mukherjee,
and other members of his group at Rensselaer Polytechnic Institute
(RPI). Rudranarayan developed the LAMMPS/POEMS interface. For
copyright information on POEMS and other details, please refer to the
documents in the poems directory distributed with LAMMPS.
</P>
<P>This fix updates the positions and velocities of the rigid atoms with
a constant-energy time integration, so you should not update the same
atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin).
</P>
<P>Each body must have a non-degenerate inertia tensor, which means if
must contain at least 3 non-collinear atoms. Which atoms are in which
bodies can be defined via several options.
</P>
<P>For option <I>group</I>, each of the listed groups is treated as a rigid
body. Note that only atoms that are also in the fix group are
included in each rigid body.
</P>
<P>For option <I>molecule</I>, each set of atoms in the group with a different
molecule ID is treated as a rigid body.
</P>
<P>For option <I>file</I>, sets of atoms are read from the specified file and
each set is treated as a rigid body. Each line of the file specifies
a rigid body in the following format:
</P>
<P>ID type atom1-ID atom2-ID atom3-ID ...
</P>
<P>ID as an integer from 1 to M (the number of rigid bodies). Type is
any integer; it is not used by the fix poems command. The remaining
arguments are IDs of atoms in the rigid body, each typically from 1 to
N (the number of atoms in the system). Only atoms that are also in
the fix group are included in each rigid body. Blank lines and lines
that begin with '#' are skipped.
</P>
<P>A connection between a pair of rigid bodies is inferred if one atom is
common to both bodies. The POEMS solver treats that atom as a
spherical joint with 3 degrees of freedom. Currently, a collection of
bodies can only be connected by joints as a linear chain. The entire
collection of rigid bodies can represent one or more chains. Other
connection topologies (tree, ring) are not allowed, but will be added
later. Note that if no joints exist, it is more efficient to use the
<A HREF = "fix_rigid.html">fix rigid</A> command to simulate the system.
</P>
<P>When the poems fix is defined, it will print out statistics on the
total # of clusters, bodies, joints, atoms involved. A cluster in
this context means a set of rigid bodies connected by joints.
</P>
<P>For computational efficiency, you should turn off pairwise and bond
interactions within each rigid body, as they no longer contribute to
the motion. The "neigh_modify exclude" and "delete_bonds" commands
can be used to do this if each rigid body is a group.
</P>
<P>For computational efficiency, you should only define one fix poems
which includes all the desired rigid bodies. LAMMPS will allow
multiple poems fixes to be defined, but it is more expensive.
</P>
<P>The degrees-of-freedom removed by coupled rigid bodies are accounted
for in temperature and pressure computations. Similarly, the rigid
body contribution to the pressure virial is also accounted for. The
latter is only correct if forces within the bodies have been turned
off, and there is only a single fix poems defined.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. No parameter of this fix can
be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "poems" package. It is only enabled if LAMMPS
+<P>This fix is part of the POEMS package. It is only enabled if LAMMPS
was built with that package, which also requires the POEMS library be
built and linked with LAMMPS. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_rigid.html">fix rigid</A>, <A HREF = "delete_bonds.html">delete_bonds</A>,
<A HREF = "neigh_modify.html">neigh_modify</A> exclude
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Anderson"></A>
<P><B>(Anderson)</B> Anderson, Mukherjee, Critchley, Ziegler, and Lipton
"POEMS: Parallelizable Open-source Efficient Multibody Software ",
Engineering With Computers (2006). (<A HREF = "http://dx.doi.org/10.1007/s00366-006-0026-x">link to
paper</A>)
</P>
</HTML>
diff --git a/doc/fix_poems.txt b/doc/fix_poems.txt
index 244b5ff0f..d90d832cb 100644
--- a/doc/fix_poems.txt
+++ b/doc/fix_poems.txt
@@ -1,136 +1,136 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix poems :h3
Syntax:
fix ID group-ID poems keyword values :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
poems = style name of this fix command :l
keyword = {group} or {file} or {molecule} :l
{group} values = list of group IDs
{molecule} values = none
{file} values = filename :pre
:ule
[Examples:]
fix 3 fluid poems group clump1 clump2 clump3
fix 3 fluid poems file cluster.list :pre
[Description:]
Treats one or more sets of atoms as coupled rigid bodies. This means
that each timestep the total force and torque on each rigid body is
computed and the coordinates and velocities of the atoms are updated
so that the collection of bodies move as a coupled set. This can be
useful for treating a large biomolecule as a collection of connected,
coarse-grained particles.
The coupling, associated motion constraints, and time integration is
performed by the software package "Parallelizable Open source
Efficient Multibody Software (POEMS)"_poems which computes the
constrained rigid-body motion of articulated (jointed) multibody
systems "(Anderson)"_#Anderson. POEMS was written and is distributed
by Prof Kurt Anderson, his graduate student Rudranarayan Mukherjee,
and other members of his group at Rensselaer Polytechnic Institute
(RPI). Rudranarayan developed the LAMMPS/POEMS interface. For
copyright information on POEMS and other details, please refer to the
documents in the poems directory distributed with LAMMPS.
:link(poems,http://www.rpi.edu/~anderk5/lab)
This fix updates the positions and velocities of the rigid atoms with
a constant-energy time integration, so you should not update the same
atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin).
Each body must have a non-degenerate inertia tensor, which means if
must contain at least 3 non-collinear atoms. Which atoms are in which
bodies can be defined via several options.
For option {group}, each of the listed groups is treated as a rigid
body. Note that only atoms that are also in the fix group are
included in each rigid body.
For option {molecule}, each set of atoms in the group with a different
molecule ID is treated as a rigid body.
For option {file}, sets of atoms are read from the specified file and
each set is treated as a rigid body. Each line of the file specifies
a rigid body in the following format:
ID type atom1-ID atom2-ID atom3-ID ...
ID as an integer from 1 to M (the number of rigid bodies). Type is
any integer; it is not used by the fix poems command. The remaining
arguments are IDs of atoms in the rigid body, each typically from 1 to
N (the number of atoms in the system). Only atoms that are also in
the fix group are included in each rigid body. Blank lines and lines
that begin with '#' are skipped.
A connection between a pair of rigid bodies is inferred if one atom is
common to both bodies. The POEMS solver treats that atom as a
spherical joint with 3 degrees of freedom. Currently, a collection of
bodies can only be connected by joints as a linear chain. The entire
collection of rigid bodies can represent one or more chains. Other
connection topologies (tree, ring) are not allowed, but will be added
later. Note that if no joints exist, it is more efficient to use the
"fix rigid"_fix_rigid.html command to simulate the system.
When the poems fix is defined, it will print out statistics on the
total # of clusters, bodies, joints, atoms involved. A cluster in
this context means a set of rigid bodies connected by joints.
For computational efficiency, you should turn off pairwise and bond
interactions within each rigid body, as they no longer contribute to
the motion. The "neigh_modify exclude" and "delete_bonds" commands
can be used to do this if each rigid body is a group.
For computational efficiency, you should only define one fix poems
which includes all the desired rigid bodies. LAMMPS will allow
multiple poems fixes to be defined, but it is more expensive.
The degrees-of-freedom removed by coupled rigid bodies are accounted
for in temperature and pressure computations. Similarly, the rigid
body contribution to the pressure virial is also accounted for. The
latter is only correct if forces within the bodies have been turned
off, and there is only a single fix poems defined.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
-This fix is part of the "poems" package. It is only enabled if LAMMPS
+This fix is part of the POEMS package. It is only enabled if LAMMPS
was built with that package, which also requires the POEMS library be
built and linked with LAMMPS. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"fix rigid"_fix_rigid.html, "delete_bonds"_delete_bonds.html,
"neigh_modify"_neigh_modify.html exclude
[Default:] none
:line
:link(Anderson)
[(Anderson)] Anderson, Mukherjee, Critchley, Ziegler, and Lipton
"POEMS: Parallelizable Open-source Efficient Multibody Software ",
Engineering With Computers (2006). ("link to
paper"_http://dx.doi.org/10.1007/s00366-006-0026-x)
diff --git a/doc/fix_pour.html b/doc/fix_pour.html
index 9e85bba92..8ef12fa78 100644
--- a/doc/fix_pour.html
+++ b/doc/fix_pour.html
@@ -1,151 +1,151 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix pour command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID pour N type seed keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>pour = style name of this fix command
<LI>N = # of atoms to insert
<LI>type = atom type to assign to inserted atoms
<LI>seed = random # seed (positive integer)
<LI>one or more keyword/value pairs may be appended to args
<LI>keyword = <I>region</I> or <I>diam</I> or <I>dens</I> or <I>vol</I> or <I>rate</I> or <I>vel</I>
<PRE> <I>region</I> value = region-ID
region-ID = ID of region to use as insertion volume
<I>diam</I> values = lo hi
lo,hi = range of diameters for inserted particles (distance units)
<I>dens</I> values = lo hi
lo,hi = range of densities for inserted particles
<I>vol</I> values = fraction Nattempt
fraction = desired volume fraction for filling insertion volume
Nattempt = max # of insertion attempts per atom
<I>rate</I> value = V
V = z velocity (3d) or y velocity (2d) at which
insertion volume moves (velocity units)
<I>vel</I> values (3d) = vxlo vxhi vylo vyhi vz
<I>vel</I> values (2d) = vxlo vxhi vy
vxlo,vxhi = range of x velocities for inserted particles (velocity units)
vylo,vyhi = range of y velocities for inserted particles (velocity units)
vz = z velocity (3d) assigned to inserted particles (velocity units)
vy = y velocity (2d) assigned to inserted particles (velocity units)
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 3 all pour 1000 2 29494 region myblock
fix 2 all pour 10000 1 19985583 region disk vol 0.33 100 rate 1.0 diam 0.9 1.1
</PRE>
<P><B>Description:</B>
</P>
<P>Insert particles into a granular run every few timesteps within a
specified region until N particles have been inserted. This is useful
for simulating the pouring of particles into a container under the
influence of gravity.
</P>
<P>Inserted particles are assigned the specified atom type and are
assigned to two groups: the default group "all" and the group
specified in the fix pour command (which can also be "all").
</P>
<P>This command must use the <I>region</I> keyword to define an insertion
volume. The specified region must have been previously defined with a
<A HREF = "region.html">region</A> command. It must be of type <I>block</I> or a z-axis
<I>cylinder</I> and must be defined with side = <I>in</I>. The cylinder style
of region can only be used with 3d simulations.
</P>
<P>Each timestep particles are inserted, they are placed randomly inside
the insertion volume so as to mimic a stream of poured particles. The
larger the volume, the more particles that can be inserted at any one
timestep. Particles are inserted again after enough time has elapsed
that the previously inserted particles fall out of the insertion
volume under the influence of gravity. Insertions continue every so
many timesteps until the desired # of particles has been inserted.
</P>
<P>All other keywords are optional with defaults as shown below. The
<I>diam</I>, <I>dens</I>, and <I>vel</I> options enable inserted particles to have a
range of diameters or densities or xy velocities. The specific values
for a particular inserted particle will be chosen randomly and
uniformly between the specified bounds. The <I>vz</I> or <I>vy</I> value for
option <I>vel</I> assigns a z-velocity (3d) or y-velocity (2d) to each
inserted particle.
</P>
<P>The <I>vol</I> option specifies what volume fraction of the insertion
volume will be filled with particles. The higher the value, the more
particles are inserted each timestep. Since inserted particles cannot
overlap, the maximum volume fraction should be no higher than about
0.6. Each timestep particles are inserted, LAMMPS will make up to a
total of M tries to insert the new particles without overlaps, where M
= # of inserted particles * Nattempt. If LAMMPS is unsuccessful at
completing all insertions, it prints a warning.
</P>
<P>The <I>rate</I> option moves the insertion volume in the z direction (3d)
or y direction (2d). This enables pouring particles from a
successively higher height over time.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. This means you must be careful when restarting a
pouring simulation, when the restart file was written in the middle of
the pouring operation. Specifically, you should use a new fix pour
command in the input script for the restarted simulation that
continues the operation. You will need to adjust the arguments of the
original fix pour command to do this.
</P>
<P>Also note that because the state of the random number generator is not
saved in restart files, you cannot do "exact" restarts with this fix,
where the simulation continues on the same as if no restart had taken
place. However, in a statistical sense, a restarted simulation should
produce the same behavior if you adjust the fix pour parameters
appropriately.
</P>
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
access by various <A HREF = "Section_howto.html#howto_15">output commands</A>. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "granular" package. It is only enabled if
+<P>This fix is part of the GRANULAR package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>For 3d simulations, a gravity fix in the -z direction must be defined
for use in conjunction with this fix. For 2d simulations, gravity
must be defined in the -y direction.
</P>
<P>The specified insertion region cannot be a "dynamic" region, as
defined by the <A HREF = "region.html">region</A> command.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_deposit.html">fix_deposit</A>, <A HREF = "fix_gravity.html">fix_gravity</A>,
<A HREF = "region.html">region</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are diam = 1.0 1.0, dens = 1.0 1.0, vol = 0.25 50,
rate = 0.0, vel = 0.0 0.0 0.0 0.0 0.0.
</P>
</HTML>
diff --git a/doc/fix_pour.txt b/doc/fix_pour.txt
index 56d4e6f73..e1521809c 100644
--- a/doc/fix_pour.txt
+++ b/doc/fix_pour.txt
@@ -1,138 +1,138 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix pour command :h3
[Syntax:]
fix ID group-ID pour N type seed keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
pour = style name of this fix command :l
N = # of atoms to insert :l
type = atom type to assign to inserted atoms :l
seed = random # seed (positive integer) :l
one or more keyword/value pairs may be appended to args :l
keyword = {region} or {diam} or {dens} or {vol} or {rate} or {vel} :l
{region} value = region-ID
region-ID = ID of region to use as insertion volume
{diam} values = lo hi
lo,hi = range of diameters for inserted particles (distance units)
{dens} values = lo hi
lo,hi = range of densities for inserted particles
{vol} values = fraction Nattempt
fraction = desired volume fraction for filling insertion volume
Nattempt = max # of insertion attempts per atom
{rate} value = V
V = z velocity (3d) or y velocity (2d) at which
insertion volume moves (velocity units)
{vel} values (3d) = vxlo vxhi vylo vyhi vz
{vel} values (2d) = vxlo vxhi vy
vxlo,vxhi = range of x velocities for inserted particles (velocity units)
vylo,vyhi = range of y velocities for inserted particles (velocity units)
vz = z velocity (3d) assigned to inserted particles (velocity units)
vy = y velocity (2d) assigned to inserted particles (velocity units) :pre
:ule
[Examples:]
fix 3 all pour 1000 2 29494 region myblock
fix 2 all pour 10000 1 19985583 region disk vol 0.33 100 rate 1.0 diam 0.9 1.1 :pre
[Description:]
Insert particles into a granular run every few timesteps within a
specified region until N particles have been inserted. This is useful
for simulating the pouring of particles into a container under the
influence of gravity.
Inserted particles are assigned the specified atom type and are
assigned to two groups: the default group "all" and the group
specified in the fix pour command (which can also be "all").
This command must use the {region} keyword to define an insertion
volume. The specified region must have been previously defined with a
"region"_region.html command. It must be of type {block} or a z-axis
{cylinder} and must be defined with side = {in}. The cylinder style
of region can only be used with 3d simulations.
Each timestep particles are inserted, they are placed randomly inside
the insertion volume so as to mimic a stream of poured particles. The
larger the volume, the more particles that can be inserted at any one
timestep. Particles are inserted again after enough time has elapsed
that the previously inserted particles fall out of the insertion
volume under the influence of gravity. Insertions continue every so
many timesteps until the desired # of particles has been inserted.
All other keywords are optional with defaults as shown below. The
{diam}, {dens}, and {vel} options enable inserted particles to have a
range of diameters or densities or xy velocities. The specific values
for a particular inserted particle will be chosen randomly and
uniformly between the specified bounds. The {vz} or {vy} value for
option {vel} assigns a z-velocity (3d) or y-velocity (2d) to each
inserted particle.
The {vol} option specifies what volume fraction of the insertion
volume will be filled with particles. The higher the value, the more
particles are inserted each timestep. Since inserted particles cannot
overlap, the maximum volume fraction should be no higher than about
0.6. Each timestep particles are inserted, LAMMPS will make up to a
total of M tries to insert the new particles without overlaps, where M
= # of inserted particles * Nattempt. If LAMMPS is unsuccessful at
completing all insertions, it prints a warning.
The {rate} option moves the insertion volume in the z direction (3d)
or y direction (2d). This enables pouring particles from a
successively higher height over time.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. This means you must be careful when restarting a
pouring simulation, when the restart file was written in the middle of
the pouring operation. Specifically, you should use a new fix pour
command in the input script for the restarted simulation that
continues the operation. You will need to adjust the arguments of the
original fix pour command to do this.
Also note that because the state of the random number generator is not
saved in restart files, you cannot do "exact" restarts with this fix,
where the simulation continues on the same as if no restart had taken
place. However, in a statistical sense, a restarted simulation should
produce the same behavior if you adjust the fix pour parameters
appropriately.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
access by various "output commands"_Section_howto.html#howto_15. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
-This fix is part of the "granular" package. It is only enabled if
+This fix is part of the GRANULAR package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
For 3d simulations, a gravity fix in the -z direction must be defined
for use in conjunction with this fix. For 2d simulations, gravity
must be defined in the -y direction.
The specified insertion region cannot be a "dynamic" region, as
defined by the "region"_region.html command.
[Related commands:]
"fix_deposit"_fix_deposit.html, "fix_gravity"_fix_gravity.html,
"region"_region.html
[Default:]
The option defaults are diam = 1.0 1.0, dens = 1.0 1.0, vol = 0.25 50,
rate = 0.0, vel = 0.0 0.0 0.0 0.0 0.0.
diff --git a/doc/fix_qeq_reax.html b/doc/fix_qeq_reax.html
index 65ed93d0d..ef970af52 100644
--- a/doc/fix_qeq_reax.html
+++ b/doc/fix_qeq_reax.html
@@ -1,100 +1,100 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix qeq/reax command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>qeq/reax = style name of this fix command
<LI>Nevery = perform QEq every this many steps
<LI>cutlo,cuthi = lo and hi cutoff for Taper radius
<LI>tolerance = precision to which charges will be equilibrated
<LI>params = reax/c or a filename
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq
</PRE>
<P><B>Description:</B>
</P>
<P>Perform the charge equilibration (QEq) method as described in <A HREF = "#Rappe_1991">(Rappe
and Goddard, 1991)</A> and formulated in <A HREF = "#Nakano_1997">(Nakano,
1997)</A>. It is typically used in conjunction with the
ReaxFF force field model as implemented in the <A HREF = "pair_reax_c.html">pair_style
reax/c</A> command, but it can be used with any
potential in LAMMPS, so long as it defines and uses charges on each
atom. The <A HREF = "fix_qeq_comb.html">fix qeq/comb</A> command should be used to
perform charge equliibration with the <A HREF = "pair_comb.html">COMB potential</A>.
For more technical details about the charge equilibration performed by
fix qeq/reax, see the "(Aktulga)" paper.
</P>
<P>The QEq method minimizes the electrostatic energy of the system by
adjusting the partial charge on individual atoms based on interactions
with their neighbors. It reqires some parameters for each atom type.
If the <I>params</I> setting above is the word "reax/c", then these are
extracted from the <A HREF = "pair_reax_c.html">pair_style reax/c</A> command and
the ReaxFF force field file it reads in. If a file name is specified
for <I>params</I>, then the parameters are taken from the specified file
and the file must contain one line for each atom type. The latter
form must be used when performing QeQ with a non-ReaxFF potential.
Each line should be formatted as follows:
</P>
<PRE>itype chi eta gamma
</PRE>
<P>where <I>itype</I> is the atom type from 1 to Ntypes, <I>chi</I> denotes the
electronegativity in eV, <I>eta</I> denotes the self-Coulomb
potential in eV, and <I>gamma</I> denotes the valence orbital
exponent. Note that these 3 quantities are also in the ReaxFF
potential file, except that eta is defined here as twice the eta value
in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
of this fix are hard-coded to be A, eV, and electronic charge.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. No global scalar or vector or per-atom
quantities are stored by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. No parameter of this fix can
be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
</P>
<P>This fix is invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "user-reaxc" package. It is only enabled if
+<P>This fix is part of the USER-REAXC package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_reax_c.html">pair_style reax/c</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Rappe_1991"></A>
<P><B>(Rappe)</B> Rappe and Goddard III, Journal of Physical Chemistry, 105,
3358-3363 (1991).
</P>
<A NAME = "Nakano_1997"></A>
<P><B>(Nakano)</B> Nakano, Computer Physics Communications, 104, 59-69 (1997).
</P>
<P>:link(Aktulga) <B>(Aktulga)</B> Aktulga, Fogarty, Pandit, Grama, Parallel
Computing, to appear (2011).
</P>
</HTML>
diff --git a/doc/fix_qeq_reax.txt b/doc/fix_qeq_reax.txt
index 8daf358fa..f57f2f254 100644
--- a/doc/fix_qeq_reax.txt
+++ b/doc/fix_qeq_reax.txt
@@ -1,93 +1,93 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix qeq/reax command :h3
[Syntax:]
fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params :pre
ID, group-ID are documented in "fix"_fix.html command
qeq/reax = style name of this fix command
Nevery = perform QEq every this many steps
cutlo,cuthi = lo and hi cutoff for Taper radius
tolerance = precision to which charges will be equilibrated
params = reax/c or a filename :ul
[Examples:]
fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq :pre
[Description:]
Perform the charge equilibration (QEq) method as described in "(Rappe
and Goddard, 1991)"_#Rappe_1991 and formulated in "(Nakano,
1997)"_#Nakano_1997. It is typically used in conjunction with the
ReaxFF force field model as implemented in the "pair_style
reax/c"_pair_reax_c.html command, but it can be used with any
potential in LAMMPS, so long as it defines and uses charges on each
atom. The "fix qeq/comb"_fix_qeq_comb.html command should be used to
perform charge equliibration with the "COMB potential"_pair_comb.html.
For more technical details about the charge equilibration performed by
fix qeq/reax, see the "(Aktulga)" paper.
The QEq method minimizes the electrostatic energy of the system by
adjusting the partial charge on individual atoms based on interactions
with their neighbors. It reqires some parameters for each atom type.
If the {params} setting above is the word "reax/c", then these are
extracted from the "pair_style reax/c"_pair_reax_c.html command and
the ReaxFF force field file it reads in. If a file name is specified
for {params}, then the parameters are taken from the specified file
and the file must contain one line for each atom type. The latter
form must be used when performing QeQ with a non-ReaxFF potential.
Each line should be formatted as follows:
itype chi eta gamma :pre
where {itype} is the atom type from 1 to Ntypes, {chi} denotes the
electronegativity in eV, {eta} denotes the self-Coulomb
potential in eV, and {gamma} denotes the valence orbital
exponent. Note that these 3 quantities are also in the ReaxFF
potential file, except that eta is defined here as twice the eta value
in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
of this fix are hard-coded to be A, eV, and electronic charge.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. No global scalar or vector or per-atom
quantities are stored by this fix for access by various "output
commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
This fix is invoked during "energy minimization"_minimize.html.
[Restrictions:]
-This fix is part of the "user-reaxc" package. It is only enabled if
+This fix is part of the USER-REAXC package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"pair_style reax/c"_pair_reax_c.html
[Default:] none
:line
:link(Rappe_1991)
[(Rappe)] Rappe and Goddard III, Journal of Physical Chemistry, 105,
3358-3363 (1991).
:link(Nakano_1997)
[(Nakano)] Nakano, Computer Physics Communications, 104, 59-69 (1997).
:link(Aktulga) [(Aktulga)] Aktulga, Fogarty, Pandit, Grama, Parallel
Computing, to appear (2011).
diff --git a/doc/fix_reax_bonds.html b/doc/fix_reax_bonds.html
index 0eb4c2691..09f23c1f1 100644
--- a/doc/fix_reax_bonds.html
+++ b/doc/fix_reax_bonds.html
@@ -1,64 +1,64 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix reax/bonds command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID reax/bonds Nevery filename
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>reax/bonds = style name of this fix command
<LI>Nevery = output interval in timesteps
<LI>filename = name of output file
</UL>
<P><B>Examples:</B>
</P>
<P>fix 1 all reax/bonds 100 bonds.tatb
</P>
<P><B>Description:</B>
</P>
<P>Write out the bond information computed by the ReaxFF potential
specified by <A HREF = "pair_reax.html">pair_style reax</A>. The bond information
is written to <I>filename</I> on timesteps that are multiples of <I>Nevery</I>,
including timestep 0.
</P>
<P>The format of the output file should be self-explantory.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. No parameter of this fix can
be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix requires that the <A HREF = "pair_reax.html">pair_style reax</A> be
-invoked. This fix is part of the "reax" package. It is only enabled
-if LAMMPS was built with that package, which also requires the REAX
+invoked. This fix is part of the REAX package. It is only enabled if
+LAMMPS was built with that package, which also requires the REAX
library be built and linked with LAMMPS. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_reax.html">pair_style reax</A>
</P>
<P><B>Default:</B>
</P>
<P>none
</P>
</HTML>
diff --git a/doc/fix_reax_bonds.txt b/doc/fix_reax_bonds.txt
index 1a42f8aa7..5ebb2a526 100644
--- a/doc/fix_reax_bonds.txt
+++ b/doc/fix_reax_bonds.txt
@@ -1,59 +1,59 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix reax/bonds command :h3
[Syntax:]
fix ID group-ID reax/bonds Nevery filename :pre
ID, group-ID are documented in "fix"_fix.html command
reax/bonds = style name of this fix command
Nevery = output interval in timesteps
filename = name of output file :ul
[Examples:]
fix 1 all reax/bonds 100 bonds.tatb
[Description:]
Write out the bond information computed by the ReaxFF potential
specified by "pair_style reax"_pair_reax.html. The bond information
is written to {filename} on timesteps that are multiples of {Nevery},
including timestep 0.
The format of the output file should be self-explantory.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix requires that the "pair_style reax"_pair_reax.html be
-invoked. This fix is part of the "reax" package. It is only enabled
-if LAMMPS was built with that package, which also requires the REAX
+invoked. This fix is part of the REAX package. It is only enabled if
+LAMMPS was built with that package, which also requires the REAX
library be built and linked with LAMMPS. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"pair_style reax"_pair_reax.html
[Default:]
none
diff --git a/doc/fix_setforce.html b/doc/fix_setforce.html
index e2194f2a4..6e713254d 100644
--- a/doc/fix_setforce.html
+++ b/doc/fix_setforce.html
@@ -1,129 +1,129 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix setforce command
</H3>
<H3>fix setforce/cuda command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID setforce fx fy fz keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>setforce = style name of this fix command
<LI>fx,fy,fz = force component values
<LI>any of fx,fy,fz can be a variable (see below)
<LI>zero or more keyword/value pairs may be appended to args
<LI>keyword = <I>region</I>
<PRE> <I>region</I> value = region-ID
region-ID = ID of region atoms must be in to have added force
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix freeze indenter setforce 0.0 0.0 0.0
fix 2 edge setforce NULL 0.0 0.0
fix 2 edge setforce NULL 0.0 v_oscillate
</PRE>
<P><B>Description:</B>
</P>
<P>Set each component of force on each atom in the group to the specified
values fx,fy,fz. This erases all previously computed forces on the
atom, though additional fixes could add new forces. This command can
be used to freeze certain atoms in the simulation by zeroing their
force, either for running dynamics or performing an energy
minimization. For dynamics, this assumes their initial velocity is
also zero.
</P>
<P>Any of the fx,fy,fz values can be specified as NULL which means do not
alter the force component in that dimension.
</P>
<P>Any of the 3 quantities defining the force components can be specified
as an equal-style or atom-style <A HREF = "variable.html">variable</A>, namely <I>fx</I>,
<I>fy</I>, <I>fz</I>. If the value is a variable, it should be specified as
v_name, where name is the variable name. In this case, the variable
will be evaluated each timestep, and its value used to determine the
force component.
</P>
<P>Equal-style variables can specify formulas with various mathematical
functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent force field.
</P>
<P>Atom-style variables can specify the same formulas as equal-style
variables but can also include per-atom values, such as atom
coordinates. Thus it is easy to specify a spatially-dependent force
field with optional time-dependence as well.
</P>
<P>If the <I>region</I> keyword is used, the atom must also be in the
specified geometric <A HREF = "region.html">region</A> in order to have force added
to it.
</P>
<HR>
<P>Styles with a <I>cuda</I> suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
<A HREF = "Section_accelerate.html">this section</A> of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix.
</P>
<P>This fix computes a global 3-vector of forces, which can be accessed
by various <A HREF = "Section_howto.html#howto_15">output commands</A>. This is the
total force on the group of atoms before the forces on individual
atoms are changed by the fix. The vector values calculated by this
fix are "extensive".
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command.
</P>
<P>The forces due to this fix are imposed during an energy minimization,
invoked by the <A HREF = "minimize.html">minimize</A> command, but you cannot set
forces to any value besides zero when performing a minimization. Use
the <A HREF = "fix_addforce.html">fix addforce</A> command if you want to apply a
non-zero force to atoms during a minimization.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_addforce.html">fix addforce</A>, <A HREF = "fix_aveforce.html">fix aveforce</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/fix_setforce.txt b/doc/fix_setforce.txt
index ee6f78341..90404f032 100644
--- a/doc/fix_setforce.txt
+++ b/doc/fix_setforce.txt
@@ -1,116 +1,116 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix setforce command :h3
fix setforce/cuda command :h3
[Syntax:]
fix ID group-ID setforce fx fy fz keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
setforce = style name of this fix command :l
fx,fy,fz = force component values :l
any of fx,fy,fz can be a variable (see below) :l
zero or more keyword/value pairs may be appended to args :l
keyword = {region} :l
{region} value = region-ID
region-ID = ID of region atoms must be in to have added force :pre
:ule
[Examples:]
fix freeze indenter setforce 0.0 0.0 0.0
fix 2 edge setforce NULL 0.0 0.0
fix 2 edge setforce NULL 0.0 v_oscillate :pre
[Description:]
Set each component of force on each atom in the group to the specified
values fx,fy,fz. This erases all previously computed forces on the
atom, though additional fixes could add new forces. This command can
be used to freeze certain atoms in the simulation by zeroing their
force, either for running dynamics or performing an energy
minimization. For dynamics, this assumes their initial velocity is
also zero.
Any of the fx,fy,fz values can be specified as NULL which means do not
alter the force component in that dimension.
Any of the 3 quantities defining the force components can be specified
as an equal-style or atom-style "variable"_variable.html, namely {fx},
{fy}, {fz}. If the value is a variable, it should be specified as
v_name, where name is the variable name. In this case, the variable
will be evaluated each timestep, and its value used to determine the
force component.
Equal-style variables can specify formulas with various mathematical
functions, and include "thermo_style"_thermo_style.html command
keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent force field.
Atom-style variables can specify the same formulas as equal-style
variables but can also include per-atom values, such as atom
coordinates. Thus it is easy to specify a spatially-dependent force
field with optional time-dependence as well.
If the {region} keyword is used, the atom must also be in the
specified geometric "region"_region.html in order to have force added
to it.
:line
Styles with a {cuda} suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
"this section"_Section_accelerate.html of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global 3-vector of forces, which can be accessed
by various "output commands"_Section_howto.html#howto_15. This is the
total force on the group of atoms before the forces on individual
atoms are changed by the fix. The vector values calculated by this
fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command, but you cannot set
forces to any value besides zero when performing a minimization. Use
the "fix addforce"_fix_addforce.html command if you want to apply a
non-zero force to atoms during a minimization.
[Restrictions:] none
[Related commands:]
"fix addforce"_fix_addforce.html, "fix aveforce"_fix_aveforce.html
[Default:] none
diff --git a/doc/fix_shake.html b/doc/fix_shake.html
index 80ec33ddf..a5aad277a 100644
--- a/doc/fix_shake.html
+++ b/doc/fix_shake.html
@@ -1,139 +1,139 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix shake command
</H3>
<H3>fix shake/cuda command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID shake tol iter N keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>shake = style name of this fix command
<LI>tol = accuracy tolerance of SHAKE solution
<LI>iter = max # of iterations in each SHAKE solution
<LI>N = print SHAKE statistics every this many timesteps (0 = never)
<LI>one or more keyword/value pairs are appended
<LI>keyword = <I>b</I> or <I>a</I> or <I>t</I> or <I>m</I>
<PRE> <I>b</I> values = one or more bond types
<I>a</I> values = one or more angle types
<I>t</I> values = one or more atom types
<I>m</I> value = one or more mass values
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 sub shake 0.0001 20 10 b 4 19 a 3 5 2
fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31
</PRE>
<P><B>Description:</B>
</P>
<P>Apply bond and angle constraints to specified bonds and angles in the
simulation. This typically enables a longer timestep.
</P>
<P>Each timestep the specified bonds and angles are reset to their
equilibrium lengths and angular values via the well-known SHAKE
algorithm. This is done by applying an additional constraint force so
that the new positions preserve the desired atom separations. The
equations for the additional force are solved via an iterative method
that typically converges to an accurate solution in a few iterations.
The desired tolerance (e.g. 1.0e-4 = 1 part in 10000) and maximum # of
iterations are specified as arguments. Setting the N argument will
print statistics to the screen and log file about regarding the
lengths of bonds and angles that are being constrained. Small delta
values mean SHAKE is doing a good job.
</P>
<P>In LAMMPS, only small clusters of atoms can be constrained. This is
so the constraint calculation for a cluster can be performed by a
single processor, to enable good parallel performance. A cluster is
defined as a central atom connected to others in the cluster by
constrained bonds. LAMMPS allows for the following kinds of clusters
to be constrained: one central atom bonded to 1 or 2 or 3 atoms, or
one central atom bonded to 2 others and the angle between the 3 atoms
also constrained. This means water molecules or CH2 or CH3 groups may
be constrained, but not all the C-C backbone bonds of a long polymer
chain.
</P>
<P>The <I>b</I> keyword lists bond types that will be constrained. The <I>t</I>
keyword lists atom types. All bonds connected to an atom of the
specified type will be constrained. The <I>m</I> keyword lists atom
masses. All bonds connected to atoms of the specified masses will be
constrained (within a fudge factor of MASSDELTA specified in
fix_shake.cpp). The <I>a</I> keyword lists angle types. If both bonds in
the angle are constrained then the angle will also be constrained if
its type is in the list.
</P>
<P>For all keywords, a particular bond is only constrained if both atoms
in the bond are in the group specified with the SHAKE fix.
</P>
<P>The degrees-of-freedom removed by SHAKE bonds and angles are accounted
for in temperature and pressure computations. Similarly, the SHAKE
contribution to the pressure of the system (virial) is also accounted
for.
</P>
<HR>
<P>Styles with a <I>cuda</I> suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
<A HREF = "Section_accelerate.html">this section</A> of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. No parameter of this fix can
be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>For computational efficiency, there can only be one shake fix defined
in a simulation.
</P>
<P>If you use a tolerance that is too large or a max-iteration count that
is too small, the constraints will not be enforced very strongly,
which can lead to poor energy conservation. You can test for this in
your system by running a constant NVE simulation with a particular set
of SHAKE parameters and monitoring the energy versus time.
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/fix_shake.txt b/doc/fix_shake.txt
index 320a02a15..dee3239bd 100644
--- a/doc/fix_shake.txt
+++ b/doc/fix_shake.txt
@@ -1,125 +1,125 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix shake command :h3
fix shake/cuda command :h3
[Syntax:]
fix ID group-ID shake tol iter N keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
shake = style name of this fix command :l
tol = accuracy tolerance of SHAKE solution :l
iter = max # of iterations in each SHAKE solution :l
N = print SHAKE statistics every this many timesteps (0 = never) :l
one or more keyword/value pairs are appended :l
keyword = {b} or {a} or {t} or {m} :l
{b} values = one or more bond types
{a} values = one or more angle types
{t} values = one or more atom types
{m} value = one or more mass values :pre
:ule
[Examples:]
fix 1 sub shake 0.0001 20 10 b 4 19 a 3 5 2
fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31 :pre
[Description:]
Apply bond and angle constraints to specified bonds and angles in the
simulation. This typically enables a longer timestep.
Each timestep the specified bonds and angles are reset to their
equilibrium lengths and angular values via the well-known SHAKE
algorithm. This is done by applying an additional constraint force so
that the new positions preserve the desired atom separations. The
equations for the additional force are solved via an iterative method
that typically converges to an accurate solution in a few iterations.
The desired tolerance (e.g. 1.0e-4 = 1 part in 10000) and maximum # of
iterations are specified as arguments. Setting the N argument will
print statistics to the screen and log file about regarding the
lengths of bonds and angles that are being constrained. Small delta
values mean SHAKE is doing a good job.
In LAMMPS, only small clusters of atoms can be constrained. This is
so the constraint calculation for a cluster can be performed by a
single processor, to enable good parallel performance. A cluster is
defined as a central atom connected to others in the cluster by
constrained bonds. LAMMPS allows for the following kinds of clusters
to be constrained: one central atom bonded to 1 or 2 or 3 atoms, or
one central atom bonded to 2 others and the angle between the 3 atoms
also constrained. This means water molecules or CH2 or CH3 groups may
be constrained, but not all the C-C backbone bonds of a long polymer
chain.
The {b} keyword lists bond types that will be constrained. The {t}
keyword lists atom types. All bonds connected to an atom of the
specified type will be constrained. The {m} keyword lists atom
masses. All bonds connected to atoms of the specified masses will be
constrained (within a fudge factor of MASSDELTA specified in
fix_shake.cpp). The {a} keyword lists angle types. If both bonds in
the angle are constrained then the angle will also be constrained if
its type is in the list.
For all keywords, a particular bond is only constrained if both atoms
in the bond are in the group specified with the SHAKE fix.
The degrees-of-freedom removed by SHAKE bonds and angles are accounted
for in temperature and pressure computations. Similarly, the SHAKE
contribution to the pressure of the system (virial) is also accounted
for.
:line
Styles with a {cuda} suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
"this section"_Section_accelerate.html of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
For computational efficiency, there can only be one shake fix defined
in a simulation.
If you use a tolerance that is too large or a max-iteration count that
is too small, the constraints will not be enforced very strongly,
which can lead to poor energy conservation. You can test for this in
your system by running a constant NVE simulation with a particular set
of SHAKE parameters and monitoring the energy versus time.
[Related commands:] none
[Default:] none
diff --git a/doc/fix_smd.html b/doc/fix_smd.html
index cf56e43fe..ececffdc4 100644
--- a/doc/fix_smd.html
+++ b/doc/fix_smd.html
@@ -1,162 +1,162 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix smd command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID smd type values keyword values
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>smd = style name of this fix command
<LI>mode = <I>cvel</I> or <I>cfor</I> to select constant velocity or constant force SMD
<PRE> <I>cvel</I> values = K vel
K = spring constant (force/distance units)
vel = velocity of pulling (distance/time units)
<I>cfor</I> values = force
force = pulling force (force units)
</PRE>
<LI>keyword = <I>tether</I> or <I>couple</I>
<PRE> <I>tether</I> values = x y z R0
x,y,z = point to which spring is tethered
R0 = distance of end of spring from tether point (distance units)
<I>couple</I> values = group-ID2 x y z R0
group-ID2 = 2nd group to couple to fix group with a spring
x,y,z = direction of spring, automatically computed with 'auto'
R0 = distance of end of spring (distance units)
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix pull cterm smd cvel 20.0 -0.00005 tether NULL NULL 100.0 0.0
fix pull cterm smd cvel 20.0 -0.0001 tether 25.0 25 25.0 0.0
fix stretch cterm smd cvel 20.0 0.0001 couple nterm auto auto auto 0.0
fix pull cterm smd cfor 5.0 tether 25.0 25.0 25.0 0.0
</PRE>
<P><B>Description:</B>
</P>
<P>This fix implements several options of steered MD (SMD) as reviewed in
<A HREF = "#Izrailev">(Izrailev)</A>, which allows to induce conformational changes
in systems and to compute the potential of mean force (PMF) along the
assumed reaction coordinate <A HREF = "#Park">(Park)</A> based on Jarzynski's
equality <A HREF = "#Jarzynski">(Jarzynski)</A>. This fix borrows a lot from <A HREF = "fix_spring.html">fix
spring</A> and <A HREF = "fix_setforce.html">fix setforce</A>.
</P>
<P>You can apply a moving spring force to a group of atoms (<I>tether</I>
style) or between two groups of atoms (<I>couple</I> style). The spring
can then be used in either constant velocity (<I>cvel</I>) mode or in
constant force (<I>cfor</I>) mode to induce transitions in your systems.
When running in <I>tether</I> style, you may need some way to fix some
other part of the system (e.g. via <A HREF = "fix_spring_self.html">fix
spring/self</A>)
</P>
<P>The <I>tether</I> style attaches a spring between a point at a distance of
R0 away from a fixed point <I>x,y,z</I> and the center of mass of the fix
group of atoms. A restoring force of magnitude K (R - R0) Mi / M is
applied to each atom in the group where <I>K</I> is the spring constant, Mi
is the mass of the atom, and M is the total mass of all atoms in the
group. Note that <I>K</I> thus represents the total force on the group of
atoms, not a per-atom force.
</P>
<P>In <I>cvel</I> mode the distance R is incremented or decremented
monotonously according to the pulling (or pushing) velocity.
In <I>cfor</I> mode a constant force is added and the actual distance
in direction of the spring is recorded.
</P>
<P>The <I>couple</I> style links two groups of atoms together. The first
group is the fix group; the second is specified by group-ID2. The
groups are coupled together by a spring that is at equilibrium when
the two groups are displaced by a vector in direction <I>x,y,z</I> with
respect to each other and at a distance R0 from that displacement.
Note that <I>x,y,z</I> only provides a direction and will be internally
normalized. But since it represents the <I>absolute</I> displacement of
group-ID2 relative to the fix group, (1,1,0) is a different spring
than (-1,-1,0). For each vector component, the displacement can be
described with the <I>auto</I> parameter. In this case the direction is
recomputed in every step, which can be useful for steering a local
process where the whole object undergoes some other change. When the
relative positions and distance between the two groups are not in
equilibrium, the same spring force described above is applied to atoms
in each of the two groups.
</P>
<P>For both the <I>tether</I> and <I>couple</I> styles, any of the x,y,z values can
be specified as NULL which means do not include that dimension in the
distance calculation or force application.
</P>
<P>For constant velocity pulling (<I>cvel</I> mode), the running integral
over the pulling force in direction of the spring is recorded and
can then later be used to compute the potential of mean force (PMF)
by averaging over multiple independent trajectories along the same
pulling path.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>The fix stores the direction of the spring, current pulling target
distance and the running PMF to <A HREF = "restart.html">binary restart files</A>.
See the <A HREF = "read_restart.html">read_restart</A> command for info on how to
re-specify a fix in an input script that reads a restart file, so that
the operation of the fix continues in an uninterrupted fashion.
</P>
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
fix.
</P>
<P>This fix computes a vector list of 7 quantities, which can be accessed
by various <A HREF = "Section_howto.html#howto_15">output commands</A>. The
quantities in the vector are in this order: the x-, y-, and
z-component of the pulling force, the total force in direction of the
pull, the equilibrium distance of the spring, the distance between the
two reference points, and finally the accumulated PMF (the sum of
pulling forces times displacement).
</P>
<P>The force is the total force on the group of atoms by the spring. In
the case of the <I>couple</I> style, it is the force on the fix group
(group-ID) or the negative of the force on the 2nd group (group-ID2).
The vector values calculated by this fix are "extensive".
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "user-misc" package. It is only enabled if
+<P>This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_drag.html">fix drag</A>, <A HREF = "fix_spring.html">fix spring</A>,
<A HREF = "fix_spring_self.html">fix spring/self</A>,
<A HREF = "fix_spring_rg.html">fix spring/rg</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Israilev"></A>
<P><B>(Izrailev)</B> Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar,
Wriggers, Schulten. Computational Molecular Dynamics: Challenges,
Methods, Ideas, volume 4 of Lecture Notes in Computational Science and
Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998.
</P>
<P><B>(Park)</B>
Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)
</P>
<P><B>(Jarzynski)</B>
Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)
</P>
</HTML>
diff --git a/doc/fix_smd.txt b/doc/fix_smd.txt
index f4ff6bd80..d58a24eb1 100644
--- a/doc/fix_smd.txt
+++ b/doc/fix_smd.txt
@@ -1,150 +1,150 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix smd command :h3
[Syntax:]
fix ID group-ID smd type values keyword values :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
smd = style name of this fix command :l
mode = {cvel} or {cfor} to select constant velocity or constant force SMD :l
{cvel} values = K vel
K = spring constant (force/distance units)
vel = velocity of pulling (distance/time units)
{cfor} values = force
force = pulling force (force units) :pre
keyword = {tether} or {couple} :l
{tether} values = x y z R0
x,y,z = point to which spring is tethered
R0 = distance of end of spring from tether point (distance units)
{couple} values = group-ID2 x y z R0
group-ID2 = 2nd group to couple to fix group with a spring
x,y,z = direction of spring, automatically computed with 'auto'
R0 = distance of end of spring (distance units) :pre
:ule
[Examples:]
fix pull cterm smd cvel 20.0 -0.00005 tether NULL NULL 100.0 0.0
fix pull cterm smd cvel 20.0 -0.0001 tether 25.0 25 25.0 0.0
fix stretch cterm smd cvel 20.0 0.0001 couple nterm auto auto auto 0.0
fix pull cterm smd cfor 5.0 tether 25.0 25.0 25.0 0.0 :pre
[Description:]
This fix implements several options of steered MD (SMD) as reviewed in
"(Izrailev)"_#Izrailev, which allows to induce conformational changes
in systems and to compute the potential of mean force (PMF) along the
assumed reaction coordinate "(Park)"_#Park based on Jarzynski's
equality "(Jarzynski)"_#Jarzynski. This fix borrows a lot from "fix
spring"_fix_spring.html and "fix setforce"_fix_setforce.html.
You can apply a moving spring force to a group of atoms ({tether}
style) or between two groups of atoms ({couple} style). The spring
can then be used in either constant velocity ({cvel}) mode or in
constant force ({cfor}) mode to induce transitions in your systems.
When running in {tether} style, you may need some way to fix some
other part of the system (e.g. via "fix
spring/self"_fix_spring_self.html)
The {tether} style attaches a spring between a point at a distance of
R0 away from a fixed point {x,y,z} and the center of mass of the fix
group of atoms. A restoring force of magnitude K (R - R0) Mi / M is
applied to each atom in the group where {K} is the spring constant, Mi
is the mass of the atom, and M is the total mass of all atoms in the
group. Note that {K} thus represents the total force on the group of
atoms, not a per-atom force.
In {cvel} mode the distance R is incremented or decremented
monotonously according to the pulling (or pushing) velocity.
In {cfor} mode a constant force is added and the actual distance
in direction of the spring is recorded.
The {couple} style links two groups of atoms together. The first
group is the fix group; the second is specified by group-ID2. The
groups are coupled together by a spring that is at equilibrium when
the two groups are displaced by a vector in direction {x,y,z} with
respect to each other and at a distance R0 from that displacement.
Note that {x,y,z} only provides a direction and will be internally
normalized. But since it represents the {absolute} displacement of
group-ID2 relative to the fix group, (1,1,0) is a different spring
than (-1,-1,0). For each vector component, the displacement can be
described with the {auto} parameter. In this case the direction is
recomputed in every step, which can be useful for steering a local
process where the whole object undergoes some other change. When the
relative positions and distance between the two groups are not in
equilibrium, the same spring force described above is applied to atoms
in each of the two groups.
For both the {tether} and {couple} styles, any of the x,y,z values can
be specified as NULL which means do not include that dimension in the
distance calculation or force application.
For constant velocity pulling ({cvel} mode), the running integral
over the pulling force in direction of the spring is recorded and
can then later be used to compute the potential of mean force (PMF)
by averaging over multiple independent trajectories along the same
pulling path.
[Restart, fix_modify, output, run start/stop, minimize info:]
The fix stores the direction of the spring, current pulling target
distance and the running PMF to "binary restart files"_restart.html.
See the "read_restart"_read_restart.html command for info on how to
re-specify a fix in an input script that reads a restart file, so that
the operation of the fix continues in an uninterrupted fashion.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix.
This fix computes a vector list of 7 quantities, which can be accessed
by various "output commands"_Section_howto.html#howto_15. The
quantities in the vector are in this order: the x-, y-, and
z-component of the pulling force, the total force in direction of the
pull, the equilibrium distance of the spring, the distance between the
two reference points, and finally the accumulated PMF (the sum of
pulling forces times displacement).
The force is the total force on the group of atoms by the spring. In
the case of the {couple} style, it is the force on the fix group
(group-ID) or the negative of the force on the 2nd group (group-ID2).
The vector values calculated by this fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
-This fix is part of the "user-misc" package. It is only enabled if
+This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"fix drag"_fix_drag.html, "fix spring"_fix_spring.html,
"fix spring/self"_fix_spring_self.html,
"fix spring/rg"_fix_spring_rg.html
[Default:] none
:line
:link(Israilev)
[(Izrailev)] Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar,
Wriggers, Schulten. Computational Molecular Dynamics: Challenges,
Methods, Ideas, volume 4 of Lecture Notes in Computational Science and
Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998.
[(Park)]
Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)
[(Jarzynski)]
Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)
diff --git a/doc/fix_srd.html b/doc/fix_srd.html
index a563e6561..df029d06f 100644
--- a/doc/fix_srd.html
+++ b/doc/fix_srd.html
@@ -1,378 +1,378 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix srd command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID srd N groupbig-ID Tsrd hgrid seed keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>srd = style name of this fix command
<LI>N = reset SRD particle velocities every this many timesteps
<LI>groupbig-ID = ID of group of large particles that SRDs interact with
<LI>Tsrd = temperature of SRD particles (temperature units)
<LI>hgrid = grid spacing for SRD grouping (distance units)
<LI>seed = random # seed (positive integer)
</UL>
<UL><LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>lamda</I> or <I>collision</I> or <I>overlap</I> or <I>inside</I> or <I>exact</I> or <I>radius</I> or <I>bounce</I> or <I>search</I> or <I>cubic</I> or <I>shift</I> or <I>stream</I>
<PRE> <I>lamda</I> value = mean free path of SRD particles (distance units)
<I>collision</I> value = <I>noslip</I> or <I>slip</I> = collision model
<I>overlap</I> value = <I>yes</I> or <I>no</I> = whether big particles may overlap
<I>inside</I> value = <I>error</I> or <I>warn</I> or <I>ignore</I> = how SRD particles which end up inside a big particle are treated
<I>exact</I> value = <I>yes</I> or <I>no</I>
<I>radius</I> value = rfactor = scale collision radius by this factor
<I>bounce</I> value = Nbounce = max # of collisions an SRD particle can undergo in one timestep
<I>search</I> value = sgrid = grid spacing for collision partner searching (distance units)
<I>cubic</I> values = style tolerance
style = <I>error</I> or <I>warn</I>
tolerance = fractional difference allowed (0 <= tol <= 1)
<I>shift</I> values = style seed
style = <I>no</I> or <I>yes</I> or <I>possible</I>
seed = random # seed (positive integer)
<I>stream</I> value = <I>yes</I> or <I>no</I> = whether or not streaming velocity is added for shear deformation
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 srd srd 10 big 1.0 0.25 482984
fix 1 srd srd 10 big 0.5 0.25 482984 collision slip search 0.5
</PRE>
<P><B>Description:</B>
</P>
<P>Treat a group of partilces as stochastic rotation dynamics (SRD)
particles that serve as a background solvent when interacting with big
(colloidal) particles in groupbig-ID. The SRD formalism is described
in <A HREF = "#Hecht">(Hecht)</A>. The key idea behind using SRD particles as a
cheap coarse-grained solvent is that SRD particles do not interact
with each other, but only with the solute particles, which in LAMMPS
can be spheroids, ellipsoids, or rigid bodies containing multiples
spherioids and ellipsoids. The collision and rotation properties of
the model imbue the SRD particles with fluid-like properties,
including an effective viscosity. Thus simulations with large solute
particles can be run more quickly, to measure solute propoerties like
diffusivity and viscosity in a background fluid. The usual LAMMPS
fixes for such simulations, such as <A HREF = "fix_deform.html">fix deform</A>, <A HREF = "fix_viscosity.html">fix
viscosity</A>, and <A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A>,
can be used in conjunction with the SRD model.
</P>
<P>For more details on how the SRD model is implemented in LAMMPS, <A HREF = "#Petersen">this
paper</A> describes the implementation and usage of pure SRD
fluids. <A HREF = "#Lechman">This paper</A>, which is nearly complete, describes
the implementation and usage of mixture systems (solute particles in
an SRD fluid). See the examples/srd directory for sample input
scripts using SRD particles in both settings.
</P>
<P>This fix does 2 things:
</P>
<P>(1) It advects the SRD particles, performing collisions between SRD
and big particles or walls every timestep, imparting force and torque
to the big particles. Collisions also change the position and
velocity of SRD particles.
</P>
<P>(2) It resets the velocity distribution of SRD particles via random
rotations every N timesteps.
</P>
<P>SRD particles have a mass, temperature, characteristic timestep
dt_SRD, and mean free path between collisions (lamda). The
fundamental equation relating these 4 quantities is
</P>
<PRE>lamda = dt_SRD * sqrt(Kboltz * Tsrd / mass)
</PRE>
<P>The mass of SRD particles is set by the <A HREF = "mass.html">mass</A> command
elsewhere in the input script. The SRD timestep dt_SRD is N times the
step dt defined by the <A HREF = "timestep.html">timestep</A> command. Big
particles move in the normal way via a time integration <A HREF = "fix.html">fix</A>
with a short timestep dt. SRD particles advect with a large timestep
dt_SRD >= dt.
</P>
<P>If the <I>lamda</I> keyword is not specified, the the SRD temperature
<I>Tsrd</I> is used in the above formula to compute lamda. If the <I>lamda</I>
keyword is specified, then the <I>Tsrd</I> setting is ignored and the above
equation is used to compute the SRD temperature.
</P>
<P>The characteristic length scale for the SRD fluid is set by <I>hgrid</I>
which is used to bin SRD particles for purposes of resetting their
velocities. Normally hgrid is set to be 1/4 of the big particle
diameter or smaller, to adequately resolve fluid properties around the
big particles.
</P>
<P>Lamda cannot be smaller than 0.6 * hgrid, else an error is generated
(unless the <I>shift</I> keyword is used, see below). The velocities of
SRD particles are bounded by Vmax, which is set so that an SRD
particle will not advect further than Dmax = 4*lamda in dt_SRD. This
means that roughly speaking, Dmax should not be larger than a big
particle diameter, else SRDs may pass thru big particles without
colliding. A warning is generated if this is the case.
</P>
<P>Collisions between SRD particles and big particles or walls are
modeled as a lightweight SRD point particle hitting a heavy big
particle of given diameter or a wall at a point on its surface and
bouncing off with a new velocity. The collision changes the momentum
of the SRD particle. It imparts a force and torque to the big
particle. It imparts a force to a wall. Static or moving SRD walls
are setup via the <A HREF = "fix_wall_srd.html">fix wall/srd</A> command. For the
remainder of this doc page, a collision of an SRD particle with a wall
can be viewed as a collision with a big particle of infinite radius
and mass.
</P>
<P>The <I>collision</I> keyword sets the style of collisions. The <I>slip</I>
style means that the tangential component of the SRD particle momentum
is preserved. Thus a force is imparted to a big particle, but no
torque. The normal component of the new SRD velocity is sampled from
a Gaussian distribution at temperature <I>Tsrd</I>.
</P>
<P>For the <I>noslip</I> style, both the normal and tangential components of
the new SRD velocity are sampled from a Gaussian distribution at
temperature <I>Tsrd</I>. Additionally, a new tangential direction for the
SRD velocity is chosen randomly. This collision style imparts torque
to a big particle. Thus a time integrator <A HREF = "fix.html">fix</A> that rotates
the big particles appropriately should be used.
</P>
<HR>
<P>The <I>overlap</I> keyword should be set to <I>yes</I> if two (or more) big
particles can ever overlap. This depends on the pair potential
interaction used for big-big interactions, or could be the case if
multiple big particles are held together as rigid bodies via the <A HREF = "fix_rigid.html">fix
rigid</A> command. If the <I>overlap</I> keyword is <I>no</I> and
big particles do in fact overlap, then SRD/big collisions can generate
an error if an SRD ends up inside two (or more) big particles at once.
How this error is treated is determined by the <I>inside</I> keyword.
Running with <I>overlap</I> set to <I>no</I> allows for faster collision
checking, so it should only be set to <I>yes</I> if needed.
</P>
<P>The <I>inside</I> keyword determines how a collision is treated if the
computation determines that the timestep started with the SRD particle
already inside a big particle. If the setting is <I>error</I> then this
generates an error message and LAMMPS stops. If the setting is <I>warn</I>
then this generates a warning message and the code continues. If the
setting is <I>ignore</I> then no message is generated. One of the output
quantities logged by the fix (see below) tallies the number of such
events, so it can be monitored. Note that once an SRD particle is
inside a big particle, it may remain there for several steps until it
drifts outside the big particle.
</P>
<P>The <I>exact</I> keyword determines how accurately collisions are computed.
A setting of <I>yes</I> computes the time and position of each collision as
SRD and big particles move together. A setting of <I>no</I> estimates the
position of each collision based on the end-of-timestep positions of
the SRD and big particle. If <I>overlap</I> is set to yes, the setting of
the <I>exact</I> keyword is ignored since time-accurate collisions are
needed.
</P>
<P>The <I>radius</I> keyword scales the effective size of big particles. If
big particles will overlap as they undergo dynamics, then this keyword
can be used to scale down their effective collision radius by an
amount <I>rfactor</I>, so that SRD particle will only collide with one big
particle at a time. For example, in a Lennard-Jones system at a
temperature of 1.0 (in reduced LJ units), the minimum separation
bewteen two big particles is as small as about 0.88 sigma. Thus an
<I>rfactor</I> value of 0.85 should prevent dual collisions.
</P>
<P>The <I>bounce</I> keyword can be used to limit the maximum number of
collisions an SRD particle undergoes in a single timestep as it
bounces between nearby big particles. Note that if the limit is
reached, the SRD can be left inside a big particle. A setting of 0 is
the same as no limit.
</P>
<HR>
<P>There are 2 kinds of bins created and maintained when running an SRD
simulation. The first are "SRD bins" which are used to bin SRD
particles and reset their velocities, as discussed above. The second
are "search bins" which are used to identify SRD/big particle
collisions.
</P>
<P>The <I>search</I> keyword can be used to choose a search bin size for
identifying SRD/big particle collisions. The default is to use the
<I>hgrid</I> parameter for SRD bins as the search bin size. Choosing a
smaller or large value may be more efficient, depending on the
problem. But, in a statistical sense, it should not change the
simulation results.
</P>
<P>The <I>cubic</I> keyword can be used to generate an error or warning when
the bin size chosen by LAMMPS creates SRD bins that are non-cubic or
different than the requested value of <I>hgrid</I> by a specified
<I>tolerance</I>. Note that using non-cubic SRD bins can lead to
undetermined behavior when rotating the velocities of SRD particles,
hence LAMMPS tries to protect you from this problem.
</P>
<P>LAMMPS attempts to set the SRD bin size to exactly <I>hgrid</I>. However,
there must be an integer number of bins in each dimension of the
simulation box. Thus the actual bin size will depend on the size and
shape of the overall simulation box. The actual bin size is printed
as part of the SRD output when a simulation begins.
</P>
<P>If the actual bin size in non-cubic by an amount exceeding the
tolerance, an error or warning is printed, depending on the style of
the <I>cubic</I> keyword. Likewise, if the actual bin size differs from
the requested <I>hgrid</I> value by an amount exceeding the tolerance, then
an error or warning is printed. The <I>tolerance</I> is a fractional
difference. E.g. a tolerance setting of 0.01 on the shape means that
if the ratio of any 2 bin dimensions exceeds (1 +/- tolerance) then an
error or warning is generated. Similarly, if the ratio of any bin
dimension with <I>hgrid</I> exceeds (1 +/- tolerance), then an error or
warning is generated.
</P>
<P>IMPORTANT NOTE: The fix srd command can be used with simluations the
size and/or shape of the simulation box changes. This can be due to
non-periodic boundary conditions or the use of fixes such as the <A HREF = "fix_deform.html">fix
deform</A> or <A HREF = "fix_wall_srd.html">fix wall/srd</A> commands
to impose a shear on an SRD fluid or an interaction with an external
wall. If the box size changes then the size of SRD bins must be
recalculated every reneighboring. This is not necessary if only the
box shape changes. This re-binning is always done so as to fit an
integer number of bins in the current box dimension, whether it be a
fixed, shrink-wrapped, or periodic boundary, as set by the
<A HREF = "boundary.html">boundary</A> command. If the box size or shape changes,
then the size of the search bins must be recalculated avery
reneighboring. Note that changing the SRD bin size may alter the
properties of the SRD fluid, such as its viscosity.
</P>
<P>The <I>shift</I> keyword determines whether the coordinates of SRD
particles are randomly shifted when binned for purposes of rotating
their velocities. When no shifting is performed, SRD particles are
binned and the velocity distribution of the set of SRD particles in
each bin is adjusted via a rotation operator. This is a statistically
valid operation if SRD particles move sufficiently far between
successive rotations. This is determined by their mean-free path
lamda. If lamda is less than 0.6 of the SRD bin size, then shifting
is required. A shift means that all of the SRD particles are shifted
by a vector whose coordinates are chosen randomly in the range [-1/2
bin size, 1/2 bin size]. Note that all particles are shifted by the
same vector. The specified random number seed is used to generate
these vectors. This operation sufficiently randomizes which SRD
particles are in the same bin, even if lamda is small.
</P>
<P>If the <I>shift</I> style is set to <I>no</I>, then no shifting is performed,
but bin data will be communicated if bins overlap processor
boundaries. An error will be generated if lamda < 0.6 of the SRD bin
size. If the <I>shift</I> style is set to <I>possible</I>, then shifting is
performed only if lamda < 0.6 of the SRD bin size. A warning is
generated to let you know this is occurring. If the <I>shift</I> style is
set to <I>yes</I> then shifting is performed regardless of the magnitude of
lamda.
</P>
<P>The shift seed is not used if the <I>shift</I> style is set to <I>no</I>, but
must still be specified.
</P>
<P>Note that shifting of SRD coordinates requires extra communication,
hence it should not normally be enabled unless required.
</P>
<P>The <I>stream</I> keyword should be used when SRD particles are used with
the <A HREF = "fix_deform.html">fix deform</A> command to perform a simulation
undergoing shear, e.g. to measure a viscosity. If the <I>stream</I> style
is set to <I>yes</I>, then the mean velocity of each bin of SRD particles
is set to the streaming velocity of the deforming box, each time SRD
velocities are reset, every N timesteps. If the <I>stream</I> style is set
to <I>no</I>, then the mean velocity is unchanged, which may mean that it
takes a long time for the SRD fluid to come to equilibrium with a
velocity profile that matches the simulation box deformation.
</P>
<HR>
<P>IMPORTANT NOTE: This fix is normally used for simulations with a huge
number of SRD particles relative to the number of big particles,
e.g. 100 to 1. In this scenario, computations that involve only big
particles (neighbor list creation, communication, time integration)
can slow down dramatically due to the large number of background SRD
particles.
</P>
<P>Three other input script commands will largely overcome this effect,
speeding up an SRD simulation by a significant amount. These are the
<A HREF = "atom_modify.html">atom_modify first</A>, <A HREF = "neigh_modify.html">neigh_modify
include</A>, and <A HREF = "communicate.html">communicate group</A>
commands. Each takes a group-ID as an argument, which in this case
should be the group-ID of the big solute particles.
</P>
<P>Additionally, when a <A HREF = "pair_style.html">pair_style</A> for big/big particle
interactions is specified, the <A HREF = "pair_coeff.html">pair_coeff</A> command
should be used to turn off big/SRD interactions, e.g. by setting their
epsilon or cutoff length to 0.0.
</P>
<P>The "delete_atoms overlap" command may be useful in setting up an SRD
simulation to insure there are no initial overlaps between big and SRD
particles.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix.
</P>
<P>This fix tabulates several SRD statistics which are stored in a vector
of length 12, which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. The vector values calculated
by this fix are "intensive", meaning they do not scale with the size
of the simulation. Technically, the first 8 do scale with the size of
the simulation, but treating them as intensive means they are not
scaled when printed as part of thermodyanmic output.
</P>
<P>These are the 12 quantities. All are values for the current timestep,
except the last three which are cummulative quantities since the
beginning of the run.
</P>
<UL><LI>(1) # of SRD/big collision checks performed
<LI>(2) # of SRDs which had a collision
<LI>(3) # of SRD/big colllisions (including multiple bounces)
<LI>(4) # of SRD particles inside a big particle
<LI>(5) # of SRD particles whose velocity was rescaled to be < Vmax
<LI>(6) # of bins for collision searching
<LI>(7) # of bins for SRD velocity rotation
<LI>(8) # of bins in which SRD temperature was computed
<LI>(9) SRD temperature
<LI>(10) # of SRD particles which have undergone max # of bounces
<LI>(11) max # of bounces any SRD particle has had in a single step
<LI>(12) # of reneighborings dues to SRD particles moving too far
</UL>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This command can only be used if LAMMPS was built with the "srd"
+<P>This command can only be used if LAMMPS was built with the SRD
package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_wall_srd.html">fix wall/srd</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are lamda inferred from Tsrd, collision = noslip,
overlap = no, inside = error, exact = yes, radius = 1.0, bounce = 0,
search = hgrid, cubic = error 0.01, shift = no, stream = yes.
</P>
<HR>
<A NAME = "Hecht"></A>
<P><B>(Hecht)</B> Hecht, Harting, Ihle, Herrmann, Phys Rev E, 72, 011408 (2005).
</P>
<A NAME = "Petersen"></A>
<P><B>(Petersen)</B> Petersen, Lechman, Plimpton, Grest, in' t Veld, Schunk, J
Chem Phys, 132, 174106 (2010).
</P>
<A NAME = "Lechman"></A>
<P><B>(Lechman)</B> Lechman, et al, in preparation (2010).
</P>
</HTML>
diff --git a/doc/fix_srd.txt b/doc/fix_srd.txt
index 12cd5332d..a45c21392 100644
--- a/doc/fix_srd.txt
+++ b/doc/fix_srd.txt
@@ -1,367 +1,367 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix srd command :h3
[Syntax:]
fix ID group-ID srd N groupbig-ID Tsrd hgrid seed keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command
srd = style name of this fix command
N = reset SRD particle velocities every this many timesteps
groupbig-ID = ID of group of large particles that SRDs interact with
Tsrd = temperature of SRD particles (temperature units)
hgrid = grid spacing for SRD grouping (distance units)
seed = random # seed (positive integer) :ul
zero or more keyword/value pairs may be appended :ulb,l
keyword = {lamda} or {collision} or {overlap} or {inside} or {exact} or {radius} or {bounce} or {search} or {cubic} or {shift} or {stream} :l
{lamda} value = mean free path of SRD particles (distance units)
{collision} value = {noslip} or {slip} = collision model
{overlap} value = {yes} or {no} = whether big particles may overlap
{inside} value = {error} or {warn} or {ignore} = how SRD particles which end up inside a big particle are treated
{exact} value = {yes} or {no}
{radius} value = rfactor = scale collision radius by this factor
{bounce} value = Nbounce = max # of collisions an SRD particle can undergo in one timestep
{search} value = sgrid = grid spacing for collision partner searching (distance units)
{cubic} values = style tolerance
style = {error} or {warn}
tolerance = fractional difference allowed (0 <= tol <= 1)
{shift} values = style seed
style = {no} or {yes} or {possible}
seed = random # seed (positive integer)
{stream} value = {yes} or {no} = whether or not streaming velocity is added for shear deformation :pre
:ule
[Examples:]
fix 1 srd srd 10 big 1.0 0.25 482984
fix 1 srd srd 10 big 0.5 0.25 482984 collision slip search 0.5 :pre
[Description:]
Treat a group of partilces as stochastic rotation dynamics (SRD)
particles that serve as a background solvent when interacting with big
(colloidal) particles in groupbig-ID. The SRD formalism is described
in "(Hecht)"_#Hecht. The key idea behind using SRD particles as a
cheap coarse-grained solvent is that SRD particles do not interact
with each other, but only with the solute particles, which in LAMMPS
can be spheroids, ellipsoids, or rigid bodies containing multiples
spherioids and ellipsoids. The collision and rotation properties of
the model imbue the SRD particles with fluid-like properties,
including an effective viscosity. Thus simulations with large solute
particles can be run more quickly, to measure solute propoerties like
diffusivity and viscosity in a background fluid. The usual LAMMPS
fixes for such simulations, such as "fix deform"_fix_deform.html, "fix
viscosity"_fix_viscosity.html, and "fix nvt/sllod"_fix_nvt_sllod.html,
can be used in conjunction with the SRD model.
For more details on how the SRD model is implemented in LAMMPS, "this
paper"_#Petersen describes the implementation and usage of pure SRD
fluids. "This paper"_#Lechman, which is nearly complete, describes
the implementation and usage of mixture systems (solute particles in
an SRD fluid). See the examples/srd directory for sample input
scripts using SRD particles in both settings.
This fix does 2 things:
(1) It advects the SRD particles, performing collisions between SRD
and big particles or walls every timestep, imparting force and torque
to the big particles. Collisions also change the position and
velocity of SRD particles.
(2) It resets the velocity distribution of SRD particles via random
rotations every N timesteps.
SRD particles have a mass, temperature, characteristic timestep
dt_SRD, and mean free path between collisions (lamda). The
fundamental equation relating these 4 quantities is
lamda = dt_SRD * sqrt(Kboltz * Tsrd / mass) :pre
The mass of SRD particles is set by the "mass"_mass.html command
elsewhere in the input script. The SRD timestep dt_SRD is N times the
step dt defined by the "timestep"_timestep.html command. Big
particles move in the normal way via a time integration "fix"_fix.html
with a short timestep dt. SRD particles advect with a large timestep
dt_SRD >= dt.
If the {lamda} keyword is not specified, the the SRD temperature
{Tsrd} is used in the above formula to compute lamda. If the {lamda}
keyword is specified, then the {Tsrd} setting is ignored and the above
equation is used to compute the SRD temperature.
The characteristic length scale for the SRD fluid is set by {hgrid}
which is used to bin SRD particles for purposes of resetting their
velocities. Normally hgrid is set to be 1/4 of the big particle
diameter or smaller, to adequately resolve fluid properties around the
big particles.
Lamda cannot be smaller than 0.6 * hgrid, else an error is generated
(unless the {shift} keyword is used, see below). The velocities of
SRD particles are bounded by Vmax, which is set so that an SRD
particle will not advect further than Dmax = 4*lamda in dt_SRD. This
means that roughly speaking, Dmax should not be larger than a big
particle diameter, else SRDs may pass thru big particles without
colliding. A warning is generated if this is the case.
Collisions between SRD particles and big particles or walls are
modeled as a lightweight SRD point particle hitting a heavy big
particle of given diameter or a wall at a point on its surface and
bouncing off with a new velocity. The collision changes the momentum
of the SRD particle. It imparts a force and torque to the big
particle. It imparts a force to a wall. Static or moving SRD walls
are setup via the "fix wall/srd"_fix_wall_srd.html command. For the
remainder of this doc page, a collision of an SRD particle with a wall
can be viewed as a collision with a big particle of infinite radius
and mass.
The {collision} keyword sets the style of collisions. The {slip}
style means that the tangential component of the SRD particle momentum
is preserved. Thus a force is imparted to a big particle, but no
torque. The normal component of the new SRD velocity is sampled from
a Gaussian distribution at temperature {Tsrd}.
For the {noslip} style, both the normal and tangential components of
the new SRD velocity are sampled from a Gaussian distribution at
temperature {Tsrd}. Additionally, a new tangential direction for the
SRD velocity is chosen randomly. This collision style imparts torque
to a big particle. Thus a time integrator "fix"_fix.html that rotates
the big particles appropriately should be used.
:line
The {overlap} keyword should be set to {yes} if two (or more) big
particles can ever overlap. This depends on the pair potential
interaction used for big-big interactions, or could be the case if
multiple big particles are held together as rigid bodies via the "fix
rigid"_fix_rigid.html command. If the {overlap} keyword is {no} and
big particles do in fact overlap, then SRD/big collisions can generate
an error if an SRD ends up inside two (or more) big particles at once.
How this error is treated is determined by the {inside} keyword.
Running with {overlap} set to {no} allows for faster collision
checking, so it should only be set to {yes} if needed.
The {inside} keyword determines how a collision is treated if the
computation determines that the timestep started with the SRD particle
already inside a big particle. If the setting is {error} then this
generates an error message and LAMMPS stops. If the setting is {warn}
then this generates a warning message and the code continues. If the
setting is {ignore} then no message is generated. One of the output
quantities logged by the fix (see below) tallies the number of such
events, so it can be monitored. Note that once an SRD particle is
inside a big particle, it may remain there for several steps until it
drifts outside the big particle.
The {exact} keyword determines how accurately collisions are computed.
A setting of {yes} computes the time and position of each collision as
SRD and big particles move together. A setting of {no} estimates the
position of each collision based on the end-of-timestep positions of
the SRD and big particle. If {overlap} is set to yes, the setting of
the {exact} keyword is ignored since time-accurate collisions are
needed.
The {radius} keyword scales the effective size of big particles. If
big particles will overlap as they undergo dynamics, then this keyword
can be used to scale down their effective collision radius by an
amount {rfactor}, so that SRD particle will only collide with one big
particle at a time. For example, in a Lennard-Jones system at a
temperature of 1.0 (in reduced LJ units), the minimum separation
bewteen two big particles is as small as about 0.88 sigma. Thus an
{rfactor} value of 0.85 should prevent dual collisions.
The {bounce} keyword can be used to limit the maximum number of
collisions an SRD particle undergoes in a single timestep as it
bounces between nearby big particles. Note that if the limit is
reached, the SRD can be left inside a big particle. A setting of 0 is
the same as no limit.
:line
There are 2 kinds of bins created and maintained when running an SRD
simulation. The first are "SRD bins" which are used to bin SRD
particles and reset their velocities, as discussed above. The second
are "search bins" which are used to identify SRD/big particle
collisions.
The {search} keyword can be used to choose a search bin size for
identifying SRD/big particle collisions. The default is to use the
{hgrid} parameter for SRD bins as the search bin size. Choosing a
smaller or large value may be more efficient, depending on the
problem. But, in a statistical sense, it should not change the
simulation results.
The {cubic} keyword can be used to generate an error or warning when
the bin size chosen by LAMMPS creates SRD bins that are non-cubic or
different than the requested value of {hgrid} by a specified
{tolerance}. Note that using non-cubic SRD bins can lead to
undetermined behavior when rotating the velocities of SRD particles,
hence LAMMPS tries to protect you from this problem.
LAMMPS attempts to set the SRD bin size to exactly {hgrid}. However,
there must be an integer number of bins in each dimension of the
simulation box. Thus the actual bin size will depend on the size and
shape of the overall simulation box. The actual bin size is printed
as part of the SRD output when a simulation begins.
If the actual bin size in non-cubic by an amount exceeding the
tolerance, an error or warning is printed, depending on the style of
the {cubic} keyword. Likewise, if the actual bin size differs from
the requested {hgrid} value by an amount exceeding the tolerance, then
an error or warning is printed. The {tolerance} is a fractional
difference. E.g. a tolerance setting of 0.01 on the shape means that
if the ratio of any 2 bin dimensions exceeds (1 +/- tolerance) then an
error or warning is generated. Similarly, if the ratio of any bin
dimension with {hgrid} exceeds (1 +/- tolerance), then an error or
warning is generated.
IMPORTANT NOTE: The fix srd command can be used with simluations the
size and/or shape of the simulation box changes. This can be due to
non-periodic boundary conditions or the use of fixes such as the "fix
deform"_fix_deform.html or "fix wall/srd"_fix_wall_srd.html commands
to impose a shear on an SRD fluid or an interaction with an external
wall. If the box size changes then the size of SRD bins must be
recalculated every reneighboring. This is not necessary if only the
box shape changes. This re-binning is always done so as to fit an
integer number of bins in the current box dimension, whether it be a
fixed, shrink-wrapped, or periodic boundary, as set by the
"boundary"_boundary.html command. If the box size or shape changes,
then the size of the search bins must be recalculated avery
reneighboring. Note that changing the SRD bin size may alter the
properties of the SRD fluid, such as its viscosity.
The {shift} keyword determines whether the coordinates of SRD
particles are randomly shifted when binned for purposes of rotating
their velocities. When no shifting is performed, SRD particles are
binned and the velocity distribution of the set of SRD particles in
each bin is adjusted via a rotation operator. This is a statistically
valid operation if SRD particles move sufficiently far between
successive rotations. This is determined by their mean-free path
lamda. If lamda is less than 0.6 of the SRD bin size, then shifting
is required. A shift means that all of the SRD particles are shifted
by a vector whose coordinates are chosen randomly in the range \[-1/2
bin size, 1/2 bin size\]. Note that all particles are shifted by the
same vector. The specified random number seed is used to generate
these vectors. This operation sufficiently randomizes which SRD
particles are in the same bin, even if lamda is small.
If the {shift} style is set to {no}, then no shifting is performed,
but bin data will be communicated if bins overlap processor
boundaries. An error will be generated if lamda < 0.6 of the SRD bin
size. If the {shift} style is set to {possible}, then shifting is
performed only if lamda < 0.6 of the SRD bin size. A warning is
generated to let you know this is occurring. If the {shift} style is
set to {yes} then shifting is performed regardless of the magnitude of
lamda.
The shift seed is not used if the {shift} style is set to {no}, but
must still be specified.
Note that shifting of SRD coordinates requires extra communication,
hence it should not normally be enabled unless required.
The {stream} keyword should be used when SRD particles are used with
the "fix deform"_fix_deform.html command to perform a simulation
undergoing shear, e.g. to measure a viscosity. If the {stream} style
is set to {yes}, then the mean velocity of each bin of SRD particles
is set to the streaming velocity of the deforming box, each time SRD
velocities are reset, every N timesteps. If the {stream} style is set
to {no}, then the mean velocity is unchanged, which may mean that it
takes a long time for the SRD fluid to come to equilibrium with a
velocity profile that matches the simulation box deformation.
:line
IMPORTANT NOTE: This fix is normally used for simulations with a huge
number of SRD particles relative to the number of big particles,
e.g. 100 to 1. In this scenario, computations that involve only big
particles (neighbor list creation, communication, time integration)
can slow down dramatically due to the large number of background SRD
particles.
Three other input script commands will largely overcome this effect,
speeding up an SRD simulation by a significant amount. These are the
"atom_modify first"_atom_modify.html, "neigh_modify
include"_neigh_modify.html, and "communicate group"_communicate.html
commands. Each takes a group-ID as an argument, which in this case
should be the group-ID of the big solute particles.
Additionally, when a "pair_style"_pair_style.html for big/big particle
interactions is specified, the "pair_coeff"_pair_coeff.html command
should be used to turn off big/SRD interactions, e.g. by setting their
epsilon or cutoff length to 0.0.
The "delete_atoms overlap" command may be useful in setting up an SRD
simulation to insure there are no initial overlaps between big and SRD
particles.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix tabulates several SRD statistics which are stored in a vector
of length 12, which can be accessed by various "output
commands"_Section_howto.html#howto_15. The vector values calculated
by this fix are "intensive", meaning they do not scale with the size
of the simulation. Technically, the first 8 do scale with the size of
the simulation, but treating them as intensive means they are not
scaled when printed as part of thermodyanmic output.
These are the 12 quantities. All are values for the current timestep,
except the last three which are cummulative quantities since the
beginning of the run.
(1) # of SRD/big collision checks performed
(2) # of SRDs which had a collision
(3) # of SRD/big colllisions (including multiple bounces)
(4) # of SRD particles inside a big particle
(5) # of SRD particles whose velocity was rescaled to be < Vmax
(6) # of bins for collision searching
(7) # of bins for SRD velocity rotation
(8) # of bins in which SRD temperature was computed
(9) SRD temperature
(10) # of SRD particles which have undergone max # of bounces
(11) max # of bounces any SRD particle has had in a single step
(12) # of reneighborings dues to SRD particles moving too far :ul
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
-This command can only be used if LAMMPS was built with the "srd"
+This command can only be used if LAMMPS was built with the SRD
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info on packages.
[Related commands:]
"fix wall/srd"_fix_wall_srd.html
[Default:]
The option defaults are lamda inferred from Tsrd, collision = noslip,
overlap = no, inside = error, exact = yes, radius = 1.0, bounce = 0,
search = hgrid, cubic = error 0.01, shift = no, stream = yes.
:line
:link(Hecht)
[(Hecht)] Hecht, Harting, Ihle, Herrmann, Phys Rev E, 72, 011408 (2005).
:link(Petersen)
[(Petersen)] Petersen, Lechman, Plimpton, Grest, in' t Veld, Schunk, J
Chem Phys, 132, 174106 (2010).
:link(Lechman)
[(Lechman)] Lechman, et al, in preparation (2010).
diff --git a/doc/fix_temp_berendsen.html b/doc/fix_temp_berendsen.html
index 70a8f7023..0762f66ee 100644
--- a/doc/fix_temp_berendsen.html
+++ b/doc/fix_temp_berendsen.html
@@ -1,166 +1,166 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix temp/berendsen command
</H3>
<H3>fix temp/berendsen/cuda command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID temp/berendsen Tstart Tstop Tdamp
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>temp/berendsen = style name of this fix command
<LI>Tstart,Tstop = desired temperature at start/end of run
<LI>Tdamp = temperature damping parameter (time units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all temp/berendsen 300.0 300.0 100.0
</PRE>
<P><B>Description:</B>
</P>
<P>Reset the temperature of a group of atoms by using a Berendsen
thermostat <A HREF = "#Berendsen">(Berendsen)</A>, which rescales their velocities
every timestep.
</P>
<P>The thermostat is applied to only the translational degrees of freedom
for the particles, which is an important consideration if extended
spherical or aspherical particles which have rotational degrees of
freedom are being thermostatted with this fix. The translational
degrees of freedom can also have a bias velocity removed from them
before thermostatting takes place; see the description below.
</P>
<P>The desired temperature at each timestep is a ramped value during the
run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I> parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
<A HREF = "units.html">units</A> command).
</P>
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nh.html">fix nvt</A> command which
performs Nose/Hoover thermostatting AND time integration, this fix
does NOT perform time integration. It only modifies velocities to
effect thermostatting. Thus you must use a separate time integration
fix, like <A HREF = "fix_nve.html">fix nve</A> to actually update the positions of
atoms using the modified velocities. Likewise, this fix should not
normally be used on atoms that also have their temperature controlled
by another fix - e.g. by <A HREF = "fix_nh.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix
langevin</A> commands.
</P>
<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
a discussion of different ways to compute temperature and perform
thermostatting.
</P>
<P>This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if this command had been
issued:
</P>
<PRE>compute fix-ID_temp group-ID temp
</PRE>
<P>See the <A HREF = "compute_temp.html">compute temp</A> command for details. Note
that the ID of the new compute is the fix-ID + underscore + "temp",
and the group for the new compute is the same as the fix group.
</P>
<P>Note that this is NOT the compute used by thermodynamic output (see
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> will have no
effect on this fix.
</P>
<P>Like other fixes that perform thermostatting, this fix can be used
with <A HREF = "compute.html">compute commands</A> that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual <A HREF = "compute.html">compute
commands</A> to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
</P>
<HR>
<P>Styles with a <I>cuda</I> suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
<A HREF = "Section_accelerate.html">this section</A> of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
fix. You can use it to assign a temperature <A HREF = "compute.html">compute</A>
you have defined to this fix which will be used in its thermostatting
procedure, as described above. For consistency, the group used by
this fix and by the compute should be the same.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change implied by a velocity rescaling to the
system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
<P>This fix computes a global scalar which can be accessed by various
<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
cummulative energy change due to this fix. The scalar value
calculated by this fix is "extensive".
</P>
<P>This fix can ramp its target temperature over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
<A HREF = "run.html">run</A> command for details of how to do this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, <A HREF = "fix_langevin.html">fix langevin</A>,
<A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "compute_temp.html">compute temp</A>,
<A HREF = "fix_press_berendsen.html">fix press/berendsen</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Berendsen"></A>
<P><B>(Berendsen)</B> Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
Phys, 81, 3684 (1984).
</P>
</HTML>
diff --git a/doc/fix_temp_berendsen.txt b/doc/fix_temp_berendsen.txt
index 5bcb03481..8dd962041 100644
--- a/doc/fix_temp_berendsen.txt
+++ b/doc/fix_temp_berendsen.txt
@@ -1,160 +1,160 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix temp/berendsen command :h3
fix temp/berendsen/cuda command :h3
[Syntax:]
fix ID group-ID temp/berendsen Tstart Tstop Tdamp :pre
ID, group-ID are documented in "fix"_fix.html command
temp/berendsen = style name of this fix command
Tstart,Tstop = desired temperature at start/end of run
Tdamp = temperature damping parameter (time units) :ul
[Examples:]
fix 1 all temp/berendsen 300.0 300.0 100.0 :pre
[Description:]
Reset the temperature of a group of atoms by using a Berendsen
thermostat "(Berendsen)"_#Berendsen, which rescales their velocities
every timestep.
The thermostat is applied to only the translational degrees of freedom
for the particles, which is an important consideration if extended
spherical or aspherical particles which have rotational degrees of
freedom are being thermostatted with this fix. The translational
degrees of freedom can also have a bias velocity removed from them
before thermostatting takes place; see the description below.
The desired temperature at each timestep is a ramped value during the
run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
"units"_units.html command).
IMPORTANT NOTE: Unlike the "fix nvt"_fix_nh.html command which
performs Nose/Hoover thermostatting AND time integration, this fix
does NOT perform time integration. It only modifies velocities to
effect thermostatting. Thus you must use a separate time integration
fix, like "fix nve"_fix_nve.html to actually update the positions of
atoms using the modified velocities. Likewise, this fix should not
normally be used on atoms that also have their temperature controlled
by another fix - e.g. by "fix nvt"_fix_nh.html or "fix
langevin"_fix_langevin.html commands.
See "this howto section"_Section_howto.html#howto_16 of the manual for
a discussion of different ways to compute temperature and perform
thermostatting.
This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if this command had been
issued:
compute fix-ID_temp group-ID temp :pre
See the "compute temp"_compute_temp.html command for details. Note
that the ID of the new compute is the fix-ID + underscore + "temp",
and the group for the new compute is the same as the fix group.
Note that this is NOT the compute used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
"compute_modify"_compute_modify.html command or print this temperature
during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} will have no
effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with "compute commands"_compute.html that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the "fix_modify"_fix_modify.html command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual "compute
commands"_compute.html to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
:line
Styles with a {cuda} suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
"this section"_Section_accelerate.html of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html.
The "fix_modify"_fix_modify.html {temp} option is supported by this
fix. You can use it to assign a temperature "compute"_compute.html
you have defined to this fix which will be used in its thermostatting
procedure, as described above. For consistency, the group used by
this fix and by the compute should be the same.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change implied by a velocity rescaling to the
system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
cummulative energy change due to this fix. The scalar value
calculated by this fix is "extensive".
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
"run"_run.html command for details of how to do this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] none
[Related commands:]
"fix nve"_fix_nve.html, "fix nvt"_fix_nh.html, "fix
temp/rescale"_fix_temp_rescale.html, "fix langevin"_fix_langevin.html,
"fix_modify"_fix_modify.html, "compute temp"_compute_temp.html,
"fix press/berendsen"_fix_press_berendsen.html
[Default:] none
:line
:link(Berendsen)
[(Berendsen)] Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
Phys, 81, 3684 (1984).
diff --git a/doc/fix_temp_rescale.html b/doc/fix_temp_rescale.html
index 5f1787131..81273ed4e 100644
--- a/doc/fix_temp_rescale.html
+++ b/doc/fix_temp_rescale.html
@@ -1,166 +1,166 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix temp/rescale command
</H3>
<H3>fix temp/rescale/cuda command
</H3>
<H3>fix temp/rescale/limit/cuda command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID temp/rescale N Tstart Tstop window fraction
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>temp/rescale = style name of this fix command
<LI>N = perform rescaling every N steps
<LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
<LI>window = only rescale if temperature is outside this window (temperature units)
<LI>fraction = rescale to target temperature by this fraction
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 3 flow temp/rescale 100 1.0 1.1 0.02 0.5
fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0
fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>Reset the temperature of a group of atoms by explicitly rescaling
their velocities.
</P>
<P>The rescaling is applied to only the translational degrees of freedom
for the particles, which is an important consideration if extended
spherical or aspherical particles which have rotational degrees of
freedom are being thermostatted with this fix. The translational
degrees of freedom can also have a bias velocity removed from them
before thermostatting takes place; see the description below.
</P>
<P>Rescaling is performed every N timesteps. The target temperature is a
ramped value between the <I>Tstart</I> and <I>Tstop</I> temperatures at the
beginning and end of the run.
</P>
<P>Rescaling is only performed if the difference between the current and
desired temperatures is greater than the <I>window</I> value. The amount
of rescaling that is applied is a <I>fraction</I> (from 0.0 to 1.0) of the
difference between the actual and desired temperature. E.g. if
<I>fraction</I> = 1.0, the temperature is reset to exactly the desired
value.
</P>
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nh.html">fix nvt</A> command which
performs Nose/Hoover thermostatting AND time integration, this fix
does NOT perform time integration. It only modifies velocities to
effect thermostatting. Thus you must use a separate time integration
fix, like <A HREF = "fix_nve.html">fix nve</A> to actually update the positions of
atoms using the modified velocities. Likewise, this fix should not
normally be used on atoms that also have their temperature controlled
by another fix - e.g. by <A HREF = "fix_nh.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix
langevin</A> commands.
</P>
<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
a discussion of different ways to compute temperature and perform
thermostatting.
</P>
<P>This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if one of this command had
been issued:
</P>
<PRE>compute fix-ID_temp group-ID temp
</PRE>
<P>See the <A HREF = "compute_temp.html">compute temp</A> for details. Note that the
ID of the new compute is the fix-ID + underscore + "temp", and the
group for the new compute is the same as the fix group.
</P>
<P>Note that this is NOT the compute used by thermodynamic output (see
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> will have no
effect on this fix.
</P>
<P>Like other fixes that perform thermostatting, this fix can be used
with <A HREF = "compute.html">compute commands</A> that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual <A HREF = "compute.html">compute
commands</A> to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
</P>
<HR>
<P>Styles with a <I>cuda</I> suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
<A HREF = "Section_accelerate.html">this section</A> of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
fix. You can use it to assign a temperature <A HREF = "compute.html">compute</A>
you have defined to this fix which will be used in its thermostatting
procedure, as described above. For consistency, the group used by
this fix and by the compute should be the same.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change implied by a velocity rescaling to the
system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
<P>This fix computes a global scalar which can be accessed by various
<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
cummulative energy change due to this fix. The scalar value
calculated by this fix is "extensive".
</P>
<P>This fix can ramp its target temperature over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
<A HREF = "run.html">run</A> command for details of how to do this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_langevin.html">fix langevin</A>, <A HREF = "fix_nh.html">fix nvt</A>,
<A HREF = "fix_modify.html">fix_modify</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/fix_temp_rescale.txt b/doc/fix_temp_rescale.txt
index 1db777f14..5fbe99e5b 100644
--- a/doc/fix_temp_rescale.txt
+++ b/doc/fix_temp_rescale.txt
@@ -1,159 +1,159 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix temp/rescale command :h3
fix temp/rescale/cuda command :h3
fix temp/rescale/limit/cuda command :h3
[Syntax:]
fix ID group-ID temp/rescale N Tstart Tstop window fraction :pre
ID, group-ID are documented in "fix"_fix.html command
temp/rescale = style name of this fix command
N = perform rescaling every N steps
Tstart,Tstop = desired temperature at start/end of run (temperature units)
window = only rescale if temperature is outside this window (temperature units)
fraction = rescale to target temperature by this fraction :ul
[Examples:]
fix 3 flow temp/rescale 100 1.0 1.1 0.02 0.5
fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0
fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0 :pre
[Description:]
Reset the temperature of a group of atoms by explicitly rescaling
their velocities.
The rescaling is applied to only the translational degrees of freedom
for the particles, which is an important consideration if extended
spherical or aspherical particles which have rotational degrees of
freedom are being thermostatted with this fix. The translational
degrees of freedom can also have a bias velocity removed from them
before thermostatting takes place; see the description below.
Rescaling is performed every N timesteps. The target temperature is a
ramped value between the {Tstart} and {Tstop} temperatures at the
beginning and end of the run.
Rescaling is only performed if the difference between the current and
desired temperatures is greater than the {window} value. The amount
of rescaling that is applied is a {fraction} (from 0.0 to 1.0) of the
difference between the actual and desired temperature. E.g. if
{fraction} = 1.0, the temperature is reset to exactly the desired
value.
IMPORTANT NOTE: Unlike the "fix nvt"_fix_nh.html command which
performs Nose/Hoover thermostatting AND time integration, this fix
does NOT perform time integration. It only modifies velocities to
effect thermostatting. Thus you must use a separate time integration
fix, like "fix nve"_fix_nve.html to actually update the positions of
atoms using the modified velocities. Likewise, this fix should not
normally be used on atoms that also have their temperature controlled
by another fix - e.g. by "fix nvt"_fix_nh.html or "fix
langevin"_fix_langevin.html commands.
See "this howto section"_Section_howto.html#howto_16 of the manual for
a discussion of different ways to compute temperature and perform
thermostatting.
This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if one of this command had
been issued:
compute fix-ID_temp group-ID temp :pre
See the "compute temp"_compute_temp.html for details. Note that the
ID of the new compute is the fix-ID + underscore + "temp", and the
group for the new compute is the same as the fix group.
Note that this is NOT the compute used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
"compute_modify"_compute_modify.html command or print this temperature
during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} will have no
effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with "compute commands"_compute.html that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the "fix_modify"_fix_modify.html command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual "compute
commands"_compute.html to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
:line
Styles with a {cuda} suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
"this section"_Section_accelerate.html of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html.
The "fix_modify"_fix_modify.html {temp} option is supported by this
fix. You can use it to assign a temperature "compute"_compute.html
you have defined to this fix which will be used in its thermostatting
procedure, as described above. For consistency, the group used by
this fix and by the compute should be the same.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change implied by a velocity rescaling to the
system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
cummulative energy change due to this fix. The scalar value
calculated by this fix is "extensive".
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
"run"_run.html command for details of how to do this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] none
[Related commands:]
"fix langevin"_fix_langevin.html, "fix nvt"_fix_nh.html,
"fix_modify"_fix_modify.html
[Default:] none
diff --git a/doc/fix_temp_rescale_eff.html b/doc/fix_temp_rescale_eff.html
index 24810091e..038e18193 100644
--- a/doc/fix_temp_rescale_eff.html
+++ b/doc/fix_temp_rescale_eff.html
@@ -1,81 +1,81 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix temp/rescale/eff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID temp/rescale/eff N Tstart Tstop window fraction
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>temp/rescale/eff = style name of this fix command
<LI>N = perform rescaling every N steps
<LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
<LI>window = only rescale if temperature is outside this window (temperature units)
<LI>fraction = rescale to target temperature by this fraction
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 3 flow temp/rescale/eff 10 1.0 100.0 0.02 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>Reset the temperature of a group of nuclei and electrons in the
<A HREF = "pair_eff.html">electron force field</A> model by explicitly rescaling
their velocities.
</P>
<P>The operation of this fix is exactly like that described by the <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A> command, except that the rescaling
is also applied to the radial electron velocity for electron
particles.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
fix. You can use it to assign a temperature <A HREF = "compute.html">compute</A>
you have defined to this fix which will be used in its thermostatting
procedure, as described above. For consistency, the group used by
this fix and by the compute should be the same.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change implied by a velocity rescaling to the
system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
<P>This fix computes a global scalar which can be accessed by various
<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
cummulative energy change due to this fix. The scalar value
calculated by this fix is "extensive".
</P>
<P>This fix can ramp its target temperature over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
<A HREF = "run.html">run</A> command for details of how to do this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "user-eff" package. It is only enabled if
+<P>This fix is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_langevin_eff.html">fix langevin/eff</A>, <A HREF = "fix_nh_eff.html">fix
nvt/eff</A>, <A HREF = "fix_modify.html">fix_modify</A>,
<A HREF = "fix_temp_rescale.html">fix_temp_rescale</A>,
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/fix_temp_rescale_eff.txt b/doc/fix_temp_rescale_eff.txt
index 184ff3a09..f96b40962 100644
--- a/doc/fix_temp_rescale_eff.txt
+++ b/doc/fix_temp_rescale_eff.txt
@@ -1,76 +1,76 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix temp/rescale/eff command :h3
[Syntax:]
fix ID group-ID temp/rescale/eff N Tstart Tstop window fraction :pre
ID, group-ID are documented in "fix"_fix.html command
temp/rescale/eff = style name of this fix command
N = perform rescaling every N steps
Tstart,Tstop = desired temperature at start/end of run (temperature units)
window = only rescale if temperature is outside this window (temperature units)
fraction = rescale to target temperature by this fraction :ul
[Examples:]
fix 3 flow temp/rescale/eff 10 1.0 100.0 0.02 1.0 :pre
[Description:]
Reset the temperature of a group of nuclei and electrons in the
"electron force field"_pair_eff.html model by explicitly rescaling
their velocities.
The operation of this fix is exactly like that described by the "fix
temp/rescale"_fix_temp_rescale.html command, except that the rescaling
is also applied to the radial electron velocity for electron
particles.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html.
The "fix_modify"_fix_modify.html {temp} option is supported by this
fix. You can use it to assign a temperature "compute"_compute.html
you have defined to this fix which will be used in its thermostatting
procedure, as described above. For consistency, the group used by
this fix and by the compute should be the same.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change implied by a velocity rescaling to the
system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
cummulative energy change due to this fix. The scalar value
calculated by this fix is "extensive".
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
"run"_run.html command for details of how to do this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
-This fix is part of the "user-eff" package. It is only enabled if
+This fix is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"fix langevin/eff"_fix_langevin_eff.html, "fix
nvt/eff"_fix_nh_eff.html, "fix_modify"_fix_modify.html,
"fix_temp_rescale"_fix_temp_rescale.html,
[Default:] none
diff --git a/doc/fix_viscous.html b/doc/fix_viscous.html
index 112301acf..fe03b9867 100644
--- a/doc/fix_viscous.html
+++ b/doc/fix_viscous.html
@@ -1,131 +1,131 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix viscous command
</H3>
<H3>fix viscous/cuda command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID viscous gamma keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>viscous = style name of this fix command
<LI>gamma = damping coefficient (force/velocity units)
<LI>zero or more keyword/value pairs may be appended
<PRE>keyword = <I>scale</I>
<I>scale</I> values = type ratio
type = atom type (1-N)
ratio = factor to scale the damping coefficient by
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 flow viscous 0.1
fix 1 damp viscous 0.5 scale 3 2.5
</PRE>
<P><B>Description:</B>
</P>
<P>Add a viscous damping force to atoms in the group that is proportional
to the velocity of the atom. The added force can be thought of as a
frictional interaction with implicit solvent, i.e. the no-slip Stokes
drag on a spherical particle. In granular simulations this can be
useful for draining the kinetic energy from the system in a controlled
fashion. If used without additional thermostatting (to add kinetic
energy to the system), it has the effect of slowly (or rapidly)
freezing the system; hence it can also be used as a simple energy
minimization technique.
</P>
<P>The damping force F is given by F = - gamma * velocity. The larger
the coefficient, the faster the kinetic energy is reduced. If the
optional keyword <I>scale</I> is used, gamma can scaled up or down by the
specified factor for atoms of that type. It can be used multiple
times to adjust gamma for several atom types.
</P>
<P>IMPORTANT NOTE: You should specify gamma in force/velocity units.
This is not the same as mass/time units, at least for some of the
LAMMPS <A HREF = "units.html">units</A> options like "real" or "metal" that are not
self-consistent.
</P>
<P>In a Brownian dynamics context, gamma = Kb T / D, where Kb =
Boltzmann's constant, T = temperature, and D = particle diffusion
coefficient. D can be written as Kb T / (3 pi eta d), where eta =
dynamic viscosity of the frictional fluid and d = diameter of
particle. This means gamma = 3 pi eta d, and thus is proportional to
the viscosity of the fluid and the particle diameter.
</P>
<P>In the current implementation, rather than have the user specify a
viscosity, gamma is specified directly in force/velocity units. If
needed, gamma can be adjusted for atoms of different sizes
(i.e. sigma) by using the <I>scale</I> keyword.
</P>
<P>Note that Brownian dynamics models also typically include a randomized
force term to thermostat the system at a chosen temperature. The <A HREF = "fix_langevin.html">fix
langevin</A> command does this. It has the same
viscous damping term as fix viscous and adds a random force to each
atom. Hence if using fix <I>langevin</I> you do not typically need to use
fix <I>viscous</I>. Also note that the gamma of fix viscous is related to
the damping parameter of <A HREF = "fix_langevin.html">fix langevin</A>, except that
the units of gamma are force/velocity and the units of damp are time,
so that it can more easily be used as a thermostat.
</P>
<HR>
<P>Styles with a <I>cuda</I> suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
<A HREF = "Section_accelerate.html">this section</A> of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+<P>These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. No parameter of this fix can
be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
</P>
<P>The forces due to this fix are imposed during an energy minimization,
invoked by the <A HREF = "minimize.html">minimize</A> command. This fix should only
be used with damped dynamics minimizers that allow for
non-conservative forces. See the <A HREF = "min_style.html">min_style</A> command
for details.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_langevin.html">fix langevin</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/fix_viscous.txt b/doc/fix_viscous.txt
index 49002a439..bfd26b726 100644
--- a/doc/fix_viscous.txt
+++ b/doc/fix_viscous.txt
@@ -1,120 +1,120 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix viscous command :h3
fix viscous/cuda command :h3
[Syntax:]
fix ID group-ID viscous gamma keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
viscous = style name of this fix command :l
gamma = damping coefficient (force/velocity units) :l
zero or more keyword/value pairs may be appended :l
keyword = {scale}
{scale} values = type ratio
type = atom type (1-N)
ratio = factor to scale the damping coefficient by :pre
:ule
[Examples:]
fix 1 flow viscous 0.1
fix 1 damp viscous 0.5 scale 3 2.5 :pre
[Description:]
Add a viscous damping force to atoms in the group that is proportional
to the velocity of the atom. The added force can be thought of as a
frictional interaction with implicit solvent, i.e. the no-slip Stokes
drag on a spherical particle. In granular simulations this can be
useful for draining the kinetic energy from the system in a controlled
fashion. If used without additional thermostatting (to add kinetic
energy to the system), it has the effect of slowly (or rapidly)
freezing the system; hence it can also be used as a simple energy
minimization technique.
The damping force F is given by F = - gamma * velocity. The larger
the coefficient, the faster the kinetic energy is reduced. If the
optional keyword {scale} is used, gamma can scaled up or down by the
specified factor for atoms of that type. It can be used multiple
times to adjust gamma for several atom types.
IMPORTANT NOTE: You should specify gamma in force/velocity units.
This is not the same as mass/time units, at least for some of the
LAMMPS "units"_units.html options like "real" or "metal" that are not
self-consistent.
In a Brownian dynamics context, gamma = Kb T / D, where Kb =
Boltzmann's constant, T = temperature, and D = particle diffusion
coefficient. D can be written as Kb T / (3 pi eta d), where eta =
dynamic viscosity of the frictional fluid and d = diameter of
particle. This means gamma = 3 pi eta d, and thus is proportional to
the viscosity of the fluid and the particle diameter.
In the current implementation, rather than have the user specify a
viscosity, gamma is specified directly in force/velocity units. If
needed, gamma can be adjusted for atoms of different sizes
(i.e. sigma) by using the {scale} keyword.
Note that Brownian dynamics models also typically include a randomized
force term to thermostat the system at a chosen temperature. The "fix
langevin"_fix_langevin.html command does this. It has the same
viscous damping term as fix viscous and adds a random force to each
atom. Hence if using fix {langevin} you do not typically need to use
fix {viscous}. Also note that the gamma of fix viscous is related to
the damping parameter of "fix langevin"_fix_langevin.html, except that
the units of gamma are force/velocity and the units of damp are time,
so that it can more easily be used as a thermostat.
:line
Styles with a {cuda} suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
"this section"_Section_accelerate.html of the manual. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda" package. They
-are only enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+These accelerated styles are part of the USER-CUDA package. They are
+only enabled if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command. This fix should only
be used with damped dynamics minimizers that allow for
non-conservative forces. See the "min_style"_min_style.html command
for details.
[Restrictions:] none
[Related commands:]
"fix langevin"_fix_langevin.html
[Default:] none
diff --git a/doc/fix_wall_gran.html b/doc/fix_wall_gran.html
index 5620f7fa0..cc8473392 100644
--- a/doc/fix_wall_gran.html
+++ b/doc/fix_wall_gran.html
@@ -1,176 +1,176 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix wall/gran command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID wall/gran Kn Kt gamma_n gamma_t xmu dampflag wallstyle args keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>wall/gran = style name of this fix command
<LI>Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
<LI>Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)
<LI>gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)
<LI>gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
<LI>xmu = static yield criterion (unitless fraction between 0.0 and 1.0)
<LI>dampflag = 0 or 1 if tangential damping force is excluded or included
<LI>wallstyle = <I>xplane</I> or <I>yplane</I> or <I>zplane</I> or <I>zcylinder</I>
<LI>args = list of arguments for a particular style
<PRE> <I>xplane</I> or <I>yplane</I> or <I>zplane</I> args = lo hi
lo,hi = position of lower and upper plane (distance units), either can be NULL)
<I>zcylinder</I> args = radius
radius = cylinder radius (distance units)
</PRE>
<LI>zero or more keyword/value pairs may be appended to args
<LI>keyword = <I>wiggle</I> or <I>shear</I>
<PRE> <I>wiggle</I> values = dim amplitude period
dim = <I>x</I> or <I>y</I> or <I>z</I>
amplitude = size of oscillation (distance units)
period = time of oscillation (time units)
<I>shear</I> values = dim vshear
dim = <I>x</I> or <I>y</I> or <I>z</I>
vshear = magnitude of shear velocity (velocity units)
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all wall/gran 200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0
fix 1 all wall/gran 200000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 NULL
fix 2 all wall/gran 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0
</PRE>
<P><B>Description:</B>
</P>
<P>Bound the simulation domain of a granular system with a frictional
wall. All particles in the group interact with the wall when they are
close enough to touch it.
</P>
<P>The first set of parameters (Kn, Kt, gamma_n, gamma_t, xmu, and
dampflag) have the same meaning as those specified with the
<A HREF = "pair_gran.html">pair_style granular</A> force fields. This means a NULL
can be used for either Kt or gamma_t as described on that page. If a
NULL is used for Kt, then a default value is used where Kt = 2/7 Kn.
If a NULL is used for gamma_t, then a default value is used where
gamma_t = 1/2 gamma_n.
</P>
<P>The nature of the wall/particle interactions are determined by which
pair_style is used in your input script: <I>hooke</I>, <I>hooke/history</I>, or
<I>hertz/history</I>. The equation for the force between the wall and
particles touching it is the same as the corresponding equation on the
<A HREF = "pair_gran.html">pair_style granular</A> doc page, in the limit of one of
the two particles going to infinite radius and mass (flat wall).
I.e. delta = radius - r = overlap of particle with wall, m_eff = mass
of particle, and sqrt(RiRj/Ri+Rj) becomes sqrt(radius of particle).
The units for Kn, Kt, gamma_n, and gamma_t are as described on that
doc page. The meaning of xmu and dampflag are also as described on
that page. Note that you can choose different values for these 6
wall/particle coefficients than for particle/particle interactions, if
you wish your wall to interact differently with the particles, e.g. if
the wall is a different material.
</P>
<P>IMPORTANT NOTE: As discussed on the doc page for <A HREF = "pair_gran.html">pair_style
granular</A>, versions of LAMMPS before 9Jan09 used a
different equation for Hertzian interactions. This means Hertizian
wall/particle interactions have also changed. They now include a
sqrt(radius) term which was not present before. Also the previous
versions used Kn and Kt from the pairwise interaction and hardwired
dampflag to 1, rather than letting them be specified directly. This
means you can set the values of the wall/particle coefficients
appropriately in the current code to reproduce the results of a
prevoius Hertzian monodisperse calculation. For example, for the
common case of a monodisperse system with particles of diameter 1, Kn,
Kt, gamma_n, and gamma_s should be set sqrt(2.0) larger than they were
previously.
</P>
<P>The <I>wallstyle</I> can be planar or cylindrical. The 3 planar options
specify a pair of walls in a dimension. Wall positions are given by
<I>lo</I> and <I>hi</I>. Either of the values can be specified as NULL if a
single wall is desired. For a <I>zcylinder</I> wallstyle, the cylinder's
axis is at x = y = 0.0, and the radius of the cylinder is specified.
</P>
<P>Optionally, the wall can be moving, if the <I>wiggle</I> or <I>shear</I>
keywords are appended. Both keywords cannot be used together.
</P>
<P>For the <I>wiggle</I> keyword, the wall oscillates sinusoidally, similar to
the oscillations of particles which can be specified by the
<A HREF = "fix_move.html">fix_move</A> command. This is useful in packing
simulations of granular particles. The arguments to the <I>wiggle</I>
keyword specify a dimension for the motion, as well as it's
<I>amplitude</I> and <I>period</I>. Note that if the dimension is in the plane
of the wall, this is effectively a shearing motion. If the dimension
is perpendicular to the wall, it is more of a shaking motion. A
<I>zcylinder</I> wall can only be wiggled in the z dimension.
</P>
<P>Each timestep, the position of a wiggled wall in the appropriate <I>dim</I>
is set according to this equation:
</P>
<PRE>position = coord + A - A cos (omega * delta)
</PRE>
<P>where <I>coord</I> is the specified initial position of the wall, <I>A</I> is
the <I>amplitude</I>, <I>omega</I> is 2 PI / <I>period</I>, and <I>delta</I> is the time
elapsed since the fix was specified. The velocity of the wall is set
to the derivative of this expression.
</P>
<P>For the <I>shear</I> keyword, the wall moves continuously in the specified
dimension with velocity <I>vshear</I>. The dimension must be tangential to
walls with a planar <I>wallstyle</I>, e.g. in the <I>y</I> or <I>z</I> directions for
an <I>xplane</I> wall. For <I>zcylinder</I> walls, a dimension of <I>z</I> means the
cylinder is moving in the z-direction along it's axis. A dimension of
<I>x</I> or <I>y</I> means the cylinder is spinning around the z-axis, either in
the clockwise direction for <I>vshear</I> > 0 or counter-clockwise for
<I>vshear</I> < 0. In this case, <I>vshear</I> is the tangential velocity of
the wall at whatever <I>radius</I> has been defined.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the shear friction state of atoms interacting with the
wall to <A HREF = "restart.html">binary restart files</A>, so that a simulation can
continue correctly if granular potentials with shear "history" effects
are being used. See the <A HREF = "read_restart.html">read_restart</A> command for
info on how to re-specify a fix in an input script that reads a
restart file, so that the operation of the fix continues in an
uninterrupted fashion.
</P>
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
access by various <A HREF = "Section_howto.html#howto_15">output commands</A>. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This fix is part of the "granular" package. It is only enabled if
+<P>This fix is part of the GRANULAR package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>Any dimension (xyz) that has a granular wall must be non-periodic.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_move.html">fix_move</A>, <A HREF = "pair_gran.html">pair_style granular</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/fix_wall_gran.txt b/doc/fix_wall_gran.txt
index f3bf272f0..f758a8364 100644
--- a/doc/fix_wall_gran.txt
+++ b/doc/fix_wall_gran.txt
@@ -1,157 +1,157 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix wall/gran command :h3
[Syntax:]
fix ID group-ID wall/gran Kn Kt gamma_n gamma_t xmu dampflag wallstyle args keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
wall/gran = style name of this fix command :l
Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) :l
Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) :l
gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) :l
gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) :l
xmu = static yield criterion (unitless fraction between 0.0 and 1.0) :l
dampflag = 0 or 1 if tangential damping force is excluded or included :l
wallstyle = {xplane} or {yplane} or {zplane} or {zcylinder} :l
args = list of arguments for a particular style :l
{xplane} or {yplane} or {zplane} args = lo hi
lo,hi = position of lower and upper plane (distance units), either can be NULL)
{zcylinder} args = radius
radius = cylinder radius (distance units) :pre
zero or more keyword/value pairs may be appended to args :l
keyword = {wiggle} or {shear} :l
{wiggle} values = dim amplitude period
dim = {x} or {y} or {z}
amplitude = size of oscillation (distance units)
period = time of oscillation (time units)
{shear} values = dim vshear
dim = {x} or {y} or {z}
vshear = magnitude of shear velocity (velocity units) :pre
:ule
[Examples:]
fix 1 all wall/gran 200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0
fix 1 all wall/gran 200000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 NULL
fix 2 all wall/gran 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0 :pre
[Description:]
Bound the simulation domain of a granular system with a frictional
wall. All particles in the group interact with the wall when they are
close enough to touch it.
The first set of parameters (Kn, Kt, gamma_n, gamma_t, xmu, and
dampflag) have the same meaning as those specified with the
"pair_style granular"_pair_gran.html force fields. This means a NULL
can be used for either Kt or gamma_t as described on that page. If a
NULL is used for Kt, then a default value is used where Kt = 2/7 Kn.
If a NULL is used for gamma_t, then a default value is used where
gamma_t = 1/2 gamma_n.
The nature of the wall/particle interactions are determined by which
pair_style is used in your input script: {hooke}, {hooke/history}, or
{hertz/history}. The equation for the force between the wall and
particles touching it is the same as the corresponding equation on the
"pair_style granular"_pair_gran.html doc page, in the limit of one of
the two particles going to infinite radius and mass (flat wall).
I.e. delta = radius - r = overlap of particle with wall, m_eff = mass
of particle, and sqrt(RiRj/Ri+Rj) becomes sqrt(radius of particle).
The units for Kn, Kt, gamma_n, and gamma_t are as described on that
doc page. The meaning of xmu and dampflag are also as described on
that page. Note that you can choose different values for these 6
wall/particle coefficients than for particle/particle interactions, if
you wish your wall to interact differently with the particles, e.g. if
the wall is a different material.
IMPORTANT NOTE: As discussed on the doc page for "pair_style
granular"_pair_gran.html, versions of LAMMPS before 9Jan09 used a
different equation for Hertzian interactions. This means Hertizian
wall/particle interactions have also changed. They now include a
sqrt(radius) term which was not present before. Also the previous
versions used Kn and Kt from the pairwise interaction and hardwired
dampflag to 1, rather than letting them be specified directly. This
means you can set the values of the wall/particle coefficients
appropriately in the current code to reproduce the results of a
prevoius Hertzian monodisperse calculation. For example, for the
common case of a monodisperse system with particles of diameter 1, Kn,
Kt, gamma_n, and gamma_s should be set sqrt(2.0) larger than they were
previously.
The {wallstyle} can be planar or cylindrical. The 3 planar options
specify a pair of walls in a dimension. Wall positions are given by
{lo} and {hi}. Either of the values can be specified as NULL if a
single wall is desired. For a {zcylinder} wallstyle, the cylinder's
axis is at x = y = 0.0, and the radius of the cylinder is specified.
Optionally, the wall can be moving, if the {wiggle} or {shear}
keywords are appended. Both keywords cannot be used together.
For the {wiggle} keyword, the wall oscillates sinusoidally, similar to
the oscillations of particles which can be specified by the
"fix_move"_fix_move.html command. This is useful in packing
simulations of granular particles. The arguments to the {wiggle}
keyword specify a dimension for the motion, as well as it's
{amplitude} and {period}. Note that if the dimension is in the plane
of the wall, this is effectively a shearing motion. If the dimension
is perpendicular to the wall, it is more of a shaking motion. A
{zcylinder} wall can only be wiggled in the z dimension.
Each timestep, the position of a wiggled wall in the appropriate {dim}
is set according to this equation:
position = coord + A - A cos (omega * delta) :pre
where {coord} is the specified initial position of the wall, {A} is
the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the time
elapsed since the fix was specified. The velocity of the wall is set
to the derivative of this expression.
For the {shear} keyword, the wall moves continuously in the specified
dimension with velocity {vshear}. The dimension must be tangential to
walls with a planar {wallstyle}, e.g. in the {y} or {z} directions for
an {xplane} wall. For {zcylinder} walls, a dimension of {z} means the
cylinder is moving in the z-direction along it's axis. A dimension of
{x} or {y} means the cylinder is spinning around the z-axis, either in
the clockwise direction for {vshear} > 0 or counter-clockwise for
{vshear} < 0. In this case, {vshear} is the tangential velocity of
the wall at whatever {radius} has been defined.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the shear friction state of atoms interacting with the
wall to "binary restart files"_restart.html, so that a simulation can
continue correctly if granular potentials with shear "history" effects
are being used. See the "read_restart"_read_restart.html command for
info on how to re-specify a fix in an input script that reads a
restart file, so that the operation of the fix continues in an
uninterrupted fashion.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
access by various "output commands"_Section_howto.html#howto_15. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
-This fix is part of the "granular" package. It is only enabled if
+This fix is part of the GRANULAR package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
Any dimension (xyz) that has a granular wall must be non-periodic.
[Related commands:]
"fix_move"_fix_move.html, "pair_style granular"_pair_gran.html
[Default:] none
diff --git a/doc/improper_class2.html b/doc/improper_class2.html
index 481ab8e3b..315163711 100644
--- a/doc/improper_class2.html
+++ b/doc/improper_class2.html
@@ -1,104 +1,104 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>improper_style class2 command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>improper_style class2
</PRE>
<P><B>Examples:</B>
</P>
<PRE>improper_style class2
improper_coeff 1 100.0 0
improper_coeff * aa 0.0 0.0 0.0 115.06 130.01 115.06
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>class2</I> improper style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/improper_class2.jpg">
</CENTER>
<P>where Ei is the improper term and Eaa is an angle-angle term. The 3 X
terms in Ei are an average over 3 out-of-plane angles.
</P>
<P>The 4 atoms in an improper quadruplet (listed in the data file read by
the <A HREF = "read_data.html">read_data</A> command) are ordered I,J,K,L. X_IJKL
refers to the angle between the plane of I,J,K and the plane of J,K,L,
and the bond JK lies in both planes. Similarly for X_KJLI and X_LJIK.
Note that atom J appears in the common bonds (JI, JK, JL) of all 3 X
terms. Thus J (the 2nd atom in the quadruplet) is the atom of
symmetry in the 3 X angles.
</P>
<P>The subscripts on the various theta's refer to different combinations
of 3 atoms (I,J,K,L) used to form a particular angle. E.g. Theta_IJL
is the angle formed by atoms I,J,L with J in the middle. Theta1,
theta2, theta3 are the equilibrium positions of those angles. Again,
atom J (the 2nd atom in the quadruplet) is the atom of symmetry in the
theta angles, since it is always the center atom.
</P>
<P>Since atom J is the atom of symmetry, normally the bonds J-I, J-K, J-L
would exist for an improper to be defined between the 4 atoms, but
this is not required.
</P>
<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
</P>
<P>Coefficients for the Ei and Eaa formulas must be defined for each
improper type via the <A HREF = "improper_coeff.html">improper_coeff</A> command as
in the example above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands.
</P>
<P>These are the 2 coefficients for the Ei formula:
</P>
<UL><LI>K (energy/radian^2)
<LI>X0 (degrees)
</UL>
<P>X0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
</P>
<P>For the Eaa formula, each line in a
<A HREF = "improper_coeff.html">improper_coeff</A> command in the input script lists
7 coefficients, the first of which is "aa" to indicate they are
AngleAngle coefficients. In a data file, these coefficients should be
listed under a "AngleAngle Coeffs" heading and you must leave out the
"aa", i.e. only list 6 coefficients after the improper type.
</P>
<UL><LI>aa
<LI>M1 (energy/distance)
<LI>M2 (energy/distance)
<LI>M3 (energy/distance)
<LI>theta1 (degrees)
<LI>theta2 (degrees)
<LI>theta3 (degrees)
</UL>
<P>The theta values are specified in degrees, but LAMMPS converts them to
radians internally; hence the units of M are in energy/radian^2.
</P>
<P><B>Restrictions:</B>
</P>
<P>This improper style can only be used if LAMMPS was built with the
-"class2" package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+CLASS2 package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "improper_coeff.html">improper_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Sun"></A>
<P><B>(Sun)</B> Sun, J Phys Chem B 102, 7338-7364 (1998).
</P>
</HTML>
diff --git a/doc/improper_class2.txt b/doc/improper_class2.txt
index e44e69a4f..156d97fa8 100644
--- a/doc/improper_class2.txt
+++ b/doc/improper_class2.txt
@@ -1,98 +1,98 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
improper_style class2 command :h3
[Syntax:]
improper_style class2 :pre
[Examples:]
improper_style class2
improper_coeff 1 100.0 0
improper_coeff * aa 0.0 0.0 0.0 115.06 130.01 115.06 :pre
[Description:]
The {class2} improper style uses the potential
:c,image(Eqs/improper_class2.jpg)
where Ei is the improper term and Eaa is an angle-angle term. The 3 X
terms in Ei are an average over 3 out-of-plane angles.
The 4 atoms in an improper quadruplet (listed in the data file read by
the "read_data"_read_data.html command) are ordered I,J,K,L. X_IJKL
refers to the angle between the plane of I,J,K and the plane of J,K,L,
and the bond JK lies in both planes. Similarly for X_KJLI and X_LJIK.
Note that atom J appears in the common bonds (JI, JK, JL) of all 3 X
terms. Thus J (the 2nd atom in the quadruplet) is the atom of
symmetry in the 3 X angles.
The subscripts on the various theta's refer to different combinations
of 3 atoms (I,J,K,L) used to form a particular angle. E.g. Theta_IJL
is the angle formed by atoms I,J,L with J in the middle. Theta1,
theta2, theta3 are the equilibrium positions of those angles. Again,
atom J (the 2nd atom in the quadruplet) is the atom of symmetry in the
theta angles, since it is always the center atom.
Since atom J is the atom of symmetry, normally the bonds J-I, J-K, J-L
would exist for an improper to be defined between the 4 atoms, but
this is not required.
See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
Coefficients for the Ei and Eaa formulas must be defined for each
improper type via the "improper_coeff"_improper_coeff.html command as
in the example above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands.
These are the 2 coefficients for the Ei formula:
K (energy/radian^2)
X0 (degrees) :ul
X0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
For the Eaa formula, each line in a
"improper_coeff"_improper_coeff.html command in the input script lists
7 coefficients, the first of which is "aa" to indicate they are
AngleAngle coefficients. In a data file, these coefficients should be
listed under a "AngleAngle Coeffs" heading and you must leave out the
"aa", i.e. only list 6 coefficients after the improper type.
aa
M1 (energy/distance)
M2 (energy/distance)
M3 (energy/distance)
theta1 (degrees)
theta2 (degrees)
theta3 (degrees) :ul
The theta values are specified in degrees, but LAMMPS converts them to
radians internally; hence the units of M are in energy/radian^2.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-"class2" package. See the "Making LAMMPS"_Section_start.html#start_3
+CLASS2 package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info on packages.
[Related commands:]
"improper_coeff"_improper_coeff.html
[Default:] none
:line
:link(Sun)
[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998).
diff --git a/doc/improper_cvff.html b/doc/improper_cvff.html
index b31a51611..9c8a3e97a 100644
--- a/doc/improper_cvff.html
+++ b/doc/improper_cvff.html
@@ -1,68 +1,68 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>improper_style cvff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>improper_style cvff
</PRE>
<P><B>Examples:</B>
</P>
<PRE>improper_style cvff
improper_coeff 1 80.0 -1 4
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>cvff</I> improper style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/improper_cvff.jpg">
</CENTER>
<P>where phi is the Wilson out-of-plane angle.
</P>
<P>If the 4 atoms in an improper quadruplet (listed in the data file read
by the <A HREF = "read_data.html">read_data</A> command) are ordered I,J,K,L then
the Wilson angle is between the plane of I,J,K and the plane of J,K,L.
This is essentially a dihedral angle, which is why the formula for
this improper style is the same as for <A HREF = "dihedral_harmonic.html">dihedral_style
harmonic</A>. Alternatively, you can think of
atoms J,K,L as being in a plane, and atom I above the plane, and the
Wilson angle as a measure of how far out-of-plane I is with respect to
the other 3 atoms.
</P>
<P>Note that defining 4 atoms to interact in this way, does not mean that
bonds necessarily exist between I-J, J-K, or K-L, as they would in a
linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an
improper to be defined between the 4 atoms.
</P>
<P>The following coefficients must be defined for each improper type via
the <A HREF = "improper_coeff.html">improper_coeff</A> command as in the example
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands:
</P>
<UL><LI>K (energy)
<LI>d (+1 or -1)
<LI>n (0,1,2,3,4,6)
</UL>
<P><B>Restrictions:</B>
</P>
<P>This improper style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "improper_coeff.html">improper_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/improper_cvff.txt b/doc/improper_cvff.txt
index 83c9f2aab..79df38298 100644
--- a/doc/improper_cvff.txt
+++ b/doc/improper_cvff.txt
@@ -1,63 +1,63 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
improper_style cvff command :h3
[Syntax:]
improper_style cvff :pre
[Examples:]
improper_style cvff
improper_coeff 1 80.0 -1 4 :pre
[Description:]
The {cvff} improper style uses the potential
:c,image(Eqs/improper_cvff.jpg)
where phi is the Wilson out-of-plane angle.
If the 4 atoms in an improper quadruplet (listed in the data file read
by the "read_data"_read_data.html command) are ordered I,J,K,L then
the Wilson angle is between the plane of I,J,K and the plane of J,K,L.
This is essentially a dihedral angle, which is why the formula for
this improper style is the same as for "dihedral_style
harmonic"_dihedral_harmonic.html. Alternatively, you can think of
atoms J,K,L as being in a plane, and atom I above the plane, and the
Wilson angle as a measure of how far out-of-plane I is with respect to
the other 3 atoms.
Note that defining 4 atoms to interact in this way, does not mean that
bonds necessarily exist between I-J, J-K, or K-L, as they would in a
linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an
improper to be defined between the 4 atoms.
The following coefficients must be defined for each improper type via
the "improper_coeff"_improper_coeff.html command as in the example
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands:
K (energy)
d (+1 or -1)
n (0,1,2,3,4,6) :ul
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"improper_coeff"_improper_coeff.html
[Default:] none
diff --git a/doc/improper_harmonic.html b/doc/improper_harmonic.html
index e5747949d..9ba2e9cce 100644
--- a/doc/improper_harmonic.html
+++ b/doc/improper_harmonic.html
@@ -1,68 +1,68 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>improper_style harmonic command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>improper_style harmonic
</PRE>
<P><B>Examples:</B>
</P>
<PRE>improper_style harmonic
improper_coeff 1 100.0 0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>harmonic</I> improper style uses the potential
</P>
<CENTER><IMG SRC = "Eqs/improper_harmonic.jpg">
</CENTER>
<P>where X is the improper angle, X0 is its equilibrium value, and K is a
prefactor. Note that the usual 1/2 factor is included in K.
</P>
<P>If the 4 atoms in an improper quadruplet (listed in the data file read
by the <A HREF = "read_data.html">read_data</A> command) are ordered I,J,K,L then X
is the angle between the plane of I,J,K and the plane of J,K,L.
Alternatively, you can think of atoms J,K,L as being in a plane, and
atom I above the plane, and X as a measure of how far out-of-plane I
is with respect to the other 3 atoms.
</P>
<P>Note that defining 4 atoms to interact in this way, does not mean that
bonds necessarily exist between I-J, J-K, or K-L, as they would in a
linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an
improper to be defined between the 4 atoms.
</P>
<P>The following coefficients must be defined for each improper type via
the <A HREF = "improper_coeff.html">improper_coeff</A> command as in the example
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands:
</P>
<UL><LI>K (energy/radian^2)
<LI>X0 (degrees)
</UL>
<P>X0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
</P>
<P><B>Restrictions:</B>
</P>
<P>This improper style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "improper_coeff.html">improper_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/improper_harmonic.txt b/doc/improper_harmonic.txt
index 91451be7a..e57ad4130 100644
--- a/doc/improper_harmonic.txt
+++ b/doc/improper_harmonic.txt
@@ -1,63 +1,63 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
improper_style harmonic command :h3
[Syntax:]
improper_style harmonic :pre
[Examples:]
improper_style harmonic
improper_coeff 1 100.0 0 :pre
[Description:]
The {harmonic} improper style uses the potential
:c,image(Eqs/improper_harmonic.jpg)
where X is the improper angle, X0 is its equilibrium value, and K is a
prefactor. Note that the usual 1/2 factor is included in K.
If the 4 atoms in an improper quadruplet (listed in the data file read
by the "read_data"_read_data.html command) are ordered I,J,K,L then X
is the angle between the plane of I,J,K and the plane of J,K,L.
Alternatively, you can think of atoms J,K,L as being in a plane, and
atom I above the plane, and X as a measure of how far out-of-plane I
is with respect to the other 3 atoms.
Note that defining 4 atoms to interact in this way, does not mean that
bonds necessarily exist between I-J, J-K, or K-L, as they would in a
linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an
improper to be defined between the 4 atoms.
The following coefficients must be defined for each improper type via
the "improper_coeff"_improper_coeff.html command as in the example
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands:
K (energy/radian^2)
X0 (degrees) :ul
X0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"improper_coeff"_improper_coeff.html
[Default:] none
diff --git a/doc/improper_hybrid.html b/doc/improper_hybrid.html
index b67f99d5f..52b68f4bd 100644
--- a/doc/improper_hybrid.html
+++ b/doc/improper_hybrid.html
@@ -1,73 +1,73 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>improper_style hybrid command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>improper_style hybrid style1 style2 ...
</PRE>
<UL><LI>style1,style2 = list of one or more improper styles
</UL>
<P><B>Examples:</B>
</P>
<PRE>improper_style hybrid harmonic helix
improper_coeff 1 harmonic 120.0 30
improper_coeff 2 cvff 20.0 -1 2
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>hybrid</I> style enables the use of multiple improper styles in one
simulation. An improper style is assigned to each improper type. For
example, impropers in a polymer flow (of improper type 1) could be
computed with a <I>harmonic</I> potential and impropers in the wall
boundary (of improper type 2) could be computed with a <I>cvff</I>
potential. The assignment of improper type to style is made via the
<A HREF = "improper_coeff.html">improper_coeff</A> command or in the data file.
</P>
<P>In the improper_coeff command, the first coefficient sets the improper
style and the remaining coefficients are those appropriate to that
style. In the example above, the 2 improper_coeff commands would set
impropers of improper type 1 to be computed with a <I>harmonic</I>
potential with coefficients 120.0, 30 for K, X0. Improper type 2
would be computed with a <I>cvff</I> potential with coefficients 20.0, -1,
2 for K, d, n.
</P>
<P>If the improper <I>class2</I> potential is one of the hybrid styles, it
requires additional AngleAngle coefficients be specified in the data
file. These lines must also have an additional "class2" argument
added after the improper type. For improper types which are assigned
to other hybrid styles, use the style name (e.g. "harmonic")
appropriate to that style. The AngleAngle coeffs for that improper
type will then be ignored.
</P>
<P>An improper style of <I>none</I> can be specified as the 2nd argument to
the improper_coeff command, if you desire to turn off certain improper
types.
</P>
<P><B>Restrictions:</B>
</P>
<P>This improper style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P>Unlike other improper styles, the hybrid improper style does not store
improper coefficient info for individual sub-styles in a <A HREF = "restart.html">binary
restart files</A>. Thus when retarting a simulation from a
restart file, you need to re-specify improper_coeff commands.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "improper_coeff.html">improper_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/improper_hybrid.txt b/doc/improper_hybrid.txt
index 9af233e33..ee9dfc571 100644
--- a/doc/improper_hybrid.txt
+++ b/doc/improper_hybrid.txt
@@ -1,68 +1,68 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
improper_style hybrid command :h3
[Syntax:]
improper_style hybrid style1 style2 ... :pre
style1,style2 = list of one or more improper styles :ul
[Examples:]
improper_style hybrid harmonic helix
improper_coeff 1 harmonic 120.0 30
improper_coeff 2 cvff 20.0 -1 2 :pre
[Description:]
The {hybrid} style enables the use of multiple improper styles in one
simulation. An improper style is assigned to each improper type. For
example, impropers in a polymer flow (of improper type 1) could be
computed with a {harmonic} potential and impropers in the wall
boundary (of improper type 2) could be computed with a {cvff}
potential. The assignment of improper type to style is made via the
"improper_coeff"_improper_coeff.html command or in the data file.
In the improper_coeff command, the first coefficient sets the improper
style and the remaining coefficients are those appropriate to that
style. In the example above, the 2 improper_coeff commands would set
impropers of improper type 1 to be computed with a {harmonic}
potential with coefficients 120.0, 30 for K, X0. Improper type 2
would be computed with a {cvff} potential with coefficients 20.0, -1,
2 for K, d, n.
If the improper {class2} potential is one of the hybrid styles, it
requires additional AngleAngle coefficients be specified in the data
file. These lines must also have an additional "class2" argument
added after the improper type. For improper types which are assigned
to other hybrid styles, use the style name (e.g. "harmonic")
appropriate to that style. The AngleAngle coeffs for that improper
type will then be ignored.
An improper style of {none} can be specified as the 2nd argument to
the improper_coeff command, if you desire to turn off certain improper
types.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
Unlike other improper styles, the hybrid improper style does not store
improper coefficient info for individual sub-styles in a "binary
restart files"_restart.html. Thus when retarting a simulation from a
restart file, you need to re-specify improper_coeff commands.
[Related commands:]
"improper_coeff"_improper_coeff.html
[Default:] none
diff --git a/doc/improper_style.html b/doc/improper_style.html
index 3a61ee8ca..db288b7a8 100644
--- a/doc/improper_style.html
+++ b/doc/improper_style.html
@@ -1,98 +1,98 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>improper_style command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>improper_style style
</PRE>
<UL><LI>style = <I>none</I> or <I>hybrid</I> or <I>class2</I> or <I>cvff</I> or <I>harmonic</I>
</UL>
<P><B>Examples:</B>
</P>
<PRE>improper_style harmonic
improper_style cvff
improper_style hybrid cvff harmonic
</PRE>
<P><B>Description:</B>
</P>
<P>Set the formula(s) LAMMPS uses to compute improper interactions
between quadruplets of atoms, which remain in force for the duration
of the simulation. The list of improper quadruplets is read in by a
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A> command
from a data or restart file. Note that the ordering of the 4 atoms in
an improper quadruplet determines the the definition of the improper
angle used in the formula for each style. See the doc pages of
individual styles for details.
</P>
<P>Hybrid models where impropers are computed using different improper
potentials can be setup using the <I>hybrid</I> improper style.
</P>
<P>The coefficients associated with an improper style can be specified in
a data or restart file or via the <A HREF = "improper_coeff.html">improper_coeff</A>
command.
</P>
<P>All improper potentials store their coefficient data in binary restart
files which means improper_style and
<A HREF = "improper_coeff.html">improper_coeff</A> commands do not need to be
re-specified in an input script that restarts a simulation. See the
<A HREF = "read_restart.html">read_restart</A> command for details on how to do
this. The one exception is that improper_style <I>hybrid</I> only stores
the list of sub-styles in the restart file; improper coefficients need
to be re-specified.
</P>
<P>IMPORTANT NOTE: When both an improper and pair style is defined, the
<A HREF = "special_bonds.html">special_bonds</A> command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
exist between a group of 4 bonded atoms.
</P>
<HR>
<P>Here is an alphabetic list of improper styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated <A HREF = "improper_coeff.html">improper_coeff</A> command:
</P>
<UL><LI><A HREF = "improper_none.html">improper_style none</A> - turn off improper interactions
<LI><A HREF = "improper_hybrid.html">improper_style hybrid</A> - define multiple styles of improper interactions
</UL>
<UL><LI><A HREF = "improper_class2.html">improper_style class2</A> - COMPASS (class 2) improper
<LI><A HREF = "improper_cvff.html">improper_style cvff</A> - CVFF improper
<LI><A HREF = "improper_harmonic.html">improper_style harmonic</A> - harmonic improper
<LI><A HREF = "improper_umbrella.html">improper_style umbrella</A> - DREIDING improper
</UL>
<P>There are also additional improper styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the improper section of <A HREF = "Section_commands.html#cmd_5">this
page</A>.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>Improper styles can only be set for atom_style choices that allow
impropers to be defined.
</P>
-<P>Most improper styles are part of the "molecular" package. They are
-only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+<P>Most improper styles are part of the MOLECULAR package. They are only
+enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
The doc pages for individual improper potentials tell if it is part of
a package.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "improper_coeff.html">improper_coeff</A>
</P>
<P><B>Default:</B>
</P>
<PRE>improper_style none
</PRE>
</HTML>
diff --git a/doc/improper_style.txt b/doc/improper_style.txt
index da255312e..d63631171 100644
--- a/doc/improper_style.txt
+++ b/doc/improper_style.txt
@@ -1,93 +1,93 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
improper_style command :h3
[Syntax:]
improper_style style :pre
style = {none} or {hybrid} or {class2} or {cvff} or {harmonic} :ul
[Examples:]
improper_style harmonic
improper_style cvff
improper_style hybrid cvff harmonic :pre
[Description:]
Set the formula(s) LAMMPS uses to compute improper interactions
between quadruplets of atoms, which remain in force for the duration
of the simulation. The list of improper quadruplets is read in by a
"read_data"_read_data.html or "read_restart"_read_restart.html command
from a data or restart file. Note that the ordering of the 4 atoms in
an improper quadruplet determines the the definition of the improper
angle used in the formula for each style. See the doc pages of
individual styles for details.
Hybrid models where impropers are computed using different improper
potentials can be setup using the {hybrid} improper style.
The coefficients associated with an improper style can be specified in
a data or restart file or via the "improper_coeff"_improper_coeff.html
command.
All improper potentials store their coefficient data in binary restart
files which means improper_style and
"improper_coeff"_improper_coeff.html commands do not need to be
re-specified in an input script that restarts a simulation. See the
"read_restart"_read_restart.html command for details on how to do
this. The one exception is that improper_style {hybrid} only stores
the list of sub-styles in the restart file; improper coefficients need
to be re-specified.
IMPORTANT NOTE: When both an improper and pair style is defined, the
"special_bonds"_special_bonds.html command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
exist between a group of 4 bonded atoms.
:line
Here is an alphabetic list of improper styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "improper_coeff"_improper_coeff.html command:
"improper_style none"_improper_none.html - turn off improper interactions
"improper_style hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul
"improper_style class2"_improper_class2.html - COMPASS (class 2) improper
"improper_style cvff"_improper_cvff.html - CVFF improper
"improper_style harmonic"_improper_harmonic.html - harmonic improper
"improper_style umbrella"_improper_umbrella.html - DREIDING improper :ul
There are also additional improper styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the improper section of "this
page"_Section_commands.html#cmd_5.
:line
[Restrictions:]
Improper styles can only be set for atom_style choices that allow
impropers to be defined.
-Most improper styles are part of the "molecular" package. They are
-only enabled if LAMMPS was built with that package. See the "Making
+Most improper styles are part of the MOLECULAR package. They are only
+enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
The doc pages for individual improper potentials tell if it is part of
a package.
[Related commands:]
"improper_coeff"_improper_coeff.html
[Default:]
improper_style none :pre
diff --git a/doc/improper_umbrella.html b/doc/improper_umbrella.html
index 3ccfd10f1..2f10f5da9 100644
--- a/doc/improper_umbrella.html
+++ b/doc/improper_umbrella.html
@@ -1,70 +1,70 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>improper_style umbrella command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>improper_style umbrella
</PRE>
<P><B>Examples:</B>
</P>
<PRE>improper_style umbrella
improper_coeff 1 100.0 180.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>umbrella</I> improper style uses the following potential, which is
commonly referred to as a classic inversion and used in the
<A HREF = "Section_howto.html#howto_4">DREIDING</A> force field:
</P>
<CENTER><IMG SRC = "Eqs/improper_umbrella.jpg">
</CENTER>
<P>where K is the force constant and omega is the angle between the IL
axis and the IJK plane:
</P>
<CENTER><IMG SRC = "Eqs/umbrella.jpg">
</CENTER>
<P>If omega0 = 0 the potential term has a minimum for the planar
structure. Otherwise it has two minima at +/- omega0, with a barrier
in between.
</P>
<P>See <A HREF = "#Mayo">(Mayo)</A> for a description of the DREIDING force field.
</P>
<P>The following coefficients must be defined for each improper type via
the <A HREF = "improper_coeff.html">improper_coeff</A> command as in the example
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands:
</P>
<UL><LI>K (energy)
<LI>omega0 (degrees)
</UL>
<P><B>Restrictions:</B>
</P>
<P>This improper style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+MOLECULAR package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "improper_coeff.html">improper_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Mayo"></A>
<P><B>(Mayo)</B> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990),
</P>
</HTML>
diff --git a/doc/improper_umbrella.txt b/doc/improper_umbrella.txt
index 232c46f68..31a7729a6 100644
--- a/doc/improper_umbrella.txt
+++ b/doc/improper_umbrella.txt
@@ -1,64 +1,64 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
improper_style umbrella command :h3
[Syntax:]
improper_style umbrella :pre
[Examples:]
improper_style umbrella
improper_coeff 1 100.0 180.0 :pre
[Description:]
The {umbrella} improper style uses the following potential, which is
commonly referred to as a classic inversion and used in the
"DREIDING"_Section_howto.html#howto_4 force field:
:c,image(Eqs/improper_umbrella.jpg)
where K is the force constant and omega is the angle between the IL
axis and the IJK plane:
:c,image(Eqs/umbrella.jpg)
If omega0 = 0 the potential term has a minimum for the planar
structure. Otherwise it has two minima at +/- omega0, with a barrier
in between.
See "(Mayo)"_#Mayo for a description of the DREIDING force field.
The following coefficients must be defined for each improper type via
the "improper_coeff"_improper_coeff.html command as in the example
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands:
K (energy)
omega0 (degrees) :ul
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-"molecular" package (which it is by default). See the "Making
+MOLECULAR package (which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.
[Related commands:]
"improper_coeff"_improper_coeff.html
[Default:] none
:line
:link(Mayo)
[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990),
diff --git a/doc/kspace_style.html b/doc/kspace_style.html
index af71e1765..018a24053 100644
--- a/doc/kspace_style.html
+++ b/doc/kspace_style.html
@@ -1,189 +1,189 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>kspace_style command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>kspace_style style value
</PRE>
<UL><LI>style = <I>none</I> or <I>ewald</I> or <I>pppm</I> or <I>pppm/cg</I> or <I>pppm/tip4p</I> or <I>ewald/n</I> or <I>pppm/gpu</I>
<PRE> <I>none</I> value = none
<I>ewald</I> value = precision
precision = desired accuracy
<I>pppm</I> value = precision
precision = desired accuracy
<I>pppm/cg</I> value = precision (smallq)
precision = desired accuracy
smallq = cutoff for charges to be considered (optional) (charge units)
<I>pppm/tip4p</I> value = precision
precision = desired accuracy
<I>ewald/n</I> value = precision
precision = desired accuracy
<I>pppm/gpu</I> value = precision
precision = desired accuracy
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>kspace_style pppm 1.0e-4
kspace_style pppm/cg 1.0e-5 1.0e-6
kspace_style none
</PRE>
<P><B>Description:</B>
</P>
<P>Define a K-space solver for LAMMPS to use each timestep to compute
long-range Coulombic interactions or long-range 1/r^N interactions.
When such a solver is used in conjunction with an appropriate pair
style, the cutoff for Coulombic or other 1/r^N interactions is
effectively infinite; each charge in the system interacts with charges
in an infinite array of periodic images of the simulation domain.
</P>
<P>The <I>ewald</I> style performs a standard Ewald summation as described in
any solid-state physics text.
</P>
<P>The <I>pppm</I> style invokes a particle-particle particle-mesh solver
<A HREF = "#Hockney">(Hockney)</A> which maps atom charge to a 3d mesh, uses 3d FFTs
to solve Poisson's equation on the mesh, then interpolates electric
fields on the mesh points back to the atoms. It is closely related to
the particle-mesh Ewald technique (PME) <A HREF = "#Darden">(Darden)</A> used in
AMBER and CHARMM. The cost of traditional Ewald summation scales as
N^(3/2) where N is the number of atoms in the system. The PPPM solver
scales as Nlog(N) due to the FFTs, so it is almost always a faster
choice <A HREF = "#Pollock">(Pollock)</A>.
</P>
<P>The <I>pppm/cg</I> style is identical to the <I>pppm</I> style except that it
has an optimization for systems where most particles are uncharged.
The optional <I>smallq</I> argument defines the cutoff for the absolute
charge value which determines whether a particle is considered charged
or not. Its default value is 1.0e-5.
</P>
<P>The <I>pppm/tip4p</I> style is identical to the <I>pppm</I> style except that it
adds a charge at the massless 4th site in each TIP4P water molecule.
It should be used with <A HREF = "pair_style.html">pair styles</A> with a
<I>long/tip4p</I> in their style name.
</P>
<P>The <I>ewald/n</I> style augments <I>ewald</I> by adding long-range dispersion
sum capabilities for 1/r^N potentials and is useful for simulation of
interfaces <A HREF = "#Veld">(Veld)</A>. It also performs standard coulombic Ewald
summations, but in a more efficient manner than the <I>ewald</I> style.
The 1/r^N capability means that Lennard-Jones or Buckingham potentials
can be used with <I>ewald/n</I> without a cutoff, i.e. they become full
long-range potentials.
</P>
<P>Currently, only the <I>ewald/n</I> style can be used with non-orthogonal
(triclinic symmetry) simulation boxes.
</P>
<P>Note that the PPPM styles can be used with single-precision FFTs by
using the compiler switch -DFFT_SINGLE for the FFT_INC setting in your
lo-level Makefile. This setting also changes some of the PPPM
operations (e.g. mapping charge to mesh and interpolating electric
fields to particles) to be performed in single precision. This option
can speed-up long-range calulations, particularly in parallel or on
GPUs. The use of the -DFFT_SINGLE flag is discussed in <A HREF = "Section_start.html#start_2_4">this
section</A> of the manual.
</P>
<HR>
<P>When a kspace style is used, a pair style that includes the
short-range correction to the pairwise Coulombic or other 1/r^N forces
must also be selected. For Coulombic interactions, these styles are
ones that have a <I>coul/long</I> in their style name. For 1/r^6
dispersion forces in a Lennard-Jones or Buckingham potential, see the
<A HREF = "pair_lj_coul.html">pair_style lj/coul</A> or <A HREF = "pair_buck_coul.html">pair_style
buck/coul</A> commands.
</P>
<P>A precision value of 1.0e-4 means one part in 10000. This setting is
used in conjunction with the pairwise cutoff to determine the number
of K-space vectors for style <I>ewald</I> or the FFT grid size for style
<I>pppm</I>.
</P>
<P>See the <A HREF = "kspace_modify.html">kspace_modify</A> command for additional
options of the K-space solvers that can be set.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <A HREF = "Section_accelerate.html">this section</A> of
the manual. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
</P>
<P>More specifically, the <I>pppm/gpu</I> style performs charge assignment and
force interpolation calculations on the GPU. These processes are
performed either in single or double precision, depending on whether
the -DFFT_SINGLE setting was specified in your lo-level Makefile, as
discussed above. The FFTs themselves are still calculated on the CPU.
If <I>pppm/gpu</I> is used with a GPU-enabled pair style, part of the PPPM
calculation can be performed concurrently on the GPU while other
calculations for non-bonded and bonded force calculation are performed
on the CPU.
</P>
-<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+<P>These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<P><B>Restrictions:</B>
</P>
<P>A simulation must be 3d and periodic in all dimensions to use an Ewald
or PPPM solver. The only exception is if the slab option is set with
<A HREF = "kspace_modify.html">kspace_modify</A>, in which case the xy dimensions
must be periodic and the z dimension must be non-periodic.
</P>
-<P>Kspace styles are part of the "kspace" package. They are only enabled
+<P>Kspace styles are part of the KSPACE package. They are only enabled
if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
-<P>The <I>ewald/n</I> style is part of the "user-ewaldn" package. It is only
+<P>The <I>ewald/n</I> style is part of the USER-EWALDN package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>When using a long-range pairwise TIP4P potential, you must use kspace
style <I>pppm/tip4p</I> and vice versa.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "kspace_modify.html">kspace_modify</A>, <A HREF = "pair_lj.html">pair_style
lj/cut/coul/long</A>, <A HREF = "pair_charmm.html">pair_style
lj/charmm/coul/long</A>, <A HREF = "pair_lj_coul.html">pair_style
lj/coul</A>, <A HREF = "pair_buck.html">pair_style buck/coul/long</A>
</P>
<P><B>Default:</B>
</P>
<PRE>kspace_style none
</PRE>
<HR>
<A NAME = "Darden"></A>
<P><B>(Darden)</B> Darden, York, Pedersen, J Chem Phys, 98, 10089 (1993).
</P>
<A NAME = "Hockney"></A>
<P><B>(Hockney)</B> Hockney and Eastwood, Computer Simulation Using Particles,
Adam Hilger, NY (1989).
</P>
<A NAME = "Pollock"></A>
<P><B>(Pollock)</B> Pollock and Glosli, Comp Phys Comm, 95, 93 (1996).
</P>
<A NAME = "Veld"></A>
<P><B>(Veld)</B> In 't Veld, Ismail, Grest, J Chem Phys, in press (2007).
</P>
</HTML>
diff --git a/doc/kspace_style.txt b/doc/kspace_style.txt
index c5d887ac9..21992d07a 100644
--- a/doc/kspace_style.txt
+++ b/doc/kspace_style.txt
@@ -1,178 +1,178 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
kspace_style command :h3
[Syntax:]
kspace_style style value :pre
style = {none} or {ewald} or {pppm} or {pppm/cg} or {pppm/tip4p} or {ewald/n} or {pppm/gpu} :ulb,l
{none} value = none
{ewald} value = precision
precision = desired accuracy
{pppm} value = precision
precision = desired accuracy
{pppm/cg} value = precision (smallq)
precision = desired accuracy
smallq = cutoff for charges to be considered (optional) (charge units)
{pppm/tip4p} value = precision
precision = desired accuracy
{ewald/n} value = precision
precision = desired accuracy
{pppm/gpu} value = precision
precision = desired accuracy :pre
:ule
[Examples:]
kspace_style pppm 1.0e-4
kspace_style pppm/cg 1.0e-5 1.0e-6
kspace_style none :pre
[Description:]
Define a K-space solver for LAMMPS to use each timestep to compute
long-range Coulombic interactions or long-range 1/r^N interactions.
When such a solver is used in conjunction with an appropriate pair
style, the cutoff for Coulombic or other 1/r^N interactions is
effectively infinite; each charge in the system interacts with charges
in an infinite array of periodic images of the simulation domain.
The {ewald} style performs a standard Ewald summation as described in
any solid-state physics text.
The {pppm} style invokes a particle-particle particle-mesh solver
"(Hockney)"_#Hockney which maps atom charge to a 3d mesh, uses 3d FFTs
to solve Poisson's equation on the mesh, then interpolates electric
fields on the mesh points back to the atoms. It is closely related to
the particle-mesh Ewald technique (PME) "(Darden)"_#Darden used in
AMBER and CHARMM. The cost of traditional Ewald summation scales as
N^(3/2) where N is the number of atoms in the system. The PPPM solver
scales as Nlog(N) due to the FFTs, so it is almost always a faster
choice "(Pollock)"_#Pollock.
The {pppm/cg} style is identical to the {pppm} style except that it
has an optimization for systems where most particles are uncharged.
The optional {smallq} argument defines the cutoff for the absolute
charge value which determines whether a particle is considered charged
or not. Its default value is 1.0e-5.
The {pppm/tip4p} style is identical to the {pppm} style except that it
adds a charge at the massless 4th site in each TIP4P water molecule.
It should be used with "pair styles"_pair_style.html with a
{long/tip4p} in their style name.
The {ewald/n} style augments {ewald} by adding long-range dispersion
sum capabilities for 1/r^N potentials and is useful for simulation of
interfaces "(Veld)"_#Veld. It also performs standard coulombic Ewald
summations, but in a more efficient manner than the {ewald} style.
The 1/r^N capability means that Lennard-Jones or Buckingham potentials
can be used with {ewald/n} without a cutoff, i.e. they become full
long-range potentials.
Currently, only the {ewald/n} style can be used with non-orthogonal
(triclinic symmetry) simulation boxes.
Note that the PPPM styles can be used with single-precision FFTs by
using the compiler switch -DFFT_SINGLE for the FFT_INC setting in your
lo-level Makefile. This setting also changes some of the PPPM
operations (e.g. mapping charge to mesh and interpolating electric
fields to particles) to be performed in single precision. This option
can speed-up long-range calulations, particularly in parallel or on
GPUs. The use of the -DFFT_SINGLE flag is discussed in "this
section"_Section_start.html#start_2_4 of the manual.
:line
When a kspace style is used, a pair style that includes the
short-range correction to the pairwise Coulombic or other 1/r^N forces
must also be selected. For Coulombic interactions, these styles are
ones that have a {coul/long} in their style name. For 1/r^6
dispersion forces in a Lennard-Jones or Buckingham potential, see the
"pair_style lj/coul"_pair_lj_coul.html or "pair_style
buck/coul"_pair_buck_coul.html commands.
A precision value of 1.0e-4 means one part in 10000. This setting is
used in conjunction with the pairwise cutoff to determine the number
of K-space vectors for style {ewald} or the FFT grid size for style
{pppm}.
See the "kspace_modify"_kspace_modify.html command for additional
options of the K-space solvers that can be set.
:line
Styles with a {cuda}, {gpu}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "this section"_Section_accelerate.html of
the manual. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
More specifically, the {pppm/gpu} style performs charge assignment and
force interpolation calculations on the GPU. These processes are
performed either in single or double precision, depending on whether
the -DFFT_SINGLE setting was specified in your lo-level Makefile, as
discussed above. The FFTs themselves are still calculated on the CPU.
If {pppm/gpu} is used with a GPU-enabled pair style, part of the PPPM
calculation can be performed concurrently on the GPU while other
calculations for non-bonded and bonded force calculation are performed
on the CPU.
-These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
[Restrictions:]
A simulation must be 3d and periodic in all dimensions to use an Ewald
or PPPM solver. The only exception is if the slab option is set with
"kspace_modify"_kspace_modify.html, in which case the xy dimensions
must be periodic and the z dimension must be non-periodic.
-Kspace styles are part of the "kspace" package. They are only enabled
+Kspace styles are part of the KSPACE package. They are only enabled
if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
-The {ewald/n} style is part of the "user-ewaldn" package. It is only
+The {ewald/n} style is part of the USER-EWALDN package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
When using a long-range pairwise TIP4P potential, you must use kspace
style {pppm/tip4p} and vice versa.
[Related commands:]
"kspace_modify"_kspace_modify.html, "pair_style
lj/cut/coul/long"_pair_lj.html, "pair_style
lj/charmm/coul/long"_pair_charmm.html, "pair_style
lj/coul"_pair_lj_coul.html, "pair_style buck/coul/long"_pair_buck.html
[Default:]
kspace_style none :pre
:line
:link(Darden)
[(Darden)] Darden, York, Pedersen, J Chem Phys, 98, 10089 (1993).
:link(Hockney)
[(Hockney)] Hockney and Eastwood, Computer Simulation Using Particles,
Adam Hilger, NY (1989).
:link(Pollock)
[(Pollock)] Pollock and Glosli, Comp Phys Comm, 95, 93 (1996).
:link(Veld)
[(Veld)] In 't Veld, Ismail, Grest, J Chem Phys, in press (2007).
diff --git a/doc/neb.html b/doc/neb.html
index 75f02c4b4..25cc68b64 100644
--- a/doc/neb.html
+++ b/doc/neb.html
@@ -1,333 +1,333 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>neb command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>neb etol ftol N1 N2 Nevery filename
</PRE>
<UL><LI>etol = stopping tolerance for energy (energy units)
<LI>ftol = stopping tolerance for force (force units)
<LI>N1 = max # of iterations (timesteps) to run initial NEB
<LI>N2 = max # of iterations (timesteps) to run barrier-climbing NEB
<LI>Nevery = print replica energies and reaction coordinates every this many timesteps
<LI>filename = file specifying final atom coordinates on other side of barrier
</UL>
<P><B>Examples:</B>
</P>
<PRE>neb 0.1 0.0 1000 500 50 coords.final
neb 0.0 0.001 1000 500 50 coords.final
</PRE>
<P><B>Description:</B>
</P>
<P>Perform a nudged elastic band (NEB) calculation using multiple
replicas of a system. Two or more replicas must be used, two of which
are the end points of the transition path.
</P>
<P>NEB is a method for finding both the atomic configurations and height
of the energy barrier associated with a transition state, e.g. for an
atom to perform a diffusive hop from one energy basin to another in a
coordinated fashion with its neighbors. The implementation in LAMMPS
follows the discussion in these 3 papers: <A HREF = "#Henkelman1">(Henkelman1)</A>,
<A HREF = "#Henkelman2">(Henkelman2)</A>, and <A HREF = "#Nakano">(Nakano)</A>.
</P>
<P>Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
switch; see <A HREF = "Section_start.html#start_6">this section</A> of the manual.
Note that if you have MPI installed, you can run a multi-replica
simulation with more replicas (partitions) than you have physical
processors, e.g you can run a 10-replica simulation on one or two
processors. You will simply not get the performance speed-up you
would see with one or more physical processors per replica. See <A HREF = "Section_howto.html#howto_5">this
section</A> of the manual for further
discussion.
</P>
<P>NOTE: The current NEB implementation in LAMMPS restricts you to having
exactly one processor per replica.
</P>
<P>When a NEB calculation is performed, it is assumed that each replica
is running the same model, though LAMMPS does not check for this.
I.e. the simulation domain, the number of atoms, the interaction
potentials, and the starting configuration when the neb command is
issued should be the same for every replica.
</P>
<P>In a NEB calculation each atom in a replica is connected to the same
atom in adjacent replicas by springs, which induce inter-replica
forces. These forces are imposed by the <A HREF = "fix_neb.html">fix neb</A>
command, which must be used in conjunction with the neb command. The
group used to define the fix neb command specifies which atoms the
inter-replica springs are applied to. These are the NEB atoms.
Additional atoms can be present in your system, e.g. to provide a
background force field or simply to hold fixed during the NEB
procedure, but they will not be part of the barrier finding procedure.
</P>
<P>The "starting configuration" for NEB should be a state with the NEB
atoms (and all other atoms) having coordinates on one side of the
energy barrier. These coordinates will be assigned to the first
replica #1. The coordinates should be close to a local energy
minimum. A perfect energy minimum is not required, since NEB runs via
damped dynamics which will tend to drive the configuration of replica
#1 to a true energy minimum, but you will typically get better
convergence if the initial state is already at a minimum. For
example, for a system with a free surface, the surface should be fully
relaxed before attempting a NEB calculation.
</P>
<P>The final configuration is specified in the input <I>filename</I>, which is
formatted as described below. Only coordinates for NEB atoms or a
subset of them should be listed in the file; they represent the state
of the system on the other side of the barrier, at or near an energy
minimum. These coordinates will be assigned to the last replica #M.
The final coordinates of atoms not listed in <I>filename</I> are set equal
to their initial coordinates. Again, a perfect energy minimum is not
required for the final configuration, since the atoms in replica #M
will tend to move during the NEB procedure to the nearest energy
minimum. Also note that a final coordinate does not need to be
specified for a NEB atom if you expect it to only displace slightly
during the NEB procedure. For example, only the final coordinate of
the single atom diffusing into a vacancy need be specified if the
surrounding atoms will only relax slightly in the final configuration.
</P>
<P>The initial coordinates of all atoms (not just NEB atoms) in the
intermediate replicas #2,#3,...,#M-1 are set to values linearly
interpolated between the corresponding atoms in replicas #1 and #M.
</P>
<P>A NEB calculation has two stages, each of which is a minimization
procedure, performed via damped dynamics. To enable this, you must
first define an appropriate <A HREF = "min_style.html">min_style</A>, such as
<I>quickmin</I> or <I>fire</I>. The <I>cg</I>, <I>sd</I>, and <I>hftn</I> styles cannot be
used, since they perform iterative line searches in their inner loop,
which cannot be easily synchronized across multiple replicas.
</P>
<P>The minimizer tolerances for energy and force are set by <I>etol</I> and <I>ftol</I>,
the same as for
the <A HREF = "minimize.html">minimize</A> command.
</P>
<P>A non-zero <I>etol</I>
means that the NEB calculation will terminate if the energy criterion is met
by every replica. The energies being compared to
<I>etol</I> do not include any contribution from the inter-replica forces, since
these are non-conservative.
A non-zero <I>ftol</I>
means that the NEB calculation will terminate if the force criterion is met
by every replica. The forces being compared to
<I>ftol</I> include the inter-replica forces between an atom and its images
in adjacent replicas.
</P>
<P>The maximum number of iterations in each stage is set by <I>N1</I> and
<I>N2</I>. These are effectively timestep counts since each iteration of
damped dynamics is like a single timestep in a dynamics
<A HREF = "run.html">run</A>. During both stages, the potential energy of each
replica and its normalized distance along the reaction path (reaction
coordinate RD) will be printed to the screen and log file every
<I>Nevery</I> timesteps. The RD is 0 and 1 for the first and last replica.
For intermediate replicas, it is the cumulative distance (normalized
by the total cumulative distance) between adjacent replicas, where
"distance" is defined as the length of the 3N-vector of differences in
atomic coordinates, where N is the number of NEB atoms involved in the
transition. These outputs allow you to monitor NEB's progress in
finding a good energy barrier. <I>N1</I> and <I>N2</I> must both be multiples
of <I>Nevery</I>.
</P>
<P>In the first stage of NEB, the set of replicas should converge toward
the minimum energy path (MEP) of conformational states that transition
over the barrier. The MEP for a barrier is defined as a sequence of
3N-dimensional states that cross the barrier at its saddle point, each
of which has a potential energy gradient parallel to the MEP itself.
The replica states will also be roughly equally spaced along the MEP
due to the inter-replica spring force added by the <A HREF = "fix_neb.html">fix
neb</A> command.
</P>
<P>In the second stage of NEB, the replica with the highest energy
is selected and the inter-replica forces on it are converted to a
force that drives its atom coordinates to the top or saddle point of
the barrier, via the barrier-climbing calculation described in
<A HREF = "#Hinkelman2">(Henkelman2)</A>. As before, the other replicas rearrange
themselves along the MEP so as to be roughly equally spaced.
</P>
<P>When both stages are complete, if the NEB calculation was successful,
one of the replicas should be an atomic configuration at the top or
saddle point of the barrier, the potential energies for the set of
replicas should represent the energy profile of the barrier along the
MEP, and the configurations of the replicas should be a sequence of
configurations along the MEP.
</P>
<HR>
<P>A few other settings in your input script are required or advised to
perform a NEB calculation.
</P>
<P>An atom map must be defined which it is not by default for <A HREF = "atom_style.html">atom_style
atomic</A> problems. The <A HREF = "atom_modify.html">atom_modify
map</A> command can be used to do this.
</P>
<P>The "atom_modify sort 0 0.0" command should be used to turn off atom
sorting.
</P>
<P>NOTE: This sorting restriction will be removed in a future version of
NEB in LAMMPS.
</P>
<P>The minimizers in LAMMPS operate on all atoms in your system, even
non-NEB atoms, as defined above. To prevent non-NEB atoms from moving
during the minimization, you should use the <A HREF = "fix_setforce.html">fix
setforce</A> command to set the force on each of those
atoms to 0.0. This is not required, and may not even be desired in
some cases, but if those atoms move too far (e.g. because the initial
state of your system was not well-minimized), it can cause problems
for the NEB procedure.
</P>
<P>The damped dynamics <A HREF = "min_style.html">minimizers</A>, such as <I>quickmin</I>
and <I>fire</I>), adjust the position and velocity of the atoms via an
Euler integration step. Thus you must define an appropriate
<A HREF = "timestep.html">timestep</A> to use with NEB. Using the same timestep
that would be used for a dynamics <A HREF = "run.html">run</A> of your system is
advised.
</P>
<HR>
<P>The specified <I>filename</I> contains atom coordinates for the final
configuration. Only atoms with coordinates different than the initial
configuration need to be specified, i.e. those geometrically near the
barrier.
</P>
<P>The file can be ASCII text or a gzipped text file (detected by a .gz
suffix). The file should contain one line per atom, formatted
with the atom ID, followed by the final x,y,z coordinates:
</P>
<PRE>125 24.97311 1.69005 23.46956
126 1.94691 2.79640 1.92799
127 0.15906 3.46099 0.79121
...
</PRE>
<P>The lines can be listed in any order.
</P>
<HR>
<P>Four kinds of output can be generated during a NEB calculation: energy
barrier statistics, thermodynamic output by each replica, dump files,
and restart files.
</P>
<P>When running with multiple partitions (each of which is a replica in
this case), the print-out to the screen and master log.lammps file
contains a line of output, printed once every <I>Nevery</I> timesteps. It
contains the timestep, the maximum force per replica, the maximum
force per atom (in any replica), potential gradients in the initial,
final, and climbing replicas,
the forward and backward energy barriers,
the total reaction coordinate (RDT), and
the normalized reaction coordinate and potential energy of each replica.
</P>
<P>The "maximum force per replica" is
the two-norm of the 3N-length force vector for the atoms in each
replica, maximized across replicas, which is what the <I>ftol</I> setting
is checking against. In this case, N is all the atoms in each
replica. The "maximum force per atom" is the maximum force component
of any atom in any replica. The potential gradients are the two-norm
of the 3N-length force vector solely due to the interaction potential i.e.
without adding in inter-replica forces. Note that inter-replica forces
are zero in the initial and final replicas, and only affect
the direction in the climbing replica. For this reason, the "maximum
force per replica" is often equal to the potential gradient in the
climbing replica. In the first stage of NEB, there is no climbing
replica, and so the potential gradient in the highest energy replica
is reported, since this replica will become the climbing replica
in the second stage of NEB.
</P>
<P>The "reaction coordinate" (RD) for each
replica is the two-norm of the 3N-length vector of distances between
its atoms and the preceding replica's atoms, added to the RD of the
preceding replica. The RD of the first replica RD1 = 0.0;
the RD of the final replica RDN = RDT, the total reaction coordinate.
The normalized RDs are divided by RDT,
so that they form a monotonically increasing sequence
from zero to one. When computing RD, N only includes the atoms
being operated on by the fix neb command.
</P>
<P>The forward (reverse) energy barrier is the potential energy of the highest
replica minus the energy of the first (last) replica.
</P>
<P>When running on multiple partitions, LAMMPS produces additional log
files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a
NEB calculation, these contain the thermodynamic output for each
replica.
</P>
<P>If <A HREF = "dump.html">dump</A> commands in the input script define a filename
that includes a <I>universe</I> or <I>uloop</I> style <A HREF = "variable.html">variable</A>,
then one dump file (per dump command) will be created for each
replica. At the end of the NEB calculation, the final snapshot in
each file will contain the sequence of snapshots that transition the
system over the energy barrier. Earlier snapshots will show the
convergence of the replicas to the MEP.
</P>
<P>Likewise, <A HREF = "restart.html">restart</A> filenames can be specified with a
<I>universe</I> or <I>uloop</I> style <A HREF = "variable.html">variable</A>, to generate
restart files for each replica. These may be useful if the NEB
calculation fails to converge properly to the MEP, and you wish to
restart the calculation from an intermediate point with altered
parameters.
</P>
<P>There are 2 Python scripts provided in the tools/python directory,
neb_combine.py and neb_final.py, which are useful in analyzing output
from a NEB calculation. Assume a NEB simulation with M replicas, and
the NEB atoms labelled with a specific atom type.
</P>
<P>The neb_combine.py script extracts atom coords for the NEB atoms from
all M dump files and creates a single dump file where each snapshot
contains the NEB atoms from all the replicas and one copy of non-NEB
atoms from the first replica (presumed to be identical in other
replicas). This can be visualized/animated to see how the NEB atoms
relax as the NEB calculation proceeds.
</P>
<P>The neb_final.py script extracts the final snapshot from each of the M
dump files to create a single dump file with M snapshots. This can be
visualized to watch the system make its transition over the energy
barrier.
</P>
<P>To illustrate, here are images from the final snapshot produced by the
neb_combine.py script run on the dump files produced by the two
example input scripts in examples/neb. Click on them to see a larger
image.
</P>
<A HREF = "JPG/hop1.jpg"><IMG SRC = "JPG/hop1_small.jpg"></A>
<A HREF = "JPG/hop2.jpg"><IMG SRC = "JPG/hop2_small.jpg"></A>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>This command can only be used if LAMMPS was built with the "replica"
+<P>This command can only be used if LAMMPS was built with the REPLICA
package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "prd.html">prd</A>, <A HREF = "temper.html">temper</A>, <A HREF = "fix_langevin.html">fix
langevin</A>, <A HREF = "fix_viscous.html">fix viscous</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Henkelman1"></A>
<P><B>(Henkelman1)</B> Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
</P>
<A NAME = "Henkelman2"></A>
<P><B>(Henkelman2)</B> Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
9901-9904 (2000).
</P>
<A NAME = "Nakano"></A>
<P><B>(Nakano)</B> Nakano, Comp Phys Comm, 178, 280-289 (2008).
</P>
</HTML>
diff --git a/doc/neb.txt b/doc/neb.txt
index 993ecd0b0..1965f2334 100644
--- a/doc/neb.txt
+++ b/doc/neb.txt
@@ -1,324 +1,324 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
neb command :h3
[Syntax:]
neb etol ftol N1 N2 Nevery filename :pre
etol = stopping tolerance for energy (energy units)
ftol = stopping tolerance for force (force units)
N1 = max # of iterations (timesteps) to run initial NEB
N2 = max # of iterations (timesteps) to run barrier-climbing NEB
Nevery = print replica energies and reaction coordinates every this many timesteps
filename = file specifying final atom coordinates on other side of barrier :ul
[Examples:]
neb 0.1 0.0 1000 500 50 coords.final
neb 0.0 0.001 1000 500 50 coords.final :pre
[Description:]
Perform a nudged elastic band (NEB) calculation using multiple
replicas of a system. Two or more replicas must be used, two of which
are the end points of the transition path.
NEB is a method for finding both the atomic configurations and height
of the energy barrier associated with a transition state, e.g. for an
atom to perform a diffusive hop from one energy basin to another in a
coordinated fashion with its neighbors. The implementation in LAMMPS
follows the discussion in these 3 papers: "(Henkelman1)"_#Henkelman1,
"(Henkelman2)"_#Henkelman2, and "(Nakano)"_#Nakano.
Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
switch; see "this section"_Section_start.html#start_6 of the manual.
Note that if you have MPI installed, you can run a multi-replica
simulation with more replicas (partitions) than you have physical
processors, e.g you can run a 10-replica simulation on one or two
processors. You will simply not get the performance speed-up you
would see with one or more physical processors per replica. See "this
section"_Section_howto.html#howto_5 of the manual for further
discussion.
NOTE: The current NEB implementation in LAMMPS restricts you to having
exactly one processor per replica.
When a NEB calculation is performed, it is assumed that each replica
is running the same model, though LAMMPS does not check for this.
I.e. the simulation domain, the number of atoms, the interaction
potentials, and the starting configuration when the neb command is
issued should be the same for every replica.
In a NEB calculation each atom in a replica is connected to the same
atom in adjacent replicas by springs, which induce inter-replica
forces. These forces are imposed by the "fix neb"_fix_neb.html
command, which must be used in conjunction with the neb command. The
group used to define the fix neb command specifies which atoms the
inter-replica springs are applied to. These are the NEB atoms.
Additional atoms can be present in your system, e.g. to provide a
background force field or simply to hold fixed during the NEB
procedure, but they will not be part of the barrier finding procedure.
The "starting configuration" for NEB should be a state with the NEB
atoms (and all other atoms) having coordinates on one side of the
energy barrier. These coordinates will be assigned to the first
replica #1. The coordinates should be close to a local energy
minimum. A perfect energy minimum is not required, since NEB runs via
damped dynamics which will tend to drive the configuration of replica
#1 to a true energy minimum, but you will typically get better
convergence if the initial state is already at a minimum. For
example, for a system with a free surface, the surface should be fully
relaxed before attempting a NEB calculation.
The final configuration is specified in the input {filename}, which is
formatted as described below. Only coordinates for NEB atoms or a
subset of them should be listed in the file; they represent the state
of the system on the other side of the barrier, at or near an energy
minimum. These coordinates will be assigned to the last replica #M.
The final coordinates of atoms not listed in {filename} are set equal
to their initial coordinates. Again, a perfect energy minimum is not
required for the final configuration, since the atoms in replica #M
will tend to move during the NEB procedure to the nearest energy
minimum. Also note that a final coordinate does not need to be
specified for a NEB atom if you expect it to only displace slightly
during the NEB procedure. For example, only the final coordinate of
the single atom diffusing into a vacancy need be specified if the
surrounding atoms will only relax slightly in the final configuration.
The initial coordinates of all atoms (not just NEB atoms) in the
intermediate replicas #2,#3,...,#M-1 are set to values linearly
interpolated between the corresponding atoms in replicas #1 and #M.
A NEB calculation has two stages, each of which is a minimization
procedure, performed via damped dynamics. To enable this, you must
first define an appropriate "min_style"_min_style.html, such as
{quickmin} or {fire}. The {cg}, {sd}, and {hftn} styles cannot be
used, since they perform iterative line searches in their inner loop,
which cannot be easily synchronized across multiple replicas.
The minimizer tolerances for energy and force are set by {etol} and {ftol},
the same as for
the "minimize"_minimize.html command.
A non-zero {etol}
means that the NEB calculation will terminate if the energy criterion is met
by every replica. The energies being compared to
{etol} do not include any contribution from the inter-replica forces, since
these are non-conservative.
A non-zero {ftol}
means that the NEB calculation will terminate if the force criterion is met
by every replica. The forces being compared to
{ftol} include the inter-replica forces between an atom and its images
in adjacent replicas.
The maximum number of iterations in each stage is set by {N1} and
{N2}. These are effectively timestep counts since each iteration of
damped dynamics is like a single timestep in a dynamics
"run"_run.html. During both stages, the potential energy of each
replica and its normalized distance along the reaction path (reaction
coordinate RD) will be printed to the screen and log file every
{Nevery} timesteps. The RD is 0 and 1 for the first and last replica.
For intermediate replicas, it is the cumulative distance (normalized
by the total cumulative distance) between adjacent replicas, where
"distance" is defined as the length of the 3N-vector of differences in
atomic coordinates, where N is the number of NEB atoms involved in the
transition. These outputs allow you to monitor NEB's progress in
finding a good energy barrier. {N1} and {N2} must both be multiples
of {Nevery}.
In the first stage of NEB, the set of replicas should converge toward
the minimum energy path (MEP) of conformational states that transition
over the barrier. The MEP for a barrier is defined as a sequence of
3N-dimensional states that cross the barrier at its saddle point, each
of which has a potential energy gradient parallel to the MEP itself.
The replica states will also be roughly equally spaced along the MEP
due to the inter-replica spring force added by the "fix
neb"_fix_neb.html command.
In the second stage of NEB, the replica with the highest energy
is selected and the inter-replica forces on it are converted to a
force that drives its atom coordinates to the top or saddle point of
the barrier, via the barrier-climbing calculation described in
"(Henkelman2)"_#Hinkelman2. As before, the other replicas rearrange
themselves along the MEP so as to be roughly equally spaced.
When both stages are complete, if the NEB calculation was successful,
one of the replicas should be an atomic configuration at the top or
saddle point of the barrier, the potential energies for the set of
replicas should represent the energy profile of the barrier along the
MEP, and the configurations of the replicas should be a sequence of
configurations along the MEP.
:line
A few other settings in your input script are required or advised to
perform a NEB calculation.
An atom map must be defined which it is not by default for "atom_style
atomic"_atom_style.html problems. The "atom_modify
map"_atom_modify.html command can be used to do this.
The "atom_modify sort 0 0.0" command should be used to turn off atom
sorting.
NOTE: This sorting restriction will be removed in a future version of
NEB in LAMMPS.
The minimizers in LAMMPS operate on all atoms in your system, even
non-NEB atoms, as defined above. To prevent non-NEB atoms from moving
during the minimization, you should use the "fix
setforce"_fix_setforce.html command to set the force on each of those
atoms to 0.0. This is not required, and may not even be desired in
some cases, but if those atoms move too far (e.g. because the initial
state of your system was not well-minimized), it can cause problems
for the NEB procedure.
The damped dynamics "minimizers"_min_style.html, such as {quickmin}
and {fire}), adjust the position and velocity of the atoms via an
Euler integration step. Thus you must define an appropriate
"timestep"_timestep.html to use with NEB. Using the same timestep
that would be used for a dynamics "run"_run.html of your system is
advised.
:line
The specified {filename} contains atom coordinates for the final
configuration. Only atoms with coordinates different than the initial
configuration need to be specified, i.e. those geometrically near the
barrier.
The file can be ASCII text or a gzipped text file (detected by a .gz
suffix). The file should contain one line per atom, formatted
with the atom ID, followed by the final x,y,z coordinates:
125 24.97311 1.69005 23.46956
126 1.94691 2.79640 1.92799
127 0.15906 3.46099 0.79121
... :pre
The lines can be listed in any order.
:line
Four kinds of output can be generated during a NEB calculation: energy
barrier statistics, thermodynamic output by each replica, dump files,
and restart files.
When running with multiple partitions (each of which is a replica in
this case), the print-out to the screen and master log.lammps file
contains a line of output, printed once every {Nevery} timesteps. It
contains the timestep, the maximum force per replica, the maximum
force per atom (in any replica), potential gradients in the initial,
final, and climbing replicas,
the forward and backward energy barriers,
the total reaction coordinate (RDT), and
the normalized reaction coordinate and potential energy of each replica.
The "maximum force per replica" is
the two-norm of the 3N-length force vector for the atoms in each
replica, maximized across replicas, which is what the {ftol} setting
is checking against. In this case, N is all the atoms in each
replica. The "maximum force per atom" is the maximum force component
of any atom in any replica. The potential gradients are the two-norm
of the 3N-length force vector solely due to the interaction potential i.e.
without adding in inter-replica forces. Note that inter-replica forces
are zero in the initial and final replicas, and only affect
the direction in the climbing replica. For this reason, the "maximum
force per replica" is often equal to the potential gradient in the
climbing replica. In the first stage of NEB, there is no climbing
replica, and so the potential gradient in the highest energy replica
is reported, since this replica will become the climbing replica
in the second stage of NEB.
The "reaction coordinate" (RD) for each
replica is the two-norm of the 3N-length vector of distances between
its atoms and the preceding replica's atoms, added to the RD of the
preceding replica. The RD of the first replica RD1 = 0.0;
the RD of the final replica RDN = RDT, the total reaction coordinate.
The normalized RDs are divided by RDT,
so that they form a monotonically increasing sequence
from zero to one. When computing RD, N only includes the atoms
being operated on by the fix neb command.
The forward (reverse) energy barrier is the potential energy of the highest
replica minus the energy of the first (last) replica.
When running on multiple partitions, LAMMPS produces additional log
files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a
NEB calculation, these contain the thermodynamic output for each
replica.
If "dump"_dump.html commands in the input script define a filename
that includes a {universe} or {uloop} style "variable"_variable.html,
then one dump file (per dump command) will be created for each
replica. At the end of the NEB calculation, the final snapshot in
each file will contain the sequence of snapshots that transition the
system over the energy barrier. Earlier snapshots will show the
convergence of the replicas to the MEP.
Likewise, "restart"_restart.html filenames can be specified with a
{universe} or {uloop} style "variable"_variable.html, to generate
restart files for each replica. These may be useful if the NEB
calculation fails to converge properly to the MEP, and you wish to
restart the calculation from an intermediate point with altered
parameters.
There are 2 Python scripts provided in the tools/python directory,
neb_combine.py and neb_final.py, which are useful in analyzing output
from a NEB calculation. Assume a NEB simulation with M replicas, and
the NEB atoms labelled with a specific atom type.
The neb_combine.py script extracts atom coords for the NEB atoms from
all M dump files and creates a single dump file where each snapshot
contains the NEB atoms from all the replicas and one copy of non-NEB
atoms from the first replica (presumed to be identical in other
replicas). This can be visualized/animated to see how the NEB atoms
relax as the NEB calculation proceeds.
The neb_final.py script extracts the final snapshot from each of the M
dump files to create a single dump file with M snapshots. This can be
visualized to watch the system make its transition over the energy
barrier.
To illustrate, here are images from the final snapshot produced by the
neb_combine.py script run on the dump files produced by the two
example input scripts in examples/neb. Click on them to see a larger
image.
:image(JPG/hop1_small.jpg,JPG/hop1.jpg)
:image(JPG/hop2_small.jpg,JPG/hop2.jpg)
:line
[Restrictions:]
-This command can only be used if LAMMPS was built with the "replica"
+This command can only be used if LAMMPS was built with the REPLICA
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info on packages.
[Related commands:]
"prd"_prd.html, "temper"_temper.html, "fix
langevin"_fix_langevin.html, "fix viscous"_fix_viscous.html
[Default:] none
:line
:link(Henkelman1)
[(Henkelman1)] Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
:link(Henkelman2)
[(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
9901-9904 (2000).
:link(Nakano)
[(Nakano)] Nakano, Comp Phys Comm, 178, 280-289 (2008).
diff --git a/doc/pair_adp.html b/doc/pair_adp.html
index 7bbfd6349..1013ed6d7 100644
--- a/doc/pair_adp.html
+++ b/doc/pair_adp.html
@@ -1,163 +1,163 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style adp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style adp
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style adp
pair_coeff * * Ta.adp Ta
pair_coeff * * ../potentials/AlCu.adp Al Al Cu
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>adp</I> computes pairwise interactions for metals and metal alloys
using the angular dependent potential (ADP) of <A HREF = "#Mishin">(Mishin)</A>,
which is a generalization of the <A HREF = "pair_eam.html">embedded atom method (EAM)
potential</A>. The LAMMPS implementation is discussed in
<A HREF = "#Singh">(Singh)</A>. The total energy Ei of an atom I is given by
</P>
<CENTER><IMG SRC = "Eqs/pair_adp.jpg">
</CENTER>
<P>where F is the embedding energy which is a function of the atomic
electron density rho, phi is a pair potential interaction, alpha and
beta are the element types of atoms I and J, and s and t = 1,2,3 and
refer to the cartesian coordinates. The mu and lambda terms represent
the dipole and quadruple distortions of the local atomic environment
which extend the original EAM framework by introducing angular forces.
</P>
<P>Note that unlike for other potentials, cutoffs for ADP potentials are
not set in the pair_style or pair_coeff command; they are specified in
the ADP potential files themselves. Likewise, the ADP potential files
list atomic masses; thus you do not need to use the <A HREF = "mass.html">mass</A>
command to specify them.
</P>
<P>The NIST WWW site distributes and documents ADP potentials:
</P>
<PRE>http://www.ctcms.nist.gov/potentials
</PRE>
<P>Note that these must be converted into the extended DYNAMO <I>setfl</I>
format discussed below.
</P>
<P>The NIST site is maintained by Chandler Becker (cbecker at nist.gov)
who is good resource for info on interatomic potentials and file
formats.
</P>
<HR>
<P>Only a single pair_coeff command is used with the <I>adp</I> style which
specifies an extended DYNAMO <I>setfl</I> file, which contains information
for M elements. These are mapped to LAMMPS atom types by specifying N
additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
</P>
<UL><LI>filename
<LI>N element names = mapping of extended <I>setfl</I> elements to atom types
</UL>
<P>As an example, the potentials/AlCu.adp file, included in the
potentials directory of the LAMMPS distrbution, is an extended <I>setfl</I>
file which has tabulated ADP values for w elements and their alloy
interactions: Cu and Al. If your LAMMPS simulation has 4 atoms types
and you want the 1st 3 to be Al, and the 4th to be Cu, you would use
the following pair_coeff command:
</P>
<PRE>pair_coeff * * AlCu.adp Al Al Al Cu
</PRE>
<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Al arguments map LAMMPS atom types 1,2,3 to the Al
element in the extended <I>setfl</I> file. The final Cu argument maps
LAMMPS atom type 4 to the Al element in the extended <I>setfl</I> file.
Note that there is no requirement that your simulation use all the
elements specified by the extended <I>setfl</I> file.
</P>
<P>If a mapping value is specified as NULL, the mapping is not performed.
This can be used when an <I>adp</I> potential is used as part of the
<I>hybrid</I> pair style. The NULL values are placeholders for atom types
that will be used with other potentials.
</P>
<P><I>Adp</I> files in the <I>potentials</I> directory of the LAMMPS distribution
have an ".adp" suffix. A DYNAMO <I>setfl</I> file extended for ADP is
formatted as follows. Basically it is the standard <I>setfl</I> format
with additional tabulated functions u and w added to the file after
the tabulated pair potentials. See the <A HREF = "pair_eam.html">pair_eam</A>
command for further details on the <I>setfl</I> format.
</P>
<UL><LI>lines 1,2,3 = comments (ignored)
<LI>line 4: Nelements Element1 Element2 ... ElementN
<LI>line 5: Nrho, drho, Nr, dr, cutoff
</UL>
<P>Following the 5 header lines are Nelements sections, one for each
element, each with the following format:
</P>
<UL><LI>line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)
<LI>embedding function F(rho) (Nrho values)
<LI>density function rho(r) (Nr values)
</UL>
<P>Following the Nelements sections, Nr values for each pair potential
phi(r) array are listed for all i,j element pairs in the same format
as other arrays. Since these interactions are symmetric (i,j = j,i)
only phi arrays with i >= j are listed, in the following order: i,j =
(1,1), (2,1), (2,2), (3,1), (3,2), (3,3), (4,1), ..., (Nelements,
Nelements).
</P>
<P>After the phi(r) arrays, each of the u(r) arrays are listed in the
same order with the same assumptions of symmetry. Directly following
the u(r), the w(r) arrays are listed.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, no special mixing rules are needed, since
the ADP potential files specify alloy interactions explicitly.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift, table, and tail options.
</P>
<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
files</A>, since it is stored in tabulated potential files.
Thus, you need to re-specify the pair_style and pair_coeff commands in
an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>This pair style is part of the "manybody" package. It is only enabled
+<P>This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default).
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_eam.html">pair_eam</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Mishin"></A>
<P><B>(Mishin)</B> Mishin, Mehl, and Papaconstantopoulos, Acta Mater, 53, 4029
(2005).
</P>
<A NAME = "Singh"></A>
<P><B>(Singh)</B> Singh and Warner, Acta Mater, 58, 5797-5805 (2010),
</P>
</HTML>
diff --git a/doc/pair_adp.txt b/doc/pair_adp.txt
index f064a89c6..cf66af91c 100644
--- a/doc/pair_adp.txt
+++ b/doc/pair_adp.txt
@@ -1,156 +1,156 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style adp command :h3
[Syntax:]
pair_style adp :pre
[Examples:]
pair_style adp
pair_coeff * * Ta.adp Ta
pair_coeff * * ../potentials/AlCu.adp Al Al Cu :pre
[Description:]
Style {adp} computes pairwise interactions for metals and metal alloys
using the angular dependent potential (ADP) of "(Mishin)"_#Mishin,
which is a generalization of the "embedded atom method (EAM)
potential"_pair_eam.html. The LAMMPS implementation is discussed in
"(Singh)"_#Singh. The total energy Ei of an atom I is given by
:c,image(Eqs/pair_adp.jpg)
where F is the embedding energy which is a function of the atomic
electron density rho, phi is a pair potential interaction, alpha and
beta are the element types of atoms I and J, and s and t = 1,2,3 and
refer to the cartesian coordinates. The mu and lambda terms represent
the dipole and quadruple distortions of the local atomic environment
which extend the original EAM framework by introducing angular forces.
Note that unlike for other potentials, cutoffs for ADP potentials are
not set in the pair_style or pair_coeff command; they are specified in
the ADP potential files themselves. Likewise, the ADP potential files
list atomic masses; thus you do not need to use the "mass"_mass.html
command to specify them.
The NIST WWW site distributes and documents ADP potentials:
http://www.ctcms.nist.gov/potentials :pre
Note that these must be converted into the extended DYNAMO {setfl}
format discussed below.
The NIST site is maintained by Chandler Becker (cbecker at nist.gov)
who is good resource for info on interatomic potentials and file
formats.
:line
Only a single pair_coeff command is used with the {adp} style which
specifies an extended DYNAMO {setfl} file, which contains information
for M elements. These are mapped to LAMMPS atom types by specifying N
additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
filename
N element names = mapping of extended {setfl} elements to atom types :ul
As an example, the potentials/AlCu.adp file, included in the
potentials directory of the LAMMPS distrbution, is an extended {setfl}
file which has tabulated ADP values for w elements and their alloy
interactions: Cu and Al. If your LAMMPS simulation has 4 atoms types
and you want the 1st 3 to be Al, and the 4th to be Cu, you would use
the following pair_coeff command:
pair_coeff * * AlCu.adp Al Al Al Cu :pre
The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Al arguments map LAMMPS atom types 1,2,3 to the Al
element in the extended {setfl} file. The final Cu argument maps
LAMMPS atom type 4 to the Al element in the extended {setfl} file.
Note that there is no requirement that your simulation use all the
elements specified by the extended {setfl} file.
If a mapping value is specified as NULL, the mapping is not performed.
This can be used when an {adp} potential is used as part of the
{hybrid} pair style. The NULL values are placeholders for atom types
that will be used with other potentials.
{Adp} files in the {potentials} directory of the LAMMPS distribution
have an ".adp" suffix. A DYNAMO {setfl} file extended for ADP is
formatted as follows. Basically it is the standard {setfl} format
with additional tabulated functions u and w added to the file after
the tabulated pair potentials. See the "pair_eam"_pair_eam.html
command for further details on the {setfl} format.
lines 1,2,3 = comments (ignored)
line 4: Nelements Element1 Element2 ... ElementN
line 5: Nrho, drho, Nr, dr, cutoff :ul
Following the 5 header lines are Nelements sections, one for each
element, each with the following format:
line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)
embedding function F(rho) (Nrho values)
density function rho(r) (Nr values) :ul
Following the Nelements sections, Nr values for each pair potential
phi(r) array are listed for all i,j element pairs in the same format
as other arrays. Since these interactions are symmetric (i,j = j,i)
only phi arrays with i >= j are listed, in the following order: i,j =
(1,1), (2,1), (2,2), (3,1), (3,2), (3,3), (4,1), ..., (Nelements,
Nelements).
After the phi(r) arrays, each of the u(r) arrays are listed in the
same order with the same assumptions of symmetry. Directly following
the u(r), the w(r) arrays are listed.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, no special mixing rules are needed, since
the ADP potential files specify alloy interactions explicitly.
This pair style does not support the "pair_modify"_pair_modify.html
shift, table, and tail options.
This pair style does not write its information to "binary restart
files"_restart.html, since it is stored in tabulated potential files.
Thus, you need to re-specify the pair_style and pair_coeff commands in
an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
-This pair style is part of the "manybody" package. It is only enabled
+This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default).
[Related commands:]
"pair_coeff"_pair_coeff.html, "pair_eam"_pair_eam.html
[Default:] none
:line
:link(Mishin)
[(Mishin)] Mishin, Mehl, and Papaconstantopoulos, Acta Mater, 53, 4029
(2005).
:link(Singh)
[(Singh)] Singh and Warner, Acta Mater, 58, 5797-5805 (2010),
diff --git a/doc/pair_airebo.html b/doc/pair_airebo.html
index 53ff4d27e..290245bed 100644
--- a/doc/pair_airebo.html
+++ b/doc/pair_airebo.html
@@ -1,171 +1,171 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style airebo command
</H3>
<H3>pair_style rebo command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style cutoff LJ_flag TORSION_flag
</PRE>
<UL><LI>style = <I>airebo</I> or <I>rebo</I>
<LI>cutoff = LJ cutoff (sigma scale factor) (AIREBO only)
<LI>LJ_flag = 0/1 to turn off/on the LJ term (AIREBO only, optional)
<LI>TORSION_flag = 0/1 to turn off/on the torsion term (AIREBO only, optional)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style airebo 3.0
pair_style airebo 2.5 1 0
pair_coeff * * ../potentials/CH.airebo H C
</PRE>
<PRE>pair_style rebo
pair_coeff * * ../potentials/CH.airebo H C
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>airebo</I> pair style computes the Adaptive Intermolecular Reactive
Empirical Bond Order (AIREBO) Potential of <A HREF = "#Stuart">(Stuart)</A> for a
system of carbon and/or hydrogen atoms. Note that this is the initial
formulation of AIREBO from 2000, not the later formulation. The
<I>rebo</I> pair style computes the Reactive Empirical Bond Order (REBO)
Potential of <A HREF = "#Brenner">(Brenner)</A>. Note that this is the so-called
2nd generation REBO from 2002, not the original REBO from 1990. As
discussed below, 2nd generation REBO is closely related to the intial
AIREBO; it is just a subset of the potential energy terms.
</P>
<P>The AIREBO potential consists of three terms:
</P>
<CENTER><IMG SRC = "Eqs/pair_airebo.jpg">
</CENTER>
<P>By default, all three terms are included. For the <I>airebo</I> style, if
the two optional flag arguments to the pair_style command are
included, the LJ and torsional terms can be turned off. Note that
both or neither of the flags must be included. If both of the LJ an
torsional terms are turned off, it becomes the 2nd-generation REBO
potential, with a small caveat on the spline fitting procedure
mentioned below. This can be specified directly as pair_style rebo
with no additional arguments.
</P>
<P>The detailed formulas for this potential are given in
<A HREF = "#Stuart">(Stuart)</A>; here we provide only a brief description.
</P>
<P>The E_REBO term has the same functional form as the hydrocarbon REBO
potential developed in <A HREF = "#Brenner">(Brenner)</A>. The coefficients for
E_REBO in AIREBO are essentially the same as Brenner's potential, but
a few fitted spline values are slightly different. For most cases the
E_REBO term in AIREBO will produce the same energies, forces and
statistical averages as the original REBO potential from which it was
derived. The E_REBO term in the AIREBO potential gives the model its
reactive capabilities and only describes short-ranged C-C, C-H and H-H
interactions (r < 2 Angstroms). These interactions have strong
coordination-dependence through a bond order parameter, which adjusts
the attraction between the I,J atoms based on the position of other
nearby atoms and thus has 3- and 4-body dependence.
</P>
<P>The E_LJ term adds longer-ranged interactions (2 < r < cutoff) using a
form similar to the standard <A HREF = "pair_lj.html">Lennard Jones potential</A>.
The E_LJ term in AIREBO contains a series of switching functions so
that the short-ranged LJ repulsion (1/r^12) does not interfere with
the energetics captured by the E_REBO term. The extent of the E_LJ
interactions is determined by the <I>cutoff</I> argument to the pair_style
command which is a scale factor. For each type pair (C-C, C-H, H-H)
the cutoff is obtained by multiplying the scale factor by the sigma
value defined in the potential file for that type pair. In the
standard AIREBO potential, sigma_CC = 3.4 Angstroms, so with a scale
factor of 3.0 (the argument in pair_style), the resulting E_LJ cutoff
would be 10.2 Angstroms.
</P>
<P>The E_TORSION term is an explicit 4-body potential that describes
various dihedral angle preferences in hydrocarbon configurations.
</P>
<P>Only a single pair_coeff command is used with the <I>airebo</I> or <I>rebo</I>
style which specifies an AIREBO potential file with parameters for C
and H. Note that the <I>rebo</I> style in LAMMPS uses the same
AIREBO-formatted potential file. These are mapped to LAMMPS atom
types by specifying N additional arguments after the filename in the
pair_coeff command, where N is the number of LAMMPS atom types:
</P>
<UL><LI>filename
<LI>N element names = mapping of AIREBO elements to atom types
</UL>
<P>As an example, if your LAMMPS simulation has 4 atom types and you want
the 1st 3 to be C, and the 4th to be H, you would use the following
pair_coeff command:
</P>
<PRE>pair_coeff * * CH.airebo C C C H
</PRE>
<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three C arguments map LAMMPS atom types 1,2,3 to the C
element in the AIREBO file. The final H argument maps LAMMPS atom
type 4 to the H element in the SW file. If a mapping value is
specified as NULL, the mapping is not performed. This can be used
when a <I>airebo</I> potential is used as part of the <I>hybrid</I> pair style.
The NULL values are placeholders for atom types that will be used with
other potentials.
</P>
<P>The parameters/coefficients for the AIREBO potentials are listed in
the CH.airebo file to agree with the original <A HREF = "#Stuart">(Stuart)</A>
paper. Thus the parameters are specific to this potential and the way
it was fit, so modifying the file should be done cautiously.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>These pair styles do not support the <A HREF = "pair_modify.html">pair_modify</A>
mix, shift, table, and tail options.
</P>
<P>These pair styles do not write their information to <A HREF = "restart.html">binary restart
files</A>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
</P>
<P>These pair styles can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. They do not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<P><B>Restrictions:</B>
</P>
-<P>These pair styles are part of the "manybody" package. They are only
+<P>These pair styles are part of the MANYBODY package. They are only
enabled if LAMMPS was built with that package (which it is by
default). See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info.
</P>
<P>These pair potentials require the <A HREF = "newton.html">newton</A> setting to be
"on" for pair interactions.
</P>
<P>The CH.airebo potential file provided with LAMMPS (see the potentials
directory) is parameterized for metal <A HREF = "units.html">units</A>. You can use
the AIREBO or REBO potential with any LAMMPS units, but you would need
to create your own AIREBO potential file with coefficients listed in
the appropriate units if your simulation doesn't use "metal" units.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Stuart"></A>
<P><B>(Stuart)</B> Stuart, Tutein, Harrison, J Chem Phys, 112, 6472-6486
(2000).
</P>
<A NAME = "Brenner"></A>
<P><B>(Brenner)</B> Brenner, Shenderova, Harrison, Stuart, Ni, Sinnott, J
Physics: Condensed Matter, 14, 783-802 (2002).
</P>
</HTML>
diff --git a/doc/pair_airebo.txt b/doc/pair_airebo.txt
index 7bff8b7d2..5d552132f 100644
--- a/doc/pair_airebo.txt
+++ b/doc/pair_airebo.txt
@@ -1,163 +1,163 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style airebo command :h3
pair_style rebo command :h3
[Syntax:]
pair_style style cutoff LJ_flag TORSION_flag :pre
style = {airebo} or {rebo}
cutoff = LJ cutoff (sigma scale factor) (AIREBO only)
LJ_flag = 0/1 to turn off/on the LJ term (AIREBO only, optional)
TORSION_flag = 0/1 to turn off/on the torsion term (AIREBO only, optional) :ul
[Examples:]
pair_style airebo 3.0
pair_style airebo 2.5 1 0
pair_coeff * * ../potentials/CH.airebo H C :pre
pair_style rebo
pair_coeff * * ../potentials/CH.airebo H C :pre
[Description:]
The {airebo} pair style computes the Adaptive Intermolecular Reactive
Empirical Bond Order (AIREBO) Potential of "(Stuart)"_#Stuart for a
system of carbon and/or hydrogen atoms. Note that this is the initial
formulation of AIREBO from 2000, not the later formulation. The
{rebo} pair style computes the Reactive Empirical Bond Order (REBO)
Potential of "(Brenner)"_#Brenner. Note that this is the so-called
2nd generation REBO from 2002, not the original REBO from 1990. As
discussed below, 2nd generation REBO is closely related to the intial
AIREBO; it is just a subset of the potential energy terms.
The AIREBO potential consists of three terms:
:c,image(Eqs/pair_airebo.jpg)
By default, all three terms are included. For the {airebo} style, if
the two optional flag arguments to the pair_style command are
included, the LJ and torsional terms can be turned off. Note that
both or neither of the flags must be included. If both of the LJ an
torsional terms are turned off, it becomes the 2nd-generation REBO
potential, with a small caveat on the spline fitting procedure
mentioned below. This can be specified directly as pair_style rebo
with no additional arguments.
The detailed formulas for this potential are given in
"(Stuart)"_#Stuart; here we provide only a brief description.
The E_REBO term has the same functional form as the hydrocarbon REBO
potential developed in "(Brenner)"_#Brenner. The coefficients for
E_REBO in AIREBO are essentially the same as Brenner's potential, but
a few fitted spline values are slightly different. For most cases the
E_REBO term in AIREBO will produce the same energies, forces and
statistical averages as the original REBO potential from which it was
derived. The E_REBO term in the AIREBO potential gives the model its
reactive capabilities and only describes short-ranged C-C, C-H and H-H
interactions (r < 2 Angstroms). These interactions have strong
coordination-dependence through a bond order parameter, which adjusts
the attraction between the I,J atoms based on the position of other
nearby atoms and thus has 3- and 4-body dependence.
The E_LJ term adds longer-ranged interactions (2 < r < cutoff) using a
form similar to the standard "Lennard Jones potential"_pair_lj.html.
The E_LJ term in AIREBO contains a series of switching functions so
that the short-ranged LJ repulsion (1/r^12) does not interfere with
the energetics captured by the E_REBO term. The extent of the E_LJ
interactions is determined by the {cutoff} argument to the pair_style
command which is a scale factor. For each type pair (C-C, C-H, H-H)
the cutoff is obtained by multiplying the scale factor by the sigma
value defined in the potential file for that type pair. In the
standard AIREBO potential, sigma_CC = 3.4 Angstroms, so with a scale
factor of 3.0 (the argument in pair_style), the resulting E_LJ cutoff
would be 10.2 Angstroms.
The E_TORSION term is an explicit 4-body potential that describes
various dihedral angle preferences in hydrocarbon configurations.
Only a single pair_coeff command is used with the {airebo} or {rebo}
style which specifies an AIREBO potential file with parameters for C
and H. Note that the {rebo} style in LAMMPS uses the same
AIREBO-formatted potential file. These are mapped to LAMMPS atom
types by specifying N additional arguments after the filename in the
pair_coeff command, where N is the number of LAMMPS atom types:
filename
N element names = mapping of AIREBO elements to atom types :ul
As an example, if your LAMMPS simulation has 4 atom types and you want
the 1st 3 to be C, and the 4th to be H, you would use the following
pair_coeff command:
pair_coeff * * CH.airebo C C C H :pre
The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three C arguments map LAMMPS atom types 1,2,3 to the C
element in the AIREBO file. The final H argument maps LAMMPS atom
type 4 to the H element in the SW file. If a mapping value is
specified as NULL, the mapping is not performed. This can be used
when a {airebo} potential is used as part of the {hybrid} pair style.
The NULL values are placeholders for atom types that will be used with
other potentials.
The parameters/coefficients for the AIREBO potentials are listed in
the CH.airebo file to agree with the original "(Stuart)"_#Stuart
paper. Thus the parameters are specific to this potential and the way
it was fit, so modifying the file should be done cautiously.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
These pair styles do not support the "pair_modify"_pair_modify.html
mix, shift, table, and tail options.
These pair styles do not write their information to "binary restart
files"_restart.html, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
These pair styles can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. They do not support the
{inner}, {middle}, {outer} keywords.
[Restrictions:]
-These pair styles are part of the "manybody" package. They are only
+These pair styles are part of the MANYBODY package. They are only
enabled if LAMMPS was built with that package (which it is by
default). See the "Making LAMMPS"_Section_start.html#start_3 section
for more info.
These pair potentials require the "newton"_newton.html setting to be
"on" for pair interactions.
The CH.airebo potential file provided with LAMMPS (see the potentials
directory) is parameterized for metal "units"_units.html. You can use
the AIREBO or REBO potential with any LAMMPS units, but you would need
to create your own AIREBO potential file with coefficients listed in
the appropriate units if your simulation doesn't use "metal" units.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Stuart)
[(Stuart)] Stuart, Tutein, Harrison, J Chem Phys, 112, 6472-6486
(2000).
:link(Brenner)
[(Brenner)] Brenner, Shenderova, Harrison, Stuart, Ni, Sinnott, J
Physics: Condensed Matter, 14, 783-802 (2002).
diff --git a/doc/pair_born.html b/doc/pair_born.html
index adf9a42c2..e396552aa 100644
--- a/doc/pair_born.html
+++ b/doc/pair_born.html
@@ -1,160 +1,160 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style born command
</H3>
<H3>pair_style born/coul/long command
</H3>
<H3>pair_style born/coul/long/cuda command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style args
</PRE>
<UL><LI>style = <I>born</I> or <I>born/coul/long</I>
<LI>args = list of arguments for a particular style
</UL>
<PRE> <I>born</I> args = cutoff
cutoff = global cutoff for non-Coulombic interactions (distance units)
<I>born/coul/long</I> args = cutoff (cutoff2)
cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style born 10.0
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
</PRE>
<PRE>pair_style born/coul/long 10.0
pair_style born/coul/long 10.0 8.0
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>born</I> style computes the Born-Mayer-Huggins or Tosi/Fumi
potential described in <A HREF = "#FumiTosi">(Fumi and Tosi)</A>, given by
</P>
<CENTER><IMG SRC = "Eqs/pair_born.jpg">
</CENTER>
<P>where sigma is an interaction-dependent length parameter, rho is an
ionic-pair dependent length parameter, and Rc is the cutoff.
</P>
<P>The <I>born/coul/long</I> style adds a Coulombic term as described for the
<A HREF = "pair_lj.html">lj/cut</A> pair styles. An additional damping factor is
applied to the Coulombic term so it can be used in conjunction with
the <A HREF = "kspace_style.html">kspace_style</A> command and its <I>ewald</I> or <I>pppm</I>
option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
</P>
<P>If one cutoff is specified for the <I>born/coulk/long</I> style, it is used
for both the A,C,D and Coulombic terms. If two cutoffs are specified,
the first is used as the cutoff for the A,C,D terms, and the second is
the cutoff for the Coulombic term.
</P>
<P>Note that these potentials are related to the <A HREF = "pair_born.html">Buckingham
potential</A>.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>A (energy units)
<LI>rho (distance units)
<LI>sigma (distance units)
<LI>C (energy units * distance units^6)
<LI>D (energy units * distance units^8)
<LI>cutoff (distance units)
</UL>
<P>The second coefficient, rho, must be greater than zero.
</P>
<P>The last coefficient is optional. If not specified, the global A,C,D
cutoff specified in the pair_style command is used.
</P>
<P>For <I>buck/coul/long</I> no Coulombic cutoff can be specified for an
individual I,J type pair. All type pairs use the same global
Coulombic cutoff specified in the pair_style command.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+<P>These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>These pair styles do not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
</P>
<P>These styles support the <A HREF = "pair_modify.html">pair_modify</A> shift option
for the energy of the exp(), 1/r^6, and 1/r^8 portion of the pair
interaction.
</P>
<P>The <I>born/coul/long</I> pair style does not support the
<A HREF = "pair_modify.html">pair_modify</A> table option since a tabulation
capability has not yet been added to this potential.
</P>
<P>These styles support the pair_modify tail option for adding long-range
tail corrections to energy and pressure.
</P>
<P>Thess styles writes thei information to binary <A HREF = "restart.html">restart</A>
files, so pair_style and pair_coeff commands do not need to be
specified in an input script that reads a restart file.
</P>
<P>These styles can only be used via the <I>pair</I> keyword of the <A HREF = "run_style.html">run_style
respa</A> command. They do not support the <I>inner</I>,
<I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>The <I>born/coul/long</I> style is part of the "kspace" package. It is
-only enabled if LAMMPS was built with that package (which it is by
+<P>The <I>born/coul/long</I> style is part of the KSPACE package. It is only
+enabled if LAMMPS was built with that package (which it is by
default). See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_buck.html">pair_style buck</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "FumiTosi"></A>
<P>Fumi and Tosi, J Phys Chem Solids, 25, 31 (1964),
Fumi and Tosi, J Phys Chem Solids, 25, 45 (1964).
</P>
</HTML>
diff --git a/doc/pair_born.txt b/doc/pair_born.txt
index 3b6939af7..56e1515da 100644
--- a/doc/pair_born.txt
+++ b/doc/pair_born.txt
@@ -1,152 +1,152 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style born command :h3
pair_style born/coul/long command :h3
pair_style born/coul/long/cuda command :h3
[Syntax:]
pair_style style args :pre
style = {born} or {born/coul/long}
args = list of arguments for a particular style :ul
{born} args = cutoff
cutoff = global cutoff for non-Coulombic interactions (distance units)
{born/coul/long} args = cutoff (cutoff2)
cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
[Examples:]
pair_style born 10.0
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
pair_style born/coul/long 10.0
pair_style born/coul/long 10.0 8.0
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
[Description:]
The {born} style computes the Born-Mayer-Huggins or Tosi/Fumi
potential described in "(Fumi and Tosi)"_#FumiTosi, given by
:c,image(Eqs/pair_born.jpg)
where sigma is an interaction-dependent length parameter, rho is an
ionic-pair dependent length parameter, and Rc is the cutoff.
The {born/coul/long} style adds a Coulombic term as described for the
"lj/cut"_pair_lj.html pair styles. An additional damping factor is
applied to the Coulombic term so it can be used in conjunction with
the "kspace_style"_kspace_style.html command and its {ewald} or {pppm}
option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
If one cutoff is specified for the {born/coulk/long} style, it is used
for both the A,C,D and Coulombic terms. If two cutoffs are specified,
the first is used as the cutoff for the A,C,D terms, and the second is
the cutoff for the Coulombic term.
Note that these potentials are related to the "Buckingham
potential"_pair_born.html.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
A (energy units)
rho (distance units)
sigma (distance units)
C (energy units * distance units^6)
D (energy units * distance units^8)
cutoff (distance units) :ul
The second coefficient, rho, must be greater than zero.
The last coefficient is optional. If not specified, the global A,C,D
cutoff specified in the pair_style command is used.
For {buck/coul/long} no Coulombic cutoff can be specified for an
individual I,J type pair. All type pairs use the same global
Coulombic cutoff specified in the pair_style command.
:line
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
These pair styles do not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
These styles support the "pair_modify"_pair_modify.html shift option
for the energy of the exp(), 1/r^6, and 1/r^8 portion of the pair
interaction.
The {born/coul/long} pair style does not support the
"pair_modify"_pair_modify.html table option since a tabulation
capability has not yet been added to this potential.
These styles support the pair_modify tail option for adding long-range
tail corrections to energy and pressure.
Thess styles writes thei information to binary "restart"_restart.html
files, so pair_style and pair_coeff commands do not need to be
specified in an input script that reads a restart file.
These styles can only be used via the {pair} keyword of the "run_style
respa"_run_style.html command. They do not support the {inner},
{middle}, {outer} keywords.
:line
[Restrictions:]
-The {born/coul/long} style is part of the "kspace" package. It is
-only enabled if LAMMPS was built with that package (which it is by
+The {born/coul/long} style is part of the KSPACE package. It is only
+enabled if LAMMPS was built with that package (which it is by
default). See the "Making LAMMPS"_Section_start.html#start_3 section
for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html, "pair_style buck"_pair_buck.html
[Default:] none
:line
:link(FumiTosi)
Fumi and Tosi, J Phys Chem Solids, 25, 31 (1964),
Fumi and Tosi, J Phys Chem Solids, 25, 45 (1964).
diff --git a/doc/pair_buck.html b/doc/pair_buck.html
index 7d26f6796..b0d50311e 100644
--- a/doc/pair_buck.html
+++ b/doc/pair_buck.html
@@ -1,172 +1,172 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style buck command
</H3>
<H3>pair_style buck/cuda command
</H3>
<H3>pair_style buck/coul/cut command
</H3>
<H3>pair_style buck/coul/cut/cuda command
</H3>
<H3>pair_style buck/coul/long command
</H3>
<H3>pair_style buck/coul/long/cuda command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style args
</PRE>
<UL><LI>style = <I>buck</I> or <I>buck/coul/cut</I> or <I>buck/coul/long</I>
<LI>args = list of arguments for a particular style
</UL>
<PRE> <I>buck</I> args = cutoff
cutoff = global cutoff for Buckingham interactions (distance units)
<I>buck/coul/cut</I> args = cutoff (cutoff2)
cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<I>buck/coul/long</I> args = cutoff (cutoff2)
cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style buck 2.5
pair_coeff * * 100.0 1.5 200.0
pair_coeff * * 100.0 1.5 200.0 3.0
</PRE>
<PRE>pair_style buck/coul/cut 10.0
pair_style buck/coul/cut 10.0 8.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff 1 1 100.0 1.5 200.0 9.0
pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0
</PRE>
<PRE>pair_style buck/coul/long 10.0
pair_style buck/coul/long 10.0 8.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff 1 1 100.0 1.5 200.0 9.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>buck</I> style computes a Buckingham potential (exp/6 instead of
Lennard-Jones 12/6) given by
</P>
<CENTER><IMG SRC = "Eqs/pair_buck.jpg">
</CENTER>
<P>where rho is an ionic-pair dependent length parameter, and Rc is the
cutoff.
</P>
<P>The <I>buck/coul/cut</I> and <I>buck/coul/long</I> styles add a Coulombic term
as described for the <A HREF = "pair_lj.html">lj/cut</A> pair styles. For
<I>buck/coul/long</I>, an additional damping factor is applied to the
Coulombic term so it can be used in conjunction with the
<A HREF = "kspace_style.html">kspace_style</A> command and its <I>ewald</I> or <I>pppm</I>
option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
</P>
<P>If one cutoff is specified for the <I>born/coul/cut</I> and
<I>born/coulk/long</I> styles, it is used for both the A,C and Coulombic
terms. If two cutoffs are specified, the first is used as the cutoff
for the A,C terms, and the second is the cutoff for the Coulombic
term.
</P>
<P>Note that these potentials are related to the <A HREF = "pair_born.html">Born-Mayer-Huggins
potential</A>.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands:
</P>
<UL><LI>A (energy units)
<LI>rho (distance units)
<LI>C (energy-distance^6 units)
<LI>cutoff (distance units)
<LI>cutoff2 (distance units)
</UL>
<P>The second coefficient, rho, must be greater than zero.
</P>
<P>The latter 2 coefficients are optional. If not specified, the global
A,C and Coulombic cutoffs are used. If only one cutoff is specified,
it is used as the cutoff for both A,C and Coulombic interactions for
this type pair. If both coefficients are specified, they are used as
the A,C and Coulombic cutoffs for this type pair. You cannot specify
2 cutoffs for style <I>buck</I>, since it has no Coulombic terms.
</P>
<P>For <I>buck/coul/long</I> only the LJ cutoff can be specified since a
Coulombic cutoff cannot be specified for an individual I,J type pair.
All type pairs use the same global Coulombic cutoff specified in the
pair_style command.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+<P>These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>These pair styles do not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
</P>
<P>These styles support the <A HREF = "pair_modify.html">pair_modify</A> shift option
for the energy of the exp() and 1/r^6 portion of the pair interaction.
</P>
<P>The <I>buck/coul/long</I> pair style does not support the
<A HREF = "pair_modify.html">pair_modify</A> table option since a tabulation
capability has not yet been added to this potential.
</P>
<P>These styles support the pair_modify tail option for adding long-range
tail corrections to energy and pressure for the A,C terms in the
pair interaction.
</P>
<P>These styles write their information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>These styles can only be used via the <I>pair</I> keyword of the <A HREF = "run_style.html">run_style
respa</A> command. They do not support the <I>inner</I>,
<I>middle</I>, <I>outer</I> keywords.
</P>
<P><B>Restrictions:</B>
</P>
-<P>The <I>buck/coul/long</I> style is part of the "kspace" package. It is
-only enabled if LAMMPS was built with that package (which it is by
+<P>The <I>buck/coul/long</I> style is part of the KSPACE package. It is only
+enabled if LAMMPS was built with that package (which it is by
default). See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_born.html">pair_style born</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/pair_buck.txt b/doc/pair_buck.txt
index c173195d9..40e095fb6 100644
--- a/doc/pair_buck.txt
+++ b/doc/pair_buck.txt
@@ -1,161 +1,161 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style buck command :h3
pair_style buck/cuda command :h3
pair_style buck/coul/cut command :h3
pair_style buck/coul/cut/cuda command :h3
pair_style buck/coul/long command :h3
pair_style buck/coul/long/cuda command :h3
[Syntax:]
pair_style style args :pre
style = {buck} or {buck/coul/cut} or {buck/coul/long}
args = list of arguments for a particular style :ul
{buck} args = cutoff
cutoff = global cutoff for Buckingham interactions (distance units)
{buck/coul/cut} args = cutoff (cutoff2)
cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{buck/coul/long} args = cutoff (cutoff2)
cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
[Examples:]
pair_style buck 2.5
pair_coeff * * 100.0 1.5 200.0
pair_coeff * * 100.0 1.5 200.0 3.0 :pre
pair_style buck/coul/cut 10.0
pair_style buck/coul/cut 10.0 8.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff 1 1 100.0 1.5 200.0 9.0
pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0 :pre
pair_style buck/coul/long 10.0
pair_style buck/coul/long 10.0 8.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff 1 1 100.0 1.5 200.0 9.0 :pre
[Description:]
The {buck} style computes a Buckingham potential (exp/6 instead of
Lennard-Jones 12/6) given by
:c,image(Eqs/pair_buck.jpg)
where rho is an ionic-pair dependent length parameter, and Rc is the
cutoff.
The {buck/coul/cut} and {buck/coul/long} styles add a Coulombic term
as described for the "lj/cut"_pair_lj.html pair styles. For
{buck/coul/long}, an additional damping factor is applied to the
Coulombic term so it can be used in conjunction with the
"kspace_style"_kspace_style.html command and its {ewald} or {pppm}
option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
If one cutoff is specified for the {born/coul/cut} and
{born/coulk/long} styles, it is used for both the A,C and Coulombic
terms. If two cutoffs are specified, the first is used as the cutoff
for the A,C terms, and the second is the cutoff for the Coulombic
term.
Note that these potentials are related to the "Born-Mayer-Huggins
potential"_pair_born.html.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands:
A (energy units)
rho (distance units)
C (energy-distance^6 units)
cutoff (distance units)
cutoff2 (distance units) :ul
The second coefficient, rho, must be greater than zero.
The latter 2 coefficients are optional. If not specified, the global
A,C and Coulombic cutoffs are used. If only one cutoff is specified,
it is used as the cutoff for both A,C and Coulombic interactions for
this type pair. If both coefficients are specified, they are used as
the A,C and Coulombic cutoffs for this type pair. You cannot specify
2 cutoffs for style {buck}, since it has no Coulombic terms.
For {buck/coul/long} only the LJ cutoff can be specified since a
Coulombic cutoff cannot be specified for an individual I,J type pair.
All type pairs use the same global Coulombic cutoff specified in the
pair_style command.
:line
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
These pair styles do not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
These styles support the "pair_modify"_pair_modify.html shift option
for the energy of the exp() and 1/r^6 portion of the pair interaction.
The {buck/coul/long} pair style does not support the
"pair_modify"_pair_modify.html table option since a tabulation
capability has not yet been added to this potential.
These styles support the pair_modify tail option for adding long-range
tail corrections to energy and pressure for the A,C terms in the
pair interaction.
These styles write their information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
These styles can only be used via the {pair} keyword of the "run_style
respa"_run_style.html command. They do not support the {inner},
{middle}, {outer} keywords.
[Restrictions:]
-The {buck/coul/long} style is part of the "kspace" package. It is
-only enabled if LAMMPS was built with that package (which it is by
+The {buck/coul/long} style is part of the KSPACE package. It is only
+enabled if LAMMPS was built with that package (which it is by
default). See the "Making LAMMPS"_Section_start.html#start_3 section
for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html, "pair_style born"_pair_born.html
[Default:] none
diff --git a/doc/pair_buck_coul.html b/doc/pair_buck_coul.html
index a9c0b7509..cfb237e58 100644
--- a/doc/pair_buck_coul.html
+++ b/doc/pair_buck_coul.html
@@ -1,154 +1,154 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style buck/coul command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style buck/coul flag_buck flag_coul cutoff (cutoff2)
</PRE>
<UL><LI>flag_buck = <I>long</I> or <I>cut</I>
<PRE> <I>long</I> = use Kspace long-range summation for the dispersion term 1/r^6
<I>cut</I> = use a cutoff
</PRE>
<LI>flag_coul = <I>long</I> or <I>off</I>
<PRE> <I>long</I> = use Kspace long-range summation for the Coulombic term 1/r
<I>off</I> = omit the Coulombic term
</PRE>
<LI>cutoff = global cutoff for Buckingham (and Coulombic if only 1 cutoff) (distance units)
<LI>cutoff2 = global cutoff for Coulombic (optional) (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style buck/coul cut off 2.5
pair_style buck/coul cut long 2.5 4.0
pair_style buck/coul long long 2.5 4.0
pair_coeff * * 1 1
pair_coeff 1 1 1 3 4
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>buck/coul</I> style computes a Buckingham potential (exp/6 instead of
Lennard-Jones 12/6) and Coulombic potential, given by
</P>
<CENTER><IMG SRC = "Eqs/pair_buck.jpg">
</CENTER>
<CENTER><IMG SRC = "Eqs/pair_coulomb.jpg">
</CENTER>
<P>Rc is the cutoff. If one cutoff is specified in the pair_style
command, it is used for both the Buckingham and Coulombic terms. If
two cutoffs are specified, they are used as cutoffs for the Buckingham
and Coulombic terms respectively.
</P>
<P>The purpose of this pair style is to capture long-range interactions
resulting from both attractive 1/r^6 Buckingham and Coulombic 1/r
interactions. This is done by use of the <I>flag_buck</I> and <I>flag_coul</I>
settings. The "<A HREF = "#Ismail">Ismail</A> paper has more details on when it is
appropriate to include long-range 1/r^6 interactions, using this
potential.
</P>
<P>If <I>flag_buck</I> is set to <I>long</I>, no cutoff is used on the Buckingham
1/r^6 dispersion term. The long-range portion is calculated by using
the <A HREF = "kspace_style.html">kspace_style ewald/n</A> command. The specified
Buckingham cutoff then determines which portion of the Buckingham
interactions are computed directly by the pair potential versus which
part is computed in reciprocal space via the Kspace style. If
<I>flag_buck</I> is set to <I>cut</I>, the Buckingham interactions are simply
cutoff, as with <A HREF = "pair_buck.html">pair_style buck</A>.
</P>
<P>If <I>flag_coul</I> is set to <I>long</I>, no cutoff is used on the Coulombic
interactions. The long-range portion is calculated by using any
style, including <I>ewald/n</I> of the <A HREF = "kspace_style.html">kspace_style</A>
command. Note that if <I>flag_buck</I> is also set to long, then only the
<I>ewald/n</I> Kspace style can perform the long-range calculations for
both the Buckingham and Coulombic interactions. If <I>flag_coul</I> is set
to <I>off</I>, Coulombic interactions are not computed.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands:
</P>
<UL><LI>A (energy units)
<LI>rho (distance units)
<LI>C (energy-distance^6 units)
<LI>cutoff (distance units)
<LI>cutoff2 (distance units)
</UL>
<P>The second coefficient, rho, must be greater than zero.
</P>
<P>The latter 2 coefficients are optional. If not specified, the global
Buckingham and Coulombic cutoffs specified in the pair_style command
are used. If only one cutoff is specified, it is used as the cutoff
for both Buckingham and Coulombic interactions for this type pair. If
both coefficients are specified, they are used as the Buckingham and
Coulombic cutoffs for this type pair. Note that if you are using
<I>flag_buck</I> set to <I>long</I>, you cannot specify a Buckingham cutoff for
an atom type pair, since only one global Buckingham cutoff is allowed.
Similarly, if you are using <I>flag_coul</I> set to <I>long</I>, you cannot
specify a Coulombic cutoff for an atom type pair, since only one
global Coulombic cutoff is allowed.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>This pair styles does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
</P>
<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
option for the energy of the exp() and 1/r^6 portion of the pair
interaction, assuming <I>flag_buck</I> is <I>cut</I>.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift option for the energy of the Buckingham portion of the pair
interaction.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
table option since a tabulation capability has not yet been added to
this potential.
</P>
<P>This pair style write its information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style supports the use of the <I>inner</I>, <I>middle</I>, and <I>outer</I>
keywords of the <A HREF = "run_style.html">run_style respa</A> command, meaning the
pairwise forces can be partitioned by distance at different levels of
the rRESPA hierarchy. See the <A HREF = "run_style.html">run_style</A> command for
details.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>This style is part of the "user-ewaldn" package. It is only enabled
-if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+<P>This style is part of the USER-EWALDN package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Ismail"></A>
<P><B>(Ismail)</B> Ismail, Tsige, In 't Veld, Grest, Molecular Physics
(accepted) (2007).
</P>
</HTML>
diff --git a/doc/pair_buck_coul.txt b/doc/pair_buck_coul.txt
index d306dc03f..16638246a 100644
--- a/doc/pair_buck_coul.txt
+++ b/doc/pair_buck_coul.txt
@@ -1,143 +1,143 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style buck/coul command :h3
[Syntax:]
pair_style buck/coul flag_buck flag_coul cutoff (cutoff2) :pre
flag_buck = {long} or {cut} :ulb,l
{long} = use Kspace long-range summation for the dispersion term 1/r^6
{cut} = use a cutoff :pre
flag_coul = {long} or {off} :l
{long} = use Kspace long-range summation for the Coulombic term 1/r
{off} = omit the Coulombic term :pre
cutoff = global cutoff for Buckingham (and Coulombic if only 1 cutoff) (distance units) :l
cutoff2 = global cutoff for Coulombic (optional) (distance units) :l,ule
[Examples:]
pair_style buck/coul cut off 2.5
pair_style buck/coul cut long 2.5 4.0
pair_style buck/coul long long 2.5 4.0
pair_coeff * * 1 1
pair_coeff 1 1 1 3 4 :pre
[Description:]
The {buck/coul} style computes a Buckingham potential (exp/6 instead of
Lennard-Jones 12/6) and Coulombic potential, given by
:c,image(Eqs/pair_buck.jpg)
:c,image(Eqs/pair_coulomb.jpg)
Rc is the cutoff. If one cutoff is specified in the pair_style
command, it is used for both the Buckingham and Coulombic terms. If
two cutoffs are specified, they are used as cutoffs for the Buckingham
and Coulombic terms respectively.
The purpose of this pair style is to capture long-range interactions
resulting from both attractive 1/r^6 Buckingham and Coulombic 1/r
interactions. This is done by use of the {flag_buck} and {flag_coul}
settings. The ""Ismail"_#Ismail paper has more details on when it is
appropriate to include long-range 1/r^6 interactions, using this
potential.
If {flag_buck} is set to {long}, no cutoff is used on the Buckingham
1/r^6 dispersion term. The long-range portion is calculated by using
the "kspace_style ewald/n"_kspace_style.html command. The specified
Buckingham cutoff then determines which portion of the Buckingham
interactions are computed directly by the pair potential versus which
part is computed in reciprocal space via the Kspace style. If
{flag_buck} is set to {cut}, the Buckingham interactions are simply
cutoff, as with "pair_style buck"_pair_buck.html.
If {flag_coul} is set to {long}, no cutoff is used on the Coulombic
interactions. The long-range portion is calculated by using any
style, including {ewald/n} of the "kspace_style"_kspace_style.html
command. Note that if {flag_buck} is also set to long, then only the
{ewald/n} Kspace style can perform the long-range calculations for
both the Buckingham and Coulombic interactions. If {flag_coul} is set
to {off}, Coulombic interactions are not computed.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands:
A (energy units)
rho (distance units)
C (energy-distance^6 units)
cutoff (distance units)
cutoff2 (distance units) :ul
The second coefficient, rho, must be greater than zero.
The latter 2 coefficients are optional. If not specified, the global
Buckingham and Coulombic cutoffs specified in the pair_style command
are used. If only one cutoff is specified, it is used as the cutoff
for both Buckingham and Coulombic interactions for this type pair. If
both coefficients are specified, they are used as the Buckingham and
Coulombic cutoffs for this type pair. Note that if you are using
{flag_buck} set to {long}, you cannot specify a Buckingham cutoff for
an atom type pair, since only one global Buckingham cutoff is allowed.
Similarly, if you are using {flag_coul} set to {long}, you cannot
specify a Coulombic cutoff for an atom type pair, since only one
global Coulombic cutoff is allowed.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
This pair styles does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
This pair style supports the "pair_modify"_pair_modify.html shift
option for the energy of the exp() and 1/r^6 portion of the pair
interaction, assuming {flag_buck} is {cut}.
This pair style does not support the "pair_modify"_pair_modify.html
shift option for the energy of the Buckingham portion of the pair
interaction.
This pair style does not support the "pair_modify"_pair_modify.html
table option since a tabulation capability has not yet been added to
this potential.
This pair style write its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style supports the use of the {inner}, {middle}, and {outer}
keywords of the "run_style respa"_run_style.html command, meaning the
pairwise forces can be partitioned by distance at different levels of
the rRESPA hierarchy. See the "run_style"_run_style.html command for
details.
:line
[Restrictions:]
-This style is part of the "user-ewaldn" package. It is only enabled
-if LAMMPS was built with that package. See the "Making
+This style is part of the USER-EWALDN package. It is only enabled if
+LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Ismail)
[(Ismail)] Ismail, Tsige, In 't Veld, Grest, Molecular Physics
(accepted) (2007).
diff --git a/doc/pair_charmm.html b/doc/pair_charmm.html
index 2d67fb2bb..0f1b7c572 100644
--- a/doc/pair_charmm.html
+++ b/doc/pair_charmm.html
@@ -1,198 +1,198 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style lj/charmm/coul/charmm command
</H3>
<H3>pair_style lj/charmm/coul/charmm/cuda command
</H3>
<H3>pair_style lj/charmm/coul/charmm/implicit command
</H3>
<H3>pair_style lj/charmm/coul/charmm/implicit/cuda command
</H3>
<H3>pair_style lj/charmm/coul/long command
</H3>
<H3>pair_style lj/charmm/coul/long/cuda command
</H3>
<H3>pair_style lj/charmm/coul/long/gpu command
</H3>
<H3>pair_style lj/charmm/coul/long/opt command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style args
</PRE>
<UL><LI>style = <I>lj/charmm/coul/charmm</I> or <I>lj/charmm/coul/charmm/implicit</I> or <I>lj/charmm/coul/long</I>
<LI>args = list of arguments for a particular style
</UL>
<PRE> <I>lj/charmm/coul/charmm</I> args = inner outer (inner2) (outer2)
inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
inner2, outer2 = global switching cutoffs for Coulombic (optional)
<I>lj/charmm/coul/charmm/implicit</I> args = inner outer (inner2) (outer2)
inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
inner2, outer2 = global switching cutoffs for Coulombic (optional)
<I>lj/charmm/coul/long</I> args = inner outer (cutoff)
inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style lj/charmm/coul/charmm 8.0 10.0
pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5
</PRE>
<PRE>pair_style lj/charmm/coul/charmm/implicit 8.0 10.0
pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5
</PRE>
<PRE>pair_style lj/charmm/coul/long 8.0 10.0
pair_style lj/charmm/coul/long 8.0 10.0 9.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>lj/charmm</I> styles compute LJ and Coulombic interactions with an
additional switching function S(r) that ramps the energy and force
smoothly to zero between an inner and outer cutoff. It is a widely
used potential in the <A HREF = "http://www.scripps.edu/brooks">CHARMM</A> MD code.
See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
field.
</P>
<CENTER><IMG SRC = "Eqs/pair_charmm.jpg">
</CENTER>
<P>Both the LJ and Coulombic terms require an inner and outer cutoff.
They can be the same for both formulas or different depending on
whether 2 or 4 arguments are used in the pair_style command. In each
case, the inner cutoff distance must be less than the outer cutoff.
It it typical to make the difference between the 2 cutoffs about 1.0
Angstrom.
</P>
<P>Style <I>lj/charmm/coul/charmm/implicit</I> computes the same formulas as
style <I>lj/charmm/coul/charmm</I> except that an additional 1/r term is
included in the Coulombic formula. The Coulombic energy thus varies
as 1/r^2. This is effectively a distance-dependent dielectric term
which is a simple model for an implicit solvent with additional
screening. It is designed for use in a simulation of an unsolvated
biomolecule (no explicit water molecules).
</P>
<P>Style <I>lj/charmm/coul/long</I> computes the same formulas as style
<I>lj/charmm/coul/charmm</I> except that an additional damping factor is
applied to the Coulombic term, as in the discussion for pair style
<I>lj/cut/coul/long</I>. Only one Coulombic cutoff is specified for
<I>lj/charmm/coul/long</I>; if only 2 arguments are used in the pair_style
command, then the outer LJ cutoff is used as the single Coulombic
cutoff.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>epsilon (energy units)
<LI>sigma (distance units)
<LI>epsilon_14 (energy units)
<LI>sigma_14 (distance units)
</UL>
<P>Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum at 2^(1/6)
sigma.
</P>
<P>The latter 2 coefficients are optional. If they are specified, they
are used in the LJ formula between 2 atoms of these types which are
also first and fourth atoms in any dihedral. No cutoffs are specified
because this CHARMM force field does not allow varying cutoffs for
individual atom pairs; all pairs use the global cutoff(s) specified in
the pair_style command.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+<P>These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14,
and sigma_14 coefficients for all of the lj/charmm pair styles can be
mixed. The default mix value is <I>arithmetic</I> to coincide with the
usual settings for the CHARMM force field. See the "pair_modify"
command for details.
</P>
<P>None of the lj/charmm pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> shift option, since the Lennard-Jones
portion of the pair interaction is smoothed to 0.0 at the cutoff.
</P>
<P>The <I>lj/charmm/coul/long</I> style supports the
<A HREF = "pair_modify.html">pair_modify</A> table option since it can tabulate the
short-range portion of the long-range Coulombic interaction.
</P>
<P>None of the lj/charmm pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> tail option for adding long-range tail
corrections to energy and pressure, since the Lennard-Jones portion of
the pair interaction is smoothed to 0.0 at the cutoff.
</P>
<P>All of the lj/charmm pair styles write their information to <A HREF = "restart.html">binary
restart files</A>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
</P>
<P>The lj/charmm/coul/long pair style supports the use of the <I>inner</I>,
<I>middle</I>, and <I>outer</I> keywords of the <A HREF = "run_style.html">run_style respa</A>
command, meaning the pairwise forces can be partitioned by distance at
different levels of the rRESPA hierarchy. The other styles only
support the <I>pair</I> keyword of run_style respa. See the
<A HREF = "run_style.html">run_style</A> command for details.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>The <I>lj/charmm/coul/charmm</I> and <I>lj/charmm/coul/charmm/implicit</I>
-styles are part of the "molecule" package. The <I>lj/charmm/coul/long</I>
-style is part of the "kspace" package. They are only enabled if
-LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
+styles are part of the MOLECULE package. The <I>lj/charmm/coul/long</I>
+style is part of the KSPACE package. They are only enabled if LAMMPS
+was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info. Note that
-the molecule and kspace packages are installed by default.
+the MOLECULE and KSPACE packages are installed by default.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "MacKerell"></A>
<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
</P>
</HTML>
diff --git a/doc/pair_charmm.txt b/doc/pair_charmm.txt
index a6540c5c3..7e38167b2 100644
--- a/doc/pair_charmm.txt
+++ b/doc/pair_charmm.txt
@@ -1,184 +1,184 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style lj/charmm/coul/charmm command :h3
pair_style lj/charmm/coul/charmm/cuda command :h3
pair_style lj/charmm/coul/charmm/implicit command :h3
pair_style lj/charmm/coul/charmm/implicit/cuda command :h3
pair_style lj/charmm/coul/long command :h3
pair_style lj/charmm/coul/long/cuda command :h3
pair_style lj/charmm/coul/long/gpu command :h3
pair_style lj/charmm/coul/long/opt command :h3
[Syntax:]
pair_style style args :pre
style = {lj/charmm/coul/charmm} or {lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long}
args = list of arguments for a particular style :ul
{lj/charmm/coul/charmm} args = inner outer (inner2) (outer2)
inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
inner2, outer2 = global switching cutoffs for Coulombic (optional)
{lj/charmm/coul/charmm/implicit} args = inner outer (inner2) (outer2)
inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
inner2, outer2 = global switching cutoffs for Coulombic (optional)
{lj/charmm/coul/long} args = inner outer (cutoff)
inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args) :pre
[Examples:]
pair_style lj/charmm/coul/charmm 8.0 10.0
pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
pair_style lj/charmm/coul/charmm/implicit 8.0 10.0
pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
pair_style lj/charmm/coul/long 8.0 10.0
pair_style lj/charmm/coul/long 8.0 10.0 9.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
[Description:]
The {lj/charmm} styles compute LJ and Coulombic interactions with an
additional switching function S(r) that ramps the energy and force
smoothly to zero between an inner and outer cutoff. It is a widely
used potential in the "CHARMM"_http://www.scripps.edu/brooks MD code.
See "(MacKerell)"_#MacKerell for a description of the CHARMM force
field.
:c,image(Eqs/pair_charmm.jpg)
Both the LJ and Coulombic terms require an inner and outer cutoff.
They can be the same for both formulas or different depending on
whether 2 or 4 arguments are used in the pair_style command. In each
case, the inner cutoff distance must be less than the outer cutoff.
It it typical to make the difference between the 2 cutoffs about 1.0
Angstrom.
Style {lj/charmm/coul/charmm/implicit} computes the same formulas as
style {lj/charmm/coul/charmm} except that an additional 1/r term is
included in the Coulombic formula. The Coulombic energy thus varies
as 1/r^2. This is effectively a distance-dependent dielectric term
which is a simple model for an implicit solvent with additional
screening. It is designed for use in a simulation of an unsolvated
biomolecule (no explicit water molecules).
Style {lj/charmm/coul/long} computes the same formulas as style
{lj/charmm/coul/charmm} except that an additional damping factor is
applied to the Coulombic term, as in the discussion for pair style
{lj/cut/coul/long}. Only one Coulombic cutoff is specified for
{lj/charmm/coul/long}; if only 2 arguments are used in the pair_style
command, then the outer LJ cutoff is used as the single Coulombic
cutoff.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
epsilon (energy units)
sigma (distance units)
epsilon_14 (energy units)
sigma_14 (distance units) :ul
Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum at 2^(1/6)
sigma.
The latter 2 coefficients are optional. If they are specified, they
are used in the LJ formula between 2 atoms of these types which are
also first and fourth atoms in any dihedral. No cutoffs are specified
because this CHARMM force field does not allow varying cutoffs for
individual atom pairs; all pairs use the global cutoff(s) specified in
the pair_style command.
:line
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14,
and sigma_14 coefficients for all of the lj/charmm pair styles can be
mixed. The default mix value is {arithmetic} to coincide with the
usual settings for the CHARMM force field. See the "pair_modify"
command for details.
None of the lj/charmm pair styles support the
"pair_modify"_pair_modify.html shift option, since the Lennard-Jones
portion of the pair interaction is smoothed to 0.0 at the cutoff.
The {lj/charmm/coul/long} style supports the
"pair_modify"_pair_modify.html table option since it can tabulate the
short-range portion of the long-range Coulombic interaction.
None of the lj/charmm pair styles support the
"pair_modify"_pair_modify.html tail option for adding long-range tail
corrections to energy and pressure, since the Lennard-Jones portion of
the pair interaction is smoothed to 0.0 at the cutoff.
All of the lj/charmm pair styles write their information to "binary
restart files"_restart.html, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
The lj/charmm/coul/long pair style supports the use of the {inner},
{middle}, and {outer} keywords of the "run_style respa"_run_style.html
command, meaning the pairwise forces can be partitioned by distance at
different levels of the rRESPA hierarchy. The other styles only
support the {pair} keyword of run_style respa. See the
"run_style"_run_style.html command for details.
:line
[Restrictions:]
The {lj/charmm/coul/charmm} and {lj/charmm/coul/charmm/implicit}
-styles are part of the "molecule" package. The {lj/charmm/coul/long}
-style is part of the "kspace" package. They are only enabled if
-LAMMPS was built with those packages. See the "Making
+styles are part of the MOLECULE package. The {lj/charmm/coul/long}
+style is part of the KSPACE package. They are only enabled if LAMMPS
+was built with those packages. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info. Note that
-the molecule and kspace packages are installed by default.
+the MOLECULE and KSPACE packages are installed by default.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(MacKerell)
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
diff --git a/doc/pair_class2.html b/doc/pair_class2.html
index 217dd9a71..f379c35fc 100644
--- a/doc/pair_class2.html
+++ b/doc/pair_class2.html
@@ -1,179 +1,179 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style lj/class2 command
</H3>
<H3>pair_style lj/class2/cuda command
</H3>
<H3>pair_style lj/class2/gpu command
</H3>
<H3>pair_style lj/class2/coul/cut command
</H3>
<H3>pair_style lj/class2/coul/cut/cuda command
</H3>
<H3>pair_style lj/class2/coul/long command
</H3>
<H3>pair_style lj/class2/coul/long/cuda command
</H3>
<H3>pair_style lj/class2/coul/long/gpu command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style args
</PRE>
<UL><LI>style = <I>lj/class2</I> or <I>lj/class2/coul/cut</I> or <I>lj/class2/coul/long</I>
<LI>args = list of arguments for a particular style
</UL>
<PRE> <I>lj/class2</I> args = cutoff
cutoff = global cutoff for class 2 interactions (distance units)
<I>lj/class2/coul/cut</I> args = cutoff (cutoff2)
cutoff = global cutoff for class 2 (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<I>lj/class2/coul/long</I> args = cutoff (cutoff2)
cutoff = global cutoff for class 2 (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style lj/class2 10.0
pair_coeff * * 100.0 2.5
pair_coeff 1 2* 100.0 2.5 9.0
</PRE>
<PRE>pair_style lj/class2/coul/cut 10.0
pair_style lj/class2/coul/cut 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
pair_coeff 1 1 100.0 3.5 9.0 9.0
</PRE>
<PRE>pair_style lj/class2/coul/long 10.0
pair_style lj/class2/coul/long 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>lj/class2</I> styles compute a 6/9 Lennard-Jones potential given by
</P>
<CENTER><IMG SRC = "Eqs/pair_class2.jpg">
</CENTER>
<P>Rc is the cutoff.
</P>
<P>The <I>lj/class2/coul/cut</I> and <I>lj/class2/coul/long</I> styles add a
Coulombic term as described for the <A HREF = "pair_lj.html">lj/cut</A> pair
styles.
</P>
<P>See <A HREF = "#Sun">(Sun)</A> for a description of the COMPASS class2 force field.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>epsilon (energy units)
<LI>sigma (distance units)
<LI>cutoff1 (distance units)
<LI>cutoff2 (distance units)
</UL>
<P>The latter 2 coefficients are optional. If not specified, the global
class 2 and Coulombic cutoffs are used. If only one cutoff is
specified, it is used as the cutoff for both class 2 and Coulombic
interactions for this type pair. If both coefficients are specified,
they are used as the class 2 and Coulombic cutoffs for this type pair.
You cannot specify 2 cutoffs for style <I>lj/class2</I>, since it has no
Coulombic terms.
</P>
<P>For <I>lj/class2/coul/long</I> only the class 2 cutoff can be specified
since a Coulombic cutoff cannot be specified for an individual I,J
type pair. All type pairs use the same global Coulombic cutoff
specified in the pair_style command.
</P>
<HR>
<P>If the pair_coeff command is not used to define coefficients for a
particular I != J type pair, the mixing rule for epsilon and sigma for
all class2 potentials is to use the <I>sixthpower</I> formulas documented
by the <A HREF = "pair_modify.html">pair_modify</A> command. The <A HREF = "pair_modify.html">pair_modify
mix</A> setting is thus ignored for class2 potentials
for epsilon and sigma. However it is still followed for mixing the
cutoff distance.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+<P>These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/class2 pair styles can be mixed.
Epsilon and sigma are always mixed with the value <I>sixthpower</I>. The
cutoff distance is mixed by whatever option is set by the pair_modify
command (default = geometric). See the "pair_modify" command for
details.
</P>
<P>All of the lj/class2 pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> shift option for the energy of the
Lennard-Jones portion of the pair interaction.
</P>
<P>The <I>lj/class2/coul/long</I> pair style does not support the
<A HREF = "pair_modify.html">pair_modify</A> table option since a tabulation
capability has not yet been added to this potential.
</P>
<P>All of the lj/class2 pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> tail option for adding a long-range
tail correction to the energy and pressure of the Lennard-Jones
portion of the pair interaction.
</P>
<P>All of the lj/class2 pair styles write their information to <A HREF = "restart.html">binary
restart files</A>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
</P>
<P>All of the lj/class2 pair styles can only be used via the <I>pair</I>
keyword of the <A HREF = "run_style.html">run_style respa</A> command. They do not
support the <I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<P><B>Restrictions:</B>
</P>
-<P>These styles are part of the "class2" package. They are only enabled
-if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+<P>These styles are part of the CLASS2 package. They are only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Sun"></A>
<P><B>(Sun)</B> Sun, J Phys Chem B 102, 7338-7364 (1998).
</P>
</HTML>
diff --git a/doc/pair_class2.txt b/doc/pair_class2.txt
index 25fa72b67..881b458f3 100644
--- a/doc/pair_class2.txt
+++ b/doc/pair_class2.txt
@@ -1,165 +1,165 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style lj/class2 command :h3
pair_style lj/class2/cuda command :h3
pair_style lj/class2/gpu command :h3
pair_style lj/class2/coul/cut command :h3
pair_style lj/class2/coul/cut/cuda command :h3
pair_style lj/class2/coul/long command :h3
pair_style lj/class2/coul/long/cuda command :h3
pair_style lj/class2/coul/long/gpu command :h3
[Syntax:]
pair_style style args :pre
style = {lj/class2} or {lj/class2/coul/cut} or {lj/class2/coul/long}
args = list of arguments for a particular style :ul
{lj/class2} args = cutoff
cutoff = global cutoff for class 2 interactions (distance units)
{lj/class2/coul/cut} args = cutoff (cutoff2)
cutoff = global cutoff for class 2 (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{lj/class2/coul/long} args = cutoff (cutoff2)
cutoff = global cutoff for class 2 (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
[Examples:]
pair_style lj/class2 10.0
pair_coeff * * 100.0 2.5
pair_coeff 1 2* 100.0 2.5 9.0 :pre
pair_style lj/class2/coul/cut 10.0
pair_style lj/class2/coul/cut 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
pair_coeff 1 1 100.0 3.5 9.0 9.0 :pre
pair_style lj/class2/coul/long 10.0
pair_style lj/class2/coul/long 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0 :pre
[Description:]
The {lj/class2} styles compute a 6/9 Lennard-Jones potential given by
:c,image(Eqs/pair_class2.jpg)
Rc is the cutoff.
The {lj/class2/coul/cut} and {lj/class2/coul/long} styles add a
Coulombic term as described for the "lj/cut"_pair_lj.html pair
styles.
See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
epsilon (energy units)
sigma (distance units)
cutoff1 (distance units)
cutoff2 (distance units) :ul
The latter 2 coefficients are optional. If not specified, the global
class 2 and Coulombic cutoffs are used. If only one cutoff is
specified, it is used as the cutoff for both class 2 and Coulombic
interactions for this type pair. If both coefficients are specified,
they are used as the class 2 and Coulombic cutoffs for this type pair.
You cannot specify 2 cutoffs for style {lj/class2}, since it has no
Coulombic terms.
For {lj/class2/coul/long} only the class 2 cutoff can be specified
since a Coulombic cutoff cannot be specified for an individual I,J
type pair. All type pairs use the same global Coulombic cutoff
specified in the pair_style command.
:line
If the pair_coeff command is not used to define coefficients for a
particular I != J type pair, the mixing rule for epsilon and sigma for
all class2 potentials is to use the {sixthpower} formulas documented
by the "pair_modify"_pair_modify.html command. The "pair_modify
mix"_pair_modify.html setting is thus ignored for class2 potentials
for epsilon and sigma. However it is still followed for mixing the
cutoff distance.
:line
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/class2 pair styles can be mixed.
Epsilon and sigma are always mixed with the value {sixthpower}. The
cutoff distance is mixed by whatever option is set by the pair_modify
command (default = geometric). See the "pair_modify" command for
details.
All of the lj/class2 pair styles support the
"pair_modify"_pair_modify.html shift option for the energy of the
Lennard-Jones portion of the pair interaction.
The {lj/class2/coul/long} pair style does not support the
"pair_modify"_pair_modify.html table option since a tabulation
capability has not yet been added to this potential.
All of the lj/class2 pair styles support the
"pair_modify"_pair_modify.html tail option for adding a long-range
tail correction to the energy and pressure of the Lennard-Jones
portion of the pair interaction.
All of the lj/class2 pair styles write their information to "binary
restart files"_restart.html, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
All of the lj/class2 pair styles can only be used via the {pair}
keyword of the "run_style respa"_run_style.html command. They do not
support the {inner}, {middle}, {outer} keywords.
[Restrictions:]
-These styles are part of the "class2" package. They are only enabled
-if LAMMPS was built with that package. See the "Making
+These styles are part of the CLASS2 package. They are only enabled if
+LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Sun)
[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998).
diff --git a/doc/pair_cmm.html b/doc/pair_cmm.html
index 255532194..766904a07 100644
--- a/doc/pair_cmm.html
+++ b/doc/pair_cmm.html
@@ -1,203 +1,203 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style cg/cmm command
</H3>
<H3>pair_style cg/cmm/cuda command
</H3>
<H3>pair_style cg/cmm/gpu command
</H3>
<H3>pair_style cg/cmm/coul/cut command
</H3>
<H3>pair_style cg/cmm/coul/cut/cuda command
</H3>
<H3>pair_style cg/cmm/coul/debye/cuda command
</H3>
<H3>pair_style cg/cmm/coul/long command
</H3>
<H3>pair_style cg/cmm/coul/long/gpu command
</H3>
<H3>pair_style cg/cmm/coul/long/cuda command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style args
</PRE>
<UL><LI>style = <I>cg/cmm</I> or <I>cg/cmm/coul/cut</I> or <I>cg/cmm/coul/long</I>
<LI>args = list of arguments for a particular style
</UL>
<PRE> <I>cg/cmm</I> args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
<I>cg/cmm/coul/cut</I> args = cutoff (cutoff2) (kappa)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
kappa = Debye length (optional, defaults to 0.0 = disabled) (inverse distance units)
<I>cg/cmm/coul/long</I> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style cg/cmm 2.5
pair_coeff 1 1 lj12_6 1 1.1 2.8
</PRE>
<PRE>pair_style cg/cmm/coul/cut 10.0 12.0
pair_coeff 1 1 lj9_6 100.0 3.5 9.0
pair_coeff 1 1 lj12_4 100.0 3.5 9.0 9.0
</PRE>
<PRE>pair_style cg/cmm/coul/long 10.0
pair_style cg/cmm/coul/long 10.0 8.0
pair_coeff 1 1 lj9_6 100.0 3.5 9.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>cg/cmm</I> styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
given by
</P>
<CENTER><IMG SRC = "Eqs/pair_cmm.jpg">
</CENTER>
<P>as required for the CMM Coarse-grained MD parametrization discussed in
<A HREF = "#Shinoda">(Shinoda)</A> and <A HREF = "#DeVane">(DeVane)</A>. Rc is the cutoff.
</P>
<P>Style <I>cg/cmm/coul/cut</I> adds a Coulombic pairwise interaction given by
</P>
<CENTER><IMG SRC = "Eqs/pair_coulomb.jpg">
</CENTER>
<P>where C is an energy-conversion constant, Qi and Qj are the charges on
the 2 atoms, and epsilon is the dielectric constant which can be set
by the <A HREF = "dielectric.html">dielectric</A> command. If one cutoff is
specified in the pair_style command, it is used for both the LJ and
Coulombic terms. If two cutoffs are specified, they are used as
cutoffs for the LJ and Coulombic terms respectively.
</P>
<P>This style also contains an additional exp() damping factor
to the Coulombic term, given by
</P>
<CENTER><IMG SRC = "Eqs/pair_debye.jpg">
</CENTER>
<P>where kappa is the Debye length (kappa=0.0 is the unscreened coulomb).
This potential is another way to mimic the screening effect of a polar
solvent.
</P>
<P>Style <I>cg/cmm/coul/long</I> computes the same Coulombic interactions as
style <I>cg/cmm/coul/cut</I> except that an additional damping factor is
applied to the Coulombic term so it can be used in conjunction with
the <A HREF = "kspace_style.html">kspace_style</A> command and its <I>ewald</I> or <I>pppm</I>
option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>cg_type (lj9_6, lj12_4, or lj12_6)
<LI>epsilon (energy units)
<LI>sigma (distance units)
<LI>cutoff1 (distance units)
<LI>cutoff2 (distance units)
</UL>
<P>Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum. The prefactors
are chosen so that the potential minimum is at -epsilon.
</P>
<P>The latter 2 coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair.
</P>
<P>For <I>cg/cmm/coul/long</I> only the LJ cutoff can be specified since a
Coulombic cutoff cannot be specified for an individual I,J type pair.
All type pairs use the same global Coulombic cutoff specified in the
pair_style command.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+<P>These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, and rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the cg/cmm pair styles <I>cannot</I> be mixed,
since different pairs may have different exponents. So all parameters
for all pairs have to be specified explicitly through the "pair_coeff"
command. Defining then in a data file is also not supported, due to
limitations of that file format.
</P>
<P>All of the cg/cmm pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> shift option for the energy of the
Lennard-Jones portion of the pair interaction.
</P>
<P>The <I>cg/cmm/coul/long</I> pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> table option since they can tabulate
the short-range portion of the long-range Coulombic interaction.
</P>
<P>All of the cg/cmm pair styles write their information to <A HREF = "restart.html">binary
restart files</A>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
</P>
<P>The cg/cmm, cg/cmm/coul/cut and lj/cut/coul/long pair styles support
the use of the <I>inner</I>, <I>middle</I>, and <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
respa</A> command, meaning the pairwise forces can be
partitioned by distance at different levels of the rRESPA hierarchy.
See the <A HREF = "run_style.html">run_style</A> command for details.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>All of the cg/cmm pair styles are part of the "user-cg-cmm" package.
-The <I>cg/cmm/coul/long</I> style also requires the "kspace" package to be
+<P>All of the cg/cmm pair styles are part of the USER-CG-CMM package.
+The <I>cg/cmm/coul/long</I> style also requires the KSPACE package to be
built (which is enabled by default). They are only enabled if LAMMPS
was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "angle_cmm.html">angle_style cg/cmm</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Shinoda"></A>
<P><B>(Shinoda)</B> Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
</P>
<A NAME = "DeVane"></A>
<P><B>(DeVane)</B> Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).
</P>
</HTML>
diff --git a/doc/pair_cmm.txt b/doc/pair_cmm.txt
index d0e5d058f..b330de491 100644
--- a/doc/pair_cmm.txt
+++ b/doc/pair_cmm.txt
@@ -1,188 +1,188 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style cg/cmm command :h3
pair_style cg/cmm/cuda command :h3
pair_style cg/cmm/gpu command :h3
pair_style cg/cmm/coul/cut command :h3
pair_style cg/cmm/coul/cut/cuda command :h3
pair_style cg/cmm/coul/debye/cuda command :h3
pair_style cg/cmm/coul/long command :h3
pair_style cg/cmm/coul/long/gpu command :h3
pair_style cg/cmm/coul/long/cuda command :h3
[Syntax:]
pair_style style args :pre
style = {cg/cmm} or {cg/cmm/coul/cut} or {cg/cmm/coul/long}
args = list of arguments for a particular style :ul
{cg/cmm} args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
{cg/cmm/coul/cut} args = cutoff (cutoff2) (kappa)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
kappa = Debye length (optional, defaults to 0.0 = disabled) (inverse distance units)
{cg/cmm/coul/long} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
[Examples:]
pair_style cg/cmm 2.5
pair_coeff 1 1 lj12_6 1 1.1 2.8 :pre
pair_style cg/cmm/coul/cut 10.0 12.0
pair_coeff 1 1 lj9_6 100.0 3.5 9.0
pair_coeff 1 1 lj12_4 100.0 3.5 9.0 9.0 :pre
pair_style cg/cmm/coul/long 10.0
pair_style cg/cmm/coul/long 10.0 8.0
pair_coeff 1 1 lj9_6 100.0 3.5 9.0 :pre
[Description:]
The {cg/cmm} styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
given by
:c,image(Eqs/pair_cmm.jpg)
as required for the CMM Coarse-grained MD parametrization discussed in
"(Shinoda)"_#Shinoda and "(DeVane)"_#DeVane. Rc is the cutoff.
Style {cg/cmm/coul/cut} adds a Coulombic pairwise interaction given by
:c,image(Eqs/pair_coulomb.jpg)
where C is an energy-conversion constant, Qi and Qj are the charges on
the 2 atoms, and epsilon is the dielectric constant which can be set
by the "dielectric"_dielectric.html command. If one cutoff is
specified in the pair_style command, it is used for both the LJ and
Coulombic terms. If two cutoffs are specified, they are used as
cutoffs for the LJ and Coulombic terms respectively.
This style also contains an additional exp() damping factor
to the Coulombic term, given by
:c,image(Eqs/pair_debye.jpg)
where kappa is the Debye length (kappa=0.0 is the unscreened coulomb).
This potential is another way to mimic the screening effect of a polar
solvent.
Style {cg/cmm/coul/long} computes the same Coulombic interactions as
style {cg/cmm/coul/cut} except that an additional damping factor is
applied to the Coulombic term so it can be used in conjunction with
the "kspace_style"_kspace_style.html command and its {ewald} or {pppm}
option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
cg_type (lj9_6, lj12_4, or lj12_6)
epsilon (energy units)
sigma (distance units)
cutoff1 (distance units)
cutoff2 (distance units) :ul
Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum. The prefactors
are chosen so that the potential minimum is at -epsilon.
The latter 2 coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair.
For {cg/cmm/coul/long} only the LJ cutoff can be specified since a
Coulombic cutoff cannot be specified for an individual I,J type pair.
All type pairs use the same global Coulombic cutoff specified in the
pair_style command.
:line
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, and rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the cg/cmm pair styles {cannot} be mixed,
since different pairs may have different exponents. So all parameters
for all pairs have to be specified explicitly through the "pair_coeff"
command. Defining then in a data file is also not supported, due to
limitations of that file format.
All of the cg/cmm pair styles support the
"pair_modify"_pair_modify.html shift option for the energy of the
Lennard-Jones portion of the pair interaction.
The {cg/cmm/coul/long} pair styles support the
"pair_modify"_pair_modify.html table option since they can tabulate
the short-range portion of the long-range Coulombic interaction.
All of the cg/cmm pair styles write their information to "binary
restart files"_restart.html, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
The cg/cmm, cg/cmm/coul/cut and lj/cut/coul/long pair styles support
the use of the {inner}, {middle}, and {outer} keywords of the "run_style
respa"_run_style.html command, meaning the pairwise forces can be
partitioned by distance at different levels of the rRESPA hierarchy.
See the "run_style"_run_style.html command for details.
:line
[Restrictions:]
-All of the cg/cmm pair styles are part of the "user-cg-cmm" package.
-The {cg/cmm/coul/long} style also requires the "kspace" package to be
+All of the cg/cmm pair styles are part of the USER-CG-CMM package.
+The {cg/cmm/coul/long} style also requires the KSPACE package to be
built (which is enabled by default). They are only enabled if LAMMPS
was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html, "angle_style cg/cmm"_angle_cmm.html
[Default:] none
:line
:link(Shinoda)
[(Shinoda)] Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
:link(DeVane)
[(DeVane)] Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).
diff --git a/doc/pair_colloid.html b/doc/pair_colloid.html
index e1a5d7bdb..7fb70fa85 100644
--- a/doc/pair_colloid.html
+++ b/doc/pair_colloid.html
@@ -1,186 +1,186 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style colloid command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style colloid cutoff
</PRE>
<UL><LI>cutoff = global cutoff for colloidal interactions (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style colloid 10.0
pair_coeff * * 25 1.0 10.0 10.0
pair_coeff 1 1 144 1.0 0.0 0.0 3.0
pair_coeff 1 2 75.398 1.0 0.0 10.0 9.0
pair_coeff 2 2 39.478 1.0 10.0 10.0 25.0
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>colloid</I> computes pairwise interactions between large colloidal
particles and small solvent particles using 3 formulas. A colloidal
particle has a size > sigma; a solvent particle is the usual
Lennard-Jones particle of size sigma.
</P>
<P>The colloid-colloid interaction energy is given by
</P>
<CENTER><IMG SRC = "Eqs/pair_colloid_cc.jpg">
</CENTER>
<P>where A_cc is the Hamaker constant, a1 and a2 are the radii of the two
colloidal particles, and Rc is the cutoff. This equation results from
describing each colloidal particle as an integrated collection of
Lennard-Jones particles of size sigma and is derived in
<A HREF = "#Everaers">(Everaers)</A>.
</P>
<P>The colloid-solvent interaction energy is given by
</P>
<CENTER><IMG SRC = "Eqs/pair_colloid_cs.jpg">
</CENTER>
<P>where A_cs is the Hamaker constant, a is the radius of the colloidal
particle, and Rc is the cutoff. This formula is derived from the
colloid-colloid interaction, letting one of the particle sizes go to
zero.
</P>
<P>The solvent-solvent interaction energy is given by the usual
Lennard-Jones formula
</P>
<CENTER><IMG SRC = "Eqs/pair_colloid_ss.jpg">
</CENTER>
<P>with A_ss set appropriately, which results from letting both particle
sizes go to zero.
</P>
<P>When used in combination with <A HREF = "pair_colloid.html">pair_style
yukawa/colloid</A>, the two terms become the so-called
DLVO potential, which combines electrostatic repulsion and van der
Waals attraction.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>A (energy units)
<LI>sigma (distance units)
<LI>d1 (distance units)
<LI>d2 (distance units)
<LI>cutoff (distance units)
</UL>
<P>A is the Hamaker energy prefactor and should typically be set as
follows:
</P>
<UL><LI>A_cc = colloid/colloid = 4 pi^2 = 39.5
<LI>A_cs = colloid/solvent = sqrt(A_cc*A_ss)
<LI>A_ss = solvent/solvent = 144 (assuming epsilon = 1, so that 144/36 = 4)
</UL>
<P>Sigma is the size of the solvent particle or the constituent particles
integrated over in the colloidal particle and should typically be set
as follows:
</P>
<UL><LI>Sigma_cc = colloid/colloid = 1.0
<LI>Sigma_cs = colloid/solvent = arithmetic mixing between colloid sigma and solvent sigma
<LI>Sigma_ss = solvent/solvent = 1.0 or whatever size the solvent particle is
</UL>
<P>Thus typically Sigma_cs = 1.0, unless the solvent particle's size !=
1.0.
</P>
<P>D1 and d2 are particle diameters, so that d1 = 2*a1 and d2 = 2*a2 in
the formulas above. Both d1 and d2 must be values >= 0. If d1 > 0
and d2 > 0, then the pair interacts via the colloid-colloid formula
above. If d1 = 0 and d2 = 0, then the pair interacts via the
solvent-solvent formula. I.e. a d value of 0 is a Lennard-Jones
particle of size sigma. If either d1 = 0 or d2 = 0 and the other is
larger, then the pair interacts via the colloid-solvent formula.
</P>
<P>Note that the diameter of a particular particle type may appear in
multiple pair_coeff commands, as it interacts with other particle
types. You should insure the particle diameter is specified
consistently each time it appears.
</P>
<P>The last coefficient is optional. If not specified, the global cutoff
specified in the pair_style command is used. However, you typically
want different cutoffs for interactions between different particle
sizes. E.g. if colloidal particles of diameter 10 are used with
solvent particles of diameter 1, then a solvent-solvent cutoff of 2.5
would correspond to a colloid-colloid cutoff of 25. A good
rule-of-thumb is to use a colloid-solvent cutoff that is half the big
diameter + 4 times the small diameter. I.e. 9 = 5 + 4 for the
colloid-solvent cutoff in this case.
</P>
<P>IMPORTANT NOTE: When using pair_style colloid for a mixture with 2 (or
more) widely different particles sizes (e.g. sigma=10 colloids in a
background sigam=1 LJ fluid), you will likely want to use these
commands for efficiency: <A HREF = "neighbor.html">neighbor multi</A> and
<A HREF = "communicate.html">communicate multi</A>.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the A, sigma, d1, and d2
coefficients and cutoff distance for this pair style can be mixed. A
is an energy value mixed like a LJ epsilon. D1 and d2 are distance
values and are mixed like sigma. The default mix value is
<I>geometric</I>. See the "pair_modify" command for details.
</P>
<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
option for the energy of the pair interaction.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
for this pair style.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding long-range tail corrections to energy and
pressure.
</P>
<P>This pair style writes its information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>This style is part of the "colloid" package. It is only enabled if
+<P>This style is part of the COLLOID package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>Normally, this pair style should be used with finite-size particles
which have a diameter, e.g. see the <A HREF = "atom_style.html">atom_style
sphere</A> command. However, this is not a requirement,
since the only definition of particle size is via the pair_coeff
parameters for each type. In other words, the physical radius of the
particle is ignored. Thus you should insure that the d1,d2 parameters
you specify are consistent with the physical size of the particles of
that type.
</P>
<P>Per-particle polydispersity is not yet supported by this pair style;
only per-type polydispersity is enabled via the pair_coeff parameters.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Everaers"></A>
<P><B>(Everaers)</B> Everaers, Ejtehadi, Phys Rev E, 67, 041710 (2003).
</P>
</HTML>
diff --git a/doc/pair_colloid.txt b/doc/pair_colloid.txt
index 4da606c03..7a519852e 100644
--- a/doc/pair_colloid.txt
+++ b/doc/pair_colloid.txt
@@ -1,180 +1,180 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style colloid command :h3
[Syntax:]
pair_style colloid cutoff :pre
cutoff = global cutoff for colloidal interactions (distance units) :ul
[Examples:]
pair_style colloid 10.0
pair_coeff * * 25 1.0 10.0 10.0
pair_coeff 1 1 144 1.0 0.0 0.0 3.0
pair_coeff 1 2 75.398 1.0 0.0 10.0 9.0
pair_coeff 2 2 39.478 1.0 10.0 10.0 25.0 :pre
[Description:]
Style {colloid} computes pairwise interactions between large colloidal
particles and small solvent particles using 3 formulas. A colloidal
particle has a size > sigma; a solvent particle is the usual
Lennard-Jones particle of size sigma.
The colloid-colloid interaction energy is given by
:c,image(Eqs/pair_colloid_cc.jpg)
where A_cc is the Hamaker constant, a1 and a2 are the radii of the two
colloidal particles, and Rc is the cutoff. This equation results from
describing each colloidal particle as an integrated collection of
Lennard-Jones particles of size sigma and is derived in
"(Everaers)"_#Everaers.
The colloid-solvent interaction energy is given by
:c,image(Eqs/pair_colloid_cs.jpg)
where A_cs is the Hamaker constant, a is the radius of the colloidal
particle, and Rc is the cutoff. This formula is derived from the
colloid-colloid interaction, letting one of the particle sizes go to
zero.
The solvent-solvent interaction energy is given by the usual
Lennard-Jones formula
:c,image(Eqs/pair_colloid_ss.jpg)
with A_ss set appropriately, which results from letting both particle
sizes go to zero.
When used in combination with "pair_style
yukawa/colloid"_pair_colloid.html, the two terms become the so-called
DLVO potential, which combines electrostatic repulsion and van der
Waals attraction.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
A (energy units)
sigma (distance units)
d1 (distance units)
d2 (distance units)
cutoff (distance units) :ul
A is the Hamaker energy prefactor and should typically be set as
follows:
A_cc = colloid/colloid = 4 pi^2 = 39.5
A_cs = colloid/solvent = sqrt(A_cc*A_ss)
A_ss = solvent/solvent = 144 (assuming epsilon = 1, so that 144/36 = 4) :ul
Sigma is the size of the solvent particle or the constituent particles
integrated over in the colloidal particle and should typically be set
as follows:
Sigma_cc = colloid/colloid = 1.0
Sigma_cs = colloid/solvent = arithmetic mixing between colloid sigma and solvent sigma
Sigma_ss = solvent/solvent = 1.0 or whatever size the solvent particle is :ul
Thus typically Sigma_cs = 1.0, unless the solvent particle's size !=
1.0.
D1 and d2 are particle diameters, so that d1 = 2*a1 and d2 = 2*a2 in
the formulas above. Both d1 and d2 must be values >= 0. If d1 > 0
and d2 > 0, then the pair interacts via the colloid-colloid formula
above. If d1 = 0 and d2 = 0, then the pair interacts via the
solvent-solvent formula. I.e. a d value of 0 is a Lennard-Jones
particle of size sigma. If either d1 = 0 or d2 = 0 and the other is
larger, then the pair interacts via the colloid-solvent formula.
Note that the diameter of a particular particle type may appear in
multiple pair_coeff commands, as it interacts with other particle
types. You should insure the particle diameter is specified
consistently each time it appears.
The last coefficient is optional. If not specified, the global cutoff
specified in the pair_style command is used. However, you typically
want different cutoffs for interactions between different particle
sizes. E.g. if colloidal particles of diameter 10 are used with
solvent particles of diameter 1, then a solvent-solvent cutoff of 2.5
would correspond to a colloid-colloid cutoff of 25. A good
rule-of-thumb is to use a colloid-solvent cutoff that is half the big
diameter + 4 times the small diameter. I.e. 9 = 5 + 4 for the
colloid-solvent cutoff in this case.
IMPORTANT NOTE: When using pair_style colloid for a mixture with 2 (or
more) widely different particles sizes (e.g. sigma=10 colloids in a
background sigam=1 LJ fluid), you will likely want to use these
commands for efficiency: "neighbor multi"_neighbor.html and
"communicate multi"_communicate.html.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the A, sigma, d1, and d2
coefficients and cutoff distance for this pair style can be mixed. A
is an energy value mixed like a LJ epsilon. D1 and d2 are distance
values and are mixed like sigma. The default mix value is
{geometric}. See the "pair_modify" command for details.
This pair style supports the "pair_modify"_pair_modify.html shift
option for the energy of the pair interaction.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
This pair style does not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
-This style is part of the "colloid" package. It is only enabled if
+This style is part of the COLLOID package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
Normally, this pair style should be used with finite-size particles
which have a diameter, e.g. see the "atom_style
sphere"_atom_style.html command. However, this is not a requirement,
since the only definition of particle size is via the pair_coeff
parameters for each type. In other words, the physical radius of the
particle is ignored. Thus you should insure that the d1,d2 parameters
you specify are consistent with the physical size of the particles of
that type.
Per-particle polydispersity is not yet supported by this pair style;
only per-type polydispersity is enabled via the pair_coeff parameters.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Everaers)
[(Everaers)] Everaers, Ejtehadi, Phys Rev E, 67, 041710 (2003).
diff --git a/doc/pair_comb.html b/doc/pair_comb.html
index 60947dba4..3c2f35f35 100644
--- a/doc/pair_comb.html
+++ b/doc/pair_comb.html
@@ -1,239 +1,239 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style comb command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style comb
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style comb
pair_coeff * * ../potentials/ffield.comb Si
pair_coeff * * ../potentials/ffield.comb Hf Si O
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>comb</I> computes a variable charge COMB (Charge-Optimized
Many-Body) potential as described in <A HREF = "#COMB_1">(COMB_1)</A> and
<A HREF = "#COMB_2">(COMB_2)</A>. The energy E of a system of atoms
is given by
</P>
<CENTER><IMG SRC = "Eqs/pair_comb1.jpg">
</CENTER>
<P>where <I>E<sub>T</sub></I> is the total potential energy of the system,
<I>E<sup>S</sup><sub>i</sub></I> is the self-energy term of atom <I>i</I>,
<I>V<sub>ij</sub></I> is the interatomic potential between the <I>i</I>th and
<I>j</I>th atoms, <I>r<sub>ij</sub></I> is the distance of the atoms <I>i</I> and
<I>j</I>, and <I>q<sub>i</sub></I> and <I>q<sub>j</sub></I> are charges of the atoms,
and <I>E<sup>BB</sup><sub>i</sub></I> is the bond-bending term of atom <I>i</I>.
</P>
<P>The interatomic potential energy <I>V<sub>ij</sub></I> consists of four
components: two-body short-range repulsion,
<I>U<sup>R</sup><sub>ij</sub></I>, many-body short-range attraction,
<I>U<sup>A</sup><sub>ij</sub></I>, long-range Coulombic electrostatic
interaction, <I>U<sup>I</sup><sub>ij</sub></I>, and van der Waals energy,
<I>U<sup>V</sup><sub>ij</sub></I>, which are defined as:
</P>
<CENTER><IMG SRC = "Eqs/pair_comb2.jpg">
</CENTER>
<P>The short-range repulsion and attraction are based on the
<A HREF = "#Tersoff">Tersoff</A> potential (see the <A HREF = "pair_tersoff.html">pair_style
tersoff</A> command); thus for a zero-charge pure
element system with no van der Waals interaction, the COMB potential
reduces to Tersoff potential, typically truncated at a short cutoff,
e.g. 3 to 4 Angstroms. The long-range Coulombic term uses the Wolf
summation method described in <A HREF = "#Wolf">Wolf</A>, spherically truncated at a
longer cutoff, e.g. 12 Angstroms.
</P>
<P>The COMB potential is a variable charge potential. The equilibrium
charge on each atom is calculated by the electronegativity
equalization (QEq) method. See <A HREF = "#Rick">Rick</A> for further details.
This is implemented by the <A HREF = "fix_qeq_comb.html">fix qeq/comb</A> command,
which should normally be specified in the input script when running a
model with the COMB potential. The <A HREF = "fix_qeq_comb.html">fix qeq/comb</A>
command has options that determine how often charge equilibration is
performed, its convergence criterion, and which atoms are included in
the calculation.
</P>
<P>Only a single pair_coeff command is used with the <I>comb</I> style which
specifies the COMB potential file with parameters for all needed
elements. These are mapped to LAMMPS atom types by specifying N
additional arguments after the potential file in the pair_coeff
command, where N is the number of LAMMPS atom types. The provided
potential file <I>ffield.comb</I> contains all currently-available COMB
parameterizations: for Si, Cu, Hf, Ti, O, their oxides and Zr, Zn and
U metals.
</P>
<P>For example, if your LAMMPS simulation of a Si/SiO<sub>2</sub>/
HfO<sub>2</sub> interface has 4 atom types, and you want the 1st and
last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would
use the following pair_coeff command:
</P>
<PRE>pair_coeff * * ../potentials/ffield.comb Si Hf O Si
</PRE>
<P>The first two arguments must be * * so as to span all LAMMPS atom
types. The first and last Si arguments map LAMMPS atom types 1 and 4
to the Si element in the <I>ffield.comb</I> file. The second Hf argument
maps LAMMPS atom type 2 to the Hf element, and the third O argument
maps LAMMPS atom type 3 to the O element in the potential file. If a
mapping value is specified as NULL, the mapping is not performed.
This can be used when a <I>comb</I> potential is used as part of the
<I>hybrid</I> pair style. The NULL values are placeholders for atom types
that will be used with other potentials.
</P>
<P>The <I>ffield.comb</I> potential file is in the <I>potentials</I> directory of
the LAMMPS distribution. Lines that are not blank or comments
(starting with #) define parameters for a triplet of elements. The 49
parameters in a single entry correspond to coefficients in the formula
above:
</P>
<UL><LI>element 1 (the center atom in a 3-body interaction)
<LI>element 2 (the atom bonded to the center atom)
<LI>element 3 (the atom influencing the 1-2 bond in a bond-order sense)
<LI>m
<LI>c
<LI>d
<LI>h (cos_theta0 (can be a value -1 or 1))
<LI>n
<LI>beta
<LI>lambda21, lambda2 of element 1 (1/distance units)
<LI>lambda22, lambda2 of element 2 (1/distance units)
<LI>B of element 1 (energy units)
<LI>B of element 2 (energy units)
<LI>R (cutoff, distance units, 0.5*(r_outer + r_inner))
<LI>D (cutoff, distance units, R - r_inner)
<LI>lambda11, lambda1 of element 1 (1/distance units)
<LI>lambda12, lambda1 of element 2 (1/distance units)
<LI>A of element 1 (energy units)
<LI>A of element 2 (energy units)
<LI>K_LP_1 (energy units, 1st order Legendre polynomial coefficient)
<LI>K_LP_3 (energy units, 3rd order Legendre polynomial coefficient)
<LI>K_LP_6 (energy units, 6th order Legendre polynomial coefficient)
<LI>A123 (cos_theta, theta = equilibrium MOM or OMO bond angles)
<LI>Aconf (cos_theta, theta = equilibrium MOM or OMO bond-bending coefficient)
<LI>addrep (energy units, additional repulsion)
<LI>R_omiga_a (unit-less scaler for A)
<LI>R_omiga_b (unit-less scaler for B)
<LI>R_omiga_c (unit-less scaler for 0.5*(lambda21+lambda22))
<LI>R_omiga_d (unit-less scaler for 0.5*(lambda11+lambda12))
<LI>QL1 (charge units, lower charge limit for element 1)
<LI>QU1 (charge units, upper charge limit for element 1)
<LI>DL1 (distance units, ion radius of element 1 with charge QL1)
<LI>DU1 (distance units, ion radius of element 1 with charge QU1)
<LI>QL2 (charge units, lower charge limit for element 2)
<LI>QU2 (charge units, upper charge limit for element 2)
<LI>DL2 (distance units, ion radius of element 2 with charge QL2)
<LI>DU2 (distance units, ion radius of element 2 with charge QU2)
<LI>chi (energy units, self energy 1st power term)
<LI>dJ (energy units, self energy 2nd power term)
<LI>dK (energy units, self energy 3rd power term)
<LI>dL (energy units, self energy 4th power term)
<LI>dM (energy units, self energy 6th power term)
<LI>esm (distance units, orbital exponent)
<LI>cmn1 (self energy penalty, rho 1 of element 1)
<LI>cml1 (self energy penalty, rho 1 of element 2)
<LI>cmn2 (self energy penalty, rho 2 of element 1)
<LI>cmn2 (self energy penalty, rho 2 of element 2)
<LI>coulcut (long range Coulombic cutoff, distance units)
<LI>hfocor (coordination term)
</UL>
<P>The parameterization of COMB potentials start with a pure element
(e.g. Si, Cu) then extend to its oxide and polymorphs
(e.g. SiO<sub>2</sub>, Cu<sub>2</sub>O). For interactions not
involving oxygen (e.g. Si-Cu or Hf-Zr), the COMB potential uses a
mixing rule to generate these parameters. For furthur details on the
parameterization and parameters, see the <A HREF = "pair_tersoff.html">Tersoff</A>
doc page and the COMB publications <A HREF = "#COMB_1">(COMB_1)</A> and
<A HREF = "#COMB_2">(COMB_2)</A>. For more details on 3-body interaction types
(e.g. SiSiO vs SiOSi), the mixing rule, and how to generate the
potential file, please see the <A HREF = "pair_tersoff.html">Tersoff</A> doc page.
</P>
<P>In the potentials directory, the file <I>ffield.comb</I> provides the
LAMMPS parameters for COMB's Si, Cu, Ti, Hf and their oxides, as well
as pure U, Zn and Zr metals. This file can be used for pure elements
(e.g. Si, Zr), binary oxides, binary alloys (e.g. SiCu, TiZr), and
complex systems. Note that alloys and complex systems require all
3-body entries be pre-defined in the potential file.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above from values in the potential file.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift, table, and tail options.
</P>
<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
files</A>, since it is stored in potential files. Thus, you
need to re-specify the pair_style, pair_coeff, and <A HREF = "fix_qeq_comb.html">fix
qeq/comb</A> commands in an input script that reads a
restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>This pair style is part of the "manybody" package. It is only enabled
+<P>This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default). See
the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
</P>
<P>This pair style requires the <A HREF = "newton.html">newton</A> setting to be "on"
for pair interactions.
</P>
<P>The COMB potentials in the <I>ffield.comb</I> file provided with LAMMPS
(see the potentials directory) are parameterized for metal
<A HREF = "units.html">units</A>. You can use the COMB potential with any LAMMPS
units, but you would need to create your own COMB potential file with
coefficients listed in the appropriate units if your simulation
doesn't use "metal" units.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_style.html">pair_style</A>, <A HREF = "pair_coeff.html">pair_coeff</A>,
<A HREF = "fix_qeq_comb.html">fix_qeq/comb</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "COMB_1"></A>
<P><B>(COMB_1)</B> J. Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007),
</P>
<A NAME = "COMB_2"></A>
<P><B>(COMB_2)</B> T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, S. R.
Phillpot, Phys Rev B, 81, 125328 (2010).
</P>
<A NAME = "Tersoff"></A>
<P><B>(Tersoff)</B> J. Tersoff, Phys Rev B, 37, 6991 (1988).
</P>
<A NAME = "Rick"></A>
<P><B>(Rick)</B> S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 16141
(1994).
</P>
<A NAME = "Wolf"></A>
<P><B>(Wolf)</B> D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem
Phys, 110, 8254 (1999).
</P>
</HTML>
diff --git a/doc/pair_comb.txt b/doc/pair_comb.txt
index 19055590f..0b2cb0ae1 100644
--- a/doc/pair_comb.txt
+++ b/doc/pair_comb.txt
@@ -1,229 +1,229 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style comb command :h3
[Syntax:]
pair_style comb :pre
[Examples:]
pair_style comb
pair_coeff * * ../potentials/ffield.comb Si
pair_coeff * * ../potentials/ffield.comb Hf Si O :pre
[Description:]
Style {comb} computes a variable charge COMB (Charge-Optimized
Many-Body) potential as described in "(COMB_1)"_#COMB_1 and
"(COMB_2)"_#COMB_2. The energy E of a system of atoms
is given by
:c,image(Eqs/pair_comb1.jpg)
where {E<sub>T</sub>} is the total potential energy of the system,
{E<sup>S</sup><sub>i</sub>} is the self-energy term of atom {i},
{V<sub>ij</sub>} is the interatomic potential between the {i}th and
{j}th atoms, {r<sub>ij</sub>} is the distance of the atoms {i} and
{j}, and {q<sub>i</sub>} and {q<sub>j</sub>} are charges of the atoms,
and {E<sup>BB</sup><sub>i</sub>} is the bond-bending term of atom {i}.
The interatomic potential energy {V<sub>ij</sub>} consists of four
components: two-body short-range repulsion,
{U<sup>R</sup><sub>ij</sub>}, many-body short-range attraction,
{U<sup>A</sup><sub>ij</sub>}, long-range Coulombic electrostatic
interaction, {U<sup>I</sup><sub>ij</sub>}, and van der Waals energy,
{U<sup>V</sup><sub>ij</sub>}, which are defined as:
:c,image(Eqs/pair_comb2.jpg)
The short-range repulsion and attraction are based on the
"Tersoff"_#Tersoff potential (see the "pair_style
tersoff"_pair_tersoff.html command); thus for a zero-charge pure
element system with no van der Waals interaction, the COMB potential
reduces to Tersoff potential, typically truncated at a short cutoff,
e.g. 3 to 4 Angstroms. The long-range Coulombic term uses the Wolf
summation method described in "Wolf"_#Wolf, spherically truncated at a
longer cutoff, e.g. 12 Angstroms.
The COMB potential is a variable charge potential. The equilibrium
charge on each atom is calculated by the electronegativity
equalization (QEq) method. See "Rick"_#Rick for further details.
This is implemented by the "fix qeq/comb"_fix_qeq_comb.html command,
which should normally be specified in the input script when running a
model with the COMB potential. The "fix qeq/comb"_fix_qeq_comb.html
command has options that determine how often charge equilibration is
performed, its convergence criterion, and which atoms are included in
the calculation.
Only a single pair_coeff command is used with the {comb} style which
specifies the COMB potential file with parameters for all needed
elements. These are mapped to LAMMPS atom types by specifying N
additional arguments after the potential file in the pair_coeff
command, where N is the number of LAMMPS atom types. The provided
potential file {ffield.comb} contains all currently-available COMB
parameterizations: for Si, Cu, Hf, Ti, O, their oxides and Zr, Zn and
U metals.
For example, if your LAMMPS simulation of a Si/SiO<sub>2</sub>/
HfO<sub>2</sub> interface has 4 atom types, and you want the 1st and
last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would
use the following pair_coeff command:
pair_coeff * * ../potentials/ffield.comb Si Hf O Si :pre
The first two arguments must be * * so as to span all LAMMPS atom
types. The first and last Si arguments map LAMMPS atom types 1 and 4
to the Si element in the {ffield.comb} file. The second Hf argument
maps LAMMPS atom type 2 to the Hf element, and the third O argument
maps LAMMPS atom type 3 to the O element in the potential file. If a
mapping value is specified as NULL, the mapping is not performed.
This can be used when a {comb} potential is used as part of the
{hybrid} pair style. The NULL values are placeholders for atom types
that will be used with other potentials.
The {ffield.comb} potential file is in the {potentials} directory of
the LAMMPS distribution. Lines that are not blank or comments
(starting with #) define parameters for a triplet of elements. The 49
parameters in a single entry correspond to coefficients in the formula
above:
element 1 (the center atom in a 3-body interaction)
element 2 (the atom bonded to the center atom)
element 3 (the atom influencing the 1-2 bond in a bond-order sense)
m
c
d
h (cos_theta0 (can be a value -1 or 1))
n
beta
lambda21, lambda2 of element 1 (1/distance units)
lambda22, lambda2 of element 2 (1/distance units)
B of element 1 (energy units)
B of element 2 (energy units)
R (cutoff, distance units, 0.5*(r_outer + r_inner))
D (cutoff, distance units, R - r_inner)
lambda11, lambda1 of element 1 (1/distance units)
lambda12, lambda1 of element 2 (1/distance units)
A of element 1 (energy units)
A of element 2 (energy units)
K_LP_1 (energy units, 1st order Legendre polynomial coefficient)
K_LP_3 (energy units, 3rd order Legendre polynomial coefficient)
K_LP_6 (energy units, 6th order Legendre polynomial coefficient)
A123 (cos_theta, theta = equilibrium MOM or OMO bond angles)
Aconf (cos_theta, theta = equilibrium MOM or OMO bond-bending coefficient)
addrep (energy units, additional repulsion)
R_omiga_a (unit-less scaler for A)
R_omiga_b (unit-less scaler for B)
R_omiga_c (unit-less scaler for 0.5*(lambda21+lambda22))
R_omiga_d (unit-less scaler for 0.5*(lambda11+lambda12))
QL1 (charge units, lower charge limit for element 1)
QU1 (charge units, upper charge limit for element 1)
DL1 (distance units, ion radius of element 1 with charge QL1)
DU1 (distance units, ion radius of element 1 with charge QU1)
QL2 (charge units, lower charge limit for element 2)
QU2 (charge units, upper charge limit for element 2)
DL2 (distance units, ion radius of element 2 with charge QL2)
DU2 (distance units, ion radius of element 2 with charge QU2)
chi (energy units, self energy 1st power term)
dJ (energy units, self energy 2nd power term)
dK (energy units, self energy 3rd power term)
dL (energy units, self energy 4th power term)
dM (energy units, self energy 6th power term)
esm (distance units, orbital exponent)
cmn1 (self energy penalty, rho 1 of element 1)
cml1 (self energy penalty, rho 1 of element 2)
cmn2 (self energy penalty, rho 2 of element 1)
cmn2 (self energy penalty, rho 2 of element 2)
coulcut (long range Coulombic cutoff, distance units)
hfocor (coordination term) :ul
The parameterization of COMB potentials start with a pure element
(e.g. Si, Cu) then extend to its oxide and polymorphs
(e.g. SiO<sub>2</sub>, Cu<sub>2</sub>O). For interactions not
involving oxygen (e.g. Si-Cu or Hf-Zr), the COMB potential uses a
mixing rule to generate these parameters. For furthur details on the
parameterization and parameters, see the "Tersoff"_pair_tersoff.html
doc page and the COMB publications "(COMB_1)"_#COMB_1 and
"(COMB_2)"_#COMB_2. For more details on 3-body interaction types
(e.g. SiSiO vs SiOSi), the mixing rule, and how to generate the
potential file, please see the "Tersoff"_pair_tersoff.html doc page.
In the potentials directory, the file {ffield.comb} provides the
LAMMPS parameters for COMB's Si, Cu, Ti, Hf and their oxides, as well
as pure U, Zn and Zr metals. This file can be used for pure elements
(e.g. Si, Zr), binary oxides, binary alloys (e.g. SiCu, TiZr), and
complex systems. Note that alloys and complex systems require all
3-body entries be pre-defined in the potential file.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above from values in the potential file.
This pair style does not support the "pair_modify"_pair_modify.html
shift, table, and tail options.
This pair style does not write its information to "binary restart
files"_restart.html, since it is stored in potential files. Thus, you
need to re-specify the pair_style, pair_coeff, and "fix
qeq/comb"_fix_qeq_comb.html commands in an input script that reads a
restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
-This pair style is part of the "manybody" package. It is only enabled
+This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default). See
the "Making LAMMPS"_Section_start.html#start_3 section for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
The COMB potentials in the {ffield.comb} file provided with LAMMPS
(see the potentials directory) are parameterized for metal
"units"_units.html. You can use the COMB potential with any LAMMPS
units, but you would need to create your own COMB potential file with
coefficients listed in the appropriate units if your simulation
doesn't use "metal" units.
[Related commands:]
"pair_style"_pair_style.html, "pair_coeff"_pair_coeff.html,
"fix_qeq/comb"_fix_qeq_comb.html
[Default:] none
:line
:link(COMB_1)
[(COMB_1)] J. Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007),
:link(COMB_2)
[(COMB_2)] T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, S. R.
Phillpot, Phys Rev B, 81, 125328 (2010).
:link(Tersoff)
[(Tersoff)] J. Tersoff, Phys Rev B, 37, 6991 (1988).
:link(Rick)
[(Rick)] S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 16141
(1994).
:link(Wolf)
[(Wolf)] D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem
Phys, 110, 8254 (1999).
diff --git a/doc/pair_coul.html b/doc/pair_coul.html
index b51638444..b0d9d858c 100644
--- a/doc/pair_coul.html
+++ b/doc/pair_coul.html
@@ -1,158 +1,158 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style coul/cut command
</H3>
<H3>pair_style coul/debye command
</H3>
<H3>pair_style coul/long command
</H3>
<H3>pair_style coul/long/gpu command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style coul/cut cutoff
pair_style coul/debye kappa cutoff
pair_style coul/long cutoff
pair_style coul/long/gpu cutoff
</PRE>
<UL><LI>cutoff = global cutoff for Coulombic interactions
<LI>kappa = Debye length (inverse distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style coul/cut 2.5
pair_coeff * *
pair_coeff 2 2 3.5
</PRE>
<PRE>pair_style coul/debye 1.4 3.0
pair_coeff * *
pair_coeff 2 2 3.5
</PRE>
<PRE>pair_style coul/long 10.0
pair_coeff * *
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>coul/cut</I> style computes the standard Coulombic interaction
potential given by
</P>
<CENTER><IMG SRC = "Eqs/pair_coulomb.jpg">
</CENTER>
<P>where C is an energy-conversion constant, Qi and Qj are the charges on
the 2 atoms, and epsilon is the dielectric constant which can be set
by the <A HREF = "dielectric.html">dielectric</A> command. The cutoff Rc truncates
the interaction distance.
</P>
<P>Style <I>coul/debye</I> adds an additional exp() damping factor to the
Coulombic term, given by
</P>
<CENTER><IMG SRC = "Eqs/pair_debye.jpg">
</CENTER>
<P>where kappa is the Debye length. This potential is another way to
mimic the screening effect of a polar solvent.
</P>
<P>Style <I>coul/long</I> computes the same Coulombic interactions as style
<I>coul/cut</I> except that an additional damping factor is applied so it
can be used in conjunction with the <A HREF = "kspace_style.html">kspace_style</A>
command and its <I>ewald</I> or <I>pppm</I> option. The Coulombic cutoff
specified for this style means that pairwise interactions within this
distance are computed directly; interactions outside that distance are
computed in reciprocal space.
</P>
<P>These potentials are designed to be combined with other pair
potentials via the <A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A>
command. This is because they have no repulsive core. Hence if they
are used by themselves, there will be no repulsion to keep two
oppositely charged particles from overlapping each other.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>cutoff (distance units)
</UL>
<P>For <I>coul/cut</I> and <I>coul/debye</I>, the cutoff coefficient is optional.
If it is not used (as in some of the examples above), the default
global value specified in the pair_style command is used.
</P>
<P>For <I>coul/long</I> no cutoff can be specified for an individual I,J type
pair via the pair_coeff command. All type pairs use the same global
Coulombic cutoff specified in the pair_style command.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+<P>These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the cutoff distance for the
<I>coul/cut</I> style can be mixed. The default mix value is <I>geometric</I>.
See the "pair_modify" command for details.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> shift option is not relevant
for these pair styles.
</P>
<P>The <I>coul/long</I> style supports the <A HREF = "pair_modify.html">pair_modify</A>
table option for tabulation of the short-range portion of the
long-range Coulombic interaction.
</P>
<P>These pair styles do not support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding long-range tail corrections to energy and
pressure.
</P>
<P>These pair styles write their information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>The <I>coul/long</I> style is part of the "kspace" package. It is only
+<P>The <I>coul/long</I> style is part of the KSPACE package. It is only
enabled if LAMMPS was built with that package (which it is by
default). See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_hybrid.html">pair_style
hybrid/overlay</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/pair_coul.txt b/doc/pair_coul.txt
index 7a17ef2d2..4fb60c269 100644
--- a/doc/pair_coul.txt
+++ b/doc/pair_coul.txt
@@ -1,150 +1,150 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style coul/cut command :h3
pair_style coul/debye command :h3
pair_style coul/long command :h3
pair_style coul/long/gpu command :h3
[Syntax:]
pair_style coul/cut cutoff
pair_style coul/debye kappa cutoff
pair_style coul/long cutoff
pair_style coul/long/gpu cutoff :pre
cutoff = global cutoff for Coulombic interactions
kappa = Debye length (inverse distance units) :ul
[Examples:]
pair_style coul/cut 2.5
pair_coeff * *
pair_coeff 2 2 3.5 :pre
pair_style coul/debye 1.4 3.0
pair_coeff * *
pair_coeff 2 2 3.5 :pre
pair_style coul/long 10.0
pair_coeff * * :pre
[Description:]
The {coul/cut} style computes the standard Coulombic interaction
potential given by
:c,image(Eqs/pair_coulomb.jpg)
where C is an energy-conversion constant, Qi and Qj are the charges on
the 2 atoms, and epsilon is the dielectric constant which can be set
by the "dielectric"_dielectric.html command. The cutoff Rc truncates
the interaction distance.
Style {coul/debye} adds an additional exp() damping factor to the
Coulombic term, given by
:c,image(Eqs/pair_debye.jpg)
where kappa is the Debye length. This potential is another way to
mimic the screening effect of a polar solvent.
Style {coul/long} computes the same Coulombic interactions as style
{coul/cut} except that an additional damping factor is applied so it
can be used in conjunction with the "kspace_style"_kspace_style.html
command and its {ewald} or {pppm} option. The Coulombic cutoff
specified for this style means that pairwise interactions within this
distance are computed directly; interactions outside that distance are
computed in reciprocal space.
These potentials are designed to be combined with other pair
potentials via the "pair_style hybrid/overlay"_pair_hybrid.html
command. This is because they have no repulsive core. Hence if they
are used by themselves, there will be no repulsion to keep two
oppositely charged particles from overlapping each other.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
cutoff (distance units) :ul
For {coul/cut} and {coul/debye}, the cutoff coefficient is optional.
If it is not used (as in some of the examples above), the default
global value specified in the pair_style command is used.
For {coul/long} no cutoff can be specified for an individual I,J type
pair via the pair_coeff command. All type pairs use the same global
Coulombic cutoff specified in the pair_style command.
:line
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the cutoff distance for the
{coul/cut} style can be mixed. The default mix value is {geometric}.
See the "pair_modify" command for details.
The "pair_modify"_pair_modify.html shift option is not relevant
for these pair styles.
The {coul/long} style supports the "pair_modify"_pair_modify.html
table option for tabulation of the short-range portion of the
long-range Coulombic interaction.
These pair styles do not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure.
These pair styles write their information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
-The {coul/long} style is part of the "kspace" package. It is only
+The {coul/long} style is part of the KSPACE package. It is only
enabled if LAMMPS was built with that package (which it is by
default). See the "Making LAMMPS"_Section_start.html#start_3 section
for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html, "pair_style
hybrid/overlay"_pair_hybrid.html
[Default:] none
diff --git a/doc/pair_dipole.html b/doc/pair_dipole.html
index 6baba2864..99d02a36e 100644
--- a/doc/pair_dipole.html
+++ b/doc/pair_dipole.html
@@ -1,190 +1,190 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style dipole/cut command
</H3>
<H3>pair_style dipole/sf command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style dipole/cut cutoff (cutoff2)
</PRE>
<PRE>pair_style dipole/sf cutoff (cutoff2)
</PRE>
<UL><LI>cutoff = global cutoff LJ (and Coulombic if only 1 arg) (distance units)
<LI>cutoff2 = global cutoff for Coulombic (optional) (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style dipole/cut 10.0
pair_coeff * * 1.0 1.0
pair_coeff 2 3 1.0 1.0 2.5 4.0
</PRE>
<PRE>pair_style dipole/sf 9.0
pair_coeff * * 1.0 1.0
pair_coeff 2 3 1.0 1.0 2.5 4.0
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>dipole/cut</I> computes interactions between pairs of particles
that each have a charge and/or a point dipole moment. In addition to
the usual Lennard-Jones interaction between the particles (Elj) the
charge-charge (Eqq), charge-dipole (Eqp), and dipole-dipole (Epp)
interactions are computed by these formulas for the energy (E), force
(F), and torque (T) between particles I and J.
</P>
<CENTER><IMG SRC = "Eqs/pair_dipole.jpg">
</CENTER>
<P>where qi and qj are the charges on the two particles, pi and pj are
the dipole moment vectors of the two particles, r is their separation
distance, and the vector r = Ri - Rj is the separation vector between
the two particles. Note that Eqq and Fqq are simply Coulombic energy
and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the
torques do not act symmetrically. These formulas are discussed in
<A HREF = "#Allen">(Allen)</A> and in <A HREF = "#Toukmaji">(Toukmaji)</A>.
</P>
<P>Style <I>dipole/sf</I> computes "shifted-force" interactions between pairs
of particles that each have a charge and/or a point dipole moment. In
general, a shifted-force potential is a (sligthly) modified potential
containing extra terms that make both the energy and its derivative go
to zero at the cutoff distance; this removes (cutoff-related) problems
in energy conservation and any numerical instability in the equations
of motion <A HREF = "#Allen">(Allen)</A>. Shifted-force interactions for the
Lennard-Jones (E_LJ), charge-charge (Eqq), charge-dipole (Eqp),
dipole-charge (Epq) and dipole-dipole (Epp) potentials are computed by
these formulas for the energy (E), force (F), and torque (T) between
particles I and J:
</P>
<CENTER><IMG SRC = "Eqs/pair_dipole_sf.jpg">
</CENTER>
<CENTER><IMG SRC = "Eqs/pair_dipole_sf2.jpg">
</CENTER>
<P>where epsilon and sigma are the standard LJ parameters, r_c is the
cutoff, qi and qj are the charges on the two particles, pi and pj are
the dipole moment vectors of the two particles, r is their separation
distance, and the vector r = Ri - Rj is the separation vector between
the two particles. Note that Eqq and Fqq are simply Coulombic energy
and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the
torques do not act symmetrically. The shifted-force formula for the
Lennard-Jones potential is reported in <A HREF = "#Stoddard">(Stoddard)</A>. The
original (unshifted) formulas for the electrostatic potentials, forces
and torques can be found in <A HREF = "#Price">(Price)</A>. The shifted-force
electrostatic potentials have been obtained by applying equation 5.13
of <A HREF = "#Allen">(Allen)</A>. The formulas for the corresponding forces and
torques have been obtained by applying the 'chain rule' as in appendix
C.3 of <A HREF = "#Allen">(Allen)</A>.
</P>
<P>If one cutoff is specified in the pair_style command, it is used for
both the LJ and Coulombic (q,p) terms. If two cutoffs are specified,
they are used as cutoffs for the LJ and Coulombic (q,p) terms
respectively.
</P>
<P>Atoms with dipole moments should be integrated using the <A HREF = "fix_nve_sphere.html">fix
nve/sphere update dipole</A> command to rotate the
dipole moments. The <A HREF = "compute_temp_sphere.html">compute temp/sphere</A>
command can be used to monitor the temperature, since it includes
rotational degrees of freedom. The <A HREF = "atom_style.html">atom_style
dipole</A> command should be used since it defines the
point dipoles and their rotational state. The magnitude of the dipole
moment for each type of particle can be defined by the
<A HREF = "dipole.html">dipole</A> command or in the "Dipoles" section of the data
file read in by the <A HREF = "read_data.html">read_data</A> command. Their initial
orientation can be defined by the <A HREF = "set.html">set dipole</A> command or in
the "Atoms" section of the data file.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>epsilon (energy units)
<LI>sigma (distance units)
<LI>cutoff1 (distance units)
<LI>cutoff2 (distance units)
</UL>
<P>The latter 2 coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distances for this pair style can be mixed. The default
mix value is <I>geometric</I>. See the "pair_modify" command for details.
</P>
<P>For atom type pairs I,J and I != J, the A, sigma, d1, and d2
coefficients and cutoff distance for this pair style can be mixed. A
is an energy value mixed like a LJ epsilon. D1 and d2 are distance
values and are mixed like sigma. The default mix value is
<I>geometric</I>. See the "pair_modify" command for details.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift option for the energy of the Lennard-Jones portion of the pair
interaction; such energy goes to zero at the cutoff by construction.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
for this pair style.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding long-range tail corrections to energy and
pressure.
</P>
<P>This pair style writes its information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<P><B>Restrictions:</B>
</P>
-<P>The <I>dipole/cut</I> style is part of the "dipole" package. It is only
+<P>The <I>dipole/cut</I> style is part of the DIPOLE package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
-<P>The <I>dipole/sf</I> style is part of the "user-misc" package. It is only
+<P>The <I>dipole/sf</I> style is part of the USER-MISC package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Allen"></A>
<P><B>(Allen)</B> Allen and Tildesley, Computer Simulation of Liquids,
Clarendon Press, Oxford, 1987.
</P>
<A NAME = "Toukmaji"></A>
<P><B>(Toukmaji)</B> Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113,
10913 (2000).
</P>
<A NAME = "Stoddard"></A>
<P><B>(Stoddard)</B> Stoddard and Ford, Phys Rev A, 8, 1504 (1973).
</P>
<A NAME = "Price"></A>
<P><B>(Price)</B> Price, Stone and Alderton, Mol Phys, 52, 987 (1984).
</P>
</HTML>
diff --git a/doc/pair_dipole.txt b/doc/pair_dipole.txt
index 55c8abf62..bb735d7a4 100755
--- a/doc/pair_dipole.txt
+++ b/doc/pair_dipole.txt
@@ -1,178 +1,178 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style dipole/cut command :h3
pair_style dipole/sf command :h3
[Syntax:]
pair_style dipole/cut cutoff (cutoff2) :pre
pair_style dipole/sf cutoff (cutoff2) :pre
cutoff = global cutoff LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units) :ul
[Examples:]
pair_style dipole/cut 10.0
pair_coeff * * 1.0 1.0
pair_coeff 2 3 1.0 1.0 2.5 4.0 :pre
pair_style dipole/sf 9.0
pair_coeff * * 1.0 1.0
pair_coeff 2 3 1.0 1.0 2.5 4.0 :pre
[Description:]
Style {dipole/cut} computes interactions between pairs of particles
that each have a charge and/or a point dipole moment. In addition to
the usual Lennard-Jones interaction between the particles (Elj) the
charge-charge (Eqq), charge-dipole (Eqp), and dipole-dipole (Epp)
interactions are computed by these formulas for the energy (E), force
(F), and torque (T) between particles I and J.
:c,image(Eqs/pair_dipole.jpg)
where qi and qj are the charges on the two particles, pi and pj are
the dipole moment vectors of the two particles, r is their separation
distance, and the vector r = Ri - Rj is the separation vector between
the two particles. Note that Eqq and Fqq are simply Coulombic energy
and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the
torques do not act symmetrically. These formulas are discussed in
"(Allen)"_#Allen and in "(Toukmaji)"_#Toukmaji.
Style {dipole/sf} computes "shifted-force" interactions between pairs
of particles that each have a charge and/or a point dipole moment. In
general, a shifted-force potential is a (sligthly) modified potential
containing extra terms that make both the energy and its derivative go
to zero at the cutoff distance; this removes (cutoff-related) problems
in energy conservation and any numerical instability in the equations
of motion "(Allen)"_#Allen. Shifted-force interactions for the
Lennard-Jones (E_LJ), charge-charge (Eqq), charge-dipole (Eqp),
dipole-charge (Epq) and dipole-dipole (Epp) potentials are computed by
these formulas for the energy (E), force (F), and torque (T) between
particles I and J:
:c,image(Eqs/pair_dipole_sf.jpg)
:c,image(Eqs/pair_dipole_sf2.jpg)
where epsilon and sigma are the standard LJ parameters, r_c is the
cutoff, qi and qj are the charges on the two particles, pi and pj are
the dipole moment vectors of the two particles, r is their separation
distance, and the vector r = Ri - Rj is the separation vector between
the two particles. Note that Eqq and Fqq are simply Coulombic energy
and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the
torques do not act symmetrically. The shifted-force formula for the
Lennard-Jones potential is reported in "(Stoddard)"_#Stoddard. The
original (unshifted) formulas for the electrostatic potentials, forces
and torques can be found in "(Price)"_#Price. The shifted-force
electrostatic potentials have been obtained by applying equation 5.13
of "(Allen)"_#Allen. The formulas for the corresponding forces and
torques have been obtained by applying the 'chain rule' as in appendix
C.3 of "(Allen)"_#Allen.
If one cutoff is specified in the pair_style command, it is used for
both the LJ and Coulombic (q,p) terms. If two cutoffs are specified,
they are used as cutoffs for the LJ and Coulombic (q,p) terms
respectively.
Atoms with dipole moments should be integrated using the "fix
nve/sphere update dipole"_fix_nve_sphere.html command to rotate the
dipole moments. The "compute temp/sphere"_compute_temp_sphere.html
command can be used to monitor the temperature, since it includes
rotational degrees of freedom. The "atom_style
dipole"_atom_style.html command should be used since it defines the
point dipoles and their rotational state. The magnitude of the dipole
moment for each type of particle can be defined by the
"dipole"_dipole.html command or in the "Dipoles" section of the data
file read in by the "read_data"_read_data.html command. Their initial
orientation can be defined by the "set dipole"_set.html command or in
the "Atoms" section of the data file.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
epsilon (energy units)
sigma (distance units)
cutoff1 (distance units)
cutoff2 (distance units) :ul
The latter 2 coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distances for this pair style can be mixed. The default
mix value is {geometric}. See the "pair_modify" command for details.
For atom type pairs I,J and I != J, the A, sigma, d1, and d2
coefficients and cutoff distance for this pair style can be mixed. A
is an energy value mixed like a LJ epsilon. D1 and d2 are distance
values and are mixed like sigma. The default mix value is
{geometric}. See the "pair_modify" command for details.
This pair style does not support the "pair_modify"_pair_modify.html
shift option for the energy of the Lennard-Jones portion of the pair
interaction; such energy goes to zero at the cutoff by construction.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
This pair style does not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
[Restrictions:]
-The {dipole/cut} style is part of the "dipole" package. It is only
+The {dipole/cut} style is part of the DIPOLE package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
-The {dipole/sf} style is part of the "user-misc" package. It is only
+The {dipole/sf} style is part of the USER-MISC package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Allen)
[(Allen)] Allen and Tildesley, Computer Simulation of Liquids,
Clarendon Press, Oxford, 1987.
:link(Toukmaji)
[(Toukmaji)] Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113,
10913 (2000).
:link(Stoddard)
[(Stoddard)] Stoddard and Ford, Phys Rev A, 8, 1504 (1973).
:link(Price)
[(Price)] Price, Stone and Alderton, Mol Phys, 52, 987 (1984).
diff --git a/doc/pair_dsmc.html b/doc/pair_dsmc.html
index 4e01bbd56..11d1481d5 100644
--- a/doc/pair_dsmc.html
+++ b/doc/pair_dsmc.html
@@ -1,144 +1,144 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style dsmc command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style dsmc max_cell_size seed weighting Tref Nrecompute Nsample
</PRE>
<UL><LI>max_cell_size = global maximum cell size for DSMC interactions (distance units)
<LI>seed = random # seed (positive integer)
<LI>weighting = macroparticle weighting
<LI>Tref = reference temperature (temperature units)
<LI>Nrecompute = recompute v*sigma_max every this many timesteps (timesteps)
<LI>Nsample = sample this many times in recomputing v*sigma_max
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style dsmc 2.5 34387 10 1.0 100 20
pair_coeff * * 1.0
pair_coeff 1 1 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>dsmc</I> computes collisions between pairs of particles for a
direct simulation Monte Carlo (DSMC) model following the exposition in
<A HREF = "#Bird">(Bird)</A>. Each collision resets the velocities of the two
particles involved. The number of pairwise collisions for each pair
or particle types and the length scale within which they occur are
determined by the parameters of the pair_style and pair_coeff
commands.
</P>
<P>Stochastic collisions are performed using the variable hard sphere
(VHS) approach, with the user-defined <I>max_cell_size</I> value used as
the maximum DSMC cell size, and reference cross-sections for
collisions given using the pair_coeff command.
</P>
<P>There is no pairwise energy or virial contributions associated with
this pair style.
</P>
<P>The following coefficient must be defined for each pair of atoms types
via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above,
or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands:
</P>
<UL><LI>sigma (area units, i.e. distance-squared)
</UL>
<P>The global DSMC <I>max_cell_size</I> determines the maximum cell length
used in the DSMC calculation. A structured mesh is overlayed on the
simulation box such that an integer number of cells are created in
each direction for each processor's sub-domain. Cell lengths are
adjusted up to the user-specified maximum cell size.
</P>
<HR>
<P>To perform a DSMC simulation with LAMMPS, several additional options
should be set in your input script, though LAMMPS does not check for
these settings.
</P>
<P>Since this pair style does not compute particle forces, you should use
the "fix nve/noforce" time integration fix for the DSMC particles,
e.g.
</P>
<PRE>fix 1 all nve/noforce
</PRE>
<P>This pair style assumes that all particles will communicated to
neighboring processors every timestep as they move. This makes it
possible to perform all collisions between pairs of particles that are
on the same processor. To ensure this occurs, you should use
these commands:
</P>
<PRE>neighbor 0.0 bin
neigh_modify every 1 delay 0 check no
communicate single cutoff 0.0
</PRE>
<P>These commands insure that LAMMPS communicates particles to
neighboring processors every timestep and that no ghost atoms are
created. The output statistics for a simulation run should indicate
there are no ghost particles or neighbors.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>This pair style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift option for the energy of the pair interaction.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
for this pair style.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding long-range tail corrections to energy and
pressure.
</P>
<P>This pair style writes its information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file. Note
that the user-specified random number seed is stored in the restart
file, so when a simulation is restarted, each processor will
re-initialize its random number generator the same way it did
initially. This means the random forces will be random, but will not
be the same as they would have been if the original simulation had
continued past the restart time.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>This style is part of the "mc" package. It is only enabled if LAMMPS
+<P>This style is part of the MC package. It is only enabled if LAMMPS
was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nve_noforce.html">fix nve/noforce</A>,
<A HREF = "neigh_modify.html">neigh_modify</A>, <A HREF = "neighbor.html">neighbor</A>,
<A HREF = "communicate.html">communicate</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Bird"></A>
<P><B>(Bird)</B> G. A. Bird, "Molecular Gas Dynamics and the Direct Simulation
of Gas Flows" (1994).
</P>
</HTML>
diff --git a/doc/pair_dsmc.txt b/doc/pair_dsmc.txt
index cc17e20fe..0f430d394 100644
--- a/doc/pair_dsmc.txt
+++ b/doc/pair_dsmc.txt
@@ -1,138 +1,138 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style dsmc command :h3
[Syntax:]
pair_style dsmc max_cell_size seed weighting Tref Nrecompute Nsample :pre
max_cell_size = global maximum cell size for DSMC interactions (distance units)
seed = random # seed (positive integer)
weighting = macroparticle weighting
Tref = reference temperature (temperature units)
Nrecompute = recompute v*sigma_max every this many timesteps (timesteps)
Nsample = sample this many times in recomputing v*sigma_max :ul
[Examples:]
pair_style dsmc 2.5 34387 10 1.0 100 20
pair_coeff * * 1.0
pair_coeff 1 1 1.0 :pre
[Description:]
Style {dsmc} computes collisions between pairs of particles for a
direct simulation Monte Carlo (DSMC) model following the exposition in
"(Bird)"_#Bird. Each collision resets the velocities of the two
particles involved. The number of pairwise collisions for each pair
or particle types and the length scale within which they occur are
determined by the parameters of the pair_style and pair_coeff
commands.
Stochastic collisions are performed using the variable hard sphere
(VHS) approach, with the user-defined {max_cell_size} value used as
the maximum DSMC cell size, and reference cross-sections for
collisions given using the pair_coeff command.
There is no pairwise energy or virial contributions associated with
this pair style.
The following coefficient must be defined for each pair of atoms types
via the "pair_coeff"_pair_coeff.html command as in the examples above,
or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands:
sigma (area units, i.e. distance-squared) :ul
The global DSMC {max_cell_size} determines the maximum cell length
used in the DSMC calculation. A structured mesh is overlayed on the
simulation box such that an integer number of cells are created in
each direction for each processor's sub-domain. Cell lengths are
adjusted up to the user-specified maximum cell size.
:line
To perform a DSMC simulation with LAMMPS, several additional options
should be set in your input script, though LAMMPS does not check for
these settings.
Since this pair style does not compute particle forces, you should use
the "fix nve/noforce" time integration fix for the DSMC particles,
e.g.
fix 1 all nve/noforce :pre
This pair style assumes that all particles will communicated to
neighboring processors every timestep as they move. This makes it
possible to perform all collisions between pairs of particles that are
on the same processor. To ensure this occurs, you should use
these commands:
neighbor 0.0 bin
neigh_modify every 1 delay 0 check no
communicate single cutoff 0.0 :pre
These commands insure that LAMMPS communicates particles to
neighboring processors every timestep and that no ghost atoms are
created. The output statistics for a simulation run should indicate
there are no ghost particles or neighbors.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
This pair style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
This pair style does not support the "pair_modify"_pair_modify.html
shift option for the energy of the pair interaction.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
This pair style does not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file. Note
that the user-specified random number seed is stored in the restart
file, so when a simulation is restarted, each processor will
re-initialize its random number generator the same way it did
initially. This means the random forces will be random, but will not
be the same as they would have been if the original simulation had
continued past the restart time.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
-This style is part of the "mc" package. It is only enabled if LAMMPS
+This style is part of the MC package. It is only enabled if LAMMPS
was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html, "fix nve/noforce"_fix_nve_noforce.html,
"neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html,
"communicate"_communicate.html
[Default:] none
:line
:link(Bird)
[(Bird)] G. A. Bird, "Molecular Gas Dynamics and the Direct Simulation
of Gas Flows" (1994).
diff --git a/doc/pair_eam.html b/doc/pair_eam.html
index 663003a10..3584d06a9 100644
--- a/doc/pair_eam.html
+++ b/doc/pair_eam.html
@@ -1,454 +1,454 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style eam command
</H3>
<H3>pair_style eam/cuda command
</H3>
<H3>pair_style eam/opt command
</H3>
<H3>pair_style eam/alloy command
</H3>
<H3>pair_style eam/alloy/cuda command
</H3>
<H3>pair_style eam/alloy/opt command
</H3>
<H3>pair_style eam/cd command
</H3>
<H3>pair_style eam/fs command
</H3>
<H3>pair_style eam/fs/cuda command
</H3>
<H3>pair_style eam/fs/opt command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style
</PRE>
<UL><LI>style = <I>eam</I> or <I>eam/alloy</I> or <I>eam/cd</I> or <I>eam/fs</I>
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style eam
pair_coeff * * cuu3
pair_coeff 1*3 1*3 niu3.eam
</PRE>
<PRE>pair_style eam/alloy
pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni
</PRE>
<PRE>pair_style eam/cd
pair_coeff * * ../potentials/FeCr.cdeam Fe Cr
</PRE>
<PRE>pair_style eam/fs
pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>eam</I> computes pairwise interactions for metals and metal alloys
using embedded-atom method (EAM) potentials <A HREF = "#Daw">(Daw)</A>. The total
energy Ei of an atom I is given by
</P>
<CENTER><IMG SRC = "Eqs/pair_eam.jpg">
</CENTER>
<P>where F is the embedding energy which is a function of the atomic
electron density rho, phi is a pair potential interaction, and alpha
and beta are the element types of atoms I and J. The multi-body
nature of the EAM potential is a result of the embedding energy term.
Both summations in the formula are over all neighbors J of atom I
within the cutoff distance.
</P>
<P>The cutoff distance and the tabulated values of the functionals F,
rho, and phi are listed in one or more files which are specified by
the <A HREF = "pair_coeff.html">pair_coeff</A> command. These are ASCII text files
in a DYNAMO-style format which is described below. DYNAMO was the
original serial EAM MD code, written by the EAM originators. Several
DYNAMO potential files for different metals are included in the
"potentials" directory of the LAMMPS distribution. All of these files
are parameterized in terms of LAMMPS <A HREF = "units.html">metal units</A>.
</P>
<P>IMPORTANT NOTE: The <I>eam</I> style reads single-element EAM potentials in
the DYNAMO <I>funcfl</I> format. Either single element or alloy systems
can be modeled using multiple <I>funcfl</I> files and style <I>eam</I>. For the
alloy case LAMMPS mixes the single-element potentials to produce alloy
potentials, the same way that DYNAMO does. Alternatively, a single
DYNAMO <I>setfl</I> file or Finnis/Sinclair EAM file can be used by LAMMPS
to model alloy systems by invoking the <I>eam/alloy</I> or <I>eam/cd</I> or
<I>eam/fs</I> styles as described below. These files require no mixing
since they specify alloy interactions explicitly.
</P>
<P>Note that unlike for other potentials, cutoffs for EAM potentials are
not set in the pair_style or pair_coeff command; they are specified in
the EAM potential files themselves. Likewise, the EAM potential files
list atomic masses; thus you do not need to use the <A HREF = "mass.html">mass</A>
command to specify them.
</P>
<P>There are several WWW sites that distribute and document EAM
potentials stored in DYNAMO or other formats:
</P>
<PRE>http://www.ctcms.nist.gov/potentials
http://cst-www.nrl.navy.mil/ccm6/ap
http://enpub.fulton.asu.edu/cms/potentials/main/main.htm
</PRE>
<P>These potentials should be usable with LAMMPS, though the alternate
formats would need to be converted to the DYNAMO format used by LAMMPS
and described on this page. The NIST site is maintained by Chandler
Becker (cbecker at nist.gov) who is good resource for info on
interatomic potentials and file formats.
</P>
<HR>
<P>For style <I>eam</I>, potential values are read from a file that is in the
DYNAMO single-element <I>funcfl</I> format. If the DYNAMO file was created
by a Fortran program, it cannot have "D" values in it for exponents.
C only recognizes "e" or "E" for scientific notation.
</P>
<P>Note that unlike for other potentials, cutoffs for EAM potentials are
not set in the pair_style or pair_coeff command; they are specified in
the EAM potential files themselves.
</P>
<P>For style <I>eam</I> a potential file must be assigned to each I,I pair of
atom types by using one or more pair_coeff commands, each with a
single argument:
</P>
<UL><LI>filename
</UL>
<P>Thus the following command
</P>
<PRE>pair_coeff *2 1*2 cuu3.eam
</PRE>
<P>will read the cuu3 potential file and use the tabulated Cu values for
F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs
1,2 and 2,1 are ignored). In effect, this makes atom types 1 and 2 in
LAMMPS be Cu atoms. Different single-element files can be assigned to
different atom types to model an alloy system. The mixing to create
alloy potentials for type pairs with I != J is done automatically the
same way that the serial DYNAMO code originally did it; you do not
need to specify coefficients for these type pairs.
</P>
<P><I>Funcfl</I> files in the <I>potentials</I> directory of the LAMMPS
distribution have an ".eam" suffix. A DYNAMO single-element <I>funcfl</I>
file is formatted as follows:
</P>
<UL><LI>line 1: comment (ignored)
<LI>line 2: atomic number, mass, lattice constant, lattice type (e.g. FCC)
<LI>line 3: Nrho, drho, Nr, dr, cutoff
</UL>
<P>On line 2, all values but the mass are ignored by LAMMPS. The mass is
in mass <A HREF = "units.html">units</A>, e.g. mass number or grams/mole for metal
units. The cubic lattice constant is in Angstroms. On line 3, Nrho
and Nr are the number of tabulated values in the subsequent arrays,
drho and dr are the spacing in density and distance space for the
values in those arrays, and the specified cutoff becomes the pairwise
cutoff used by LAMMPS for the potential. The units of dr are
Angstroms; I'm not sure of the units for drho - some measure of
electron density.
</P>
<P>Following the three header lines are three arrays of tabulated values:
</P>
<UL><LI>embedding function F(rho) (Nrho values)
<LI>effective charge function Z(r) (Nr values)
<LI>density function rho(r) (Nr values)
</UL>
<P>The values for each array can be listed as multiple values per line,
so long as each array starts on a new line. For example, the
individual Z(r) values are for r = 0,dr,2*dr, ... (Nr-1)*dr.
</P>
<P>The units for the embedding function F are eV. The units for the
density function rho are the same as for drho (see above, electron
density). The units for the effective charge Z are "atomic charge" or
sqrt(Hartree * Bohr-radii). For two interacting atoms i,j this is used
by LAMMPS to compute the pair potential term in the EAM energy
expression as r*phi, in units of eV-Angstroms, via the formula
</P>
<PRE>r*phi = 27.2 * 0.529 * Zi * Zj
</PRE>
<P>where 1 Hartree = 27.2 eV and 1 Bohr = 0.529 Angstroms.
</P>
<HR>
<P>Style <I>eam/alloy</I> computes pairwise interactions using the same
formula as style <I>eam</I>. However the associated
<A HREF = "pair_coeff.html">pair_coeff</A> command reads a DYNAMO <I>setfl</I> file
instead of a <I>funcfl</I> file. <I>Setfl</I> files can be used to model a
single-element or alloy system. In the alloy case, as explained
above, <I>setfl</I> files contain explicit tabulated values for alloy
interactions. Thus they allow more generality than <I>funcfl</I> files for
modeling alloys.
</P>
<P>For style <I>eam/alloy</I>, potential values are read from a file that is
in the DYNAMO multi-element <I>setfl</I> format, except that element names
(Ni, Cu, etc) are added to one of the lines in the file. If the
DYNAMO file was created by a Fortran program, it cannot have "D"
values in it for exponents. C only recognizes "e" or "E" for
scientific notation.
</P>
<P>Only a single pair_coeff command is used with the <I>eam/alloy</I> style
which specifies a DYNAMO <I>setfl</I> file, which contains information for
M elements. These are mapped to LAMMPS atom types by specifying N
additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
</P>
<UL><LI>filename
<LI>N element names = mapping of <I>setfl</I> elements to atom types
</UL>
<P>As an example, the potentials/NiAlH_jea.eam.alloy file is a <I>setfl</I>
file which has tabulated EAM values for 3 elements and their alloy
interactions: Ni, Al, and H. If your LAMMPS simulation has 4 atoms
types and you want the 1st 3 to be Ni, and the 4th to be Al, you would
use the following pair_coeff command:
</P>
<PRE>pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al
</PRE>
<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Ni arguments map LAMMPS atom types 1,2,3 to the Ni
element in the <I>setfl</I> file. The final Al argument maps LAMMPS atom
type 4 to the Al element in the <I>setfl</I> file. Note that there is no
requirement that your simulation use all the elements specified by the
<I>setfl</I> file.
</P>
<P>If a mapping value is specified as NULL, the mapping is not performed.
This can be used when an <I>eam/alloy</I> potential is used as part of the
<I>hybrid</I> pair style. The NULL values are placeholders for atom types
that will be used with other potentials.
</P>
<P><I>Setfl</I> files in the <I>potentials</I> directory of the LAMMPS distribution
have an ".eam.alloy" suffix. A DYNAMO multi-element <I>setfl</I> file is
formatted as follows:
</P>
<UL><LI>lines 1,2,3 = comments (ignored)
<LI>line 4: Nelements Element1 Element2 ... ElementN
<LI>line 5: Nrho, drho, Nr, dr, cutoff
</UL>
<P>In a DYNAMO <I>setfl</I> file, line 4 only lists Nelements = the # of
elements in the <I>setfl</I> file. For LAMMPS, the element name (Ni, Cu,
etc) of each element must be added to the line, in the order the
elements appear in the file.
</P>
<P>The meaning and units of the values in line 5 is the same as for the
<I>funcfl</I> file described above. Note that the cutoff (in Angstroms) is
a global value, valid for all pairwise interactions for all element
pairings.
</P>
<P>Following the 5 header lines are Nelements sections, one for each
element, each with the following format:
</P>
<UL><LI>line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)
<LI>embedding function F(rho) (Nrho values)
<LI>density function rho(r) (Nr values)
</UL>
<P>As with the <I>funcfl</I> files, only the mass (in mass <A HREF = "units.html">units</A>,
e.g. mass number or grams/mole for metal units) is used by LAMMPS from
the 1st line. The cubic lattice constant is in Angstroms. The F and
rho arrays are unique to a single element and have the same format and
units as in a <I>funcfl</I> file.
</P>
<P>Following the Nelements sections, Nr values for each pair potential
phi(r) array are listed for all i,j element pairs in the same format
as other arrays. Since these interactions are symmetric (i,j = j,i)
only phi arrays with i >= j are listed, in the following order: i,j =
(1,1), (2,1), (2,2), (3,1), (3,2), (3,3), (4,1), ..., (Nelements,
Nelements). Unlike the effective charge array Z(r) in <I>funcfl</I> files,
the tabulated values for each phi function are listed in <I>setfl</I> files
directly as r*phi (in units of eV-Angstroms), since they are for atom
pairs.
</P>
<HR>
<P>Style <I>eam/cd</I> is similar to the <I>eam/alloy</I> style, except that it
computes alloy pairwise interactions using the concentration-dependent
embedded-atom method (CD-EAM). This model can reproduce the enthalpy
of mixing of alloys over the full composition range, as described in
<A HREF = "#Stukowski">(Stukowski)</A>.
</P>
<P>The pair_coeff command is specified the same as for the <I>eam/alloy</I>
style. However the DYNAMO <I>setfl</I> file must has two
lines added to it, at the end of the file:
</P>
<UL><LI>line 1: Comment line (ignored)
<LI>line 2: N Coefficient0 Coefficient1 ... CoeffincientN
</UL>
<P>The last line begins with the degree <I>N</I> of the polynomial function
<I>h(x)</I> that modifies the cross interaction between A and B elements.
Then <I>N+1</I> coefficients for the terms of the polynomial are then
listed.
</P>
<P>Modified EAM <I>setfl</I> files used with the <I>eam/cd</I> style must contain
exactly two elements, i.e. in the current implementation the <I>eam/cd</I>
style only supports binary alloys. The first and second elements in
the input EAM file are always taken as the <I>A</I> and <I>B</I> species.
</P>
<P><I>CD-EAM</I> files in the <I>potentials</I> directory of the LAMMPS
distribution have a ".cdeam" suffix.
</P>
<HR>
<P>Style <I>eam/fs</I> computes pairwise interactions for metals and metal
alloys using a generalized form of EAM potentials due to Finnis and
Sinclair <A HREF = "#Finnis">(Finnis)</A>. The total energy Ei of an atom I is
given by
</P>
<CENTER><IMG SRC = "Eqs/pair_eam_fs.jpg">
</CENTER>
<P>This has the same form as the EAM formula above, except that rho is
now a functional specific to the atomic types of both atoms I and J,
so that different elements can contribute differently to the total
electron density at an atomic site depending on the identity of the
element at that atomic site.
</P>
<P>The associated <A HREF = "pair_coeff.html">pair_coeff</A> command for style <I>eam/fs</I>
reads a DYNAMO <I>setfl</I> file that has been extended to include
additional rho_alpha_beta arrays of tabulated values. A discussion of
how FS EAM differs from conventional EAM alloy potentials is given in
<A HREF = "#Ackland1">(Ackland1)</A>. An example of such a potential is the same
author's Fe-P FS potential <A HREF = "#Ackland2">(Ackland2)</A>. Note that while FS
potentials always specify the embedding energy with a square root
dependence on the total density, the implementation in LAMMPS does not
require that; the user can tabulate any functional form desired in the
FS potential files.
</P>
<P>For style <I>eam/fs</I>, the form of the pair_coeff command is exactly the
same as for style <I>eam/alloy</I>, e.g.
</P>
<PRE>pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al
</PRE>
<P>where there are N additional arguments after the filename, where N is
the number of LAMMPS atom types. The N values determine the mapping
of LAMMPS atom types to EAM elements in the file, as described above
for style <I>eam/alloy</I>. As with <I>eam/alloy</I>, if a mapping value is
NULL, the mapping is not performed. This can be used when an <I>eam/fs</I>
potential is used as part of the <I>hybrid</I> pair style. The NULL values
are used as placeholders for atom types that will be used with other
potentials.
</P>
<P>FS EAM files include more information than the DYNAMO <I>setfl</I> format
files read by <I>eam/alloy</I>, in that i,j density functionals for all
pairs of elements are included as needed by the Finnis/Sinclair
formulation of the EAM.
</P>
<P>FS EAM files in the <I>potentials</I> directory of the LAMMPS distribution
have an ".eam.fs" suffix. They are formatted as follows:
</P>
<UL><LI>lines 1,2,3 = comments (ignored)
<LI>line 4: Nelements Element1 Element2 ... ElementN
<LI>line 5: Nrho, drho, Nr, dr, cutoff
</UL>
<P>The 5-line header section is identical to an EAM <I>setfl</I> file.
</P>
<P>Following the header are Nelements sections, one for each element I,
each with the following format:
</P>
<UL><LI>line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)
<LI>embedding function F(rho) (Nrho values)
<LI>density function rho(r) for element I at element 1 (Nr values)
<LI>density function rho(r) for element I at element 2
<LI>...
<LI>density function rho(r) for element I at element Nelement
</UL>
<P>The units of these quantities in line 1 are the same as for <I>setfl</I>
files. Note that the rho(r) arrays in Finnis/Sinclair can be
asymmetric (i,j != j,i) so there are Nelements^2 of them listed in the
file.
</P>
<P>Following the Nelements sections, Nr values for each pair potential
phi(r) array are listed in the same manner (r*phi, units of
eV-Angstroms) as in EAM <I>setfl</I> files. Note that in Finnis/Sinclair,
the phi(r) arrays are still symmetric, so only phi arrays for i >= j
are listed.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+<P>These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above with the individual styles. You never need to specify
a pair_coeff command with I != J arguments for the eam styles.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift, table, and tail options.
</P>
<P>The eam pair styles do not write their information to <A HREF = "restart.html">binary restart
files</A>, since it is stored in tabulated potential files.
Thus, you need to re-specify the pair_style and pair_coeff commands in
an input script that reads a restart file.
</P>
<P>The eam pair styles can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. They do not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>All of these styles except the <I>eam/cd</I> style are part of the
-"manybody" package. They are only enabled if LAMMPS was built with
-that package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
+<P>All of these styles except the <I>eam/cd</I> style are part of the MANYBODY
+package. They are only enabled if LAMMPS was built with that package
+(which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
-<P>The <I>eam/cd</I> style is part of the "user-misc" package and also
-requires the "manybody" package. It is only enabled if LAMMPS was
-built with those packages. See the <A HREF = "Section_start.html#start_3">Making
-LAMMPS</A> section for more info.
+<P>The <I>eam/cd</I> style is part of the USER-MISC package and also requires
+the MANYBODY package. It is only enabled if LAMMPS was built with
+those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
+section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Ackland1"></A>
<P><B>(Ackland1)</B> Ackland, Condensed Matter (2005).
</P>
<A NAME = "Ackland2"></A>
<P><B>(Ackland2)</B> Ackland, Mendelev, Srolovitz, Han and Barashev, Journal
of Physics: Condensed Matter, 16, S2629 (2004).
</P>
<A NAME = "Daw"></A>
<P><B>(Daw)</B> Daw, Baskes, Phys Rev Lett, 50, 1285 (1983).
Daw, Baskes, Phys Rev B, 29, 6443 (1984).
</P>
<A NAME = "Finnis"></A>
<P><B>(Finnis)</B> Finnis, Sinclair, Philosophical Magazine A, 50, 45 (1984).
</P>
<A NAME = "Stukowski"></A>
<P><B>(Stukowski)</B> Stukowski, Sadigh, Erhart, Caro; Modeling Simulation
Materials Science & Engineering, 7, 075005 (2009).
</P>
</HTML>
diff --git a/doc/pair_eam.txt b/doc/pair_eam.txt
index 7153cef70..5bc1779cb 100644
--- a/doc/pair_eam.txt
+++ b/doc/pair_eam.txt
@@ -1,435 +1,435 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style eam command :h3
pair_style eam/cuda command :h3
pair_style eam/opt command :h3
pair_style eam/alloy command :h3
pair_style eam/alloy/cuda command :h3
pair_style eam/alloy/opt command :h3
pair_style eam/cd command :h3
pair_style eam/fs command :h3
pair_style eam/fs/cuda command :h3
pair_style eam/fs/opt command :h3
[Syntax:]
pair_style style :pre
style = {eam} or {eam/alloy} or {eam/cd} or {eam/fs} :ul
[Examples:]
pair_style eam
pair_coeff * * cuu3
pair_coeff 1*3 1*3 niu3.eam :pre
pair_style eam/alloy
pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni :pre
pair_style eam/cd
pair_coeff * * ../potentials/FeCr.cdeam Fe Cr :pre
pair_style eam/fs
pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni :pre
[Description:]
Style {eam} computes pairwise interactions for metals and metal alloys
using embedded-atom method (EAM) potentials "(Daw)"_#Daw. The total
energy Ei of an atom I is given by
:c,image(Eqs/pair_eam.jpg)
where F is the embedding energy which is a function of the atomic
electron density rho, phi is a pair potential interaction, and alpha
and beta are the element types of atoms I and J. The multi-body
nature of the EAM potential is a result of the embedding energy term.
Both summations in the formula are over all neighbors J of atom I
within the cutoff distance.
The cutoff distance and the tabulated values of the functionals F,
rho, and phi are listed in one or more files which are specified by
the "pair_coeff"_pair_coeff.html command. These are ASCII text files
in a DYNAMO-style format which is described below. DYNAMO was the
original serial EAM MD code, written by the EAM originators. Several
DYNAMO potential files for different metals are included in the
"potentials" directory of the LAMMPS distribution. All of these files
are parameterized in terms of LAMMPS "metal units"_units.html.
IMPORTANT NOTE: The {eam} style reads single-element EAM potentials in
the DYNAMO {funcfl} format. Either single element or alloy systems
can be modeled using multiple {funcfl} files and style {eam}. For the
alloy case LAMMPS mixes the single-element potentials to produce alloy
potentials, the same way that DYNAMO does. Alternatively, a single
DYNAMO {setfl} file or Finnis/Sinclair EAM file can be used by LAMMPS
to model alloy systems by invoking the {eam/alloy} or {eam/cd} or
{eam/fs} styles as described below. These files require no mixing
since they specify alloy interactions explicitly.
Note that unlike for other potentials, cutoffs for EAM potentials are
not set in the pair_style or pair_coeff command; they are specified in
the EAM potential files themselves. Likewise, the EAM potential files
list atomic masses; thus you do not need to use the "mass"_mass.html
command to specify them.
There are several WWW sites that distribute and document EAM
potentials stored in DYNAMO or other formats:
http://www.ctcms.nist.gov/potentials
http://cst-www.nrl.navy.mil/ccm6/ap
http://enpub.fulton.asu.edu/cms/potentials/main/main.htm :pre
These potentials should be usable with LAMMPS, though the alternate
formats would need to be converted to the DYNAMO format used by LAMMPS
and described on this page. The NIST site is maintained by Chandler
Becker (cbecker at nist.gov) who is good resource for info on
interatomic potentials and file formats.
:line
For style {eam}, potential values are read from a file that is in the
DYNAMO single-element {funcfl} format. If the DYNAMO file was created
by a Fortran program, it cannot have "D" values in it for exponents.
C only recognizes "e" or "E" for scientific notation.
Note that unlike for other potentials, cutoffs for EAM potentials are
not set in the pair_style or pair_coeff command; they are specified in
the EAM potential files themselves.
For style {eam} a potential file must be assigned to each I,I pair of
atom types by using one or more pair_coeff commands, each with a
single argument:
filename :ul
Thus the following command
pair_coeff *2 1*2 cuu3.eam :pre
will read the cuu3 potential file and use the tabulated Cu values for
F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs
1,2 and 2,1 are ignored). In effect, this makes atom types 1 and 2 in
LAMMPS be Cu atoms. Different single-element files can be assigned to
different atom types to model an alloy system. The mixing to create
alloy potentials for type pairs with I != J is done automatically the
same way that the serial DYNAMO code originally did it; you do not
need to specify coefficients for these type pairs.
{Funcfl} files in the {potentials} directory of the LAMMPS
distribution have an ".eam" suffix. A DYNAMO single-element {funcfl}
file is formatted as follows:
line 1: comment (ignored)
line 2: atomic number, mass, lattice constant, lattice type (e.g. FCC)
line 3: Nrho, drho, Nr, dr, cutoff :ul
On line 2, all values but the mass are ignored by LAMMPS. The mass is
in mass "units"_units.html, e.g. mass number or grams/mole for metal
units. The cubic lattice constant is in Angstroms. On line 3, Nrho
and Nr are the number of tabulated values in the subsequent arrays,
drho and dr are the spacing in density and distance space for the
values in those arrays, and the specified cutoff becomes the pairwise
cutoff used by LAMMPS for the potential. The units of dr are
Angstroms; I'm not sure of the units for drho - some measure of
electron density.
Following the three header lines are three arrays of tabulated values:
embedding function F(rho) (Nrho values)
effective charge function Z(r) (Nr values)
density function rho(r) (Nr values) :ul
The values for each array can be listed as multiple values per line,
so long as each array starts on a new line. For example, the
individual Z(r) values are for r = 0,dr,2*dr, ... (Nr-1)*dr.
The units for the embedding function F are eV. The units for the
density function rho are the same as for drho (see above, electron
density). The units for the effective charge Z are "atomic charge" or
sqrt(Hartree * Bohr-radii). For two interacting atoms i,j this is used
by LAMMPS to compute the pair potential term in the EAM energy
expression as r*phi, in units of eV-Angstroms, via the formula
r*phi = 27.2 * 0.529 * Zi * Zj :pre
where 1 Hartree = 27.2 eV and 1 Bohr = 0.529 Angstroms.
:line
Style {eam/alloy} computes pairwise interactions using the same
formula as style {eam}. However the associated
"pair_coeff"_pair_coeff.html command reads a DYNAMO {setfl} file
instead of a {funcfl} file. {Setfl} files can be used to model a
single-element or alloy system. In the alloy case, as explained
above, {setfl} files contain explicit tabulated values for alloy
interactions. Thus they allow more generality than {funcfl} files for
modeling alloys.
For style {eam/alloy}, potential values are read from a file that is
in the DYNAMO multi-element {setfl} format, except that element names
(Ni, Cu, etc) are added to one of the lines in the file. If the
DYNAMO file was created by a Fortran program, it cannot have "D"
values in it for exponents. C only recognizes "e" or "E" for
scientific notation.
Only a single pair_coeff command is used with the {eam/alloy} style
which specifies a DYNAMO {setfl} file, which contains information for
M elements. These are mapped to LAMMPS atom types by specifying N
additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
filename
N element names = mapping of {setfl} elements to atom types :ul
As an example, the potentials/NiAlH_jea.eam.alloy file is a {setfl}
file which has tabulated EAM values for 3 elements and their alloy
interactions: Ni, Al, and H. If your LAMMPS simulation has 4 atoms
types and you want the 1st 3 to be Ni, and the 4th to be Al, you would
use the following pair_coeff command:
pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al :pre
The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Ni arguments map LAMMPS atom types 1,2,3 to the Ni
element in the {setfl} file. The final Al argument maps LAMMPS atom
type 4 to the Al element in the {setfl} file. Note that there is no
requirement that your simulation use all the elements specified by the
{setfl} file.
If a mapping value is specified as NULL, the mapping is not performed.
This can be used when an {eam/alloy} potential is used as part of the
{hybrid} pair style. The NULL values are placeholders for atom types
that will be used with other potentials.
{Setfl} files in the {potentials} directory of the LAMMPS distribution
have an ".eam.alloy" suffix. A DYNAMO multi-element {setfl} file is
formatted as follows:
lines 1,2,3 = comments (ignored)
line 4: Nelements Element1 Element2 ... ElementN
line 5: Nrho, drho, Nr, dr, cutoff :ul
In a DYNAMO {setfl} file, line 4 only lists Nelements = the # of
elements in the {setfl} file. For LAMMPS, the element name (Ni, Cu,
etc) of each element must be added to the line, in the order the
elements appear in the file.
The meaning and units of the values in line 5 is the same as for the
{funcfl} file described above. Note that the cutoff (in Angstroms) is
a global value, valid for all pairwise interactions for all element
pairings.
Following the 5 header lines are Nelements sections, one for each
element, each with the following format:
line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)
embedding function F(rho) (Nrho values)
density function rho(r) (Nr values) :ul
As with the {funcfl} files, only the mass (in mass "units"_units.html,
e.g. mass number or grams/mole for metal units) is used by LAMMPS from
the 1st line. The cubic lattice constant is in Angstroms. The F and
rho arrays are unique to a single element and have the same format and
units as in a {funcfl} file.
Following the Nelements sections, Nr values for each pair potential
phi(r) array are listed for all i,j element pairs in the same format
as other arrays. Since these interactions are symmetric (i,j = j,i)
only phi arrays with i >= j are listed, in the following order: i,j =
(1,1), (2,1), (2,2), (3,1), (3,2), (3,3), (4,1), ..., (Nelements,
Nelements). Unlike the effective charge array Z(r) in {funcfl} files,
the tabulated values for each phi function are listed in {setfl} files
directly as r*phi (in units of eV-Angstroms), since they are for atom
pairs.
:line
Style {eam/cd} is similar to the {eam/alloy} style, except that it
computes alloy pairwise interactions using the concentration-dependent
embedded-atom method (CD-EAM). This model can reproduce the enthalpy
of mixing of alloys over the full composition range, as described in
"(Stukowski)"_#Stukowski.
The pair_coeff command is specified the same as for the {eam/alloy}
style. However the DYNAMO {setfl} file must has two
lines added to it, at the end of the file:
line 1: Comment line (ignored)
line 2: N Coefficient0 Coefficient1 ... CoeffincientN :ul
The last line begins with the degree {N} of the polynomial function
{h(x)} that modifies the cross interaction between A and B elements.
Then {N+1} coefficients for the terms of the polynomial are then
listed.
Modified EAM {setfl} files used with the {eam/cd} style must contain
exactly two elements, i.e. in the current implementation the {eam/cd}
style only supports binary alloys. The first and second elements in
the input EAM file are always taken as the {A} and {B} species.
{CD-EAM} files in the {potentials} directory of the LAMMPS
distribution have a ".cdeam" suffix.
:line
Style {eam/fs} computes pairwise interactions for metals and metal
alloys using a generalized form of EAM potentials due to Finnis and
Sinclair "(Finnis)"_#Finnis. The total energy Ei of an atom I is
given by
:c,image(Eqs/pair_eam_fs.jpg)
This has the same form as the EAM formula above, except that rho is
now a functional specific to the atomic types of both atoms I and J,
so that different elements can contribute differently to the total
electron density at an atomic site depending on the identity of the
element at that atomic site.
The associated "pair_coeff"_pair_coeff.html command for style {eam/fs}
reads a DYNAMO {setfl} file that has been extended to include
additional rho_alpha_beta arrays of tabulated values. A discussion of
how FS EAM differs from conventional EAM alloy potentials is given in
"(Ackland1)"_#Ackland1. An example of such a potential is the same
author's Fe-P FS potential "(Ackland2)"_#Ackland2. Note that while FS
potentials always specify the embedding energy with a square root
dependence on the total density, the implementation in LAMMPS does not
require that; the user can tabulate any functional form desired in the
FS potential files.
For style {eam/fs}, the form of the pair_coeff command is exactly the
same as for style {eam/alloy}, e.g.
pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al :pre
where there are N additional arguments after the filename, where N is
the number of LAMMPS atom types. The N values determine the mapping
of LAMMPS atom types to EAM elements in the file, as described above
for style {eam/alloy}. As with {eam/alloy}, if a mapping value is
NULL, the mapping is not performed. This can be used when an {eam/fs}
potential is used as part of the {hybrid} pair style. The NULL values
are used as placeholders for atom types that will be used with other
potentials.
FS EAM files include more information than the DYNAMO {setfl} format
files read by {eam/alloy}, in that i,j density functionals for all
pairs of elements are included as needed by the Finnis/Sinclair
formulation of the EAM.
FS EAM files in the {potentials} directory of the LAMMPS distribution
have an ".eam.fs" suffix. They are formatted as follows:
lines 1,2,3 = comments (ignored)
line 4: Nelements Element1 Element2 ... ElementN
line 5: Nrho, drho, Nr, dr, cutoff :ul
The 5-line header section is identical to an EAM {setfl} file.
Following the header are Nelements sections, one for each element I,
each with the following format:
line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)
embedding function F(rho) (Nrho values)
density function rho(r) for element I at element 1 (Nr values)
density function rho(r) for element I at element 2
...
density function rho(r) for element I at element Nelement :ul
The units of these quantities in line 1 are the same as for {setfl}
files. Note that the rho(r) arrays in Finnis/Sinclair can be
asymmetric (i,j != j,i) so there are Nelements^2 of them listed in the
file.
Following the Nelements sections, Nr values for each pair potential
phi(r) array are listed in the same manner (r*phi, units of
eV-Angstroms) as in EAM {setfl} files. Note that in Finnis/Sinclair,
the phi(r) arrays are still symmetric, so only phi arrays for i >= j
are listed.
:line
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above with the individual styles. You never need to specify
a pair_coeff command with I != J arguments for the eam styles.
This pair style does not support the "pair_modify"_pair_modify.html
shift, table, and tail options.
The eam pair styles do not write their information to "binary restart
files"_restart.html, since it is stored in tabulated potential files.
Thus, you need to re-specify the pair_style and pair_coeff commands in
an input script that reads a restart file.
The eam pair styles can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. They do not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
-All of these styles except the {eam/cd} style are part of the
-"manybody" package. They are only enabled if LAMMPS was built with
-that package (which it is by default). See the "Making
+All of these styles except the {eam/cd} style are part of the MANYBODY
+package. They are only enabled if LAMMPS was built with that package
+(which it is by default). See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
-The {eam/cd} style is part of the "user-misc" package and also
-requires the "manybody" package. It is only enabled if LAMMPS was
-built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+The {eam/cd} style is part of the USER-MISC package and also requires
+the MANYBODY package. It is only enabled if LAMMPS was built with
+those packages. See the "Making LAMMPS"_Section_start.html#start_3
+section for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Ackland1)
[(Ackland1)] Ackland, Condensed Matter (2005).
:link(Ackland2)
[(Ackland2)] Ackland, Mendelev, Srolovitz, Han and Barashev, Journal
of Physics: Condensed Matter, 16, S2629 (2004).
:link(Daw)
[(Daw)] Daw, Baskes, Phys Rev Lett, 50, 1285 (1983).
Daw, Baskes, Phys Rev B, 29, 6443 (1984).
:link(Finnis)
[(Finnis)] Finnis, Sinclair, Philosophical Magazine A, 50, 45 (1984).
:link(Stukowski)
[(Stukowski)] Stukowski, Sadigh, Erhart, Caro; Modeling Simulation
Materials Science & Engineering, 7, 075005 (2009).
diff --git a/doc/pair_eff.html b/doc/pair_eff.html
index 3bf46fef4..a2aaa1a88 100644
--- a/doc/pair_eff.html
+++ b/doc/pair_eff.html
@@ -1,290 +1,290 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style eff/cut command
</H3>
<P><B>Syntax:</B>
</P>
<P>pair_style eff/cut cutoff eradius_limit_flag pressure_flag
</P>
<UL><LI>cutoff = global cutoff for Coulombic interactions
<LI>eradius_limit_flag = 0 or 1 for whether electron size is restrained (optional)
<LI>pressure_flag = 0 or 1 to define the type of pressure calculation (optional)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style eff/cut 39.7
pair_style eff/cut 40.0 1 1
pair_coeff * *
pair_coeff 2 2 20.0
</PRE>
<P><B>Description:</B>
</P>
<P>This pair style contains a LAMMPS implementation of the electron Force
Field (eFF) potential currently under development at Caltech, as
described in <A HREF = "#Jaramillo-Botero">(Jaramillo-Botero)</A>. The eFF was
first introduced by <A HREF = "#Su">(Su)</A> in 2007.
</P>
<P>eFF can be viewed as an approximation to QM wave packet dynamics and
Fermionic molecular dynamics, combining the ability of electronic
structure methods to describe atomic structure, bonding, and chemistry
in materials, and of plasma methods to describe nonequilibrium
dynamics of large systems with a large number of highly excited
electrons. Yet, eFF relies on a simplification of the electronic
wavefunction in which electrons are described as floating Gaussian
wave packets whose position and size respond to the various dynamic
forces between interacting classical nuclear particles and spherical
Gaussian electron wavepackets. The wavefunction is taken to be a
Hartree product of the wave packets. To compensate for the lack of
explicit antisymmetry in the resulting wavefunction, a spin-dependent
Pauli potential is included in the Hamiltonian. Substituting this
wavefunction into the time-dependent Schrodinger equation produces
equations of motion that correspond - to second order - to classical
Hamiltonian relations between electron position and size, and their
conjugate momenta. The N-electron wavefunction is described as a
product of one-electron Gaussian functions, whose size is a dynamical
variable and whose position is not constrained to a nuclear
center. This form allows for straightforward propagation of the
wavefunction, with time, using a simple formulation from which the
equations of motion are then integrated with conventional MD
algorithms. In addition to this spin-dependent Pauli repulsion
potential term between Gaussians, eFF includes the electron kinetic
energy from the Gaussians. These two terms are based on
first-principles quantum mechanics. On the other hand, nuclei are
described as point charges, which interact with other nuclei and
electrons through standard electrostatic potential forms.
</P>
<P>The full Hamiltonian (shown below), contains then a standard
description for electrostatic interactions between a set of
delocalized point and Gaussian charges which include, nuclei-nuclei
(NN), electron-electron (ee), and nuclei-electron (Ne). Thus, eFF is a
mixed QM-classical mechanics method rather than a conventional force
field method (in which electron motions are averaged out into ground
state nuclear motions, i.e a single electronic state, and particle
interactions are described via empirically parameterized interatomic
potential functions). This makes eFF uniquely suited to simulate
materials over a wide range of temperatures and pressures where
electronically excited and ionized states of matter can occur and
coexist. Furthermore, the interactions between particles -nuclei and
electrons- reduce to the sum of a set of effective pairwise potentials
in the eFF formulation. The <I>eff/cut</I> style computes the pairwise
Coulomb interactions between nuclei and electrons (E_NN,E_Ne,E_ee),
and the quantum-derived Pauli (E_PR) and Kinetic energy interactions
potentials between electrons (E_KE) for a total energy expression
given as,
</P>
<CENTER><IMG SRC = "Eqs/eff_energy_expression.jpg">
</CENTER>
<P>The individual terms are defined as follows:
</P>
<CENTER><IMG SRC = "Eqs/eff_KE.jpg">
</CENTER>
<CENTER><IMG SRC = "Eqs/eff_NN.jpg">
</CENTER>
<CENTER><IMG SRC = "Eqs/eff_Ne.jpg">
</CENTER>
<CENTER><IMG SRC = "Eqs/eff_ee.jpg">
</CENTER>
<CENTER><IMG SRC = "Eqs/eff_Pauli.jpg">
</CENTER>
<P>where, s_i correspond to the electron sizes, the sigmas i's to the
fixed spins of the electrons, Z_i to the charges on the nuclei, R_ij
to the distances between the nuclei or the nuclei and electrons, and
r_ij to the distances between electrons. For additional details see
<A HREF = "#Jaramillo-Botero">(Jaramillo-Botero)</A>.
</P>
<P>The overall electrostatics energy is given in Hartree units of energy
by default and can be modified by an energy-conversion constant,
according to the units chosen (see <A HREF = "units.html">electron_units</A>). The
cutoff Rc, given in Bohrs (by default), truncates the interaction
distance. The recommended cutoff for this pair style should follow
the minimum image criterion, i.e. half of the minimum unit cell
length.
</P>
<P>Style <I>eff/long</I> (not yet available) computes the same interactions as
style <I>eff/cut</I> except that an additional damping factor is applied so
it can be used in conjunction with the
<A HREF = "kspace_style.html">kspace_style</A> command and its <I>ewald</I> or <I>pppm</I>
option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
</P>
<P>This potential is designed to be used with <A HREF = "atom_style.html">atom_style
electron</A> definitions, in order to handle the
description of systems with interacting nuclei and explicit electrons.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>cutoff (distance units)
</UL>
<P>For <I>eff/cut</I>, the cutoff coefficient is optional. If it is not used
(as in some of the examples above), the default global value specified
in the pair_style command is used.
</P>
<P>For <I>eff/long</I> (not yet available) no cutoff will be specified for an
individual I,J type pair via the <A HREF = "pair_coeff.html">pair_coeff</A> command.
All type pairs use the same global cutoff specified in the pair_style
command.
</P>
<P>The <I>eradius_limit_flag</I> and <I>pressure_flag</I> settings are optional.
Neither or both must be specified. If not specified they are
both set to 0 by default.
</P>
<P>The <I>eradius_limit_flag</I> is used to restrain electrons from becoming
unbounded in size at very high temperatures were the Gaussian wave
packet representation breaks down, and from expanding as free
particles to infinite size. A setting of 0 means do not impose this
restraint. A setting of 1 imposes the restraint. The restraining
harmonic potential takes the form E = 1/2k_ss^2 for s > L_box/2, where
k_s = 1 Hartrees/Bohr^2.
</P>
<P>The <I>pressure_flag</I> is used to control between two types of pressure
computation: if set to 0, the computed pressure does not include the
electronic radial virials contributions to the total pressure (scalar
or tensor). If set to 1, the computed pressure will include the
electronic radial virial contributions to the total pressure (scalar
and tensor).
</P>
<P>IMPORTANT NOTE: there are two different pressures that can be reported
for eFF when defining this pair_style, one (default) that considers
electrons do not contribute radial virial components (i.e. electrons
treated as incompressible 'rigid' spheres) and one that does. The
radial electronic contributions to the virials are only tallied if the
flexible pressure option is set, and this will affect both global and
per-atom quantities. In principle, the true pressure of a system is
somewhere in between the rigid and the flexible eFF pressures, but,
for most cases, the difference between these two pressures will not be
significant over long-term averaged runs (i.e. even though the energy
partitioning changes, the total energy remains similar).
</P>
<HR>
<P>IMPORTANT NOTE: The currently implemented eFF gives a reasonably
accurate description for systems containing nuclei from Z = 1-6.
Users interested in applying eFF should restrict to systems where
electrons are s-like, or contain p character only insofar as a single
lobe of electron density is shifted away from the nuclear center. See
further details about some of the virtues and current limitations of
the method in <A HREF = "#Jaramillo-Botero">(Jaramillo-Botero)</A>.
</P>
<P>Work is underway to extend the eFF to higher Z elements with
increasingly non-spherical electrons (p-block and d-block), to provide
explicit terms for electron correlation/exchange, and to improve its
computational efficiency via atom models with fixed 2 s core electrons
and atom models represented as pseudo-cores plus valence electrons.
</P>
<P>The current version adds support for models with fixed-core and
effective pseudo-core (i.e. effective core pseudopotentials, ECP)
definitions. to enable larger timesteps (i.e. by avoiding the high
frequency vibrational modes -translational and radial- of the 2 s
electrons), and in the ECP case to reduce the p-character effects in
higher Z elements (e.g. Silicon). A fixed-core should be defined with
a mass that includes the corresponding nuclear mass plus the 2 s
electrons in atomic mass units (2x5.4857990943e-4), and a radius
equivalent to that of minimized 1s electrons (see examples under
/examples/USER/eff/fixed-core). An pseudo-core should be described
with a mass that includes the corresponding nuclear mass, plus all the
core electrons (i.e no outer shell electrons), and a radius equivalent
to that of a corresponding minimized full-electron system. The charge
for a pseudo-core atom should be given by the number of outer shell
electrons.
</P>
<P>In general, eFF excels at computing the properties of materials in
extreme conditions and tracing the system dynamics over multi-picosend
timescales; this is particularly relevant where electron excitations
can change significantly the nature of bonding in the system. It can
capture with surprising accuracy the behavior of such systems because
it describes consistently and in an unbiased manner many different
kinds of bonds, including covalent, ionic, multicenter, ionic, and
plasma, and how they interconvert and/or change when they become
excited. eFF also excels in computing the relative thermochemistry of
isodemic reactions and conformational changes, where the bonds of the
reactants are of the same type as the bonds of the products. eFF
assumes that kinetic energy differences dominate the overall exchange
energy, which is true when the electrons present are nearly spherical
and nodeless and valid for covalent compounds such as dense hydrogen,
hydrocarbons, and diamond; alkali metals (e.g. lithium), alkali earth
metals (e.g. beryllium) and semimetals such as boron; and various
compounds containing ionic and/or multicenter bonds, such as boron
dihydride.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the cutoff distance for the
<I>eff/cut</I> style can be mixed. The default mix value is <I>geometric</I>.
See the "pair_modify" command for details.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> shift option is not relevant for
these pair styles.
</P>
<P>The <I>eff/long</I> (not yet available) style supports the
<A HREF = "pair_modify.html">pair_modify</A> table option for tabulation of the
short-range portion of the long-range Coulombic interaction.
</P>
<P>These pair styles do not support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding long-range tail corrections to energy and
pressure.
</P>
<P>These pair styles write their information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>These pair styles can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. They do not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>These pair styles will only be enabled if LAMMPS is built with the
-"user-eff" package. It will only be enabled if LAMMPS was built with
+USER-EFF package. It will only be enabled if LAMMPS was built with
that package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>These pair styles require that particles store electron attributes
such as radius, radial velocity, and radital force, as defined by the
<A HREF = "atom_style.html">atom_style</A>. The <I>electron</I> atom style does all of
this.
</P>
<P>Thes pair styles require you to use the <A HREF = "communicate.html">communicate vel
yes</A> option so that velocites are stored by ghost
atoms.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B>
</P>
<P>If not specified, eradius_limit_flag = 0 and pressure_flag = 0.
</P>
<HR>
<A NAME = "Su"></A>
<P><B>(Su)</B> Su and Goddard, Excited Electron Dynamics Modeling of Warm
Dense Matter, Phys Rev Lett, 99:185003 (2007).
</P>
<A NAME = "Jaramillo-Botero"></A>
<P><B>(Jaramillo-Botero)</B> Jaramillo-Botero, Su, Qi, Goddard, Large-scale,
Long-term Non-adiabatic Electron Molecular Dynamics for Describing
Material Properties and Phenomena in Extreme Environments, J Comp
Chem, 32, 497-512 (2011).
</P>
</HTML>
diff --git a/doc/pair_eff.txt b/doc/pair_eff.txt
index 11f0fb960..7e3877010 100644
--- a/doc/pair_eff.txt
+++ b/doc/pair_eff.txt
@@ -1,283 +1,283 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style eff/cut command :h3
[Syntax:]
pair_style eff/cut cutoff eradius_limit_flag pressure_flag
cutoff = global cutoff for Coulombic interactions
eradius_limit_flag = 0 or 1 for whether electron size is restrained (optional)
pressure_flag = 0 or 1 to define the type of pressure calculation (optional) :ul
[Examples:]
pair_style eff/cut 39.7
pair_style eff/cut 40.0 1 1
pair_coeff * *
pair_coeff 2 2 20.0 :pre
[Description:]
This pair style contains a LAMMPS implementation of the electron Force
Field (eFF) potential currently under development at Caltech, as
described in "(Jaramillo-Botero)"_#Jaramillo-Botero. The eFF was
first introduced by "(Su)"_#Su in 2007.
eFF can be viewed as an approximation to QM wave packet dynamics and
Fermionic molecular dynamics, combining the ability of electronic
structure methods to describe atomic structure, bonding, and chemistry
in materials, and of plasma methods to describe nonequilibrium
dynamics of large systems with a large number of highly excited
electrons. Yet, eFF relies on a simplification of the electronic
wavefunction in which electrons are described as floating Gaussian
wave packets whose position and size respond to the various dynamic
forces between interacting classical nuclear particles and spherical
Gaussian electron wavepackets. The wavefunction is taken to be a
Hartree product of the wave packets. To compensate for the lack of
explicit antisymmetry in the resulting wavefunction, a spin-dependent
Pauli potential is included in the Hamiltonian. Substituting this
wavefunction into the time-dependent Schrodinger equation produces
equations of motion that correspond - to second order - to classical
Hamiltonian relations between electron position and size, and their
conjugate momenta. The N-electron wavefunction is described as a
product of one-electron Gaussian functions, whose size is a dynamical
variable and whose position is not constrained to a nuclear
center. This form allows for straightforward propagation of the
wavefunction, with time, using a simple formulation from which the
equations of motion are then integrated with conventional MD
algorithms. In addition to this spin-dependent Pauli repulsion
potential term between Gaussians, eFF includes the electron kinetic
energy from the Gaussians. These two terms are based on
first-principles quantum mechanics. On the other hand, nuclei are
described as point charges, which interact with other nuclei and
electrons through standard electrostatic potential forms.
The full Hamiltonian (shown below), contains then a standard
description for electrostatic interactions between a set of
delocalized point and Gaussian charges which include, nuclei-nuclei
(NN), electron-electron (ee), and nuclei-electron (Ne). Thus, eFF is a
mixed QM-classical mechanics method rather than a conventional force
field method (in which electron motions are averaged out into ground
state nuclear motions, i.e a single electronic state, and particle
interactions are described via empirically parameterized interatomic
potential functions). This makes eFF uniquely suited to simulate
materials over a wide range of temperatures and pressures where
electronically excited and ionized states of matter can occur and
coexist. Furthermore, the interactions between particles -nuclei and
electrons- reduce to the sum of a set of effective pairwise potentials
in the eFF formulation. The {eff/cut} style computes the pairwise
Coulomb interactions between nuclei and electrons (E_NN,E_Ne,E_ee),
and the quantum-derived Pauli (E_PR) and Kinetic energy interactions
potentials between electrons (E_KE) for a total energy expression
given as,
:c,image(Eqs/eff_energy_expression.jpg)
The individual terms are defined as follows:
:c,image(Eqs/eff_KE.jpg)
:c,image(Eqs/eff_NN.jpg)
:c,image(Eqs/eff_Ne.jpg)
:c,image(Eqs/eff_ee.jpg)
:c,image(Eqs/eff_Pauli.jpg)
where, s_i correspond to the electron sizes, the sigmas i's to the
fixed spins of the electrons, Z_i to the charges on the nuclei, R_ij
to the distances between the nuclei or the nuclei and electrons, and
r_ij to the distances between electrons. For additional details see
"(Jaramillo-Botero)"_#Jaramillo-Botero.
The overall electrostatics energy is given in Hartree units of energy
by default and can be modified by an energy-conversion constant,
according to the units chosen (see "electron_units"_units.html). The
cutoff Rc, given in Bohrs (by default), truncates the interaction
distance. The recommended cutoff for this pair style should follow
the minimum image criterion, i.e. half of the minimum unit cell
length.
Style {eff/long} (not yet available) computes the same interactions as
style {eff/cut} except that an additional damping factor is applied so
it can be used in conjunction with the
"kspace_style"_kspace_style.html command and its {ewald} or {pppm}
option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
This potential is designed to be used with "atom_style
electron"_atom_style.html definitions, in order to handle the
description of systems with interacting nuclei and explicit electrons.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
cutoff (distance units) :ul
For {eff/cut}, the cutoff coefficient is optional. If it is not used
(as in some of the examples above), the default global value specified
in the pair_style command is used.
For {eff/long} (not yet available) no cutoff will be specified for an
individual I,J type pair via the "pair_coeff"_pair_coeff.html command.
All type pairs use the same global cutoff specified in the pair_style
command.
The {eradius_limit_flag} and {pressure_flag} settings are optional.
Neither or both must be specified. If not specified they are
both set to 0 by default.
The {eradius_limit_flag} is used to restrain electrons from becoming
unbounded in size at very high temperatures were the Gaussian wave
packet representation breaks down, and from expanding as free
particles to infinite size. A setting of 0 means do not impose this
restraint. A setting of 1 imposes the restraint. The restraining
harmonic potential takes the form E = 1/2k_ss^2 for s > L_box/2, where
k_s = 1 Hartrees/Bohr^2.
The {pressure_flag} is used to control between two types of pressure
computation: if set to 0, the computed pressure does not include the
electronic radial virials contributions to the total pressure (scalar
or tensor). If set to 1, the computed pressure will include the
electronic radial virial contributions to the total pressure (scalar
and tensor).
IMPORTANT NOTE: there are two different pressures that can be reported
for eFF when defining this pair_style, one (default) that considers
electrons do not contribute radial virial components (i.e. electrons
treated as incompressible 'rigid' spheres) and one that does. The
radial electronic contributions to the virials are only tallied if the
flexible pressure option is set, and this will affect both global and
per-atom quantities. In principle, the true pressure of a system is
somewhere in between the rigid and the flexible eFF pressures, but,
for most cases, the difference between these two pressures will not be
significant over long-term averaged runs (i.e. even though the energy
partitioning changes, the total energy remains similar).
:line
IMPORTANT NOTE: The currently implemented eFF gives a reasonably
accurate description for systems containing nuclei from Z = 1-6.
Users interested in applying eFF should restrict to systems where
electrons are s-like, or contain p character only insofar as a single
lobe of electron density is shifted away from the nuclear center. See
further details about some of the virtues and current limitations of
the method in "(Jaramillo-Botero)"_#Jaramillo-Botero.
Work is underway to extend the eFF to higher Z elements with
increasingly non-spherical electrons (p-block and d-block), to provide
explicit terms for electron correlation/exchange, and to improve its
computational efficiency via atom models with fixed 2 s core electrons
and atom models represented as pseudo-cores plus valence electrons.
The current version adds support for models with fixed-core and
effective pseudo-core (i.e. effective core pseudopotentials, ECP)
definitions. to enable larger timesteps (i.e. by avoiding the high
frequency vibrational modes -translational and radial- of the 2 s
electrons), and in the ECP case to reduce the p-character effects in
higher Z elements (e.g. Silicon). A fixed-core should be defined with
a mass that includes the corresponding nuclear mass plus the 2 s
electrons in atomic mass units (2x5.4857990943e-4), and a radius
equivalent to that of minimized 1s electrons (see examples under
/examples/USER/eff/fixed-core). An pseudo-core should be described
with a mass that includes the corresponding nuclear mass, plus all the
core electrons (i.e no outer shell electrons), and a radius equivalent
to that of a corresponding minimized full-electron system. The charge
for a pseudo-core atom should be given by the number of outer shell
electrons.
In general, eFF excels at computing the properties of materials in
extreme conditions and tracing the system dynamics over multi-picosend
timescales; this is particularly relevant where electron excitations
can change significantly the nature of bonding in the system. It can
capture with surprising accuracy the behavior of such systems because
it describes consistently and in an unbiased manner many different
kinds of bonds, including covalent, ionic, multicenter, ionic, and
plasma, and how they interconvert and/or change when they become
excited. eFF also excels in computing the relative thermochemistry of
isodemic reactions and conformational changes, where the bonds of the
reactants are of the same type as the bonds of the products. eFF
assumes that kinetic energy differences dominate the overall exchange
energy, which is true when the electrons present are nearly spherical
and nodeless and valid for covalent compounds such as dense hydrogen,
hydrocarbons, and diamond; alkali metals (e.g. lithium), alkali earth
metals (e.g. beryllium) and semimetals such as boron; and various
compounds containing ionic and/or multicenter bonds, such as boron
dihydride.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the cutoff distance for the
{eff/cut} style can be mixed. The default mix value is {geometric}.
See the "pair_modify" command for details.
The "pair_modify"_pair_modify.html shift option is not relevant for
these pair styles.
The {eff/long} (not yet available) style supports the
"pair_modify"_pair_modify.html table option for tabulation of the
short-range portion of the long-range Coulombic interaction.
These pair styles do not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure.
These pair styles write their information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
These pair styles can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. They do not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
These pair styles will only be enabled if LAMMPS is built with the
-"user-eff" package. It will only be enabled if LAMMPS was built with
+USER-EFF package. It will only be enabled if LAMMPS was built with
that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
These pair styles require that particles store electron attributes
such as radius, radial velocity, and radital force, as defined by the
"atom_style"_atom_style.html. The {electron} atom style does all of
this.
Thes pair styles require you to use the "communicate vel
yes"_communicate.html option so that velocites are stored by ghost
atoms.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:]
If not specified, eradius_limit_flag = 0 and pressure_flag = 0.
:line
:link(Su)
[(Su)] Su and Goddard, Excited Electron Dynamics Modeling of Warm
Dense Matter, Phys Rev Lett, 99:185003 (2007).
:link(Jaramillo-Botero)
[(Jaramillo-Botero)] Jaramillo-Botero, Su, Qi, Goddard, Large-scale,
Long-term Non-adiabatic Electron Molecular Dynamics for Describing
Material Properties and Phenomena in Extreme Environments, J Comp
Chem, 32, 497-512 (2011).
diff --git a/doc/pair_eim.html b/doc/pair_eim.html
index cfeead5d9..b43368617 100644
--- a/doc/pair_eim.html
+++ b/doc/pair_eim.html
@@ -1,153 +1,153 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style eim command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style
</PRE>
<UL><LI>style = <I>eim</I>
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style eim
pair_coeff * * Na Cl ../potentials/ffield.eim Na Cl
pair_coeff * * Na Cl ffield.eim Na Na Na Cl
pair_coeff * * Na Cl ../potentials/ffield.eim Cl NULL Na
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>eim</I> computes pairwise interactions for ionic compounds
using embedded-ion method (EIM) potentials <A HREF = "#Zhou">(Zhou)</A>. The
energy of the system E is given by
</P>
<CENTER><IMG SRC = "Eqs/pair_eim1.jpg">
</CENTER>
<P>The first term is a double pairwise sum over the J neighbors of all I
atoms, where phi_ij is a pair potential. The second term sums over
the embedding energy E_i of atom I, which is a function of its charge
q_i and the electrical potential sigma_i at its location. E_i, q_i,
and sigma_i are calculated as
</P>
<CENTER><IMG SRC = "Eqs/pair_eim2.jpg">
</CENTER>
<P>where eta_ji is a pairwise function describing electron flow from atom
I to atom J, and psi_ij is another pairwise function. The multi-body
nature of the EIM potential is a result of the embedding energy term.
A complete list of all the pair functions used in EIM is summarized
below
</P>
<CENTER><IMG SRC = "Eqs/pair_eim3.jpg">
</CENTER>
<P>Here E_b, r_e, r_(c,phi), alpha, beta, A_(psi), zeta, r_(s,psi),
r_(c,psi), A_(eta), r_(s,eta), r_(c,eta), chi, and pair function type
p are parameters, with subscripts ij indicating the two species of
atoms in the atomic pair.
</P>
<P>IMPORTANT NOTE: Even though the EIM potential is treating atoms as
charged ions, you should not use a LAMMPS <A HREF = "atom_style.html">atom_style</A>
that stores a charge on each atom and thus requires you to assign a
charge to each atom, e.g. the <I>charge</I> or <I>full</I> atom styles. This is
because the EIM potential infers the charge on an atom from the
equation above for q_i; you do not assign charges explicitly.
</P>
<HR>
<P>All the EIM parameters are listed in a potential file which is
specified by the <A HREF = "pair_coeff.html">pair_coeff</A> command. This is an
ASCII text file in a format described below. The "ffield.eim" file
included in the "potentials" directory of the LAMMPS distribution
currently includes nine elements Li, Na, K, Rb, Cs, F, Cl, Br, and I.
A system with any combination of these elements can be modeled. This
file is parameterized in terms of LAMMPS <A HREF = "units.html">metal units</A>.
</P>
<P>Note that unlike other potentials, cutoffs for EIM potentials are not
set in the pair_style or pair_coeff command; they are specified in the
EIM potential file itself. Likewise, the EIM potential file lists
atomic masses; thus you do not need to use the <A HREF = "mass.html">mass</A>
command to specify them.
</P>
<P>Only a single pair_coeff command is used with the <I>eim</I> style which
specifies an EIM potential file and the element(s) to extract
information for. The EIM elements are mapped to LAMMPS atom types by
specifying N additional arguments after the filename in the pair_coeff
command, where N is the number of LAMMPS atom types:
</P>
<UL><LI>Elem1, Elem2, ...
<LI>EIM potential file
<LI>N element names = mapping of EIM elements to atom types
</UL>
<P>As an example like one of those above, suppose you want to model a
system with Na and Cl atoms. If your LAMMPS simulation has 4 atoms
types and you want the 1st 3 to be Na, and the 4th to be Cl, you would
use the following pair_coeff command:
</P>
<PRE>pair_coeff * * Na Cl ffield.eim Na Na Na Cl
</PRE>
<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The filename is the EIM potential file. The Na and Cl arguments
(before the file name) are the two elements for which info will be
extracted from the potentail file. The first three trailing Na
arguments map LAMMPS atom types 1,2,3 to the EIM Na element. The
final Cl argument maps LAMMPS atom type 4 to the EIM Cl element.
</P>
<P>If a mapping value is specified as NULL, the mapping is not performed.
This can be used when an <I>eim</I> potential is used as part of the
<I>hybrid</I> pair style. The NULL values are placeholders for atom types
that will be used with other potentials.
</P>
<P>The ffield.eim file in the <I>potentials</I> directory of the LAMMPS
distribution is formated as follows:
</P>
<P>Lines starting with # are comments and are ignored by LAMMPS. Lines
starting with "global:" include three global values. The first value
divides the cations from anions, i.e., any elements with
electronegativity above this value are viewed as anions, and any
elements with electronegativity below this value are viewed as
cations. The second and third values are related to the cutoff
function - i.e. the 0.510204, 1.64498, and 0.010204 shown in the above
equation can be derived from these values.
</P>
<P>Lines starting with "element:" are formatted as follows: name of
element, atomic number, atomic mass, electronic negativity, atomic
radius (LAMMPS ignores it), ionic radius (LAMMPS ignores it), cohesive
energy (LAMMPS ignores it), and q0 (must be 0).
</P>
<P>Lines starting with "pair:" are entered as: element 1, element 2,
r_(c,phi), r_(c,phi) (redundant for historical reasons), E_b, r_e,
alpha, beta, r_(c,eta), A_(eta), r_(s,eta), r_(c,psi), A_(psi), zeta,
r_(s,psi), and p.
</P>
<P>The lines in the file can be in any order; LAMMPS extracts the info it
needs.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>This style is part of the "manybody" package. It is only enabled if
+<P>This style is part of the MANYBODY package. It is only enabled if
LAMMPS was built with that package (which it is by default).
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Zhou"></A>
<P><B>(Zhou)</B> Zhou, submitted for publication (2010). Please contact
Xiaowang Zhou (Sandia) for details via email at xzhou at sandia.gov.
</P>
</HTML>
diff --git a/doc/pair_eim.txt b/doc/pair_eim.txt
index 411f64c25..240e551b8 100644
--- a/doc/pair_eim.txt
+++ b/doc/pair_eim.txt
@@ -1,147 +1,147 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style eim command :h3
[Syntax:]
pair_style style :pre
style = {eim} :ul
[Examples:]
pair_style eim
pair_coeff * * Na Cl ../potentials/ffield.eim Na Cl
pair_coeff * * Na Cl ffield.eim Na Na Na Cl
pair_coeff * * Na Cl ../potentials/ffield.eim Cl NULL Na :pre
[Description:]
Style {eim} computes pairwise interactions for ionic compounds
using embedded-ion method (EIM) potentials "(Zhou)"_#Zhou. The
energy of the system E is given by
:c,image(Eqs/pair_eim1.jpg)
The first term is a double pairwise sum over the J neighbors of all I
atoms, where phi_ij is a pair potential. The second term sums over
the embedding energy E_i of atom I, which is a function of its charge
q_i and the electrical potential sigma_i at its location. E_i, q_i,
and sigma_i are calculated as
:c,image(Eqs/pair_eim2.jpg)
where eta_ji is a pairwise function describing electron flow from atom
I to atom J, and psi_ij is another pairwise function. The multi-body
nature of the EIM potential is a result of the embedding energy term.
A complete list of all the pair functions used in EIM is summarized
below
:c,image(Eqs/pair_eim3.jpg)
Here E_b, r_e, r_(c,phi), alpha, beta, A_(psi), zeta, r_(s,psi),
r_(c,psi), A_(eta), r_(s,eta), r_(c,eta), chi, and pair function type
p are parameters, with subscripts ij indicating the two species of
atoms in the atomic pair.
IMPORTANT NOTE: Even though the EIM potential is treating atoms as
charged ions, you should not use a LAMMPS "atom_style"_atom_style.html
that stores a charge on each atom and thus requires you to assign a
charge to each atom, e.g. the {charge} or {full} atom styles. This is
because the EIM potential infers the charge on an atom from the
equation above for q_i; you do not assign charges explicitly.
:line
All the EIM parameters are listed in a potential file which is
specified by the "pair_coeff"_pair_coeff.html command. This is an
ASCII text file in a format described below. The "ffield.eim" file
included in the "potentials" directory of the LAMMPS distribution
currently includes nine elements Li, Na, K, Rb, Cs, F, Cl, Br, and I.
A system with any combination of these elements can be modeled. This
file is parameterized in terms of LAMMPS "metal units"_units.html.
Note that unlike other potentials, cutoffs for EIM potentials are not
set in the pair_style or pair_coeff command; they are specified in the
EIM potential file itself. Likewise, the EIM potential file lists
atomic masses; thus you do not need to use the "mass"_mass.html
command to specify them.
Only a single pair_coeff command is used with the {eim} style which
specifies an EIM potential file and the element(s) to extract
information for. The EIM elements are mapped to LAMMPS atom types by
specifying N additional arguments after the filename in the pair_coeff
command, where N is the number of LAMMPS atom types:
Elem1, Elem2, ...
EIM potential file
N element names = mapping of EIM elements to atom types :ul
As an example like one of those above, suppose you want to model a
system with Na and Cl atoms. If your LAMMPS simulation has 4 atoms
types and you want the 1st 3 to be Na, and the 4th to be Cl, you would
use the following pair_coeff command:
pair_coeff * * Na Cl ffield.eim Na Na Na Cl :pre
The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The filename is the EIM potential file. The Na and Cl arguments
(before the file name) are the two elements for which info will be
extracted from the potentail file. The first three trailing Na
arguments map LAMMPS atom types 1,2,3 to the EIM Na element. The
final Cl argument maps LAMMPS atom type 4 to the EIM Cl element.
If a mapping value is specified as NULL, the mapping is not performed.
This can be used when an {eim} potential is used as part of the
{hybrid} pair style. The NULL values are placeholders for atom types
that will be used with other potentials.
The ffield.eim file in the {potentials} directory of the LAMMPS
distribution is formated as follows:
Lines starting with # are comments and are ignored by LAMMPS. Lines
starting with "global:" include three global values. The first value
divides the cations from anions, i.e., any elements with
electronegativity above this value are viewed as anions, and any
elements with electronegativity below this value are viewed as
cations. The second and third values are related to the cutoff
function - i.e. the 0.510204, 1.64498, and 0.010204 shown in the above
equation can be derived from these values.
Lines starting with "element:" are formatted as follows: name of
element, atomic number, atomic mass, electronic negativity, atomic
radius (LAMMPS ignores it), ionic radius (LAMMPS ignores it), cohesive
energy (LAMMPS ignores it), and q0 (must be 0).
Lines starting with "pair:" are entered as: element 1, element 2,
r_(c,phi), r_(c,phi) (redundant for historical reasons), E_b, r_e,
alpha, beta, r_(c,eta), A_(eta), r_(s,eta), r_(c,psi), A_(psi), zeta,
r_(s,psi), and p.
The lines in the file can be in any order; LAMMPS extracts the info it
needs.
:line
[Restrictions:]
-This style is part of the "manybody" package. It is only enabled if
+This style is part of the MANYBODY package. It is only enabled if
LAMMPS was built with that package (which it is by default).
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Zhou)
[(Zhou)] Zhou, submitted for publication (2010). Please contact
Xiaowang Zhou (Sandia) for details via email at xzhou at sandia.gov.
diff --git a/doc/pair_gayberne.html b/doc/pair_gayberne.html
index 77e11eaa0..e3d249ae4 100644
--- a/doc/pair_gayberne.html
+++ b/doc/pair_gayberne.html
@@ -1,238 +1,238 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style gayberne command
</H3>
<H3>pair_style gayberne/gpu command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style gayberne gamma upsilon mu cutoff
</PRE>
<UL><LI>gamma = shift for potential minimum (typically 1)
<LI>upsilon = exponent for eta orientation-dependent energy function
<LI>mu = exponent for chi orientation-dependent energy function
<LI>cutoff = global cutoff for interactions (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style gayberne 1.0 1.0 1.0 10.0
pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>gayberne</I> styles compute a Gay-Berne anisotropic LJ interaction
<A HREF = "#Berardi">(Berardi)</A> between pairs of ellipsoidal particles or an
ellipsoidal and spherical particle via the formulas
</P>
<CENTER><IMG SRC = "Eqs/pair_gayberne.jpg">
</CENTER>
<P>where A1 and A2 are the transformation matrices from the simulation
box frame to the body frame and r12 is the center to center vector
between the particles. Ur controls the shifted distance dependent
interaction based on the distance of closest approach of the two
particles (h12) and the user-specified shift parameter gamma. When
both particles are spherical, the formula reduces to the usual
Lennard-Jones interaction (see details below for when Gay-Berne treats
a particle as "spherical").
</P>
<P>For large uniform molecules it has been shown that the energy
parameters are approximately representable in terms of local contact
curvatures <A HREF = "#Everaers">(Everaers)</A>:
</P>
<CENTER><IMG SRC = "Eqs/pair_gayberne2.jpg">
</CENTER>
<P>The variable names utilized as potential parameters are for the most
part taken from <A HREF = "#Everaers">(Everaers)</A> in order to be consistent with
the <A HREF = "pair_resquared.html">RE-squared pair potential</A>. Details on the
upsilon and mu parameters are given
<A HREF = "PDF/pair_resquared_extra.pdf">here</A>.
</P>
<P>More details of the Gay-Berne formulation are given in the references
listed below and in <A HREF = "PDF/pair_gayberne_extra.pdf">this supplementary
document</A>.
</P>
<P>Use of this pair style requires the NVE, NVT, or NPT fixes with the
<I>asphere</I> extension (e.g. <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>) in
order to integrate particle rotation. Additionally, <A HREF = "atom_style.html">atom_style
ellipsoid</A> should be used since it defines the
rotational state and the size and shape of each ellipsoidal particle.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>epsilon = well depth (energy units)
<LI>sigma = minimum effective particle radii (distance units)
<LI>epsilon_i_a = relative well depth of type I for side-to-side interactions
<LI>epsilon_i_b = relative well depth of type I for face-to-face interactions
<LI>epsilon_i_c = relative well depth of type I for end-to-end interactions
<LI>epsilon_j_a = relative well depth of type J for side-to-side interactions
<LI>epsilon_j_b = relative well depth of type J for face-to-face interactions
<LI>epsilon_j_c = relative well depth of type J for end-to-end interactions
<LI>cutoff (distance units)
</UL>
<P>The last coefficient is optional. If not specified, the global
cutoff specified in the pair_style command is used.
</P>
<P>It is typical with the Gay-Berne potential to define <I>sigma</I> as the
minimum of the 3 shape diameters of the particles involved in an I,I
interaction, though this is not required. Note that this is a
different meaning for <I>sigma</I> than the <A HREF = "pair_resquared.html">pair_style
resquared</A> potential uses.
</P>
<P>The epsilon_i and epsilon_j coefficients are actually defined for atom
types, not for pairs of atom types. Thus, in a series of pair_coeff
commands, they only need to be specified once for each atom type.
</P>
<P>Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are
non-zero, the three values are assigned to atom type I. If all the
epsilon_i values are zero, they are ignored. If any of epsilon_j_a,
epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned
to atom type J. If all three epsilon_i values are zero, they are
ignored. Thus the typical way to define the epsilon_i and epsilon_j
coefficients is to list their values in "pair_coeff I J" commands when
I = J, but set them to 0.0 when I != J. If you do list them when I !=
J, you should insure they are consistent with their values in other
pair_coeff commands.
</P>
<P>Note that if this potential is being used as a sub-style of
<A HREF = "pair_hybrid.html">pair_style hybrid</A>, and there is no "pair_coeff I I"
setting made for Gay-Berne for a particular type I (because I-I
interactions are computed by another hybrid pair potential), then you
still need to insure the epsilon a,b,c coefficients are assigned to
that type in a "pair_coeff I J" command.
</P>
<P>IMPORTANT NOTE: If the epsilon a = b = c for an atom type, and if the
shape of the particle itself is spherical, meaning its 3 shape
parameters are all the same, then the particle is treated as an LJ
sphere by the Gay-Berne potential. This is significant because if two
LJ spheres interact, then the simple Lennard-Jones formula is used to
compute their interaction energy/force using the specified epsilon and
sigma as the standard LJ parameters. This is much cheaper to compute
than the full Gay-Berne formula. To treat the particle as a LJ sphere
with sigma = D, you should normally set epsilon a = b = c = 1.0, set
the pair_coeff sigma = D, and also set the 3 shape parameters for the
particle to D. The one exception is that if the 3 shape parameters
are set to 0.0, which is a valid way in LAMMPS to specify a point
particle, then the Gay-Berne potential will treat that as shape
parameters of 1.0 (i.e. a LJ particle with sigma = 1), since it
requires finite-size particles. In this case you should still set the
pair_coeff sigma to 1.0 as well.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+<P>These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for this pair style can be mixed. The default mix
value is <I>geometric</I>. See the "pair_modify" command for details.
</P>
<P>This pair styles supports the <A HREF = "pair_modify.html">pair_modify</A> shift
option for the energy of the Lennard-Jones portion of the pair
interaction, but only for sphere-sphere interactions. There is no
shifting performed for ellipsoidal interactions due to the anisotropic
dependence of the interaction.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
for this pair style.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding long-range tail corrections to energy and
pressure.
</P>
<P>This pair style writes its information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>The <I>gayberne</I> style is part of the "asphere" package. It is only
+<P>The <I>gayberne</I> style is part of the ASPHERE package. It is only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>These pair style require that atoms store torque and a quaternion to
represent their orientation, as defined by the
<A HREF = "atom_style.html">atom_style</A>. It also require they store a per-type
<A HREF = "shape.html">shape</A>. The particles cannot store a per-particle
diameter.
</P>
<P>This pair style requires that atoms be ellipsoids as defined by the
<A HREF = "atom_style.html">atom_style ellipsoid</A> command.
</P>
<P>Particles acted on by the potential can be extended aspherical or
spherical particles, or point particles. Spherical particles have all
3 of their shape parameters equal to each other. Point particles have
all 3 of their shape parameters equal to 0.0.
</P>
<P>The Gay-Berne potential does not become isotropic as r increases
<A HREF = "#Everaers">(Everaers)</A>. The distance-of-closest-approach
approximation used by LAMMPS becomes less accurate when high-aspect
ratio ellipsoids are used.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>,
<A HREF = "compute_temp_asphere.html">compute temp/asphere</A>, <A HREF = "pair_resquared.html">pair_style
resquared</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Everaers"></A>
<P><B>(Everaers)</B> Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).
</P>
<A NAME = "Berardi"></A>
<P><B>(Berardi)</B> Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998).
Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008).
</P>
<A NAME = "Perram"></A>
<P><B>(Perram)</B> Perram and Rasmussen, Phys Rev E, 54, 6565-6572 (1996).
</P>
<A NAME = "Allen"></A>
<P><B>(Allen)</B> Allen and Germano, Mol Phys 104, 3225-3235 (2006).
</P>
</HTML>
diff --git a/doc/pair_gayberne.txt b/doc/pair_gayberne.txt
index 6a0f7f5bc..6ff0f16dd 100755
--- a/doc/pair_gayberne.txt
+++ b/doc/pair_gayberne.txt
@@ -1,228 +1,228 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style gayberne command :h3
pair_style gayberne/gpu command :h3
[Syntax:]
pair_style gayberne gamma upsilon mu cutoff :pre
gamma = shift for potential minimum (typically 1)
upsilon = exponent for eta orientation-dependent energy function
mu = exponent for chi orientation-dependent energy function
cutoff = global cutoff for interactions (distance units) :ul
[Examples:]
pair_style gayberne 1.0 1.0 1.0 10.0
pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0 :pre
[Description:]
The {gayberne} styles compute a Gay-Berne anisotropic LJ interaction
"(Berardi)"_#Berardi between pairs of ellipsoidal particles or an
ellipsoidal and spherical particle via the formulas
:c,image(Eqs/pair_gayberne.jpg)
where A1 and A2 are the transformation matrices from the simulation
box frame to the body frame and r12 is the center to center vector
between the particles. Ur controls the shifted distance dependent
interaction based on the distance of closest approach of the two
particles (h12) and the user-specified shift parameter gamma. When
both particles are spherical, the formula reduces to the usual
Lennard-Jones interaction (see details below for when Gay-Berne treats
a particle as "spherical").
For large uniform molecules it has been shown that the energy
parameters are approximately representable in terms of local contact
curvatures "(Everaers)"_#Everaers:
:c,image(Eqs/pair_gayberne2.jpg)
The variable names utilized as potential parameters are for the most
part taken from "(Everaers)"_#Everaers in order to be consistent with
the "RE-squared pair potential"_pair_resquared.html. Details on the
upsilon and mu parameters are given
"here"_PDF/pair_resquared_extra.pdf.
More details of the Gay-Berne formulation are given in the references
listed below and in "this supplementary
document"_PDF/pair_gayberne_extra.pdf.
Use of this pair style requires the NVE, NVT, or NPT fixes with the
{asphere} extension (e.g. "fix nve/asphere"_fix_nve_asphere.html) in
order to integrate particle rotation. Additionally, "atom_style
ellipsoid"_atom_style.html should be used since it defines the
rotational state and the size and shape of each ellipsoidal particle.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
epsilon = well depth (energy units)
sigma = minimum effective particle radii (distance units)
epsilon_i_a = relative well depth of type I for side-to-side interactions
epsilon_i_b = relative well depth of type I for face-to-face interactions
epsilon_i_c = relative well depth of type I for end-to-end interactions
epsilon_j_a = relative well depth of type J for side-to-side interactions
epsilon_j_b = relative well depth of type J for face-to-face interactions
epsilon_j_c = relative well depth of type J for end-to-end interactions
cutoff (distance units) :ul
The last coefficient is optional. If not specified, the global
cutoff specified in the pair_style command is used.
It is typical with the Gay-Berne potential to define {sigma} as the
minimum of the 3 shape diameters of the particles involved in an I,I
interaction, though this is not required. Note that this is a
different meaning for {sigma} than the "pair_style
resquared"_pair_resquared.html potential uses.
The epsilon_i and epsilon_j coefficients are actually defined for atom
types, not for pairs of atom types. Thus, in a series of pair_coeff
commands, they only need to be specified once for each atom type.
Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are
non-zero, the three values are assigned to atom type I. If all the
epsilon_i values are zero, they are ignored. If any of epsilon_j_a,
epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned
to atom type J. If all three epsilon_i values are zero, they are
ignored. Thus the typical way to define the epsilon_i and epsilon_j
coefficients is to list their values in "pair_coeff I J" commands when
I = J, but set them to 0.0 when I != J. If you do list them when I !=
J, you should insure they are consistent with their values in other
pair_coeff commands.
Note that if this potential is being used as a sub-style of
"pair_style hybrid"_pair_hybrid.html, and there is no "pair_coeff I I"
setting made for Gay-Berne for a particular type I (because I-I
interactions are computed by another hybrid pair potential), then you
still need to insure the epsilon a,b,c coefficients are assigned to
that type in a "pair_coeff I J" command.
IMPORTANT NOTE: If the epsilon a = b = c for an atom type, and if the
shape of the particle itself is spherical, meaning its 3 shape
parameters are all the same, then the particle is treated as an LJ
sphere by the Gay-Berne potential. This is significant because if two
LJ spheres interact, then the simple Lennard-Jones formula is used to
compute their interaction energy/force using the specified epsilon and
sigma as the standard LJ parameters. This is much cheaper to compute
than the full Gay-Berne formula. To treat the particle as a LJ sphere
with sigma = D, you should normally set epsilon a = b = c = 1.0, set
the pair_coeff sigma = D, and also set the 3 shape parameters for the
particle to D. The one exception is that if the 3 shape parameters
are set to 0.0, which is a valid way in LAMMPS to specify a point
particle, then the Gay-Berne potential will treat that as shape
parameters of 1.0 (i.e. a LJ particle with sigma = 1), since it
requires finite-size particles. In this case you should still set the
pair_coeff sigma to 1.0 as well.
:line
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for this pair style can be mixed. The default mix
value is {geometric}. See the "pair_modify" command for details.
This pair styles supports the "pair_modify"_pair_modify.html shift
option for the energy of the Lennard-Jones portion of the pair
interaction, but only for sphere-sphere interactions. There is no
shifting performed for ellipsoidal interactions due to the anisotropic
dependence of the interaction.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
This pair style does not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
-The {gayberne} style is part of the "asphere" package. It is only
+The {gayberne} style is part of the ASPHERE package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
These pair style require that atoms store torque and a quaternion to
represent their orientation, as defined by the
"atom_style"_atom_style.html. It also require they store a per-type
"shape"_shape.html. The particles cannot store a per-particle
diameter.
This pair style requires that atoms be ellipsoids as defined by the
"atom_style ellipsoid"_atom_style.html command.
Particles acted on by the potential can be extended aspherical or
spherical particles, or point particles. Spherical particles have all
3 of their shape parameters equal to each other. Point particles have
all 3 of their shape parameters equal to 0.0.
The Gay-Berne potential does not become isotropic as r increases
"(Everaers)"_#Everaers. The distance-of-closest-approach
approximation used by LAMMPS becomes less accurate when high-aspect
ratio ellipsoids are used.
[Related commands:]
"pair_coeff"_pair_coeff.html, "fix nve/asphere"_fix_nve_asphere.html,
"compute temp/asphere"_compute_temp_asphere.html, "pair_style
resquared"_pair_resquared.html
[Default:] none
:line
:link(Everaers)
[(Everaers)] Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).
:link(Berardi)
[(Berardi)] Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998).
Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008).
:link(Perram)
[(Perram)] Perram and Rasmussen, Phys Rev E, 54, 6565-6572 (1996).
:link(Allen)
[(Allen)] Allen and Germano, Mol Phys 104, 3225-3235 (2006).
diff --git a/doc/pair_gran.html b/doc/pair_gran.html
index 9e42833bf..9e1bd6cdd 100644
--- a/doc/pair_gran.html
+++ b/doc/pair_gran.html
@@ -1,247 +1,247 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style gran/hooke command
</H3>
<H3>pair_style gran/cuda command
</H3>
<H3>pair_style gran/hooke/history command
</H3>
<H3>pair_style gran/hertz/history command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style Kn Kt gamma_n gamma_t xmu dampflag
</PRE>
<UL><LI>style = <I>gran/hooke</I> or <I>gran/hooke/history</I> or <I>gran/hertz/history</I>
<LI>Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
<LI>Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)
<LI>gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)
<LI>gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
<LI>xmu = static yield criterion (unitless fraction between 0.0 and 1.0)
<LI>dampflag = 0 or 1 if tangential damping force is excluded or included
</UL>
<P>IMPORTANT NOTE: Versions of LAMMPS before 9Jan09 had different style
names for granular force fields. This is to emphasize the fact that
the Hertzian equation has changed to model polydispersity more
accurately. A side effect of the change is that the Kn, Kt, gamma_n,
and gamma_t coefficients in the pair_style command must be specified
with different values in order to reproduce calculations made with
earlier versions of LAMMPS, even for monodisperse systems. See the
NOTE below for details.
</P>
<P><B>Examples:</B>
</P>
<PRE>pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 1
pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>gran</I> styles use the following formulas for the frictional force
between two granular particles, as described in
<A HREF = "#Brilliantov">(Brilliantov)</A>, <A HREF = "#Silbert">(Silbert)</A>, and
<A HREF = "#Zhang">(Zhang)</A>, when the distance r between two particles of radii
Ri and Rj is less than their contact distance d = Ri + Rj. There is
no force between the particles when r > d.
</P>
<P>The two Hookean styles use this formula:
</P>
<CENTER><IMG SRC = "Eqs/pair_gran_hooke.jpg">
</CENTER>
<P>The Hertzian style uses this formula:
</P>
<CENTER><IMG SRC = "Eqs/pair_gran_hertz.jpg">
</CENTER>
<P>In both equations the first parenthesized term is the normal force
between the two particles and the second parenthesized term is the
tangential force. The normal force has 2 terms, a contact force and a
damping force. The tangential force also has 2 terms: a shear force
and a damping force. The shear force is a "history" effect that
accounts for the tangential displacement between the particles for the
duration of the time they are in contact. This term is included in
pair styles <I>hooke/history</I> and <I>hertz/history</I>, but is not included
in pair style <I>hooke</I>. The tangential damping force term is included
in all three pair styles if <I>dampflag</I> is set to 1; it is not included
if <I>dampflag</I> is set to 0.
</P>
<P>The other quantities in the equations are as follows:
</P>
<UL><LI>delta = d - r = overlap distance of 2 particles
<LI>Kn = elastic constant for normal contact
<LI>Kt = elastic constant for tangential contact
<LI>gamma_n = viscoelastic damping constant for normal contact
<LI>gamma_t = viscoelastic damping constant for tangential contact
<LI>m_eff = Mi Mj / (Mi + Mj) = effective mass of 2 particles of mass Mi and Mj
<LI>Delta St = tangential displacement vector between 2 spherical particles which is truncated to satisfy a frictional yield criterion
<LI>n_ij = unit vector along the line connecting the centers of the 2 particles
<LI>Vn = normal component of the relative velocity of the 2 particles
<LI>Vt = tangential component of the relative velocity of the 2 particles
</UL>
<P>The Kn, Kt, gamma_n, and gamma_t coefficients are specified as
parameters to the pair_style command. If a NULL is used for Kt, then
a default value is used where Kt = 2/7 Kn. If a NULL is used for
gamma_t, then a default value is used where gamma_t = 1/2 gamma_n.
</P>
<P>The interpretation and units for these 4 coefficients are different in
the Hookean versus Hertzian equations.
</P>
<P>The Hookean model is one where the normal push-back force for two
overlapping particles is a linear function of the overlap distance.
Thus the specified Kn is in units of (force/distance). Note that this
push-back force is independent of absolute particle size (in the
monodisperse case) and of the relative sizes of the two particles (in
the polydisperse case). This model also applies to the other terms in
the force equation so that the specified gamma_n is in units of
(1/time), Kt is in units of (force/distance), and gamma_t is in units
of (1/time).
</P>
<P>The Hertzian model is one where the normal push-back force for two
overlapping particles is proportional to the area of overlap of the
two particles, and is thus a non-linear function of overlap distance.
Thus Kn has units of force per area and is thus specified in units of
(pressure). The effects of absolute particle size (monodispersity)
and relative size (polydispersity) are captured in the radii-dependent
pre-factors. When these pre-factors are carried through to the other
terms in the force equation it means that the specified gamma_n is in
units of (1/(time*distance)), Kt is in units of (pressure), and
gamma_t is in units of (1/(time*distance)).
</P>
<P>Note that in the Hookean case, Kn can be thought of as a linear spring
constant with units of force/distance. In the Hertzian case, Kn is
like a non-linear spring constant with units of force/area or
pressure, and as shown in the <A HREF = "#Zhang">(Zhang)</A> paper, Kn = 4G /
(3(1-nu)) where nu = the Poisson ratio, G = shear modulus = E /
(2(1+nu)), and E = Young's modulus. Similarly, Kt = 8G / (2-nu).
Thus in the Hertzian case Kn and Kt can be set to values that
corresponds to properties of the material being modeled. This is also
true in the Hookean case, except that a spring constant must be chosen
that is appropriate for the absolute size of particles in the model.
Since relative particle sizes are not accounted for, the Hookean
styles may not be a suitable model for polydisperse systems.
</P>
<P>IMPORTANT NOTE: In versions of LAMMPS before 9Jan09, the equation for
Hertzian interactions did not include the sqrt(RiRj/Ri+Rj) term and
thus was not as accurate for polydisperse systems. For monodisperse
systems, sqrt(RiRj/Ri+Rj) is a constant factor that effectively scales
all 4 coefficients: Kn, Kt, gamma_n, gamma_t. Thus you can set the
values of these 4 coefficients appropriately in the current code to
reproduce the results of a previous Hertzian monodisperse calculation.
For example, for the common case of a monodisperse system with
particles of diameter 1, all 4 of these coefficients should now be set
2x larger than they were previously.
</P>
<P>Xmu is also specified in the pair_style command and is the upper limit
of the tangential force through the Coulomb criterion Ft = xmu*Fn,
where Ft and Fn are the total tangential and normal force components
in the formulas above. Thus in the Hookean case, the tangential force
between 2 particles grows according to a tangential spring and
dash-pot model until Ft/Fn = xmu and is then held at Ft = Fn*xmu until
the particles lose contact. In the Hertzian case, a similar analogy
holds, though the spring is no longer linear.
</P>
<P>For granular styles there are no additional coefficients to set for
each pair of atom types via the <A HREF = "pair_coeff.html">pair_coeff</A> command.
All settings are global and are made via the pair_style command.
However you must still use the <A HREF = "pair_coeff.html">pair_coeff</A> for all
pairs of granular atom types. For example the command
</P>
<PRE>pair_coeff * *
</PRE>
<P>should be used if all atoms in the simulation interact via a granular
potential (i.e. one of the pair styles above is used). If a granular
potential is used as a sub-style of <A HREF = "pair_hybrid.html">pair_style
hybrid</A>, then specific atom types can be used in the
pair_coeff command to determine which atoms interact via a granular
potential.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+<P>These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> mix, shift, table, and tail options
are not relevant for granular pair styles.
</P>
<P>These pair styles write their information to <A HREF = "restart.html">binary restart
files</A>, so a pair_style command does not need to be
specified in an input script that reads a restart file.
</P>
<P>These pair styles can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. They do not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B> none
</P>
-<P>All the granular pair styles are part of the "granular" package. It
-is only enabled if LAMMPS was built with that package. See the
-<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+<P>All the granular pair styles are part of the GRANULAR package. It is
+only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
</P>
<P>These pair styles require that atoms store torque and angular velocity
(omega) as defined by the <A HREF = "atom_style.html">atom_style</A>. They also
require a per-particle radius is stored. The <I>sphere</I> atom style does
all of this.
</P>
<P>This pair style requires you to use the <A HREF = "communicate.html">communicate vel
yes</A> option so that velocites are stored by ghost
atoms.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Brilliantov"></A>
<P><B>(Brilliantov)</B> Brilliantov, Spahn, Hertzsch, Poschel, Phys Rev E, 53,
p 5382-5392 (1996).
</P>
<A NAME = "Silbert"></A>
<P><B>(Silbert)</B> Silbert, Ertas, Grest, Halsey, Levine, Plimpton, Phys Rev
E, 64, p 051302 (2001).
</P>
<A NAME = "Zhang"></A>
<P><B>(Zhang)</B> Zhang and Makse, Phys Rev E, 72, p 011301 (2005).
</P>
</HTML>
diff --git a/doc/pair_gran.txt b/doc/pair_gran.txt
index c1ea6710c..ec11abea3 100644
--- a/doc/pair_gran.txt
+++ b/doc/pair_gran.txt
@@ -1,231 +1,231 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style gran/hooke command :h3
pair_style gran/cuda command :h3
pair_style gran/hooke/history command :h3
pair_style gran/hertz/history command :h3
[Syntax:]
pair_style style Kn Kt gamma_n gamma_t xmu dampflag :pre
style = {gran/hooke} or {gran/hooke/history} or {gran/hertz/history} :ulb,l
Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) :l
Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) :l
gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) :l
gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) :l
xmu = static yield criterion (unitless fraction between 0.0 and 1.0) :l
dampflag = 0 or 1 if tangential damping force is excluded or included :l,ule
IMPORTANT NOTE: Versions of LAMMPS before 9Jan09 had different style
names for granular force fields. This is to emphasize the fact that
the Hertzian equation has changed to model polydispersity more
accurately. A side effect of the change is that the Kn, Kt, gamma_n,
and gamma_t coefficients in the pair_style command must be specified
with different values in order to reproduce calculations made with
earlier versions of LAMMPS, even for monodisperse systems. See the
NOTE below for details.
[Examples:]
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 1
pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0 :pre
[Description:]
The {gran} styles use the following formulas for the frictional force
between two granular particles, as described in
"(Brilliantov)"_#Brilliantov, "(Silbert)"_#Silbert, and
"(Zhang)"_#Zhang, when the distance r between two particles of radii
Ri and Rj is less than their contact distance d = Ri + Rj. There is
no force between the particles when r > d.
The two Hookean styles use this formula:
:c,image(Eqs/pair_gran_hooke.jpg)
The Hertzian style uses this formula:
:c,image(Eqs/pair_gran_hertz.jpg)
In both equations the first parenthesized term is the normal force
between the two particles and the second parenthesized term is the
tangential force. The normal force has 2 terms, a contact force and a
damping force. The tangential force also has 2 terms: a shear force
and a damping force. The shear force is a "history" effect that
accounts for the tangential displacement between the particles for the
duration of the time they are in contact. This term is included in
pair styles {hooke/history} and {hertz/history}, but is not included
in pair style {hooke}. The tangential damping force term is included
in all three pair styles if {dampflag} is set to 1; it is not included
if {dampflag} is set to 0.
The other quantities in the equations are as follows:
delta = d - r = overlap distance of 2 particles
Kn = elastic constant for normal contact
Kt = elastic constant for tangential contact
gamma_n = viscoelastic damping constant for normal contact
gamma_t = viscoelastic damping constant for tangential contact
m_eff = Mi Mj / (Mi + Mj) = effective mass of 2 particles of mass Mi and Mj
Delta St = tangential displacement vector between 2 spherical particles \
which is truncated to satisfy a frictional yield criterion
n_ij = unit vector along the line connecting the centers of the 2 particles
Vn = normal component of the relative velocity of the 2 particles
Vt = tangential component of the relative velocity of the 2 particles :ul
The Kn, Kt, gamma_n, and gamma_t coefficients are specified as
parameters to the pair_style command. If a NULL is used for Kt, then
a default value is used where Kt = 2/7 Kn. If a NULL is used for
gamma_t, then a default value is used where gamma_t = 1/2 gamma_n.
The interpretation and units for these 4 coefficients are different in
the Hookean versus Hertzian equations.
The Hookean model is one where the normal push-back force for two
overlapping particles is a linear function of the overlap distance.
Thus the specified Kn is in units of (force/distance). Note that this
push-back force is independent of absolute particle size (in the
monodisperse case) and of the relative sizes of the two particles (in
the polydisperse case). This model also applies to the other terms in
the force equation so that the specified gamma_n is in units of
(1/time), Kt is in units of (force/distance), and gamma_t is in units
of (1/time).
The Hertzian model is one where the normal push-back force for two
overlapping particles is proportional to the area of overlap of the
two particles, and is thus a non-linear function of overlap distance.
Thus Kn has units of force per area and is thus specified in units of
(pressure). The effects of absolute particle size (monodispersity)
and relative size (polydispersity) are captured in the radii-dependent
pre-factors. When these pre-factors are carried through to the other
terms in the force equation it means that the specified gamma_n is in
units of (1/(time*distance)), Kt is in units of (pressure), and
gamma_t is in units of (1/(time*distance)).
Note that in the Hookean case, Kn can be thought of as a linear spring
constant with units of force/distance. In the Hertzian case, Kn is
like a non-linear spring constant with units of force/area or
pressure, and as shown in the "(Zhang)"_#Zhang paper, Kn = 4G /
(3(1-nu)) where nu = the Poisson ratio, G = shear modulus = E /
(2(1+nu)), and E = Young's modulus. Similarly, Kt = 8G / (2-nu).
Thus in the Hertzian case Kn and Kt can be set to values that
corresponds to properties of the material being modeled. This is also
true in the Hookean case, except that a spring constant must be chosen
that is appropriate for the absolute size of particles in the model.
Since relative particle sizes are not accounted for, the Hookean
styles may not be a suitable model for polydisperse systems.
IMPORTANT NOTE: In versions of LAMMPS before 9Jan09, the equation for
Hertzian interactions did not include the sqrt(RiRj/Ri+Rj) term and
thus was not as accurate for polydisperse systems. For monodisperse
systems, sqrt(RiRj/Ri+Rj) is a constant factor that effectively scales
all 4 coefficients: Kn, Kt, gamma_n, gamma_t. Thus you can set the
values of these 4 coefficients appropriately in the current code to
reproduce the results of a previous Hertzian monodisperse calculation.
For example, for the common case of a monodisperse system with
particles of diameter 1, all 4 of these coefficients should now be set
2x larger than they were previously.
Xmu is also specified in the pair_style command and is the upper limit
of the tangential force through the Coulomb criterion Ft = xmu*Fn,
where Ft and Fn are the total tangential and normal force components
in the formulas above. Thus in the Hookean case, the tangential force
between 2 particles grows according to a tangential spring and
dash-pot model until Ft/Fn = xmu and is then held at Ft = Fn*xmu until
the particles lose contact. In the Hertzian case, a similar analogy
holds, though the spring is no longer linear.
For granular styles there are no additional coefficients to set for
each pair of atom types via the "pair_coeff"_pair_coeff.html command.
All settings are global and are made via the pair_style command.
However you must still use the "pair_coeff"_pair_coeff.html for all
pairs of granular atom types. For example the command
pair_coeff * * :pre
should be used if all atoms in the simulation interact via a granular
potential (i.e. one of the pair styles above is used). If a granular
potential is used as a sub-style of "pair_style
hybrid"_pair_hybrid.html, then specific atom types can be used in the
pair_coeff command to determine which atoms interact via a granular
potential.
:line
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
The "pair_modify"_pair_modify.html mix, shift, table, and tail options
are not relevant for granular pair styles.
These pair styles write their information to "binary restart
files"_restart.html, so a pair_style command does not need to be
specified in an input script that reads a restart file.
These pair styles can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. They do not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:] none
-All the granular pair styles are part of the "granular" package. It
-is only enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+All the granular pair styles are part of the GRANULAR package. It is
+only enabled if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
These pair styles require that atoms store torque and angular velocity
(omega) as defined by the "atom_style"_atom_style.html. They also
require a per-particle radius is stored. The {sphere} atom style does
all of this.
This pair style requires you to use the "communicate vel
yes"_communicate.html option so that velocites are stored by ghost
atoms.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Brilliantov)
[(Brilliantov)] Brilliantov, Spahn, Hertzsch, Poschel, Phys Rev E, 53,
p 5382-5392 (1996).
:link(Silbert)
[(Silbert)] Silbert, Ertas, Grest, Halsey, Levine, Plimpton, Phys Rev
E, 64, p 051302 (2001).
:link(Zhang)
[(Zhang)] Zhang and Makse, Phys Rev E, 72, p 011301 (2005).
diff --git a/doc/pair_gromacs.html b/doc/pair_gromacs.html
index 322549cfa..9b17b0993 100644
--- a/doc/pair_gromacs.html
+++ b/doc/pair_gromacs.html
@@ -1,161 +1,161 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style lj/gromacs command
</H3>
<H3>pair_style lj/gromacs/cuda command
</H3>
<H3>pair_style lj/gromacs/coul/gromacs command
</H3>
<H3>pair_style lj/gromacs/coul/gromacs/cuda command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style args
</PRE>
<UL><LI>style = <I>lj/gromacs</I> or <I>lj/gromacs/coul/gromacs</I>
<LI>args = list of arguments for a particular style
</UL>
<PRE> <I>lj/gromacs</I> args = inner outer
inner, outer = global switching cutoffs for Lennard Jones
<I>lj/gromacs/coul/gromacs</I> args = inner outer (inner2) (outer2)
inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
inner2, outer2 = global switching cutoffs for Coulombic (optional)
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style lj/gromacs 9.0 12.0
pair_coeff * * 100.0 2.0
pair_coeff 2 2 100.0 2.0 8.0 10.0
</PRE>
<PRE>pair_style lj/gromacs/coul/gromacs 9.0 12.0
pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0
pair_coeff * * 100.0 2.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>lj/gromacs</I> styles compute shifted LJ and Coulombic interactions
with an additional switching function S(r) that ramps the energy and force
smoothly to zero between an inner and outer cutoff. It is a commonly
used potential in the <A HREF = "http://www.gromacs.org">GROMACS</A> MD code and for
the coarse-grained models of <A HREF = "#Marrink">(Marrink)</A>.
</P>
<CENTER><IMG SRC = "Eqs/pair_gromacs.jpg">
</CENTER>
<P>R1 is the inner cutoff; Rc is the outer cutoff. The coefficients A, B,
and C are computed by LAMMPS to perform the shifting and smoothing.
The function
S(r) is actually applied once to each term of the LJ formula and once
to the Coulombic formula, so there are 2 or 3 sets of A,B,C coefficients
depending on which pair_style is used. The boundary conditions
applied to the smoothing function are as follows: S(r1) = S'(r1) = 0,
S(rc) = -F(rc), S'(rc) = -F'(rc), where F(r) is the corresponding term
in the LJ or Coulombic potential energy function and a
single quote represents a derivative with respect to r.
</P>
<P>The inner and outer cutoff for the LJ and Coulombic terms can be the
same or different depending on whether 2 or 4 arguments are used in
the pair_style command. The inner LJ cutoff must be > 0, but the
inner Coulombic cutoff can be >= 0.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>epsilon (energy units)
<LI>sigma (distance units)
<LI>inner (distance units)
<LI>outer (distance units)
</UL>
<P>Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum at 2^(1/6)
sigma.
</P>
<P>The last 2 coefficients are optional inner and outer cutoffs for style
<I>lj/gromacs</I>. If not specified, the global <I>inner</I> and <I>outer</I> values
are used.
</P>
<P>The last 2 coefficients cannot be used with style
<I>lj/gromacs/coul/gromacs</I> because this force field does not allow
varying cutoffs for individual atom pairs; all pairs use the global
cutoff(s) specified in the pair_style command.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+<P>These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
The default mix value is <I>geometric</I>. See the "pair_modify" command
for details.
</P>
<P>None of the GROMACS pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> shift option, since the Lennard-Jones
portion of the pair interaction is already smoothed to 0.0 at the
cutoff.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
for this pair style.
</P>
<P>None of the GROMACS pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> tail option for adding long-range tail
corrections to energy and pressure, since there are no corrections for
a potential that goes to 0.0 at the cutoff.
</P>
<P>All of the GROMACS pair styles write their information to <A HREF = "restart.html">binary
restart files</A>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
</P>
<P>All of the GROMACS pair styles can only be used via the <I>pair</I>
keyword of the <A HREF = "run_style.html">run_style respa</A> command. They do not
support the <I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Marrink"></A>
<P><B>(Marrink)</B> Marrink, de Vries, Mark, J Phys Chem B, 108, 750-760 (2004).
</P>
</HTML>
diff --git a/doc/pair_gromacs.txt b/doc/pair_gromacs.txt
index 344f51e96..a57253568 100644
--- a/doc/pair_gromacs.txt
+++ b/doc/pair_gromacs.txt
@@ -1,151 +1,151 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style lj/gromacs command :h3
pair_style lj/gromacs/cuda command :h3
pair_style lj/gromacs/coul/gromacs command :h3
pair_style lj/gromacs/coul/gromacs/cuda command :h3
[Syntax:]
pair_style style args :pre
style = {lj/gromacs} or {lj/gromacs/coul/gromacs}
args = list of arguments for a particular style :ul
{lj/gromacs} args = inner outer
inner, outer = global switching cutoffs for Lennard Jones
{lj/gromacs/coul/gromacs} args = inner outer (inner2) (outer2)
inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
inner2, outer2 = global switching cutoffs for Coulombic (optional) :pre
[Examples:]
pair_style lj/gromacs 9.0 12.0
pair_coeff * * 100.0 2.0
pair_coeff 2 2 100.0 2.0 8.0 10.0 :pre
pair_style lj/gromacs/coul/gromacs 9.0 12.0
pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0
pair_coeff * * 100.0 2.0 :pre
[Description:]
The {lj/gromacs} styles compute shifted LJ and Coulombic interactions
with an additional switching function S(r) that ramps the energy and force
smoothly to zero between an inner and outer cutoff. It is a commonly
used potential in the "GROMACS"_http://www.gromacs.org MD code and for
the coarse-grained models of "(Marrink)"_#Marrink.
:c,image(Eqs/pair_gromacs.jpg)
R1 is the inner cutoff; Rc is the outer cutoff. The coefficients A, B,
and C are computed by LAMMPS to perform the shifting and smoothing.
The function
S(r) is actually applied once to each term of the LJ formula and once
to the Coulombic formula, so there are 2 or 3 sets of A,B,C coefficients
depending on which pair_style is used. The boundary conditions
applied to the smoothing function are as follows: S(r1) = S'(r1) = 0,
S(rc) = -F(rc), S'(rc) = -F'(rc), where F(r) is the corresponding term
in the LJ or Coulombic potential energy function and a
single quote represents a derivative with respect to r.
The inner and outer cutoff for the LJ and Coulombic terms can be the
same or different depending on whether 2 or 4 arguments are used in
the pair_style command. The inner LJ cutoff must be > 0, but the
inner Coulombic cutoff can be >= 0.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
epsilon (energy units)
sigma (distance units)
inner (distance units)
outer (distance units) :ul
Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum at 2^(1/6)
sigma.
The last 2 coefficients are optional inner and outer cutoffs for style
{lj/gromacs}. If not specified, the global {inner} and {outer} values
are used.
The last 2 coefficients cannot be used with style
{lj/gromacs/coul/gromacs} because this force field does not allow
varying cutoffs for individual atom pairs; all pairs use the global
cutoff(s) specified in the pair_style command.
:line
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
The default mix value is {geometric}. See the "pair_modify" command
for details.
None of the GROMACS pair styles support the
"pair_modify"_pair_modify.html shift option, since the Lennard-Jones
portion of the pair interaction is already smoothed to 0.0 at the
cutoff.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
None of the GROMACS pair styles support the
"pair_modify"_pair_modify.html tail option for adding long-range tail
corrections to energy and pressure, since there are no corrections for
a potential that goes to 0.0 at the cutoff.
All of the GROMACS pair styles write their information to "binary
restart files"_restart.html, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
All of the GROMACS pair styles can only be used via the {pair}
keyword of the "run_style respa"_run_style.html command. They do not
support the {inner}, {middle}, {outer} keywords.
:line
[Restrictions:] none
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Marrink)
[(Marrink)] Marrink, de Vries, Mark, J Phys Chem B, 108, 750-760 (2004).
diff --git a/doc/pair_lj.html b/doc/pair_lj.html
index a15688735..53a058b32 100644
--- a/doc/pair_lj.html
+++ b/doc/pair_lj.html
@@ -1,253 +1,253 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style lj/cut command
</H3>
<H3>pair_style lj/cut/cuda command
</H3>
<H3>pair_style lj/cut/experimental/cuda command
</H3>
<H3>pair_style lj/cut/gpu command
</H3>
<H3>pair_style lj/cut/opt command
</H3>
<H3>pair_style lj/cut/coul/cut command
</H3>
<H3>pair_style lj/cut/coul/cut/cuda command
</H3>
<H3>pair_style lj/cut/coul/cut/gpu command
</H3>
<H3>pair_style lj/cut/coul/debye command
</H3>
<H3>pair_style lj/cut/coul/debye/cuda command
</H3>
<H3>pair_style lj/cut/coul/long command
</H3>
<H3>pair_style lj/cut/coul/long/cuda command
</H3>
<H3>pair_style lj/cut/coul/long/gpu command
</H3>
<H3>pair_style lj/cut/coul/long/tip4p command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style args
</PRE>
<UL><LI>style = <I>lj/cut</I> or <I>lj/cut/coul/cut</I> or <I>lj/cut/coul/debye</I> or <I>lj/cut/coul/long</I> or <I>lj/cut/coul/long/tip4p</I>
<LI>args = list of arguments for a particular style
</UL>
<PRE> <I>lj/cut</I> args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
<I>lj/cut/coul/cut</I> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<I>lj/cut/coul/debye</I> args = kappa cutoff (cutoff2)
kappa = Debye length (inverse distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<I>lj/cut/coul/long</I> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<I>lj/cut/coul/long/tip4p</I> args = otype htype btype atype qdist cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
qdist = distance from O atom to massless charge (distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style lj/cut 2.5
pair_coeff * * 1 1
pair_coeff 1 1 1 1.1 2.8
</PRE>
<PRE>pair_style lj/cut/coul/cut 10.0
pair_style lj/cut/coul/cut 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
pair_coeff 1 1 100.0 3.5 9.0 9.0
</PRE>
<PRE>pair_style lj/cut/coul/debye 1.5 3.0
pair_style lj/cut/coul/debye 1.5 2.5 5.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.5 2.5
pair_coeff 1 1 1.0 1.5 2.5 5.0
</PRE>
<PRE>pair_style lj/cut/coul/long 10.0
pair_style lj/cut/coul/long 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
</PRE>
<PRE>pair_style lj/cut/coul/long/tip4p 1 2 7 8 0.3 12.0
pair_style lj/cut/coul/long/tip4p 1 2 7 8 0.3 12.0 10.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>lj/cut</I> styles compute the standard 12/6 Lennard-Jones potential,
given by
</P>
<CENTER><IMG SRC = "Eqs/pair_lj.jpg">
</CENTER>
<P>Rc is the cutoff.
</P>
<P>Style <I>lj/cut/coul/cut</I> adds a Coulombic pairwise interaction given by
</P>
<CENTER><IMG SRC = "Eqs/pair_coulomb.jpg">
</CENTER>
<P>where C is an energy-conversion constant, Qi and Qj are the charges on
the 2 atoms, and epsilon is the dielectric constant which can be set
by the <A HREF = "dielectric.html">dielectric</A> command. If one cutoff is
specified in the pair_style command, it is used for both the LJ and
Coulombic terms. If two cutoffs are specified, they are used as
cutoffs for the LJ and Coulombic terms respectively.
</P>
<P>Style <I>lj/cut/coul/debye</I> adds an additional exp() damping factor
to the Coulombic term, given by
</P>
<CENTER><IMG SRC = "Eqs/pair_debye.jpg">
</CENTER>
<P>where kappa is the Debye length. This potential is another way to
mimic the screening effect of a polar solvent.
</P>
<P>Style <I>lj/cut/coul/long</I> computes the same Coulombic interactions as
style <I>lj/cut/coul/cut</I> except that an additional damping factor is
applied to the Coulombic term so it can be used in conjunction with
the <A HREF = "kspace_style.html">kspace_style</A> command and its <I>ewald</I> or <I>pppm</I>
option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
</P>
<P>Style <I>lj/cut/coul/long/tip4p</I> implements the TIP4P water model of
<A HREF = "#Jorgensen">(Jorgensen)</A>, which introduces a massless site located a
short distance away from the oxygen atom along the bisector of the HOH
angle. The atomic types of the oxygen and hydrogen atoms, the bond
and angle types for OH and HOH interactions, and the distance to the
massless charge site are specified as pair_style arguments.
</P>
<P>IMPORTANT NOTE: For each TIP4P water molecule in your system, the atom
IDs for the O and 2 H atoms must be consecutive, with the O atom
first. This is to enable LAMMPS to "find" the 2 H atoms associated
with each O atom. For example, if the atom ID of an O atom in a TIP4P
water molecule is 500, then its 2 H atoms must have IDs 501 and 502.
</P>
<P>See the <A HREF = "Section_howto.html#howto_8">howto section</A> for more
information on how to use the TIP4P pair style.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>epsilon (energy units)
<LI>sigma (distance units)
<LI>cutoff1 (distance units)
<LI>cutoff2 (distance units)
</UL>
<P>Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum at 2^(1/6)
sigma.
</P>
<P>The latter 2 coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair. You cannot specify 2 cutoffs for style <I>lj/cut</I>, since it
has no Coulombic terms.
</P>
<P>For <I>lj/cut/coul/long</I> and <I>lj/cut/coul/long/tip4p</I> only the LJ cutoff
can be specified since a Coulombic cutoff cannot be specified for an
individual I,J type pair. All type pairs use the same global
Coulombic cutoff specified in the pair_style command.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+<P>These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
The default mix value is <I>geometric</I>. See the "pair_modify" command
for details.
</P>
<P>All of the lj/cut pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> shift option for the energy of the
Lennard-Jones portion of the pair interaction.
</P>
<P>The <I>lj/cut/coul/long</I> and <I>lj/cut/coul/long/tip4p</I> pair styles
support the <A HREF = "pair_modify.html">pair_modify</A> table option since they can
tabulate the short-range portion of the long-range Coulombic
interaction.
</P>
<P>All of the lj/cut pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> tail option for adding a long-range
tail correction to the energy and pressure for the Lennard-Jones
portion of the pair interaction.
</P>
<P>All of the lj/cut pair styles write their information to <A HREF = "restart.html">binary
restart files</A>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
</P>
<P>The lj/cut and lj/cut/coul/long pair styles support the use of the
<I>inner</I>, <I>middle</I>, and <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
respa</A> command, meaning the pairwise forces can be
partitioned by distance at different levels of the rRESPA hierarchy.
The other styles only support the <I>pair</I> keyword of run_style respa.
See the <A HREF = "run_style.html">run_style</A> command for details.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>The <I>lj/cut/coul/long</I> and <I>lj/cut/coul/long/tip4p</I> styles are part of
-the "kspace" package. They are only enabled if LAMMPS was built with
+the KSPACE package. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
-section for more info. Note that the kspace package is installed by
+section for more info. Note that the KSPACE package is installed by
default.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Jorgensen"></A>
<P><B>(Jorgensen)</B> Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).
</P>
</HTML>
diff --git a/doc/pair_lj.txt b/doc/pair_lj.txt
index 93f371cba..09441a9d5 100644
--- a/doc/pair_lj.txt
+++ b/doc/pair_lj.txt
@@ -1,233 +1,233 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style lj/cut command :h3
pair_style lj/cut/cuda command :h3
pair_style lj/cut/experimental/cuda command :h3
pair_style lj/cut/gpu command :h3
pair_style lj/cut/opt command :h3
pair_style lj/cut/coul/cut command :h3
pair_style lj/cut/coul/cut/cuda command :h3
pair_style lj/cut/coul/cut/gpu command :h3
pair_style lj/cut/coul/debye command :h3
pair_style lj/cut/coul/debye/cuda command :h3
pair_style lj/cut/coul/long command :h3
pair_style lj/cut/coul/long/cuda command :h3
pair_style lj/cut/coul/long/gpu command :h3
pair_style lj/cut/coul/long/tip4p command :h3
[Syntax:]
pair_style style args :pre
style = {lj/cut} or {lj/cut/coul/cut} or {lj/cut/coul/debye} or {lj/cut/coul/long} or {lj/cut/coul/long/tip4p}
args = list of arguments for a particular style :ul
{lj/cut} args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
{lj/cut/coul/cut} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{lj/cut/coul/debye} args = kappa cutoff (cutoff2)
kappa = Debye length (inverse distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{lj/cut/coul/long} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{lj/cut/coul/long/tip4p} args = otype htype btype atype qdist cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
qdist = distance from O atom to massless charge (distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
[Examples:]
pair_style lj/cut 2.5
pair_coeff * * 1 1
pair_coeff 1 1 1 1.1 2.8 :pre
pair_style lj/cut/coul/cut 10.0
pair_style lj/cut/coul/cut 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
pair_coeff 1 1 100.0 3.5 9.0 9.0 :pre
pair_style lj/cut/coul/debye 1.5 3.0
pair_style lj/cut/coul/debye 1.5 2.5 5.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.5 2.5
pair_coeff 1 1 1.0 1.5 2.5 5.0 :pre
pair_style lj/cut/coul/long 10.0
pair_style lj/cut/coul/long 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0 :pre
pair_style lj/cut/coul/long/tip4p 1 2 7 8 0.3 12.0
pair_style lj/cut/coul/long/tip4p 1 2 7 8 0.3 12.0 10.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0 :pre
[Description:]
The {lj/cut} styles compute the standard 12/6 Lennard-Jones potential,
given by
:c,image(Eqs/pair_lj.jpg)
Rc is the cutoff.
Style {lj/cut/coul/cut} adds a Coulombic pairwise interaction given by
:c,image(Eqs/pair_coulomb.jpg)
where C is an energy-conversion constant, Qi and Qj are the charges on
the 2 atoms, and epsilon is the dielectric constant which can be set
by the "dielectric"_dielectric.html command. If one cutoff is
specified in the pair_style command, it is used for both the LJ and
Coulombic terms. If two cutoffs are specified, they are used as
cutoffs for the LJ and Coulombic terms respectively.
Style {lj/cut/coul/debye} adds an additional exp() damping factor
to the Coulombic term, given by
:c,image(Eqs/pair_debye.jpg)
where kappa is the Debye length. This potential is another way to
mimic the screening effect of a polar solvent.
Style {lj/cut/coul/long} computes the same Coulombic interactions as
style {lj/cut/coul/cut} except that an additional damping factor is
applied to the Coulombic term so it can be used in conjunction with
the "kspace_style"_kspace_style.html command and its {ewald} or {pppm}
option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
Style {lj/cut/coul/long/tip4p} implements the TIP4P water model of
"(Jorgensen)"_#Jorgensen, which introduces a massless site located a
short distance away from the oxygen atom along the bisector of the HOH
angle. The atomic types of the oxygen and hydrogen atoms, the bond
and angle types for OH and HOH interactions, and the distance to the
massless charge site are specified as pair_style arguments.
IMPORTANT NOTE: For each TIP4P water molecule in your system, the atom
IDs for the O and 2 H atoms must be consecutive, with the O atom
first. This is to enable LAMMPS to "find" the 2 H atoms associated
with each O atom. For example, if the atom ID of an O atom in a TIP4P
water molecule is 500, then its 2 H atoms must have IDs 501 and 502.
See the "howto section"_Section_howto.html#howto_8 for more
information on how to use the TIP4P pair style.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
epsilon (energy units)
sigma (distance units)
cutoff1 (distance units)
cutoff2 (distance units) :ul
Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum at 2^(1/6)
sigma.
The latter 2 coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair. You cannot specify 2 cutoffs for style {lj/cut}, since it
has no Coulombic terms.
For {lj/cut/coul/long} and {lj/cut/coul/long/tip4p} only the LJ cutoff
can be specified since a Coulombic cutoff cannot be specified for an
individual I,J type pair. All type pairs use the same global
Coulombic cutoff specified in the pair_style command.
:line
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
The default mix value is {geometric}. See the "pair_modify" command
for details.
All of the lj/cut pair styles support the
"pair_modify"_pair_modify.html shift option for the energy of the
Lennard-Jones portion of the pair interaction.
The {lj/cut/coul/long} and {lj/cut/coul/long/tip4p} pair styles
support the "pair_modify"_pair_modify.html table option since they can
tabulate the short-range portion of the long-range Coulombic
interaction.
All of the lj/cut pair styles support the
"pair_modify"_pair_modify.html tail option for adding a long-range
tail correction to the energy and pressure for the Lennard-Jones
portion of the pair interaction.
All of the lj/cut pair styles write their information to "binary
restart files"_restart.html, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
The lj/cut and lj/cut/coul/long pair styles support the use of the
{inner}, {middle}, and {outer} keywords of the "run_style
respa"_run_style.html command, meaning the pairwise forces can be
partitioned by distance at different levels of the rRESPA hierarchy.
The other styles only support the {pair} keyword of run_style respa.
See the "run_style"_run_style.html command for details.
:line
[Restrictions:]
The {lj/cut/coul/long} and {lj/cut/coul/long/tip4p} styles are part of
-the "kspace" package. They are only enabled if LAMMPS was built with
+the KSPACE package. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info. Note that the kspace package is installed by
+section for more info. Note that the KSPACE package is installed by
default.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Jorgensen)
[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).
diff --git a/doc/pair_lj96.html b/doc/pair_lj96.html
index 6e0cbbb84..f32391b9a 100644
--- a/doc/pair_lj96.html
+++ b/doc/pair_lj96.html
@@ -1,113 +1,113 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style lj96/cut command
</H3>
<H3>pair_style lj96/cut/cuda command
</H3>
<H3>pair_style lj96/cut/gpu command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style lj96/cut cutoff
</PRE>
<UL><LI>cutoff = global cutoff for lj96/cut interactions (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style lj96/cut 2.5
pair_coeff * * 1.0 1.0 4.0
pair_coeff 1 1 1.0 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>lj96/cut</I> style compute a 9/6 Lennard-Jones potential, instead
of the standard 12/6 potential, given by
</P>
<CENTER><IMG SRC = "Eqs/pair_lj96.jpg">
</CENTER>
<P>Rc is the cutoff.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>epsilon (energy units)
<LI>sigma (distance units)
<LI>cutoff (distance units)
</UL>
<P>The last coefficient is optional. If not specified, the global LJ
cutoff specified in the pair_style command is used.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+<P>These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
The default mix value is <I>geometric</I>. See the "pair_modify" command
for details.
</P>
<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
option for the energy of the pair interaction.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
for this pair style.
</P>
<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> tail
option for adding a long-range tail correction to the energy and
pressure of the pair interaction.
</P>
<P>This pair style writes its information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style supports the use of the <I>inner</I>, <I>middle</I>, and <I>outer</I>
keywords of the <A HREF = "run_style.html">run_style respa</A> command, meaning the
pairwise forces can be partitioned by distance at different levels of
the rRESPA hierarchy. See the <A HREF = "run_style.html">run_style</A> command for
details.
</P>
<HR>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/pair_lj96.txt b/doc/pair_lj96.txt
index 84ddd5b2b..96fe64076 100644
--- a/doc/pair_lj96.txt
+++ b/doc/pair_lj96.txt
@@ -1,106 +1,106 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style lj96/cut command :h3
pair_style lj96/cut/cuda command :h3
pair_style lj96/cut/gpu command :h3
[Syntax:]
pair_style lj96/cut cutoff :pre
cutoff = global cutoff for lj96/cut interactions (distance units) :ul
[Examples:]
pair_style lj96/cut 2.5
pair_coeff * * 1.0 1.0 4.0
pair_coeff 1 1 1.0 1.0 :pre
[Description:]
The {lj96/cut} style compute a 9/6 Lennard-Jones potential, instead
of the standard 12/6 potential, given by
:c,image(Eqs/pair_lj96.jpg)
Rc is the cutoff.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
epsilon (energy units)
sigma (distance units)
cutoff (distance units) :ul
The last coefficient is optional. If not specified, the global LJ
cutoff specified in the pair_style command is used.
:line
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
The default mix value is {geometric}. See the "pair_modify" command
for details.
This pair style supports the "pair_modify"_pair_modify.html shift
option for the energy of the pair interaction.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
This pair style supports the "pair_modify"_pair_modify.html tail
option for adding a long-range tail correction to the energy and
pressure of the pair interaction.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style supports the use of the {inner}, {middle}, and {outer}
keywords of the "run_style respa"_run_style.html command, meaning the
pairwise forces can be partitioned by distance at different levels of
the rRESPA hierarchy. See the "run_style"_run_style.html command for
details.
:line
[Restrictions:] none
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
diff --git a/doc/pair_lj_coul.html b/doc/pair_lj_coul.html
index a93365fd9..b495c4d56 100644
--- a/doc/pair_lj_coul.html
+++ b/doc/pair_lj_coul.html
@@ -1,157 +1,157 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style lj/coul command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style lj/coul flag_lj flag_coul cutoff (cutoff2)
</PRE>
<UL><LI>flag_lj = <I>long</I> or <I>cut</I>
<PRE> <I>long</I> = use Kspace long-range summation for the dispersion term 1/r^6
<I>cut</I> = use a cutoff
</PRE>
<LI>flag_coul = <I>long</I> or <I>off</I>
<PRE> <I>long</I> = use Kspace long-range summation for the Coulombic term 1/r
<I>off</I> = omit the Coulombic term
</PRE>
<LI>cutoff = global cutoff for LJ (and Coulombic if only 1 cutoff) (distance units)
<LI>cutoff2 = global cutoff for Coulombic (optional) (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style lj/coul cut off 2.5
pair_style lj/coul cut long 2.5 4.0
pair_style lj/coul long long 2.5 4.0
pair_coeff * * 1 1
pair_coeff 1 1 1 3 4
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>lj/coul</I> style computes the standard 12/6 Lennard-Jones and
Coulombic potentials, given by
</P>
<CENTER><IMG SRC = "Eqs/pair_lj.jpg">
</CENTER>
<CENTER><IMG SRC = "Eqs/pair_coulomb.jpg">
</CENTER>
<P>where C is an energy-conversion constant, Qi and Qj are the charges on
the 2 atoms, epsilon is the dielectric constant which can be set by
the <A HREF = "dielectric.html">dielectric</A> command, and Rc is the cutoff. If
one cutoff is specified in the pair_style command, it is used for both
the LJ and Coulombic terms. If two cutoffs are specified, they are
used as cutoffs for the LJ and Coulombic terms respectively.
</P>
<P>The purpose of this pair style is to capture long-range interactions
resulting from both attractive 1/r^6 Lennard-Jones and Coulombic 1/r
interactions. This is done by use of the <I>flag_lj</I> and <I>flag_coul</I>
settings. The <A HREF = "#Veld">In 't Veld</A> paper has more details on when it is
appropriate to include long-range 1/r^6 interactions, using this
potential.
</P>
<P>If <I>flag_lj</I> is set to <I>long</I>, no cutoff is used on the LJ 1/r^6
dispersion term. The long-range portion is calculated by using the
<A HREF = "kspace_style.html">kspace_style ewald/n</A> command. The specified LJ
cutoff then determines which portion of the LJ interactions are
computed directly by the pair potential versus which part is computed
in reciprocal space via the Kspace style. If <I>flag_lj</I> is set to
<I>cut</I>, the LJ interactions are simply cutoff, as with <A HREF = "pair_lj.html">pair_style
lj/cut</A>.
</P>
<P>If <I>flag_coul</I> is set to <I>long</I>, no cutoff is used on the Coulombic
interactions. The long-range portion is calculated by using any
style, including <I>ewald/n</I> of the <A HREF = "kspace_style.html">kspace_style</A>
command. Note that if <I>flag_lj</I> is also set to long, then only the
<I>ewald/n</I> Kspace style can perform the long-range calculations for
both the LJ and Coulombic interactions. If <I>flag_coul</I> is set to
<I>off</I>, Coulombic interactions are not computed.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>epsilon (energy units)
<LI>sigma (distance units)
<LI>cutoff1 (distance units)
<LI>cutoff2 (distance units)
</UL>
<P>Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum at 2^(1/6)
sigma.
</P>
<P>The latter 2 coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair. Note that if you are using <I>flag_lj</I> set to <I>long</I>, you
cannot specify a LJ cutoff for an atom type pair, since only one
global LJ cutoff is allowed. Similarly, if you are using <I>flag_coul</I>
set to <I>long</I>, you cannot specify a Coulombic cutoff for an atom type
pair, since only one global Coulombic cutoff is allowed.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
The default mix value is <I>geometric</I>. See the "pair_modify" command
for details.
</P>
<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
option for the energy of the Lennard-Jones portion of the pair
interaction, assuming <I>flag_lj</I> is <I>cut</I>.
</P>
<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> table
option since it can tabulate the short-range portion of the long-range
Coulombic interaction.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding a long-range tail correction to the
Lennard-Jones portion of the energy and pressure.
</P>
<P>This pair style writes its information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style supports the use of the <I>inner</I>, <I>middle</I>, and <I>outer</I>
keywords of the <A HREF = "run_style.html">run_style respa</A> command, meaning the
pairwise forces can be partitioned by distance at different levels of
the rRESPA hierarchy. See the <A HREF = "run_style.html">run_style</A> command for
details.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>This style is part of the "user-ewaldn" package. It is only enabled
-if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+<P>This style is part of the USER-EWALDN package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Veld"></A>
<P><B>(In 't Veld)</B> In 't Veld, Ismail, Grest, J Chem Phys (accepted) (2007).
</P>
</HTML>
diff --git a/doc/pair_lj_coul.txt b/doc/pair_lj_coul.txt
index af695001e..e731ee342 100644
--- a/doc/pair_lj_coul.txt
+++ b/doc/pair_lj_coul.txt
@@ -1,146 +1,146 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style lj/coul command :h3
[Syntax:]
pair_style lj/coul flag_lj flag_coul cutoff (cutoff2) :pre
flag_lj = {long} or {cut} :ulb,l
{long} = use Kspace long-range summation for the dispersion term 1/r^6
{cut} = use a cutoff :pre
flag_coul = {long} or {off} :l
{long} = use Kspace long-range summation for the Coulombic term 1/r
{off} = omit the Coulombic term :pre
cutoff = global cutoff for LJ (and Coulombic if only 1 cutoff) (distance units) :l
cutoff2 = global cutoff for Coulombic (optional) (distance units) :l,ule
[Examples:]
pair_style lj/coul cut off 2.5
pair_style lj/coul cut long 2.5 4.0
pair_style lj/coul long long 2.5 4.0
pair_coeff * * 1 1
pair_coeff 1 1 1 3 4 :pre
[Description:]
The {lj/coul} style computes the standard 12/6 Lennard-Jones and
Coulombic potentials, given by
:c,image(Eqs/pair_lj.jpg)
:c,image(Eqs/pair_coulomb.jpg)
where C is an energy-conversion constant, Qi and Qj are the charges on
the 2 atoms, epsilon is the dielectric constant which can be set by
the "dielectric"_dielectric.html command, and Rc is the cutoff. If
one cutoff is specified in the pair_style command, it is used for both
the LJ and Coulombic terms. If two cutoffs are specified, they are
used as cutoffs for the LJ and Coulombic terms respectively.
The purpose of this pair style is to capture long-range interactions
resulting from both attractive 1/r^6 Lennard-Jones and Coulombic 1/r
interactions. This is done by use of the {flag_lj} and {flag_coul}
settings. The "In 't Veld"_#Veld paper has more details on when it is
appropriate to include long-range 1/r^6 interactions, using this
potential.
If {flag_lj} is set to {long}, no cutoff is used on the LJ 1/r^6
dispersion term. The long-range portion is calculated by using the
"kspace_style ewald/n"_kspace_style.html command. The specified LJ
cutoff then determines which portion of the LJ interactions are
computed directly by the pair potential versus which part is computed
in reciprocal space via the Kspace style. If {flag_lj} is set to
{cut}, the LJ interactions are simply cutoff, as with "pair_style
lj/cut"_pair_lj.html.
If {flag_coul} is set to {long}, no cutoff is used on the Coulombic
interactions. The long-range portion is calculated by using any
style, including {ewald/n} of the "kspace_style"_kspace_style.html
command. Note that if {flag_lj} is also set to long, then only the
{ewald/n} Kspace style can perform the long-range calculations for
both the LJ and Coulombic interactions. If {flag_coul} is set to
{off}, Coulombic interactions are not computed.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
epsilon (energy units)
sigma (distance units)
cutoff1 (distance units)
cutoff2 (distance units) :ul
Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum at 2^(1/6)
sigma.
The latter 2 coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair. Note that if you are using {flag_lj} set to {long}, you
cannot specify a LJ cutoff for an atom type pair, since only one
global LJ cutoff is allowed. Similarly, if you are using {flag_coul}
set to {long}, you cannot specify a Coulombic cutoff for an atom type
pair, since only one global Coulombic cutoff is allowed.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
The default mix value is {geometric}. See the "pair_modify" command
for details.
This pair style supports the "pair_modify"_pair_modify.html shift
option for the energy of the Lennard-Jones portion of the pair
interaction, assuming {flag_lj} is {cut}.
This pair style supports the "pair_modify"_pair_modify.html table
option since it can tabulate the short-range portion of the long-range
Coulombic interaction.
This pair style does not support the "pair_modify"_pair_modify.html
tail option for adding a long-range tail correction to the
Lennard-Jones portion of the energy and pressure.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style supports the use of the {inner}, {middle}, and {outer}
keywords of the "run_style respa"_run_style.html command, meaning the
pairwise forces can be partitioned by distance at different levels of
the rRESPA hierarchy. See the "run_style"_run_style.html command for
details.
:line
[Restrictions:]
-This style is part of the "user-ewaldn" package. It is only enabled
-if LAMMPS was built with that package. See the "Making
+This style is part of the USER-EWALDN package. It is only enabled if
+LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Veld)
[(In 't Veld)] In 't Veld, Ismail, Grest, J Chem Phys (accepted) (2007).
diff --git a/doc/pair_lj_expand.html b/doc/pair_lj_expand.html
index c1c421261..29b56468c 100644
--- a/doc/pair_lj_expand.html
+++ b/doc/pair_lj_expand.html
@@ -1,117 +1,117 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style lj/expand command
</H3>
<H3>pair_style lj/expand/cuda command
</H3>
<H3>pair_style lj/expand/gpu command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style lj/expand cutoff
</PRE>
<UL><LI>cutoff = global cutoff for lj/expand interactions (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style lj/expand 2.5
pair_coeff * * 1.0 1.0 0.5
pair_coeff 1 1 1.0 1.0 -0.2 2.0
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>lj/expand</I> computes a LJ interaction with a distance shifted by
delta which can be useful when particles are of different sizes, since
it is different that using different sigma values in a standard LJ
formula:
</P>
<CENTER><IMG SRC = "Eqs/pair_lj_expand.jpg">
</CENTER>
<P>Rc is the cutoff which does not include the delta distance. I.e. the
actual force cutoff is the sum of cutoff + delta.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>epsilon (energy units)
<LI>sigma (distance units)
<LI>delta (distance units)
<LI>cutoff (distance units)
</UL>
<P>The delta values can be positive or negative. The last coefficient is
optional. If not specified, the global LJ cutoff is used.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+<P>These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon, sigma, and shift
coefficients and cutoff distance for this pair style can be mixed.
Shift is always mixed via an <I>arithmetic</I> rule. The other
coefficients are mixed according to the pair_modify mix value. The
default mix value is <I>geometric</I>. See the "pair_modify" command for
details.
</P>
<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
option for the energy of the pair interaction.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
for this pair style.
</P>
<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> tail
option for adding a long-range tail correction to the energy and
pressure of the pair interaction.
</P>
<P>This pair style writes its information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/pair_lj_expand.txt b/doc/pair_lj_expand.txt
index 7ec8b8e8c..4efad1203 100644
--- a/doc/pair_lj_expand.txt
+++ b/doc/pair_lj_expand.txt
@@ -1,110 +1,110 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style lj/expand command :h3
pair_style lj/expand/cuda command :h3
pair_style lj/expand/gpu command :h3
[Syntax:]
pair_style lj/expand cutoff :pre
cutoff = global cutoff for lj/expand interactions (distance units) :ul
[Examples:]
pair_style lj/expand 2.5
pair_coeff * * 1.0 1.0 0.5
pair_coeff 1 1 1.0 1.0 -0.2 2.0 :pre
[Description:]
Style {lj/expand} computes a LJ interaction with a distance shifted by
delta which can be useful when particles are of different sizes, since
it is different that using different sigma values in a standard LJ
formula:
:c,image(Eqs/pair_lj_expand.jpg)
Rc is the cutoff which does not include the delta distance. I.e. the
actual force cutoff is the sum of cutoff + delta.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
epsilon (energy units)
sigma (distance units)
delta (distance units)
cutoff (distance units) :ul
The delta values can be positive or negative. The last coefficient is
optional. If not specified, the global LJ cutoff is used.
:line
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon, sigma, and shift
coefficients and cutoff distance for this pair style can be mixed.
Shift is always mixed via an {arithmetic} rule. The other
coefficients are mixed according to the pair_modify mix value. The
default mix value is {geometric}. See the "pair_modify" command for
details.
This pair style supports the "pair_modify"_pair_modify.html shift
option for the energy of the pair interaction.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
This pair style supports the "pair_modify"_pair_modify.html tail
option for adding a long-range tail correction to the energy and
pressure of the pair interaction.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:] none
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
diff --git a/doc/pair_lj_sf.html b/doc/pair_lj_sf.html
index 42cad6d0e..71034f613 100644
--- a/doc/pair_lj_sf.html
+++ b/doc/pair_lj_sf.html
@@ -1,96 +1,96 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style lj/sf command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style lj/sf cutoff
</PRE>
<UL><LI>cutoff = global cutoff for Lennard-Jones interactions (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style lj/sf 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.0 3.0
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>lj/sf</I> computes a truncated and force-shifted LJ interaction
(Shifted Force Lennard-Jones), so that both the potential and the
force go continuously to zero at the cutoff <A HREF = "#Toxvaerd">(Toxvaerd)</A>:
</P>
<CENTER><IMG SRC = "Eqs/pair_lj_sf.jpg">
</CENTER>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>epsilon (energy units)
<LI>sigma (distance units)
<LI>cutoff (distance units)
</UL>
<P>The last coefficient is optional. If not specified, the global
LJ cutoff specified in the pair_style command is used.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma
coefficients and cutoff distance for this pair style can be mixed.
Rin is a cutoff value and is mixed like the cutoff. The
default mix value is <I>geometric</I>. See the "pair_modify" command for
details.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> shift option is not relevant for
this pair style, since the pair interaction goes to 0.0 at the cutoff.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
for this pair style.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding long-range tail corrections to energy and
pressure, since the energy of the pair interaction is smoothed to 0.0
at the cutoff.
</P>
<P>This pair style writes its information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>This pair style is part of the "user-misc" package. It is only
-enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+<P>This pair style is part of the USER-MISC package. It is only enabled
+if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Toxvaerd"></A>
<P><B>(Toxvaerd)</B> Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011).
</P>
</HTML>
diff --git a/doc/pair_lj_sf.txt b/doc/pair_lj_sf.txt
index 8c0b65da2..aade3f97a 100644
--- a/doc/pair_lj_sf.txt
+++ b/doc/pair_lj_sf.txt
@@ -1,90 +1,90 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style lj/sf command :h3
[Syntax:]
pair_style lj/sf cutoff :pre
cutoff = global cutoff for Lennard-Jones interactions (distance units) :ul
[Examples:]
pair_style lj/sf 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.0 3.0 :pre
[Description:]
Style {lj/sf} computes a truncated and force-shifted LJ interaction
(Shifted Force Lennard-Jones), so that both the potential and the
force go continuously to zero at the cutoff "(Toxvaerd)"_#Toxvaerd:
:c,image(Eqs/pair_lj_sf.jpg)
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
epsilon (energy units)
sigma (distance units)
cutoff (distance units) :ul
The last coefficient is optional. If not specified, the global
LJ cutoff specified in the pair_style command is used.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma
coefficients and cutoff distance for this pair style can be mixed.
Rin is a cutoff value and is mixed like the cutoff. The
default mix value is {geometric}. See the "pair_modify" command for
details.
The "pair_modify"_pair_modify.html shift option is not relevant for
this pair style, since the pair interaction goes to 0.0 at the cutoff.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
This pair style does not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure, since the energy of the pair interaction is smoothed to 0.0
at the cutoff.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
-This pair style is part of the "user-misc" package. It is only
-enabled if LAMMPS was built with that package. See the "Making
+This pair style is part of the USER-MISC package. It is only enabled
+if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Toxvaerd)
[(Toxvaerd)] Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011).
diff --git a/doc/pair_lj_smooth.html b/doc/pair_lj_smooth.html
index d8ad196c7..bffb1716e 100644
--- a/doc/pair_lj_smooth.html
+++ b/doc/pair_lj_smooth.html
@@ -1,126 +1,126 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style lj/smooth command
</H3>
<H3>pair_style lj/smooth/cuda command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style lj/smooth Rin Rc
</PRE>
<UL><LI>Rin = inner cutoff beyond which force smoothing will be applied (distance units)
<LI>Rc = outer cutoff for lj/smooth interactions (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style lj/smooth 8.0 10.0
pair_coeff * * 10.0 1.5
pair_coeff 1 1 20.0 1.3 7.0 9.0
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>lj/smooth</I> computes a LJ interaction with a force smoothing
applied between the inner and outer cutoff.
</P>
<CENTER><IMG SRC = "Eqs/pair_lj_smooth.jpg">
</CENTER>
<P>The polynomial coefficients C1, C2, C3, C4 are computed by LAMMPS to
cause the force to vary smoothly from the inner cutoff Rin to the
outer cutoff Rc.
</P>
<P>At the inner cutoff the force and its 1st derivative
will match the unsmoothed LJ formula. At the outer cutoff the force
and its 1st derivative will be 0.0. The inner cutoff cannot be 0.0.
</P>
<P>IMPORTANT NOTE: this force smoothing causes the energy to be
discontinuous both in its values and 1st derivative. This can lead to
poor energy conservation and may require the use of a thermostat.
Plot the energy and force resulting from this formula via the
<A HREF = "pair_write.html">pair_write</A> command to see the effect.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>epsilon (energy units)
<LI>sigma (distance units)
<LI>innner (distance units)
<LI>outer (distance units)
</UL>
<P>The last 2 coefficients are optional inner and outer cutoffs. If not
specified, the global values for Rin and Rc are used.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+<P>These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon, sigma, Rin
coefficients and the cutoff distance for this pair style can be mixed.
Rin is a cutoff value and is mixed like the cutoff. The other
coefficients are mixed according to the pair_modify mix option. The
default mix value is <I>geometric</I>. See the "pair_modify" command for
details.
</P>
<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
option for the energy of the pair interaction.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
for this pair style.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding long-range tail corrections to energy and
pressure, since the energy of the pair interaction is smoothed to 0.0
at the cutoff.
</P>
<P>This pair style writes its information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/pair_lj_smooth.txt b/doc/pair_lj_smooth.txt
index e11954d46..5bbf2c48d 100644
--- a/doc/pair_lj_smooth.txt
+++ b/doc/pair_lj_smooth.txt
@@ -1,120 +1,120 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style lj/smooth command :h3
pair_style lj/smooth/cuda command :h3
[Syntax:]
pair_style lj/smooth Rin Rc :pre
Rin = inner cutoff beyond which force smoothing will be applied (distance units)
Rc = outer cutoff for lj/smooth interactions (distance units) :ul
[Examples:]
pair_style lj/smooth 8.0 10.0
pair_coeff * * 10.0 1.5
pair_coeff 1 1 20.0 1.3 7.0 9.0 :pre
[Description:]
Style {lj/smooth} computes a LJ interaction with a force smoothing
applied between the inner and outer cutoff.
:c,image(Eqs/pair_lj_smooth.jpg)
The polynomial coefficients C1, C2, C3, C4 are computed by LAMMPS to
cause the force to vary smoothly from the inner cutoff Rin to the
outer cutoff Rc.
At the inner cutoff the force and its 1st derivative
will match the unsmoothed LJ formula. At the outer cutoff the force
and its 1st derivative will be 0.0. The inner cutoff cannot be 0.0.
IMPORTANT NOTE: this force smoothing causes the energy to be
discontinuous both in its values and 1st derivative. This can lead to
poor energy conservation and may require the use of a thermostat.
Plot the energy and force resulting from this formula via the
"pair_write"_pair_write.html command to see the effect.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
epsilon (energy units)
sigma (distance units)
innner (distance units)
outer (distance units) :ul
The last 2 coefficients are optional inner and outer cutoffs. If not
specified, the global values for Rin and Rc are used.
:line
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon, sigma, Rin
coefficients and the cutoff distance for this pair style can be mixed.
Rin is a cutoff value and is mixed like the cutoff. The other
coefficients are mixed according to the pair_modify mix option. The
default mix value is {geometric}. See the "pair_modify" command for
details.
This pair style supports the "pair_modify"_pair_modify.html shift
option for the energy of the pair interaction.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
This pair style does not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure, since the energy of the pair interaction is smoothed to 0.0
at the cutoff.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:] none
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
diff --git a/doc/pair_lubricate.html b/doc/pair_lubricate.html
index 90455f041..63df12a6d 100644
--- a/doc/pair_lubricate.html
+++ b/doc/pair_lubricate.html
@@ -1,154 +1,154 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style lubricate command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style lubricate mu squeeze shear pump twist cutinner cutoff T_target seed
</PRE>
<UL><LI>mu = dynamic viscosity (dynamic viscosity units)
<LI>squeeze = 0/1 for squeeze force off/on
<LI>shear = 0/1 for shear force off/on
<LI>pump = 0/1 for pump force off/on
<LI>twist = 0/1 for twist force off/on
<LI>cutinner = (distance units)
<LI>cutoff = outer cutoff for interactions (distance units)
<LI>T_target = desired temperature (temperature units)
<LI>seed = random number seed (positive integer)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style lubricate 1.5 1 1 1 0 2.3 2.4 1.3 5878598
pair_coeff 1 1 1.8 2.0
pair_coeff * *
</PRE>
<PRE>pair_style lubricate 1.0 1 1 1 0 2.3 2.4 1.3 5878598
pair_coeff * *
variable mu equal ramp(1,2)
fix 1 all adapt 1 pair lubricate mu * * v_mu
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>lubricate</I> computes pairwise interactions between mono-disperse
spherical particles via this formula from <A HREF = "#Ball">(Ball and Melrose)</A>
</P>
<CENTER><IMG SRC = "Eqs/pair_lubricate.jpg">
</CENTER>
<P>which represents the dissipation W between two nearby particles due to
their relative velocities in the presence of a background solvent with
viscosity mu. Note that this is dynamic viscosity which has units of
mass/distance/time, not kinematic viscosity.
</P>
<P>The viscosity mu can be varied in a time-dependent manner over the
course of a simluation, in which case in which case the pair_style
setting for mu will be overridden. See the <A HREF = "fix_adapt.html">fix adapt</A>
command for details.
</P>
<P>Rc is the outer cutoff specified in the pair_style command, the
translational velocities of the 2 particles are v1 and v2, the angular
velocities are w1 and w2, and n is the unit vector in the direction
from particle 1 to 2. The 4 terms represent four modes of pairwise
interaction: squeezing, shearing, pumping, and twisting. The 4 flags
in the pair_style command turn on or off each of these modes by
including or excluding each term. The 4 coefficients on each term are
functions of the separation distance of the particles and the
viscosity. Details are given in <A HREF = "#Ball">(Ball and Melrose)</A>, including
the forces and torques that result from taking derivatives of this
equation with respect to velocity (see Appendix A).
</P>
<P>Unlike most pair potentials, the two specified cutoffs (cutinner and
cutoff) refer to the surface-to-surface separation between two
particles, not center-to-center distance. Currently, this pair style
can only be used for mono-disperse extended spheres (same radii), so
that separation is r_ij - 2*radius, where r_ij is the center-to-center
distance between the particles. Within the inner cutoff <I>cutinner</I>,
the forces and torques are evaluated at a separation of cutinner. The
outer <I>cutoff</I> is the separation distance beyond which the pair-wise
forces are zero.
</P>
<P>A Langevin thermostatting term is also added to the pairwise force,
similar to that provided by the <A HREF = "fix_langevin.html">fix langevin</A> or
<A HREF = "pair_dpd.html">pair_style dpd</A> commands. The target temperature for
the thermostat is the specified <I>T_target</I>. The <I>seed</I> is used for
the random numbers generated for the thermostat.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>cutinner (distance units)
<LI>cutoff (distance units)
</UL>
<P>The two coefficients are optional. If neither is specified, the two
cutoffs specified in the pair_style command are used. Otherwise both
must be specified.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the two cutoff distances for this
pair style can be mixed. The default mix value is <I>geometric</I>. See
the "pair_modify" command for details.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift option for the energy of the pair interaction.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
for this pair style.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding long-range tail corrections to energy and
pressure.
</P>
<P>This pair style writes its information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>This style is part of the "colloid" package. It is only enabled if
+<P>This style is part of the COLLOID package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>This pair style requires that atoms be finite-size spheres with a
diameter, as defined by the <A HREF = "atom_style.html">atom_style sphere</A>
command.
</P>
<P>Per-particle or per-type polydispersity is not yet supported by this
pair style; all particles must have the same diameter.
</P>
<P>This pair style requires you to use the <A HREF = "communicate.html">communicate vel
yes</A> option so that velocites are stored by ghost
atoms.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Ball"></A>
<P><B>(Ball)</B> Ball and Melrose, Physica A, 247, 444-472 (1997).
</P>
</HTML>
diff --git a/doc/pair_lubricate.txt b/doc/pair_lubricate.txt
index cb925f428..b8f758cb8 100644
--- a/doc/pair_lubricate.txt
+++ b/doc/pair_lubricate.txt
@@ -1,148 +1,148 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style lubricate command :h3
[Syntax:]
pair_style lubricate mu squeeze shear pump twist cutinner cutoff T_target seed :pre
mu = dynamic viscosity (dynamic viscosity units)
squeeze = 0/1 for squeeze force off/on
shear = 0/1 for shear force off/on
pump = 0/1 for pump force off/on
twist = 0/1 for twist force off/on
cutinner = (distance units)
cutoff = outer cutoff for interactions (distance units)
T_target = desired temperature (temperature units)
seed = random number seed (positive integer) :ul
[Examples:]
pair_style lubricate 1.5 1 1 1 0 2.3 2.4 1.3 5878598
pair_coeff 1 1 1.8 2.0
pair_coeff * * :pre
pair_style lubricate 1.0 1 1 1 0 2.3 2.4 1.3 5878598
pair_coeff * *
variable mu equal ramp(1,2)
fix 1 all adapt 1 pair lubricate mu * * v_mu :pre
[Description:]
Style {lubricate} computes pairwise interactions between mono-disperse
spherical particles via this formula from "(Ball and Melrose)"_#Ball
:c,image(Eqs/pair_lubricate.jpg)
which represents the dissipation W between two nearby particles due to
their relative velocities in the presence of a background solvent with
viscosity mu. Note that this is dynamic viscosity which has units of
mass/distance/time, not kinematic viscosity.
The viscosity mu can be varied in a time-dependent manner over the
course of a simluation, in which case in which case the pair_style
setting for mu will be overridden. See the "fix adapt"_fix_adapt.html
command for details.
Rc is the outer cutoff specified in the pair_style command, the
translational velocities of the 2 particles are v1 and v2, the angular
velocities are w1 and w2, and n is the unit vector in the direction
from particle 1 to 2. The 4 terms represent four modes of pairwise
interaction: squeezing, shearing, pumping, and twisting. The 4 flags
in the pair_style command turn on or off each of these modes by
including or excluding each term. The 4 coefficients on each term are
functions of the separation distance of the particles and the
viscosity. Details are given in "(Ball and Melrose)"_#Ball, including
the forces and torques that result from taking derivatives of this
equation with respect to velocity (see Appendix A).
Unlike most pair potentials, the two specified cutoffs (cutinner and
cutoff) refer to the surface-to-surface separation between two
particles, not center-to-center distance. Currently, this pair style
can only be used for mono-disperse extended spheres (same radii), so
that separation is r_ij - 2*radius, where r_ij is the center-to-center
distance between the particles. Within the inner cutoff {cutinner},
the forces and torques are evaluated at a separation of cutinner. The
outer {cutoff} is the separation distance beyond which the pair-wise
forces are zero.
A Langevin thermostatting term is also added to the pairwise force,
similar to that provided by the "fix langevin"_fix_langevin.html or
"pair_style dpd"_pair_dpd.html commands. The target temperature for
the thermostat is the specified {T_target}. The {seed} is used for
the random numbers generated for the thermostat.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
cutinner (distance units)
cutoff (distance units) :ul
The two coefficients are optional. If neither is specified, the two
cutoffs specified in the pair_style command are used. Otherwise both
must be specified.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the two cutoff distances for this
pair style can be mixed. The default mix value is {geometric}. See
the "pair_modify" command for details.
This pair style does not support the "pair_modify"_pair_modify.html
shift option for the energy of the pair interaction.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
This pair style does not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
-This style is part of the "colloid" package. It is only enabled if
+This style is part of the COLLOID package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
This pair style requires that atoms be finite-size spheres with a
diameter, as defined by the "atom_style sphere"_atom_style.html
command.
Per-particle or per-type polydispersity is not yet supported by this
pair style; all particles must have the same diameter.
This pair style requires you to use the "communicate vel
yes"_communicate.html option so that velocites are stored by ghost
atoms.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Ball)
[(Ball)] Ball and Melrose, Physica A, 247, 444-472 (1997).
diff --git a/doc/pair_meam.html b/doc/pair_meam.html
index 4001a5cae..8d5868201 100644
--- a/doc/pair_meam.html
+++ b/doc/pair_meam.html
@@ -1,379 +1,379 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style meam command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style meam
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style meam
pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si
pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni
</PRE>
<P><B>Description:</B>
</P>
<P>NOTE: The behavior of the MEAM potential for alloy systems has changed
as of November 2010; see description below of the mixture_ref_t
parameter
</P>
<P>Style <I>meam</I> computes pairwise interactions for a variety of materials
using modified embedded-atom method (MEAM) potentials
<A HREF = "#Baskes">(Baskes)</A>. Conceptually, it is an extension to the original
<A HREF = "pair_eam.html">EAM potentials</A> which adds angular forces. It is
thus suitable for modeling metals and alloys with fcc, bcc, hcp and
diamond cubic structures, as well as covalently bonded materials like
silicon and carbon.
</P>
<P>In the MEAM formulation, the total energy E of a system of atoms is
given by:
</P>
<CENTER><IMG SRC = "Eqs/pair_meam.jpg">
</CENTER>
<P>where F is the embedding energy which is a function of the atomic
electron density rho, and phi is a pair potential interaction. The
pair interaction is summed over all neighbors J of atom I within the
cutoff distance. As with EAM, the multi-body nature of the MEAM
potential is a result of the embedding energy term. Details of the
computation of the embedding and pair energies, as implemented in
LAMMPS, are given in <A HREF = "#Gullet">(Gullet)</A> and references therein.
</P>
<P>The various parameters in the MEAM formulas are listed in two files
which are specified by the <A HREF = "pair_coeff.html">pair_coeff</A> command.
These are ASCII text files in a format consistent with other MD codes
that implement MEAM potentials, such as the serial DYNAMO code and
Warp. Several MEAM potential files with parameters for different
materials are included in the "potentials" directory of the LAMMPS
distribution with a ".meam" suffix. All of these are parameterized in
terms of LAMMPS <A HREF = "units.html">metal units</A>.
</P>
<P>Note that unlike for other potentials, cutoffs for MEAM potentials are
not set in the pair_style or pair_coeff command; they are specified in
the MEAM potential files themselves.
</P>
<P>Only a single pair_coeff command is used with the <I>meam</I> style which
specifies two MEAM files and the element(s) to extract information
for. The MEAM elements are mapped to LAMMPS atom types by specifying
N additional arguments after the 2nd filename in the pair_coeff
command, where N is the number of LAMMPS atom types:
</P>
<UL><LI>MEAM library file
<LI>Elem1, Elem2, ...
<LI>MEAM parameter file
<LI>N element names = mapping of MEAM elements to atom types
</UL>
<P>As an example, the potentials/library.meam file has generic MEAM
settings for a variety of elements. The potentials/sic.meam file has
specific parameter settings for a Si and C alloy system. If your
LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si,
and the 4th to be C, you would use the following pair_coeff command:
</P>
<PRE>pair_coeff * * library.meam Si C sic.meam Si Si Si C
</PRE>
<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The two filenames are for the library and parameter file respectively.
The Si and C arguments (between the file names) are the two elements
for which info will be extracted from the library file. The first
three trailing Si arguments map LAMMPS atom types 1,2,3 to the MEAM Si
element. The final C argument maps LAMMPS atom type 4 to the MEAM C
element.
</P>
<P>If the 2nd filename is specified as NULL, no parameter file is read,
which simply means the generic parameters in the library file are
used. Use of the NULL specification for the parameter file is
discouraged for systems with more than a single element type
(e.g. alloys), since the parameter file is expected to set element
interaction terms that are not captured by the information in the
library file.
</P>
<P>If a mapping value is specified as NULL, the mapping is not performed.
This can be used when a <I>meam</I> potential is used as part of the
<I>hybrid</I> pair style. The NULL values are placeholders for atom types
that will be used with other potentials.
</P>
<P>The MEAM library file provided with LAMMPS has the name
potentials/library.meam. It is the "meamf" file used by other MD
codes. Aside from blank and comment lines (start with #) which can
appear anywhere, it is formatted as a series of entries, each of which
has 19 parameters and can span multiple lines:
</P>
<P>elt, lat, z, ielement, atwt, alpha, b0, b1, b2, b3, alat, esub, asub,
t0, t1, t2, t3, rozero, ibar
</P>
<P>The "elt" and "lat" parameters are text strings, such as elt = Si or
Cu and lat = dia or fcc. Because the library file is used by Fortran
MD codes, these strings may be enclosed in single quotes, but this is
not required. The other numeric parameters match values in the
formulas above. The value of the "elt" string is what is used in the
pair_coeff command to identify which settings from the library file
you wish to read in. There can be multiple entries in the library
file with the same "elt" value; LAMMPS reads the 1st matching entry it
finds and ignores the rest.
</P>
<P>Other parameters in the MEAM library file correspond to single-element
potential parameters:
</P>
<PRE>lat = lattice structure of reference configuration
z = number of nearest neighbors in the reference structure
ielement = atomic number
atwt = atomic weight
alat = lattice constant of reference structure
esub = energy per atom (eV) in the reference structure at equilibrium
asub = "A" parameter for MEAM (see e.g. <A HREF = "#Baskes">(Baskes)</A>)
</PRE>
<P>The alpha, b0, b1, b2, b3, t0, t1, t2, t3 parameters correspond to the
standard MEAM parameters in the literature <A HREF = "#Baskes">(Baskes)</A> (the b
parameters are the standard beta parameters). The rozero parameter is
an element-dependent density scaling that weights the reference
background density (see e.g. equation 4.5 in <A HREF = "#Gullet">(Gullet)</A>) and
is typically 1.0 for single-element systems. The ibar parameter
selects the form of the function G(Gamma) used to compute the electron
density; options are
</P>
<PRE> 0 => G = sqrt(1+Gamma)
1 => G = exp(Gamma/2)
2 => not implemented
3 => G = 2/(1+exp(-Gamma))
4 => G = sqrt(1+Gamma)
-5 => G = +-sqrt(abs(1+Gamma))
</PRE>
<P>If used, the MEAM parameter file contains settings that override or
complement the library file settings. Examples of such parameter
files are in the potentials directory with a ".meam" suffix. Their
format is the same as is read by other Fortran MD codes. Aside from
blank and comment lines (start with #) which can appear anywhere, each
line has one of the following forms. Each line can also have a
trailing comment (starting with #) which is ignored.
</P>
<PRE>keyword = value
keyword(I) = value
keyword(I,J) = value
keyword(I,J,K) = value
</PRE>
<P>The recognized keywords are as follows:
</P>
<P>Ec, alpha, rho0, delta, lattce, attrac, repuls, nn2, Cmin, Cmax, rc, delr,
augt1, gsmooth_factor, re
</P>
<P>where
</P>
<PRE>rc = cutoff radius for cutoff function; default = 4.0
delr = length of smoothing distance for cutoff function; default = 0.1
rho0(I) = relative density for element I (overwrites value
read from meamf file)
Ec(I,J) = cohesive energy of reference structure for I-J mixture
delta(I,J) = heat of formation for I-J alloy; if Ec_IJ is input as
zero, then LAMMPS sets Ec_IJ = (Ec_II + Ec_JJ)/2 - delta_IJ
alpha(I,J) = alpha parameter for pair potential between I and J (can
be computed from bulk modulus of reference structure
re(I,J) = equilibrium distance between I and J in the reference
structure
Cmax(I,J,K) = Cmax screening parameter when I-J pair is screened
by K (I<=J); default = 2.8
Cmin(I,J,K) = Cmin screening parameter when I-J pair is screened
by K (I<=J); default = 2.0
lattce(I,J) = lattice structure of I-J reference structure:
dia = diamond (interlaced fcc for alloy)
fcc = face centered cubic
bcc = body centered cubic
dim = dimer
b1 = rock salt (NaCl structure)
hcp = hexagonal close-packed
c11 = MoSi2 structure
l12 = Cu3Au structure (lower case L, followed by 12)
b2 = CsCl structure (interpenetrating simple cubic)
nn2(I,J) = turn on second-nearest neighbor MEAM formulation for
I-J pair (see for example <A HREF = "#Lee">(Lee)</A>).
0 = second-nearest neighbor formulation off
1 = second-nearest neighbor formulation on
default = 0
attrac(I,J) = additional cubic attraction term in Rose energy I-J pair potential
default = 0
repuls(I,J) = additional cubic repulsive term in Rose energy I-J pair potential
default = 0
zbl(I,J) = blend the MEAM I-J pair potential with the ZBL potential for small
atom separations <A HREF = "#ZBL">(ZBL)</A>
default = 1
gsmooth_factor = factor determining the length of the G-function smoothing
region; only significant for ibar=0 or ibar=4.
99.0 = short smoothing region, sharp step
0.5 = long smoothing region, smooth step
default = 99.0
augt1 = integer flag for whether to augment t1 parameter by
3/5*t3 to account for old vs. new meam formulations;
0 = don't augment t1
1 = augment t1
default = 1
ialloy = integer flag to use alternative averaging rule for t parameters,
for comparison with the DYNAMO MEAM code
0 = standard averaging (matches ialloy=0 in DYNAMO)
1 = alternative averaging (matches ialloy=1 in DYNAMO)
2 = no averaging of t (use single-element values)
default = 0
mixture_ref_t = integer flag to use mixture average of t to compute the background
reference density for alloys, instead of the single-element values
(see description and warning elsewhere in this doc page)
0 = do not use mixture averaging for t in the reference density
1 = use mixture averaging for t in the reference density
default = 0
erose_form = integer value to select the form of the Rose energy function
(see description below).
default = 0
emb_lin_neg = integer value to select embedding function for negative densities
0 = F(rho)=0
1 = F(rho) = -asub*esub*rho (linear in rho, matches DYNAMO)
default = 0
bkgd_dyn = integer value to select background density formula
0 = rho_bkgd = rho_ref_meam(a) (as in the reference structure)
1 = rho_bkgd = rho0_meam(a)*Z_meam(a) (matches DYNAMO)
default = 0
</PRE>
<P>Rc, delr, re are in distance units (Angstroms in the case of metal
units). Ec and delta are in energy units (eV in the case of metal
units).
</P>
<P>Each keyword represents a quantity which is either a scalar, vector,
2d array, or 3d array and must be specified with the correct
corresponding array syntax. The indices I,J,K each run from 1 to N
where N is the number of MEAM elements being used.
</P>
<P>Thus these lines
</P>
<PRE>rho0(2) = 2.25
alpha(1,2) = 4.37
</PRE>
<P>set rho0 for the 2nd element to the value 2.25 and set alpha for the
alloy interaction between elements 1 and 2 to 4.37.
</P>
<P>The augt1 parameter is related to modifications in the MEAM
formulation of the partial electron density function. In recent
literature, an extra term is included in the expression for the
third-order density in order to make the densities orthogonal (see for
example <A HREF = "#Wang">(Wang)</A>, equation 3d); this term is included in the
MEAM implementation in lammps. However, in earlier published work
this term was not included when deriving parameters, including most of
those provided in the library.meam file included with lammps, and to
account for this difference the parameter t1 must be augmented by
3/5*t3. If augt1=1, the default, this augmentation is done
automatically. When parameter values are fit using the modified
density function, as in more recent literature, augt1 should be set to
0.
</P>
<P>The mixture_ref_t parameter is available to match results with those
of previous versions of lammps (before January 2011). Newer versions
of lammps, by default, use the single-element values of the t
parameters to compute the background reference density. This is the
proper way to compute these parameters. Earlier versions of lammps
used an alloy mixture averaged value of t to compute the background
reference density. Setting mixture_ref_t=1 gives the old behavior.
WARNING: using mixture_ref_t=1 will give results that are demonstrably
incorrect for second-neighbor MEAM, and non-standard for
first-neighbor MEAM; this option is included only for matching with
previous versions of lammps and should be avoided if possible.
</P>
<P>The parameters attrac and repuls, along with the integer selection
parameter erose_form, can be used to modify the Rose energy function
used to compute the pair potential. This function gives the energy of
the reference state as a function of interatomic spacing. The form of
this function is:
</P>
<PRE>astar = alpha * (r/re - 1.d0)
if erose_form = 0: erose = -Ec*(1+astar+a3*(astar**3)/(r/re))*exp(-astar)
if erose_form = 1: erose = -Ec*(1+astar+(-attrac+repuls/r)*(astar**3))*exp(-astar)
if erose_form = 2: erose = -Ec*(1 +astar + a3*(astar**3))*exp(-astar)
a3 = repuls, astar < 0
a3 = attrac, astar >= 0
</PRE>
<P>Most published MEAM parameter sets use the default values attrac=repulse=0.
Setting repuls=attrac=delta corresponds to the form used in several
recent published MEAM parameter sets, such as <A HREF = "#Vallone">(Vallone)</A>
</P>
<P>NOTE: The default form of the erose expression in LAMMPS was corrected
in March 2009. The current version is correct, but may show different
behavior compared with earlier versions of lammps with the attrac
and/or repuls parameters are non-zero. To obtain the previous default
form, use erose_form = 1 (this form does not seem to appear in the
literature). An alternative form (see e.g. <A HREF = "#Lee2">(Lee2)</A>) is
available using erose_form = 2.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS with
user-specifiable parameters as described above. You never need to
specify a pair_coeff command with I != J arguments for this style.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift, table, and tail options.
</P>
<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
files</A>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>This style is part of the "meam" package. It is only enabled if
-LAMMPS was built with that package, which also requires the MEAM
-library be built and linked with LAMMPS. See the <A HREF = "Section_start.html#start_3">Making
+<P>This style is part of the MEAM package. It is only enabled if LAMMPS
+was built with that package, which also requires the MEAM library be
+built and linked with LAMMPS. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_eam.html">pair_style eam</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Baskes"></A>
<P><B>(Baskes)</B> Baskes, Phys Rev B, 46, 2727-2742 (1992).
</P>
<A NAME = "Gullet"></A>
<P><B>(Gullet)</B> Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003).
This report may be accessed on-line via <A HREF = "http://infoserve.sandia.gov/sand_doc/2003/038782.pdf">this link</A>.
</P>
<A NAME = "Lee"></A>
<P><B>(Lee)</B> Lee, Baskes, Phys. Rev. B, 62, 8564-8567 (2000).
</P>
<A NAME = "Lee2"></A>
<P><B>(Lee2)</B> Lee, Baskes, Kim, Cho. Phys. Rev. B, 64, 184102 (2001).
</P>
<A NAME = "Valone"></A>
<P><B>(Valone)</B> Valone, Baskes, Martin, Phys. Rev. B, 73, 214209 (2006).
</P>
<A NAME = "Wang"></A>
<P><B>(Wang)</B> Wang, Van Hove, Ross, Baskes, J. Chem. Phys., 121, 5410 (2004).
</P>
<A NAME = "ZBL"></A>
-<P><B>(ZBL)</B> J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges
-of Ions in Matter' Vol 1, 1985, Pergamon Press.
+<P><B>(ZBL)</B> J.F. Ziegler, J.P. Biersack, U. Littmark, "Stopping and Ranges
+of Ions in Matter", Vol 1, 1985, Pergamon Press.
</P>
</HTML>
diff --git a/doc/pair_meam.txt b/doc/pair_meam.txt
index 12bae3092..b787345ae 100644
--- a/doc/pair_meam.txt
+++ b/doc/pair_meam.txt
@@ -1,368 +1,367 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style meam command :h3
[Syntax:]
pair_style meam :pre
[Examples:]
pair_style meam
pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si
pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni :pre
[Description:]
NOTE: The behavior of the MEAM potential for alloy systems has changed
as of November 2010; see description below of the mixture_ref_t
parameter
Style {meam} computes pairwise interactions for a variety of materials
using modified embedded-atom method (MEAM) potentials
"(Baskes)"_#Baskes. Conceptually, it is an extension to the original
"EAM potentials"_pair_eam.html which adds angular forces. It is
thus suitable for modeling metals and alloys with fcc, bcc, hcp and
diamond cubic structures, as well as covalently bonded materials like
silicon and carbon.
In the MEAM formulation, the total energy E of a system of atoms is
given by:
:c,image(Eqs/pair_meam.jpg)
where F is the embedding energy which is a function of the atomic
electron density rho, and phi is a pair potential interaction. The
pair interaction is summed over all neighbors J of atom I within the
cutoff distance. As with EAM, the multi-body nature of the MEAM
potential is a result of the embedding energy term. Details of the
computation of the embedding and pair energies, as implemented in
LAMMPS, are given in "(Gullet)"_#Gullet and references therein.
The various parameters in the MEAM formulas are listed in two files
which are specified by the "pair_coeff"_pair_coeff.html command.
These are ASCII text files in a format consistent with other MD codes
that implement MEAM potentials, such as the serial DYNAMO code and
Warp. Several MEAM potential files with parameters for different
materials are included in the "potentials" directory of the LAMMPS
distribution with a ".meam" suffix. All of these are parameterized in
terms of LAMMPS "metal units"_units.html.
Note that unlike for other potentials, cutoffs for MEAM potentials are
not set in the pair_style or pair_coeff command; they are specified in
the MEAM potential files themselves.
Only a single pair_coeff command is used with the {meam} style which
specifies two MEAM files and the element(s) to extract information
for. The MEAM elements are mapped to LAMMPS atom types by specifying
N additional arguments after the 2nd filename in the pair_coeff
command, where N is the number of LAMMPS atom types:
MEAM library file
Elem1, Elem2, ...
MEAM parameter file
N element names = mapping of MEAM elements to atom types :ul
As an example, the potentials/library.meam file has generic MEAM
settings for a variety of elements. The potentials/sic.meam file has
specific parameter settings for a Si and C alloy system. If your
LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si,
and the 4th to be C, you would use the following pair_coeff command:
pair_coeff * * library.meam Si C sic.meam Si Si Si C :pre
The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The two filenames are for the library and parameter file respectively.
The Si and C arguments (between the file names) are the two elements
for which info will be extracted from the library file. The first
three trailing Si arguments map LAMMPS atom types 1,2,3 to the MEAM Si
element. The final C argument maps LAMMPS atom type 4 to the MEAM C
element.
If the 2nd filename is specified as NULL, no parameter file is read,
which simply means the generic parameters in the library file are
used. Use of the NULL specification for the parameter file is
discouraged for systems with more than a single element type
(e.g. alloys), since the parameter file is expected to set element
interaction terms that are not captured by the information in the
library file.
If a mapping value is specified as NULL, the mapping is not performed.
This can be used when a {meam} potential is used as part of the
{hybrid} pair style. The NULL values are placeholders for atom types
that will be used with other potentials.
The MEAM library file provided with LAMMPS has the name
potentials/library.meam. It is the "meamf" file used by other MD
codes. Aside from blank and comment lines (start with #) which can
appear anywhere, it is formatted as a series of entries, each of which
has 19 parameters and can span multiple lines:
elt, lat, z, ielement, atwt, alpha, b0, b1, b2, b3, alat, esub, asub,
t0, t1, t2, t3, rozero, ibar
The "elt" and "lat" parameters are text strings, such as elt = Si or
Cu and lat = dia or fcc. Because the library file is used by Fortran
MD codes, these strings may be enclosed in single quotes, but this is
not required. The other numeric parameters match values in the
formulas above. The value of the "elt" string is what is used in the
pair_coeff command to identify which settings from the library file
you wish to read in. There can be multiple entries in the library
file with the same "elt" value; LAMMPS reads the 1st matching entry it
finds and ignores the rest.
Other parameters in the MEAM library file correspond to single-element
potential parameters:
lat = lattice structure of reference configuration
z = number of nearest neighbors in the reference structure
ielement = atomic number
atwt = atomic weight
alat = lattice constant of reference structure
esub = energy per atom (eV) in the reference structure at equilibrium
asub = "A" parameter for MEAM (see e.g. "(Baskes)"_#Baskes) :pre
The alpha, b0, b1, b2, b3, t0, t1, t2, t3 parameters correspond to the
standard MEAM parameters in the literature "(Baskes)"_#Baskes (the b
parameters are the standard beta parameters). The rozero parameter is
an element-dependent density scaling that weights the reference
background density (see e.g. equation 4.5 in "(Gullet)"_#Gullet) and
is typically 1.0 for single-element systems. The ibar parameter
selects the form of the function G(Gamma) used to compute the electron
density; options are
0 => G = sqrt(1+Gamma)
1 => G = exp(Gamma/2)
2 => not implemented
3 => G = 2/(1+exp(-Gamma))
4 => G = sqrt(1+Gamma)
-5 => G = +-sqrt(abs(1+Gamma)) :pre
If used, the MEAM parameter file contains settings that override or
complement the library file settings. Examples of such parameter
files are in the potentials directory with a ".meam" suffix. Their
format is the same as is read by other Fortran MD codes. Aside from
blank and comment lines (start with #) which can appear anywhere, each
line has one of the following forms. Each line can also have a
trailing comment (starting with #) which is ignored.
keyword = value
keyword(I) = value
keyword(I,J) = value
keyword(I,J,K) = value :pre
The recognized keywords are as follows:
Ec, alpha, rho0, delta, lattce, attrac, repuls, nn2, Cmin, Cmax, rc, delr,
augt1, gsmooth_factor, re
where
rc = cutoff radius for cutoff function; default = 4.0
delr = length of smoothing distance for cutoff function; default = 0.1
rho0(I) = relative density for element I (overwrites value
read from meamf file)
Ec(I,J) = cohesive energy of reference structure for I-J mixture
delta(I,J) = heat of formation for I-J alloy; if Ec_IJ is input as
zero, then LAMMPS sets Ec_IJ = (Ec_II + Ec_JJ)/2 - delta_IJ
alpha(I,J) = alpha parameter for pair potential between I and J (can
be computed from bulk modulus of reference structure
re(I,J) = equilibrium distance between I and J in the reference
structure
Cmax(I,J,K) = Cmax screening parameter when I-J pair is screened
by K (I<=J); default = 2.8
Cmin(I,J,K) = Cmin screening parameter when I-J pair is screened
by K (I<=J); default = 2.0
lattce(I,J) = lattice structure of I-J reference structure:
dia = diamond (interlaced fcc for alloy)
fcc = face centered cubic
bcc = body centered cubic
dim = dimer
b1 = rock salt (NaCl structure)
hcp = hexagonal close-packed
c11 = MoSi2 structure
l12 = Cu3Au structure (lower case L, followed by 12)
b2 = CsCl structure (interpenetrating simple cubic)
nn2(I,J) = turn on second-nearest neighbor MEAM formulation for
I-J pair (see for example "(Lee)"_#Lee).
0 = second-nearest neighbor formulation off
1 = second-nearest neighbor formulation on
default = 0
attrac(I,J) = additional cubic attraction term in Rose energy I-J pair potential
default = 0
repuls(I,J) = additional cubic repulsive term in Rose energy I-J pair potential
default = 0
zbl(I,J) = blend the MEAM I-J pair potential with the ZBL potential for small
atom separations "(ZBL)"_#ZBL
default = 1
gsmooth_factor = factor determining the length of the G-function smoothing
region; only significant for ibar=0 or ibar=4.
99.0 = short smoothing region, sharp step
0.5 = long smoothing region, smooth step
default = 99.0
augt1 = integer flag for whether to augment t1 parameter by
3/5*t3 to account for old vs. new meam formulations;
0 = don't augment t1
1 = augment t1
default = 1
ialloy = integer flag to use alternative averaging rule for t parameters,
for comparison with the DYNAMO MEAM code
0 = standard averaging (matches ialloy=0 in DYNAMO)
1 = alternative averaging (matches ialloy=1 in DYNAMO)
2 = no averaging of t (use single-element values)
default = 0
mixture_ref_t = integer flag to use mixture average of t to compute the background
reference density for alloys, instead of the single-element values
(see description and warning elsewhere in this doc page)
0 = do not use mixture averaging for t in the reference density
1 = use mixture averaging for t in the reference density
default = 0
erose_form = integer value to select the form of the Rose energy function
(see description below).
default = 0
emb_lin_neg = integer value to select embedding function for negative densities
0 = F(rho)=0
1 = F(rho) = -asub*esub*rho (linear in rho, matches DYNAMO)
default = 0
bkgd_dyn = integer value to select background density formula
0 = rho_bkgd = rho_ref_meam(a) (as in the reference structure)
1 = rho_bkgd = rho0_meam(a)*Z_meam(a) (matches DYNAMO)
default = 0 :pre
Rc, delr, re are in distance units (Angstroms in the case of metal
units). Ec and delta are in energy units (eV in the case of metal
units).
Each keyword represents a quantity which is either a scalar, vector,
2d array, or 3d array and must be specified with the correct
corresponding array syntax. The indices I,J,K each run from 1 to N
where N is the number of MEAM elements being used.
Thus these lines
rho0(2) = 2.25
alpha(1,2) = 4.37 :pre
set rho0 for the 2nd element to the value 2.25 and set alpha for the
alloy interaction between elements 1 and 2 to 4.37.
The augt1 parameter is related to modifications in the MEAM
formulation of the partial electron density function. In recent
literature, an extra term is included in the expression for the
third-order density in order to make the densities orthogonal (see for
example "(Wang)"_#Wang, equation 3d); this term is included in the
MEAM implementation in lammps. However, in earlier published work
this term was not included when deriving parameters, including most of
those provided in the library.meam file included with lammps, and to
account for this difference the parameter t1 must be augmented by
3/5*t3. If augt1=1, the default, this augmentation is done
automatically. When parameter values are fit using the modified
density function, as in more recent literature, augt1 should be set to
0.
The mixture_ref_t parameter is available to match results with those
of previous versions of lammps (before January 2011). Newer versions
of lammps, by default, use the single-element values of the t
parameters to compute the background reference density. This is the
proper way to compute these parameters. Earlier versions of lammps
used an alloy mixture averaged value of t to compute the background
reference density. Setting mixture_ref_t=1 gives the old behavior.
WARNING: using mixture_ref_t=1 will give results that are demonstrably
incorrect for second-neighbor MEAM, and non-standard for
first-neighbor MEAM; this option is included only for matching with
previous versions of lammps and should be avoided if possible.
The parameters attrac and repuls, along with the integer selection
parameter erose_form, can be used to modify the Rose energy function
used to compute the pair potential. This function gives the energy of
the reference state as a function of interatomic spacing. The form of
this function is:
astar = alpha * (r/re - 1.d0)
if erose_form = 0: erose = -Ec*(1+astar+a3*(astar**3)/(r/re))*exp(-astar)
if erose_form = 1: erose = -Ec*(1+astar+(-attrac+repuls/r)*(astar**3))*exp(-astar)
if erose_form = 2: erose = -Ec*(1 +astar + a3*(astar**3))*exp(-astar)
a3 = repuls, astar < 0
a3 = attrac, astar >= 0 :pre
Most published MEAM parameter sets use the default values attrac=repulse=0.
Setting repuls=attrac=delta corresponds to the form used in several
recent published MEAM parameter sets, such as "(Vallone)"_#Vallone
NOTE: The default form of the erose expression in LAMMPS was corrected
in March 2009. The current version is correct, but may show different
behavior compared with earlier versions of lammps with the attrac
and/or repuls parameters are non-zero. To obtain the previous default
form, use erose_form = 1 (this form does not seem to appear in the
literature). An alternative form (see e.g. "(Lee2)"_#Lee2) is
available using erose_form = 2.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS with
user-specifiable parameters as described above. You never need to
specify a pair_coeff command with I != J arguments for this style.
This pair style does not support the "pair_modify"_pair_modify.html
shift, table, and tail options.
This pair style does not write its information to "binary restart
files"_restart.html, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
-This style is part of the "meam" package. It is only enabled if
-LAMMPS was built with that package, which also requires the MEAM
-library be built and linked with LAMMPS. See the "Making
+This style is part of the MEAM package. It is only enabled if LAMMPS
+was built with that package, which also requires the MEAM library be
+built and linked with LAMMPS. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html, "pair_style eam"_pair_eam.html
[Default:] none
:line
:link(Baskes)
[(Baskes)] Baskes, Phys Rev B, 46, 2727-2742 (1992).
:link(Gullet)
[(Gullet)] Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003).
This report may be accessed on-line via "this link"_sandreport.
:link(sandreport,http://infoserve.sandia.gov/sand_doc/2003/038782.pdf)
:link(Lee)
[(Lee)] Lee, Baskes, Phys. Rev. B, 62, 8564-8567 (2000).
:link(Lee2)
[(Lee2)] Lee, Baskes, Kim, Cho. Phys. Rev. B, 64, 184102 (2001).
:link(Valone)
[(Valone)] Valone, Baskes, Martin, Phys. Rev. B, 73, 214209 (2006).
:link(Wang)
[(Wang)] Wang, Van Hove, Ross, Baskes, J. Chem. Phys., 121, 5410 (2004).
:link(ZBL)
-[(ZBL)] J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges
-of Ions in Matter' Vol 1, 1985, Pergamon Press.
-
+[(ZBL)] J.F. Ziegler, J.P. Biersack, U. Littmark, "Stopping and Ranges
+of Ions in Matter", Vol 1, 1985, Pergamon Press.
diff --git a/doc/pair_morse.html b/doc/pair_morse.html
index 8aaf1b4de..bdb1af654 100644
--- a/doc/pair_morse.html
+++ b/doc/pair_morse.html
@@ -1,111 +1,111 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style morse command
</H3>
<H3>pair_style morse/cuda command
</H3>
<H3>pair_style morse/gpu command
</H3>
<H3>pair_style morse/opt command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style morse cutoff
</PRE>
<UL><LI>cutoff = global cutoff for Morse interactions (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style morse 2.5
pair_coeff * * 100.0 2.0 1.5
pair_coeff 1 1 100.0 2.0 1.5 3.0
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>morse</I> computes pairwise interactions with the formula
</P>
<CENTER><IMG SRC = "Eqs/pair_morse.jpg">
</CENTER>
<P>Rc is the cutoff.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands:
</P>
<UL><LI>D0 (energy units)
<LI>alpha (1/distance units)
<LI>r0 (distance units)
<LI>cutoff (distance units)
</UL>
<P>The last coefficient is optional. If not specified, the global morse
cutoff is used.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+<P>These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>None of these pair styles support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
</P>
<P>All of these pair styles support the <A HREF = "pair_modify.html">pair_modify</A>
shift option for the energy of the pair interaction.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table options is not relevant for
the Morse pair styles.
</P>
<P>None of these pair styles support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding long-range tail corrections to energy and
pressure.
</P>
<P>All of these pair styles write their information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>These pair styles can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. They do not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/pair_morse.txt b/doc/pair_morse.txt
index d6f8a6fd3..eb9d78cf6 100644
--- a/doc/pair_morse.txt
+++ b/doc/pair_morse.txt
@@ -1,103 +1,103 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style morse command :h3
pair_style morse/cuda command :h3
pair_style morse/gpu command :h3
pair_style morse/opt command :h3
[Syntax:]
pair_style morse cutoff :pre
cutoff = global cutoff for Morse interactions (distance units) :ul
[Examples:]
pair_style morse 2.5
pair_coeff * * 100.0 2.0 1.5
pair_coeff 1 1 100.0 2.0 1.5 3.0 :pre
[Description:]
Style {morse} computes pairwise interactions with the formula
:c,image(Eqs/pair_morse.jpg)
Rc is the cutoff.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands:
D0 (energy units)
alpha (1/distance units)
r0 (distance units)
cutoff (distance units) :ul
The last coefficient is optional. If not specified, the global morse
cutoff is used.
:line
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
None of these pair styles support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
All of these pair styles support the "pair_modify"_pair_modify.html
shift option for the energy of the pair interaction.
The "pair_modify"_pair_modify.html table options is not relevant for
the Morse pair styles.
None of these pair styles support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure.
All of these pair styles write their information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
These pair styles can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. They do not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:] none
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
diff --git a/doc/pair_peri.html b/doc/pair_peri.html
index b119d01a0..4dbf57a00 100644
--- a/doc/pair_peri.html
+++ b/doc/pair_peri.html
@@ -1,130 +1,130 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style peri/pmb command
</H3>
<H3>pair_style peri/lps command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style
</PRE>
<UL><LI>style = <I>peri/pmb</I> or <I>peri/lps</I>
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style peri/pmb
pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
</PRE>
<PRE>pair_style peri/lps
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25
</PRE>
<P><B>Description:</B>
</P>
<P>The peridynamic pair styles implement material models that can be used
at the mescscopic and macroscopic scales.
</P>
<P>Style <I>peri/pmb</I> implements the Peridynamic bond-based prototype
microelastic brittle (PMB) model.
</P>
<P>Style <I>peri/lps</I> implements the Peridynamic state-based linear
peridynamic solid (LPS) model.
</P>
<P>The canonical papers on Peridynamics are <A HREF = "#Silling2000">(Silling 2000)</A>
and <A HREF = "#Silling2007">(Silling 2007)</A>. The implementation of Peridynamics
in LAMMPS is described in <A HREF = "#Parks">(Parks)</A>. Also see the <A HREF = "http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf">PDLAMMPS
user guide</A> for
more details about the implementation of peridynamics in LAMMPS.
</P>
<P>The following coefficients must be defined for each pair of atom types
via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above,
or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below.
</P>
<P>For the <I>peri/pmb</I> style:
</P>
<UL><LI>c (energy/distance/volume^2 units)
<LI>horizon (distance units)
<LI>s00 (unitless)
<LI>alpha (unitless)
</UL>
<P>C is the effectively a spring constant for Peridynamic bonds, the
horizon is a cutoff distance for truncating interactions, and s00 and
alpha are used as a bond breaking criteria. The units of c are such
that c/distance = stiffness/volume^2, where stiffness is
energy/distance^2 and volume is distance^3. See the users guide for
more details.
</P>
<P>For the <I>peri/lps</I> style:
</P>
<UL><LI>K (force/area units)
<LI>G (force/area units)
<LI>horizon (distance units)
<LI>s00 (unitless)
<LI>alpha (unitless)
</UL>
<P>K is the bulk modulus and G is the shear modulus. The horizon is a
cutoff distance for truncating interactions, and s00 and alpha are
used as a bond breaking criteria. See the users guide for more
details.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>These pair styles do not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
</P>
<P>These pair styles do not support the <A HREF = "pair_modify.html">pair_modify</A>
shift option.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table and tail options are not
relevant for these pair styles.
</P>
<P>These pair styles write their information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>These pair styles can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. They do not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>The <I>peri/pmb</I> and <I>peri/lps</I> styles are part of the "peri"
+<P>The <I>peri/pmb</I> and <I>peri/lps</I> styles are part of the PERI
package. They are only enabled if LAMMPS was built with that package.
See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more
info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Parks"></A>
<P><B>(Parks)</B> Parks, Lehoucq, Plimpton, Silling, Comp Phys Comm, 179(11), 777-783 (2008).
</P>
<A NAME = "Silling2000"></A>
<P><B>(Silling 2000)</B> Silling, J Mech Phys Solids, 48, 175-209 (2000).
</P>
<A NAME = "Silling2007"></A>
<P><B>(Silling 2007)</B> Silling, Epton, Weckner, Xu, Askari, J Elasticity, 88, 151-184 (2007).
</P>
</HTML>
diff --git a/doc/pair_peri.txt b/doc/pair_peri.txt
index 3a7747794..080508b37 100644
--- a/doc/pair_peri.txt
+++ b/doc/pair_peri.txt
@@ -1,121 +1,121 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style peri/pmb command :h3
pair_style peri/lps command :h3
[Syntax:]
pair_style style :pre
style = {peri/pmb} or {peri/lps} :ul
[Examples:]
pair_style peri/pmb
pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25 :pre
pair_style peri/lps
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 :pre
[Description:]
The peridynamic pair styles implement material models that can be used
at the mescscopic and macroscopic scales.
Style {peri/pmb} implements the Peridynamic bond-based prototype
microelastic brittle (PMB) model.
Style {peri/lps} implements the Peridynamic state-based linear
peridynamic solid (LPS) model.
The canonical papers on Peridynamics are "(Silling 2000)"_#Silling2000
and "(Silling 2007)"_#Silling2007. The implementation of Peridynamics
in LAMMPS is described in "(Parks)"_#Parks. Also see the "PDLAMMPS
user guide"_http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf for
more details about the implementation of peridynamics in LAMMPS.
The following coefficients must be defined for each pair of atom types
via the "pair_coeff"_pair_coeff.html command as in the examples above,
or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below.
For the {peri/pmb} style:
c (energy/distance/volume^2 units)
horizon (distance units)
s00 (unitless)
alpha (unitless) :ul
C is the effectively a spring constant for Peridynamic bonds, the
horizon is a cutoff distance for truncating interactions, and s00 and
alpha are used as a bond breaking criteria. The units of c are such
that c/distance = stiffness/volume^2, where stiffness is
energy/distance^2 and volume is distance^3. See the users guide for
more details.
For the {peri/lps} style:
K (force/area units)
G (force/area units)
horizon (distance units)
s00 (unitless)
alpha (unitless) :ul
K is the bulk modulus and G is the shear modulus. The horizon is a
cutoff distance for truncating interactions, and s00 and alpha are
used as a bond breaking criteria. See the users guide for more
details.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
These pair styles do not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
These pair styles do not support the "pair_modify"_pair_modify.html
shift option.
The "pair_modify"_pair_modify.html table and tail options are not
relevant for these pair styles.
These pair styles write their information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
These pair styles can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. They do not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
-The {peri/pmb} and {peri/lps} styles are part of the "peri"
+The {peri/pmb} and {peri/lps} styles are part of the PERI
package. They are only enabled if LAMMPS was built with that package.
See the "Making LAMMPS"_Section_start.html#start_3 section for more
info.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Parks)
[(Parks)] Parks, Lehoucq, Plimpton, Silling, Comp Phys Comm, 179(11), 777-783 (2008).
:link(Silling2000)
[(Silling 2000)] Silling, J Mech Phys Solids, 48, 175-209 (2000).
:link(Silling2007)
[(Silling 2007)] Silling, Epton, Weckner, Xu, Askari, J Elasticity, 88, 151-184 (2007).
diff --git a/doc/pair_reax_c.html b/doc/pair_reax_c.html
index 94c3e5322..c4a27801e 100644
--- a/doc/pair_reax_c.html
+++ b/doc/pair_reax_c.html
@@ -1,280 +1,280 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style reax/c command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style reax/c cfile keyword value
</PRE>
<UL><LI>cfile = NULL or name of a control file
</UL>
<PRE>one keyword value pair may be appended
keyword = <I>checkqeq</I>
<I>checkqeq</I> value = <I>yes</I> or <I>no</I> = whether or not to require qeq/reax fix
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style reax/c NULL
pair_style reax/c controlfile checkqeq no
pair_coeff * * ffield.reax 1 2 2 3
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>reax/c</I> computes the ReaxFF potential of van Duin, Goddard and
co-workers. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
energy. There is more than one version of ReaxFF. The version
implemented in LAMMPS uses the functional forms documented in the
supplemental information of the following paper: <A HREF = "#Chenoweth_2008">(Chenoweth et al.,
2008)</A>. The version integrated into LAMMPS matches
the most up-to-date version of ReaxFF as of summer 2010. For more
technical details about the pair reax/c implementation of ReaxFF, see
the "(Aktulga)" paper.
</P>
<P>The <I>reax/c</I> style differs from the <A HREF = "pair_reax.html">pair_style reax</A>
command in the lo-level implementation details. The <I>reax</I> style is a
Fortran library, linked to LAMMPS. The <I>reax/c</I> style was initially
implemented as stand-alone C code and is now integrated into LAMMPS as
a package.
</P>
<P>LAMMPS provides several different versions of ffield.reax in its
potentials dir, each called potentials/ffield.reax.label. These are
documented in potentials/README.reax. The default ffield.reax
contains parameterizations for the following elements: C, H, O, N, S.
</P>
<P>The format of these files is identical to that used originally by van
Duin. We have tested the accuracy of <I>pair_style reax/c</I> potential
against the original ReaxFF code for the systems mentioned above. You
can use other ffield files for specific chemical systems that may be
available elsewhere (but note that their accuracy may not have been
tested).
</P>
<P>The <I>cfile</I> setting can be specified as NULL, in which case default
settings are used. Or a control file can be specified which contains
cutoff values for the ReaxFF potential in addition to some performance
and output controls. Each line in the control specifies the value for
a control variable. The format of the control file is described
below.
</P>
<P>Two examples using <I>pair_style reax/c</I> are provided in the examples/reax
sub-directory, along with corresponding examples for
<A HREF = "pair_reax.html">pair_style reax</A>.
</P>
<P>Use of this pair style requires that a charge be defined for every
atom. See the <A HREF = "atom_style.html">atom_style</A> and
<A HREF = "read_data.html">read_data</A> commands for details on how to specify
charges.
</P>
<P>The ReaxFF parameter files provided were created using a charge
equilibration (QEq) model for handling the electrostatic interactions.
Therefore, by default, LAMMPS requires that the <A HREF = "fix_qeq_reax.html">fix
qeq/reax</A> command be used with <I>pair_style reax/c</I>
when simulating a ReaxFF model, to equilibrate charge each timestep.
Using the keyword <I>checkqeq</I> with the value <I>no</I>
turns off the check for <I>fix qeq/reax</I>,
allowing a simulation to be run without charge equilibration.
In this case, the static charges you
assign to each atom will be used for computing the electrostatic
interactions in the system.
See the <A HREF = "fix_qeq_reax.html">fix qeq/reax</A> command for details.
</P>
<P>The thermo variable <I>evdwl</I> stores the sum of all the ReaxFF potential
energy contributions, with the exception of the Coulombic and charge
equilibration contributions which are stored in the thermo variable
<I>ecoul</I>. The output of these quantities is controlled by the
<A HREF = "thermo.html">thermo</A> command.
</P>
<P>This pair style tallies a breakdown of the total ReaxFF potential
energy into sub-categories, which can be accessed via the <A HREF = "compute_pair.html">compute
pair</A> command as a vector of values of length 14.
The 14 values correspond to the following sub-categories (the variable
names in italics match those used in the original FORTRAN ReaxFF code):
</P>
<OL><LI><I>eb</I> = bond energy
<LI><I>ea</I> = atom energy
<LI><I>elp</I> = lone-pair energy
<LI><I>emol</I> = molecule energy (always 0.0)
<LI><I>ev</I> = valence angle energy
<LI><I>epen</I> = double-bond valence angle penalty
<LI><I>ecoa</I> = valence angle conjugation energy
<LI><I>ehb</I> = hydrogen bond energy
<LI><I>et</I> = torsion energy
<LI><I>eco</I> = conjugation energy
<LI><I>ew</I> = van der Waals energy
<LI><I>ep</I> = Coulomb energy
<LI><I>efi</I> = electric field energy (always 0.0)
<LI><I>eqeq</I> = charge equilibration energy
</OL>
<P>To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:
</P>
<PRE>compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
...
variable eqeq equal c_reax[14]
thermo_style custom step temp epair v_eb v_ea ... v_eqeq
</PRE>
<P>Only a single pair_coeff command is used with the <I>reax/c</I> style which
specifies a ReaxFF potential file with parameters for all needed
elements. These are mapped to LAMMPS atom types by specifying N
additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
</P>
<UL><LI>filename
<LI>N indices = mapping of ReaxFF elements to atom types
</UL>
<P>The filename is the ReaxFF potential file. Unlike for the <I>reax</I>
pair style, any filename can be used.
</P>
<P>In the ReaxFF potential file, near the top, after the general
parameters, is the atomic parameters section that contains element
names, each with a couple dozen numeric parameters. If there are M
elements specified in the <I>ffield</I> file, think of these as numbered 1
to M. Each of the N indices you specify for the N atom types of LAMMPS
atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will
be mapped to whatever element you specify as the first index value,
etc. If a mapping value is specified as NULL, the mapping is not
performed. This can be used when the <I>reax/c</I> style is used as part
of the <I>hybrid</I> pair style. The NULL values are placeholders for atom
types that will be used with other potentials.
</P>
<P>IMPORTANT NOTE: Currently the reax/c pair style cannot be used as part
of the <I>hybrid</I> pair style. Some additional work still need to be
done to enable this.
</P>
<P>As an example, say your LAMMPS simulation has 4 atom types and the
elements are ordered as C, H, O, N in the <I>ffield</I> file. If you want
the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
H, you would use the following pair_coeff command:
</P>
<PRE>pair_coeff * * ffield.reax 1 1 4 2
</PRE>
<HR>
<P>The format of a line in the control file is as follows:
</P>
<PRE>variable_name value
</PRE>
<P>and it may be followed by an "!" character and a trailing comment.
</P>
<P>If the value of a control variable is not specified, then default
values are used. What follows is the list of variables along with a
brief description of their use and default values.
</P>
<P>simulation_name: Output files produced by <I>pair_style reax/c</I> carry
this name + extensions specific to their contents. Partial energies
are reported with a ".pot" extension, while the trajectory file has
".trj" extension.
</P>
<P>tabulate_long_range: To improve performance, long range interactions
can optionally be tabulated (0 means no tabulation). Value of this
variable denotes the size of the long range interaction table. The
range from 0 to long range cutoff (defined in the <I>ffield</I> file) is
divided into <I>tabulate_long_range</I> points. Then at the start of
simulation, we fill in the entries of the long range interaction table
by computing the energies and forces resulting from van der Waals and
Coulomb interactions between every possible atom type pairs present in
the input system. During the simulation we consult to the long range
interaction table to estimate the energy and forces between a pair of
atoms. Linear interpolation is used for estimation. (default value =
0)
</P>
<P>energy_update_freq: Denotes the frequency (in number of steps) of
writes into the partial energies file. (default value = 0)
</P>
<P>nbrhood_cutoff: Denotes the near neighbors cutoff (in Angstroms)
regarding the bonded interactions. (default value = 4)
</P>
<P>hbond_cutoff: Denotes the cutoff distance (in Angstroms) for hydrogen
bond interactions.(default value = 0 - means no hydrogen bonds are
present)
</P>
<P>bond_graph_cutoff: is the threshold used in determining what is a
physical bond, what is not. Bonds and angles reported in the
trajectory file rely on this cutoff. (default value = 0.3)
</P>
<P>thb_cutoff: cutoff value for the strength of bonds to be considered in
three body interactions. (default value = 0.001)
</P>
<P>write_freq: Frequency of writes into the trajectory file. (default
value = 0)
</P>
<P>traj_title: Title of the trajectory - not the name of the trajectory
file.
</P>
<P>atom_info: 1 means print only atomic positions + charge (default = 0)
</P>
<P>atom_forces: 1 adds net forces to atom lines in the trajectory file
(default = 0)
</P>
<P>atom_velocities: 1 adds atomic velocities to atoms line (default = 0)
</P>
<P>bond_info: 1 prints bonds in the trajectory file (default = 0)
</P>
<P>angle_info: 1 prints angles in the trajectory file (default = 0)
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
mix, shift, table, and tail options.
</P>
<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
files</A>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<P><B>Restrictions:</B>
</P>
-<P>This pair style is part of the "user-reaxc" package. It is only
-enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+<P>This pair style is part of the USER-REAXC package. It is only enabled
+if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>The ReaxFF potential files provided with LAMMPS in the potentials
directory are parameterized for real <A HREF = "units.html">units</A>. You can use
the ReaxFF potential with any LAMMPS units, but you would need to
create your own potential file with coefficients listed in the
appropriate units if your simulation doesn't use "real" units.
</P>
<P>This pair style cannot yet compute per-atom energy or stress. If you
use another command that tries to calculate these quantities using
this pair style, a warning message will be printed and the quantities
will be 0.0.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_qeq_reax.html">fix_qeq_reax</A>,
<A HREF = "pair_reax.html">pair_style reax</A>
</P>
<P><B>Default:</B>
</P>
<P>The keyword default is checkqeq = yes.
</P>
<HR>
<A NAME = "Chenoweth_2008"></A>
<P><B>(Chenoweth_2008)</B> Chenoweth, van Duin and Goddard,
Journal of Physical Chemistry A, 112, 1040-1053 (2008).
</P>
<P>:link(Aktulga) <B>(Aktulga)</B> Aktulga, Fogarty, Pandit, Grama, Parallel
Computing, to appear (2011).
</P>
</HTML>
diff --git a/doc/pair_reax_c.txt b/doc/pair_reax_c.txt
index 5c4c16433..6706ab687 100644
--- a/doc/pair_reax_c.txt
+++ b/doc/pair_reax_c.txt
@@ -1,273 +1,273 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style reax/c command :h3
[Syntax:]
pair_style reax/c cfile keyword value :pre
cfile = NULL or name of a control file :ul
one keyword value pair may be appended
keyword = {checkqeq}
{checkqeq} value = {yes} or {no} = whether or not to require qeq/reax fix :pre
:ule
[Examples:]
pair_style reax/c NULL
pair_style reax/c controlfile checkqeq no
pair_coeff * * ffield.reax 1 2 2 3 :pre
[Description:]
Style {reax/c} computes the ReaxFF potential of van Duin, Goddard and
co-workers. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
energy. There is more than one version of ReaxFF. The version
implemented in LAMMPS uses the functional forms documented in the
supplemental information of the following paper: "(Chenoweth et al.,
2008)"_#Chenoweth_2008. The version integrated into LAMMPS matches
the most up-to-date version of ReaxFF as of summer 2010. For more
technical details about the pair reax/c implementation of ReaxFF, see
the "(Aktulga)" paper.
The {reax/c} style differs from the "pair_style reax"_pair_reax.html
command in the lo-level implementation details. The {reax} style is a
Fortran library, linked to LAMMPS. The {reax/c} style was initially
implemented as stand-alone C code and is now integrated into LAMMPS as
a package.
LAMMPS provides several different versions of ffield.reax in its
potentials dir, each called potentials/ffield.reax.label. These are
documented in potentials/README.reax. The default ffield.reax
contains parameterizations for the following elements: C, H, O, N, S.
The format of these files is identical to that used originally by van
Duin. We have tested the accuracy of {pair_style reax/c} potential
against the original ReaxFF code for the systems mentioned above. You
can use other ffield files for specific chemical systems that may be
available elsewhere (but note that their accuracy may not have been
tested).
The {cfile} setting can be specified as NULL, in which case default
settings are used. Or a control file can be specified which contains
cutoff values for the ReaxFF potential in addition to some performance
and output controls. Each line in the control specifies the value for
a control variable. The format of the control file is described
below.
Two examples using {pair_style reax/c} are provided in the examples/reax
sub-directory, along with corresponding examples for
"pair_style reax"_pair_reax.html.
Use of this pair style requires that a charge be defined for every
atom. See the "atom_style"_atom_style.html and
"read_data"_read_data.html commands for details on how to specify
charges.
The ReaxFF parameter files provided were created using a charge
equilibration (QEq) model for handling the electrostatic interactions.
Therefore, by default, LAMMPS requires that the "fix
qeq/reax"_fix_qeq_reax.html command be used with {pair_style reax/c}
when simulating a ReaxFF model, to equilibrate charge each timestep.
Using the keyword {checkqeq} with the value {no}
turns off the check for {fix qeq/reax},
allowing a simulation to be run without charge equilibration.
In this case, the static charges you
assign to each atom will be used for computing the electrostatic
interactions in the system.
See the "fix qeq/reax"_fix_qeq_reax.html command for details.
The thermo variable {evdwl} stores the sum of all the ReaxFF potential
energy contributions, with the exception of the Coulombic and charge
equilibration contributions which are stored in the thermo variable
{ecoul}. The output of these quantities is controlled by the
"thermo"_thermo.html command.
This pair style tallies a breakdown of the total ReaxFF potential
energy into sub-categories, which can be accessed via the "compute
pair"_compute_pair.html command as a vector of values of length 14.
The 14 values correspond to the following sub-categories (the variable
names in italics match those used in the original FORTRAN ReaxFF code):
{eb} = bond energy
{ea} = atom energy
{elp} = lone-pair energy
{emol} = molecule energy (always 0.0)
{ev} = valence angle energy
{epen} = double-bond valence angle penalty
{ecoa} = valence angle conjugation energy
{ehb} = hydrogen bond energy
{et} = torsion energy
{eco} = conjugation energy
{ew} = van der Waals energy
{ep} = Coulomb energy
{efi} = electric field energy (always 0.0)
{eqeq} = charge equilibration energy :ol
To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:
compute reax all pair reax/c
variable eb equal c_reax\[1\]
variable ea equal c_reax\[2\]
...
variable eqeq equal c_reax\[14\]
thermo_style custom step temp epair v_eb v_ea ... v_eqeq :pre
Only a single pair_coeff command is used with the {reax/c} style which
specifies a ReaxFF potential file with parameters for all needed
elements. These are mapped to LAMMPS atom types by specifying N
additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
filename
N indices = mapping of ReaxFF elements to atom types :ul
The filename is the ReaxFF potential file. Unlike for the {reax}
pair style, any filename can be used.
In the ReaxFF potential file, near the top, after the general
parameters, is the atomic parameters section that contains element
names, each with a couple dozen numeric parameters. If there are M
elements specified in the {ffield} file, think of these as numbered 1
to M. Each of the N indices you specify for the N atom types of LAMMPS
atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will
be mapped to whatever element you specify as the first index value,
etc. If a mapping value is specified as NULL, the mapping is not
performed. This can be used when the {reax/c} style is used as part
of the {hybrid} pair style. The NULL values are placeholders for atom
types that will be used with other potentials.
IMPORTANT NOTE: Currently the reax/c pair style cannot be used as part
of the {hybrid} pair style. Some additional work still need to be
done to enable this.
As an example, say your LAMMPS simulation has 4 atom types and the
elements are ordered as C, H, O, N in the {ffield} file. If you want
the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
H, you would use the following pair_coeff command:
pair_coeff * * ffield.reax 1 1 4 2 :pre
:line
The format of a line in the control file is as follows:
variable_name value :pre
and it may be followed by an "!" character and a trailing comment.
If the value of a control variable is not specified, then default
values are used. What follows is the list of variables along with a
brief description of their use and default values.
simulation_name: Output files produced by {pair_style reax/c} carry
this name + extensions specific to their contents. Partial energies
are reported with a ".pot" extension, while the trajectory file has
".trj" extension.
tabulate_long_range: To improve performance, long range interactions
can optionally be tabulated (0 means no tabulation). Value of this
variable denotes the size of the long range interaction table. The
range from 0 to long range cutoff (defined in the {ffield} file) is
divided into {tabulate_long_range} points. Then at the start of
simulation, we fill in the entries of the long range interaction table
by computing the energies and forces resulting from van der Waals and
Coulomb interactions between every possible atom type pairs present in
the input system. During the simulation we consult to the long range
interaction table to estimate the energy and forces between a pair of
atoms. Linear interpolation is used for estimation. (default value =
0)
energy_update_freq: Denotes the frequency (in number of steps) of
writes into the partial energies file. (default value = 0)
nbrhood_cutoff: Denotes the near neighbors cutoff (in Angstroms)
regarding the bonded interactions. (default value = 4)
hbond_cutoff: Denotes the cutoff distance (in Angstroms) for hydrogen
bond interactions.(default value = 0 - means no hydrogen bonds are
present)
bond_graph_cutoff: is the threshold used in determining what is a
physical bond, what is not. Bonds and angles reported in the
trajectory file rely on this cutoff. (default value = 0.3)
thb_cutoff: cutoff value for the strength of bonds to be considered in
three body interactions. (default value = 0.001)
write_freq: Frequency of writes into the trajectory file. (default
value = 0)
traj_title: Title of the trajectory - not the name of the trajectory
file.
atom_info: 1 means print only atomic positions + charge (default = 0)
atom_forces: 1 adds net forces to atom lines in the trajectory file
(default = 0)
atom_velocities: 1 adds atomic velocities to atoms line (default = 0)
bond_info: 1 prints bonds in the trajectory file (default = 0)
angle_info: 1 prints angles in the trajectory file (default = 0)
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
This pair style does not support the "pair_modify"_pair_modify.html
mix, shift, table, and tail options.
This pair style does not write its information to "binary restart
files"_restart.html, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
[Restrictions:]
-This pair style is part of the "user-reaxc" package. It is only
-enabled if LAMMPS was built with that package. See the "Making
+This pair style is part of the USER-REAXC package. It is only enabled
+if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
The ReaxFF potential files provided with LAMMPS in the potentials
directory are parameterized for real "units"_units.html. You can use
the ReaxFF potential with any LAMMPS units, but you would need to
create your own potential file with coefficients listed in the
appropriate units if your simulation doesn't use "real" units.
This pair style cannot yet compute per-atom energy or stress. If you
use another command that tries to calculate these quantities using
this pair style, a warning message will be printed and the quantities
will be 0.0.
[Related commands:]
"pair_coeff"_pair_coeff.html, "fix_qeq_reax"_fix_qeq_reax.html,
"pair_style reax"_pair_reax.html
[Default:]
The keyword default is checkqeq = yes.
:line
:link(Chenoweth_2008)
[(Chenoweth_2008)] Chenoweth, van Duin and Goddard,
Journal of Physical Chemistry A, 112, 1040-1053 (2008).
:link(Aktulga) [(Aktulga)] Aktulga, Fogarty, Pandit, Grama, Parallel
Computing, to appear (2011).
diff --git a/doc/pair_resquared.html b/doc/pair_resquared.html
index 6dc4367b5..c5bd317a7 100644
--- a/doc/pair_resquared.html
+++ b/doc/pair_resquared.html
@@ -1,241 +1,241 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style resquared command
</H3>
<H3>pair_style resquared/gpu command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style resquared cutoff
</PRE>
<UL><LI>cutoff = global cutoff for interactions (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style resquared 10.0
pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>resquared</I> computes the RE-squared anisotropic interaction
<A HREF = "#Everaers">(Everaers)</A>, <A HREF = "#Babadi">(Babadi)</A> between pairs of
ellipsoidal and/or spherical Lennard-Jones particles. For ellipsoidal
interactions, the potential considers the ellipsoid as being comprised
of small spheres of size sigma. LJ particles are a single sphere of
size sigma. The distinction is made to allow the pair style to make
efficient calculations of ellipsoid/solvent interactions.
</P>
<P>Details for the equations used are given in the references below and
in <A HREF = "PDF/pair_resquared_extra.pdf">this supplementary document</A>.
</P>
<P>Use of this pair style requires the NVE, NVT, or NPT fixes with the
<I>asphere</I> extension (e.g. <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>) in
order to integrate particle rotation. Additionally, <A HREF = "atom_style.html">atom_style
ellipsoid</A> should be used since it defines the
rotational state and the size and shape of each ellipsoidal particle.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands:
</P>
<UL><LI>A12 = Energy Prefactor/Hamaker constant (energy units)
<LI>sigma = atomic interaction diameter (distance units)
<LI>epsilon_i_a = relative well depth of type I for side-to-side interactions
<LI>epsilon_i_b = relative well depth of type I for face-to-face interactions
<LI>epsilon_i_c = relative well depth of type I for end-to-end interactions
<LI>epsilon_j_a = relative well depth of type J for side-to-side interactions
<LI>epsilon_j_b = relative well depth of type J for face-to-face interactions
<LI>epsilon_j_c = relative well depth of type J for end-to-end interactions
<LI>cutoff (distance units)
</UL>
<P>The parameters used depend on the type of the interacting particles,
i.e. ellipsoids or LJ spheres. The type of a particle is determined
by the diameters specified for its 3 shape paramters. If all 3 shape
parameters = 0.0, then the particle is treated as an LJ sphere. The
epsilon_i_* or epsilon_j_* parameters are ignored for LJ spheres. If
the 3 shape paraemters are > 0.0, then the particle is treated as an
ellipsoid (even if the 3 parameters are equal to each other).
</P>
<P>A12 specifies the energy prefactor which depends on the types of the
two interacting particles.
</P>
<P>For ellipsoid/ellipsoid interactions, the interaction is computed by
the formulas in the supplementary docuement referenced above. A12 is
the Hamaker constant as described in <A HREF = "#Everaers">(Everaers)</A>. In LJ
units:
</P>
<CENTER><IMG SRC = "Eqs/pair_resquared.jpg">
</CENTER>
<P>where rho gives the number density of the spherical particles
composing the ellipsoids and epsilon_LJ determines the interaction
strength of the spherical particles.
</P>
<P>For ellipsoid/LJ sphere interactions, the interaction is also computed
by the formulas in the supplementary docuement referenced above. A12
has a modifed form (see <A HREF = "PDF/pair_resquared_extra.pdf">here</A> for
details):
</P>
<CENTER><IMG SRC = "Eqs/pair_resquared2.jpg">
</CENTER>
<P>For ellipsoid/LJ sphere interactions, a correction to the distance-
of-closest approach equation has been implemented to reduce the error
from two particles of disparate sizes; see <A HREF = "PDF/pair_resquared_extra.pdf">this supplementary
document</A>.
</P>
<P>For LJ sphere/LJ sphere interactions, the interaction is computed
using the standard Lennard-Jones formula, which is much cheaper to
compute than the ellipsoidal formulas. A12 is used as epsilon in the
standard LJ formula:
</P>
<CENTER><IMG SRC = "Eqs/pair_resquared3.jpg">
</CENTER>
<P>and the specified <I>sigma</I> is used as the sigma in the standard LJ
formula.
</P>
<P>When one of both of the interacting particles are ellipsoids, then
<I>sigma</I> specifies the diameter of the continuous distribution of
constituent particles within each ellipsoid used to model the
RE-squared potential. Note that this is a different meaning for
<I>sigma</I> than the <A HREF = "pair_gayberne.html">pair_style gayberne</A> potential
uses.
</P>
<P>The epsilon_i and epsilon_j coefficients are defined for atom types,
not for pairs of atom types. Thus, in a series of pair_coeff
commands, they only need to be specified once for each atom type.
</P>
<P>Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are
non-zero, the three values are assigned to atom type I. If all the
epsilon_i values are zero, they are ignored. If any of epsilon_j_a,
epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned
to atom type J. If all three epsilon_i values are zero, they are
ignored. Thus the typical way to define the epsilon_i and epsilon_j
coefficients is to list their values in "pair_coeff I J" commands when
I = J, but set them to 0.0 when I != J. If you do list them when I !=
J, you should insure they are consistent with their values in other
pair_coeff commands.
</P>
<P>Note that if this potential is being used as a sub-style of
<A HREF = "pair_hybrid.html">pair_style hybrid</A>, and there is no "pair_coeff I I"
setting made for RE-squared for a particular type I (because I-I
interactions are computed by another hybrid pair potential), then you
still need to insure the epsilon a,b,c coefficients are assigned to
that type in a "pair_coeff I J" command.
</P>
<P>For large uniform molecules it has been shown that the epsilon_*_*
energy parameters are approximately representable in terms of local
contact curvatures <A HREF = "#Everaers">(Everaers)</A>:
</P>
<CENTER><IMG SRC = "Eqs/pair_resquared4.jpg">
</CENTER>
<P>where a, b, and c give the particle diameters.
</P>
<P>The last coefficient is optional. If not specified, the global cutoff
specified in the pair_style command is used.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, or <I>opt</I> suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
-<P>These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+<P>These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">this section</A> of the manual for more
instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance can be mixed, but only for sphere pairs. The
default mix value is <I>geometric</I>. See the "pair_modify" command for
details. Other type pairs cannot be mixed, due to the different
meanings of the energy prefactors used to calculate the interactions
and the implicit dependence of the ellipsoid-sphere interaction on the
equation for the Hamaker constant presented here. Mixing of sigma and
epsilon followed by calculation of the energy prefactors using the
equations above is recommended.
</P>
<P>This pair styles supports the <A HREF = "pair_modify.html">pair_modify</A> shift
option for the energy of the Lennard-Jones portion of the pair
interaction, but only for sphere-sphere interactions. There is no
shifting performed for ellipsoidal interactions due to the anisotropic
dependence of the interaction.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
for this pair style.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding long-range tail corrections to energy and
pressure.
</P>
<P>This pair style writes its information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
command</A>.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>This style is part of the "asphere" package. It is only enabled if
+<P>This style is part of the ASPHERE package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>This pair style requires that atoms be ellipsoids as defined by the
<A HREF = "atom_style.html">atom_style ellipsoid</A> command.
</P>
<P>Particles acted on by the potential can be extended aspherical or
spherical particles, or point particles. Spherical particles have all
3 of their shape parameters equal to each other. Point particles have
all 3 of their shape parameters equal to 0.0.
</P>
<P>The distance-of-closest-approach approximation used by LAMMPS becomes
less accurate when high-aspect ratio ellipsoids are used.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>,
<A HREF = "compute_temp_asphere.html">compute temp/asphere</A>, <A HREF = "pair_gayberne.html">pair_style
gayberne</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Everaers"></A>
<P><B>(Everaers)</B> Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).
</P>
<A NAME = "Babadi"></A>
<P><B>(Berardi)</B> Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006).
</P>
</HTML>
diff --git a/doc/pair_resquared.txt b/doc/pair_resquared.txt
index 1315cc4e8..71d50e8eb 100755
--- a/doc/pair_resquared.txt
+++ b/doc/pair_resquared.txt
@@ -1,233 +1,233 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style resquared command :h3
pair_style resquared/gpu command :h3
[Syntax:]
pair_style resquared cutoff :pre
cutoff = global cutoff for interactions (distance units) :ul
[Examples:]
pair_style resquared 10.0
pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0 :pre
[Description:]
Style {resquared} computes the RE-squared anisotropic interaction
"(Everaers)"_#Everaers, "(Babadi)"_#Babadi between pairs of
ellipsoidal and/or spherical Lennard-Jones particles. For ellipsoidal
interactions, the potential considers the ellipsoid as being comprised
of small spheres of size sigma. LJ particles are a single sphere of
size sigma. The distinction is made to allow the pair style to make
efficient calculations of ellipsoid/solvent interactions.
Details for the equations used are given in the references below and
in "this supplementary document"_PDF/pair_resquared_extra.pdf.
Use of this pair style requires the NVE, NVT, or NPT fixes with the
{asphere} extension (e.g. "fix nve/asphere"_fix_nve_asphere.html) in
order to integrate particle rotation. Additionally, "atom_style
ellipsoid"_atom_style.html should be used since it defines the
rotational state and the size and shape of each ellipsoidal particle.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands:
A12 = Energy Prefactor/Hamaker constant (energy units)
sigma = atomic interaction diameter (distance units)
epsilon_i_a = relative well depth of type I for side-to-side interactions
epsilon_i_b = relative well depth of type I for face-to-face interactions
epsilon_i_c = relative well depth of type I for end-to-end interactions
epsilon_j_a = relative well depth of type J for side-to-side interactions
epsilon_j_b = relative well depth of type J for face-to-face interactions
epsilon_j_c = relative well depth of type J for end-to-end interactions
cutoff (distance units) :ul
The parameters used depend on the type of the interacting particles,
i.e. ellipsoids or LJ spheres. The type of a particle is determined
by the diameters specified for its 3 shape paramters. If all 3 shape
parameters = 0.0, then the particle is treated as an LJ sphere. The
epsilon_i_* or epsilon_j_* parameters are ignored for LJ spheres. If
the 3 shape paraemters are > 0.0, then the particle is treated as an
ellipsoid (even if the 3 parameters are equal to each other).
A12 specifies the energy prefactor which depends on the types of the
two interacting particles.
For ellipsoid/ellipsoid interactions, the interaction is computed by
the formulas in the supplementary docuement referenced above. A12 is
the Hamaker constant as described in "(Everaers)"_#Everaers. In LJ
units:
:c,image(Eqs/pair_resquared.jpg)
where rho gives the number density of the spherical particles
composing the ellipsoids and epsilon_LJ determines the interaction
strength of the spherical particles.
For ellipsoid/LJ sphere interactions, the interaction is also computed
by the formulas in the supplementary docuement referenced above. A12
has a modifed form (see "here"_PDF/pair_resquared_extra.pdf for
details):
:c,image(Eqs/pair_resquared2.jpg)
For ellipsoid/LJ sphere interactions, a correction to the distance-
of-closest approach equation has been implemented to reduce the error
from two particles of disparate sizes; see "this supplementary
document"_PDF/pair_resquared_extra.pdf.
For LJ sphere/LJ sphere interactions, the interaction is computed
using the standard Lennard-Jones formula, which is much cheaper to
compute than the ellipsoidal formulas. A12 is used as epsilon in the
standard LJ formula:
:c,image(Eqs/pair_resquared3.jpg)
and the specified {sigma} is used as the sigma in the standard LJ
formula.
When one of both of the interacting particles are ellipsoids, then
{sigma} specifies the diameter of the continuous distribution of
constituent particles within each ellipsoid used to model the
RE-squared potential. Note that this is a different meaning for
{sigma} than the "pair_style gayberne"_pair_gayberne.html potential
uses.
The epsilon_i and epsilon_j coefficients are defined for atom types,
not for pairs of atom types. Thus, in a series of pair_coeff
commands, they only need to be specified once for each atom type.
Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are
non-zero, the three values are assigned to atom type I. If all the
epsilon_i values are zero, they are ignored. If any of epsilon_j_a,
epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned
to atom type J. If all three epsilon_i values are zero, they are
ignored. Thus the typical way to define the epsilon_i and epsilon_j
coefficients is to list their values in "pair_coeff I J" commands when
I = J, but set them to 0.0 when I != J. If you do list them when I !=
J, you should insure they are consistent with their values in other
pair_coeff commands.
Note that if this potential is being used as a sub-style of
"pair_style hybrid"_pair_hybrid.html, and there is no "pair_coeff I I"
setting made for RE-squared for a particular type I (because I-I
interactions are computed by another hybrid pair potential), then you
still need to insure the epsilon a,b,c coefficients are assigned to
that type in a "pair_coeff I J" command.
For large uniform molecules it has been shown that the epsilon_*_*
energy parameters are approximately representable in terms of local
contact curvatures "(Everaers)"_#Everaers:
:c,image(Eqs/pair_resquared4.jpg)
where a, b, and c give the particle diameters.
The last coefficient is optional. If not specified, the global cutoff
specified in the pair_style command is used.
:line
Styles with a {cuda}, {gpu}, or {opt} suffix are functionally the same
as the corresponding style without the suffix. They have been
optimized to run faster, depending on your available hardware, as
discussed in "this section"_Section_accelerate.html of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
-These accelerated styles are part of the "user-cuda", "gpu", and "opt"
+These accelerated styles are part of the USER-CUDA, GPU, and OPT
packages respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "this section"_Section_accelerate.html of the manual for more
instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance can be mixed, but only for sphere pairs. The
default mix value is {geometric}. See the "pair_modify" command for
details. Other type pairs cannot be mixed, due to the different
meanings of the energy prefactors used to calculate the interactions
and the implicit dependence of the ellipsoid-sphere interaction on the
equation for the Hamaker constant presented here. Mixing of sigma and
epsilon followed by calculation of the energy prefactors using the
equations above is recommended.
This pair styles supports the "pair_modify"_pair_modify.html shift
option for the energy of the Lennard-Jones portion of the pair
interaction, but only for sphere-sphere interactions. There is no
shifting performed for ellipsoidal interactions due to the anisotropic
dependence of the interaction.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
This pair style does not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords of the "run_style
command"_run_style.html.
:line
[Restrictions:]
-This style is part of the "asphere" package. It is only enabled if
+This style is part of the ASPHERE package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
This pair style requires that atoms be ellipsoids as defined by the
"atom_style ellipsoid"_atom_style.html command.
Particles acted on by the potential can be extended aspherical or
spherical particles, or point particles. Spherical particles have all
3 of their shape parameters equal to each other. Point particles have
all 3 of their shape parameters equal to 0.0.
The distance-of-closest-approach approximation used by LAMMPS becomes
less accurate when high-aspect ratio ellipsoids are used.
[Related commands:]
"pair_coeff"_pair_coeff.html, "fix nve/asphere"_fix_nve_asphere.html,
"compute temp/asphere"_compute_temp_asphere.html, "pair_style
gayberne"_pair_gayberne.html
[Default:] none
:line
:link(Everaers)
[(Everaers)] Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).
:link(Babadi)
[(Berardi)] Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006).
diff --git a/doc/pair_sph_heatconduction.html b/doc/pair_sph_heatconduction.html
new file mode 100644
index 000000000..570a324b8
--- /dev/null
+++ b/doc/pair_sph_heatconduction.html
@@ -0,0 +1,68 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style sph/heatconduction command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style sph/heatconduction
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style sph/heatconduction
+pair_coeff * * 1.0 2.4
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The sph/heatconduction style computes heat transport between SPH particles.
+The transport model is the diffusion euqation for the internal energy.
+</P>
+<P>See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+LAMMPS.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above.
+</P>
+<UL><LI>D diffusion coefficient (length^2/time units)
+<LI>h kernel function cutoff (distance units)
+</UL>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>This style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This style does not write information to <A HREF = "restart.html">binary restart
+files</A>. Thus, you need to re-specify the pair_style and
+pair_coeff commands in an input script that reads a restart file.
+</P>
+<P>This style can only be used via the <I>pair</I> keyword of the <A HREF = "run_style.html">run_style
+respa</A> command. It does not support the <I>inner</I>,
+<I>middle</I>, <I>outer</I> keywords.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style is part of the USER-SPH package. It is only enabled
+if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, pair_sph/rhosum
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/pair_sph_heatconduction.txt b/doc/pair_sph_heatconduction.txt
new file mode 100644
index 000000000..d25debe91
--- /dev/null
+++ b/doc/pair_sph_heatconduction.txt
@@ -0,0 +1,63 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+pair_style sph/heatconduction command :h3
+
+[Syntax:]
+
+pair_style sph/heatconduction :pre
+
+[Examples:]
+
+pair_style sph/heatconduction
+pair_coeff * * 1.0 2.4 :pre
+
+[Description:]
+
+The sph/heatconduction style computes heat transport between SPH particles.
+The transport model is the diffusion euqation for the internal energy.
+
+See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in
+LAMMPS.
+
+The following coefficients must be defined for each pair of atoms
+types via the "pair_coeff"_pair_coeff.html command as in the examples
+above.
+
+D diffusion coefficient (length^2/time units)
+h kernel function cutoff (distance units) :ul
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+This style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+This style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+This style does not write information to "binary restart
+files"_restart.html. Thus, you need to re-specify the pair_style and
+pair_coeff commands in an input script that reads a restart file.
+
+This style can only be used via the {pair} keyword of the "run_style
+respa"_run_style.html command. It does not support the {inner},
+{middle}, {outer} keywords.
+
+[Restrictions:]
+
+This pair style is part of the USER-SPH package. It is only enabled
+if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html, pair_sph/rhosum
+
+[Default:] none
diff --git a/doc/pair_sph_idealgas.html b/doc/pair_sph_idealgas.html
new file mode 100644
index 000000000..4d45b2959
--- /dev/null
+++ b/doc/pair_sph_idealgas.html
@@ -0,0 +1,82 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style sph/idealgas command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style sph/idealgas
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style sph/idealgas
+pair_coeff * * 1.0 2.4
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The sph/idealgas style computes pressure forces between particles
+according to the ideal gas equation of state:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_sph_ideal.jpg">
+</CENTER>
+<P>where gamma = 1.4 is the heat capacity ratio, rho is the local
+density, and e is the internal energy per unit mass. This pair style
+also computes Monaghan's artificial viscosity to prevent particles
+from interpentrating <A HREF = "#Monoghan">(Monaghan)</A>.
+</P>
+<P>See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+LAMMPS.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above.
+</P>
+<UL><LI>nu artificial viscosity (no units)
+<LI>h kernel function cutoff (distance units)
+</UL>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>This style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This style does not write information to <A HREF = "restart.html">binary restart
+files</A>. Thus, you need to re-specify the pair_style and
+pair_coeff commands in an input script that reads a restart file.
+</P>
+<P>This style can only be used via the <I>pair</I> keyword of the <A HREF = "run_style.html">run_style
+respa</A> command. It does not support the <I>inner</I>,
+<I>middle</I>, <I>outer</I> keywords.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style is part of the USER-SPH package. It is only enabled
+if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, pair_sph/rhosum
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Monoghan"></A>
+
+<P><B>(Monaghan)</B> Monaghan and Gingold, Journal of Computational Physics,
+52, 374-389 (1983).
+</P>
+</HTML>
diff --git a/doc/pair_sph_idealgas.txt b/doc/pair_sph_idealgas.txt
new file mode 100644
index 000000000..f28d26265
--- /dev/null
+++ b/doc/pair_sph_idealgas.txt
@@ -0,0 +1,77 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+pair_style sph/idealgas command :h3
+
+[Syntax:]
+
+pair_style sph/idealgas :pre
+
+[Examples:]
+
+pair_style sph/idealgas
+pair_coeff * * 1.0 2.4 :pre
+
+[Description:]
+
+The sph/idealgas style computes pressure forces between particles
+according to the ideal gas equation of state:
+
+:c,image(Eqs/pair_sph_ideal.jpg)
+
+where gamma = 1.4 is the heat capacity ratio, rho is the local
+density, and e is the internal energy per unit mass. This pair style
+also computes Monaghan's artificial viscosity to prevent particles
+from interpentrating "(Monaghan)"_#Monoghan.
+
+See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in
+LAMMPS.
+
+The following coefficients must be defined for each pair of atoms
+types via the "pair_coeff"_pair_coeff.html command as in the examples
+above.
+
+nu artificial viscosity (no units)
+h kernel function cutoff (distance units) :ul
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+This style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+This style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+This style does not write information to "binary restart
+files"_restart.html. Thus, you need to re-specify the pair_style and
+pair_coeff commands in an input script that reads a restart file.
+
+This style can only be used via the {pair} keyword of the "run_style
+respa"_run_style.html command. It does not support the {inner},
+{middle}, {outer} keywords.
+
+[Restrictions:]
+
+This pair style is part of the USER-SPH package. It is only enabled
+if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html, pair_sph/rhosum
+
+[Default:] none
+
+:line
+
+:link(Monoghan)
+[(Monaghan)] Monaghan and Gingold, Journal of Computational Physics,
+52, 374-389 (1983).
+
diff --git a/doc/pair_sph_lj.html b/doc/pair_sph_lj.html
new file mode 100644
index 000000000..60cbdc67c
--- /dev/null
+++ b/doc/pair_sph_lj.html
@@ -0,0 +1,86 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style sph/lj command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style sph/lj
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style sph/lj
+pair_coeff * * 1.0 2.4
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The sph/lj style computes pressure forces between particles according
+to the Lennard-Jones equation of state, which is computed according to
+Ree's 1980 polynomial fit <A HREF = "#Ree">(Ree)</A>. The Lennard-Jones parameters
+epsilon and sigma are set to unity. This pair style also computes
+Monaghan's artificial viscosity to prevent particles from
+interpentrating <A HREF = "#Monoghan">(Monaghan)</A>.
+</P>
+<P>See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+LAMMPS.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above.
+</P>
+<UL><LI>nu artificial viscosity (no units)
+<LI>h kernel function cutoff (distance units)
+</UL>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>This style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This style does not write information to <A HREF = "restart.html">binary restart
+files</A>. Thus, you need to re-specify the pair_style and
+pair_coeff commands in an input script that reads a restart file.
+</P>
+<P>This style can only be used via the <I>pair</I> keyword of the <A HREF = "run_style.html">run_style
+respa</A> command. It does not support the <I>inner</I>,
+<I>middle</I>, <I>outer</I> keywords.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>As noted above, the Lennard-Jones parameters epsilon and sigma are set
+to unity.
+</P>
+<P>This pair style is part of the USER-SPH package. It is only enabled
+if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, pair_sph/rhosum
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Ree"></A>
+
+<P><B>(Ree)</B> Ree, Journal of Chemical Physics, 73, 5401 (1980).
+</P>
+<A NAME = "Monoghan"></A>
+
+<P><B>(Monaghan)</B> Monaghan and Gingold, Journal of Computational Physics,
+52, 374-389 (1983).
+</P>
+</HTML>
diff --git a/doc/pair_sph_lj.txt b/doc/pair_sph_lj.txt
new file mode 100644
index 000000000..849884113
--- /dev/null
+++ b/doc/pair_sph_lj.txt
@@ -0,0 +1,79 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+pair_style sph/lj command :h3
+
+[Syntax:]
+
+pair_style sph/lj :pre
+
+[Examples:]
+
+pair_style sph/lj
+pair_coeff * * 1.0 2.4 :pre
+
+[Description:]
+
+The sph/lj style computes pressure forces between particles according
+to the Lennard-Jones equation of state, which is computed according to
+Ree's 1980 polynomial fit "(Ree)"_#Ree. The Lennard-Jones parameters
+epsilon and sigma are set to unity. This pair style also computes
+Monaghan's artificial viscosity to prevent particles from
+interpentrating "(Monaghan)"_#Monoghan.
+
+See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in
+LAMMPS.
+
+The following coefficients must be defined for each pair of atoms
+types via the "pair_coeff"_pair_coeff.html command as in the examples
+above.
+
+nu artificial viscosity (no units)
+h kernel function cutoff (distance units) :ul
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+This style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+This style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+This style does not write information to "binary restart
+files"_restart.html. Thus, you need to re-specify the pair_style and
+pair_coeff commands in an input script that reads a restart file.
+
+This style can only be used via the {pair} keyword of the "run_style
+respa"_run_style.html command. It does not support the {inner},
+{middle}, {outer} keywords.
+
+[Restrictions:]
+
+As noted above, the Lennard-Jones parameters epsilon and sigma are set
+to unity.
+
+This pair style is part of the USER-SPH package. It is only enabled
+if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html, pair_sph/rhosum
+
+[Default:] none
+
+:line
+
+:link(Ree)
+[(Ree)] Ree, Journal of Chemical Physics, 73, 5401 (1980).
+
+:link(Monoghan)
+[(Monaghan)] Monaghan and Gingold, Journal of Computational Physics,
+52, 374-389 (1983).
diff --git a/doc/pair_sph_rhosum.html b/doc/pair_sph_rhosum.html
new file mode 100644
index 000000000..7e3f38a91
--- /dev/null
+++ b/doc/pair_sph_rhosum.html
@@ -0,0 +1,69 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style sph/rhosum command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style sph/rhosum Nstep
+</PRE>
+<UL><LI>Nstep = timestep interval
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style sph/rhosum 10
+pair_coeff * * 2.4
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The sph/rhosum style computes the local particle mass density rho for
+SPH particles by kernel function interpolation, every Nstep timesteps.
+</P>
+<P>See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+LAMMPS.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above.
+</P>
+<UL><LI>h (distance units)
+</UL>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>This style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This style does not write information to <A HREF = "restart.html">binary restart
+files</A>. Thus, you need to re-specify the pair_style and
+pair_coeff commands in an input script that reads a restart file.
+</P>
+<P>This style can only be used via the <I>pair</I> keyword of the <A HREF = "run_style.html">run_style
+respa</A> command. It does not support the <I>inner</I>,
+<I>middle</I>, <I>outer</I> keywords.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style is part of the USER-SPH package. It is only enabled
+if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, pair_sph/taitwater
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/pair_sph_rhosum.txt b/doc/pair_sph_rhosum.txt
new file mode 100644
index 000000000..352e717f7
--- /dev/null
+++ b/doc/pair_sph_rhosum.txt
@@ -0,0 +1,64 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+pair_style sph/rhosum command :h3
+
+[Syntax:]
+
+pair_style sph/rhosum Nstep :pre
+
+Nstep = timestep interval :ul
+
+[Examples:]
+
+pair_style sph/rhosum 10
+pair_coeff * * 2.4 :pre
+
+[Description:]
+
+The sph/rhosum style computes the local particle mass density rho for
+SPH particles by kernel function interpolation, every Nstep timesteps.
+
+See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in
+LAMMPS.
+
+The following coefficients must be defined for each pair of atoms
+types via the "pair_coeff"_pair_coeff.html command as in the examples
+above.
+
+h (distance units) :ul
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+This style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+This style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+This style does not write information to "binary restart
+files"_restart.html. Thus, you need to re-specify the pair_style and
+pair_coeff commands in an input script that reads a restart file.
+
+This style can only be used via the {pair} keyword of the "run_style
+respa"_run_style.html command. It does not support the {inner},
+{middle}, {outer} keywords.
+
+[Restrictions:]
+
+This pair style is part of the USER-SPH package. It is only enabled
+if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html, pair_sph/taitwater
+
+[Default:] none
diff --git a/doc/pair_sph_taitwater.html b/doc/pair_sph_taitwater.html
new file mode 100644
index 000000000..7c350f2f3
--- /dev/null
+++ b/doc/pair_sph_taitwater.html
@@ -0,0 +1,85 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style sph/taitwater command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style sph/taitwater
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style sph/taitwater
+pair_coeff * * 1000.0 1430.0 1.0 2.4
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The sph/taitwater style computes pressure forces between SPH particles
+according to Tait's equation of state:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_sph_tait.jpg">
+</CENTER>
+<P>where gamma = 7 and B = c_0^2 rho_0 / gamma, with rho_0 being the
+reference density and c_0 the reference speed of sound.
+</P>
+<P>This pair style also computes Monaghan's artificial viscosity to
+prevent particles from interpentrating <A HREF = "#Monaghan">(Monaghan)</A>.
+</P>
+<P>See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+LAMMPS.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above.
+</P>
+<UL><LI>rho0 reference density (mass/volume units)
+<LI>c0 reference soundspeed (distance/time units)
+<LI>nu artificial viscosity (no units)
+<LI>h kernel function cutoff (distance units)
+</UL>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>This style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This style does not write information to <A HREF = "restart.html">binary restart
+files</A>. Thus, you need to re-specify the pair_style and
+pair_coeff commands in an input script that reads a restart file.
+</P>
+<P>This style can only be used via the <I>pair</I> keyword of the <A HREF = "run_style.html">run_style
+respa</A> command. It does not support the <I>inner</I>,
+<I>middle</I>, <I>outer</I> keywords.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style is part of the USER-SPH package. It is only enabled
+if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, pair_sph/rhosum
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Monoghan"></A>
+
+<P><B>(Monaghan)</B> Monaghan and Gingold, Journal of Computational Physics,
+52, 374-389 (1983).
+</P>
+</HTML>
diff --git a/doc/pair_sph_taitwater.txt b/doc/pair_sph_taitwater.txt
new file mode 100644
index 000000000..5f6fbeb5b
--- /dev/null
+++ b/doc/pair_sph_taitwater.txt
@@ -0,0 +1,79 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+pair_style sph/taitwater command :h3
+
+[Syntax:]
+
+pair_style sph/taitwater :pre
+
+[Examples:]
+
+pair_style sph/taitwater
+pair_coeff * * 1000.0 1430.0 1.0 2.4 :pre
+
+[Description:]
+
+The sph/taitwater style computes pressure forces between SPH particles
+according to Tait's equation of state:
+
+:c,image(Eqs/pair_sph_tait.jpg)
+
+where gamma = 7 and B = c_0^2 rho_0 / gamma, with rho_0 being the
+reference density and c_0 the reference speed of sound.
+
+This pair style also computes Monaghan's artificial viscosity to
+prevent particles from interpentrating "(Monaghan)"_#Monaghan.
+
+See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in
+LAMMPS.
+
+The following coefficients must be defined for each pair of atoms
+types via the "pair_coeff"_pair_coeff.html command as in the examples
+above.
+
+rho0 reference density (mass/volume units)
+c0 reference soundspeed (distance/time units)
+nu artificial viscosity (no units)
+h kernel function cutoff (distance units) :ul
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+This style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+This style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+This style does not write information to "binary restart
+files"_restart.html. Thus, you need to re-specify the pair_style and
+pair_coeff commands in an input script that reads a restart file.
+
+This style can only be used via the {pair} keyword of the "run_style
+respa"_run_style.html command. It does not support the {inner},
+{middle}, {outer} keywords.
+
+[Restrictions:]
+
+This pair style is part of the USER-SPH package. It is only enabled
+if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html, pair_sph/rhosum
+
+[Default:] none
+
+:line
+
+:link(Monoghan)
+[(Monaghan)] Monaghan and Gingold, Journal of Computational Physics,
+52, 374-389 (1983).
diff --git a/doc/pair_sph_taitwater_morris.html b/doc/pair_sph_taitwater_morris.html
new file mode 100644
index 000000000..4abffb4c5
--- /dev/null
+++ b/doc/pair_sph_taitwater_morris.html
@@ -0,0 +1,83 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>pair_style sph/taitwater/morris command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style sph/taitwater/morris
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style sph/taitwater/morris
+pair_coeff * * 1000.0 1430.0 1.0 2.4
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The sph/taitwater/morris style computes pressure forces between SPH
+particles according to Tait's equation of state:
+</P>
+<CENTER><IMG SRC = "Eqs/pair_sph_tait.jpg">
+</CENTER>
+<P>where gamma = 7 and B = c_0^2 rho_0 / gamma, with rho_0 being the
+reference density and c_0 the reference speed of sound.
+</P>
+<P>This pair style also computes laminar viscosity <A HREF = "#Morris">(Morris)</A>.
+</P>
+<P>See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
+LAMMPS.
+</P>
+<P>The following coefficients must be defined for each pair of atoms
+types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
+above.
+</P>
+<UL><LI>rho0 reference density (mass/volume units)
+<LI>c0 reference soundspeed (distance/time units)
+<LI>nu dynamic viscosity (mass*distance/time units)
+<LI>h kernel function cutoff (distance units)
+</UL>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+</P>
+<P>This style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+shift, table, and tail options.
+</P>
+<P>This style does not write information to <A HREF = "restart.html">binary restart
+files</A>. Thus, you need to re-specify the pair_style and
+pair_coeff commands in an input script that reads a restart file.
+</P>
+<P>This style can only be used via the <I>pair</I> keyword of the <A HREF = "run_style.html">run_style
+respa</A> command. It does not support the <I>inner</I>,
+<I>middle</I>, <I>outer</I> keywords.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This pair style is part of the USER-SPH package. It is only enabled
+if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, pair_sph/rhosum
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Morris"></A>
+
+<P><B>(Morris)</B> Morris, Fox, Zhu, J Comp Physics, 136, 214–226 (1997).
+</P>
+</HTML>
diff --git a/doc/pair_sph_taitwater_morris.txt b/doc/pair_sph_taitwater_morris.txt
new file mode 100644
index 000000000..8bedfd499
--- /dev/null
+++ b/doc/pair_sph_taitwater_morris.txt
@@ -0,0 +1,79 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+pair_style sph/taitwater/morris command :h3
+
+[Syntax:]
+
+pair_style sph/taitwater/morris :pre
+
+[Examples:]
+
+pair_style sph/taitwater/morris
+pair_coeff * * 1000.0 1430.0 1.0 2.4 :pre
+
+[Description:]
+
+The sph/taitwater/morris style computes pressure forces between SPH
+particles according to Tait's equation of state:
+
+:c,image(Eqs/pair_sph_tait.jpg)
+
+where gamma = 7 and B = c_0^2 rho_0 / gamma, with rho_0 being the
+reference density and c_0 the reference speed of sound.
+
+This pair style also computes laminar viscosity "(Morris)"_#Morris.
+
+See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in
+LAMMPS.
+
+The following coefficients must be defined for each pair of atoms
+types via the "pair_coeff"_pair_coeff.html command as in the examples
+above.
+
+rho0 reference density (mass/volume units)
+c0 reference soundspeed (distance/time units)
+nu dynamic viscosity (mass*distance/time units)
+h kernel function cutoff (distance units) :ul
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+This style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+This style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+This style does not write information to "binary restart
+files"_restart.html. Thus, you need to re-specify the pair_style and
+pair_coeff commands in an input script that reads a restart file.
+
+This style can only be used via the {pair} keyword of the "run_style
+respa"_run_style.html command. It does not support the {inner},
+{middle}, {outer} keywords.
+
+[Restrictions:]
+
+This pair style is part of the USER-SPH package. It is only enabled
+if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html, pair_sph/rhosum
+
+[Default:] none
+
+:line
+
+:link(Morris)
+[(Morris)] Morris, Fox, Zhu, J Comp Physics, 136, 214–226 (1997).
+
+
diff --git a/doc/pair_sw.html b/doc/pair_sw.html
index 9789f23e3..6267d6ba2 100644
--- a/doc/pair_sw.html
+++ b/doc/pair_sw.html
@@ -1,187 +1,187 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style sw command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style sw
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style sw
pair_coeff * * si.sw Si
pair_coeff * * GaN.sw Ga N Ga
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>sw</I> style computes a 3-body <A HREF = "#Stillinger">Stillinger-Weber</A>
potential for the energy E of a system of atoms as
</P>
<CENTER><IMG SRC = "Eqs/pair_sw.jpg">
</CENTER>
<P>where phi2 is a two-body term and phi3 is a three-body term. The
summations in the formula are over all neighbors J and K of atom I
within a cutoff distance = a*sigma.
</P>
<P>Only a single pair_coeff command is used with the <I>sw</I> style which
specifies a Stillinger-Weber potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
</P>
<UL><LI>filename
<LI>N element names = mapping of SW elements to atom types
</UL>
<P>As an example, imagine a file SiC.sw has Stillinger-Weber values for
Si and C. If your LAMMPS simulation has 4 atoms types and you want
the 1st 3 to be Si, and the 4th to be C, you would use the following
pair_coeff command:
</P>
<PRE>pair_coeff * * SiC.sw Si Si Si C
</PRE>
<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
element in the SW file. The final C argument maps LAMMPS atom type 4
to the C element in the SW file. If a mapping value is specified as
NULL, the mapping is not performed. This can be used when a <I>sw</I>
potential is used as part of the <I>hybrid</I> pair style. The NULL values
are placeholders for atom types that will be used with other
potentials.
</P>
<P>Stillinger-Weber files in the <I>potentials</I> directory of the LAMMPS
distribution have a ".sw" suffix. Lines that are not blank or
comments (starting with #) define parameters for a triplet of
elements. The parameters in a single entry correspond to the two-body
and three-body coefficients in the formula above:
</P>
<UL><LI>element 1 (the center atom in a 3-body interaction)
<LI>element 2
<LI>element 3
<LI>epsilon (energy units)
<LI>sigma (distance units)
<LI>a
<LI>lambda
<LI>gamma
<LI>costheta0
<LI>A
<LI>B
<LI>p
<LI>q
<LI>tol
</UL>
<P>The A, B, p, and q parameters are used only for two-body
interactions. The lambda and costheta0 parameters are used only for
three-body interactions. The epsilon, sigma and a parameters are used
for both two-body and three-body interactions. gamma is used only in the
three-body interactions, but is defined for pairs of atoms.
The non-annotated parameters are unitless.
</P>
<P>LAMMPS introduces an additional performance-optimization parameter tol
that is used for both two-body and three-body interactions. In the
Stillinger-Weber potential, the interaction energies become negligibly
small at atomic separations substantially less than the theoretical
cutoff distances. LAMMPS therefore defines a virtual cutoff distance
based on a user defined tolerance tol. The use of the virtual cutoff
distance in constructing atom neighbor lists can significantly reduce
the neighbor list sizes and therefore the computational cost. LAMMPS
provides a <I>tol</I> value for each of the three-body entries so that they
can be separately controlled. If tol = 0.0, then the standard
Stillinger-Weber cutoff is used.
</P>
<P>The Stillinger-Weber potential file must contain entries for all the
elements listed in the pair_coeff command. It can also contain
entries for additional elements not being used in a particular
simulation; LAMMPS ignores those entries.
</P>
<P>For a single-element simulation, only a single entry is required
(e.g. SiSiSi). For a two-element simulation, the file must contain 8
entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
specify SW parameters for all permutations of the two elements
interacting in three-body configurations. Thus for 3 elements, 27
entries would be required, etc.
</P>
<P>As annotated above, the first element in the entry is the center atom
in a three-body interaction. Thus an entry for SiCC means a Si atom
with 2 C atoms as neighbors. The parameter values used for the
two-body interaction come from the entry where the 2nd and 3rd
elements are the same. Thus the two-body parameters for Si
interacting with C, comes from the SiCC entry. The three-body
parameters can in principle be specific to the three elements of the
configuration. In the literature, however, the three-body parameters
are usually defined by simple formulas involving two sets of pair-wise
parameters, corresponding to the ij and ik pairs, where i is the
center atom. The user must ensure that the correct combining rule is
used to calculate the values of the threebody parameters for
alloys. Note also that the function phi3 contains two exponential
screening factors with parameter values from the ij pair and ik
pairs. So phi3 for a C atom bonded to a Si atom and a second C atom
will depend on the three-body parameters for the CSiC entry, and also
on the two-body parameters for the CCC and CSiSi entries. Since the
order of the two neighbors is arbitrary, the threebody parameters for
entries CSiC and CCSi should be the same. Similarly, the two-body
parameters for entries SiCC and CSiSi should also be the same. The
parameters used only for two-body interactions (A, B, p, and q) in
entries whose 2nd and 3rd element are different (e.g. SiCSi) are not
used for anything and can be set to 0.0 if desired.
This is also true for the parameters in phi3 that are
taken from the ij and ik pairs (sigma, a, gamma)
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above from values in the potential file.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift, table, and tail options.
</P>
<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
files</A>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>This pair style is part of the "manybody" package. It is only enabled
+<P>This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default). See
the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
</P>
<P>This pair style requires the <A HREF = "newton.html">newton</A> setting to be "on"
for pair interactions.
</P>
<P>The Stillinger-Weber potential files provided with LAMMPS (see the
potentials directory) are parameterized for metal <A HREF = "units.html">units</A>.
You can use the SW potential with any LAMMPS units, but you would need
to create your own SW potential file with coefficients listed in the
appropriate units if your simulation doesn't use "metal" units.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Stillinger"></A>
<P><B>(Stillinger)</B> Stillinger and Weber, Phys Rev B, 31, 5262 (1985).
</P>
</HTML>
diff --git a/doc/pair_sw.txt b/doc/pair_sw.txt
index c6083a3fe..1b62af869 100644
--- a/doc/pair_sw.txt
+++ b/doc/pair_sw.txt
@@ -1,181 +1,181 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style sw command :h3
[Syntax:]
pair_style sw :pre
[Examples:]
pair_style sw
pair_coeff * * si.sw Si
pair_coeff * * GaN.sw Ga N Ga :pre
[Description:]
The {sw} style computes a 3-body "Stillinger-Weber"_#Stillinger
potential for the energy E of a system of atoms as
:c,image(Eqs/pair_sw.jpg)
where phi2 is a two-body term and phi3 is a three-body term. The
summations in the formula are over all neighbors J and K of atom I
within a cutoff distance = a*sigma.
Only a single pair_coeff command is used with the {sw} style which
specifies a Stillinger-Weber potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
filename
N element names = mapping of SW elements to atom types :ul
As an example, imagine a file SiC.sw has Stillinger-Weber values for
Si and C. If your LAMMPS simulation has 4 atoms types and you want
the 1st 3 to be Si, and the 4th to be C, you would use the following
pair_coeff command:
pair_coeff * * SiC.sw Si Si Si C :pre
The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
element in the SW file. The final C argument maps LAMMPS atom type 4
to the C element in the SW file. If a mapping value is specified as
NULL, the mapping is not performed. This can be used when a {sw}
potential is used as part of the {hybrid} pair style. The NULL values
are placeholders for atom types that will be used with other
potentials.
Stillinger-Weber files in the {potentials} directory of the LAMMPS
distribution have a ".sw" suffix. Lines that are not blank or
comments (starting with #) define parameters for a triplet of
elements. The parameters in a single entry correspond to the two-body
and three-body coefficients in the formula above:
element 1 (the center atom in a 3-body interaction)
element 2
element 3
epsilon (energy units)
sigma (distance units)
a
lambda
gamma
costheta0
A
B
p
q
tol :ul
The A, B, p, and q parameters are used only for two-body
interactions. The lambda and costheta0 parameters are used only for
three-body interactions. The epsilon, sigma and a parameters are used
for both two-body and three-body interactions. gamma is used only in the
three-body interactions, but is defined for pairs of atoms.
The non-annotated parameters are unitless.
LAMMPS introduces an additional performance-optimization parameter tol
that is used for both two-body and three-body interactions. In the
Stillinger-Weber potential, the interaction energies become negligibly
small at atomic separations substantially less than the theoretical
cutoff distances. LAMMPS therefore defines a virtual cutoff distance
based on a user defined tolerance tol. The use of the virtual cutoff
distance in constructing atom neighbor lists can significantly reduce
the neighbor list sizes and therefore the computational cost. LAMMPS
provides a {tol} value for each of the three-body entries so that they
can be separately controlled. If tol = 0.0, then the standard
Stillinger-Weber cutoff is used.
The Stillinger-Weber potential file must contain entries for all the
elements listed in the pair_coeff command. It can also contain
entries for additional elements not being used in a particular
simulation; LAMMPS ignores those entries.
For a single-element simulation, only a single entry is required
(e.g. SiSiSi). For a two-element simulation, the file must contain 8
entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
specify SW parameters for all permutations of the two elements
interacting in three-body configurations. Thus for 3 elements, 27
entries would be required, etc.
As annotated above, the first element in the entry is the center atom
in a three-body interaction. Thus an entry for SiCC means a Si atom
with 2 C atoms as neighbors. The parameter values used for the
two-body interaction come from the entry where the 2nd and 3rd
elements are the same. Thus the two-body parameters for Si
interacting with C, comes from the SiCC entry. The three-body
parameters can in principle be specific to the three elements of the
configuration. In the literature, however, the three-body parameters
are usually defined by simple formulas involving two sets of pair-wise
parameters, corresponding to the ij and ik pairs, where i is the
center atom. The user must ensure that the correct combining rule is
used to calculate the values of the threebody parameters for
alloys. Note also that the function phi3 contains two exponential
screening factors with parameter values from the ij pair and ik
pairs. So phi3 for a C atom bonded to a Si atom and a second C atom
will depend on the three-body parameters for the CSiC entry, and also
on the two-body parameters for the CCC and CSiSi entries. Since the
order of the two neighbors is arbitrary, the threebody parameters for
entries CSiC and CCSi should be the same. Similarly, the two-body
parameters for entries SiCC and CSiSi should also be the same. The
parameters used only for two-body interactions (A, B, p, and q) in
entries whose 2nd and 3rd element are different (e.g. SiCSi) are not
used for anything and can be set to 0.0 if desired.
This is also true for the parameters in phi3 that are
taken from the ij and ik pairs (sigma, a, gamma)
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above from values in the potential file.
This pair style does not support the "pair_modify"_pair_modify.html
shift, table, and tail options.
This pair style does not write its information to "binary restart
files"_restart.html, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
-This pair style is part of the "manybody" package. It is only enabled
+This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default). See
the "Making LAMMPS"_Section_start.html#start_3 section for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
The Stillinger-Weber potential files provided with LAMMPS (see the
potentials directory) are parameterized for metal "units"_units.html.
You can use the SW potential with any LAMMPS units, but you would need
to create your own SW potential file with coefficients listed in the
appropriate units if your simulation doesn't use "metal" units.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Stillinger)
[(Stillinger)] Stillinger and Weber, Phys Rev B, 31, 5262 (1985).
diff --git a/doc/pair_tersoff.html b/doc/pair_tersoff.html
index bcec40982..ed15a307a 100644
--- a/doc/pair_tersoff.html
+++ b/doc/pair_tersoff.html
@@ -1,217 +1,217 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style tersoff command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style tersoff
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style tersoff
pair_coeff * * Si.tersoff Si
pair_coeff * * SiC.tersoff Si C Si
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>tersoff</I> style computes a 3-body Tersoff potential
<A HREF = "#Tersoff_1">(Tersoff_1)</A> for the energy E of a system of atoms as
</P>
<CENTER><IMG SRC = "Eqs/pair_tersoff_1.jpg">
</CENTER>
<P>where f_R is a two-body term and f_A includes three-body interactions.
The summations in the formula are over all neighbors J and K of atom I
within a cutoff distance = R + D.
</P>
<P>Only a single pair_coeff command is used with the <I>tersoff</I> style
which specifies a Tersoff potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
</P>
<UL><LI>filename
<LI>N element names = mapping of Tersoff elements to atom types
</UL>
<P>As an example, imagine the SiC.tersoff file has Tersoff values for Si
and C. If your LAMMPS simulation has 4 atoms types and you want the
1st 3 to be Si, and the 4th to be C, you would use the following
pair_coeff command:
</P>
<PRE>pair_coeff * * SiC.tersoff Si Si Si C
</PRE>
<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
element in the Tersoff file. The final C argument maps LAMMPS atom
type 4 to the C element in the Tersoff file. If a mapping value is
specified as NULL, the mapping is not performed. This can be used
when a <I>tersoff</I> potential is used as part of the <I>hybrid</I> pair style.
The NULL values are placeholders for atom types that will be used with
other potentials.
</P>
<P>Tersoff files in the <I>potentials</I> directory of the LAMMPS distribution
have a ".tersoff" suffix. Lines that are not blank or comments
(starting with #) define parameters for a triplet of elements. The
parameters in a single entry correspond to coefficients in the formula
above:
</P>
<UL><LI>element 1 (the center atom in a 3-body interaction)
<LI>element 2 (the atom bonded to the center atom)
<LI>element 3 (the atom influencing the 1-2 bond in a bond-order sense)
<LI>m
<LI>gamma
<LI>lambda3 (1/distance units)
<LI>c
<LI>d
<LI>costheta0 (can be a value < -1 or > 1)
<LI>n
<LI>beta
<LI>lambda2 (1/distance units)
<LI>B (energy units)
<LI>R (distance units)
<LI>D (distance units)
<LI>lambda1 (1/distance units)
<LI>A (energy units)
</UL>
<P>The n, beta, lambda2, B, lambda1, and A parameters are only used for
two-body interactions. The m, gamma, lambda3, c, d, and costheta0
parameters are only used for three-body interactions. The R and D
parameters are used for both two-body and three-body interactions. The
non-annotated parameters are unitless. The value of m must be 3 or 1.
</P>
<P>The Tersoff potential file must contain entries for all the elements
listed in the pair_coeff command. It can also contain entries for
additional elements not being used in a particular simulation; LAMMPS
ignores those entries.
</P>
<P>For a single-element simulation, only a single entry is required
(e.g. SiSiSi). For a two-element simulation, the file must contain 8
entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
specify Tersoff parameters for all permutations of the two elements
interacting in three-body configurations. Thus for 3 elements, 27
entries would be required, etc.
</P>
<P>As annotated above, the first element in the entry is the center atom
in a three-body interaction and it is bonded to the 2nd atom and the
bond is influenced by the 3rd atom. Thus an entry for SiCC means Si
bonded to a C with another C atom influencing the bond. Thus
three-body parameters for SiCSi and SiSiC entries will not, in
general, be the same. The parameters used for the two-body
interaction come from the entry where the 2nd element is repeated.
Thus the two-body parameters for Si interacting with C, comes from the
SiCC entry.
</P>
<P>The parameters used for a particular
three-body interaction come from the entry with the corresponding
three elements. The parameters used only for two-body interactions
(n, beta, lambda2, B, lambda1, and A) in entries whose 2nd and 3rd
element are different (e.g. SiCSi) are not used for anything and can
be set to 0.0 if desired.
</P>
<P>Note that the twobody parameters in entries such as SiCC and CSiSi
are often the same, due to the common use of symmetric mixing rules,
but this is not always the case. For example, the beta and n parameters in
Tersoff_2 <A HREF = "#Tersoff_2">(Tersoff_2)</A> are not symmetric.
</P>
<P>We chose the above form so as to enable users to define all commonly
used variants of the Tersoff potential. In particular, our form
reduces to the original Tersoff form when m = 3 and gamma = 1, while
it reduces to the form of <A HREF = "#Albe">Albe et al.</A> when beta = 1 and m = 1.
Note that in the current Tersoff implementation in LAMMPS, m must be
specified as either 3 or 1. Tersoff used a slightly different but
equivalent form for alloys, which we will refer to as Tersoff_2
potential <A HREF = "#Tersoff_2">(Tersoff_2)</A>.
</P>
<P>LAMMPS parameter values for Tersoff_2 can be obtained as follows:
gamma = 1, just as for Tersoff_1, but now lambda3 = 0 and the value of
m has no effect. The parameters for species i and j can be calculated
using the Tersoff_2 mixing rules:
</P>
<CENTER><IMG SRC = "Eqs/pair_tersoff_2.jpg">
</CENTER>
<P>Tersoff_2 parameters R and S must be converted to the LAMMPS
parameters R and D (R is different in both forms), using the following
relations: R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the
Tersoff_2 parameters.
</P>
<P>In the potentials directory, the file SiCGe.tersoff provides the
LAMMPS parameters for Tersoff's various versions of Si, as well as his
alloy parameters for Si, C, and Ge. This file can be used for pure Si,
(three different versions), pure C, pure Ge, binary SiC, and binary
SiGe. LAMMPS will generate an error if this file is used with any
combination involving C and Ge, since there are no entries for the GeC
interactions (Tersoff did not publish parameters for this
cross-interaction.) Tersoff files are also provided for the SiC alloy
(SiC.tersoff) and the GaN (GaN.tersoff) alloys.
</P>
<P>Many thanks to Rutuparna Narulkar, David Farrell, and Xiaowang Zhou
for helping clarify how Tersoff parameters for alloys have been
defined in various papers.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above from values in the potential file.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift, table, and tail options.
</P>
<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
files</A>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>This pair style is part of the "manybody" package. It is only enabled
+<P>This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default). See
the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
</P>
<P>This pair style requires the <A HREF = "newton.html">newton</A> setting to be "on"
for pair interactions.
</P>
<P>The Tersoff potential files provided with LAMMPS (see the potentials
directory) are parameterized for metal <A HREF = "units.html">units</A>. You can
use the Tersoff potential with any LAMMPS units, but you would need to
create your own Tersoff potential file with coefficients listed in the
appropriate units if your simulation doesn't use "metal" units.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Tersoff_1"></A>
<P><B>(Tersoff_1)</B> J. Tersoff, Phys Rev B, 37, 6991 (1988).
</P>
<A NAME = "Albe"></A>
<P><B>(Albe)</B> J. Nord, K. Albe, P. Erhart, and K. Nordlund, J. Phys.:
Condens. Matter, 15, 5649(2003).
</P>
<A NAME = "Tersoff_2"></A>
<P><B>(Tersoff_2)</B> J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248)
</P>
</HTML>
diff --git a/doc/pair_tersoff.txt b/doc/pair_tersoff.txt
index d5c9eb857..f6cfd8316 100644
--- a/doc/pair_tersoff.txt
+++ b/doc/pair_tersoff.txt
@@ -1,209 +1,209 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style tersoff command :h3
[Syntax:]
pair_style tersoff :pre
[Examples:]
pair_style tersoff
pair_coeff * * Si.tersoff Si
pair_coeff * * SiC.tersoff Si C Si :pre
[Description:]
The {tersoff} style computes a 3-body Tersoff potential
"(Tersoff_1)"_#Tersoff_1 for the energy E of a system of atoms as
:c,image(Eqs/pair_tersoff_1.jpg)
where f_R is a two-body term and f_A includes three-body interactions.
The summations in the formula are over all neighbors J and K of atom I
within a cutoff distance = R + D.
Only a single pair_coeff command is used with the {tersoff} style
which specifies a Tersoff potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
filename
N element names = mapping of Tersoff elements to atom types :ul
As an example, imagine the SiC.tersoff file has Tersoff values for Si
and C. If your LAMMPS simulation has 4 atoms types and you want the
1st 3 to be Si, and the 4th to be C, you would use the following
pair_coeff command:
pair_coeff * * SiC.tersoff Si Si Si C :pre
The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
element in the Tersoff file. The final C argument maps LAMMPS atom
type 4 to the C element in the Tersoff file. If a mapping value is
specified as NULL, the mapping is not performed. This can be used
when a {tersoff} potential is used as part of the {hybrid} pair style.
The NULL values are placeholders for atom types that will be used with
other potentials.
Tersoff files in the {potentials} directory of the LAMMPS distribution
have a ".tersoff" suffix. Lines that are not blank or comments
(starting with #) define parameters for a triplet of elements. The
parameters in a single entry correspond to coefficients in the formula
above:
element 1 (the center atom in a 3-body interaction)
element 2 (the atom bonded to the center atom)
element 3 (the atom influencing the 1-2 bond in a bond-order sense)
m
gamma
lambda3 (1/distance units)
c
d
costheta0 (can be a value < -1 or > 1)
n
beta
lambda2 (1/distance units)
B (energy units)
R (distance units)
D (distance units)
lambda1 (1/distance units)
A (energy units) :ul
The n, beta, lambda2, B, lambda1, and A parameters are only used for
two-body interactions. The m, gamma, lambda3, c, d, and costheta0
parameters are only used for three-body interactions. The R and D
parameters are used for both two-body and three-body interactions. The
non-annotated parameters are unitless. The value of m must be 3 or 1.
The Tersoff potential file must contain entries for all the elements
listed in the pair_coeff command. It can also contain entries for
additional elements not being used in a particular simulation; LAMMPS
ignores those entries.
For a single-element simulation, only a single entry is required
(e.g. SiSiSi). For a two-element simulation, the file must contain 8
entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
specify Tersoff parameters for all permutations of the two elements
interacting in three-body configurations. Thus for 3 elements, 27
entries would be required, etc.
As annotated above, the first element in the entry is the center atom
in a three-body interaction and it is bonded to the 2nd atom and the
bond is influenced by the 3rd atom. Thus an entry for SiCC means Si
bonded to a C with another C atom influencing the bond. Thus
three-body parameters for SiCSi and SiSiC entries will not, in
general, be the same. The parameters used for the two-body
interaction come from the entry where the 2nd element is repeated.
Thus the two-body parameters for Si interacting with C, comes from the
SiCC entry.
The parameters used for a particular
three-body interaction come from the entry with the corresponding
three elements. The parameters used only for two-body interactions
(n, beta, lambda2, B, lambda1, and A) in entries whose 2nd and 3rd
element are different (e.g. SiCSi) are not used for anything and can
be set to 0.0 if desired.
Note that the twobody parameters in entries such as SiCC and CSiSi
are often the same, due to the common use of symmetric mixing rules,
but this is not always the case. For example, the beta and n parameters in
Tersoff_2 "(Tersoff_2)"_#Tersoff_2 are not symmetric.
We chose the above form so as to enable users to define all commonly
used variants of the Tersoff potential. In particular, our form
reduces to the original Tersoff form when m = 3 and gamma = 1, while
it reduces to the form of "Albe et al."_#Albe when beta = 1 and m = 1.
Note that in the current Tersoff implementation in LAMMPS, m must be
specified as either 3 or 1. Tersoff used a slightly different but
equivalent form for alloys, which we will refer to as Tersoff_2
potential "(Tersoff_2)"_#Tersoff_2.
LAMMPS parameter values for Tersoff_2 can be obtained as follows:
gamma = 1, just as for Tersoff_1, but now lambda3 = 0 and the value of
m has no effect. The parameters for species i and j can be calculated
using the Tersoff_2 mixing rules:
:c,image(Eqs/pair_tersoff_2.jpg)
Tersoff_2 parameters R and S must be converted to the LAMMPS
parameters R and D (R is different in both forms), using the following
relations: R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the
Tersoff_2 parameters.
In the potentials directory, the file SiCGe.tersoff provides the
LAMMPS parameters for Tersoff's various versions of Si, as well as his
alloy parameters for Si, C, and Ge. This file can be used for pure Si,
(three different versions), pure C, pure Ge, binary SiC, and binary
SiGe. LAMMPS will generate an error if this file is used with any
combination involving C and Ge, since there are no entries for the GeC
interactions (Tersoff did not publish parameters for this
cross-interaction.) Tersoff files are also provided for the SiC alloy
(SiC.tersoff) and the GaN (GaN.tersoff) alloys.
Many thanks to Rutuparna Narulkar, David Farrell, and Xiaowang Zhou
for helping clarify how Tersoff parameters for alloys have been
defined in various papers.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above from values in the potential file.
This pair style does not support the "pair_modify"_pair_modify.html
shift, table, and tail options.
This pair style does not write its information to "binary restart
files"_restart.html, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
-This pair style is part of the "manybody" package. It is only enabled
+This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default). See
the "Making LAMMPS"_Section_start.html#start_3 section for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
The Tersoff potential files provided with LAMMPS (see the potentials
directory) are parameterized for metal "units"_units.html. You can
use the Tersoff potential with any LAMMPS units, but you would need to
create your own Tersoff potential file with coefficients listed in the
appropriate units if your simulation doesn't use "metal" units.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Tersoff_1)
[(Tersoff_1)] J. Tersoff, Phys Rev B, 37, 6991 (1988).
:link(Albe)
[(Albe)] J. Nord, K. Albe, P. Erhart, and K. Nordlund, J. Phys.:
Condens. Matter, 15, 5649(2003).
:link(Tersoff_2)
[(Tersoff_2)] J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248)
diff --git a/doc/pair_tersoff_zbl.html b/doc/pair_tersoff_zbl.html
index 8fda7458d..84e4c85fe 100644
--- a/doc/pair_tersoff_zbl.html
+++ b/doc/pair_tersoff_zbl.html
@@ -1,243 +1,243 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style tersoff/zbl command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style tersoff/zbl
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style tersoff/zbl
pair_coeff * * SiC.tersoff.zbl Si C Si
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>tersoff/zbl</I> style computes a 3-body Tersoff potential
<A HREF = "#Tersoff_1">(Tersoff_1)</A> with a close-separation pairwise modification
based on a Coulomb potential and the Ziegler-Biersack-Littmark
universal screening function <A HREF = "#ZBL">(ZBL)</A>, giving the energy E of a
system of atoms as
</P>
<CENTER><IMG SRC = "Eqs/pair_tersoff_zbl.jpg">
</CENTER>
<P>The f_F term is a fermi-like function used to smoothly connect the ZBL
repulsive potential with the Tersoff potential. There are 2
parameters used to adjust it: A_F and r_C. A_F controls how "sharp"
the transition is between the two, and r_C is essentially the cutoff
for the ZBL potential.
</P>
<P>For the ZBL portion, there are two terms. The first is the Coulomb
repulsive term, with Z1, Z2 as the number of protons in each nucleus,
e as the electron charge (1 for metal and real units) and epsilon0 as
the permittivity of vacuum. The second part is the ZBL universal
screening function, with a0 being the Bohr radius (typically 0.529
Angstroms), and the remainder of the coefficients provided by the
original paper. This screening function should be applicable to most
systems. However, it is only accurate for small separations
(i.e. less than 1 Angstrom).
</P>
<P>For the Tersoff portion, f_R is a two-body term and f_A includes
three-body interactions. The summations in the formula are over all
neighbors J and K of atom I within a cutoff distance = R + D.
</P>
<P>Only a single pair_coeff command is used with the <I>tersoff/zbl</I> style
which specifies a Tersoff/ZBL potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
</P>
<UL><LI>filename
<LI>N element names = mapping of Tersoff/ZBL elements to atom types
</UL>
<P>As an example, imagine the SiC.tersoff.zbl file has Tersoff/ZBL values
for Si and C. If your LAMMPS simulation has 4 atoms types and you
want the 1st 3 to be Si, and the 4th to be C, you would use the
following pair_coeff command:
</P>
<PRE>pair_coeff * * SiC.tersoff Si Si Si C
</PRE>
<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
element in the Tersoff/ZBL file. The final C argument maps LAMMPS
atom type 4 to the C element in the Tersoff/ZBL file. If a mapping
value is specified as NULL, the mapping is not performed. This can be
used when a <I>tersoff/zbl</I> potential is used as part of the <I>hybrid</I>
pair style. The NULL values are placeholders for atom types that will
be used with other potentials.
</P>
<P>Tersoff/ZBL files in the <I>potentials</I> directory of the LAMMPS
distribution have a ".tersoff.zbl" suffix. Lines that are not blank
or comments (starting with #) define parameters for a triplet of
elements. The parameters in a single entry correspond to coefficients
in the formula above:
</P>
<UL><LI>element 1 (the center atom in a 3-body interaction)
<LI>element 2 (the atom bonded to the center atom)
<LI>element 3 (the atom influencing the 1-2 bond in a bond-order sense)
<LI>m
<LI>gamma
<LI>lambda3 (1/distance units)
<LI>c
<LI>d
<LI>costheta0 (can be a value < -1 or > 1)
<LI>n
<LI>beta
<LI>lambda2 (1/distance units)
<LI>B (energy units)
<LI>R (distance units)
<LI>D (distance units)
<LI>lambda1 (1/distance units)
<LI>A (energy units)
<LI>Z_i
<LI>Z_j
<LI>ZBLcut (distance units)
<LI>ZBLexpscale (1/distance units)
</UL>
<P>The n, beta, lambda2, B, lambda1, and A parameters are only used for
two-body interactions. The m, gamma, lambda3, c, d, and costheta0
parameters are only used for three-body interactions. The R and D
parameters are used for both two-body and three-body interactions. The
Z_i,Z_j, ZBLcut, ZBLexpscale parameters are used in the ZBL repulsive
portion of the potential and in the Fermi-like function. The
non-annotated parameters are unitless. The value of m must be 3 or 1.
</P>
<P>The Tersoff/ZBL potential file must contain entries for all the
elements listed in the pair_coeff command. It can also contain
entries for additional elements not being used in a particular
simulation; LAMMPS ignores those entries.
</P>
<P>For a single-element simulation, only a single entry is required
(e.g. SiSiSi). For a two-element simulation, the file must contain 8
entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
specify Tersoff parameters for all permutations of the two elements
interacting in three-body configurations. Thus for 3 elements, 27
entries would be required, etc.
</P>
<P>As annotated above, the first element in the entry is the center atom
in a three-body interaction and it is bonded to the 2nd atom and the
bond is influenced by the 3rd atom. Thus an entry for SiCC means Si
bonded to a C with another C atom influencing the bond. Thus
three-body parameters for SiCSi and SiSiC entries will not, in
general, be the same. The parameters used for the two-body
interaction come from the entry where the 2nd element is repeated.
Thus the two-body parameters for Si interacting with C, comes from the
SiCC entry. By symmetry, the twobody parameters in the SiCC and CSiSi
entries should thus be the same. The parameters used for a particular
three-body interaction come from the entry with the corresponding
three elements. The parameters used only for two-body interactions
(n, beta, lambda2, B, lambda1, and A) in entries whose 2nd and 3rd
element are different (e.g. SiCSi) are not used for anything and can
be set to 0.0 if desired.
</P>
<P>We chose the above form so as to enable users to define all commonly
used variants of the Tersoff portion of the potential. In particular,
our form reduces to the original Tersoff form when m = 3 and gamma =
1, while it reduces to the form of <A HREF = "#Albe">Albe et al.</A> when beta = 1
and m = 1. Note that in the current Tersoff implementation in LAMMPS,
m must be specified as either 3 or 1. Tersoff used a slightly
different but equivalent form for alloys, which we will refer to as
Tersoff_2 potential <A HREF = "#Tersoff_2">(Tersoff_2)</A>.
</P>
<P>LAMMPS parameter values for Tersoff_2 can be obtained as follows:
gamma = 1, just as for Tersoff_1, but now lambda3 = 0 and the value of
m has no effect. The parameters for species i and j can be calculated
using the Tersoff_2 mixing rules:
</P>
<CENTER><IMG SRC = "Eqs/pair_tersoff_2.jpg">
</CENTER>
<P>Values not shown are determined by the first atom type. Finally, the
Tersoff_2 parameters R and S must be converted to the LAMMPS
parameters R and D (R is different in both forms), using the following
relations: R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the
Tersoff_2 parameters.
</P>
<P>In the potentials directory, the file SiCGe.tersoff provides the
LAMMPS parameters for Tersoff's various versions of Si, as well as his
alloy parameters for Si, C, and Ge. This file can be used for pure Si,
(three different versions), pure C, pure Ge, binary SiC, and binary
SiGe. LAMMPS will generate an error if this file is used with any
combination involving C and Ge, since there are no entries for the GeC
interactions (Tersoff did not publish parameters for this
cross-interaction.) Tersoff files are also provided for the SiC alloy
(SiC.tersoff) and the GaN (GaN.tersoff) alloys.
</P>
<P>Many thanks to Rutuparna Narulkar, David Farrell, and Xiaowang Zhou
for helping clarify how Tersoff parameters for alloys have been
defined in various papers. Also thanks to Ram Devanathan for
providing the base ZBL implementation.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above from values in the potential file.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift, table, and tail options.
</P>
<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
files</A>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>This pair style is part of the "manybody" package. It is only enabled
+<P>This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default). See
the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
</P>
<P>This pair style requires the <A HREF = "newton.html">newton</A> setting to be "on"
for pair interactions.
</P>
<P>The Tersoff/ZBL potential files provided with LAMMPS (see the
potentials directory) are parameterized for metal <A HREF = "units.html">units</A>.
You can use the Tersoff potential with any LAMMPS units, but you would
need to create your own Tersoff potential file with coefficients
listed in the appropriate units if your simulation doesn't use "metal"
units.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Tersoff_1"></A>
<P><B>(Tersoff_1)</B> J. Tersoff, Phys Rev B, 37, 6991 (1988).
</P>
<A NAME = "ZBL"></A>
<P><B>(ZBL)</B> J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges
of Ions in Matter' Vol 1, 1985, Pergamon Press.
</P>
<A NAME = "Albe"></A>
<P><B>(Albe)</B> J. Nord, K. Albe, P. Erhartand K. Nordlund, J. Phys.:
Condens. Matter, 15, 5649(2003).
</P>
<A NAME = "Tersoff_2"></A>
<P><B>(Tersoff_2)</B> J. Tersoff, Phys Rev B, 39, 5566 (1989)
</P>
</HTML>
diff --git a/doc/pair_tersoff_zbl.txt b/doc/pair_tersoff_zbl.txt
index 34aa45a2c..ade09bd52 100644
--- a/doc/pair_tersoff_zbl.txt
+++ b/doc/pair_tersoff_zbl.txt
@@ -1,234 +1,234 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style tersoff/zbl command :h3
[Syntax:]
pair_style tersoff/zbl :pre
[Examples:]
pair_style tersoff/zbl
pair_coeff * * SiC.tersoff.zbl Si C Si :pre
[Description:]
The {tersoff/zbl} style computes a 3-body Tersoff potential
"(Tersoff_1)"_#Tersoff_1 with a close-separation pairwise modification
based on a Coulomb potential and the Ziegler-Biersack-Littmark
universal screening function "(ZBL)"_#ZBL, giving the energy E of a
system of atoms as
:c,image(Eqs/pair_tersoff_zbl.jpg)
The f_F term is a fermi-like function used to smoothly connect the ZBL
repulsive potential with the Tersoff potential. There are 2
parameters used to adjust it: A_F and r_C. A_F controls how "sharp"
the transition is between the two, and r_C is essentially the cutoff
for the ZBL potential.
For the ZBL portion, there are two terms. The first is the Coulomb
repulsive term, with Z1, Z2 as the number of protons in each nucleus,
e as the electron charge (1 for metal and real units) and epsilon0 as
the permittivity of vacuum. The second part is the ZBL universal
screening function, with a0 being the Bohr radius (typically 0.529
Angstroms), and the remainder of the coefficients provided by the
original paper. This screening function should be applicable to most
systems. However, it is only accurate for small separations
(i.e. less than 1 Angstrom).
For the Tersoff portion, f_R is a two-body term and f_A includes
three-body interactions. The summations in the formula are over all
neighbors J and K of atom I within a cutoff distance = R + D.
Only a single pair_coeff command is used with the {tersoff/zbl} style
which specifies a Tersoff/ZBL potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
filename
N element names = mapping of Tersoff/ZBL elements to atom types :ul
As an example, imagine the SiC.tersoff.zbl file has Tersoff/ZBL values
for Si and C. If your LAMMPS simulation has 4 atoms types and you
want the 1st 3 to be Si, and the 4th to be C, you would use the
following pair_coeff command:
pair_coeff * * SiC.tersoff Si Si Si C :pre
The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
element in the Tersoff/ZBL file. The final C argument maps LAMMPS
atom type 4 to the C element in the Tersoff/ZBL file. If a mapping
value is specified as NULL, the mapping is not performed. This can be
used when a {tersoff/zbl} potential is used as part of the {hybrid}
pair style. The NULL values are placeholders for atom types that will
be used with other potentials.
Tersoff/ZBL files in the {potentials} directory of the LAMMPS
distribution have a ".tersoff.zbl" suffix. Lines that are not blank
or comments (starting with #) define parameters for a triplet of
elements. The parameters in a single entry correspond to coefficients
in the formula above:
element 1 (the center atom in a 3-body interaction)
element 2 (the atom bonded to the center atom)
element 3 (the atom influencing the 1-2 bond in a bond-order sense)
m
gamma
lambda3 (1/distance units)
c
d
costheta0 (can be a value < -1 or > 1)
n
beta
lambda2 (1/distance units)
B (energy units)
R (distance units)
D (distance units)
lambda1 (1/distance units)
A (energy units)
Z_i
Z_j
ZBLcut (distance units)
ZBLexpscale (1/distance units) :ul
The n, beta, lambda2, B, lambda1, and A parameters are only used for
two-body interactions. The m, gamma, lambda3, c, d, and costheta0
parameters are only used for three-body interactions. The R and D
parameters are used for both two-body and three-body interactions. The
Z_i,Z_j, ZBLcut, ZBLexpscale parameters are used in the ZBL repulsive
portion of the potential and in the Fermi-like function. The
non-annotated parameters are unitless. The value of m must be 3 or 1.
The Tersoff/ZBL potential file must contain entries for all the
elements listed in the pair_coeff command. It can also contain
entries for additional elements not being used in a particular
simulation; LAMMPS ignores those entries.
For a single-element simulation, only a single entry is required
(e.g. SiSiSi). For a two-element simulation, the file must contain 8
entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that
specify Tersoff parameters for all permutations of the two elements
interacting in three-body configurations. Thus for 3 elements, 27
entries would be required, etc.
As annotated above, the first element in the entry is the center atom
in a three-body interaction and it is bonded to the 2nd atom and the
bond is influenced by the 3rd atom. Thus an entry for SiCC means Si
bonded to a C with another C atom influencing the bond. Thus
three-body parameters for SiCSi and SiSiC entries will not, in
general, be the same. The parameters used for the two-body
interaction come from the entry where the 2nd element is repeated.
Thus the two-body parameters for Si interacting with C, comes from the
SiCC entry. By symmetry, the twobody parameters in the SiCC and CSiSi
entries should thus be the same. The parameters used for a particular
three-body interaction come from the entry with the corresponding
three elements. The parameters used only for two-body interactions
(n, beta, lambda2, B, lambda1, and A) in entries whose 2nd and 3rd
element are different (e.g. SiCSi) are not used for anything and can
be set to 0.0 if desired.
We chose the above form so as to enable users to define all commonly
used variants of the Tersoff portion of the potential. In particular,
our form reduces to the original Tersoff form when m = 3 and gamma =
1, while it reduces to the form of "Albe et al."_#Albe when beta = 1
and m = 1. Note that in the current Tersoff implementation in LAMMPS,
m must be specified as either 3 or 1. Tersoff used a slightly
different but equivalent form for alloys, which we will refer to as
Tersoff_2 potential "(Tersoff_2)"_#Tersoff_2.
LAMMPS parameter values for Tersoff_2 can be obtained as follows:
gamma = 1, just as for Tersoff_1, but now lambda3 = 0 and the value of
m has no effect. The parameters for species i and j can be calculated
using the Tersoff_2 mixing rules:
:c,image(Eqs/pair_tersoff_2.jpg)
Values not shown are determined by the first atom type. Finally, the
Tersoff_2 parameters R and S must be converted to the LAMMPS
parameters R and D (R is different in both forms), using the following
relations: R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the
Tersoff_2 parameters.
In the potentials directory, the file SiCGe.tersoff provides the
LAMMPS parameters for Tersoff's various versions of Si, as well as his
alloy parameters for Si, C, and Ge. This file can be used for pure Si,
(three different versions), pure C, pure Ge, binary SiC, and binary
SiGe. LAMMPS will generate an error if this file is used with any
combination involving C and Ge, since there are no entries for the GeC
interactions (Tersoff did not publish parameters for this
cross-interaction.) Tersoff files are also provided for the SiC alloy
(SiC.tersoff) and the GaN (GaN.tersoff) alloys.
Many thanks to Rutuparna Narulkar, David Farrell, and Xiaowang Zhou
for helping clarify how Tersoff parameters for alloys have been
defined in various papers. Also thanks to Ram Devanathan for
providing the base ZBL implementation.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above from values in the potential file.
This pair style does not support the "pair_modify"_pair_modify.html
shift, table, and tail options.
This pair style does not write its information to "binary restart
files"_restart.html, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
-This pair style is part of the "manybody" package. It is only enabled
+This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default). See
the "Making LAMMPS"_Section_start.html#start_3 section for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
The Tersoff/ZBL potential files provided with LAMMPS (see the
potentials directory) are parameterized for metal "units"_units.html.
You can use the Tersoff potential with any LAMMPS units, but you would
need to create your own Tersoff potential file with coefficients
listed in the appropriate units if your simulation doesn't use "metal"
units.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Tersoff_1)
[(Tersoff_1)] J. Tersoff, Phys Rev B, 37, 6991 (1988).
:link(ZBL)
[(ZBL)] J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges
of Ions in Matter' Vol 1, 1985, Pergamon Press.
:link(Albe)
[(Albe)] J. Nord, K. Albe, P. Erhartand K. Nordlund, J. Phys.:
Condens. Matter, 15, 5649(2003).
:link(Tersoff_2)
[(Tersoff_2)] J. Tersoff, Phys Rev B, 39, 5566 (1989)
diff --git a/doc/pair_yukawa_colloid.html b/doc/pair_yukawa_colloid.html
index 4c5d472a4..cdd706450 100644
--- a/doc/pair_yukawa_colloid.html
+++ b/doc/pair_yukawa_colloid.html
@@ -1,128 +1,128 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style yukawa/colloid command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style yukawa/colloid kappa cutoff
</PRE>
<UL><LI>kappa = screening length (inverse distance units)
<LI>cutoff = global cutoff for colloidal Yukawa interactions (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style yukawa/colloid 2.0 2.5
pair_coeff 1 1 100.0 2.3
pair_coeff * * 100.0
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>yukawa/colloid</I> computes pairwise interactions with the formula
</P>
<CENTER><IMG SRC = "Eqs/pair_yukawa_colloid.jpg">
</CENTER>
<P>where Ri and Rj are the radii of the two particles and Rc is the
cutoff.
</P>
<P>In contrast to <A HREF = "pair_yukawa.html">pair_style yukawa</A>, this functional
form arises from the Coulombic interaction between two colloid
particles, screened due to the presence of an electrolyte.
<A HREF = "pair_yukawa.html">Pair_style yukawa</A> is a screened Coulombic potential
between two point-charges and uses no such approximation.
</P>
<P>This potential applies to nearby particle pairs for which the Derjagin
approximation holds, meaning h << Ri + Rj, where h is the
surface-to-surface separation of the two particles.
</P>
<P>When used in combination with <A HREF = "pair_colloid.html">pair_style colloid</A>,
the two terms become the so-called DLVO potential, which combines
electrostatic repulsion and van der Waals attraction.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
</P>
<UL><LI>A (energy/distance units)
<LI>cutoff (distance units)
</UL>
<P>The prefactor A is determined from the relationship between surface
charge and surface potential due to the presence of electrolyte. Note
that the A for this potential style has different units than the A
used in <A HREF = "pair_yukawa.html">pair_style yukawa</A>. For low surface
potentials, i.e. less than about 25 mV, A can be written as:
</P>
<PRE>A = 2 * PI * R*eps*eps0 * kappa * psi^2
</PRE>
<P>where
</P>
<UL><LI>R = colloid radius (distance units)
<LI>eps0 = permittivity of free space (charge^2/energy/distance units)
<LI>eps = relative permittivity of fluid medium (dimensionless)
<LI>kappa = inverse screening length (1/distance units)
<LI>psi = surface potential (energy/charge units)
</UL>
<P>The last coefficient is optional. If not specified, the global
yukawa/colloid cutoff is used.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the A coefficient and cutoff
distance for this pair style can be mixed. A is an energy value mixed
like a LJ epsilon. The default mix value is <I>geometric</I>. See the
"pair_modify" command for details.
</P>
<P>This pair style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
option for the energy of the pair interaction.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
for this pair style.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding long-range tail corrections to energy and
pressure.
</P>
<P>This pair style writes its information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>This style is part of the "colloid" package. It is only enabled if
+<P>This style is part of the COLLOID package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>This pair style requires that atoms be finite-size spheres with a
diameter, as defined by the <A HREF = "atom_style.html">atom_style sphere</A>
command.
</P>
<P>Per-particle polydispersity is not yet supported by this pair style;
per-type polydispersity is allowed. This means all particles of the
same type must have the same diameter. Each type can have a different
diameter.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/pair_yukawa_colloid.txt b/doc/pair_yukawa_colloid.txt
index 4cce25340..ee09adf69 100644
--- a/doc/pair_yukawa_colloid.txt
+++ b/doc/pair_yukawa_colloid.txt
@@ -1,123 +1,123 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style yukawa/colloid command :h3
[Syntax:]
pair_style yukawa/colloid kappa cutoff :pre
kappa = screening length (inverse distance units)
cutoff = global cutoff for colloidal Yukawa interactions (distance units) :ul
[Examples:]
pair_style yukawa/colloid 2.0 2.5
pair_coeff 1 1 100.0 2.3
pair_coeff * * 100.0 :pre
[Description:]
Style {yukawa/colloid} computes pairwise interactions with the formula
:c,image(Eqs/pair_yukawa_colloid.jpg)
where Ri and Rj are the radii of the two particles and Rc is the
cutoff.
In contrast to "pair_style yukawa"_pair_yukawa.html, this functional
form arises from the Coulombic interaction between two colloid
particles, screened due to the presence of an electrolyte.
"Pair_style yukawa"_pair_yukawa.html is a screened Coulombic potential
between two point-charges and uses no such approximation.
This potential applies to nearby particle pairs for which the Derjagin
approximation holds, meaning h << Ri + Rj, where h is the
surface-to-surface separation of the two particles.
When used in combination with "pair_style colloid"_pair_colloid.html,
the two terms become the so-called DLVO potential, which combines
electrostatic repulsion and van der Waals attraction.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
A (energy/distance units)
cutoff (distance units) :ul
The prefactor A is determined from the relationship between surface
charge and surface potential due to the presence of electrolyte. Note
that the A for this potential style has different units than the A
used in "pair_style yukawa"_pair_yukawa.html. For low surface
potentials, i.e. less than about 25 mV, A can be written as:
A = 2 * PI * R*eps*eps0 * kappa * psi^2 :pre
where
R = colloid radius (distance units)
eps0 = permittivity of free space (charge^2/energy/distance units)
eps = relative permittivity of fluid medium (dimensionless)
kappa = inverse screening length (1/distance units)
psi = surface potential (energy/charge units) :ul
The last coefficient is optional. If not specified, the global
yukawa/colloid cutoff is used.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the A coefficient and cutoff
distance for this pair style can be mixed. A is an energy value mixed
like a LJ epsilon. The default mix value is {geometric}. See the
"pair_modify" command for details.
This pair style supports the "pair_modify"_pair_modify.html shift
option for the energy of the pair interaction.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
This pair style does not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
-This style is part of the "colloid" package. It is only enabled if
+This style is part of the COLLOID package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
This pair style requires that atoms be finite-size spheres with a
diameter, as defined by the "atom_style sphere"_atom_style.html
command.
Per-particle polydispersity is not yet supported by this pair style;
per-type polydispersity is allowed. This means all particles of the
same type must have the same diameter. Each type can have a different
diameter.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
diff --git a/doc/prd.html b/doc/prd.html
index ae9cbcda4..270a48c0a 100644
--- a/doc/prd.html
+++ b/doc/prd.html
@@ -1,314 +1,314 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>prd command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>prd N t_event n_dephase t_dephase t_correlate compute-ID seed keyword value ...
</PRE>
<UL><LI>N = # of timesteps to run (not including dephasing/quenching)
<LI>t_event = timestep interval between event checks
<LI>n_dephase = number of velocity randomizations to perform in each dephase run
<LI>t_dephase = number of timesteps to run dynamics after each velocity randomization during dephase
<LI>t_correlate = number of timesteps within which 2 consecutive events are considered to be correlated
<LI>compute-ID = ID of the compute used for event detection
<LI>random_seed = random # seed (positive integer)
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>min</I> or <I>temp</I> or <I>vel</I>
<PRE> <I>min</I> values = etol ftol maxiter maxeval
etol = stopping tolerance for energy, used in quenching
ftol = stopping tolerance for force, used in quenching
maxiter = max iterations of minimize, used in quenching
maxeval = max number of force/energy evaluations, used in quenching
<I>temp</I> value = Tdephase
Tdephase = target temperature for velocity randomization, used in dephasing
<I>vel</I> values = loop dist
loop = <I>all</I> or <I>local</I> or <I>geom</I>, used in dephasing
dist = <I>uniform</I> or <I>gaussian</I>, used in dephasing
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>prd 5000 100 10 10 100 1 54982
prd 5000 100 10 10 100 1 54982 min 0.1 0.1 100 200
</PRE>
<P><B>Description:</B>
</P>
<P>Run a parallel replica dynamics (PRD) simulation using multiple
replicas of a system. One or more replicas can be used.
</P>
<P>PRD is described in <A HREF = "#Voter">this paper</A> by Art Voter. It is a method
for performing accelerated dynamics that is suitable for
infrequent-event systems that obey first-order kinetics. A good
overview of accelerated dynamics methods for such systems in given in
<A HREF = "#Voter2">this review paper</A> from the same group. To quote from the
paper: "The dynamical evolution is characterized by vibrational
excursions within a potential basin, punctuated by occasional
transitions between basins." The transition probability is
characterized by p(t) = k*exp(-kt) where k is the rate constant.
Running multiple replicas gives an effective enhancement in the
timescale spanned by the multiple simulations, while waiting for an
event to occur.
</P>
<P>Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
switch; see <A HREF = "Section_start.html#start_6">this section</A> of the manual.
Note that if you have MPI installed, you can run a multi-replica
simulation with more replicas (partitions) than you have physical
processors, e.g you can run a 10-replica simulation on one or two
processors. For PRD, this makes little sense, since this offers no
effective parallel speed-up in searching for infrequent events. See
<A HREF = "Section_howto.html#howto_5">this section</A> of the manual for further
discussion.
</P>
<P>When a PRD simulation is performed, it is assumed that each replica is
running the same model, though LAMMPS does not check for this.
I.e. the simulation domain, the number of atoms, the interaction
potentials, etc should be the same for every replica.
</P>
<P>A PRD run has several stages, which are repeated each time an "event"
occurs in one of the replicas, as defined below. The logic for a PRD
run is as follows:
</P>
<PRE>while (time remains):
dephase for n_dephase*t_dephase steps
until (event occurs on some replica):
run dynamics for t_event steps
quench
check for uncorrelated event on any replica
until (no correlated event occurs):
run dynamics for t_correlate steps
quench
check for correlated event on this replica
event replica shares state with all replicas
</PRE>
<P>Before this loop begins, the state of the system on replica 0 is
shared with all replicas, so that all replicas begin from the same
initial state. The first potential energy basin is identified by
quenching (an energy minimization, see below) the initial state and
storing the resulting coordinates for reference.
</P>
<P>In the first stage, dephasing is performed by each replica
independently to eliminate correlations between replicas. This is
done by choosing a random set of velocities, based on the
<I>random_seed</I> that is specified, and running <I>t_dephase</I> timesteps of
dynamics. This is repeated <I>n_dephase</I> times. If the <I>temp</I> keyword
is not specified, the target temperature for velocity randomization
for each replica is the current temperature of that replica.
Otherwise, it is the specified <I>Tdephase</I> temperature. The style of
velocity randomization is controlled using the keyword <I>vel</I> with
arguments that have the same meaning as their counterparts in the
<A HREF = "velocity.html">velocity</A> command.
</P>
<P>In the second stage, each replica runs dynamics continuously, stopping
every <I>t_event</I> steps to check if a transition event has occurred.
This check is performed by quenching the system and comparing the
resulting atom coordinates to the coordinates from the previous basin.
The first time through the PRD loop, the "previous basin" is the set
of quenched coordinates from the initial state of the system.
</P>
<P>A quench is an energy minimization and is performed by whichever
algorithm has been defined by the <A HREF = "min_style.html">min_style</A> command.
Minimization parameters may be set via the
<A HREF = "min_modify.html">min_modify</A> command and by the <I>min</I> keyword of the
PRD command. The latter are the settings that would be used with the
<A HREF = "minimize.html">minimize</A> command. Note that typically, you do not
need to perform a highly-converged minimization to detect a transition
event.
</P>
<P>The event check is performed by a compute with the specified
<I>compute-ID</I>. Currently there is only one compute that works with the
PRD commmand, which is the <A HREF = "compute_event_displace.html">compute
event/displace</A> command. Other
event-checking computes may be added. <A HREF = "compute_event_displace.html">Compute
event/displace</A> checks whether any atom in
the compute group has moved further than a specified threshold
distance. If so, an "event" has occurred.
</P>
<P>In the third stage, the replica on which the event occurred (event
replica) continues to run dynamics to search for correlated events.
This is done by running dynamics for <I>t_correlate</I> steps, quenching
every <I>t_event</I> steps, and checking if another event has occurred.
The first time no correlated event occurs, the final state of the
event replica is shared with all replicas, the new basin reference
coordinates are updated with the quenched state, and the outer loop
begins again. While the replica event is searching for correlated
events, all the other replicas also run dynamics and event checking
with the same schedule, but the final states are always overwritten by
the state of the event replica.
</P>
<HR>
<P>Four kinds of output can be generated during a PRD run: event
statistics, thermodynamic output by each replica, dump files, and
restart files.
</P>
<P>When running with multiple partitions (each of which is a replica in
this case), the print-out to the screen and master log.lammps file is
limited to event statistics. Note that if a PRD run is performed on
only a single replica then the event statistics will be intermixed
with the usual thermodynamic output discussed below.
</P>
<P>The quantities printed each time an event occurs are the timestep,
CPU time, clock, event number, a correlation flag,
the number of coincident events, and the replica number of the chosen event.
</P>
<P>The timestep is the usual LAMMPS timestep, except that time does not
advance during dephasing or quenches, but only during dynamics. Note
that are two kinds of dynamics in the PRD loop listed above. The
first is when all replicas are performing independent dynamics. The
second is when correlated events are being searched for and only one
replica is running dynamics.
</P>
<P>The CPU time is the total processor time since the start of the PRD
run.
</P>
<P>The clock is the same as the timestep except that it advances by M
steps every timestep during the first kind of dynamics when the M
replicas are running independently. The clock represents the real
time that effectively elapses during a PRD simulation of <I>N</I> steps on
M replicas. If most of the PRD run is spent in the second stage of
the loop above, searching for infrequent events, then the clock will
advance nearly N*M steps. Note the clock time between events will be
drawn from p(t).
</P>
<P>The event number is a counter that increments with each event, whether
it is uncorrelated or correlated.
</P>
<P>The correlation flag will be 0 when an uncorrelated event occurs
during the second stage of the loop listed above, i.e. when all
replicas are running independently. The correlation flag will be 1
when a correlated event occurs during the third stage of the loop
listed above, i.e. when only one replica is running dynamics.
</P>
<P>When more than one replica detects an event at the end of the second
stage, then one of them is chosen at random. The number of coincident
events is the number of replicas that detected an event. Normally, we
expect this value to be 1. If it is often greater than 1, then either
the number of replicas is too large, or <I>t_event</I> is too large.
</P>
<P>The replica number is the ID of the replica (from 0 to M-1) that
found the event.
</P>
<HR>
<P>When running on multiple partitions, LAMMPS produces additional log
files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For
the PRD command, these contain the thermodynamic output for each
replica. You will see short runs and minimizations corresponding to
the dynamics and quench operations of the loop listed above. The
timestep will be reset aprpopriately depending on whether the
operation advances time or not.
</P>
<P>After the PRD command completes, timing statistics for the PRD run are
printed in each replica's log file, giving a breakdown of how much CPU
time was spent in each stage (dephasing, dynamics, quenching, etc).
</P>
<HR>
<P>Any <A HREF = "dump.html">dump files</A> defined in the input script, will be
written to during a PRD run at timesteps corresponding to both
uncorrelated and correlated events. This means the the requested dump
frequency in the <A HREF = "dump.html">dump</A> command is ignored. There will be
one dump file (per dump command) created for all partitions.
</P>
<P>The atom coordinates of the dump snapshot are those of the minimum
energy configuration resulting from quenching following a transition
event. The timesteps written into the dump files correspond to the
timestep at which the event occurred and NOT the clock. A dump
snapshot corresponding to the initial minimum state used for event
detection is written to the dump file at the beginning of each PRD
run.
</P>
<HR>
<P>If the <A HREF = "restart.html">restart</A> command is used, a single restart file
for all the partitions is generated, which allows a PRD run to be
continued by a new input script in the usual manner.
</P>
<P>The restart file is generated at the end of the loop listed above. If
no correlated events are found, this means it contains a snapshot of
the system at time T + <I>t_correlate</I>, where T is the time at which the
uncorrelated event occurred. If correlated events were found, then it
contains a snapshot of the system at time T + <I>t_correlate</I>, where T
is the time of the last correlated event.
</P>
<P>The restart frequency specified in the <A HREF = "restart.html">restart</A> command
is interpreted differently when performing a PRD run. It does not
mean the timestep interval between restart files. Instead it means an
event interval for uncorrelated events. Thus a frequency of 1 means
write a restart file every time an uncorrelated event occurs. A
frequency of 10 means write a restart file every 10th uncorrelated
event.
</P>
<P>When an input script reads a restart file from a previous PRD run, the
new script can be run on a different number of replicas or processors.
However, it is assumed that <I>t_correlate</I> in the new PRD command is
the same as it was previously. If not, the calculation of the "clock"
value for the first event in the new run will be slightly off.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>This command can only be used if LAMMPS was built with the "replica"
+<P>This command can only be used if LAMMPS was built with the REPLICA
package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info on packages.
</P>
<P><I>N</I> and <I>t_correlate</I> settings must be integer multiples of
<I>t_event</I>.
</P>
<P>Runs restarted from restart file written during a PRD run will not
produce identical results due to changes in the random numbers used
for dephasing.
</P>
<P>This command cannot be used when any fixes are defined that keep track
of elapsed time to perform time-dependent operations. Examples
include the "ave" fixes such as <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A>. Also <A HREF = "fix_dt_reset.html">fix
dt/reset</A> and <A HREF = "fix_deposit.html">fix deposit</A>.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_event_displace.html">compute event/displace</A>,
<A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_style.html">min_style</A>,
<A HREF = "run_style.html">run_style</A>, <A HREF = "minimize.html">minimize</A>,
<A HREF = "velocity.html">velocity</A>, <A HREF = "temper.html">temper</A>, <A HREF = "neb.html">neb</A>,
<A HREF = "tad.html">tad</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are <I>min</I> = 0.1 0.1 40 50, no <I>temp</I> setting, and
<I>vel</I> = <I>geom</I> <I>gaussian</I>.
</P>
<HR>
<A NAME = "Voter"></A>
<P><B>(Voter)</B> Voter, Phys Rev B, 57, 13985 (1998).
</P>
<A NAME = "Voter2"></A>
<P><B>(Voter2)</B> Voter, Montalenti, Germann, Annual Review of Materials
Research 32, 321 (2002).
</P>
</HTML>
diff --git a/doc/prd.txt b/doc/prd.txt
index 52f6820d8..33130c17b 100644
--- a/doc/prd.txt
+++ b/doc/prd.txt
@@ -1,297 +1,297 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
prd command :h3
[Syntax:]
prd N t_event n_dephase t_dephase t_correlate compute-ID seed keyword value ... :pre
N = # of timesteps to run (not including dephasing/quenching) :ulb,l
t_event = timestep interval between event checks :l
n_dephase = number of velocity randomizations to perform in each dephase run :l
t_dephase = number of timesteps to run dynamics after each velocity randomization during dephase :l
t_correlate = number of timesteps within which 2 consecutive events are considered to be correlated :l
compute-ID = ID of the compute used for event detection :l
random_seed = random # seed (positive integer) :l
zero or more keyword/value pairs may be appended :l
keyword = {min} or {temp} or {vel} :l
{min} values = etol ftol maxiter maxeval
etol = stopping tolerance for energy, used in quenching
ftol = stopping tolerance for force, used in quenching
maxiter = max iterations of minimize, used in quenching
maxeval = max number of force/energy evaluations, used in quenching
{temp} value = Tdephase
Tdephase = target temperature for velocity randomization, used in dephasing
{vel} values = loop dist
loop = {all} or {local} or {geom}, used in dephasing
dist = {uniform} or {gaussian}, used in dephasing :pre
:ule
[Examples:]
prd 5000 100 10 10 100 1 54982
prd 5000 100 10 10 100 1 54982 min 0.1 0.1 100 200 :pre
[Description:]
Run a parallel replica dynamics (PRD) simulation using multiple
replicas of a system. One or more replicas can be used.
PRD is described in "this paper"_#Voter by Art Voter. It is a method
for performing accelerated dynamics that is suitable for
infrequent-event systems that obey first-order kinetics. A good
overview of accelerated dynamics methods for such systems in given in
"this review paper"_#Voter2 from the same group. To quote from the
paper: "The dynamical evolution is characterized by vibrational
excursions within a potential basin, punctuated by occasional
transitions between basins." The transition probability is
characterized by p(t) = k*exp(-kt) where k is the rate constant.
Running multiple replicas gives an effective enhancement in the
timescale spanned by the multiple simulations, while waiting for an
event to occur.
Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
switch; see "this section"_Section_start.html#start_6 of the manual.
Note that if you have MPI installed, you can run a multi-replica
simulation with more replicas (partitions) than you have physical
processors, e.g you can run a 10-replica simulation on one or two
processors. For PRD, this makes little sense, since this offers no
effective parallel speed-up in searching for infrequent events. See
"this section"_Section_howto.html#howto_5 of the manual for further
discussion.
When a PRD simulation is performed, it is assumed that each replica is
running the same model, though LAMMPS does not check for this.
I.e. the simulation domain, the number of atoms, the interaction
potentials, etc should be the same for every replica.
A PRD run has several stages, which are repeated each time an "event"
occurs in one of the replicas, as defined below. The logic for a PRD
run is as follows:
while (time remains):
dephase for n_dephase*t_dephase steps
until (event occurs on some replica):
run dynamics for t_event steps
quench
check for uncorrelated event on any replica
until (no correlated event occurs):
run dynamics for t_correlate steps
quench
check for correlated event on this replica
event replica shares state with all replicas :pre
Before this loop begins, the state of the system on replica 0 is
shared with all replicas, so that all replicas begin from the same
initial state. The first potential energy basin is identified by
quenching (an energy minimization, see below) the initial state and
storing the resulting coordinates for reference.
In the first stage, dephasing is performed by each replica
independently to eliminate correlations between replicas. This is
done by choosing a random set of velocities, based on the
{random_seed} that is specified, and running {t_dephase} timesteps of
dynamics. This is repeated {n_dephase} times. If the {temp} keyword
is not specified, the target temperature for velocity randomization
for each replica is the current temperature of that replica.
Otherwise, it is the specified {Tdephase} temperature. The style of
velocity randomization is controlled using the keyword {vel} with
arguments that have the same meaning as their counterparts in the
"velocity"_velocity.html command.
In the second stage, each replica runs dynamics continuously, stopping
every {t_event} steps to check if a transition event has occurred.
This check is performed by quenching the system and comparing the
resulting atom coordinates to the coordinates from the previous basin.
The first time through the PRD loop, the "previous basin" is the set
of quenched coordinates from the initial state of the system.
A quench is an energy minimization and is performed by whichever
algorithm has been defined by the "min_style"_min_style.html command.
Minimization parameters may be set via the
"min_modify"_min_modify.html command and by the {min} keyword of the
PRD command. The latter are the settings that would be used with the
"minimize"_minimize.html command. Note that typically, you do not
need to perform a highly-converged minimization to detect a transition
event.
The event check is performed by a compute with the specified
{compute-ID}. Currently there is only one compute that works with the
PRD commmand, which is the "compute
event/displace"_compute_event_displace.html command. Other
event-checking computes may be added. "Compute
event/displace"_compute_event_displace.html checks whether any atom in
the compute group has moved further than a specified threshold
distance. If so, an "event" has occurred.
In the third stage, the replica on which the event occurred (event
replica) continues to run dynamics to search for correlated events.
This is done by running dynamics for {t_correlate} steps, quenching
every {t_event} steps, and checking if another event has occurred.
The first time no correlated event occurs, the final state of the
event replica is shared with all replicas, the new basin reference
coordinates are updated with the quenched state, and the outer loop
begins again. While the replica event is searching for correlated
events, all the other replicas also run dynamics and event checking
with the same schedule, but the final states are always overwritten by
the state of the event replica.
:line
Four kinds of output can be generated during a PRD run: event
statistics, thermodynamic output by each replica, dump files, and
restart files.
When running with multiple partitions (each of which is a replica in
this case), the print-out to the screen and master log.lammps file is
limited to event statistics. Note that if a PRD run is performed on
only a single replica then the event statistics will be intermixed
with the usual thermodynamic output discussed below.
The quantities printed each time an event occurs are the timestep,
CPU time, clock, event number, a correlation flag,
the number of coincident events, and the replica number of the chosen event.
The timestep is the usual LAMMPS timestep, except that time does not
advance during dephasing or quenches, but only during dynamics. Note
that are two kinds of dynamics in the PRD loop listed above. The
first is when all replicas are performing independent dynamics. The
second is when correlated events are being searched for and only one
replica is running dynamics.
The CPU time is the total processor time since the start of the PRD
run.
The clock is the same as the timestep except that it advances by M
steps every timestep during the first kind of dynamics when the M
replicas are running independently. The clock represents the real
time that effectively elapses during a PRD simulation of {N} steps on
M replicas. If most of the PRD run is spent in the second stage of
the loop above, searching for infrequent events, then the clock will
advance nearly N*M steps. Note the clock time between events will be
drawn from p(t).
The event number is a counter that increments with each event, whether
it is uncorrelated or correlated.
The correlation flag will be 0 when an uncorrelated event occurs
during the second stage of the loop listed above, i.e. when all
replicas are running independently. The correlation flag will be 1
when a correlated event occurs during the third stage of the loop
listed above, i.e. when only one replica is running dynamics.
When more than one replica detects an event at the end of the second
stage, then one of them is chosen at random. The number of coincident
events is the number of replicas that detected an event. Normally, we
expect this value to be 1. If it is often greater than 1, then either
the number of replicas is too large, or {t_event} is too large.
The replica number is the ID of the replica (from 0 to M-1) that
found the event.
:line
When running on multiple partitions, LAMMPS produces additional log
files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For
the PRD command, these contain the thermodynamic output for each
replica. You will see short runs and minimizations corresponding to
the dynamics and quench operations of the loop listed above. The
timestep will be reset aprpopriately depending on whether the
operation advances time or not.
After the PRD command completes, timing statistics for the PRD run are
printed in each replica's log file, giving a breakdown of how much CPU
time was spent in each stage (dephasing, dynamics, quenching, etc).
:line
Any "dump files"_dump.html defined in the input script, will be
written to during a PRD run at timesteps corresponding to both
uncorrelated and correlated events. This means the the requested dump
frequency in the "dump"_dump.html command is ignored. There will be
one dump file (per dump command) created for all partitions.
The atom coordinates of the dump snapshot are those of the minimum
energy configuration resulting from quenching following a transition
event. The timesteps written into the dump files correspond to the
timestep at which the event occurred and NOT the clock. A dump
snapshot corresponding to the initial minimum state used for event
detection is written to the dump file at the beginning of each PRD
run.
:line
If the "restart"_restart.html command is used, a single restart file
for all the partitions is generated, which allows a PRD run to be
continued by a new input script in the usual manner.
The restart file is generated at the end of the loop listed above. If
no correlated events are found, this means it contains a snapshot of
the system at time T + {t_correlate}, where T is the time at which the
uncorrelated event occurred. If correlated events were found, then it
contains a snapshot of the system at time T + {t_correlate}, where T
is the time of the last correlated event.
The restart frequency specified in the "restart"_restart.html command
is interpreted differently when performing a PRD run. It does not
mean the timestep interval between restart files. Instead it means an
event interval for uncorrelated events. Thus a frequency of 1 means
write a restart file every time an uncorrelated event occurs. A
frequency of 10 means write a restart file every 10th uncorrelated
event.
When an input script reads a restart file from a previous PRD run, the
new script can be run on a different number of replicas or processors.
However, it is assumed that {t_correlate} in the new PRD command is
the same as it was previously. If not, the calculation of the "clock"
value for the first event in the new run will be slightly off.
:line
[Restrictions:]
-This command can only be used if LAMMPS was built with the "replica"
+This command can only be used if LAMMPS was built with the REPLICA
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info on packages.
{N} and {t_correlate} settings must be integer multiples of
{t_event}.
Runs restarted from restart file written during a PRD run will not
produce identical results due to changes in the random numbers used
for dephasing.
This command cannot be used when any fixes are defined that keep track
of elapsed time to perform time-dependent operations. Examples
include the "ave" fixes such as "fix
ave/spatial"_fix_ave_spatial.html. Also "fix
dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposit.html.
[Related commands:]
"compute event/displace"_compute_event_displace.html,
"min_modify"_min_modify.html, "min_style"_min_style.html,
"run_style"_run_style.html, "minimize"_minimize.html,
"velocity"_velocity.html, "temper"_temper.html, "neb"_neb.html,
"tad"_tad.html
[Default:]
The option defaults are {min} = 0.1 0.1 40 50, no {temp} setting, and
{vel} = {geom} {gaussian}.
:line
:link(Voter)
[(Voter)] Voter, Phys Rev B, 57, 13985 (1998).
:link(Voter2)
[(Voter2)] Voter, Montalenti, Germann, Annual Review of Materials
Research 32, 321 (2002).
diff --git a/doc/read_data.html b/doc/read_data.html
index 1bfc95bbb..bd2e87918 100644
--- a/doc/read_data.html
+++ b/doc/read_data.html
@@ -1,733 +1,737 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>read_data command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>read_data file
</PRE>
<UL><LI>file = name of data file to read in
</UL>
<P><B>Examples:</B>
</P>
<PRE>read_data data.lj
read_data ../run7/data.polymer.gz
</PRE>
<P><B>Description:</B>
</P>
<P>Read in a data file containing information LAMMPS needs to run a
simulation. The file can be ASCII text or a gzipped text file
(detected by a .gz suffix). This is one of 3 ways to specify initial
atom coordinates; see the <A HREF = "read_restart.html">read_restart</A> and
<A HREF = "create_atoms.html">create_atoms</A> commands for alternative methods.
</P>
<P>The structure of the data file is important, though many settings and
sections are optional or can come in any order. See the examples
directory for sample data files for different problems.
</P>
<P>A data file has a header and a body. The header appears first. The
first line of the header is always skipped; it typically contains a
description of the file. Then lines are read one at a time. Lines
can have a trailing comment starting with '#' that is ignored. If the
line is blank (only whitespace after comment is deleted), it is
skipped. If the line contains a header keyword, the corresponding
value(s) is read from the line. If it doesn't contain a header
keyword, the line begins the body of the file.
</P>
<P>The body of the file contains zero or more sections. The first line
of a section has only a keyword. The next line is skipped. The
remaining lines of the section contain values. The number of lines
depends on the section keyword as described below. Zero or more blank
lines can be used between sections. Sections can appear in any order,
with a few exceptions as noted below.
</P>
<P>The formatting of individual lines in the data file (indentation,
spacing between words and numbers) is not important except that header
and section keywords (e.g. atoms, xlo xhi, Masses, Bond Coeffs) must
be capitalized as shown and can't have extra white space between their
words - e.g. two spaces or a tab between "Bond" and "Coeffs" is not
valid.
</P>
<HR>
<P>These are the recognized header keywords. Header lines can come in
any order. The value(s) are read from the beginning of the line.
Thus the keyword <I>atoms</I> should be in a line like "1000 atoms"; the
keyword <I>ylo yhi</I> should be in a line like "-10.0 10.0 ylo yhi"; the
keyword <I>xy xz yz</I> should be in a line like "0.0 5.0 6.0 xy xz yz".
All these settings have a default value of 0, except the lo/hi box
size defaults are -0.5 and 0.5. A line need only appear if the value
is different than the default.
</P>
<UL><LI><I>atoms</I> = # of atoms in system
<LI><I>bonds</I> = # of bonds in system
<LI><I>angles</I> = # of angles in system
<LI><I>dihedrals</I> = # of dihedrals in system
<LI><I>impropers</I> = # of impropers in system
<LI><I>atom types</I> = # of atom types in system
<LI><I>bond types</I> = # of bond types in system
<LI><I>angle types</I> = # of angle types in system
<LI><I>dihedral types</I> = # of dihedral types in system
<LI><I>improper types</I> = # of improper types in system
<LI><I>extra bond per atom</I> = leave space for this many new bonds per atom
<LI><I>ellipsoids</I> = # of ellipsoids in system
<LI><I>xlo xhi</I> = simulation box boundaries in x dimension
<LI><I>ylo yhi</I> = simulation box boundaries in y dimension
<LI><I>zlo zhi</I> = simulation box boundaries in z dimension
<LI><I>xy xz yz</I> = simulation box tilt factors for triclinic system
</UL>
<P>The initial simulation box size is determined by the lo/hi settings.
In any dimension, the system may be periodic or non-periodic; see the
<A HREF = "boundary.html">boundary</A> command.
</P>
<P>If the <I>xy xz yz</I> line does not appear, LAMMPS will set up an
axis-aligned (orthogonal) simulation box. If the line does appear,
LAMMPS creates a non-orthogonal simulation domain shaped as a
parallelepiped with triclinic symmetry. The parallelepiped has its
"origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting
from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C =
(xz,yz,zhi-zlo). <I>Xy,xz,yz</I> can be 0.0 or positive or negative values
and are called "tilt factors" because they are the amount of
displacement applied to faces of an originally orthogonal box to
transform it into the parallelepiped.
</P>
<P>The tilt factors (xy,xz,yz) can not skew the box more than half the
distance of the corresponding parallel box length. For example, if
xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt
factor must be between -5 and 5. Similarly, both xz and yz must be
between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a
limitation, since if the maximum tilt factor is 5 (as in this
example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
... are all geometrically equivalent.
</P>
<P>See <A HREF = "Section_howto.html#howto_12">this section</A> of the doc pages for a
geometric description of triclinic boxes, as defined by LAMMPS, and
how to transform these parameters to and from other commonly used
triclinic representations.
</P>
<P>When a triclinic system is used, the simulation domain must be
periodic in any dimensions with a non-zero tilt factor, as defined by
the <A HREF = "boundary.html">boundary</A> command. I.e. if the xy tilt factor is
non-zero, then both the x and y dimensions must be periodic.
Similarly, x and z must be periodic if xz is non-zero and y and z must
be periodic if yz is non-zero. Also note that if your simulation will
tilt the box, e.g. via the <A HREF = "fix_deform.html">fix deform</A> command, the
simulation box must be defined as triclinic, even if the tilt factors
are initially 0.0.
</P>
<P>For 2d simulations, the <I>zlo zhi</I> values should be set to bound the z
coords for atoms that appear in the file; the default of -0.5 0.5 is
valid if all z coords are 0.0. For 2d triclinic simulations, the xz
and yz tilt factors must be 0.0.
</P>
<P>If the system is periodic (in a dimension), then atom coordinates can
be outside the bounds (in that dimension); they will be remapped (in a
periodic sense) back inside the box.
</P>
<P>IMPORTANT NOTE: If the system is non-periodic (in a dimension), then
all atoms in the data file must have coordinates (in that dimension)
that are "greater than or equal to" the lo value and "less than or
equal to" the hi value. If the non-periodic dimension is of style
"fixed" (see the <A HREF = "boundary.html">boundary</A> command), then the atom
coords must be strictly "less than" the hi value, due to the way
LAMMPS assign atoms to processors. Note that you should not make the
lo/hi values radically smaller/larger than the extent of the atoms.
For example, if your atoms extend from 0 to 50, you should not specify
the box bounds as -10000 and 10000. This is because LAMMPS uses the
specified box size to layout the 3d grid of processors. A huge
(mostly empty) box will be sub-optimal for performance when using
"fixed" boundary conditions (see the <A HREF = "boundary.html">boundary</A>
command). When using "shrink-wrap" boundary conditions (see the
<A HREF = "boundary.html">boundary</A> command), a huge (mostly empty) box may cause
a parallel simulation to lose atoms the first time that LAMMPS
shrink-wraps the box around the atoms.
</P>
<P>The "extra bond per atom" setting should be used if new bonds will be
added to the system when a simulation runs, e.g. by using the <A HREF = "fix_bond_create.html">fix
bond/create</A> command. This will pre-allocate
space in LAMMPS data structures for storing the new bonds.
</P>
<P>The "ellipsoids<A HREF = "atom_style.html"> setting is only used with atom_style
ellipsoid</A> and specifies how many of the atoms are
finite-size ellipsoids; the remainder are point particles. See the
discussion of ellipseflag and the <I>Ellipsoids</I> section below.
</P>
<HR>
<P>These are the section keywords for the body of the file.
</P>
<UL><LI><I>Atoms, Velocities, Ellipsoids, Masses</I> = atom-property sections
<LI><I>Bonds, Angles, Dihedrals, Impropers</I> = molecular topology sections
<LI><I>Pair Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs</I> = force field sections
<LI><I>BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, BondBond13 Coeffs, AngleAngle Coeffs</I> = class 2 force field sections
</UL>
<P>Each section is listed below in alphabetic order. The format of each
section is described including the number of lines it must contain and
rules (if any) for where it can appear in the data file.
</P>
<P>Any individual line in the various sections can have a trailing
comment starting with "#" for annotation purposes. E.g. in the
Atoms section:
</P>
<PRE>10 1 17 -1.0 10.0 5.0 6.0 # salt ion
</PRE>
<HR>
<P><I>Angle Coeffs</I> section:
</P>
<UL><LI>one line per angle type
<LI>line syntax: ID coeffs
<PRE> ID = angle type (1-N)
coeffs = list of coeffs
</PRE>
<LI>example:
<PRE> 6 70 108.5 0 0
</PRE>
</UL>
<P>The number and meaning of the coefficients are specific to the defined
angle style. See the <A HREF = "angle_style.html">angle_style</A> and
<A HREF = "angle_coeff.html">angle_coeff</A> commands for details. Coefficients can
also be set via the <A HREF = "angle_coeff.html">angle_coeff</A> command in the
input script.
</P>
<HR>
<P><I>AngleAngle Coeffs</I> section:
</P>
<UL><LI>one line per improper type
<LI>line syntax: ID coeffs
<PRE> ID = improper type (1-N)
coeffs = list of coeffs (see <A HREF = "improper_coeff.html">improper_coeff</A>)
</PRE>
</UL>
<HR>
<P><I>AngleAngleTorsion Coeffs</I> section:
</P>
<UL><LI>one line per dihedral type
<LI>line syntax: ID coeffs
<PRE> ID = dihedral type (1-N)
coeffs = list of coeffs (see <A HREF = "dihedral_coeff.html">dihedral_coeff</A>)
</PRE>
</UL>
<HR>
<P><I>Angles</I> section:
</P>
<UL><LI>one line per angle
<LI>line syntax: ID type atom1 atom2 atom3
<PRE> ID = number of angle (1-Nangles)
type = angle type (1-Nangletype)
atom1,atom2,atom3 = IDs of 1st,2nd,3rd atoms in angle
</PRE>
example:
<BR>
<PRE> 2 2 17 29 430
</PRE>
</UL>
<P>The 3 atoms are ordered linearly within the angle. Thus the central
atom (around which the angle is computed) is the atom2 in the list.
E.g. H,O,H for a water molecule. The <I>Angles</I> section must appear
after the <I>Atoms</I> section. All values in this section must be
integers (1, not 1.0).
</P>
<HR>
<P><I>AngleTorsion Coeffs</I> section:
</P>
<UL><LI>one line per dihedral type
<LI>line syntax: ID coeffs
<PRE> ID = dihedral type (1-N)
coeffs = list of coeffs (see <A HREF = "dihedral_coeff.html">dihedral_coeff</A>)
</PRE>
</UL>
<HR>
<P><I>Atoms</I> section:
</P>
<UL><LI>one line per atom
<LI>line syntax: depends on atom style
</UL>
<P>An <I>Atoms</I> section must appear in the data file if natoms > 0 in the
header section. The atoms can be listed in any order. These are the
line formats for each <A HREF = "atom_style.html">atom style</A> in LAMMPS. As
discussed below, each line can optionally have 3 flags (nx,ny,nz)
appended to it, which indicate which image of a periodic simulation
box the atom is in. These may be important to include for some kinds
of analysis.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >angle</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
<TR><TD >atomic</TD><TD > atom-ID atom-type x y z</TD></TR>
<TR><TD >bond</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
<TR><TD >charge</TD><TD > atom-ID atom-type q x y z</TD></TR>
<TR><TD >dipole</TD><TD > atom-ID atom-type q x y z mux muy muz</TD></TR>
<TR><TD >electron</TD><TD > atom-ID atom-type q spin eradius x y z</TD></TR>
<TR><TD >ellipsoid</TD><TD > atom-ID atom-type ellipsoidflag density x y z</TD></TR>
<TR><TD >full</TD><TD > atom-ID molecule-ID atom-type q x y z</TD></TR>
+<TR><TD >meso</TD><TD > atom-ID atom-type rho e cv x y z</TD></TR>
<TR><TD >molecular</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
<TR><TD >peri</TD><TD > atom-ID atom-type volume density x y z</TD></TR>
<TR><TD >sphere</TD><TD > atom-ID atom-type diameter density x y z</TD></TR>
<TR><TD >wavepacket</TD><TD > atom-ID atom-type charge spin eradius etag cs_re cs_im x y z</TD></TR>
<TR><TD >hybrid</TD><TD > atom-ID atom-type x y z sub-style1 sub-style2 ...
</TD></TR></TABLE></DIV>
<P>The keywords have these meanings:
</P>
<UL><LI>atom-ID = integer ID of atom
<LI>molecule-ID = integer ID of molecule the atom belongs to
<LI>atom-type = type of atom (1-Ntype)
<LI>q = charge on atom (charge units)
<LI>diameter = diameter of spherical atom (distance units)
<LI>ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
<LI>density = density of atom (mass/distance^3 units)
<LI>volume = volume of atom (distance^3 units)
<LI>x,y,z = coordinates of atom
<LI>mux,muy,muz = components of dipole moment of atom (dipole units)
+<LI>rho = density (need units) for SPH particles
+<LI>e = energy (need units) for SPH particles
+<LI>cv = heat capacity (need units) for SPH particles
<LI>spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
<LI>eradius = electron radius (or fixed-core radius)
<LI>etag = integer ID of electron that each wavepacket belongs to
<LI>cs_re,cs_im = real/imaginary parts of wavepacket coefficients
</UL>
<P>The units for these quantities depend on the unit style; see the
<A HREF = "units.html">units</A> command for details.
</P>
<P>For 2d simulations specify z as 0.0, or a value within the <I>zlo zhi</I>
setting in the data file header.
</P>
<P>The atom-ID is used to identify the atom throughout the simulation and
in dump files. Normally, it is a unique value from 1 to Natoms for
each atom. Unique values larger than Natoms can be used, but they
will cause extra memory to be allocated on each processor, if an atom
map array is used (see the <A HREF = "atom_modify.html">atom_modify</A> command).
If an atom map array is not used (e.g. an atomic system with no
bonds), and velocities are not assigned in the data file, and you
don't care if unique atom IDs appear in dump files, then the atom-IDs
can all be set to 0.
</P>
<P>The molecule ID is a 2nd identifier attached to an atom. Normally, it
is a number from 1 to N, identifying which molecule the atom belongs
to. It can be 0 if it is an unbonded atom or if you don't care to
keep track of molecule assignments.
</P>
<P>The diameter specifies the size of a finite-size spherical particle.
It can be set to 0.0, which means that atom is a point particle.
</P>
<P>The ellipseflag determines whether the particle is a finite-size
ellipsoid of finite size, or a point particle. Additional attributes
must be defined for each ellipsoid in the <I>Ellipsoids</I> section.
</P>
<P>Some pair styles and fixes and computes that operate on finite-size
particles allow for a mixture of finite-size and point particles. See
the doc pages of individual commands for details.
</P>
<P>The density is used in conjunction with the particle volume for
finite-size particles to set the mass of the particle as mass =
density * volume. If the volume is 0.0, meaning a point particle,
then the density value is used as the mass.
</P>
<P>For atom_style hybrid, following the 5 initial values (ID,type,x,y,z),
specific values for each sub-style must be listed. The order of the
sub-styles is the same as they were listed in the
<A HREF = "atom_style.html">atom_style</A> command. The sub-style specific values
are those that are not the 5 standard ones (ID,type,x,y,z). For
example, for the "charge" sub-style, a "q" value would appear. For
the "full" sub-style, a "molecule-ID" and "q" would appear. These are
listed in the same order they appear as listed above. Thus if
</P>
<PRE>atom_style hybrid charge sphere
</PRE>
<P>were used in the input script, each atom line would have these fields:
</P>
<PRE>atom-ID atom-type x y z q diameter density
</PRE>
<P>Atom lines (all lines or none of them) can optionally list 3 trailing
integer values: nx,ny,nz. For periodic dimensions, they specify which
image of the simulation box the atom is considered to be in. An image
of 0 means it is inside the box as defined. A value of 2 means add 2
box lengths to get the true value. A value of -1 means subtract 1 box
length to get the true value. LAMMPS updates these flags as atoms
cross periodic boundaries during the simulation. The flags can be
output with atom snapshots via the <A HREF = "dump.html">dump</A> command.
</P>
<P>If nx,ny,nz values are not set in the data file, LAMMPS initializes
them to 0. If image information is needed for later analysis and they
are not all initially 0, it's important to set them correctly in the
data file. Also, if you plan to use the <A HREF = "replicate.html">replicate</A>
command to generate a larger system, these flags must be listed
correctly for bonded atoms when the bond crosses a periodic boundary.
I.e. the values of the image flags should be different by 1 (in the
appropriate dimension) for the two atoms in such a bond.
</P>
<P>Atom velocities and other atom quantities not defined above are set to
0.0 when the <I>Atoms</I> section is read. Velocities can be set later by
a <I>Velocities</I> section in the data file or by a
<A HREF = "velocity.html">velocity</A> or <A HREF = "set.html">set</A> command in the input
script.
</P>
<HR>
<P><I>Bond Coeffs</I> section:
</P>
<UL><LI>one line per bond type
<LI>line syntax: ID coeffs
<PRE> ID = bond type (1-N)
coeffs = list of coeffs
</PRE>
<LI>example:
<PRE> 4 250 1.49
</PRE>
</UL>
<P>The number and meaning of the coefficients are specific to the defined
bond style. See the <A HREF = "bond_style.html">bond_style</A> and
<A HREF = "bond_coeff.html">bond_coeff</A> commands for details. Coefficients can
also be set via the <A HREF = "bond_coeff.html">bond_coeff</A> command in the input
script.
</P>
<HR>
<P><I>BondAngle Coeffs</I> section:
</P>
<UL><LI>one line per angle type
<LI>line syntax: ID coeffs
<PRE> ID = angle type (1-N)
coeffs = list of coeffs (see class 2 section of <A HREF = "angle_coeff.html">angle_coeff</A>)
</PRE>
</UL>
<HR>
<P><I>BondBond Coeffs</I> section:
</P>
<UL><LI>one line per angle type
<LI>line syntax: ID coeffs
<PRE> ID = angle type (1-N)
coeffs = list of coeffs (see class 2 section of <A HREF = "angle_coeff.html">angle_coeff</A>)
</PRE>
</UL>
<HR>
<P><I>BondBond13 Coeffs</I> section:
</P>
<UL><LI>one line per dihedral type
<LI>line syntax: ID coeffs
<PRE> ID = dihedral type (1-N)
coeffs = list of coeffs (see class 2 section of <A HREF = "dihedral_coeff.html">dihedral_coeff</A>)
</PRE>
</UL>
<HR>
<P><I>Bonds</I> section:
</P>
<UL><LI>one line per bond
<LI>line syntax: ID type atom1 atom2
<PRE> ID = bond number (1-Nbonds)
type = bond type (1-Nbondtype)
atom1,atom2 = IDs of 1st,2nd atoms in bond
</PRE>
<LI>example:
<PRE> 12 3 17 29
</PRE>
</UL>
<P>The <I>Bonds</I> section must appear after the <I>Atoms</I> section. All values
in this section must be integers (1, not 1.0).
</P>
<HR>
<P><I>Dihedral Coeffs</I> section:
</P>
<UL><LI>one line per dihedral type
<LI>line syntax: ID coeffs
<PRE> ID = dihedral type (1-N)
coeffs = list of coeffs
</PRE>
<LI>example:
<PRE> 3 0.6 1 0 1
</PRE>
</UL>
<P>The number and meaning of the coefficients are specific to the defined
dihedral style. See the <A HREF = "dihedral_style.html">dihedral_style</A> and
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> commands for details.
Coefficients can also be set via the
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script.
</P>
<HR>
<P><I>Dihedrals</I> section:
</P>
<UL><LI>one line per dihedral
<LI>line syntax: ID type atom1 atom2 atom3 atom4
<PRE> ID = number of dihedral (1-Ndihedrals)
type = dihedral type (1-Ndihedraltype)
atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in dihedral
</PRE>
<LI>example:
<PRE> 12 4 17 29 30 21
</PRE>
</UL>
<P>The 4 atoms are ordered linearly within the dihedral. The <I>Dihedrals</I>
section must appear after the <I>Atoms</I> section. All values in this
section must be integers (1, not 1.0).
</P>
<HR>
<P><I>Ellipsoids</I> section:
</P>
<UL><LI>one line per ellipsoid
<LI>line syntax: atom-ID shapex shapey shapez quatw quati quatj quatk
<PRE> atom-ID = ID of atom which is an ellipsoid
shapex,shapey,shapez = 3 diameters of ellipsoid (distance units)
quatw,quati,quatj,quatk = quaternion components for orientation of atom
type = bond type (1-Nbondtype)
atom1,atom2 = IDs of 1st,2nd atoms in bond
</PRE>
<LI>example:
<PRE> 12 3 17 29
</PRE>
</UL>
<P>The <I>Ellipsoids</I> section must appear if <A HREF = "atom_style.html">atom_style
ellipsoid</A> is used and any atoms are listed in the
<I>Atoms</I> section with an ellipsoidflag = 1. The number of ellipsoids
should be specified in the header section via the "ellipsoids"
keyword.
</P>
<P>The 3 shape values specify the 3 diameters or aspect ratios of a
finite-size ellipsoidal particle, when it is oriented along the 3
coordinate axes. They must all be non-zero values.
</P>
<P>The values <I>quatw</I>, <I>quati</I>, <I>quatj</I>, and <I>quatk</I> set the orientation
of the atom as a quaternion (4-vector). Note that the shape
attributes specify the aspect ratios of an ellipsoidal particle, which
is oriented by default with its x-axis along the simulation box's
x-axis, and similarly for y and z. If this body is rotated (via the
right-hand rule) by an angle theta around a unit vector (a,b,c), then
the quaternion that represents its new orientation is given by
(cos(theta/2), a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). These
4 components are quatw, quati, quatj, and quatk as specified above.
LAMMPS normalizes each atom's quaternion in case (a,b,c) is not
specified as a unit vector.
</P>
<P>The <I>Ellipsoids</I> section must appear after the <I>Atoms</I> section.
</P>
<HR>
<P><I>EndBondTorsion Coeffs</I> section:
</P>
<UL><LI>one line per dihedral type
<LI>line syntax: ID coeffs
<PRE> ID = dihedral type (1-N)
coeffs = list of coeffs (see class 2 section of <A HREF = "dihedral_coeff.html">dihedral_coeff</A>)
</PRE>
</UL>
<HR>
<P><I>Improper Coeffs</I> section:
</P>
<UL><LI>one line per improper type
<LI>line syntax: ID coeffs
<PRE> ID = improper type (1-N)
coeffs = list of coeffs
</PRE>
<LI>example:
<PRE> 2 20 0.0548311
</PRE>
</UL>
<P>The number and meaning of the coefficients are specific to the defined
improper style. See the <A HREF = "improper_style.html">improper_style</A> and
<A HREF = "improper_coeff.html">improper_coeff</A> commands for details.
Coefficients can also be set via the
<A HREF = "improper_coeff.html">improper_coeff</A> command in the input script.
</P>
<HR>
<P><I>Impropers</I> section:
</P>
<UL><LI>one line per improper
<LI>line syntax: ID type atom1 atom2 atom3 atom4
<PRE> ID = number of improper (1-Nimpropers)
type = improper type (1-Nimpropertype)
atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in improper
</PRE>
<LI>example:
<PRE> 12 3 17 29 13 100
</PRE>
</UL>
<P>The ordering of the 4 atoms determines the definition of the improper
angle used in the formula for each <A HREF = "improper_style.html">improper
style</A>. See the doc pages for individual styles
for details.
</P>
<P>The <I>Impropers</I> section must appear after the <I>Atoms</I> section. All
values in this section must be integers (1, not 1.0).
</P>
<HR>
<P><I>Masses</I> section:
</P>
<UL><LI>one line per atom type
<LI>line syntax: ID mass
<PRE> ID = atom type (1-N)
mass = mass value
</PRE>
<LI>example:
<PRE> 3 1.01
</PRE>
</UL>
<P>This defines the mass of each atom type. This can also be set via the
<A HREF = "mass.html">mass</A> command in the input script. This section cannot be
used for atom styles that define a mass for individual atoms -
e.g. <A HREF = "atom_style.html">atom_style sphere</A>.
</P>
<HR>
<P><I>MiddleBondTorsion Coeffs</I> section:
</P>
<UL><LI>one line per dihedral type
<LI>line syntax: ID coeffs
<PRE> ID = dihedral type (1-N)
coeffs = list of coeffs (see class 2 section of <A HREF = "dihedral_coeff.html">dihedral_coeff</A>)
</PRE>
</UL>
<HR>
<P><I>Pair Coeffs</I> section:
</P>
<UL><LI>one line per atom type
<LI>line syntax: ID coeffs
<PRE> ID = atom type (1-N)
coeffs = list of coeffs
</PRE>
<LI>example:
<PRE> 3 0.022 2.35197 0.022 2.35197
</PRE>
</UL>
<P>The number and meaning of the coefficients are specific to the defined
pair style. See the <A HREF = "pair_style.html">pair_style</A> and
<A HREF = "pair_coeff.html">pair_coeff</A> commands for details. Coefficients can
also be set via the <A HREF = "pair_coeff.html">pair_coeff</A> command in the input
script.
</P>
<HR>
<P><I>Velocities</I> section:
</P>
<UL><LI>one line per atom
<LI>line syntax: depends on atom style
</UL>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >all styles except those listed</TD><TD > atom-ID vx vy vz</TD></TR>
<TR><TD >dipole</TD><TD > atom-ID vx vy vz wx wy wz</TD></TR>
<TR><TD >electron</TD><TD > atom-ID vx vy vz evel</TD></TR>
<TR><TD >ellipsoid</TD><TD > atom-ID vx vy vz lx ly lz</TD></TR>
<TR><TD >sphere</TD><TD > atom-ID vx vy vz wx wy wz
</TD></TR></TABLE></DIV>
<P>where the keywords have these meanings:
</P>
<P>vx,vy,vz = translational velocity of atom
lx,ly,lz = angular momentum of aspherical atom
wx,wy,wz = angular velocity of spherical atom
evel = electron radial velocity (0 for fixed-core):ul
</P>
<P>The velocity lines can appear in any order. This section can only be
used after an <I>Atoms</I> section. This is because the <I>Atoms</I> section
must have assigned a unique atom ID to each atom so that velocities
can be assigned to them.
</P>
<P>Vx, vy, vz, and evel are in <A HREF = "units.html">units</A> of velocity. Lx, ly,
lz are in units of angular momentum (distance-velocity-mass). Wx, Wy,
Wz are in units of angular velocity (radians/time).
</P>
<P>Translational velocities can also be set by the
<A HREF = "velocity.html">velocity</A> command in the input script.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>To read gzipped data files, you must compile LAMMPS with the
-DLAMMPS_GZIP option - see the <A HREF = "Section_start.html#start_2">Making
LAMMPS</A> section of the documentation.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "read_restart.html">read_restart</A>, <A HREF = "create_atoms.html">create_atoms</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/read_data.txt b/doc/read_data.txt
index 593b93e57..e2d1c0437 100644
--- a/doc/read_data.txt
+++ b/doc/read_data.txt
@@ -1,648 +1,652 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
read_data command :h3
[Syntax:]
read_data file :pre
file = name of data file to read in :ul
[Examples:]
read_data data.lj
read_data ../run7/data.polymer.gz :pre
[Description:]
Read in a data file containing information LAMMPS needs to run a
simulation. The file can be ASCII text or a gzipped text file
(detected by a .gz suffix). This is one of 3 ways to specify initial
atom coordinates; see the "read_restart"_read_restart.html and
"create_atoms"_create_atoms.html commands for alternative methods.
The structure of the data file is important, though many settings and
sections are optional or can come in any order. See the examples
directory for sample data files for different problems.
A data file has a header and a body. The header appears first. The
first line of the header is always skipped; it typically contains a
description of the file. Then lines are read one at a time. Lines
can have a trailing comment starting with '#' that is ignored. If the
line is blank (only whitespace after comment is deleted), it is
skipped. If the line contains a header keyword, the corresponding
value(s) is read from the line. If it doesn't contain a header
keyword, the line begins the body of the file.
The body of the file contains zero or more sections. The first line
of a section has only a keyword. The next line is skipped. The
remaining lines of the section contain values. The number of lines
depends on the section keyword as described below. Zero or more blank
lines can be used between sections. Sections can appear in any order,
with a few exceptions as noted below.
The formatting of individual lines in the data file (indentation,
spacing between words and numbers) is not important except that header
and section keywords (e.g. atoms, xlo xhi, Masses, Bond Coeffs) must
be capitalized as shown and can't have extra white space between their
words - e.g. two spaces or a tab between "Bond" and "Coeffs" is not
valid.
:line
These are the recognized header keywords. Header lines can come in
any order. The value(s) are read from the beginning of the line.
Thus the keyword {atoms} should be in a line like "1000 atoms"; the
keyword {ylo yhi} should be in a line like "-10.0 10.0 ylo yhi"; the
keyword {xy xz yz} should be in a line like "0.0 5.0 6.0 xy xz yz".
All these settings have a default value of 0, except the lo/hi box
size defaults are -0.5 and 0.5. A line need only appear if the value
is different than the default.
{atoms} = # of atoms in system
{bonds} = # of bonds in system
{angles} = # of angles in system
{dihedrals} = # of dihedrals in system
{impropers} = # of impropers in system
{atom types} = # of atom types in system
{bond types} = # of bond types in system
{angle types} = # of angle types in system
{dihedral types} = # of dihedral types in system
{improper types} = # of improper types in system
{extra bond per atom} = leave space for this many new bonds per atom
{ellipsoids} = # of ellipsoids in system
{xlo xhi} = simulation box boundaries in x dimension
{ylo yhi} = simulation box boundaries in y dimension
{zlo zhi} = simulation box boundaries in z dimension
{xy xz yz} = simulation box tilt factors for triclinic system :ul
The initial simulation box size is determined by the lo/hi settings.
In any dimension, the system may be periodic or non-periodic; see the
"boundary"_boundary.html command.
If the {xy xz yz} line does not appear, LAMMPS will set up an
axis-aligned (orthogonal) simulation box. If the line does appear,
LAMMPS creates a non-orthogonal simulation domain shaped as a
parallelepiped with triclinic symmetry. The parallelepiped has its
"origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting
from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C =
(xz,yz,zhi-zlo). {Xy,xz,yz} can be 0.0 or positive or negative values
and are called "tilt factors" because they are the amount of
displacement applied to faces of an originally orthogonal box to
transform it into the parallelepiped.
The tilt factors (xy,xz,yz) can not skew the box more than half the
distance of the corresponding parallel box length. For example, if
xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt
factor must be between -5 and 5. Similarly, both xz and yz must be
between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a
limitation, since if the maximum tilt factor is 5 (as in this
example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
... are all geometrically equivalent.
See "this section"_Section_howto.html#howto_12 of the doc pages for a
geometric description of triclinic boxes, as defined by LAMMPS, and
how to transform these parameters to and from other commonly used
triclinic representations.
When a triclinic system is used, the simulation domain must be
periodic in any dimensions with a non-zero tilt factor, as defined by
the "boundary"_boundary.html command. I.e. if the xy tilt factor is
non-zero, then both the x and y dimensions must be periodic.
Similarly, x and z must be periodic if xz is non-zero and y and z must
be periodic if yz is non-zero. Also note that if your simulation will
tilt the box, e.g. via the "fix deform"_fix_deform.html command, the
simulation box must be defined as triclinic, even if the tilt factors
are initially 0.0.
For 2d simulations, the {zlo zhi} values should be set to bound the z
coords for atoms that appear in the file; the default of -0.5 0.5 is
valid if all z coords are 0.0. For 2d triclinic simulations, the xz
and yz tilt factors must be 0.0.
If the system is periodic (in a dimension), then atom coordinates can
be outside the bounds (in that dimension); they will be remapped (in a
periodic sense) back inside the box.
IMPORTANT NOTE: If the system is non-periodic (in a dimension), then
all atoms in the data file must have coordinates (in that dimension)
that are "greater than or equal to" the lo value and "less than or
equal to" the hi value. If the non-periodic dimension is of style
"fixed" (see the "boundary"_boundary.html command), then the atom
coords must be strictly "less than" the hi value, due to the way
LAMMPS assign atoms to processors. Note that you should not make the
lo/hi values radically smaller/larger than the extent of the atoms.
For example, if your atoms extend from 0 to 50, you should not specify
the box bounds as -10000 and 10000. This is because LAMMPS uses the
specified box size to layout the 3d grid of processors. A huge
(mostly empty) box will be sub-optimal for performance when using
"fixed" boundary conditions (see the "boundary"_boundary.html
command). When using "shrink-wrap" boundary conditions (see the
"boundary"_boundary.html command), a huge (mostly empty) box may cause
a parallel simulation to lose atoms the first time that LAMMPS
shrink-wraps the box around the atoms.
The "extra bond per atom" setting should be used if new bonds will be
added to the system when a simulation runs, e.g. by using the "fix
bond/create"_fix_bond_create.html command. This will pre-allocate
space in LAMMPS data structures for storing the new bonds.
The "ellipsoids" setting is only used with atom_style
ellipsoid"_atom_style.html and specifies how many of the atoms are
finite-size ellipsoids; the remainder are point particles. See the
discussion of ellipseflag and the {Ellipsoids} section below.
:line
These are the section keywords for the body of the file.
{Atoms, Velocities, Ellipsoids, Masses} = atom-property sections
{Bonds, Angles, Dihedrals, Impropers} = molecular topology sections
{Pair Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, \
Improper Coeffs} = force field sections
{BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, \
EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, \
BondBond13 Coeffs, AngleAngle Coeffs} = class 2 force field sections :ul
Each section is listed below in alphabetic order. The format of each
section is described including the number of lines it must contain and
rules (if any) for where it can appear in the data file.
Any individual line in the various sections can have a trailing
comment starting with "#" for annotation purposes. E.g. in the
Atoms section:
10 1 17 -1.0 10.0 5.0 6.0 # salt ion :pre
:line
{Angle Coeffs} section:
one line per angle type :ulb,l
line syntax: ID coeffs :l
ID = angle type (1-N)
coeffs = list of coeffs :pre
example: :l
6 70 108.5 0 0 :pre
:ule
The number and meaning of the coefficients are specific to the defined
angle style. See the "angle_style"_angle_style.html and
"angle_coeff"_angle_coeff.html commands for details. Coefficients can
also be set via the "angle_coeff"_angle_coeff.html command in the
input script.
:line
{AngleAngle Coeffs} section:
one line per improper type :ulb,l
line syntax: ID coeffs :l
ID = improper type (1-N)
coeffs = list of coeffs (see "improper_coeff"_improper_coeff.html) :pre
:ule
:line
{AngleAngleTorsion Coeffs} section:
one line per dihedral type :ulb,l
line syntax: ID coeffs :l
ID = dihedral type (1-N)
coeffs = list of coeffs (see "dihedral_coeff"_dihedral_coeff.html) :pre
:ule
:line
{Angles} section:
one line per angle :ulb,l
line syntax: ID type atom1 atom2 atom3 :l
ID = number of angle (1-Nangles)
type = angle type (1-Nangletype)
atom1,atom2,atom3 = IDs of 1st,2nd,3rd atoms in angle :pre
example: :b
2 2 17 29 430 :pre
:ule
The 3 atoms are ordered linearly within the angle. Thus the central
atom (around which the angle is computed) is the atom2 in the list.
E.g. H,O,H for a water molecule. The {Angles} section must appear
after the {Atoms} section. All values in this section must be
integers (1, not 1.0).
:line
{AngleTorsion Coeffs} section:
one line per dihedral type :ulb,l
line syntax: ID coeffs :l
ID = dihedral type (1-N)
coeffs = list of coeffs (see "dihedral_coeff"_dihedral_coeff.html) :pre
:ule
:line
{Atoms} section:
one line per atom
line syntax: depends on atom style :ul
An {Atoms} section must appear in the data file if natoms > 0 in the
header section. The atoms can be listed in any order. These are the
line formats for each "atom style"_atom_style.html in LAMMPS. As
discussed below, each line can optionally have 3 flags (nx,ny,nz)
appended to it, which indicate which image of a periodic simulation
box the atom is in. These may be important to include for some kinds
of analysis.
angle: atom-ID molecule-ID atom-type x y z
atomic: atom-ID atom-type x y z
bond: atom-ID molecule-ID atom-type x y z
charge: atom-ID atom-type q x y z
dipole: atom-ID atom-type q x y z mux muy muz
electron: atom-ID atom-type q spin eradius x y z
ellipsoid: atom-ID atom-type ellipsoidflag density x y z
full: atom-ID molecule-ID atom-type q x y z
+meso: atom-ID atom-type rho e cv x y z
molecular: atom-ID molecule-ID atom-type x y z
peri: atom-ID atom-type volume density x y z
sphere: atom-ID atom-type diameter density x y z
wavepacket: atom-ID atom-type charge spin eradius etag cs_re cs_im x y z
hybrid: atom-ID atom-type x y z sub-style1 sub-style2 ... :tb(s=:)
The keywords have these meanings:
atom-ID = integer ID of atom
molecule-ID = integer ID of molecule the atom belongs to
atom-type = type of atom (1-Ntype)
q = charge on atom (charge units)
diameter = diameter of spherical atom (distance units)
ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
density = density of atom (mass/distance^3 units)
volume = volume of atom (distance^3 units)
x,y,z = coordinates of atom
mux,muy,muz = components of dipole moment of atom (dipole units)
+rho = density (need units) for SPH particles
+e = energy (need units) for SPH particles
+cv = heat capacity (need units) for SPH particles
spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
eradius = electron radius (or fixed-core radius)
etag = integer ID of electron that each wavepacket belongs to
cs_re,cs_im = real/imaginary parts of wavepacket coefficients :ul
The units for these quantities depend on the unit style; see the
"units"_units.html command for details.
For 2d simulations specify z as 0.0, or a value within the {zlo zhi}
setting in the data file header.
The atom-ID is used to identify the atom throughout the simulation and
in dump files. Normally, it is a unique value from 1 to Natoms for
each atom. Unique values larger than Natoms can be used, but they
will cause extra memory to be allocated on each processor, if an atom
map array is used (see the "atom_modify"_atom_modify.html command).
If an atom map array is not used (e.g. an atomic system with no
bonds), and velocities are not assigned in the data file, and you
don't care if unique atom IDs appear in dump files, then the atom-IDs
can all be set to 0.
The molecule ID is a 2nd identifier attached to an atom. Normally, it
is a number from 1 to N, identifying which molecule the atom belongs
to. It can be 0 if it is an unbonded atom or if you don't care to
keep track of molecule assignments.
The diameter specifies the size of a finite-size spherical particle.
It can be set to 0.0, which means that atom is a point particle.
The ellipseflag determines whether the particle is a finite-size
ellipsoid of finite size, or a point particle. Additional attributes
must be defined for each ellipsoid in the {Ellipsoids} section.
Some pair styles and fixes and computes that operate on finite-size
particles allow for a mixture of finite-size and point particles. See
the doc pages of individual commands for details.
The density is used in conjunction with the particle volume for
finite-size particles to set the mass of the particle as mass =
density * volume. If the volume is 0.0, meaning a point particle,
then the density value is used as the mass.
For atom_style hybrid, following the 5 initial values (ID,type,x,y,z),
specific values for each sub-style must be listed. The order of the
sub-styles is the same as they were listed in the
"atom_style"_atom_style.html command. The sub-style specific values
are those that are not the 5 standard ones (ID,type,x,y,z). For
example, for the "charge" sub-style, a "q" value would appear. For
the "full" sub-style, a "molecule-ID" and "q" would appear. These are
listed in the same order they appear as listed above. Thus if
atom_style hybrid charge sphere :pre
were used in the input script, each atom line would have these fields:
atom-ID atom-type x y z q diameter density :pre
Atom lines (all lines or none of them) can optionally list 3 trailing
integer values: nx,ny,nz. For periodic dimensions, they specify which
image of the simulation box the atom is considered to be in. An image
of 0 means it is inside the box as defined. A value of 2 means add 2
box lengths to get the true value. A value of -1 means subtract 1 box
length to get the true value. LAMMPS updates these flags as atoms
cross periodic boundaries during the simulation. The flags can be
output with atom snapshots via the "dump"_dump.html command.
If nx,ny,nz values are not set in the data file, LAMMPS initializes
them to 0. If image information is needed for later analysis and they
are not all initially 0, it's important to set them correctly in the
data file. Also, if you plan to use the "replicate"_replicate.html
command to generate a larger system, these flags must be listed
correctly for bonded atoms when the bond crosses a periodic boundary.
I.e. the values of the image flags should be different by 1 (in the
appropriate dimension) for the two atoms in such a bond.
Atom velocities and other atom quantities not defined above are set to
0.0 when the {Atoms} section is read. Velocities can be set later by
a {Velocities} section in the data file or by a
"velocity"_velocity.html or "set"_set.html command in the input
script.
:line
{Bond Coeffs} section:
one line per bond type :ulb,l
line syntax: ID coeffs :l
ID = bond type (1-N)
coeffs = list of coeffs :pre
example: :l
4 250 1.49 :pre
:ule
The number and meaning of the coefficients are specific to the defined
bond style. See the "bond_style"_bond_style.html and
"bond_coeff"_bond_coeff.html commands for details. Coefficients can
also be set via the "bond_coeff"_bond_coeff.html command in the input
script.
:line
{BondAngle Coeffs} section:
one line per angle type :ulb,l
line syntax: ID coeffs :l
ID = angle type (1-N)
coeffs = list of coeffs (see class 2 section of "angle_coeff"_angle_coeff.html) :pre
:ule
:line
{BondBond Coeffs} section:
one line per angle type :ulb,l
line syntax: ID coeffs :l
ID = angle type (1-N)
coeffs = list of coeffs (see class 2 section of "angle_coeff"_angle_coeff.html) :pre
:ule
:line
{BondBond13 Coeffs} section:
one line per dihedral type :ulb,l
line syntax: ID coeffs :l
ID = dihedral type (1-N)
coeffs = list of coeffs (see class 2 section of "dihedral_coeff"_dihedral_coeff.html) :pre
:ule
:line
{Bonds} section:
one line per bond :ulb,l
line syntax: ID type atom1 atom2 :l
ID = bond number (1-Nbonds)
type = bond type (1-Nbondtype)
atom1,atom2 = IDs of 1st,2nd atoms in bond :pre
example: :l
12 3 17 29 :pre
:ule
The {Bonds} section must appear after the {Atoms} section. All values
in this section must be integers (1, not 1.0).
:line
{Dihedral Coeffs} section:
one line per dihedral type :ulb,l
line syntax: ID coeffs :l
ID = dihedral type (1-N)
coeffs = list of coeffs :pre
example: :l
3 0.6 1 0 1 :pre
:ule
The number and meaning of the coefficients are specific to the defined
dihedral style. See the "dihedral_style"_dihedral_style.html and
"dihedral_coeff"_dihedral_coeff.html commands for details.
Coefficients can also be set via the
"dihedral_coeff"_dihedral_coeff.html command in the input script.
:line
{Dihedrals} section:
one line per dihedral :ulb,l
line syntax: ID type atom1 atom2 atom3 atom4 :l
ID = number of dihedral (1-Ndihedrals)
type = dihedral type (1-Ndihedraltype)
atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in dihedral :pre
example: :l
12 4 17 29 30 21 :pre
:ule
The 4 atoms are ordered linearly within the dihedral. The {Dihedrals}
section must appear after the {Atoms} section. All values in this
section must be integers (1, not 1.0).
:line
{Ellipsoids} section:
one line per ellipsoid :ulb,l
line syntax: atom-ID shapex shapey shapez quatw quati quatj quatk :l
atom-ID = ID of atom which is an ellipsoid
shapex,shapey,shapez = 3 diameters of ellipsoid (distance units)
quatw,quati,quatj,quatk = quaternion components for orientation of atom
type = bond type (1-Nbondtype)
atom1,atom2 = IDs of 1st,2nd atoms in bond :pre
example: :l
12 3 17 29 :pre
:ule
The {Ellipsoids} section must appear if "atom_style
ellipsoid"_atom_style.html is used and any atoms are listed in the
{Atoms} section with an ellipsoidflag = 1. The number of ellipsoids
should be specified in the header section via the "ellipsoids"
keyword.
The 3 shape values specify the 3 diameters or aspect ratios of a
finite-size ellipsoidal particle, when it is oriented along the 3
coordinate axes. They must all be non-zero values.
The values {quatw}, {quati}, {quatj}, and {quatk} set the orientation
of the atom as a quaternion (4-vector). Note that the shape
attributes specify the aspect ratios of an ellipsoidal particle, which
is oriented by default with its x-axis along the simulation box's
x-axis, and similarly for y and z. If this body is rotated (via the
right-hand rule) by an angle theta around a unit vector (a,b,c), then
the quaternion that represents its new orientation is given by
(cos(theta/2), a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). These
4 components are quatw, quati, quatj, and quatk as specified above.
LAMMPS normalizes each atom's quaternion in case (a,b,c) is not
specified as a unit vector.
The {Ellipsoids} section must appear after the {Atoms} section.
:line
{EndBondTorsion Coeffs} section:
one line per dihedral type :ulb,l
line syntax: ID coeffs :l
ID = dihedral type (1-N)
coeffs = list of coeffs (see class 2 section of "dihedral_coeff"_dihedral_coeff.html) :pre
:ule
:line
{Improper Coeffs} section:
one line per improper type :ulb,l
line syntax: ID coeffs :l
ID = improper type (1-N)
coeffs = list of coeffs :pre
example: :l
2 20 0.0548311 :pre
:ule
The number and meaning of the coefficients are specific to the defined
improper style. See the "improper_style"_improper_style.html and
"improper_coeff"_improper_coeff.html commands for details.
Coefficients can also be set via the
"improper_coeff"_improper_coeff.html command in the input script.
:line
{Impropers} section:
one line per improper :ulb,l
line syntax: ID type atom1 atom2 atom3 atom4 :l
ID = number of improper (1-Nimpropers)
type = improper type (1-Nimpropertype)
atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in improper :pre
example: :l
12 3 17 29 13 100 :pre
:ule
The ordering of the 4 atoms determines the definition of the improper
angle used in the formula for each "improper
style"_improper_style.html. See the doc pages for individual styles
for details.
The {Impropers} section must appear after the {Atoms} section. All
values in this section must be integers (1, not 1.0).
:line
{Masses} section:
one line per atom type :ulb,l
line syntax: ID mass :l
ID = atom type (1-N)
mass = mass value :pre
example: :l
3 1.01 :pre
:ule
This defines the mass of each atom type. This can also be set via the
"mass"_mass.html command in the input script. This section cannot be
used for atom styles that define a mass for individual atoms -
e.g. "atom_style sphere"_atom_style.html.
:line
{MiddleBondTorsion Coeffs} section:
one line per dihedral type :ulb,l
line syntax: ID coeffs :l
ID = dihedral type (1-N)
coeffs = list of coeffs (see class 2 section of "dihedral_coeff"_dihedral_coeff.html) :pre
:ule
:line
{Pair Coeffs} section:
one line per atom type :ulb,l
line syntax: ID coeffs :l
ID = atom type (1-N)
coeffs = list of coeffs :pre
example: :l
3 0.022 2.35197 0.022 2.35197 :pre
:ule
The number and meaning of the coefficients are specific to the defined
pair style. See the "pair_style"_pair_style.html and
"pair_coeff"_pair_coeff.html commands for details. Coefficients can
also be set via the "pair_coeff"_pair_coeff.html command in the input
script.
:line
{Velocities} section:
one line per atom
line syntax: depends on atom style :ul
all styles except those listed: atom-ID vx vy vz
dipole: atom-ID vx vy vz wx wy wz
electron: atom-ID vx vy vz evel
ellipsoid: atom-ID vx vy vz lx ly lz
sphere: atom-ID vx vy vz wx wy wz :tb(s=:)
where the keywords have these meanings:
vx,vy,vz = translational velocity of atom
lx,ly,lz = angular momentum of aspherical atom
wx,wy,wz = angular velocity of spherical atom
evel = electron radial velocity (0 for fixed-core):ul
The velocity lines can appear in any order. This section can only be
used after an {Atoms} section. This is because the {Atoms} section
must have assigned a unique atom ID to each atom so that velocities
can be assigned to them.
Vx, vy, vz, and evel are in "units"_units.html of velocity. Lx, ly,
lz are in units of angular momentum (distance-velocity-mass). Wx, Wy,
Wz are in units of angular velocity (radians/time).
Translational velocities can also be set by the
"velocity"_velocity.html command in the input script.
:line
[Restrictions:]
To read gzipped data files, you must compile LAMMPS with the
-DLAMMPS_GZIP option - see the "Making
LAMMPS"_Section_start.html#start_2 section of the documentation.
[Related commands:]
"read_restart"_read_restart.html, "create_atoms"_create_atoms.html
[Default:] none
diff --git a/doc/set.html b/doc/set.html
index e70cd6a1b..a1feb65a3 100644
--- a/doc/set.html
+++ b/doc/set.html
@@ -1,259 +1,268 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>set command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>set style ID keyword values ...
</PRE>
<UL><LI>style = <I>atom</I> or <I>type</I> or <I>mol</I> or <I>group</I> or <I>region</I>
<LI>ID = atom ID range or type range or mol ID range or group ID or region ID
<LI>one or more keyword/value pairs may be appended
<LI>keyword = <I>type</I> or <I>type/fraction</I> or <I>mol</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>charge</I> or <I>dipole</I> or <I>dipole/random</I> or <I>quat</I> or <I>quat/random</I> or <I>diameter</I> or <I>shape</I> or <I>mass</I> or <I>density</I> or <I>volume</I> or <I>image</I> or
- <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I>
+ <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or
+ <I>meso_e</I> or <I>meso_cv</I> or <I>meso_rho</I>
<PRE> <I>type</I> value = atom type
<I>type/fraction</I> values = type fraction seed
type = new atom type
fraction = fraction of selected atoms to set to new atom type
seed = random # seed (positive integer)
<I>mol</I> value = molecule ID
<I>x</I>,<I>y</I>,<I>z</I> value = atom coordinate (distance units)
<I>charge</I> value = atomic charge (charge units)
<I>dipole</I> values = x y z
x,y,z = orientation of dipole moment vector
<I>dipole/random</I> value = seed Dlen
seed = random # seed (positive integer) for dipole moment orientations
Dlen = magnitude of dipole moment (dipole units)
<I>quat</I> values = a b c theta
a,b,c = unit vector to rotate particle around via right-hand rule
theta = rotation angle in degrees
<I>quat/random</I> value = seed
seed = random # seed (positive integer) for quaternion orientations
<I>diameter</I> value = diameter of spherical particle (distance units)
<I>shape</I> value = Sx Sy Sz
Sx,Sy,Sz = 3 diameters of ellipsoid (distance units)
<I>mass</I> value = per-atom mass (mass units)
<I>density</I> value = particle density for sphere or ellipsoid (mass/distance^3 units)
<I>volume</I> value = particle volume for Peridynamic particle (distance^3 units)
<I>image</I> nx ny nz
nx,ny,nz = which periodic image of the simulation box the atom is in
<I>bond</I> value = bond type for all bonds between selected atoms
<I>angle</I> value = angle type for all angles between selected atoms
<I>dihedral</I> value = dihedral type for all dihedrals between selected atoms
- <I>improper</I> value = improper type for all impropers between selected atoms
+ <I>improper</I> value = improper type for all impropers between selected atoms
+ <I>meso_e</I> value = energy of SPH particles (need units)
+ <I>meso_cv</I> value = heat capacity of SPH particles (need units)
+ <I>meso_rho</I> value = density of SPH particles (need units)
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>set group solvent type 2
set group solvent type/fraction 2 0.5 12393
set group edge bond 4
set region half charge 0.5
set type 3 charge 0.5
set type 1*3 charge 0.5
set atom 100*200 x 0.5 y 1.0
set atom 1492 type 3
</PRE>
<P><B>Description:</B>
</P>
<P>Set one or more properties of one or more atoms. Since atom
properties are initially assigned by the <A HREF = "read_data.html">read_data</A>,
<A HREF = "read_restart.html">read_restart</A> or <A HREF = "create_atoms.html">create_atoms</A>
commands, this command changes those assignments. This can be useful
for overriding the default values assigned by the
<A HREF = "create_atoms.html">create_atoms</A> command (e.g. charge = 0.0). It can
be useful for altering pairwise and molecular force interactions,
since force-field coefficients are defined in terms of types. It can
be used to change the labeling of atoms by atom type or molecule ID
when they are output in <A HREF = "dump.html">dump</A> files. It can be useful for
debugging purposes; i.e. positioning an atom at a precise location to
compute subsequent forces or energy.
</P>
<P>The style <I>atom</I> selects all the atoms in a range of atom IDs. The
style <I>type</I> selects all the atoms in a range of types. The style
<I>mol</I> selects all the atoms in a range of molecule IDs.
</P>
<P>In each of the range cases, a single value can be specified, or a
wildcard asterisk can be used to specify a range of values. This
takes the form "*" or "*n" or "n*" or "m*n". For example, for the
style <I>type</I>, if N = the number of atom types, then an asterisk with
no numeric values means all types from 1 to N. A leading asterisk
means all types from 1 to n (inclusive). A trailing asterisk means
all types from n to N (inclusive). A middle asterisk means all types
from m to n (inclusive). Note that the loweest value for the wildcard
is 1, not 0, so you cannot not use this form to select atoms
with molecule ID = 0, for example.
</P>
<P>The style <I>group</I> selects all the atoms in the specified group. The
style <I>region</I> selects all the atoms in the specified geometric
region. See the <A HREF = "group.html">group</A> and <A HREF = "region.html">region</A> commands
for details of how to specify a group or region.
</P>
<HR>
<P>Keyword <I>type</I> sets the atom type for all selected atoms. The
specified value must be from 1 to ntypes, where ntypes was set by the
<A HREF = "create_box.html">create_box</A> command or the <I>atom types</I> field in the
header of the data file read by the <A HREF = "read_data.html">read_data</A>
command.
</P>
<P>Keyword <I>type/fraction</I> sets the atom type for a fraction of the
selected atoms. The actual number of atoms changed is not guaranteed
to be exactly the requested fraction, but should be statistically
close. Random numbers are used in such a way that a particular atom
is changed or not changed, regardless of how many processors are being
used.
</P>
<P>Keyword <I>mol</I> sets the molecule ID for all selected atoms. The <A HREF = "atom_style.html">atom
style</A> being used must support the use of molecule
IDs.
</P>
<P>Keywords <I>x</I>, <I>y</I>, <I>z</I>, and <I>charge</I> set the coordinates or charge of
all selected atoms. For <I>charge</I>, the <A HREF = "atom_style.html">atom style</A>
being used must support the use of atomic charge.
</P>
<P>Keyword <I>dipole</I> uses the specified x,y,z values as components of a
vector to set as the orientation of the dipole moment vectors of the
selected atoms. The magnitude of the dipole moment is set
by the length of this orientation vector.
</P>
<P>Keyword <I>dipole/random</I> randomizes the orientation of the dipole
moment vectors of the selected atoms and sets the magnitude of each to
the specified <I>Dlen</I> value. For 2d systems, the z component of the
orientation is set to 0.0. Random numbers are used in such a way that
the orientation of a particular atom is the same, regardless of how
many processors are being used.
</P>
<P>Keyword <I>quat</I> uses the specified values to create a quaternion
(4-vector) that represents the orientation of the selected atoms.
Note that particles defined by <A HREF = "atom_style.html">atom_style ellipsoid</A>
have 3 shape parameters. The 3 values must be non-zero for each
particle set by this command. They are used to specify the aspect
ratios of an ellipsoidal particle, which is oriented by default with
its x-axis along the simulation box's x-axis, and similarly for y and
z. If this body is rotated (via the right-hand rule) by an angle
theta around a unit rotation vector (a,b,c), then the quaternion that
represents its new orientation is given by (cos(theta/2),
a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). The theta and a,b,c
values are the arguments to the <I>quat</I> keyword. LAMMPS normalizes the
quaternion in case (a,b,c) was not specified as a unit vector. For 2d
systems, the a,b,c values are ignored, since a rotation vector of
(0,0,1) is the only valid choice.
</P>
<P>Keyword <I>quat/random</I> randomizes the orientation of the quaternion of
the selected atoms. Random numbers are used in such a way that the
orientation of a particular atom is the same, regardless of how many
processors are being used. For 2d systems, only orientations in the
xy plane are generated. As with keyword <I>quat</I>, the 3 shape values
must be non-zero for each particle set by this command.
</P>
<P>Keyword <I>diameter</I> sets the size of the selected atoms. The particles
must be finite-size spheres as defined by the <A HREF = "atom_style.html">atom_style
sphere</A> command. The diameter of a particle can be
set to 0.0, which means they will be treated as point particles. Note
that this command does not adjust the particle mass, even if it was
defined with a density, e.g. via the <A HREF = "read_data.html">read_data</A>
command.
</P>
<P>Keyword <I>shape</I> sets the size and shape of the selected atoms. The
particles must be aspherical ellipsoids as defined by the <A HREF = "atom_style.html">atom_style
ellipsoid</A> command. The <I>Sx</I>, <I>Sy</I>, <I>Sz</I> settings are
the 3 diameters of the ellipsoid in each direction. All 3 can be set
to the same value, which means the ellipsoid is effectively a sphere.
They can also all be set to 0.0 which means the particle will be
treated as a point particle. Note that this command does not adjust
the particle mass, even if it was defined with a density, e.g. via the
<A HREF = "read_data.html">read_data</A> command.
</P>
<P>Keyword <I>mass</I> sets the mass of all selected particles. The particles
must have a per-atom mass attribute, as defined by the
<A HREF = "atom_style.html">atom_style</A> command. See the "mass" command for how
to set mass values on a per-type basis.
</P>
<P>Keyword <I>density</I> sets the mass of all selected particles. The
particles must have a per-atom mass attribute, as defined by the
<A HREF = "atom_style.html">atom_style</A> command. See the "mass" command for how
to set mass values on a per-type basis. If the atom has a radius
attribute (see <A HREF = "atom_style.html">atom_style sphere</A>) and its radius is
non-zero, its mass is set from the density and particle volume. The
same is true if the atom has a shape attribute (see <A HREF = "atom_style.html">atom_style
ellipsoid</A>) and its 3 shape parameters are non-zero.
Otherwise the mass is set to the density value directly.
</P>
<P>Keyword <I>volume</I> sets the volume of all selected particles.
Currently, only the <A HREF = "atom_style.html">atom_style peri</A> command defines
particles with a volume attribute. Note that this command does not
adjust the particle mass.
</P>
<P>Keyword <I>image</I> sets which image of the simulation box the atom is
considered to be in. An image of 0 means it is inside the box as
defined. A value of 2 means add 2 box lengths to get the true value.
A value of -1 means subtract 1 box length to get the true value.
LAMMPS updates these flags as atoms cross periodic boundaries during
the simulation. The flags can be output with atom snapshots via the
<A HREF = "dump.html">dump</A> command. If a value of NULL is specified for any of
nx,ny,nz, then the current image value for that dimension is
unchanged. For non-periodic dimensions only a value of 0 can be
specified.
</P>
<P>This command can be useful after a system has been equilibrated and
atoms have diffused one or more box lengths in various directions.
This command can then reset the image values for atoms so that they
are effectively inside the simulation box, e.g if a diffusion
coefficient is about to be measured via the <A HREF = "compute_msd.html">compute
msd</A> command. Care should be taken not to reset the
image flags of two atoms in a bond to the same value if the bond
straddles a periodic boundary (rather they should be different by +/-
1). This will not affect the dynamics of a simulation, but may mess
up analysis of the trajectories if a LAMMPS diagnostic or your own
analysis relies on the image flags to unwrap a molecule which
straddles the periodic box.
</P>
<P>Keywords <I>bond</I>, <I>angle</I>, <I>dihedral</I>, and <I>improper</I>, set the bond
type (angle type, etc) of all bonds (angles, etc) of selected atoms to
the specified value from 1 to nbondtypes (nangletypes, etc). All
atoms in a particular bond (angle, etc) must be selected atoms in
order for the change to be made. The value of nbondtype (nangletypes,
etc) was set by the <I>bond types</I> (<I>angle types</I>, etc) field in the
header of the data file read by the <A HREF = "read_data.html">read_data</A>
command.
</P>
+<P>Keywords <I>meso_e</I>, <I>meso_cv</I>, and <I>meso_rho</I> set the energy, heat
+capacity, and density of smmothed particle hydrodynamics (SPH)
+particles. See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to
+using SPH in LAMMPS.
+</P>
<P><B>Restrictions:</B>
</P>
<P>You cannot set an atom attribute (e.g. <I>mol</I> or <I>q</I> or <I>volume</I>) if
the <A HREF = "atom_style.html">atom_style</A> does not have that attribute.
</P>
<P>This command requires inter-processor communication to coordinate the
setting of bond types (angle types, etc). This means that your system
must be ready to perform a simulation before using one of these
keywords (force fields set, atom mass set, etc). This is not
necessary for other keywords.
</P>
<P>Using the <I>region</I> style with the bond (angle, etc) keywords can give
unpredictable results if there are bonds (angles, etc) that straddle
periodic boundaries. This is because the region may only extend up to
the boundary and partner atoms in the bond (angle, etc) may have
coordinates outside the simulation box if they are ghost atoms.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "create_box.html">create_box</A>, <A HREF = "create_atoms.html">create_atoms</A>,
<A HREF = "read_data.html">read_data</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/set.txt b/doc/set.txt
index a768576f1..8f37b29f1 100644
--- a/doc/set.txt
+++ b/doc/set.txt
@@ -1,252 +1,261 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
set command :h3
[Syntax:]
set style ID keyword values ... :pre
style = {atom} or {type} or {mol} or {group} or {region} :ulb,l
ID = atom ID range or type range or mol ID range or group ID or region ID :l
one or more keyword/value pairs may be appended :l
keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
{charge} or {dipole} or {dipole/random} or {quat} or \
{quat/random} or {diameter} or {shape} or {mass} or \
{density} or {volume} or {image} or
- {bond} or {angle} or {dihedral} or {improper} :l
+ {bond} or {angle} or {dihedral} or {improper} or
+ {meso_e} or {meso_cv} or {meso_rho} :l
{type} value = atom type
{type/fraction} values = type fraction seed
type = new atom type
fraction = fraction of selected atoms to set to new atom type
seed = random # seed (positive integer)
{mol} value = molecule ID
{x},{y},{z} value = atom coordinate (distance units)
{charge} value = atomic charge (charge units)
{dipole} values = x y z
x,y,z = orientation of dipole moment vector
{dipole/random} value = seed Dlen
seed = random # seed (positive integer) for dipole moment orientations
Dlen = magnitude of dipole moment (dipole units)
{quat} values = a b c theta
a,b,c = unit vector to rotate particle around via right-hand rule
theta = rotation angle in degrees
{quat/random} value = seed
seed = random # seed (positive integer) for quaternion orientations
{diameter} value = diameter of spherical particle (distance units)
{shape} value = Sx Sy Sz
Sx,Sy,Sz = 3 diameters of ellipsoid (distance units)
{mass} value = per-atom mass (mass units)
{density} value = particle density for sphere or ellipsoid (mass/distance^3 units)
{volume} value = particle volume for Peridynamic particle (distance^3 units)
{image} nx ny nz
nx,ny,nz = which periodic image of the simulation box the atom is in
{bond} value = bond type for all bonds between selected atoms
{angle} value = angle type for all angles between selected atoms
{dihedral} value = dihedral type for all dihedrals between selected atoms
- {improper} value = improper type for all impropers between selected atoms :pre
+ {improper} value = improper type for all impropers between selected atoms
+ {meso_e} value = energy of SPH particles (need units)
+ {meso_cv} value = heat capacity of SPH particles (need units)
+ {meso_rho} value = density of SPH particles (need units) :pre
:ule
[Examples:]
set group solvent type 2
set group solvent type/fraction 2 0.5 12393
set group edge bond 4
set region half charge 0.5
set type 3 charge 0.5
set type 1*3 charge 0.5
set atom 100*200 x 0.5 y 1.0
set atom 1492 type 3 :pre
[Description:]
Set one or more properties of one or more atoms. Since atom
properties are initially assigned by the "read_data"_read_data.html,
"read_restart"_read_restart.html or "create_atoms"_create_atoms.html
commands, this command changes those assignments. This can be useful
for overriding the default values assigned by the
"create_atoms"_create_atoms.html command (e.g. charge = 0.0). It can
be useful for altering pairwise and molecular force interactions,
since force-field coefficients are defined in terms of types. It can
be used to change the labeling of atoms by atom type or molecule ID
when they are output in "dump"_dump.html files. It can be useful for
debugging purposes; i.e. positioning an atom at a precise location to
compute subsequent forces or energy.
The style {atom} selects all the atoms in a range of atom IDs. The
style {type} selects all the atoms in a range of types. The style
{mol} selects all the atoms in a range of molecule IDs.
In each of the range cases, a single value can be specified, or a
wildcard asterisk can be used to specify a range of values. This
takes the form "*" or "*n" or "n*" or "m*n". For example, for the
style {type}, if N = the number of atom types, then an asterisk with
no numeric values means all types from 1 to N. A leading asterisk
means all types from 1 to n (inclusive). A trailing asterisk means
all types from n to N (inclusive). A middle asterisk means all types
from m to n (inclusive). Note that the loweest value for the wildcard
is 1, not 0, so you cannot not use this form to select atoms
with molecule ID = 0, for example.
The style {group} selects all the atoms in the specified group. The
style {region} selects all the atoms in the specified geometric
region. See the "group"_group.html and "region"_region.html commands
for details of how to specify a group or region.
:line
Keyword {type} sets the atom type for all selected atoms. The
specified value must be from 1 to ntypes, where ntypes was set by the
"create_box"_create_box.html command or the {atom types} field in the
header of the data file read by the "read_data"_read_data.html
command.
Keyword {type/fraction} sets the atom type for a fraction of the
selected atoms. The actual number of atoms changed is not guaranteed
to be exactly the requested fraction, but should be statistically
close. Random numbers are used in such a way that a particular atom
is changed or not changed, regardless of how many processors are being
used.
Keyword {mol} sets the molecule ID for all selected atoms. The "atom
style"_atom_style.html being used must support the use of molecule
IDs.
Keywords {x}, {y}, {z}, and {charge} set the coordinates or charge of
all selected atoms. For {charge}, the "atom style"_atom_style.html
being used must support the use of atomic charge.
Keyword {dipole} uses the specified x,y,z values as components of a
vector to set as the orientation of the dipole moment vectors of the
selected atoms. The magnitude of the dipole moment is set
by the length of this orientation vector.
Keyword {dipole/random} randomizes the orientation of the dipole
moment vectors of the selected atoms and sets the magnitude of each to
the specified {Dlen} value. For 2d systems, the z component of the
orientation is set to 0.0. Random numbers are used in such a way that
the orientation of a particular atom is the same, regardless of how
many processors are being used.
Keyword {quat} uses the specified values to create a quaternion
(4-vector) that represents the orientation of the selected atoms.
Note that particles defined by "atom_style ellipsoid"_atom_style.html
have 3 shape parameters. The 3 values must be non-zero for each
particle set by this command. They are used to specify the aspect
ratios of an ellipsoidal particle, which is oriented by default with
its x-axis along the simulation box's x-axis, and similarly for y and
z. If this body is rotated (via the right-hand rule) by an angle
theta around a unit rotation vector (a,b,c), then the quaternion that
represents its new orientation is given by (cos(theta/2),
a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). The theta and a,b,c
values are the arguments to the {quat} keyword. LAMMPS normalizes the
quaternion in case (a,b,c) was not specified as a unit vector. For 2d
systems, the a,b,c values are ignored, since a rotation vector of
(0,0,1) is the only valid choice.
Keyword {quat/random} randomizes the orientation of the quaternion of
the selected atoms. Random numbers are used in such a way that the
orientation of a particular atom is the same, regardless of how many
processors are being used. For 2d systems, only orientations in the
xy plane are generated. As with keyword {quat}, the 3 shape values
must be non-zero for each particle set by this command.
Keyword {diameter} sets the size of the selected atoms. The particles
must be finite-size spheres as defined by the "atom_style
sphere"_atom_style.html command. The diameter of a particle can be
set to 0.0, which means they will be treated as point particles. Note
that this command does not adjust the particle mass, even if it was
defined with a density, e.g. via the "read_data"_read_data.html
command.
Keyword {shape} sets the size and shape of the selected atoms. The
particles must be aspherical ellipsoids as defined by the "atom_style
ellipsoid"_atom_style.html command. The {Sx}, {Sy}, {Sz} settings are
the 3 diameters of the ellipsoid in each direction. All 3 can be set
to the same value, which means the ellipsoid is effectively a sphere.
They can also all be set to 0.0 which means the particle will be
treated as a point particle. Note that this command does not adjust
the particle mass, even if it was defined with a density, e.g. via the
"read_data"_read_data.html command.
Keyword {mass} sets the mass of all selected particles. The particles
must have a per-atom mass attribute, as defined by the
"atom_style"_atom_style.html command. See the "mass" command for how
to set mass values on a per-type basis.
Keyword {density} sets the mass of all selected particles. The
particles must have a per-atom mass attribute, as defined by the
"atom_style"_atom_style.html command. See the "mass" command for how
to set mass values on a per-type basis. If the atom has a radius
attribute (see "atom_style sphere"_atom_style.html) and its radius is
non-zero, its mass is set from the density and particle volume. The
same is true if the atom has a shape attribute (see "atom_style
ellipsoid"_atom_style.html) and its 3 shape parameters are non-zero.
Otherwise the mass is set to the density value directly.
Keyword {volume} sets the volume of all selected particles.
Currently, only the "atom_style peri"_atom_style.html command defines
particles with a volume attribute. Note that this command does not
adjust the particle mass.
Keyword {image} sets which image of the simulation box the atom is
considered to be in. An image of 0 means it is inside the box as
defined. A value of 2 means add 2 box lengths to get the true value.
A value of -1 means subtract 1 box length to get the true value.
LAMMPS updates these flags as atoms cross periodic boundaries during
the simulation. The flags can be output with atom snapshots via the
"dump"_dump.html command. If a value of NULL is specified for any of
nx,ny,nz, then the current image value for that dimension is
unchanged. For non-periodic dimensions only a value of 0 can be
specified.
This command can be useful after a system has been equilibrated and
atoms have diffused one or more box lengths in various directions.
This command can then reset the image values for atoms so that they
are effectively inside the simulation box, e.g if a diffusion
coefficient is about to be measured via the "compute
msd"_compute_msd.html command. Care should be taken not to reset the
image flags of two atoms in a bond to the same value if the bond
straddles a periodic boundary (rather they should be different by +/-
1). This will not affect the dynamics of a simulation, but may mess
up analysis of the trajectories if a LAMMPS diagnostic or your own
analysis relies on the image flags to unwrap a molecule which
straddles the periodic box.
Keywords {bond}, {angle}, {dihedral}, and {improper}, set the bond
type (angle type, etc) of all bonds (angles, etc) of selected atoms to
the specified value from 1 to nbondtypes (nangletypes, etc). All
atoms in a particular bond (angle, etc) must be selected atoms in
order for the change to be made. The value of nbondtype (nangletypes,
etc) was set by the {bond types} ({angle types}, etc) field in the
header of the data file read by the "read_data"_read_data.html
command.
+Keywords {meso_e}, {meso_cv}, and {meso_rho} set the energy, heat
+capacity, and density of smmothed particle hydrodynamics (SPH)
+particles. See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to
+using SPH in LAMMPS.
+
[Restrictions:]
You cannot set an atom attribute (e.g. {mol} or {q} or {volume}) if
the "atom_style"_atom_style.html does not have that attribute.
This command requires inter-processor communication to coordinate the
setting of bond types (angle types, etc). This means that your system
must be ready to perform a simulation before using one of these
keywords (force fields set, atom mass set, etc). This is not
necessary for other keywords.
Using the {region} style with the bond (angle, etc) keywords can give
unpredictable results if there are bonds (angles, etc) that straddle
periodic boundaries. This is because the region may only extend up to
the boundary and partner atoms in the bond (angle, etc) may have
coordinates outside the simulation box if they are ghost atoms.
[Related commands:]
"create_box"_create_box.html, "create_atoms"_create_atoms.html,
"read_data"_read_data.html
[Default:] none
diff --git a/doc/tad.html b/doc/tad.html
index ff74027e2..a454bf867 100644
--- a/doc/tad.html
+++ b/doc/tad.html
@@ -1,314 +1,314 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>tad command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>tad N t_event T_lo T_hi delta tmax compute-ID seed keyword value ...
</PRE>
<UL><LI>N = # of timesteps to run (not including dephasing/quenching)
<LI>t_event = timestep interval between event checks
<LI>T_lo = temperature at which event times are desired
<LI>T_hi = temperature at which MD simulation is performed
<LI>delta = desired confidence level for stopping criterion
<LI>tmax = reciprocal of lowest expected preexponential factor (time units)
<LI>compute-ID = ID of the compute used for event detection
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>min</I> or <I>neb</I> or <I>min_style</I> or <I>neb_style</I> or <I>neb_log</I>
<PRE> <I>min</I> values = etol ftol maxiter maxeval
etol = stopping tolerance for energy (energy units)
ftol = stopping tolerance for force (force units)
maxiter = max iterations of minimize
maxeval = max number of force/energy evaluations
<I>neb</I> values = ftol N1 N2 Nevery
etol = stopping tolerance for energy (energy units)
ftol = stopping tolerance for force (force units)
N1 = max # of iterations (timesteps) to run initial NEB
N2 = max # of iterations (timesteps) to run barrier-climbing NEB
Nevery = print NEB statistics every this many timesteps
<I>min_style</I> value = <I>cg</I> or <I>hftn</I> or <I>sd</I> or <I>quickmin</I> or <I>fire</I>
<I>neb_style</I> value = <I>quickmin</I> or <I>fire</I>
<I>neb_log</I> value = file where NEB statistics are printed
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>tad 2000 50 1800 2300 0.01 0.01 event 54985
tad 2000 50 1800 2300 0.01 0.01 event 54985 &
min 1e-05 1e-05 100 100 &
neb 0.0 0.01 200 200 20 &
min_style cg &
neb_style fire &
neb_log log.neb
</PRE>
<P><B>Description:</B>
</P>
<P>Run a temperature accelerated dynamics (TAD) simulation. This method
requires two or more partitions to perform NEB transition state
searches.
</P>
<P>TAD is described in <A HREF = "#Voter">this paper</A> by Art Voter. It is a method
that uses accelerated dynamics at an elevated temperature to generate
results at a specified lower temperature. A good overview of
accelerated dynamics methods for such systems is given in <A HREF = "#Voter2">this review
paper</A> from the same group. In general, these methods assume
that the long-time dynamics is dominated by infrequent events i.e. the
system is is confined to low energy basins for long periods,
punctuated by brief, randomly-occurring transitions to adjacent
basins. TAD is suitable for infrequent-event systems, where in
addition, the transition kinetics are well-approximated by harmonic
transition state theory (hTST). In hTST, the temperature dependence of
transition rates follows the Arrhenius relation. As a consequence a
set of event times generated in a high-temperature simulation can be
mapped to a set of much longer estimated times in the low-temperature
system. However, because this mapping involves the energy barrier of
the transition event, which is different for each event, the first
event at the high temperature may not be the earliest event at the low
temperature. TAD handles this by first generating a set of possible
events from the current basin. After each event, the simulation is
reflected backwards into the current basin. This is repeated until
the stopping criterion is satisfied, at which point the event with the
earliest low-temperature occurrence time is selected. The stopping
criterion is that the confidence measure be greater than
1-<I>delta</I>. The confidence measure is the probability that no earlier
low-temperature event will occur at some later time in the
high-temperature simulation. hTST provides an lower bound for this
probability, based on the user-specified minimum pre-exponential
factor (reciprocal of <I>tmax</I>).
</P>
<P>In order to estimate the energy barrier for each event, the TAD method
invokes the <A HREF = "neb.html">NEB</A> method. Each NEB replica runs on a
partition of processors. The current NEB implementation in LAMMPS
restricts you to having exactly one processor per replica. For more
information, see the documentation for the <A HREF = "neb.html">neb</A> command. In
the current LAMMPS implementation of TAD, all the non-NEB TAD
operations are performed on the first partition, while the other
partitions remain idle. See <A HREF = "Section_howto.html#howto_5">this section</A>
of the manual for further discussion of multi-replica simulations.
</P>
<P>A TAD run has several stages, which are repeated each time an event is
performed. The logic for a TAD run is as follows:
</P>
<PRE>while (time remains):
while (time < tstop):
until (event occurs):
run dynamics for t_event steps
quench
run neb calculation using all replicas
compute tlo from energy barrier
update earliest event
update tstop
reflect back into current basin
execute earliest event
</PRE>
<P>Before this outer loop begins, the initial potential energy basin is
identified by quenching (an energy minimization, see below) the
initial state and storing the resulting coordinates for reference.
</P>
<P>Inside the inner loop, dynamics is run continuously according to
whatever integrator has been specified by the user, stopping every
<I>t_event</I> steps to check if a transition event has occurred. This
check is performed by quenching the system and comparing the resulting
atom coordinates to the coordinates from the previous basin.
</P>
<P>A quench is an energy minimization and is performed by whichever
algorithm has been defined by the <I>min</I> and <I>min_style</I> keywords or
their default values. Note that typically, you do not need to perform
a highly-converged minimization to detect a transition event.
</P>
<P>The event check is performed by a compute with the specified
<I>compute-ID</I>. Currently there is only one compute that works with the
TAD commmand, which is the <A HREF = "compute_event_displace.html">compute
event/displace</A> command. Other
event-checking computes may be added. <A HREF = "compute_event_displace.html">Compute
event/displace</A> checks whether any atom in
the compute group has moved further than a specified threshold
distance. If so, an "event" has occurred.
</P>
<P>The neb calculation is similar to that invoked by the <A HREF = "neb.html">neb</A>
command, except that the final state is generated internally, instead
of being read in from a file. The TAD implementation provides default
values for the NEB settings, which can be overridden using the <I>neb</I>
and <I>neb_style</I> keywords.
</P>
<HR>
<P>A key aspect of the TAD method is setting the stopping criterion
appropriately. If this criterion is too conservative, then many
events must be generated before one is finally executed. Conversely,
if this criterion is too aggressive, high-entropy high-barrier events
will be over-sampled, while low-entropy low-barrier events will be
under-sampled. If the lowest pre-exponential factor is known fairly
accurately, then it can be used to estimate <I>tmax</I>, and the value of
<I>delta</I> can be set to the desired confidence level e.g. <I>delta</I> = 0.05
corresponds to 95% confidence. However, for systems where the dynamics
are not well characterized (the most common case), it will be
necessary to experiment with the values of <I>delta</I> and <I>tmax</I> to get a
good trade-off between accuracy and performance.
</P>
<P>A second key aspect is the choice of <I>t_hi</I>. A larger value greatly
increases the rate at which new events are generated. However, too
large a value introduces errors due to anharmonicity (not accounted
for within hTST). Once again, for any given system, experimentation is
necessary to determine the best value of <I>t_hi</I>.
</P>
<HR>
<P>Five kinds of output can be generated during a TAD run: event
statistics, NEB statistics, thermodynamic output by each replica, dump
files, and restart files.
</P>
<P>Event statistics are printed to the screen and master log.lammps file
each time an event is executed. The quantities are the timestep, CPU
time, global event number <I>N</I>, local event number <I>M</I>, event status,
energy barrier, time margin, <I>t_lo</I> and <I>delt_lo</I>. The timestep is
the usual LAMMPS timestep, which corresponds to the high-temperature
time at which the event was detected, in units of timestep. The CPU
time is the total processor time since the start of the TAD run. The
global event number <I>N</I> is a counter that increments with each
executed event. The local event number <I>M</I> is a counter that resets to
zero upon entering each new basin. The event status is <I>E</I> when an
event is executed, and is <I>D</I> for an event that is detected, while
<I>DF</I> is for a detected event that is also the earliest (first) event
at the low temperature.
</P>
<P>The time margin is the ratio of the high temperature time in the
current basin to the stopping time. This last number can be used to
judge whether the stopping time is too short or too long (see above).
</P>
<P><I>t_lo</I> is the low-temperature event time when the current basin was
entered, in units of timestep. del<I>t_lo</I> is the time of each detected
event, measured relative to <I>t_lo</I>. <I>delt_lo</I> is equal to the
high-temperature time since entering the current basin, scaled by an
exponential factor that depends on the hi/lo temperature ratio and the
energy barrier for that event.
</P>
<P>On lines for executed events, with status <I>E</I>, the global event number
is incremented by one, and the timestep, local event number, energy
barrier, <I>t_lo</I>, and <I>delt_lo</I> match the last event with status <I>DF</I>
in the immediately preceding block of detected events.
</P>
<P>The NEB statistics are written to the file specified by the <I>neb_log</I>
keyword. If the keyword value is "none", then no NEB statistics are
printed out. The statistics are written every <I>Nevery</I> timesteps. See
the <A HREF = "neb.html">neb</A> command for a full description of the NEB
statistics. When invoked from TAD, NEB statistics are never printed to
the screen.
</P>
<P>Because the NEB calculation must run on multiple partitions, LAMMPS
produces additional screen and log files for each partition,
e.g. log.lammps.0, log.lammps.1, etc. For the TAD command, these
contain the thermodynamic output of each NEB replica. In addition, the
log file for the first partition, log.lammps.0, will contain
thermodynamic output from short runs and minimizations corresponding
to the dynamics and quench operations, as well as a line for each new
detected event, as described above.
</P>
<P>After the TAD command completes, timing statistics for the TAD run are
printed in each replica's log file, giving a breakdown of how much CPU
time was spent in each stage (NEB, dynamics, quenching, etc).
</P>
<P>Any <A HREF = "dump.html">dump files</A> defined in the input script will be written
to during a TAD run at timesteps when an event is executed. This
means the the requested dump frequency in the <A HREF = "dump.html">dump</A> command
is ignored. There will be one dump file (per dump command) created
for all partitions. The atom coordinates of the dump snapshot are
those of the minimum energy configuration resulting from quenching
following the executed event. The timesteps written into the dump
files correspond to the timestep at which the event occurred and NOT
the clock. A dump snapshot corresponding to the initial minimum state
used for event detection is written to the dump file at the beginning
of each TAD run.
</P>
<P>If the <A HREF = "restart.html">restart</A> command is used, a single restart file
for all the partitions is generated, which allows a TAD run to be
continued by a new input script in the usual manner. The restart file
is generated after an event is executed. The restart file contains a
snapshot of the system in the new quenched state, including the event
number and the low-temperature time. The restart frequency specified
in the <A HREF = "restart.html">restart</A> command is interpreted differently when
performing a TAD run. It does not mean the timestep interval between
restart files. Instead it means an event interval for executed
events. Thus a frequency of 1 means write a restart file every time
an event is executed. A frequency of 10 means write a restart file
every 10th executed event. When an input script reads a restart file
from a previous TAD run, the new script can be run on a different
number of replicas or processors.
</P>
<P>Note that within a single state, the dynamics will typically
temporarily continue beyond the event that is ultimately chosen, until
the stopping criterionis satisfied. When the event is eventually
executed, the timestep counter is reset to the value when the event
was detected. Similarly, after each quench and NEB minimization, the
timestep counter is reset to the value at the start of the
minimization. This means that the timesteps listed in the replica log
files do not always increase monotonically. However, the timestep
values printed to the master log file, dump files, and restart files
are always monotonically increasing.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>This command can only be used if LAMMPS was built with the "replica"
+<P>This command can only be used if LAMMPS was built with the REPLICA
package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info on packages.
</P>
<P><I>N</I> setting must be integer multiple of <I>t_event</I>.
</P>
<P>Runs restarted from restart files written during a TAD run will only
produce identical results if the user-specified integrator supports
exact restarts. So <A HREF = "fix_nh.html">fix nvt</A> will produce an exact
restart, but <A HREF = "fix_langevin.html">fix langevin</A> will not.
</P>
<P>This command cannot be used when any fixes are defined that keep track
of elapsed time to perform time-dependent operations. Examples
include the "ave" fixes such as <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A>. Also <A HREF = "fix_dt_reset.html">fix
dt/reset</A> and <A HREF = "fix_deposit.html">fix deposit</A>.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_event_displace.html">compute event/displace</A>,
<A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_style.html">min_style</A>,
<A HREF = "run_style.html">run_style</A>, <A HREF = "minimize.html">minimize</A>,
<A HREF = "temper.html">temper</A>, <A HREF = "neb.html">neb</A>,
<A HREF = "prd.html">prd</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are <I>min</I> = 0.1 0.1 40 50, <I>neb</I> = 0.01 100 100
10, <I>min_style</I> = <I>cg</I>, <I>neb_style</I> = <I>quickmin</I>, and <I>neb_log</I> =
"none"
</P>
<HR>
<A NAME = "Voter"></A>
<P><B>(Voter)</B> Sørensen and Voter, J Chem Phys, 112, 9599 (2000)
</P>
<A NAME = "Voter2"></A>
<P><B>(Voter2)</B> Voter, Montalenti, Germann, Annual Review of Materials
Research 32, 321 (2002).
</P>
</HTML>
diff --git a/doc/tad.txt b/doc/tad.txt
index 85115cfa2..f18edb067 100644
--- a/doc/tad.txt
+++ b/doc/tad.txt
@@ -1,300 +1,300 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
tad command :h3
[Syntax:]
tad N t_event T_lo T_hi delta tmax compute-ID \
seed keyword value ... :pre
N = # of timesteps to run (not including dephasing/quenching) :ulb,l
t_event = timestep interval between event checks :l
T_lo = temperature at which event times are desired :l
T_hi = temperature at which MD simulation is performed :l
delta = desired confidence level for stopping criterion :l
tmax = reciprocal of lowest expected preexponential factor (time units) :l
compute-ID = ID of the compute used for event detection :l
zero or more keyword/value pairs may be appended :l
keyword = {min} or {neb} or {min_style} or {neb_style} or {neb_log} :l
{min} values = etol ftol maxiter maxeval
etol = stopping tolerance for energy (energy units)
ftol = stopping tolerance for force (force units)
maxiter = max iterations of minimize
maxeval = max number of force/energy evaluations
{neb} values = ftol N1 N2 Nevery
etol = stopping tolerance for energy (energy units)
ftol = stopping tolerance for force (force units)
N1 = max # of iterations (timesteps) to run initial NEB
N2 = max # of iterations (timesteps) to run barrier-climbing NEB
Nevery = print NEB statistics every this many timesteps
{min_style} value = {cg} or {hftn} or {sd} or {quickmin} or {fire}
{neb_style} value = {quickmin} or {fire}
{neb_log} value = file where NEB statistics are printed :pre
:ule
[Examples:]
tad 2000 50 1800 2300 0.01 0.01 event 54985
tad 2000 50 1800 2300 0.01 0.01 event 54985 &
min 1e-05 1e-05 100 100 &
neb 0.0 0.01 200 200 20 &
min_style cg &
neb_style fire &
neb_log log.neb :pre
[Description:]
Run a temperature accelerated dynamics (TAD) simulation. This method
requires two or more partitions to perform NEB transition state
searches.
TAD is described in "this paper"_#Voter by Art Voter. It is a method
that uses accelerated dynamics at an elevated temperature to generate
results at a specified lower temperature. A good overview of
accelerated dynamics methods for such systems is given in "this review
paper"_#Voter2 from the same group. In general, these methods assume
that the long-time dynamics is dominated by infrequent events i.e. the
system is is confined to low energy basins for long periods,
punctuated by brief, randomly-occurring transitions to adjacent
basins. TAD is suitable for infrequent-event systems, where in
addition, the transition kinetics are well-approximated by harmonic
transition state theory (hTST). In hTST, the temperature dependence of
transition rates follows the Arrhenius relation. As a consequence a
set of event times generated in a high-temperature simulation can be
mapped to a set of much longer estimated times in the low-temperature
system. However, because this mapping involves the energy barrier of
the transition event, which is different for each event, the first
event at the high temperature may not be the earliest event at the low
temperature. TAD handles this by first generating a set of possible
events from the current basin. After each event, the simulation is
reflected backwards into the current basin. This is repeated until
the stopping criterion is satisfied, at which point the event with the
earliest low-temperature occurrence time is selected. The stopping
criterion is that the confidence measure be greater than
1-{delta}. The confidence measure is the probability that no earlier
low-temperature event will occur at some later time in the
high-temperature simulation. hTST provides an lower bound for this
probability, based on the user-specified minimum pre-exponential
factor (reciprocal of {tmax}).
In order to estimate the energy barrier for each event, the TAD method
invokes the "NEB"_neb.html method. Each NEB replica runs on a
partition of processors. The current NEB implementation in LAMMPS
restricts you to having exactly one processor per replica. For more
information, see the documentation for the "neb"_neb.html command. In
the current LAMMPS implementation of TAD, all the non-NEB TAD
operations are performed on the first partition, while the other
partitions remain idle. See "this section"_Section_howto.html#howto_5
of the manual for further discussion of multi-replica simulations.
A TAD run has several stages, which are repeated each time an event is
performed. The logic for a TAD run is as follows:
while (time remains):
while (time < tstop):
until (event occurs):
run dynamics for t_event steps
quench
run neb calculation using all replicas
compute tlo from energy barrier
update earliest event
update tstop
reflect back into current basin
execute earliest event :pre
Before this outer loop begins, the initial potential energy basin is
identified by quenching (an energy minimization, see below) the
initial state and storing the resulting coordinates for reference.
Inside the inner loop, dynamics is run continuously according to
whatever integrator has been specified by the user, stopping every
{t_event} steps to check if a transition event has occurred. This
check is performed by quenching the system and comparing the resulting
atom coordinates to the coordinates from the previous basin.
A quench is an energy minimization and is performed by whichever
algorithm has been defined by the {min} and {min_style} keywords or
their default values. Note that typically, you do not need to perform
a highly-converged minimization to detect a transition event.
The event check is performed by a compute with the specified
{compute-ID}. Currently there is only one compute that works with the
TAD commmand, which is the "compute
event/displace"_compute_event_displace.html command. Other
event-checking computes may be added. "Compute
event/displace"_compute_event_displace.html checks whether any atom in
the compute group has moved further than a specified threshold
distance. If so, an "event" has occurred.
The neb calculation is similar to that invoked by the "neb"_neb.html
command, except that the final state is generated internally, instead
of being read in from a file. The TAD implementation provides default
values for the NEB settings, which can be overridden using the {neb}
and {neb_style} keywords.
:line
A key aspect of the TAD method is setting the stopping criterion
appropriately. If this criterion is too conservative, then many
events must be generated before one is finally executed. Conversely,
if this criterion is too aggressive, high-entropy high-barrier events
will be over-sampled, while low-entropy low-barrier events will be
under-sampled. If the lowest pre-exponential factor is known fairly
accurately, then it can be used to estimate {tmax}, and the value of
{delta} can be set to the desired confidence level e.g. {delta} = 0.05
corresponds to 95% confidence. However, for systems where the dynamics
are not well characterized (the most common case), it will be
necessary to experiment with the values of {delta} and {tmax} to get a
good trade-off between accuracy and performance.
A second key aspect is the choice of {t_hi}. A larger value greatly
increases the rate at which new events are generated. However, too
large a value introduces errors due to anharmonicity (not accounted
for within hTST). Once again, for any given system, experimentation is
necessary to determine the best value of {t_hi}.
:line
Five kinds of output can be generated during a TAD run: event
statistics, NEB statistics, thermodynamic output by each replica, dump
files, and restart files.
Event statistics are printed to the screen and master log.lammps file
each time an event is executed. The quantities are the timestep, CPU
time, global event number {N}, local event number {M}, event status,
energy barrier, time margin, {t_lo} and {delt_lo}. The timestep is
the usual LAMMPS timestep, which corresponds to the high-temperature
time at which the event was detected, in units of timestep. The CPU
time is the total processor time since the start of the TAD run. The
global event number {N} is a counter that increments with each
executed event. The local event number {M} is a counter that resets to
zero upon entering each new basin. The event status is {E} when an
event is executed, and is {D} for an event that is detected, while
{DF} is for a detected event that is also the earliest (first) event
at the low temperature.
The time margin is the ratio of the high temperature time in the
current basin to the stopping time. This last number can be used to
judge whether the stopping time is too short or too long (see above).
{t_lo} is the low-temperature event time when the current basin was
entered, in units of timestep. del{t_lo} is the time of each detected
event, measured relative to {t_lo}. {delt_lo} is equal to the
high-temperature time since entering the current basin, scaled by an
exponential factor that depends on the hi/lo temperature ratio and the
energy barrier for that event.
On lines for executed events, with status {E}, the global event number
is incremented by one, and the timestep, local event number, energy
barrier, {t_lo}, and {delt_lo} match the last event with status {DF}
in the immediately preceding block of detected events.
The NEB statistics are written to the file specified by the {neb_log}
keyword. If the keyword value is "none", then no NEB statistics are
printed out. The statistics are written every {Nevery} timesteps. See
the "neb"_neb.html command for a full description of the NEB
statistics. When invoked from TAD, NEB statistics are never printed to
the screen.
Because the NEB calculation must run on multiple partitions, LAMMPS
produces additional screen and log files for each partition,
e.g. log.lammps.0, log.lammps.1, etc. For the TAD command, these
contain the thermodynamic output of each NEB replica. In addition, the
log file for the first partition, log.lammps.0, will contain
thermodynamic output from short runs and minimizations corresponding
to the dynamics and quench operations, as well as a line for each new
detected event, as described above.
After the TAD command completes, timing statistics for the TAD run are
printed in each replica's log file, giving a breakdown of how much CPU
time was spent in each stage (NEB, dynamics, quenching, etc).
Any "dump files"_dump.html defined in the input script will be written
to during a TAD run at timesteps when an event is executed. This
means the the requested dump frequency in the "dump"_dump.html command
is ignored. There will be one dump file (per dump command) created
for all partitions. The atom coordinates of the dump snapshot are
those of the minimum energy configuration resulting from quenching
following the executed event. The timesteps written into the dump
files correspond to the timestep at which the event occurred and NOT
the clock. A dump snapshot corresponding to the initial minimum state
used for event detection is written to the dump file at the beginning
of each TAD run.
If the "restart"_restart.html command is used, a single restart file
for all the partitions is generated, which allows a TAD run to be
continued by a new input script in the usual manner. The restart file
is generated after an event is executed. The restart file contains a
snapshot of the system in the new quenched state, including the event
number and the low-temperature time. The restart frequency specified
in the "restart"_restart.html command is interpreted differently when
performing a TAD run. It does not mean the timestep interval between
restart files. Instead it means an event interval for executed
events. Thus a frequency of 1 means write a restart file every time
an event is executed. A frequency of 10 means write a restart file
every 10th executed event. When an input script reads a restart file
from a previous TAD run, the new script can be run on a different
number of replicas or processors.
Note that within a single state, the dynamics will typically
temporarily continue beyond the event that is ultimately chosen, until
the stopping criterionis satisfied. When the event is eventually
executed, the timestep counter is reset to the value when the event
was detected. Similarly, after each quench and NEB minimization, the
timestep counter is reset to the value at the start of the
minimization. This means that the timesteps listed in the replica log
files do not always increase monotonically. However, the timestep
values printed to the master log file, dump files, and restart files
are always monotonically increasing.
:line
[Restrictions:]
-This command can only be used if LAMMPS was built with the "replica"
+This command can only be used if LAMMPS was built with the REPLICA
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info on packages.
{N} setting must be integer multiple of {t_event}.
Runs restarted from restart files written during a TAD run will only
produce identical results if the user-specified integrator supports
exact restarts. So "fix nvt"_fix_nh.html will produce an exact
restart, but "fix langevin"_fix_langevin.html will not.
This command cannot be used when any fixes are defined that keep track
of elapsed time to perform time-dependent operations. Examples
include the "ave" fixes such as "fix
ave/spatial"_fix_ave_spatial.html. Also "fix
dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposit.html.
[Related commands:]
"compute event/displace"_compute_event_displace.html,
"min_modify"_min_modify.html, "min_style"_min_style.html,
"run_style"_run_style.html, "minimize"_minimize.html,
"temper"_temper.html, "neb"_neb.html,
"prd"_prd.html
[Default:]
The option defaults are {min} = 0.1 0.1 40 50, {neb} = 0.01 100 100
10, {min_style} = {cg}, {neb_style} = {quickmin}, and {neb_log} =
"none"
:line
:link(Voter)
[(Voter)] Sørensen and Voter, J Chem Phys, 112, 9599 (2000)
:link(Voter2)
[(Voter2)] Voter, Montalenti, Germann, Annual Review of Materials
Research 32, 321 (2002).
diff --git a/doc/temper.html b/doc/temper.html
index ce9f7e8b4..790cc891e 100644
--- a/doc/temper.html
+++ b/doc/temper.html
@@ -1,137 +1,137 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>temper command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>temper N M temp fix-ID seed1 seed2 index
</PRE>
<UL><LI>N = total # of timesteps to run
<LI>M = attempt a tempering swap every this many steps
<LI>temp = initial temperature for this ensemble
<LI>fix-ID = ID of the fix that will control temperature during the run
<LI>seed1 = random # seed used to decide on adjacent temperature to partner with
<LI>seed2 = random # seed for Boltzmann factor in Metropolis swap
<LI>index = which temperature (0 to N-1) I am simulating (optional)
</UL>
<P><B>Examples:</B>
</P>
<PRE>temper 100000 100 $t tempfix 0 58728
temper 40000 100 $t tempfix 0 32285 $w
</PRE>
<P><B>Description:</B>
</P>
<P>Run a parallel tempering or replica exchange simulation using multiple
replicas (ensembles) of a system. Two or more replicas must be used.
</P>
<P>Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
switch; see <A HREF = "Section_start.html#start_6">this section</A> of the manual.
Note that if you have MPI installed, you can run a multi-replica
simulation with more replicas (partitions) than you have physical
processors, e.g you can run a 10-replica simulation on one or two
processors. You will simply not get the performance speed-up you
would see with one or more physical processors per replica. See <A HREF = "Section_howto.html#howto_5">this
section</A> of the manual for further
discussion.
</P>
<P>Each replica's temperature is controlled at a different value by a fix
with <I>fix-ID</I> that controls temperature. Possible fix styles are
<A HREF = "fix_nh.html">nvt</A>, <A HREF = "fix_nh.html">temp/berendsen</A>,
<A HREF = "fix_langevin.html">langevin</A> and <A HREF = "fix_temp_rescale.html">temp/rescale</A>.
The desired temperature is specified by <I>temp</I>, which is typically a
variable previously set in the input script, so that each partition is
assigned a different temperature. See the <A HREF = "variable.html">variable</A>
command for more details. For example:
</P>
<PRE>variable t world 300.0 310.0 320.0 330.0
fix myfix all nvt $t $t 100.0
temper 100000 100 $t myfix 3847 58382
</PRE>
<P>would define 4 temperatures, and assign one of them to the thermostat
used by each replica, and to the temper command.
</P>
<P>As the tempering simulation runs for <I>N</I> timesteps, a temperature swap
between adjacent ensembles will be attempted every <I>M</I> timesteps. If
<I>seed1</I> is 0, then the swap attempts will alternate between odd and
even pairings. If <I>seed1</I> is non-zero then it is used as a seed in a
random number generator to randomly choose an odd or even pairing each
time. Each attempted swap of temperatures is either accepted or
rejected based on a Boltzmann-weighted Metropolis criterion which uses
<I>seed2</I> in the random number generator.
</P>
<P>As a tempering run proceeds, multiple log files and screen output
files are created, one per replica. By default these files are named
log.lammps.M and screen.M where M is the replica number from 0 to N-1,
with N = # of replicas. See the <A HREF = "Section_start.html#start_6">section on command-line
switches</A> for info on how to change these
names.
</P>
<P>The main screen and log file (log.lammps) will list information about
which temperature is assigned to each replica at each thermodynamic
output timestep. E.g. for a simulation with 16 replicas:
</P>
<PRE>Running on 16 partitions of processors
Step T0 T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11 T12 T13 T14 T15
0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
500 1 0 3 2 5 4 6 7 8 9 10 11 12 13 14 15
1000 2 0 4 1 5 3 6 7 8 9 10 11 12 14 13 15
1500 2 1 4 0 5 3 6 7 9 8 10 11 12 14 13 15
2000 2 1 3 0 6 4 5 7 10 8 9 11 12 14 13 15
2500 2 1 3 0 6 4 5 7 11 8 9 10 12 14 13 15
...
</PRE>
<P>The column headings T0 to TN-1 mean which temperature is currently
assigned to the replica 0 to N-1. Thus the columns represent replicas
and the value in each column is its temperature (also numbered 0 to
N-1). For example, a 0 in the 4th column (column T3, step 2500) means
that the 4th replica is assigned temperature 0, i.e. the lowest
temperature. You can verify this time sequence of temperature
assignments for the Nth replica by comparing the Nth column of screen
output to the thermodynamic data in the corresponding log.lammps.N or
screen.N files as time proceeds.
</P>
<P>The last argument <I>index</I> in the temper command is optional and is
used when restarting a tempering run from a set of restart files (one
for each replica) which had previously swapped to new temperatures.
The <I>index</I> value (from 0 to N-1, where N is the # of replicas)
identifies which temperature the replica was simulating on the
timestep the restart files were written. Obviously, this argument
must be a variable so that each partition has the correct value. Set
the variable to the <I>N</I> values listed in the log file for the previous
run for the replica temperatures at that timestep. For example if the
log file listed the following for a simulation with 5 replicas:
</P>
<PRE>500000 2 4 0 1 3
</PRE>
<P>then a setting of
</P>
<PRE>variable w proc 2 4 0 1 3
</PRE>
<P>would be used to restart the run with a tempering command like the
example above with $w as the last argument.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>This command can only be used if LAMMPS was built with the "replica"
+<P>This command can only be used if LAMMPS was built with the REPLICA
package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "variable.html">variable</A>, <A HREF = "prd.html">prd</A>, <A HREF = "neb.html">neb</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/temper.txt b/doc/temper.txt
index ac79b6e5d..c7cda7cbe 100644
--- a/doc/temper.txt
+++ b/doc/temper.txt
@@ -1,132 +1,132 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
temper command :h3
[Syntax:]
temper N M temp fix-ID seed1 seed2 index :pre
N = total # of timesteps to run
M = attempt a tempering swap every this many steps
temp = initial temperature for this ensemble
fix-ID = ID of the fix that will control temperature during the run
seed1 = random # seed used to decide on adjacent temperature to partner with
seed2 = random # seed for Boltzmann factor in Metropolis swap
index = which temperature (0 to N-1) I am simulating (optional) :ul
[Examples:]
temper 100000 100 $t tempfix 0 58728
temper 40000 100 $t tempfix 0 32285 $w :pre
[Description:]
Run a parallel tempering or replica exchange simulation using multiple
replicas (ensembles) of a system. Two or more replicas must be used.
Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
switch; see "this section"_Section_start.html#start_6 of the manual.
Note that if you have MPI installed, you can run a multi-replica
simulation with more replicas (partitions) than you have physical
processors, e.g you can run a 10-replica simulation on one or two
processors. You will simply not get the performance speed-up you
would see with one or more physical processors per replica. See "this
section"_Section_howto.html#howto_5 of the manual for further
discussion.
Each replica's temperature is controlled at a different value by a fix
with {fix-ID} that controls temperature. Possible fix styles are
"nvt"_fix_nh.html, "temp/berendsen"_fix_nh.html,
"langevin"_fix_langevin.html and "temp/rescale"_fix_temp_rescale.html.
The desired temperature is specified by {temp}, which is typically a
variable previously set in the input script, so that each partition is
assigned a different temperature. See the "variable"_variable.html
command for more details. For example:
variable t world 300.0 310.0 320.0 330.0
fix myfix all nvt $t $t 100.0
temper 100000 100 $t myfix 3847 58382 :pre
would define 4 temperatures, and assign one of them to the thermostat
used by each replica, and to the temper command.
As the tempering simulation runs for {N} timesteps, a temperature swap
between adjacent ensembles will be attempted every {M} timesteps. If
{seed1} is 0, then the swap attempts will alternate between odd and
even pairings. If {seed1} is non-zero then it is used as a seed in a
random number generator to randomly choose an odd or even pairing each
time. Each attempted swap of temperatures is either accepted or
rejected based on a Boltzmann-weighted Metropolis criterion which uses
{seed2} in the random number generator.
As a tempering run proceeds, multiple log files and screen output
files are created, one per replica. By default these files are named
log.lammps.M and screen.M where M is the replica number from 0 to N-1,
with N = # of replicas. See the "section on command-line
switches"_Section_start.html#start_6 for info on how to change these
names.
The main screen and log file (log.lammps) will list information about
which temperature is assigned to each replica at each thermodynamic
output timestep. E.g. for a simulation with 16 replicas:
Running on 16 partitions of processors
Step T0 T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11 T12 T13 T14 T15
0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
500 1 0 3 2 5 4 6 7 8 9 10 11 12 13 14 15
1000 2 0 4 1 5 3 6 7 8 9 10 11 12 14 13 15
1500 2 1 4 0 5 3 6 7 9 8 10 11 12 14 13 15
2000 2 1 3 0 6 4 5 7 10 8 9 11 12 14 13 15
2500 2 1 3 0 6 4 5 7 11 8 9 10 12 14 13 15
... :pre
The column headings T0 to TN-1 mean which temperature is currently
assigned to the replica 0 to N-1. Thus the columns represent replicas
and the value in each column is its temperature (also numbered 0 to
N-1). For example, a 0 in the 4th column (column T3, step 2500) means
that the 4th replica is assigned temperature 0, i.e. the lowest
temperature. You can verify this time sequence of temperature
assignments for the Nth replica by comparing the Nth column of screen
output to the thermodynamic data in the corresponding log.lammps.N or
screen.N files as time proceeds.
The last argument {index} in the temper command is optional and is
used when restarting a tempering run from a set of restart files (one
for each replica) which had previously swapped to new temperatures.
The {index} value (from 0 to N-1, where N is the # of replicas)
identifies which temperature the replica was simulating on the
timestep the restart files were written. Obviously, this argument
must be a variable so that each partition has the correct value. Set
the variable to the {N} values listed in the log file for the previous
run for the replica temperatures at that timestep. For example if the
log file listed the following for a simulation with 5 replicas:
500000 2 4 0 1 3 :pre
then a setting of
variable w proc 2 4 0 1 3 :pre
would be used to restart the run with a tempering command like the
example above with $w as the last argument.
:line
[Restrictions:]
-This command can only be used if LAMMPS was built with the "replica"
+This command can only be used if LAMMPS was built with the REPLICA
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info on packages.
[Related commands:]
"variable"_variable.html, "prd"_prd.html, "neb"_neb.html
[Default:] none
diff --git a/examples/USER/sph/README b/examples/USER/sph/README
new file mode 100644
index 000000000..b5a1acc61
--- /dev/null
+++ b/examples/USER/sph/README
@@ -0,0 +1 @@
+see the USER-SPH user's guide for a detailed explanation of these examples.
diff --git a/examples/USER/sph/cavity_flow/cavity_flow.lmp b/examples/USER/sph/cavity_flow/cavity_flow.lmp
new file mode 100644
index 000000000..3348c42b9
--- /dev/null
+++ b/examples/USER/sph/cavity_flow/cavity_flow.lmp
@@ -0,0 +1,63 @@
+dimension 2
+units si
+atom_style meso
+
+# create simulation box
+region box block -0.050e-3 1.044e-3 -0.05e-3 1.044e-3 -1.0e-6 1.0e-6 units box
+create_box 3 box
+
+# create fluid particles
+region fluid block 0.0001e-3 0.999e-3 0.0001e-3 0.999e-3 EDGE EDGE side in units box
+lattice sq 0.025e-3
+create_atoms 1 region fluid
+
+# create bottom, left, and right wall
+region walls block 0.0001e-3 0.999e-3 0.0001e-3 EDGE EDGE EDGE side out units box
+lattice sq2 0.025e-3
+create_atoms 2 region walls
+
+# create a driver strip of particles, which exerts shear forces on the fluid
+region driver block EDGE EDGE 0.999e-3 EDGE EDGE EDGE side in units box
+create_atoms 3 region driver
+
+group fluid type 1
+group walls type 2
+group driver type 3
+group integrate_full union fluid driver
+
+mass 3 2.0e-7
+mass 2 2.0e-7
+mass 1 4.0e-7
+set group all meso_rho 1000.0
+
+# use Tait's EOS in combination with Morris' laminar viscosity.
+# We set rho_0 = 1000 kg/m^3, c = 0.1 m/s, h = 6.5e-5 m.
+# The dynamic viscosity is set to 1.0e-3 Pa s, corresponding to a kinematic viscosity of 1.0e-6 m^2/s
+pair_style hybrid sph/taitwater/morris
+pair_coeff * * sph/taitwater/morris 1000 0.1 1.0e-3 6.5e-5
+pair_coeff 2 3 none # exclude interaction between walls and shear driver
+
+compute rho_peratom all meso_rho/atom
+compute e_peratom all meso_e/atom
+compute ke_peratom all ke/atom
+compute esph all reduce sum c_e_peratom
+compute ke all ke
+variable etot equal c_ke+c_esph
+
+# assign a constant velocity to shear driver
+velocity driver set 0.001 0.0 0.0 units box
+fix freeze_fix driver setforce 0.0 0.0 0.0
+
+# do full time integration for shear driver and fluid, but keep walls stationary
+fix integrate_fix_full integrate_full meso
+fix integrate_fix_stationary walls meso/stationary
+
+dump dump_id all custom 100 dump.lammpstrj id type xs ys zs vx vy c_rho_peratom c_e_peratom
+dump_modify dump_id first yes
+thermo 100
+thermo_style custom step c_esph v_etot
+thermo_modify norm no
+
+neighbor 3.0e-6 bin
+timestep 5.0e-5
+run 4000
diff --git a/examples/USER/sph/heatconduction/compare_analytic.gpl b/examples/USER/sph/heatconduction/compare_analytic.gpl
new file mode 100755
index 000000000..602da6a69
--- /dev/null
+++ b/examples/USER/sph/heatconduction/compare_analytic.gpl
@@ -0,0 +1,24 @@
+#!/usr/bin/gnuplot
+
+# compare sph/heatconduction output with analytic solution to diffusion equation
+
+alpha = 1.0e-4
+time = 4.0
+
+analytic_profile(x) = 1.5 + 0.5*erf((x-49.5e-2)/sqrt(4.0*alpha*time))
+
+set ylabel "internal energy per particle"
+set xlabel "x position [m]"
+
+plot [][0.5:2.5]'dump.last' u 3:6 ti "SPH simulation", analytic_profile(x) ti "analytic solution"
+
+pause -1
+#set terminal postscript color enhanced lw 2
+#set out "heat_profile.ps"
+set table "simu.dat"
+plot [0:1][0.5:2.5]'dump.last' u 3:6
+
+set table "analytic.dat"
+set samples 1000
+plot [0:1][0.5:2.5] analytic_profile(x)
+#replot
diff --git a/examples/USER/sph/heatconduction/sph_heat_conduction_2d.lmp b/examples/USER/sph/heatconduction/sph_heat_conduction_2d.lmp
new file mode 100644
index 000000000..2538a2fab
--- /dev/null
+++ b/examples/USER/sph/heatconduction/sph_heat_conduction_2d.lmp
@@ -0,0 +1,51 @@
+# mesoscopic heat conduction
+# heat flow from hot right region to cold left region
+# compare the temperature profile at the end opf the simulation,
+# contained in file dump.last, to analytic solution.
+#
+#
+dimension 2
+units si
+atom_style meso
+boundary f p p
+
+lattice sq 0.01
+region box block 0 100 0 10 0 0.1
+create_box 1 box
+create_atoms 1 box
+mass 1 1.0e-5
+
+region left block EDGE 49.9 EDGE EDGE EDGE EDGE
+region right block 50 EDGE EDGE EDGE EDGE EDGE
+set region left meso_e 1.0 # internal energies
+set region right meso_e 2.0
+set group all meso_rho 0.1 # mesoscopic density is also needed for this pair style
+# For correct temperature profiles, mescoscopic density and mass * number density must coincide!
+
+pair_style sph/heatconduction
+# i j diffusion coeff. cutoff
+pair_coeff 1 1 1.0e-4 2.0e-2
+
+compute ie_atom all meso_e/atom
+compute ie all reduce sum c_ie_atom
+
+thermo 10
+thermo_style custom step temp c_ie
+timestep 0.25e-1
+neighbor 0.2e-2 bin
+fix integrate_fix all meso/stationary
+
+dump dump_fix all custom 10 dump.heat id type x y z c_ie_atom
+dump_modify dump_fix first yes
+run 160
+undump dump_fix
+
+dump dump_fix all custom 10 dump.last id type x y z c_ie_atom
+dump_modify dump_fix first yes
+run 0
+undump dump_fix
+
+dump dump_fix all custom 10 dump.last.xs id type xs ys zs c_ie_atom
+dump_modify dump_fix first yes
+run 0
+undump dump_fix
diff --git a/examples/USER/sph/heatconduction/sph_heat_conduction_3d.lmp b/examples/USER/sph/heatconduction/sph_heat_conduction_3d.lmp
new file mode 100644
index 000000000..f34cc054c
--- /dev/null
+++ b/examples/USER/sph/heatconduction/sph_heat_conduction_3d.lmp
@@ -0,0 +1,49 @@
+# mesoscopic heat conduction
+# heat flow from hot right region to cold left region
+# compare the temperature profile at the end opf the simulation,
+# contained in file dump.last, to analytic solution.
+#
+#
+units si
+atom_style meso
+newton on
+boundary f p p
+
+lattice sc 0.01
+region box block 0 100 0 10 0 10
+create_box 1 box
+create_atoms 1 box
+mass 1 1.0e-5
+
+region left block EDGE 49.9 EDGE EDGE EDGE EDGE
+region right block 50 EDGE EDGE EDGE EDGE EDGE
+set region left meso_e 1.0 # internal energies
+set region right meso_e 2.0
+set group all meso_rho 10.0 # mesoscopic density is also needed for this pair style
+# For correct temperature profiles, mescoscopic density and mass * number density must coincide!
+
+pair_style sph/heatconduction
+# i j diffusion coeff. cutoff
+pair_coeff 1 1 1.0e-4 2.0e-2
+neighbor 0.2e-2 bin
+neigh_modify every 20 delay 0 check no
+
+compute ie_atom all meso_e/atom
+compute ie all reduce sum c_ie_atom
+
+thermo_style custom step temp c_ie
+thermo_modify norm no
+
+fix integrate_fix all meso/stationary
+
+thermo 10
+timestep 0.25e-1
+
+dump dump_fix all custom 10 dump.heat id type x y z c_ie_atom
+dump_modify dump_fix first yes
+run 160
+undump dump_fix
+
+dump dump_fix all custom 10 dump.last id type x y z c_ie_atom
+dump_modify dump_fix first yes
+run 0
diff --git a/examples/USER/sph/shock_tube/compare_exact.gpl b/examples/USER/sph/shock_tube/compare_exact.gpl
new file mode 100755
index 000000000..2dfef9c65
--- /dev/null
+++ b/examples/USER/sph/shock_tube/compare_exact.gpl
@@ -0,0 +1,6 @@
+#!/usr/bin/gnuplot
+
+# compare SPH shock output with exact solution
+plot 'dump.3d.last' u 3:6, "exact_solution.dat" w l
+pause -1
+
diff --git a/examples/USER/sph/shock_tube/exact_solution.dat b/examples/USER/sph/shock_tube/exact_solution.dat
new file mode 100755
index 000000000..22f960158
--- /dev/null
+++ b/examples/USER/sph/shock_tube/exact_solution.dat
@@ -0,0 +1,501 @@
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+ 4.700000E+01 2.500000E-01 0.000000E+00 2.500000E-01
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diff --git a/examples/USER/sph/shock_tube/shock2d.lmp b/examples/USER/sph/shock_tube/shock2d.lmp
new file mode 100755
index 000000000..70eb4039c
--- /dev/null
+++ b/examples/USER/sph/shock_tube/shock2d.lmp
@@ -0,0 +1,45 @@
+atom_style meso
+dimension 2
+boundary s p p
+
+region box block -100 150 -4 4 -0.1 0.1 units box
+create_box 2 box
+lattice sq 1.0
+create_atoms 1 box
+
+region left block EDGE 0.0 EDGE EDGE EDGE EDGE units box
+region right block 1 EDGE EDGE EDGE EDGE EDGE units box
+set region right type 2
+
+mass 1 1
+mass 2 0.25
+set type 1 meso_e 2.5 # internal energy corresponding to p=1, rho=1
+set type 2 meso_e 0.625 # internal energy corresponding to p=0.25, rho=0.25
+set type 1 meso_rho 1.0
+set type 2 meso_rho 0.25
+
+pair_style hybrid/overlay sph/rhosum 1 sph/idealgas
+pair_coeff * * sph/rhosum 4.0
+pair_coeff * * sph/idealgas 0.75 4.0
+
+compute rhoatom all meso_rho/atom
+compute ieatom all meso_e/atom
+compute emeso all reduce sum c_ieatom # total internal energy
+compute ke all ke
+variable etot equal c_ke+c_emeso # total energy
+
+# dump positions and local density
+dump dump_id all custom 100 dump.2d id type x z y c_rhoatom
+dump_modify dump_id first yes
+
+neighbor 0.5 bin
+neigh_modify every 5 delay 0 check yes
+thermo 10
+thermo_style custom step c_ke c_emeso v_etot
+thermo_modify norm no
+
+fix integration_fix all meso
+fix 1 all setforce NULL 0.0 0.0 # treat as a quasi 1d problem
+timestep 0.05
+log log.2d
+run 400 # run for t=20
diff --git a/examples/USER/sph/shock_tube/shock3d.lmp b/examples/USER/sph/shock_tube/shock3d.lmp
new file mode 100644
index 000000000..22a3710e3
--- /dev/null
+++ b/examples/USER/sph/shock_tube/shock3d.lmp
@@ -0,0 +1,48 @@
+atom_style meso
+boundary s p p
+
+region box block -100 150 -4 4 -4 4 units box
+create_box 2 box
+lattice sc 1.0
+create_atoms 1 box
+
+region left block EDGE 0.0 EDGE EDGE EDGE EDGE units box
+region right block 1 EDGE EDGE EDGE EDGE EDGE units box
+set region right type 2
+
+mass 1 1
+mass 2 0.25
+set type 1 meso_e 2.5 # internal energy corresponding to p=1, rho=1
+set type 2 meso_e 0.625 # internal energy corresponding to p=0.25, rho=0.25
+set type 1 meso_rho 1.0
+set type 2 meso_rho 0.25
+
+pair_style hybrid/overlay sph/rhosum 1 sph/idealgas
+pair_coeff * * sph/rhosum 4.0
+pair_coeff * * sph/idealgas 0.75 4.0
+
+compute rhoatom all meso_rho/atom
+compute ieatom all meso_e/atom
+compute emeso all reduce sum c_ieatom # total internal energy
+compute ke all ke
+variable etot equal c_ke+c_emeso # total energy
+
+# dump positions and local density
+dump dump_id all custom 100 dump.3d id type x z y c_rhoatom
+dump_modify dump_id first yes
+
+neighbor 0.5 bin
+neigh_modify every 5 delay 0 check yes
+thermo 10
+thermo_style custom step c_ke c_emeso v_etot
+thermo_modify norm no
+
+fix integration_fix all meso
+fix 1 all setforce NULL 0.0 0.0 # treat as a quasi 1d problem
+timestep 0.05
+log log.3d
+run 400 # run for t=20
+
+undump dump_id
+dump dump_id all custom 100 dump.3d.last id type x z y c_rhoatom
+run 0
diff --git a/examples/USER/sph/water_collapse/data.initial b/examples/USER/sph/water_collapse/data.initial
new file mode 100644
index 000000000..9a78b6034
--- /dev/null
+++ b/examples/USER/sph/water_collapse/data.initial
@@ -0,0 +1,31424 @@
+LAMMPS data file from restart file: timestep = 0, procs = 4
+
+15702 atoms
+
+2 atom types
+
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+0.0000000000000000e+00 8.0009999999999994e+00 ylo yhi
+-1.0000000000000000e-03 1.0000000000000000e-03 zlo zhi
+
+Masses
+
+1 0.2
+2 0.1
+
+Atoms
+
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diff --git a/examples/USER/sph/water_collapse/water_collapse.lmp b/examples/USER/sph/water_collapse/water_collapse.lmp
new file mode 100644
index 000000000..f259da6a3
--- /dev/null
+++ b/examples/USER/sph/water_collapse/water_collapse.lmp
@@ -0,0 +1,49 @@
+processors 4 1 1 # manually assign processors to spatial regions
+atom_style meso
+dimension 2
+newton on
+boundary f f p
+units lj
+read_data data.initial
+
+variable h equal 0.03
+variable c equal 10.0 # soundspeed for Tait's EOS
+variable dt equal 0.1*${h}/${c} # upper limit of timestep based on CFL-like criterion
+variable nrun equal 15.0/${dt} # roughly estimate number of timesteps needed for 7.5 seconds
+
+group bc type 2 # assign group name "bc" to boundary particles (type 2)
+group water type 1 # assign group name "water" to water particles (type 1)
+
+# use hybrid pairstyle which does density summation with cutoff ${h} every timestep (1)
+pair_style hybrid/overlay sph/rhosum 1 sph/taitwater
+pair_coeff * * sph/taitwater 1000.0 ${c} 1.0 ${h} # use target density of 1000, soundspeed ${c} for Tait's EOS
+pair_coeff 1 1 sph/rhosum ${h}
+
+fix gfix water gravity -9.81 vector 0 1 0 # add gravity. This fix also computes potential energy of mass in gravity field.
+fix 2d_fix all enforce2d
+
+compute rho_peratom all meso_rho/atom
+compute e_peratom all meso_e/atom
+compute esph all reduce sum c_e_peratom
+compute ke all ke
+variable etot equal c_esph+c_ke+f_gfix
+
+# adjust nevery | min. allowed dt | max. allowed dt | max. travel distance per dt # // ${dt} ~= CFL criterion 0.1*h/c
+fix dtfix all dt/reset 1 NULL ${dt} 0.0005 units box # use a variable timestep
+
+# time-integrate position, velocities, internal energy and density of water particles
+fix integrate_water_fix water meso
+
+# time-integrate only internal energy and density of boundary particles
+fix integrate_bc_fix bc meso/stationary
+dump dump_id all custom 100 dump.lammpstrj id type xs ys zs c_rho_peratom c_e_peratom fx fy
+dump_modify dump_id first yes
+thermo 10
+thermo_style custom step ke c_esph v_etot f_gfix press f_dtfix[1] f_dtfix
+thermo_modify norm no
+
+neigh_modify every 5 delay 0 check no
+variable skin equal 0.3*${h}
+neighbor ${skin} bin # set Verlet list skin distance
+
+run ${nrun}
diff --git a/src/Makefile b/src/Makefile
index acb35bb08..c95e423ba 100755
--- a/src/Makefile
+++ b/src/Makefile
@@ -1,201 +1,197 @@
# LAMMPS multiple-machine Makefile
SHELL = /bin/bash
#.IGNORE:
# Definitions
ROOT = lmp
EXE = $(ROOT)_$@
SRC = $(wildcard *.cpp)
INC = $(wildcard *.h)
OBJ = $(SRC:.cpp=.o)
# Package variables
PACKAGE = asphere class2 colloid dipole gpu granular \
kspace manybody mc meam molecule opt peri poems reax replica \
shock srd xtc
PACKUSER = user-misc user-atc user-awpmd user-cg-cmm \
- user-cuda user-eff user-ewaldn user-omp user-reaxc
+ user-cuda user-eff user-ewaldn user-omp user-reaxc user-sph
PACKALL = $(PACKAGE) $(PACKUSER)
PACKAGEUC = $(shell echo $(PACKAGE) | tr a-z A-Z)
PACKUSERUC = $(shell echo $(PACKUSER) | tr a-z A-Z)
YESDIR = $(shell echo $(@:yes-%=%) | tr a-z A-Z)
NODIR = $(shell echo $(@:no-%=%) | tr a-z A-Z)
# List of all targets
help:
@echo ''
@echo 'make clean-all delete all object files'
@echo 'make clean-machine delete object files for one machine'
@echo 'make tar lmp_src.tar.gz of src dir and packages'
@echo 'make makelib update Makefile.lib for library build'
@echo 'make makelist update Makefile.list used by old makes'
@echo ''
@echo 'make package list available packages'
@echo 'make package-status status of all packages'
@echo 'make yes-package install a single package in src dir'
@echo 'make no-package remove a single package from src dir'
@echo 'make yes-all install all packages in src dir'
@echo 'make no-all remove all packages from src dir'
@echo 'make yes-standard install all standard packages'
@echo 'make no-standard remove all standard packages'
@echo 'make yes-user install all user packages'
@echo 'make no-user remove all user packages'
@echo ''
@echo 'make package-update replace src files with package files'
@echo 'make package-overwrite replace package files with src files'
@echo 'make package-diff diff src files against package files'
@echo ''
@echo 'make machine build LAMMPS where machine is one of:'
@echo ''
@files="`ls MAKE/Makefile.*`"; \
for file in $$files; do head -1 $$file; done
@echo ''
# Build the code
.DEFAULT:
@test -f MAKE/Makefile.$@
@if [ ! -d Obj_$@ ]; then mkdir Obj_$@; fi
@$(SHELL) Make.sh style
@cp -p *.cpp *.h Obj_$@
@cp MAKE/Makefile.$@ Obj_$@/Makefile
- @if [ ! -e Makefile.package ]; then make package-regenerate; fi
- @if [ ! -e Makefile.package.settings ]; then make package-regenerate; fi
+ @if [ ! -e Makefile.package ]; \
+ then cp Makefile.package.empty Makefile.package; fi
+ @if [ ! -e Makefile.package.settings ]; \
+ then cp Makefile.package.settings.empty Makefile.package.settings; fi
@cp Makefile.package Makefile.package.settings Obj_$@
@cd Obj_$@; \
- $(MAKE) $(MFLAGS) "OBJ = $(OBJ)" "INC = $(INC)" "EXE = ../$(EXE)" ../$(EXE)
+ $(MAKE) $(MFLAGS) "OBJ = $(OBJ)" "INC = $(INC)" \
+ "EXE = ../$(EXE)" ../$(EXE)
@if [ -d Obj_$@ ]; then cd Obj_$@; rm -f $(SRC) $(INC) Makefile*; fi
# Remove machine-specific object files
clean:
@echo 'make clean-all delete all object files'
@echo 'make clean-machine delete object files for one machine'
clean-all:
rm -rf Obj_*
clean-%:
rm -rf Obj_$(@:clean-%=%)
# Create a tarball of src dir and packages
tar:
@cd STUBS; make clean
@cd ..; tar cvzf src/$(ROOT)_src.tar.gz \
src/Make* src/Package.sh src/MAKE src/*.cpp src/*.h src/STUBS \
$(patsubst %,src/%,$(PACKAGEUC)) $(patsubst %,src/%,$(PACKUSERUC)) \
--exclude=*/.svn
@cd STUBS; make
@echo "Created $(ROOT)_src.tar.gz"
# Make MPI STUBS lib
stubs:
@cd STUBS; make clean; make
# Update Makefile.lib and Makefile.list
makelib:
@$(SHELL) Make.sh style
@$(SHELL) Make.sh Makefile.lib
makelist:
@$(SHELL) Make.sh style
@$(SHELL) Make.sh Makefile.list
# Package management
package:
@echo 'Standard packages:' $(PACKAGE)
@echo ''
@echo 'User-contributed packages:' $(PACKUSER)
@echo ''
@echo 'make package list available packages'
@echo 'make package-status status of all packages'
@echo 'make yes-package install a single package in src dir'
@echo 'make no-package remove a single package from src dir'
@echo 'make yes-all install all packages in src dir'
@echo 'make no-all remove all packages from src dir'
@echo 'make yes-standard install all standard packages'
@echo 'make no-standard remove all standard packages'
@echo 'make yes-user install all user packages'
@echo 'make no-user remove all user packages'
@echo ''
@echo 'make package-update replace src files with package files'
@echo 'make package-overwrite replace package files with src files'
@echo 'make package-diff diff src files against package file'
yes-all:
@for p in $(PACKALL); do $(MAKE) yes-$$p; done
no-all:
@for p in $(PACKALL); do $(MAKE) no-$$p; done
yes-standard:
@for p in $(PACKAGE); do $(MAKE) yes-$$p; done
no-standard:
@for p in $(PACKAGE); do $(MAKE) no-$$p; done
yes-user:
@for p in $(PACKUSER); do $(MAKE) yes-$$p; done
no-user:
@for p in $(PACKUSER); do $(MAKE) no-$$p; done
yes-%:
@if [ ! -e $(YESDIR) ]; then \
echo "Package $(@:yes-%=%) does not exist"; \
else \
echo "Installing package $(@:yes-%=%)"; \
cd $(YESDIR); $(SHELL) Install.sh 1; cd ..; $(SHELL) Depend.sh 1; \
fi;
no-%:
@if [ ! -e $(NODIR) ]; then \
echo "Package $(@:no-%=%) does not exist"; \
else \
echo "Uninstalling package $(@:no-%=%)"; \
cd $(NODIR); $(SHELL) Install.sh 0; cd ..; $(SHELL) Depend.sh 0; \
fi;
# status = list src files that differ from package files
# update = replace src files with newer package files
# overwrite = overwrite package files with newer src files
-# regenerate = regenerate Makefile.package from Makefile.package.empty
# diff = show differences between src and package files
package-status:
@for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p status; done
@echo ''
@for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p status; done
package-update:
@for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p update; done
@echo ''
@for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p update; done
package-overwrite:
@for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p overwrite; done
@echo ''
@for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p overwrite; done
-package-regenerate:
- @cp Makefile.package.empty Makefile.package
- @cp Makefile.package.settings.empty Makefile.package.settings
- @for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p regenerate; done
- @for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p regenerate; done
-
package-diff:
@for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p diff; done
@echo ''
@for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p diff; done
diff --git a/src/Package.sh b/src/Package.sh
index fb3694bb4..78b7b7a10 100644
--- a/src/Package.sh
+++ b/src/Package.sh
@@ -1,114 +1,105 @@
# Package.sh = package management, called from Makefile
-# Syntax: sh Package.sh DIR status/update/overwrite/regenerate/diff
+# Syntax: sh Package.sh DIR status/update/overwrite/diff
# style used to translate dir name to package name
style=`echo $1 | sed 'y/-ABCDEFGHIJKLMNOPQRSTUVWXYZ/_abcdefghijklmnopqrstuvwxyz/'`
# package is already installed if any package *.cpp or *.h file is in src
# else not installed
cd $1
installed=0
for file in *.cpp *.h; do
if (test -e ../$file) then
installed=1
fi
done
# status
# if installed:
# issue warning if any package file is not in src or is different
if (test $2 = "status") then
if (test $installed = 1) then
echo "Installed YES: package $1"
for file in *.cpp *.h; do
if (test ! -e ../$file) then
echo " src/$file does not exist"
elif (test "`diff --brief $file ../$file`" != "") then
echo " src/$file and $1/$file are different"
fi
done
else
echo "Installed NO: package $1"
fi
# update
# if installed:
# cp package file to src if doesn't exist or is different
elif (test $2 = "update") then
echo "Updating src files from $1 package files"
if (test $installed = 1) then
if (test ! -e Package.sh) then
for file in *.cpp *.h; do
if (test ! -e ../$file) then
echo " creating src/$file"
cp $file ..
elif (test "`diff --brief $file ../$file`" != "") then
echo " updating src/$file"
cp $file ..
fi
done
else
/bin/sh Package.sh
fi
else
echo " $1 package is not installed, no action"
fi
# overwrite
# if installed:
# if package file not in src, issue warning
# if src file different than package file, overwrite package file
elif (test $2 = "overwrite") then
echo "Overwriting $1 package files with src files"
if (test $installed = 1) then
for file in *.cpp *.h; do
if (test ! -e ../$file) then
echo " src/$file does not exist"
elif (test "`diff --brief $file ../$file`" != "") then
echo " overwriting $1/$file"
cp ../$file .
fi
done
else
echo " $1 package is not installed, no action"
fi
-# regenenate Makefile.package from Makefile.package.empty
-# if installed:
-# re-install so Install.sh will edit Makefile.package
-
-elif (test $2 = "regenerate") then
- if (test $installed = 1) then
- /bin/sh Install.sh 1
- fi
-
# diff
# if installed:
# show any differences between src files and package files
elif (test $2 = "diff") then
if (test $installed = 1) then
echo "Installed YES: package $1"
for file in *.cpp *.h; do
if (test ! -e ../$file) then
echo "************************************************************************"
echo " src/$file does not exist"
echo "************************************************************************"
elif (test "`diff --brief $file ../$file`" != "") then
echo "************************************************************************"
echo "diff $1/$file src/$file "
echo "************************************************************************"
diff $file ../$file
fi
done
fi
fi
diff --git a/src/USER-ATC/README b/src/USER-ATC/README
index 3e8466904..85e2c1a57 100644
--- a/src/USER-ATC/README
+++ b/src/USER-ATC/README
@@ -1,15 +1,20 @@
-The files in this directory are a user-contributed package for LAMMPS.
-
-The primary people who created these files are Reese Jones
-(rjones@sandia.gov), Jeremy Templeton (jatemple@sandia.gov) and Jon
-Zimmerman (jzimmer@sandia.gov). Contact them directly if you have
-questions.
-
This package implements a "fix atc" command which can be used in a
LAMMPS input script. This fix can be employed to either do concurrent
coupling of MD with FE-based physics surrogates or on-the-fly
-post-processing of atomic information to continuum fields. See the
-doc page for the fix atc command to get started.
+post-processing of atomic information to continuum fields.
+
+See the doc page for the fix atc command to get started. At the
+bottom of the doc page are many links to additional documentation
+contained in the doc/USER/atc directory.
+
+There are example scripts for using this package in examples/USER/atc.
+
+This package uses an external library in lib/atc which must be
+compiled before making LAMMPS. See the lib/atc/README file and the
+LAMMPS manual for information on building LAMMPS with external
+libraries.
-There are example scripts for using this package with LAMMPS in
-examples/USER/atc.
+The primary people who created this package are Reese Jones
+(rjones at sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon
+Zimmerman (jzimmer at sandia.gov) at Sandia. Contact them directly if
+you have questions.
diff --git a/src/USER-AWPMD/README b/src/USER-AWPMD/README
index 66378cd45..4dd16fca4 100644
--- a/src/USER-AWPMD/README
+++ b/src/USER-AWPMD/README
@@ -1,24 +1,23 @@
-The files in this directory are a user-contributed package for LAMMPS.
+This package contains a LAMMPS implementation of the Antisymmetrized
+Wave Packet Molecular Dynamics (AWPMD) method.
-The person who created these files is Ilya Valuev
-(valuev@physik.hu-berlin.de). Contact him directly if you have
-questions.
+See the doc page for the pair_style awpmd/cut command to get started.
-PACKAGE DESCRIPTION:
+There are example scripts for using this package in
+examples/USER/awpmd.
-Contains a LAMMPS implementation of the Antisymmetrized Wave Packet
-Molecular Dynamics (AWPMD) method.
+This package uses an external library in lib/awpmd which must be
+compiled before making LAMMPS. See the lib/awpmd/README file and the
+LAMMPS manual for information on building LAMMPS with external
+libraries.
-INSTALLATION:
-
-- compile the awpmd library in lib/awpmd
-- follow a normal LAMMPS package installation: make yes-user-awpmd
-
-OTHERS FILES INCLUDED:
-
-User examples are under examples/USER/awpmd
+The person who created this package is Ilya Valuev at the JIHT in
+Russia (valuev at physik.hu-berlin.de). Contact him directly if you
+have questions.
+
+----------------------
ACKNOWLEDGMENTS:
Thanks to Steve Plimpton and Aidan Thompson for their help in
adaptation of the AWPMD code to LAMMPS.
diff --git a/src/USER-CG-CMM/README b/src/USER-CG-CMM/README
index a7ff592f0..e93e739b1 100644
--- a/src/USER-CG-CMM/README
+++ b/src/USER-CG-CMM/README
@@ -1,36 +1,36 @@
-The files in this directory are a user-contributed package for LAMMPS.
-
-The person who created these files is Axel Kohlmeyer
-(akohlmey@gmail.com). Contact him directly if you have questions.
-
-The current version of this package should be considered beta
-quality. The CG potentials work correctly and well, but there will be
-optimizations, cleanups and additional tools to aid in setting up and
-analyzing simulations with this package added in the next months.
-
This package implements 4 commands which can be used in a LAMMPS input
script:
pair_style cg/cmm
pair_style cg/cmm/coul/cut
pair_style cg/cmm/coul/long
-and angle_style cg/cmm.
-
-See the documentation files for these commands for details.
-
-There are example scripts for using this package with LAMMPS in
-examples/USER/cg-cmm.
+angle_style cg/cmm :ul
These styles allow coarse grained MD simulations with the
parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
(cg/cmm), with extensions to simulate ionic liquids, electrolytes,
lipids and charged amino acids (to be published soon).
+See the doc pages for these commands for details.
+
+There are example scripts for using this package in
+examples/USER/cg-cmm.
+
+The current version of this package should be considered beta
+quality. The CG potentials work correctly and well, but there will be
+optimizations, cleanups and additional tools to aid in setting up and
+analyzing simulations with this package added in the next months.
+
+The person who created this package is Axel Kohlmeyer at Temple U
+(akohlmey at gmail.com). Contact him directly if you have questions.
+
+---------------------------------
+
Thanks for contributions, support and testing goes to
Wataru Shinoda (AIST, Tsukuba)
Russell DeVane (CMM / U Penn, Philadelphia)
Balasubramanian Sundaram (JNCASR, Bangalore)
Michael L. Klein (CMM / U Penn, Philadelphia)
version: 0.98 / 2008-01-31
diff --git a/src/USER-CUDA/README b/src/USER-CUDA/README
index c98ef0327..74e5ad60c 100644
--- a/src/USER-CUDA/README
+++ b/src/USER-CUDA/README
@@ -1,16 +1,19 @@
-The files in this directory are a user-contributed package for LAMMPS.
+This package provides acceleration of various LAMMPS pair styles, fix
+styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
+GPUs.
+
+See this section of the manual to get started:
-The person who created these files is Christian Trott at the
-University of Technology Ilmenau, Germany
-(christian.trott@tu-ilmenau.de). Contact him directly if you have
-questions.
+doc/Section_accelerate.html, sub-section 5.4
-The USER-CUDA package provides acceleration of various LAMMPS pair
-styles, fix styles, compute styles, and long-range Coulombics via PPPM
-on NVIDIA GPUs.
+There are example scripts for using this package in
+examples/USER/cuda.
-It's use is documented in this file:
-lammps/doc/Section_accelerate.html
+This package uses an external library in lib/cuda which must be
+compiled before making LAMMPS. See the lib/cuda/README file and the
+LAMMPS manual for information on building LAMMPS with external
+libraries.
-Examples input scripts that use the USER-CUDA package are provided in
-lammps/examples/USER/cuda.
+The person who created this package is Christian Trott at the
+University of Technology Ilmenau, Germany (christian.trott at
+tu-ilmenau.de). Contact him directly if you have questions.
diff --git a/src/USER-EFF/README b/src/USER-EFF/README
index c1c2453ec..6bae419b1 100644
--- a/src/USER-EFF/README
+++ b/src/USER-EFF/README
@@ -1,80 +1,76 @@
-The files in this directory are a user-contributed package for LAMMPS.
-
-The person who created these files is Andres Jaramillo-Botero at
-CalTech (ajaramil@wag.caltech.edu). Contact him directly if you have
-questions.
-
---------------------------------------
-
-Andres Jaramillo-Botero
-California Institute of Technology (Caltech)
-Chemistry and Chemical Engineering, 139-74
-1200 E. California Blvd., Pasadena, CA 91125
-Phone: (626) 395-3591
-e-mail: ajaramil@wag.caltech.edu
-
-Co-Authors:
-Julius Su (jsu@wag.caltech.edu)
-William A. Goddard III (wag@wag.caltech.edu)
-
-PACKAGE DESCRIPTION:
-
-Contains a LAMMPS implementation of the electron Force Field (eFF)
-currently under development at Caltech, as described in
+This package contains a LAMMPS implementation of the electron Force
+Field (eFF) currently under development at Caltech, as described in
A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
2010. The eFF potential was first introduced by Su and Goddard, in
2007.
eFF can be viewed as an approximation to QM wave packet dynamics and
Fermionic molecular dynamics, combining the ability of electronic
structure methods to describe atomic structure, bonding, and chemistry
in materials, and of plasma methods to describe nonequilibrium
dynamics of large systems with a large number of highly excited
electrons. We classify it as a mixed QM-classical approach rather than
a conventional force field method, which introduces QM-based terms (a
spin-dependent repulsion term to account for the Pauli exclusion
principle and the electron wavefunction kinetic energy associated with
the Heisenberg principle) that reduce, along with classical
electrostatic terms between nuclei and electrons, to the sum of a set
of effective pairwise potentials. This makes eFF uniquely suited to
simulate materials over a wide range of temperatures and pressures
where electronically excited and ionized states of matter can occur
and coexist.
The necessary customizations to the LAMMPS core are in place to
enable the correct handling of explicit electron properties during
minimization and dynamics.
-INSTALLATION:
+See the doc page for the pair_style eff/cut command to get started.
+
+There are example scripts for using this package in
+examples/USER/eff.
-via a normal LAMMPS package installation: make yes-user-eff
+There are auxiliary tools for using this package in tools/eff.
-OTHERS FILES INCLUDED:
+The person who created this package is Andres Jaramillo-Botero at
+CalTech (ajaramil at wag.caltech.edu). Contact him directly if you
+have questions.
-User examples are under examples/USER/eff
-eFF tools are under tools/eff
+-------------------------
+
+AUTHOR INFORMATION:
+
+Andres Jaramillo-Botero
+California Institute of Technology (Caltech)
+Chemistry and Chemical Engineering, 139-74
+1200 E. California Blvd., Pasadena, CA 91125
+Phone: (626) 395-3591
+e-mail: ajaramil@wag.caltech.edu
+
+Co-Authors:
+Julius Su (jsu@wag.caltech.edu)
+William A. Goddard III (wag@wag.caltech.edu)
ACKNOWLEDGMENTS:
Thanks to Steve Plimpton and Aidan Thompson for their input on the
LAMMPS architecture and for their help in customizing some of the
required LAMMPS core modules.
Version 01/2010: Special thanks to:
- Hai Xiao (Caltech) for reviewing the fixed-core implementation and
providing useful insights to improve it, and for his work on the effective core pseudopotential.
- Vaclav Cvicek (Caltech) for thoroughly revising the units, for finding a bug in the
fix_langevin_eff radial scaling factors, and for suggesting changes to clean-up the code.
- Patrick Theofanis (Caltech) for providing an optimized set of parameters for the Si ECP
(default) and for providing basic cases.
- Qi An (Caltech) for providing feedback on usage, application cases, and testing.
VERSION NOTES:
-01/2010: Added support for fixed-core and effective core pseudopotentials [ECP]
-(useful for C, Al, Si, O and other elements). Cleaned up the code to make it
-easier to maintain, revised support for real units, upgraded post-processing
-and visualization tools, added support for "compute pair eff" to allow thermo
-prints with the different eFF energy components (eke, epauli, ecoul and errestrain),
-fixed radial scaling factors in the eff langevin thermostat.
-
+01/2010: Added support for fixed-core and effective core
+pseudopotentials [ECP] (useful for C, Al, Si, O and other elements).
+Cleaned up the code to make it easier to maintain, revised support for
+real units, upgraded post-processing and visualization tools, added
+support for "compute pair eff" to allow thermo prints with the
+different eFF energy components (eke, epauli, ecoul and errestrain),
+fixed radial scaling factors in the eff langevin thermostat.
diff --git a/src/USER-EWALDN/README b/src/USER-EWALDN/README
index 77295f017..e88839bd2 100644
--- a/src/USER-EWALDN/README
+++ b/src/USER-EWALDN/README
@@ -1,23 +1,23 @@
-The files in this directory are a user-contributed package for LAMMPS.
-
-The person who created these files is Pieter in' t Veld while at
-Sandia. He is now at BASF (pieter.intveld@basf.com). Contact him
-directly if you have questions.
-
This package implements 3 commands which can be used in a LAMMPS input
script: pair_style lj/coul, pair_style buck/coul, and kspace_style
-ewald/n. See the documentation files for these commands for details.
+ewald/n.
The "kspace_style ewald/n" command is similar to standard Ewald for
charges, but also enables the Lennard-Jones interaction, or any 1/r^N
interaction to be of infinite extent, instead of being cutoff. LAMMPS
pair potentials for long-range Coulombic interactions, such as
lj/cut/coul/long can be used with ewald/n. The two new pair_style
commands provide the modifications for the short-range LJ and
Buckingham interactions that can also be used with ewald/n.
Another advantage of kspace_style ewald/n is that it can be used with
non-orthogonal (triclinic symmetry) simulation boxes, either for just
long-range Coulombic interactions, or for both Coulombic and 1/r^N LJ
or Buckingham, which is not currently possible for other kspace styles
such as PPPM and ewald.
+
+See the doc pages for these commands for details.
+
+The person who created these files is Pieter in' t Veld while at
+Sandia. He is now at BASF (pieter.intveld at basf.com). Contact him
+directly if you have questions.
diff --git a/src/USER-MISC/README b/src/USER-MISC/README
index d3724d17b..6cc149a77 100644
--- a/src/USER-MISC/README
+++ b/src/USER-MISC/README
@@ -1,31 +1,33 @@
-The files in this directory are a potpourri of (mostly) unrelated
+The files in this package are a potpourri of (mostly) unrelated
features contributed to LAMMPS by users. Each feature is a single
-file (actually a *.cpp and *.h file).
+pair of files (*.cpp and *.h).
More information about each feature can be found by reading its doc
-page in the LAMMPS doc directory. This link points to the doc
-page for all LAMMPS input script commands:
+page in the LAMMPS doc directory. The doc page which lists all LAMMPS
+input script commands is as follows:
-http://lammps.sandia.gov/doc/Section_commands.html#3_5\
+doc/Section_commands.html, subsection 3.5
User-contributed features are listed at the bottom of the fix,
compute, pair, etc sections.
-You should contact the author if you have specific questions about the
-feature or its code.
+The list of features and author of each is given below.
+
+You should contact the author directly if you have specific questions
+about the feature or its coding.
------------------------------------------------------------
angle_style cosine/shift, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
angle_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
bond_style harmonic/shift, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
bond_style harmonic/shift/cut, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
compute ackland/atom, Gerolf Ziegenhain, gerolf at ziegenhain.com, 4 Oct 2007
compute temp/rotate, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
dihedral_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
fix imd, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 2009
fix smd, Axel Kohlmeyer, akohlmey at gmail.com, 19 May 2008
pair dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11
pair eam/cd, Alexander Stukowski, stukowski at mm.tu-darmstadt.de,
pair lj/sf, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
diff --git a/src/USER-REAXC/README b/src/USER-REAXC/README
index 9d1c8b1ac..823978804 100644
--- a/src/USER-REAXC/README
+++ b/src/USER-REAXC/README
@@ -1,68 +1,61 @@
-The files in this directory are a user-contributed package for LAMMPS.
+This package contains a implementation for LAMMPS of the ReaxFF force
+field. ReaxFF uses distance-dependent bond-order functions to
+represent the contributions of chemical bonding to the potential
+energy. It was originally developed by Adri van Duin and the Goddard
+group at CalTech.
-The person who created this package is Hasan Metin Aktulga, haktulga
-at cs.purdue.edu, while at Purdue University. Contact him directly,
-or Aidan Thompson (Sandia) at athomps at sandia.gov, if you have
-questions.
+The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in
+C, should give identical or very similar results to pair_style reax,
+which is a ReaxFF implementation on top of a Fortran library, a
+version of which library was originally authored by Adri van Duin.
+
+The reax/c version should be somewhat faster and more scalable,
+particularly with respect to the charge equilibration calculation. It
+should also be easier to build and use since there are no complicating
+issues with Fortran memory allocation or linking to a Fortran library.
For technical details about this implemention of ReaxFF, see
this paper:
Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods
and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty,
S. A. Pandit, A. Y. Grama, Parallel Computing, to appear (2011).
---------------------------------------
-
-Note that the files with names starting with "reaxc" in this package
-are from PuReMD, the Purdue ReaxFF Molecular Dynamics Program. Its
-copyright info and authorship info are listed below.
-
-PACKAGE DESCRIPTION:
-
-Contains a implementation for LAMMPS of the ReaxFF force field.
-ReaxFF uses distance-dependent bond-order functions to represent the
-contributions of chemical bonding to the potential energy. It was
-originally developed by Adri van Duin and the Goddard group at
-CalTech.
+See the doc page for the pair_style reax/c command for details
+of how to use it in LAMMPS.
-The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in
-C, should give identical or very similar results to pair_style reax,
-which is a ReaxFF implementation on top of a Fortran library, a
-version of which was originally authored by Adri van Duin.
-
-The reax/c version should be somewhat faster and more scalable,
-particularly with respect to the charge equilibration calculation. It
-should also be easier to build and use since there are no complicating
-issues due to linking to a Fortran library.
-
-OTHERS FILES INCLUDED:
+The person who created this package is Hasan Metin Aktulga (hmaktulga
+at lbl.gov), while at Purdue University. Contact him directly, or
+Aidan Thompson at Sandia (athomps at sandia.gov), if you have
+questions.
-User examples for pair_style reax/c are in examples/reax.
+--------------------------------------
Thanks to Steve Plimpton and Aidan Thompson for their input on the
LAMMPS architecture and for their help in understanding and
customizing some of the required LAMMPS interfaces.
---------------------------------------
+Note that files in the package with names starting with "reaxc" are
+from PuReMD, the Purdue ReaxFF Molecular Dynamics Program. Its
+copyright info and authorship info are listed below.
The reaxc files in this directory have the following header:
PuReMD - Purdue ReaxFF Molecular Dynamics Program
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
diff --git a/src/USER-SPH/Install.sh b/src/USER-SPH/Install.sh
new file mode 100644
index 000000000..56b8b50b5
--- /dev/null
+++ b/src/USER-SPH/Install.sh
@@ -0,0 +1,59 @@
+# Install/unInstall package files in LAMMPS
+
+if (test $1 = 1) then
+
+ cp -p atom_vec_meso.cpp ..
+ cp -p pair_sph_heatconduction.cpp ..
+ cp -p pair_sph_idealgas.cpp ..
+ cp -p pair_sph_lj.cpp ..
+ cp -p pair_sph_rhosum.cpp ..
+ cp -p pair_sph_taitwater.cpp ..
+ cp -p pair_sph_taitwater_morris.cpp ..
+ cp -p compute_meso_e_atom.cpp ..
+ cp -p compute_meso_rho_atom.cpp ..
+ cp -p compute_meso_t_atom.cpp ..
+ cp -p fix_meso.cpp ..
+ cp -p fix_meso_stationary.cpp ..
+
+ cp -p atom_vec_meso.h ..
+ cp -p pair_sph_heatconduction.h ..
+ cp -p pair_sph_idealgas.h ..
+ cp -p pair_sph_lj.h ..
+ cp -p pair_sph_rhosum.h ..
+ cp -p pair_sph_taitwater.h ..
+ cp -p pair_sph_taitwater_morris.h ..
+ cp -p compute_meso_e_atom.h ..
+ cp -p compute_meso_rho_atom.h ..
+ cp -p compute_meso_t_atom.h ..
+ cp -p fix_meso.h ..
+ cp -p fix_meso_stationary.h ..
+
+elif (test $1 = 0) then
+
+ rm -f ../atom_vec_meso.cpp
+ rm -f ../pair_sph_heatconduction.cpp
+ rm -f ../pair_sph_idealgas.cpp
+ rm -f ../pair_sph_lj.cpp
+ rm -f ../pair_sph_rhosum.cpp
+ rm -f ../pair_sph_taitwater.cpp
+ rm -f ../pair_sph_taitwater_morris.cpp
+ rm -f ../compute_meso_e_atom.cpp
+ rm -f ../compute_meso_rho_atom.cpp
+ rm -f ../compute_meso_t_atom.cpp
+ rm -f ../fix_meso.cpp
+ rm -f ../fix_meso_stationary.cpp
+
+ rm -f ../atom_vec_meso.h
+ rm -f ../pair_sph_heatconduction.h
+ rm -f ../pair_sph_idealgas.h
+ rm -f ../pair_sph_lj.h
+ rm -f ../pair_sph_rhosum.h
+ rm -f ../pair_sph_taitwater.h
+ rm -f ../pair_sph_taitwater_morris.h
+ rm -f ../compute_meso_e_atom.h
+ rm -f ../compute_meso_rho_atom.h
+ rm -f ../compute_meso_t_atom.h
+ rm -f ../fix_meso.h
+ rm -f ../fix_meso_stationary.h
+
+fi
diff --git a/src/USER-SPH/README b/src/USER-SPH/README
new file mode 100644
index 000000000..1658ff2f7
--- /dev/null
+++ b/src/USER-SPH/README
@@ -0,0 +1,20 @@
+This package implements smoothed particle hydrodynamics (SPH) in
+LAMMPS. Currently, the package has the following features:
+
+* Tait, ideal gas, Lennard-Jones equation of states, full support for
+ complete (i.e. internal-energy dependent) equations of state
+* plain or Monaghans XSPH integration of the equations of motion
+* density continuity or density summation to propagate the density field
+* commands to set internal energy and density of particles from the
+ input script
+* output commands to access internal energy and density for dumping and
+ thermo output
+
+See the file doc/USER/sph/SPH_LAMMPS_userguide.pdf to get started.
+
+There are example scripts for using this package in examples/USER/sph.
+
+The person who created this package is Georg Ganzenmuller at the
+Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
+Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
+you have questions.
diff --git a/src/USER-SPH/atom_vec_meso.cpp b/src/USER-SPH/atom_vec_meso.cpp
new file mode 100644
index 000000000..c977a8e32
--- /dev/null
+++ b/src/USER-SPH/atom_vec_meso.cpp
@@ -0,0 +1,868 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+ ------------------------------------------------------------------------- */
+
+#include "stdlib.h"
+#include "atom_vec_meso.h"
+#include "atom.h"
+#include "domain.h"
+#include "modify.h"
+#include "fix.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define DELTA 10000
+
+/* ---------------------------------------------------------------------- */
+
+AtomVecMeso::AtomVecMeso(LAMMPS *lmp, int narg, char **arg) :
+ AtomVec(lmp, narg, arg) {
+ molecular = 0;
+ mass_type = 1;
+
+ comm_x_only = 0; // we communicate not only x forward but also vest ...
+ comm_f_only = 0; // we also communicate de and drho in reverse direction
+ size_forward = 8; // 3 + rho + e + vest[3], that means we may only communicate 5 in hybrid
+ size_reverse = 5; // 3 + drho + de
+ size_border = 12; // 6 + rho + e + vest[3] + cv
+ size_velocity = 3;
+ size_data_atom = 8;
+ size_data_vel = 4;
+ xcol_data = 6;
+
+ atom->e_flag = 1;
+ atom->rho_flag = 1;
+ atom->cv_flag = 1;
+ atom->vest_flag = 1;
+}
+
+/* ----------------------------------------------------------------------
+ grow atom arrays
+ n = 0 grows arrays by DELTA
+ n > 0 allocates arrays to size n
+ ------------------------------------------------------------------------- */
+
+void AtomVecMeso::grow(int n) {
+ if (n == 0)
+ nmax += DELTA;
+ else
+ nmax = n;
+ atom->nmax = nmax;
+ if (nmax < 0 || nmax > MAXSMALLINT)
+ error->one("Per-processor system is too big");
+
+ tag = memory->grow(atom->tag, nmax, "atom:tag");
+ type = memory->grow(atom->type, nmax, "atom:type");
+ mask = memory->grow(atom->mask, nmax, "atom:mask");
+ image = memory->grow(atom->image, nmax, "atom:image");
+ x = memory->grow(atom->x, nmax, 3, "atom:x");
+ v = memory->grow(atom->v, nmax, 3, "atom:v");
+ f = memory->grow(atom->f, nmax, 3, "atom:f");
+
+ rho = memory->grow(atom->rho, nmax, "atom:rho");
+ drho = memory->grow(atom->drho, nmax, "atom:drho");
+ e = memory->grow(atom->e, nmax, "atom:e");
+ de = memory->grow(atom->de, nmax, "atom:de");
+ vest = memory->grow(atom->vest, nmax, 3, "atom:vest");
+ cv = memory->grow(atom->cv, nmax, "atom:cv");
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
+}
+
+/* ----------------------------------------------------------------------
+ reset local array ptrs
+ ------------------------------------------------------------------------- */
+
+void AtomVecMeso::grow_reset() {
+ tag = atom->tag;
+ type = atom->type;
+ mask = atom->mask;
+ image = atom->image;
+ x = atom->x;
+ v = atom->v;
+ f = atom->f;
+ rho = atom->rho;
+ drho = atom->drho;
+ e = atom->e;
+ de = atom->de;
+ vest = atom->vest;
+ cv = atom->cv;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecMeso::copy(int i, int j, int delflag) {
+ //printf("in AtomVecMeso::copy\n");
+ tag[j] = tag[i];
+ type[j] = type[i];
+ mask[j] = mask[i];
+ image[j] = image[i];
+ x[j][0] = x[i][0];
+ x[j][1] = x[i][1];
+ x[j][2] = x[i][2];
+ v[j][0] = v[i][0];
+ v[j][1] = v[i][1];
+ v[j][2] = v[i][2];
+
+ rho[j] = rho[i];
+ drho[j] = drho[i];
+ e[j] = e[i];
+ de[j] = de[i];
+ cv[j] = cv[i];
+ vest[j][0] = vest[i][0];
+ vest[j][1] = vest[i][1];
+ vest[j][2] = vest[i][2];
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ modify->fix[atom->extra_grow[iextra]]->copy_arrays(i, j);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMeso::pack_comm_hybrid(int n, int *list, double *buf) {
+ //printf("in AtomVecMeso::pack_comm_hybrid\n");
+ int i, j, m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = rho[j];
+ buf[m++] = e[j];
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2];
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMeso::unpack_comm_hybrid(int n, int first, double *buf) {
+ //printf("in AtomVecMeso::unpack_comm_hybrid\n");
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ rho[i] = buf[m++];
+ e[i] = buf[m++];
+ vest[i][0] = buf[m++];
+ vest[i][1] = buf[m++];
+ vest[i][2] = buf[m++];
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMeso::pack_border_hybrid(int n, int *list, double *buf) {
+ //printf("in AtomVecMeso::pack_border_hybrid\n");
+ int i, j, m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = rho[j];
+ buf[m++] = e[j];
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2];
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMeso::unpack_border_hybrid(int n, int first, double *buf) {
+ //printf("in AtomVecMeso::unpack_border_hybrid\n");
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ rho[i] = buf[m++];
+ e[i] = buf[m++];
+ vest[i][0] = buf[m++];
+ vest[i][1] = buf[m++];
+ vest[i][2] = buf[m++];
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMeso::pack_reverse_hybrid(int n, int first, double *buf) {
+ //printf("in AtomVecMeso::pack_reverse_hybrid\n");
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ buf[m++] = drho[i];
+ buf[m++] = de[i];
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMeso::unpack_reverse_hybrid(int n, int *list, double *buf) {
+ //printf("in AtomVecMeso::unpack_reverse_hybrid\n");
+ int i, j, m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ drho[j] += buf[m++];
+ de[j] += buf[m++];
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMeso::pack_comm(int n, int *list, double *buf, int pbc_flag,
+ int *pbc) {
+ //printf("in AtomVecMeso::pack_comm\n");
+ int i, j, m;
+ double dx, dy, dz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0];
+ buf[m++] = x[j][1];
+ buf[m++] = x[j][2];
+ buf[m++] = rho[j];
+ buf[m++] = e[j];
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2];
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0] * domain->xprd;
+ dy = pbc[1] * domain->yprd;
+ dz = pbc[2] * domain->zprd;
+ } else {
+ dx = pbc[0] * domain->xprd + pbc[5] * domain->xy + pbc[4] * domain->xz;
+ dy = pbc[1] * domain->yprd + pbc[3] * domain->yz;
+ dz = pbc[2] * domain->zprd;
+ }
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = rho[j];
+ buf[m++] = e[j];
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2];
+ }
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMeso::pack_comm_vel(int n, int *list, double *buf, int pbc_flag,
+ int *pbc) {
+ //printf("in AtomVecMeso::pack_comm_vel\n");
+ int i, j, m;
+ double dx, dy, dz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0];
+ buf[m++] = x[j][1];
+ buf[m++] = x[j][2];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ buf[m++] = rho[j];
+ buf[m++] = e[j];
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2];
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0] * domain->xprd;
+ dy = pbc[1] * domain->yprd;
+ dz = pbc[2] * domain->zprd;
+ } else {
+ dx = pbc[0] * domain->xprd + pbc[5] * domain->xy + pbc[4] * domain->xz;
+ dy = pbc[1] * domain->yprd + pbc[3] * domain->yz;
+ dz = pbc[2] * domain->zprd;
+ }
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ buf[m++] = rho[j];
+ buf[m++] = e[j];
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2];
+ }
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecMeso::unpack_comm(int n, int first, double *buf) {
+ //printf("in AtomVecMeso::unpack_comm\n");
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ x[i][0] = buf[m++];
+ x[i][1] = buf[m++];
+ x[i][2] = buf[m++];
+ rho[i] = buf[m++];
+ e[i] = buf[m++];
+ vest[i][0] = buf[m++];
+ vest[i][1] = buf[m++];
+ vest[i][2] = buf[m++];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecMeso::unpack_comm_vel(int n, int first, double *buf) {
+ //printf("in AtomVecMeso::unpack_comm_vel\n");
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ x[i][0] = buf[m++];
+ x[i][1] = buf[m++];
+ x[i][2] = buf[m++];
+ v[i][0] = buf[m++];
+ v[i][1] = buf[m++];
+ v[i][2] = buf[m++];
+ rho[i] = buf[m++];
+ e[i] = buf[m++];
+ vest[i][0] = buf[m++];
+ vest[i][1] = buf[m++];
+ vest[i][2] = buf[m++];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMeso::pack_reverse(int n, int first, double *buf) {
+ //printf("in AtomVecMeso::pack_reverse\n");
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ buf[m++] = f[i][0];
+ buf[m++] = f[i][1];
+ buf[m++] = f[i][2];
+ buf[m++] = drho[i];
+ buf[m++] = de[i];
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecMeso::unpack_reverse(int n, int *list, double *buf) {
+ //printf("in AtomVecMeso::unpack_reverse\n");
+ int i, j, m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ f[j][0] += buf[m++];
+ f[j][1] += buf[m++];
+ f[j][2] += buf[m++];
+ drho[j] += buf[m++];
+ de[j] += buf[m++];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMeso::pack_border(int n, int *list, double *buf, int pbc_flag,
+ int *pbc) {
+ //printf("in AtomVecMeso::pack_border\n");
+ int i, j, m;
+ double dx, dy, dz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0];
+ buf[m++] = x[j][1];
+ buf[m++] = x[j][2];
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = rho[j];
+ buf[m++] = e[j];
+ buf[m++] = cv[j];
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2];
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0] * domain->xprd;
+ dy = pbc[1] * domain->yprd;
+ dz = pbc[2] * domain->zprd;
+ } else {
+ dx = pbc[0];
+ dy = pbc[1];
+ dz = pbc[2];
+ }
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = rho[j];
+ buf[m++] = e[j];
+ buf[m++] = cv[j];
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2];
+ }
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMeso::pack_border_vel(int n, int *list, double *buf, int pbc_flag,
+ int *pbc) {
+ //printf("in AtomVecMeso::pack_border_vel\n");
+ int i, j, m;
+ double dx, dy, dz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0];
+ buf[m++] = x[j][1];
+ buf[m++] = x[j][2];
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ buf[m++] = rho[j];
+ buf[m++] = e[j];
+ buf[m++] = cv[j];
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2];
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0] * domain->xprd;
+ dy = pbc[1] * domain->yprd;
+ dz = pbc[2] * domain->zprd;
+ } else {
+ dx = pbc[0];
+ dy = pbc[1];
+ dz = pbc[2];
+ }
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0] + dx;
+ buf[m++] = x[j][1] + dy;
+ buf[m++] = x[j][2] + dz;
+ buf[m++] = tag[j];
+ buf[m++] = type[j];
+ buf[m++] = mask[j];
+ buf[m++] = v[j][0];
+ buf[m++] = v[j][1];
+ buf[m++] = v[j][2];
+ buf[m++] = rho[j];
+ buf[m++] = e[j];
+ buf[m++] = cv[j];
+ buf[m++] = vest[j][0];
+ buf[m++] = vest[j][1];
+ buf[m++] = vest[j][2];
+ }
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecMeso::unpack_border(int n, int first, double *buf) {
+ //printf("in AtomVecMeso::unpack_border\n");
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ if (i == nmax)
+ grow(0);
+ x[i][0] = buf[m++];
+ x[i][1] = buf[m++];
+ x[i][2] = buf[m++];
+ tag[i] = static_cast<int> (buf[m++]);
+ type[i] = static_cast<int> (buf[m++]);
+ mask[i] = static_cast<int> (buf[m++]);
+ rho[i] = buf[m++];
+ e[i] = buf[m++];
+ cv[i] = buf[m++];
+ vest[i][0] = buf[m++];
+ vest[i][1] = buf[m++];
+ vest[i][2] = buf[m++];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecMeso::unpack_border_vel(int n, int first, double *buf) {
+ //printf("in AtomVecMeso::unpack_border_vel\n");
+ int i, m, last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ if (i == nmax)
+ grow(0);
+ x[i][0] = buf[m++];
+ x[i][1] = buf[m++];
+ x[i][2] = buf[m++];
+ tag[i] = static_cast<int> (buf[m++]);
+ type[i] = static_cast<int> (buf[m++]);
+ mask[i] = static_cast<int> (buf[m++]);
+ v[i][0] = buf[m++];
+ v[i][1] = buf[m++];
+ v[i][2] = buf[m++];
+ rho[i] = buf[m++];
+ e[i] = buf[m++];
+ cv[i] = buf[m++];
+ vest[i][0] = buf[m++];
+ vest[i][1] = buf[m++];
+ vest[i][2] = buf[m++];
+ }
+}
+
+/* ----------------------------------------------------------------------
+ pack data for atom I for sending to another proc
+ xyz must be 1st 3 values, so comm::exchange() can test on them
+ ------------------------------------------------------------------------- */
+
+int AtomVecMeso::pack_exchange(int i, double *buf) {
+ //printf("in AtomVecMeso::pack_exchange\n");
+ int m = 1;
+ buf[m++] = x[i][0];
+ buf[m++] = x[i][1];
+ buf[m++] = x[i][2];
+ buf[m++] = v[i][0];
+ buf[m++] = v[i][1];
+ buf[m++] = v[i][2];
+ buf[m++] = tag[i];
+ buf[m++] = type[i];
+ buf[m++] = mask[i];
+ buf[m++] = image[i];
+ buf[m++] = rho[i];
+ buf[m++] = e[i];
+ buf[m++] = cv[i];
+ buf[m++] = vest[i][0];
+ buf[m++] = vest[i][1];
+ buf[m++] = vest[i][2];
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i, &buf[m]);
+
+ buf[0] = m;
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMeso::unpack_exchange(double *buf) {
+ //printf("in AtomVecMeso::unpack_exchange\n");
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax)
+ grow(0);
+
+ int m = 1;
+ x[nlocal][0] = buf[m++];
+ x[nlocal][1] = buf[m++];
+ x[nlocal][2] = buf[m++];
+ v[nlocal][0] = buf[m++];
+ v[nlocal][1] = buf[m++];
+ v[nlocal][2] = buf[m++];
+ tag[nlocal] = static_cast<int> (buf[m++]);
+ type[nlocal] = static_cast<int> (buf[m++]);
+ mask[nlocal] = static_cast<int> (buf[m++]);
+ image[nlocal] = static_cast<int> (buf[m++]);
+ rho[nlocal] = buf[m++];
+ e[nlocal] = buf[m++];
+ cv[nlocal] = buf[m++];
+ vest[nlocal][0] = buf[m++];
+ vest[nlocal][1] = buf[m++];
+ vest[nlocal][2] = buf[m++];
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ m += modify->fix[atom->extra_grow[iextra]]-> unpack_exchange(nlocal,
+ &buf[m]);
+
+ atom->nlocal++;
+ return m;
+}
+
+/* ----------------------------------------------------------------------
+ size of restart data for all atoms owned by this proc
+ include extra data stored by fixes
+ ------------------------------------------------------------------------- */
+
+int AtomVecMeso::size_restart() {
+ int i;
+
+ int nlocal = atom->nlocal;
+ int n = 17 * nlocal; // 11 + rho + e + cv + vest[3]
+
+ if (atom->nextra_restart)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (i = 0; i < nlocal; i++)
+ n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+
+ return n;
+}
+
+/* ----------------------------------------------------------------------
+ pack atom I's data for restart file including extra quantities
+ xyz must be 1st 3 values, so that read_restart can test on them
+ molecular types may be negative, but write as positive
+ ------------------------------------------------------------------------- */
+
+int AtomVecMeso::pack_restart(int i, double *buf) {
+ int m = 1;
+ buf[m++] = x[i][0];
+ buf[m++] = x[i][1];
+ buf[m++] = x[i][2];
+ buf[m++] = tag[i];
+ buf[m++] = type[i];
+ buf[m++] = mask[i];
+ buf[m++] = image[i];
+ buf[m++] = v[i][0];
+ buf[m++] = v[i][1];
+ buf[m++] = v[i][2];
+ buf[m++] = rho[i];
+ buf[m++] = e[i];
+ buf[m++] = cv[i];
+ buf[m++] = vest[i][0];
+ buf[m++] = vest[i][1];
+ buf[m++] = vest[i][2];
+
+ if (atom->nextra_restart)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i, &buf[m]);
+
+ buf[0] = m;
+ return m;
+}
+
+/* ----------------------------------------------------------------------
+ unpack data for one atom from restart file including extra quantities
+ ------------------------------------------------------------------------- */
+
+int AtomVecMeso::unpack_restart(double *buf) {
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) {
+ grow(0);
+ if (atom->nextra_store)
+ memory->grow(atom->extra, nmax, atom->nextra_store, "atom:extra");
+ }
+
+ int m = 1;
+ x[nlocal][0] = buf[m++];
+ x[nlocal][1] = buf[m++];
+ x[nlocal][2] = buf[m++];
+ tag[nlocal] = static_cast<int> (buf[m++]);
+ type[nlocal] = static_cast<int> (buf[m++]);
+ mask[nlocal] = static_cast<int> (buf[m++]);
+ image[nlocal] = static_cast<int> (buf[m++]);
+ v[nlocal][0] = buf[m++];
+ v[nlocal][1] = buf[m++];
+ v[nlocal][2] = buf[m++];
+ rho[nlocal] = buf[m++];
+ e[nlocal] = buf[m++];
+ cv[nlocal] = buf[m++];
+ vest[nlocal][0] = buf[m++];
+ vest[nlocal][1] = buf[m++];
+ vest[nlocal][2] = buf[m++];
+
+ double **extra = atom->extra;
+ if (atom->nextra_store) {
+ int size = static_cast<int> (buf[0]) - m;
+ for (int i = 0; i < size; i++)
+ extra[nlocal][i] = buf[m++];
+ }
+
+ atom->nlocal++;
+ return m;
+}
+
+/* ----------------------------------------------------------------------
+ create one atom of itype at coord
+ set other values to defaults
+ ------------------------------------------------------------------------- */
+
+void AtomVecMeso::create_atom(int itype, double *coord) {
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax)
+ grow(0);
+
+ tag[nlocal] = 0;
+ type[nlocal] = itype;
+ x[nlocal][0] = coord[0];
+ x[nlocal][1] = coord[1];
+ x[nlocal][2] = coord[2];
+ mask[nlocal] = 1;
+ image[nlocal] = (512 << 20) | (512 << 10) | 512;
+ v[nlocal][0] = 0.0;
+ v[nlocal][1] = 0.0;
+ v[nlocal][2] = 0.0;
+ rho[nlocal] = 0.0;
+ e[nlocal] = 0.0;
+ cv[nlocal] = 1.0;
+ vest[nlocal][0] = 0.0;
+ vest[nlocal][1] = 0.0;
+ vest[nlocal][2] = 0.0;
+ de[nlocal] = 0.0;
+ drho[nlocal] = 0.0;
+
+ atom->nlocal++;
+}
+
+/* ----------------------------------------------------------------------
+ unpack one line from Atoms section of data file
+ initialize other atom quantities
+ ------------------------------------------------------------------------- */
+
+void AtomVecMeso::data_atom(double *coord, int imagetmp, char **values) {
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax)
+ grow(0);
+
+ tag[nlocal] = atoi(values[0]);
+ if (tag[nlocal] <= 0)
+ error->one("Invalid atom ID in Atoms section of data file");
+
+ type[nlocal] = atoi(values[1]);
+ if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
+ error->one("Invalid atom type in Atoms section of data file");
+
+ rho[nlocal] = atof(values[2]);
+ e[nlocal] = atof(values[3]);
+ cv[nlocal] = atof(values[4]);
+
+ x[nlocal][0] = coord[0];
+ x[nlocal][1] = coord[1];
+ x[nlocal][2] = coord[2];
+
+ //printf("rho=%f, e=%f, cv=%f, x=%f\n", rho[nlocal], e[nlocal], cv[nlocal], x[nlocal][0]);
+
+ image[nlocal] = imagetmp;
+
+ mask[nlocal] = 1;
+ v[nlocal][0] = 0.0;
+ v[nlocal][1] = 0.0;
+ v[nlocal][2] = 0.0;
+
+ vest[nlocal][0] = 0.0;
+ vest[nlocal][1] = 0.0;
+ vest[nlocal][2] = 0.0;
+
+ de[nlocal] = 0.0;
+ drho[nlocal] = 0.0;
+
+ atom->nlocal++;
+}
+
+/* ----------------------------------------------------------------------
+ unpack hybrid quantities from one line in Atoms section of data file
+ initialize other atom quantities for this sub-style
+ ------------------------------------------------------------------------- */
+
+int AtomVecMeso::data_atom_hybrid(int nlocal, char **values) {
+
+ rho[nlocal] = atof(values[0]);
+ e[nlocal] = atof(values[1]);
+ cv[nlocal] = atof(values[2]);
+
+ return 3;
+}
+
+/* ----------------------------------------------------------------------
+ return # of bytes of allocated memory
+ ------------------------------------------------------------------------- */
+
+bigint AtomVecMeso::memory_usage() {
+ bigint bytes = 0;
+
+ if (atom->memcheck("tag"))
+ bytes += memory->usage(tag, nmax);
+ if (atom->memcheck("type"))
+ bytes += memory->usage(type, nmax);
+ if (atom->memcheck("mask"))
+ bytes += memory->usage(mask, nmax);
+ if (atom->memcheck("image"))
+ bytes += memory->usage(image, nmax);
+ if (atom->memcheck("x"))
+ bytes += memory->usage(x, nmax);
+ if (atom->memcheck("v"))
+ bytes += memory->usage(v, nmax);
+ if (atom->memcheck("f"))
+ bytes += memory->usage(f, nmax);
+ if (atom->memcheck("rho"))
+ bytes += memory->usage(rho, nmax);
+ if (atom->memcheck("drho"))
+ bytes += memory->usage(drho, nmax);
+ if (atom->memcheck("e"))
+ bytes += memory->usage(e, nmax);
+ if (atom->memcheck("de"))
+ bytes += memory->usage(de, nmax);
+ if (atom->memcheck("cv"))
+ bytes += memory->usage(cv, nmax);
+ if (atom->memcheck("vest"))
+ bytes += memory->usage(vest, nmax);
+
+ return bytes;
+}
diff --git a/src/USER-SPH/atom_vec_meso.h b/src/USER-SPH/atom_vec_meso.h
new file mode 100644
index 000000000..b187198c0
--- /dev/null
+++ b/src/USER-SPH/atom_vec_meso.h
@@ -0,0 +1,74 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef ATOM_CLASS
+
+AtomStyle(meso,AtomVecMeso)
+
+#else
+
+#ifndef LMP_ATOM_VEC_MESO_H
+#define LMP_ATOM_VEC_MESO_H
+
+#include "atom_vec.h"
+
+namespace LAMMPS_NS {
+
+class AtomVecMeso : public AtomVec {
+ public:
+ AtomVecMeso(class LAMMPS *, int, char **);
+ ~AtomVecMeso() {}
+ void grow(int);
+ void grow_reset();
+ void copy(int, int, int);
+ int pack_comm(int, int *, double *, int, int *);
+ int pack_comm_vel(int, int *, double *, int, int *);
+ void unpack_comm(int, int, double *);
+ void unpack_comm_vel(int, int, double *);
+ int pack_reverse(int, int, double *);
+ void unpack_reverse(int, int *, double *);
+
+ int pack_comm_hybrid(int, int *, double *);
+ int unpack_comm_hybrid(int, int, double *);
+
+ int pack_border_hybrid(int, int *, double *);
+ int unpack_border_hybrid(int, int, double *);
+
+ int pack_reverse_hybrid(int, int, double *);
+ int unpack_reverse_hybrid(int, int *, double *);
+
+ int pack_border(int, int *, double *, int, int *);
+ int pack_border_vel(int, int *, double *, int, int *);
+ void unpack_border(int, int, double *);
+ void unpack_border_vel(int, int, double *);
+ int pack_exchange(int, double *);
+ int unpack_exchange(double *);
+ int size_restart();
+ int pack_restart(int, double *);
+ int unpack_restart(double *);
+ void create_atom(int, double *);
+ void data_atom(double *, int, char **);
+ int data_atom_hybrid(int, char **);
+ bigint memory_usage();
+
+ private:
+ int *tag,*type,*mask,*image;
+ double **x,**v,**f;
+ double *rho, *drho, *e, *de, *cv;
+ double **vest; // estimated velocity during force computation
+};
+
+}
+
+#endif
+#endif
diff --git a/src/USER-SPH/compute_meso_e_atom.cpp b/src/USER-SPH/compute_meso_e_atom.cpp
new file mode 100644
index 000000000..934818584
--- /dev/null
+++ b/src/USER-SPH/compute_meso_e_atom.cpp
@@ -0,0 +1,97 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "string.h"
+#include "compute_meso_e_atom.h"
+#include "atom.h"
+#include "update.h"
+#include "modify.h"
+#include "comm.h"
+#include "force.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputeMesoEAtom::ComputeMesoEAtom(LAMMPS *lmp, int narg, char **arg) :
+ Compute(lmp, narg, arg)
+{
+ if (narg != 3) error->all("Number of arguments for compute meso_e/atom command != 3");
+ if (atom->e_flag != 1) error->all("compute meso_e/atom command requires atom_style with energy (e.g. meso)");
+
+ peratom_flag = 1;
+ size_peratom_cols = 0;
+
+ nmax = 0;
+ evector = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeMesoEAtom::~ComputeMesoEAtom()
+{
+ memory->sfree(evector);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeMesoEAtom::init()
+{
+
+ int count = 0;
+ for (int i = 0; i < modify->ncompute; i++)
+ if (strcmp(modify->compute[i]->style,"evector/atom") == 0) count++;
+ if (count > 1 && comm->me == 0)
+ error->warning("More than one compute evector/atom");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeMesoEAtom::compute_peratom()
+{
+ invoked_peratom = update->ntimestep;
+
+ // grow evector array if necessary
+
+ if (atom->nlocal > nmax) {
+ memory->sfree(evector);
+ nmax = atom->nmax;
+ evector = (double *) memory->smalloc(nmax*sizeof(double),"evector/atom:evector");
+ vector_atom = evector;
+ }
+
+ double *e = atom->e;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ evector[i] = e[i];
+ }
+ else {
+ evector[i] = 0.0;
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ memory usage of local atom-based array
+------------------------------------------------------------------------- */
+
+double ComputeMesoEAtom::memory_usage()
+{
+ double bytes = nmax * sizeof(double);
+ return bytes;
+}
diff --git a/src/verlet.h b/src/USER-SPH/compute_meso_e_atom.h
similarity index 59%
copy from src/verlet.h
copy to src/USER-SPH/compute_meso_e_atom.h
index 8b8c90b7a..07fc01c92 100644
--- a/src/verlet.h
+++ b/src/USER-SPH/compute_meso_e_atom.h
@@ -1,48 +1,43 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#ifdef INTEGRATE_CLASS
+#ifdef COMPUTE_CLASS
-IntegrateStyle(verlet,Verlet)
+ComputeStyle(meso_e/atom,ComputeMesoEAtom)
#else
-#ifndef LMP_VERLET_H
-#define LMP_VERLET_H
+#ifndef LMP_COMPUTE_MESO_E_ATOM_H
+#define LMP_COMPUTE_MESO_E_ATOM_H
-#include "integrate.h"
+#include "compute.h"
namespace LAMMPS_NS {
-class Verlet : public Integrate {
+class ComputeMesoEAtom : public Compute {
public:
- Verlet(class LAMMPS *, int, char **);
- virtual ~Verlet() {}
+ ComputeMesoEAtom(class LAMMPS *, int, char **);
+ ~ComputeMesoEAtom();
void init();
- void setup();
- void setup_minimal(int);
- void run(int);
- void cleanup();
+ void compute_peratom();
+ double memory_usage();
- protected:
- int triclinic; // 0 if domain is orthog, 1 if triclinic
- int torqueflag; // zero out arrays every step
- int erforceflag;
-
- void force_clear();
+ private:
+ int nmax;
+ double *evector;
};
}
#endif
#endif
diff --git a/src/USER-SPH/compute_meso_rho_atom.cpp b/src/USER-SPH/compute_meso_rho_atom.cpp
new file mode 100644
index 000000000..98aab3ad7
--- /dev/null
+++ b/src/USER-SPH/compute_meso_rho_atom.cpp
@@ -0,0 +1,99 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "string.h"
+#include "compute_meso_rho_atom.h"
+#include "atom.h"
+#include "update.h"
+#include "modify.h"
+#include "comm.h"
+#include "force.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputeMesoRhoAtom::ComputeMesoRhoAtom(LAMMPS *lmp, int narg, char **arg) :
+ Compute(lmp, narg, arg)
+{
+ if (narg != 3) error->all("Illegal compute meso_rho/atom command");
+ if (atom->rho_flag != 1) error->all("compute meso_rho/atom command requires atom_style with density (e.g. meso)");
+
+ peratom_flag = 1;
+ size_peratom_cols = 0;
+
+ nmax = 0;
+ rhoVector = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeMesoRhoAtom::~ComputeMesoRhoAtom()
+{
+ memory->sfree(rhoVector);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeMesoRhoAtom::init()
+{
+
+ int count = 0;
+ for (int i = 0; i < modify->ncompute; i++)
+ if (strcmp(modify->compute[i]->style,"rhoVector/atom") == 0) count++;
+ if (count > 1 && comm->me == 0)
+ error->warning("More than one compute rhoVector/atom");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeMesoRhoAtom::compute_peratom()
+{
+ invoked_peratom = update->ntimestep;
+
+ // grow rhoVector array if necessary
+
+ if (atom->nlocal > nmax) {
+ memory->sfree(rhoVector);
+ nmax = atom->nmax;
+ rhoVector = (double *) memory->smalloc(nmax*sizeof(double),"atom:rhoVector");
+ vector_atom = rhoVector;
+ }
+
+ // compute kinetic energy for each atom in group
+
+ double *rho = atom->rho;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ rhoVector[i] = rho[i];
+ }
+ else {
+ rhoVector[i] = 0.0;
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ memory usage of local atom-based array
+------------------------------------------------------------------------- */
+
+double ComputeMesoRhoAtom::memory_usage()
+{
+ double bytes = nmax * sizeof(double);
+ return bytes;
+}
diff --git a/src/verlet.h b/src/USER-SPH/compute_meso_rho_atom.h
similarity index 59%
copy from src/verlet.h
copy to src/USER-SPH/compute_meso_rho_atom.h
index 8b8c90b7a..e1100a2f8 100644
--- a/src/verlet.h
+++ b/src/USER-SPH/compute_meso_rho_atom.h
@@ -1,48 +1,43 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#ifdef INTEGRATE_CLASS
+#ifdef COMPUTE_CLASS
-IntegrateStyle(verlet,Verlet)
+ComputeStyle(meso_rho/atom,ComputeMesoRhoAtom)
#else
-#ifndef LMP_VERLET_H
-#define LMP_VERLET_H
+#ifndef LMP_COMPUTE_MESO_RHO_ATOM_H
+#define LMP_COMPUTE_MESO_RHO_ATOM_H
-#include "integrate.h"
+#include "compute.h"
namespace LAMMPS_NS {
-class Verlet : public Integrate {
+class ComputeMesoRhoAtom : public Compute {
public:
- Verlet(class LAMMPS *, int, char **);
- virtual ~Verlet() {}
+ ComputeMesoRhoAtom(class LAMMPS *, int, char **);
+ ~ComputeMesoRhoAtom();
void init();
- void setup();
- void setup_minimal(int);
- void run(int);
- void cleanup();
+ void compute_peratom();
+ double memory_usage();
- protected:
- int triclinic; // 0 if domain is orthog, 1 if triclinic
- int torqueflag; // zero out arrays every step
- int erforceflag;
-
- void force_clear();
+ private:
+ int nmax;
+ double *rhoVector;
};
}
#endif
#endif
diff --git a/src/USER-SPH/compute_meso_t_atom.cpp b/src/USER-SPH/compute_meso_t_atom.cpp
new file mode 100644
index 000000000..21a9a4d66
--- /dev/null
+++ b/src/USER-SPH/compute_meso_t_atom.cpp
@@ -0,0 +1,101 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "string.h"
+#include "compute_meso_t_atom.h"
+#include "atom.h"
+#include "update.h"
+#include "modify.h"
+#include "comm.h"
+#include "force.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputeMesoTAtom::ComputeMesoTAtom(LAMMPS *lmp, int narg, char **arg) :
+ Compute(lmp, narg, arg)
+{
+ if (narg != 3) error->all("Number of arguments for compute meso_t/atom command != 3");
+ if ((atom->e_flag != 1) || (atom->cv_flag != 1))
+ error->all("compute meso_e/atom command requires atom_style with both energy and heat capacity (e.g. meso)");
+
+ peratom_flag = 1;
+ size_peratom_cols = 0;
+
+ nmax = 0;
+ tvector = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeMesoTAtom::~ComputeMesoTAtom()
+{
+ memory->sfree(tvector);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeMesoTAtom::init()
+{
+
+ int count = 0;
+ for (int i = 0; i < modify->ncompute; i++)
+ if (strcmp(modify->compute[i]->style,"meso_t/atom") == 0) count++;
+ if (count > 1 && comm->me == 0)
+ error->warning("More than one compute meso_t/atom");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeMesoTAtom::compute_peratom()
+{
+ invoked_peratom = update->ntimestep;
+
+ // grow tvector array if necessary
+
+ if (atom->nlocal > nmax) {
+ memory->sfree(tvector);
+ nmax = atom->nmax;
+ tvector = (double *) memory->smalloc(nmax*sizeof(double),"tvector/atom:tvector");
+ vector_atom = tvector;
+ }
+
+ double *e = atom->e;
+ double *cv = atom->cv;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ if (cv[i] > 0.0) {
+ tvector[i] = e[i] / cv[i];
+ }
+ }
+ else {
+ tvector[i] = 0.0;
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ memory usage of local atom-based array
+------------------------------------------------------------------------- */
+
+double ComputeMesoTAtom::memory_usage()
+{
+ double bytes = nmax * sizeof(double);
+ return bytes;
+}
diff --git a/src/verlet.h b/src/USER-SPH/compute_meso_t_atom.h
similarity index 59%
copy from src/verlet.h
copy to src/USER-SPH/compute_meso_t_atom.h
index 8b8c90b7a..279d749f8 100644
--- a/src/verlet.h
+++ b/src/USER-SPH/compute_meso_t_atom.h
@@ -1,48 +1,43 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#ifdef INTEGRATE_CLASS
+#ifdef COMPUTE_CLASS
-IntegrateStyle(verlet,Verlet)
+ComputeStyle(meso_t/atom,ComputeMesoTAtom)
#else
-#ifndef LMP_VERLET_H
-#define LMP_VERLET_H
+#ifndef LMP_COMPUTE_MESO_T_ATOM_H
+#define LMP_COMPUTE_MESO_T_ATOM_H
-#include "integrate.h"
+#include "compute.h"
namespace LAMMPS_NS {
-class Verlet : public Integrate {
+class ComputeMesoTAtom : public Compute {
public:
- Verlet(class LAMMPS *, int, char **);
- virtual ~Verlet() {}
+ ComputeMesoTAtom(class LAMMPS *, int, char **);
+ ~ComputeMesoTAtom();
void init();
- void setup();
- void setup_minimal(int);
- void run(int);
- void cleanup();
+ void compute_peratom();
+ double memory_usage();
- protected:
- int triclinic; // 0 if domain is orthog, 1 if triclinic
- int torqueflag; // zero out arrays every step
- int erforceflag;
-
- void force_clear();
+ private:
+ int nmax;
+ double *tvector;
};
}
#endif
#endif
diff --git a/src/USER-SPH/fix_meso.cpp b/src/USER-SPH/fix_meso.cpp
new file mode 100644
index 000000000..0b8576f38
--- /dev/null
+++ b/src/USER-SPH/fix_meso.cpp
@@ -0,0 +1,167 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+ ------------------------------------------------------------------------- */
+
+#include "stdio.h"
+#include "string.h"
+#include "fix_meso.h"
+#include "math.h"
+#include "stdlib.h"
+#include "string.h"
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "update.h"
+#include "integrate.h"
+#include "respa.h"
+#include "memory.h"
+#include "error.h"
+#include "pair.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+FixMeso::FixMeso(LAMMPS *lmp, int narg, char **arg) :
+ Fix(lmp, narg, arg) {
+
+ if ((atom->e_flag != 1) || (atom->rho_flag != 1))
+ error->all(
+ "fix meso command requires atom_style with both energy and density");
+
+ if (narg != 3)
+ error->all("Illegal number of arguments for fix meso command");
+
+ time_integrate = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixMeso::setmask() {
+ int mask = 0;
+ mask |= INITIAL_INTEGRATE;
+ mask |= FINAL_INTEGRATE;
+ return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixMeso::init() {
+ dtv = update->dt;
+ dtf = 0.5 * update->dt * force->ftm2v;
+}
+
+/* ----------------------------------------------------------------------
+ allow for both per-type and per-atom mass
+ ------------------------------------------------------------------------- */
+
+void FixMeso::initial_integrate(int vflag) {
+ // update v and x and rho and e of atoms in group
+
+ double **x = atom->x;
+ double **v = atom->v;
+ double **f = atom->f;
+ double **vest = atom->vest;
+ double *rho = atom->rho;
+ double *drho = atom->drho;
+ double *e = atom->e;
+ double *de = atom->de;
+ double *mass = atom->mass;
+ double *rmass = atom->rmass;
+ int rmass_flag = atom->rmass_flag;
+
+ int *type = atom->type;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ int i;
+ double dtfm;
+
+ if (igroup == atom->firstgroup)
+ nlocal = atom->nfirst;
+
+ for (i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ if (rmass_flag) {
+ dtfm = dtf / rmass[i];
+ } else {
+ dtfm = dtf / mass[type[i]];
+ }
+
+ e[i] += dtf * de[i]; // half-step update of particle internal energy
+ rho[i] += dtf * drho[i]; // ... and density
+
+ // extrapolate velocity for use with velocity-dependent potentials, e.g. SPH
+ vest[i][0] = v[i][0] + 2.0 * dtfm * f[i][0];
+ vest[i][1] = v[i][1] + 2.0 * dtfm * f[i][1];
+ vest[i][2] = v[i][2] + 2.0 * dtfm * f[i][2];
+
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
+
+ x[i][0] += dtv * v[i][0];
+ x[i][1] += dtv * v[i][1];
+ x[i][2] += dtv * v[i][2];
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixMeso::final_integrate() {
+
+ // update v, rho, and e of atoms in group
+
+ double **v = atom->v;
+ double **f = atom->f;
+ double *e = atom->e;
+ double *de = atom->de;
+ double *rho = atom->rho;
+ double *drho = atom->drho;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ double *mass = atom->mass;
+ int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup)
+ nlocal = atom->nfirst;
+ double dtfm;
+ double *rmass = atom->rmass;
+ int rmass_flag = atom->rmass_flag;
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+
+ if (rmass_flag) {
+ dtfm = dtf / rmass[i];
+ } else {
+ dtfm = dtf / mass[type[i]];
+ }
+ v[i][0] += dtfm * f[i][0];
+ v[i][1] += dtfm * f[i][1];
+ v[i][2] += dtfm * f[i][2];
+
+ e[i] += dtf * de[i];
+ rho[i] += dtf * drho[i];
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixMeso::reset_dt() {
+ dtv = update->dt;
+ dtf = 0.5 * update->dt * force->ftm2v;
+}
+
diff --git a/src/fix_gravity.h b/src/USER-SPH/fix_meso.h
similarity index 61%
copy from src/fix_gravity.h
copy to src/USER-SPH/fix_meso.h
index 248a9ffa1..eee5ee1d4 100644
--- a/src/fix_gravity.h
+++ b/src/USER-SPH/fix_meso.h
@@ -1,52 +1,49 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
-FixStyle(gravity,FixGravity)
+FixStyle(meso,FixMeso)
#else
-#ifndef LMP_FIX_GRAVITY_H
-#define LMP_FIX_GRAVITY_H
+#ifndef LMP_FIX_MESO_H
+#define LMP_FIX_MESO_H
#include "fix.h"
namespace LAMMPS_NS {
-class FixGravity : public Fix {
- friend class FixPour;
-
+class FixMeso : public Fix {
public:
- FixGravity(class LAMMPS *, int, char **);
+ FixMeso(class LAMMPS *, int, char **);
int setmask();
- void init();
- void setup(int);
- void post_force(int);
- void post_force_respa(int, int, int);
+ virtual void init();
+ virtual void initial_integrate(int);
+ virtual void final_integrate();
+ void reset_dt();
private:
- int style;
- double magnitude,dt;
- double phi,theta,phigrad,thetagrad;
- double xdir,ydir,zdir;
- double xgrav,ygrav,zgrav,xacc,yacc,zacc;
- double degree2rad;
- int nlevels_respa;
- int time_origin;
+ class NeighList *list;
+ protected:
+ double dtv,dtf;
+ double *step_respa;
+ int mass_require;
+
+ class Pair *pair;
};
}
#endif
#endif
diff --git a/src/USER-SPH/fix_meso_stationary.cpp b/src/USER-SPH/fix_meso_stationary.cpp
new file mode 100644
index 000000000..9a08d28fd
--- /dev/null
+++ b/src/USER-SPH/fix_meso_stationary.cpp
@@ -0,0 +1,122 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+ ------------------------------------------------------------------------- */
+
+#include "stdio.h"
+#include "string.h"
+#include "fix_meso_stationary.h"
+#include "math.h"
+#include "stdlib.h"
+#include "string.h"
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "update.h"
+#include "integrate.h"
+#include "respa.h"
+#include "memory.h"
+#include "error.h"
+#include "pair.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+FixMesoStationary::FixMesoStationary(LAMMPS *lmp, int narg, char **arg) :
+ Fix(lmp, narg, arg) {
+
+ if ((atom->e_flag != 1) || (atom->rho_flag != 1))
+ error->all(
+ "fix meso/stationary command requires atom_style with both energy and density, e.g. meso");
+
+ if (narg != 3)
+ error->all("Illegal number of arguments for fix meso/stationary command");
+
+ time_integrate = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixMesoStationary::setmask() {
+ int mask = 0;
+ mask |= INITIAL_INTEGRATE;
+ mask |= FINAL_INTEGRATE;
+ return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixMesoStationary::init() {
+ dtv = update->dt;
+ dtf = 0.5 * update->dt * force->ftm2v;
+}
+
+/* ----------------------------------------------------------------------
+ allow for both per-type and per-atom mass
+ ------------------------------------------------------------------------- */
+
+void FixMesoStationary::initial_integrate(int vflag) {
+
+ double *rho = atom->rho;
+ double *drho = atom->drho;
+ double *e = atom->e;
+ double *de = atom->de;
+
+ int *type = atom->type;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ int i;
+
+ if (igroup == atom->firstgroup)
+ nlocal = atom->nfirst;
+
+ for (i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ e[i] += dtf * de[i]; // half-step update of particle internal energy
+ rho[i] += dtf * drho[i]; // ... and density
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixMesoStationary::final_integrate() {
+
+ double *e = atom->e;
+ double *de = atom->de;
+ double *rho = atom->rho;
+ double *drho = atom->drho;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ double *mass = atom->mass;
+ int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup)
+ nlocal = atom->nfirst;
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ e[i] += dtf * de[i];
+ rho[i] += dtf * drho[i];
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixMesoStationary::reset_dt() {
+ dtv = update->dt;
+ dtf = 0.5 * update->dt * force->ftm2v;
+}
+
diff --git a/src/fix_gravity.h b/src/USER-SPH/fix_meso_stationary.h
similarity index 61%
copy from src/fix_gravity.h
copy to src/USER-SPH/fix_meso_stationary.h
index 248a9ffa1..08869d210 100644
--- a/src/fix_gravity.h
+++ b/src/USER-SPH/fix_meso_stationary.h
@@ -1,52 +1,49 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
-FixStyle(gravity,FixGravity)
+FixStyle(meso/stationary,FixMesoStationary)
#else
-#ifndef LMP_FIX_GRAVITY_H
-#define LMP_FIX_GRAVITY_H
+#ifndef LMP_FIX_MESO_STATIONARY_H
+#define LMP_FIX_MESO_STATIONARY_H
#include "fix.h"
namespace LAMMPS_NS {
-class FixGravity : public Fix {
- friend class FixPour;
-
+class FixMesoStationary : public Fix {
public:
- FixGravity(class LAMMPS *, int, char **);
+ FixMesoStationary(class LAMMPS *, int, char **);
int setmask();
- void init();
- void setup(int);
- void post_force(int);
- void post_force_respa(int, int, int);
+ virtual void init();
+ virtual void initial_integrate(int);
+ virtual void final_integrate();
+ void reset_dt();
private:
- int style;
- double magnitude,dt;
- double phi,theta,phigrad,thetagrad;
- double xdir,ydir,zdir;
- double xgrav,ygrav,zgrav,xacc,yacc,zacc;
- double degree2rad;
- int nlevels_respa;
- int time_origin;
+ class NeighList *list;
+ protected:
+ double dtv,dtf;
+ double *step_respa;
+ int mass_require;
+
+ class Pair *pair;
};
}
#endif
#endif
diff --git a/src/USER-SPH/pair_sph_heatconduction.cpp b/src/USER-SPH/pair_sph_heatconduction.cpp
new file mode 100644
index 000000000..e4af6f766
--- /dev/null
+++ b/src/USER-SPH/pair_sph_heatconduction.cpp
@@ -0,0 +1,221 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+ ------------------------------------------------------------------------- */
+
+#include "math.h"
+#include "stdlib.h"
+#include "pair_sph_heatconduction.h"
+#include "atom.h"
+#include "force.h"
+#include "comm.h"
+#include "memory.h"
+#include "error.h"
+#include "neigh_list.h"
+#include "domain.h"
+
+using namespace LAMMPS_NS;
+
+#define MIN(a,b) ((a) < (b) ? (a) : (b))
+#define MAX(a,b) ((a) > (b) ? (a) : (b))
+
+/* ---------------------------------------------------------------------- */
+
+PairSPHHeatConduction::PairSPHHeatConduction(LAMMPS *lmp) :
+ Pair(lmp) {
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairSPHHeatConduction::~PairSPHHeatConduction() {
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+ memory->destroy(cut);
+ memory->destroy(alpha);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairSPHHeatConduction::compute(int eflag, int vflag) {
+ int i, j, ii, jj, inum, jnum, itype, jtype;
+ double xtmp, ytmp, ztmp, delx, dely, delz;
+
+ int *ilist, *jlist, *numneigh, **firstneigh;
+ double imass, jmass, h, ih, ihsq;
+ double rsq, wfd, D, deltaE;
+
+ if (eflag || vflag)
+ ev_setup(eflag, vflag);
+ else
+ evflag = vflag_fdotr = 0;
+
+ double **x = atom->x;
+ double *e = atom->e;
+ double *de = atom->de;
+ double *mass = atom->mass;
+ double *rho = atom->rho;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ int newton_pair = force->newton_pair;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // loop over neighbors of my atoms and do heat diffusion
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ itype = type[i];
+
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ imass = mass[itype];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx * delx + dely * dely + delz * delz;
+ jtype = type[j];
+ jmass = mass[jtype];
+
+ if (rsq < cutsq[itype][jtype]) {
+ h = cut[itype][jtype];
+ ih = 1.0 / h;
+ ihsq = ih * ih;
+
+ // kernel function
+ wfd = h - sqrt(rsq);
+ if (domain->dimension == 3) {
+ // Lucy Kernel, 3d
+ // Note that wfd, the derivative of the weight function with respect to r,
+ // is lacking a factor of r.
+ // The missing factor of r is recovered by
+ // deltaE, which is missing a factor of 1/r
+ wfd = -25.066903536973515383e0 * wfd * wfd * ihsq * ihsq * ihsq * ih;
+ } else {
+ // Lucy Kernel, 2d
+ wfd = -19.098593171027440292e0 * wfd * wfd * ihsq * ihsq * ihsq;
+ }
+
+ jmass = mass[jtype];
+ D = alpha[itype][jtype]; // diffusion coefficient
+
+ deltaE = 2.0 * imass * jmass / (imass+jmass);
+ deltaE *= (rho[i] + rho[j]) / (rho[i] * rho[j]);
+ deltaE *= D * (e[i] - e[j]) * wfd;
+
+ de[i] += deltaE;
+ if (newton_pair || j < nlocal) {
+ de[j] -= deltaE;
+ }
+
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ allocate all arrays
+ ------------------------------------------------------------------------- */
+
+void PairSPHHeatConduction::allocate() {
+ allocated = 1;
+ int n = atom->ntypes;
+
+ memory->create(setflag, n + 1, n + 1, "pair:setflag");
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ setflag[i][j] = 0;
+
+ memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
+ memory->create(cut, n + 1, n + 1, "pair:cut");
+ memory->create(alpha, n + 1, n + 1, "pair:alpha");
+}
+
+/* ----------------------------------------------------------------------
+ global settings
+ ------------------------------------------------------------------------- */
+
+void PairSPHHeatConduction::settings(int narg, char **arg) {
+ if (narg != 0)
+ error->all(
+ "Illegal number of setting arguments for pair_style sph/heatconduction");
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs for one or more type pairs
+ ------------------------------------------------------------------------- */
+
+void PairSPHHeatConduction::coeff(int narg, char **arg) {
+ if (narg != 4)
+ error->all("Incorrect number of args for pair_style sph/heatconduction coefficients");
+ if (!allocated)
+ allocate();
+
+ int ilo, ihi, jlo, jhi;
+ force->bounds(arg[0], atom->ntypes, ilo, ihi);
+ force->bounds(arg[1], atom->ntypes, jlo, jhi);
+
+ double alpha_one = force->numeric(arg[2]);
+ double cut_one = force->numeric(arg[3]);
+
+ int count = 0;
+ for (int i = ilo; i <= ihi; i++) {
+ for (int j = MAX(jlo,i); j <= jhi; j++) {
+ //printf("setting cut[%d][%d] = %f\n", i, j, cut_one);
+ cut[i][j] = cut_one;
+ alpha[i][j] = alpha_one;
+ setflag[i][j] = 1;
+ count++;
+ }
+ }
+
+ if (count == 0)
+ error->all("Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+ init for one type pair i,j and corresponding j,i
+ ------------------------------------------------------------------------- */
+
+double PairSPHHeatConduction::init_one(int i, int j) {
+
+ if (setflag[i][j] == 0) {
+ error->all("All pair sph/heatconduction coeffs are not set");
+ }
+
+ cut[j][i] = cut[i][j];
+ alpha[j][i] = alpha[i][j];
+
+ return cut[i][j];
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairSPHHeatConduction::single(int i, int j, int itype, int jtype,
+ double rsq, double factor_coul, double factor_lj, double &fforce) {
+ fforce = 0.0;
+
+ return 0.0;
+}
diff --git a/src/verlet.h b/src/USER-SPH/pair_sph_heatconduction.h
similarity index 56%
copy from src/verlet.h
copy to src/USER-SPH/pair_sph_heatconduction.h
index 8b8c90b7a..81402fda2 100644
--- a/src/verlet.h
+++ b/src/USER-SPH/pair_sph_heatconduction.h
@@ -1,48 +1,45 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#ifdef INTEGRATE_CLASS
+#ifdef PAIR_CLASS
-IntegrateStyle(verlet,Verlet)
+PairStyle(sph/heatconduction,PairSPHHeatConduction)
#else
-#ifndef LMP_VERLET_H
-#define LMP_VERLET_H
+#ifndef LMP_PAIR_SPH_HEATCONDUCTION_H
+#define LMP_PAIR_SPH_HEATCONDUCTION_H
-#include "integrate.h"
+#include "pair.h"
namespace LAMMPS_NS {
-class Verlet : public Integrate {
+class PairSPHHeatConduction : public Pair {
public:
- Verlet(class LAMMPS *, int, char **);
- virtual ~Verlet() {}
- void init();
- void setup();
- void setup_minimal(int);
- void run(int);
- void cleanup();
+ PairSPHHeatConduction(class LAMMPS *);
+ virtual ~PairSPHHeatConduction();
+ virtual void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ virtual double init_one(int, int);
+ virtual double single(int, int, int, int, double, double, double, double &);
protected:
- int triclinic; // 0 if domain is orthog, 1 if triclinic
- int torqueflag; // zero out arrays every step
- int erforceflag;
-
- void force_clear();
+ double **cut, **alpha;
+ void allocate();
};
}
#endif
#endif
diff --git a/src/USER-SPH/pair_sph_idealgas.cpp b/src/USER-SPH/pair_sph_idealgas.cpp
new file mode 100644
index 000000000..35baf218c
--- /dev/null
+++ b/src/USER-SPH/pair_sph_idealgas.cpp
@@ -0,0 +1,262 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+ ------------------------------------------------------------------------- */
+
+#include "math.h"
+#include "stdlib.h"
+#include "pair_sph_idealgas.h"
+#include "atom.h"
+#include "force.h"
+#include "comm.h"
+#include "neigh_list.h"
+#include "memory.h"
+#include "error.h"
+#include "domain.h"
+
+using namespace LAMMPS_NS;
+
+#define MIN(a,b) ((a) < (b) ? (a) : (b))
+#define MAX(a,b) ((a) > (b) ? (a) : (b))
+
+/* ---------------------------------------------------------------------- */
+
+PairSPHIdealGas::PairSPHIdealGas(LAMMPS *lmp) :
+ Pair(lmp) {
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairSPHIdealGas::~PairSPHIdealGas() {
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+
+ memory->destroy(cut);
+ memory->destroy(viscosity);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairSPHIdealGas::compute(int eflag, int vflag) {
+ int i, j, ii, jj, inum, jnum, itype, jtype;
+ double xtmp, ytmp, ztmp, delx, dely, delz, fpair;
+
+ int *ilist, *jlist, *numneigh, **firstneigh;
+ double vxtmp, vytmp, vztmp, imass, jmass, fi, fj, fvisc, h, ih, ihsq;
+ double rsq, wfd, delVdotDelR, mu, deltaE, ci, cj;
+
+ if (eflag || vflag)
+ ev_setup(eflag, vflag);
+ else
+ evflag = vflag_fdotr = 0;
+
+ double **v = atom->vest;
+ double **x = atom->x;
+ double **f = atom->f;
+ double *rho = atom->rho;
+ double *mass = atom->mass;
+ double *de = atom->de;
+ double *e = atom->e;
+ double *drho = atom->drho;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ int newton_pair = force->newton_pair;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // loop over neighbors of my atoms
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ vxtmp = v[i][0];
+ vytmp = v[i][1];
+ vztmp = v[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ imass = mass[itype];
+
+ fi = 0.4 * e[i] / imass / rho[i]; // ideal gas EOS; this expression is fi = pressure / rho^2
+ ci = sqrt(0.4*e[i]/imass); // speed of sound with heat capacity ratio gamma=1.4
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx * delx + dely * dely + delz * delz;
+ jtype = type[j];
+ jmass = mass[jtype];
+
+ if (rsq < cutsq[itype][jtype]) {
+ h = cut[itype][jtype];
+ ih = 1. / h;
+ ihsq = ih * ih;
+
+ wfd = h - sqrt(rsq);
+ if (domain->dimension == 3) {
+ // Lucy Kernel, 3d
+ // Note that wfd, the derivative of the weight function with respect to r,
+ // is lacking a factor of r.
+ // The missing factor of r is recovered by
+ // (1) using delV . delX instead of delV . (delX/r) and
+ // (2) using f[i][0] += delx * fpair instead of f[i][0] += (delx/r) * fpair
+ wfd = -25.066903536973515383e0 * wfd * wfd * ihsq * ihsq * ihsq * ih;
+ } else {
+ // Lucy Kernel, 2d
+ wfd = -19.098593171027440292e0 * wfd * wfd * ihsq * ihsq * ihsq;
+ }
+
+ fj = 0.4 * e[j] / jmass / rho[j];
+
+ // dot product of velocity delta and distance vector
+ delVdotDelR = delx * (vxtmp - v[j][0]) + dely * (vytmp - v[j][1])
+ + delz * (vztmp - v[j][2]);
+
+ // artificial viscosity (Monaghan 1992)
+ if (delVdotDelR < 0.) {
+ cj = sqrt(0.4*e[j]/jmass);
+ mu = h * delVdotDelR / (rsq + 0.01 * h * h);
+ fvisc = -viscosity[itype][jtype] * (ci + cj) * mu / (rho[i] + rho[j]);
+ } else {
+ fvisc = 0.;
+ }
+
+ // total pair force & thermal energy increment
+ fpair = -imass * jmass * (fi + fj + fvisc) * wfd;
+ deltaE = -0.5 * fpair * delVdotDelR;
+
+ f[i][0] += delx * fpair;
+ f[i][1] += dely * fpair;
+ f[i][2] += delz * fpair;
+
+ // and change in density
+ drho[i] += jmass * delVdotDelR * wfd;
+
+ // change in thermal energy
+ de[i] += deltaE;
+
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx * fpair;
+ f[j][1] -= dely * fpair;
+ f[j][2] -= delz * fpair;
+ de[j] += deltaE;
+ drho[j] += imass * delVdotDelR * wfd;
+ }
+
+ if (evflag)
+ ev_tally(i, j, nlocal, newton_pair, 0.0, 0.0, fpair, delx, dely, delz);
+
+ if (evflag)
+ ev_tally(i, j, nlocal, newton_pair, 0.0, 0.0, fpair, delx, dely,
+ delz);
+ }
+ }
+ }
+
+ if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ----------------------------------------------------------------------
+ allocate all arrays
+ ------------------------------------------------------------------------- */
+
+void PairSPHIdealGas::allocate() {
+ allocated = 1;
+ int n = atom->ntypes;
+
+ memory->create(setflag, n + 1, n + 1, "pair:setflag");
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ setflag[i][j] = 0;
+
+ memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
+
+ memory->create(cut, n + 1, n + 1, "pair:cut");
+ memory->create(viscosity, n + 1, n + 1, "pair:viscosity");
+}
+
+/* ----------------------------------------------------------------------
+ global settings
+ ------------------------------------------------------------------------- */
+
+void PairSPHIdealGas::settings(int narg, char **arg) {
+ if (narg != 0)
+ error->all(
+ "Illegal number of setting arguments for pair_style sph/idealgas");
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs for one or more type pairs
+ ------------------------------------------------------------------------- */
+
+void PairSPHIdealGas::coeff(int narg, char **arg) {
+ if (narg != 4)
+ error->all("Incorrect number of args for pair_style sph/idealgas coefficients");
+ if (!allocated)
+ allocate();
+
+ int ilo, ihi, jlo, jhi;
+ force->bounds(arg[0], atom->ntypes, ilo, ihi);
+ force->bounds(arg[1], atom->ntypes, jlo, jhi);
+
+ double viscosity_one = force->numeric(arg[2]);
+ double cut_one = force->numeric(arg[3]);
+
+ int count = 0;
+ for (int i = ilo; i <= ihi; i++) {
+ for (int j = MAX(jlo,i); j <= jhi; j++) {
+ viscosity[i][j] = viscosity_one;
+ //printf("setting cut[%d][%d] = %f\n", i, j, cut_one);
+ cut[i][j] = cut_one;
+ setflag[i][j] = 1;
+ count++;
+ }
+ }
+
+ if (count == 0)
+ error->all("Incorrect args for pair sph/idealgas coefficients");
+}
+
+/* ----------------------------------------------------------------------
+ init for one type pair i,j and corresponding j,i
+ ------------------------------------------------------------------------- */
+
+double PairSPHIdealGas::init_one(int i, int j) {
+
+ if (setflag[i][j] == 0) {
+ error->all("All pair sph/idealgas coeffs are not set");
+ }
+
+ cut[j][i] = cut[i][j];
+
+ return cut[i][j];
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairSPHIdealGas::single(int i, int j, int itype, int jtype,
+ double rsq, double factor_coul, double factor_lj, double &fforce) {
+ fforce = 0.0;
+
+ return 0.0;
+}
diff --git a/src/verlet.h b/src/USER-SPH/pair_sph_idealgas.h
similarity index 58%
copy from src/verlet.h
copy to src/USER-SPH/pair_sph_idealgas.h
index 8b8c90b7a..540789afe 100644
--- a/src/verlet.h
+++ b/src/USER-SPH/pair_sph_idealgas.h
@@ -1,48 +1,46 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#ifdef INTEGRATE_CLASS
+#ifdef PAIR_CLASS
-IntegrateStyle(verlet,Verlet)
+PairStyle(sph/idealgas,PairSPHIdealGas)
#else
-#ifndef LMP_VERLET_H
-#define LMP_VERLET_H
+#ifndef LMP_PAIR_IDEALGAS_H
+#define LMP_PAIR_IDEALGAS_H
-#include "integrate.h"
+#include "pair.h"
namespace LAMMPS_NS {
-class Verlet : public Integrate {
+class PairSPHIdealGas : public Pair {
public:
- Verlet(class LAMMPS *, int, char **);
- virtual ~Verlet() {}
- void init();
- void setup();
- void setup_minimal(int);
- void run(int);
- void cleanup();
+ PairSPHIdealGas(class LAMMPS *);
+ virtual ~PairSPHIdealGas();
+ virtual void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ virtual double init_one(int, int);
+ virtual double single(int, int, int, int, double, double, double, double &);
protected:
- int triclinic; // 0 if domain is orthog, 1 if triclinic
- int torqueflag; // zero out arrays every step
- int erforceflag;
+ double **cut,**viscosity;
- void force_clear();
+ void allocate();
};
}
#endif
#endif
diff --git a/src/USER-SPH/pair_sph_lj.cpp b/src/USER-SPH/pair_sph_lj.cpp
new file mode 100644
index 000000000..fd92cddc8
--- /dev/null
+++ b/src/USER-SPH/pair_sph_lj.cpp
@@ -0,0 +1,368 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+ ------------------------------------------------------------------------- */
+
+#include "math.h"
+#include "stdlib.h"
+#include "pair_sph_lj.h"
+#include "atom.h"
+#include "force.h"
+#include "comm.h"
+#include "neigh_list.h"
+#include "memory.h"
+#include "error.h"
+#include "domain.h"
+
+using namespace LAMMPS_NS;
+
+#define MIN(a,b) ((a) < (b) ? (a) : (b))
+#define MAX(a,b) ((a) > (b) ? (a) : (b))
+
+/* ---------------------------------------------------------------------- */
+
+PairSPHLJ::PairSPHLJ(LAMMPS *lmp) :
+ Pair(lmp) {
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairSPHLJ::~PairSPHLJ() {
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+
+ memory->destroy(cut);
+ memory->destroy(viscosity);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairSPHLJ::compute(int eflag, int vflag) {
+ int i, j, ii, jj, inum, jnum, itype, jtype;
+ double xtmp, ytmp, ztmp, delx, dely, delz, fpair;
+
+ int *ilist, *jlist, *numneigh, **firstneigh;
+ double vxtmp, vytmp, vztmp, imass, jmass, fi, fj, fvisc, h, ih, ihsq, ihcub;
+ double rsq, wfd, delVdotDelR, mu, deltaE, ci, cj, lrc;
+
+ if (eflag || vflag)
+ ev_setup(eflag, vflag);
+ else
+ evflag = vflag_fdotr = 0;
+
+ double **v = atom->vest;
+ double **x = atom->x;
+ double **f = atom->f;
+ double *rho = atom->rho;
+ double *mass = atom->mass;
+ double *de = atom->de;
+ double *e = atom->e;
+ double *cv = atom->cv;
+ double *drho = atom->drho;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ int newton_pair = force->newton_pair;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // loop over neighbors of my atoms
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ vxtmp = v[i][0];
+ vytmp = v[i][1];
+ vztmp = v[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ imass = mass[itype];
+
+ // compute pressure of particle i with LJ EOS
+ LJEOS2(rho[i], e[i], cv[i], &fi, &ci);
+ fi /= (rho[i] * rho[i]);
+ //printf("fi = %f\n", fi);
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx * delx + dely * dely + delz * delz;
+ jtype = type[j];
+ jmass = mass[jtype];
+
+ if (rsq < cutsq[itype][jtype]) {
+ h = cut[itype][jtype];
+ ih = 1.0 / h;
+ ihsq = ih * ih;
+ ihcub = ihsq * ih;
+
+ wfd = h - sqrt(rsq);
+ if (domain->dimension == 3) {
+ // Lucy Kernel, 3d
+ // Note that wfd, the derivative of the weight function with respect to r,
+ // is lacking a factor of r.
+ // The missing factor of r is recovered by
+ // (1) using delV . delX instead of delV . (delX/r) and
+ // (2) using f[i][0] += delx * fpair instead of f[i][0] += (delx/r) * fpair
+ wfd = -25.066903536973515383e0 * wfd * wfd * ihsq * ihsq * ihsq * ih;
+ } else {
+ // Lucy Kernel, 2d
+ wfd = -19.098593171027440292e0 * wfd * wfd * ihsq * ihsq * ihsq;
+ }
+
+ // function call to LJ EOS
+ LJEOS2(rho[j], e[j], cv[j], &fj, &cj);
+ fj /= (rho[j] * rho[j]);
+
+ // apply long-range correction to model a LJ fluid with cutoff
+ // this implies that the modelled LJ fluid has cutoff == SPH cutoff
+ lrc = - 11.1701 * (ihcub * ihcub * ihcub - 1.5 * ihcub);
+ fi += lrc;
+ fj += lrc;
+
+ // dot product of velocity delta and distance vector
+ delVdotDelR = delx * (vxtmp - v[j][0]) + dely * (vytmp - v[j][1])
+ + delz * (vztmp - v[j][2]);
+
+ // artificial viscosity (Monaghan 1992)
+ if (delVdotDelR < 0.) {
+ mu = h * delVdotDelR / (rsq + 0.01 * h * h);
+ fvisc = -viscosity[itype][jtype] * (ci + cj) * mu / (rho[i] + rho[j]);
+ } else {
+ fvisc = 0.;
+ }
+
+ // total pair force & thermal energy increment
+ fpair = -imass * jmass * (fi + fj + fvisc) * wfd;
+ deltaE = -0.5 * fpair * delVdotDelR;
+
+ f[i][0] += delx * fpair;
+ f[i][1] += dely * fpair;
+ f[i][2] += delz * fpair;
+
+ // and change in density
+ drho[i] += jmass * delVdotDelR * wfd;
+
+ // change in thermal energy
+ de[i] += deltaE;
+
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx * fpair;
+ f[j][1] -= dely * fpair;
+ f[j][2] -= delz * fpair;
+ de[j] += deltaE;
+ drho[j] += imass * delVdotDelR * wfd;
+ }
+
+ if (evflag)
+ ev_tally(i, j, nlocal, newton_pair, 0.0, 0.0, fpair, delx, dely, delz);
+ }
+ }
+ }
+
+ if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ----------------------------------------------------------------------
+ allocate all arrays
+ ------------------------------------------------------------------------- */
+
+void PairSPHLJ::allocate() {
+ allocated = 1;
+ int n = atom->ntypes;
+
+ memory->create(setflag, n + 1, n + 1, "pair:setflag");
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ setflag[i][j] = 0;
+
+ memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
+
+ memory->create(cut, n + 1, n + 1, "pair:cut");
+ memory->create(viscosity, n + 1, n + 1, "pair:viscosity");
+}
+
+/* ----------------------------------------------------------------------
+ global settings
+ ------------------------------------------------------------------------- */
+
+void PairSPHLJ::settings(int narg, char **arg) {
+ if (narg != 0)
+ error->all(
+ "Illegal number of setting arguments for pair_style sph/lj");
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs for one or more type pairs
+ ------------------------------------------------------------------------- */
+
+void PairSPHLJ::coeff(int narg, char **arg) {
+ if (narg != 4)
+ error->all(
+ "Incorrect args for pair_style sph/lj coefficients");
+ if (!allocated)
+ allocate();
+
+ int ilo, ihi, jlo, jhi;
+ force->bounds(arg[0], atom->ntypes, ilo, ihi);
+ force->bounds(arg[1], atom->ntypes, jlo, jhi);
+
+ double viscosity_one = force->numeric(arg[2]);
+ double cut_one = force->numeric(arg[3]);
+
+ int count = 0;
+ for (int i = ilo; i <= ihi; i++) {
+ for (int j = MAX(jlo,i); j <= jhi; j++) {
+ viscosity[i][j] = viscosity_one;
+ printf("setting cut[%d][%d] = %f\n", i, j, cut_one);
+ cut[i][j] = cut_one;
+ setflag[i][j] = 1;
+ count++;
+ }
+ }
+
+ if (count == 0)
+ error->all("Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+ init for one type pair i,j and corresponding j,i
+ ------------------------------------------------------------------------- */
+
+double PairSPHLJ::init_one(int i, int j) {
+
+ if (setflag[i][j] == 0) {
+ error->all("All pair sph/lj coeffs are not set");
+ }
+
+ cut[j][i] = cut[i][j];
+ viscosity[j][i] = viscosity[i][j];
+
+ return cut[i][j];
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairSPHLJ::single(int i, int j, int itype, int jtype,
+ double rsq, double factor_coul, double factor_lj, double &fforce) {
+ fforce = 0.0;
+
+ return 0.0;
+}
+
+
+/*double PairSPHLJ::LJEOS2(double rho, double e, double cv) {
+
+
+ double T = e / cv;
+ if (T < 1.e-2) T = 1.e-2;
+ //printf("%f %f\n", T, rho);
+ double iT = 0.1e1 / T;
+ //double itpow1_4 = exp(0.25 * log(iT)); //pow(iT, 0.1e1 / 0.4e1);
+ double itpow1_4 = pow(iT, 0.1e1 / 0.4e1);
+ double x = rho * itpow1_4;
+ double xsq = x * x;
+ double xpow3 = xsq * x;
+ double xpow4 = xsq * xsq;
+ double xpow9 = xpow3 * xpow3 * xpow3;
+
+
+ return (0.1e1 + rho * (0.3629e1 + 0.7264e1 * x + 0.104925e2 * xsq + 0.11460e2
+ * xpow3 + 0.21760e1 * xpow9 - itpow1_4 * itpow1_4 * (0.5369e1 + 0.13160e2
+ * x + 0.18525e2 * xsq - 0.17076e2 * xpow3 + 0.9320e1 * xpow4) + iT
+ * (-0.3492e1 + 0.18698e2 * x - 0.35505e2 * xsq + 0.31816e2 * xpow3
+ - 0.11195e2 * xpow4)) * itpow1_4) * rho * T;
+}*/
+
+
+/* --------------------------------------------------------------------------------------------- */
+/* Lennard-Jones EOS,
+ Francis H. Ree
+ "Analytic representation of thermodynamic data for the Lennard‐Jones fluid",
+ Journal of Chemical Physics 73 pp. 5401-5403 (1980)
+*/
+
+void PairSPHLJ::LJEOS2(double rho, double e, double cv, double *p, double *c) {
+ double T = e/cv;
+ double beta = 1.0 / T;
+ double beta_sqrt = sqrt(beta);
+ double x = rho * sqrt(beta_sqrt);
+
+ double xsq = x * x;
+ double xpow3 = xsq * x;
+ double xpow4 = xsq * xsq;
+
+ /* differential of Helmholtz free energy w.r.t. x */
+ double diff_A_NkT = 3.629 + 7.264*x - beta*(3.492 - 18.698*x + 35.505*xsq - 31.816*xpow3 + 11.195*xpow4)
+ - beta_sqrt*(5.369 + 13.16*x + 18.525*xsq - 17.076*xpow3 + 9.32*xpow4)
+ + 10.4925*xsq + 11.46*xpow3 + 2.176*xpow4*xpow4*x;
+
+ /* differential of Helmholtz free energy w.r.t. x^2 */
+ double d2A_dx2 = 7.264 + 20.985*x \
+ + beta*(18.698 - 71.01*x + 95.448*xsq - 44.78*xpow3)\
+ - beta_sqrt*(13.16 + 37.05*x - 51.228*xsq + 37.28*xpow3)\
+ + 34.38*xsq + 19.584*xpow4*xpow4;
+
+ // p = rho k T * (1 + rho * d(A/(NkT))/drho)
+ // dx/drho = rho/x
+ *p = rho * T * (1.0 + diff_A_NkT * x); // pressure
+ double csq = T * (1.0 + 2.0 * diff_A_NkT * x + d2A_dx2 * x * x); // soundspeed squared
+ if (csq > 0.0) {
+ *c = sqrt(csq); // soundspeed
+ } else {
+ *c = 0.0;
+ }
+}
+
+/* ------------------------------------------------------------------------------ */
+
+/* Jirí Kolafa, Ivo Nezbeda
+ * "The Lennard-Jones fluid: an accurate analytic and theoretically-based equation of state",
+ * Fluid Phase Equilibria 100 pp. 1-34 (1994) */
+/*double PairSPHLJ::LJEOS2(double rho, double e, double cv) {
+ double T = e / cv;
+
+ double sT = sqrt(T);
+ double isT = 1.0 / sT;
+ double dC = -0.063920968 * log(T) + 0.011117524 / T - 0.076383859 / sT
+ + 1.080142248 + 0.000693129 * sT;
+ double eta = 3.141592654 / 6. * rho * (dC * dC * dC);
+ double zHS = (1 + eta * (1 + eta * (1 - eta / 1.5 * (1 + eta))))
+ / ((1. - eta) * (1. - eta) * (1. - eta));
+ double BC = (((((-0.58544978 * isT + 0.43102052) * isT + .87361369) * isT
+ - 4.13749995) * isT + 2.90616279) * isT - 7.02181962) / T + 0.02459877;
+ double gammaBH = 1.92907278;
+
+ double sum = ((2.01546797 * 2 + rho * ((-28.17881636) * 3 + rho
+ * (28.28313847 * 4 + rho * (-10.42402873) * 5))) + (-19.58371655 * 2
+ + rho * (+75.62340289 * 3 + rho * ((-120.70586598) * 4 + rho
+ * (+93.92740328 * 5 + rho * (-27.37737354) * 6)))) / sqrt(T)
+ + ((29.34470520 * 2 + rho * ((-112.35356937) * 3 + rho * (+170.64908980
+ * 4 + rho * ((-123.06669187) * 5 + rho * 34.42288969 * 6))))
+ + ((-13.37031968) * 2 + rho * (65.38059570 * 3 + rho
+ * ((-115.09233113) * 4 + rho * (88.91973082 * 5 + rho
+ * (-25.62099890) * 6)))) / T) / T) * rho * rho;
+ return ((zHS + BC / exp(gammaBH * rho * rho) * rho * (1 - 2 * gammaBH * rho
+ * rho)) * T + sum) * rho;
+ }
+*/
diff --git a/src/verlet.h b/src/USER-SPH/pair_sph_lj.h
similarity index 57%
copy from src/verlet.h
copy to src/USER-SPH/pair_sph_lj.h
index 8b8c90b7a..244ee044a 100644
--- a/src/verlet.h
+++ b/src/USER-SPH/pair_sph_lj.h
@@ -1,48 +1,48 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#ifdef INTEGRATE_CLASS
+#ifdef PAIR_CLASS
-IntegrateStyle(verlet,Verlet)
+PairStyle(sph/lj,PairSPHLJ)
#else
-#ifndef LMP_VERLET_H
-#define LMP_VERLET_H
+#ifndef LMP_PAIR_LJ_H
+#define LMP_PAIR_LJ_H
-#include "integrate.h"
+#include "pair.h"
namespace LAMMPS_NS {
-class Verlet : public Integrate {
+class PairSPHLJ : public Pair {
public:
- Verlet(class LAMMPS *, int, char **);
- virtual ~Verlet() {}
- void init();
- void setup();
- void setup_minimal(int);
- void run(int);
- void cleanup();
+ PairSPHLJ(class LAMMPS *);
+ virtual ~PairSPHLJ();
+ virtual void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ virtual double init_one(int, int);
+ virtual double single(int, int, int, int, double, double, double, double &);
+ //double LJEOS(int);
+ void LJEOS2(double, double, double, double *, double *);
protected:
- int triclinic; // 0 if domain is orthog, 1 if triclinic
- int torqueflag; // zero out arrays every step
- int erforceflag;
+ double **cut,**viscosity;
- void force_clear();
+ void allocate();
};
}
#endif
#endif
diff --git a/src/USER-SPH/pair_sph_rhosum.cpp b/src/USER-SPH/pair_sph_rhosum.cpp
new file mode 100644
index 000000000..b846b1bb4
--- /dev/null
+++ b/src/USER-SPH/pair_sph_rhosum.cpp
@@ -0,0 +1,316 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+ ------------------------------------------------------------------------- */
+
+#include "math.h"
+#include "stdlib.h"
+#include "pair_sph_rhosum.h"
+#include "atom.h"
+#include "force.h"
+#include "comm.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "memory.h"
+#include "error.h"
+#include "neighbor.h"
+#include "update.h"
+#include "domain.h"
+
+using namespace LAMMPS_NS;
+
+#define MIN(a,b) ((a) < (b) ? (a) : (b))
+#define MAX(a,b) ((a) > (b) ? (a) : (b))
+
+/* ---------------------------------------------------------------------- */
+
+PairSPHRhoSum::PairSPHRhoSum(LAMMPS *lmp) :
+ Pair(lmp) {
+
+ // set comm size needed by this Pair
+
+ comm_forward = 1;
+ first = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairSPHRhoSum::~PairSPHRhoSum() {
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+
+ memory->destroy(cut);
+ }
+}
+
+/* ----------------------------------------------------------------------
+ init specific to this pair style
+ ------------------------------------------------------------------------- */
+
+void PairSPHRhoSum::init_style() {
+ // need a full neighbor list
+ int irequest = neighbor->request(this);
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->full = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairSPHRhoSum::compute(int eflag, int vflag) {
+ int i, j, ii, jj, jnum, itype, jtype;
+ double xtmp, ytmp, ztmp, delx, dely, delz;
+ double r, rsq, imass, h, ih, ihsq;
+ int *jlist;
+ double wf;
+ // neighbor list variables
+ int inum, *ilist, *numneigh, **firstneigh;
+
+ if (eflag || vflag)
+ ev_setup(eflag, vflag);
+ else
+ evflag = vflag_fdotr = 0;
+
+ double **x = atom->x;
+ double *rho = atom->rho;
+ int *type = atom->type;
+ double *mass = atom->mass;
+
+ // check consistency of pair coefficients
+
+ if (first) {
+ for (i = 1; i <= atom->ntypes; i++) {
+ for (j = 1; i <= atom->ntypes; i++) {
+ if (cutsq[i][j] > 0.0) {
+ if (!setflag[i][i] || !setflag[j][j]) {
+ if (comm->me == 0) {
+ printf(
+ "SPH particle types %d and %d interact, but not all of their single particle properties are set.\n",
+ i, j);
+ }
+ }
+ }
+ }
+ }
+ first = 0;
+ }
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // recompute density
+ // we use a full neighborlist here
+
+ if (nstep != 0) {
+ if ((update->ntimestep % nstep) == 0) {
+
+ // initialize density with self-contribution,
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ itype = type[i];
+ imass = mass[itype];
+
+ h = cut[itype][itype];
+ if (domain->dimension == 3) {
+ /*
+ // Lucy kernel, 3d
+ wf = 2.0889086280811262819e0 / (h * h * h);
+ */
+
+ // quadric kernel, 3d
+ wf = 2.1541870227086614782 / (h * h * h);
+ } else {
+ /*
+ // Lucy kernel, 2d
+ wf = 1.5915494309189533576e0 / (h * h);
+ */
+
+ // quadric kernel, 2d
+ wf = 1.5915494309189533576e0 / (h * h);
+ }
+
+ rho[i] = imass * wf;
+ }
+
+ // add density at each atom via kernel function overlap
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ jtype = type[j];
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx * delx + dely * dely + delz * delz;
+
+ if (rsq < cutsq[itype][jtype]) {
+ h = cut[itype][jtype];
+ ih = 1.0 / h;
+ ihsq = ih * ih;
+
+ if (domain->dimension == 3) {
+ /*
+ // Lucy kernel, 3d
+ r = sqrt(rsq);
+ wf = (h - r) * ihsq;
+ wf = 2.0889086280811262819e0 * (h + 3. * r) * wf * wf * wf * ih;
+ */
+
+ // quadric kernel, 3d
+ wf = 1.0 - rsq * ihsq;
+ wf = wf * wf;
+ wf = wf * wf;
+ wf = 2.1541870227086614782e0 * wf * ihsq * ih;
+ } else {
+ // Lucy kernel, 2d
+ //r = sqrt(rsq);
+ //wf = (h - r) * ihsq;
+ //wf = 1.5915494309189533576e0 * (h + 3. * r) * wf * wf * wf;
+
+ // quadric kernel, 2d
+ wf = 1.0 - rsq * ihsq;
+ wf = wf * wf;
+ wf = wf * wf;
+ wf = 1.5915494309189533576e0 * wf * ihsq;
+ }
+
+ rho[i] += mass[jtype] * wf;
+ }
+
+ }
+ }
+ }
+ }
+
+ // communicate densities
+ comm->forward_comm_pair(this);
+}
+
+/* ----------------------------------------------------------------------
+ allocate all arrays
+ ------------------------------------------------------------------------- */
+
+void PairSPHRhoSum::allocate() {
+ allocated = 1;
+ int n = atom->ntypes;
+
+ memory->create(setflag, n + 1, n + 1, "pair:setflag");
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ setflag[i][j] = 0;
+
+ memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
+
+ memory->create(cut, n + 1, n + 1, "pair:cut");
+}
+
+/* ----------------------------------------------------------------------
+ global settings
+ ------------------------------------------------------------------------- */
+
+void PairSPHRhoSum::settings(int narg, char **arg) {
+ if (narg != 1)
+ error->all(
+ "Illegal number of setting arguments for pair_style sph/rhosum");
+ nstep = force->inumeric(arg[0]);
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs for one or more type pairs
+ ------------------------------------------------------------------------- */
+
+void PairSPHRhoSum::coeff(int narg, char **arg) {
+ if (narg != 3)
+ error->all("Incorrect number of args for sph/rhosum coefficients");
+ if (!allocated)
+ allocate();
+
+ int ilo, ihi, jlo, jhi;
+ force->bounds(arg[0], atom->ntypes, ilo, ihi);
+ force->bounds(arg[1], atom->ntypes, jlo, jhi);
+
+ double cut_one = force->numeric(arg[2]);
+
+ int count = 0;
+ for (int i = ilo; i <= ihi; i++) {
+ for (int j = MAX(jlo,i); j <= jhi; j++) {
+ //printf("setting cut[%d][%d] = %f\n", i, j, cut_one);
+ cut[i][j] = cut_one;
+ setflag[i][j] = 1;
+ count++;
+ }
+ }
+
+ if (count == 0)
+ error->all("Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+ init for one type pair i,j and corresponding j,i
+ ------------------------------------------------------------------------- */
+
+double PairSPHRhoSum::init_one(int i, int j) {
+ if (setflag[i][j] == 0) {
+ error->all("All pair sph/rhosum coeffs are not set");
+ }
+
+ cut[j][i] = cut[i][j];
+
+ return cut[i][j];
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairSPHRhoSum::single(int i, int j, int itype, int jtype, double rsq,
+ double factor_coul, double factor_lj, double &fforce) {
+ fforce = 0.0;
+
+ return 0.0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int PairSPHRhoSum::pack_comm(int n, int *list, double *buf, int pbc_flag,
+ int *pbc) {
+ int i, j, m;
+ double *rho = atom->rho;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = rho[j];
+ }
+ return 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairSPHRhoSum::unpack_comm(int n, int first, double *buf) {
+ int i, m, last;
+ double *rho = atom->rho;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++)
+ rho[i] = buf[m++];
+}
+
diff --git a/src/verlet.h b/src/USER-SPH/pair_sph_rhosum.h
similarity index 53%
copy from src/verlet.h
copy to src/USER-SPH/pair_sph_rhosum.h
index 8b8c90b7a..227cdef95 100644
--- a/src/verlet.h
+++ b/src/USER-SPH/pair_sph_rhosum.h
@@ -1,48 +1,50 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#ifdef INTEGRATE_CLASS
+#ifdef PAIR_CLASS
-IntegrateStyle(verlet,Verlet)
+PairStyle(sph/rhosum,PairSPHRhoSum)
#else
-#ifndef LMP_VERLET_H
-#define LMP_VERLET_H
+#ifndef LMP_PAIR_SPH_RHOSUM_H
+#define LMP_PAIR_SPH_RHOSUM_H
-#include "integrate.h"
+#include "pair.h"
namespace LAMMPS_NS {
-class Verlet : public Integrate {
+class PairSPHRhoSum : public Pair {
public:
- Verlet(class LAMMPS *, int, char **);
- virtual ~Verlet() {}
- void init();
- void setup();
- void setup_minimal(int);
- void run(int);
- void cleanup();
+ PairSPHRhoSum(class LAMMPS *);
+ virtual ~PairSPHRhoSum();
+ void init_style();
+ virtual void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ virtual double init_one(int, int);
+ virtual double single(int, int, int, int, double, double, double, double &);
+ int pack_comm(int, int *, double *, int, int *);
+ void unpack_comm(int, int, double *);
protected:
- int triclinic; // 0 if domain is orthog, 1 if triclinic
- int torqueflag; // zero out arrays every step
- int erforceflag;
+ double **cut;
+ int nstep, first;
- void force_clear();
+ void allocate();
};
}
#endif
#endif
diff --git a/src/USER-SPH/pair_sph_taitwater.cpp b/src/USER-SPH/pair_sph_taitwater.cpp
new file mode 100644
index 000000000..0226d8fed
--- /dev/null
+++ b/src/USER-SPH/pair_sph_taitwater.cpp
@@ -0,0 +1,303 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+ ------------------------------------------------------------------------- */
+
+#include "math.h"
+#include "stdlib.h"
+#include "pair_sph_taitwater.h"
+#include "atom.h"
+#include "force.h"
+#include "comm.h"
+#include "neigh_list.h"
+#include "memory.h"
+#include "error.h"
+#include "domain.h"
+
+using namespace LAMMPS_NS;
+
+#define MIN(a,b) ((a) < (b) ? (a) : (b))
+#define MAX(a,b) ((a) > (b) ? (a) : (b))
+
+/* ---------------------------------------------------------------------- */
+
+PairSPHTaitwater::PairSPHTaitwater(LAMMPS *lmp) :
+ Pair(lmp) {
+
+ first = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairSPHTaitwater::~PairSPHTaitwater() {
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+
+ memory->destroy(cut);
+ memory->destroy(rho0);
+ memory->destroy(soundspeed);
+ memory->destroy(B);
+ memory->destroy(viscosity);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairSPHTaitwater::compute(int eflag, int vflag) {
+ int i, j, ii, jj, inum, jnum, itype, jtype;
+ double xtmp, ytmp, ztmp, delx, dely, delz, fpair;
+
+ int *ilist, *jlist, *numneigh, **firstneigh;
+ double vxtmp, vytmp, vztmp, imass, jmass, fi, fj, fvisc, h, ih, ihsq;
+ double rsq, tmp, wfd, delVdotDelR, mu, deltaE;
+
+ if (eflag || vflag)
+ ev_setup(eflag, vflag);
+ else
+ evflag = vflag_fdotr = 0;
+
+ double **v = atom->vest;
+ double **x = atom->x;
+ double **f = atom->f;
+ double *rho = atom->rho;
+ double *mass = atom->mass;
+ double *de = atom->de;
+ double *drho = atom->drho;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ int newton_pair = force->newton_pair;
+
+ // check consistency of pair coefficients
+
+ if (first) {
+ for (i = 1; i <= atom->ntypes; i++) {
+ for (j = 1; i <= atom->ntypes; i++) {
+ if (cutsq[i][j] > 1.e-32) {
+ if (!setflag[i][i] || !setflag[j][j]) {
+ if (comm->me == 0) {
+ printf(
+ "SPH particle types %d and %d interact with cutoff=%g, but not all of their single particle properties are set.\n",
+ i, j, sqrt(cutsq[i][j]));
+ }
+ }
+ }
+ }
+ }
+ first = 0;
+ }
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // loop over neighbors of my atoms
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ vxtmp = v[i][0];
+ vytmp = v[i][1];
+ vztmp = v[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ imass = mass[itype];
+
+ // compute pressure of atom i with Tait EOS
+ tmp = rho[i] / rho0[itype];
+ fi = tmp * tmp * tmp;
+ fi = B[itype] * (fi * fi * tmp - 1.0) / (rho[i] * rho[i]);
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx * delx + dely * dely + delz * delz;
+ jtype = type[j];
+ jmass = mass[jtype];
+
+ if (rsq < cutsq[itype][jtype]) {
+
+ h = cut[itype][jtype];
+ ih = 1.0 / h;
+ ihsq = ih * ih;
+
+ wfd = h - sqrt(rsq);
+ if (domain->dimension == 3) {
+ // Lucy Kernel, 3d
+ // Note that wfd, the derivative of the weight function with respect to r,
+ // is lacking a factor of r.
+ // The missing factor of r is recovered by
+ // (1) using delV . delX instead of delV . (delX/r) and
+ // (2) using f[i][0] += delx * fpair instead of f[i][0] += (delx/r) * fpair
+ wfd = -25.066903536973515383e0 * wfd * wfd * ihsq * ihsq * ihsq * ih;
+ } else {
+ // Lucy Kernel, 2d
+ wfd = -19.098593171027440292e0 * wfd * wfd * ihsq * ihsq * ihsq;
+ }
+
+ // compute pressure of atom j with Tait EOS
+ tmp = rho[j] / rho0[jtype];
+ fj = tmp * tmp * tmp;
+ fj = B[jtype] * (fj * fj * tmp - 1.0) / (rho[j] * rho[j]);
+
+ // dot product of velocity delta and distance vector
+ delVdotDelR = delx * (vxtmp - v[j][0]) + dely * (vytmp - v[j][1])
+ + delz * (vztmp - v[j][2]);
+
+ // artificial viscosity (Monaghan 1992)
+ if (delVdotDelR < 0.) {
+ mu = h * delVdotDelR / (rsq + 0.01 * h * h);
+ fvisc = -viscosity[itype][jtype] * (soundspeed[itype]
+ + soundspeed[jtype]) * mu / (rho[i] + rho[j]);
+ } else {
+ fvisc = 0.;
+ }
+
+ // total pair force & thermal energy increment
+ fpair = -imass * jmass * (fi + fj + fvisc) * wfd;
+ deltaE = -0.5 * fpair * delVdotDelR;
+
+ f[i][0] += delx * fpair;
+ f[i][1] += dely * fpair;
+ f[i][2] += delz * fpair;
+
+ // and change in density
+ drho[i] += jmass * delVdotDelR * wfd;
+
+ // change in thermal energy
+ de[i] += deltaE;
+
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx * fpair;
+ f[j][1] -= dely * fpair;
+ f[j][2] -= delz * fpair;
+ de[j] += deltaE;
+ drho[j] += imass * delVdotDelR * wfd;
+ }
+
+ if (evflag)
+ ev_tally(i, j, nlocal, newton_pair, 0.0, 0.0, fpair, delx, dely, delz);
+ }
+ }
+ }
+
+ if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ----------------------------------------------------------------------
+ allocate all arrays
+ ------------------------------------------------------------------------- */
+
+void PairSPHTaitwater::allocate() {
+ allocated = 1;
+ int n = atom->ntypes;
+
+ memory->create(setflag, n + 1, n + 1, "pair:setflag");
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ setflag[i][j] = 0;
+
+ memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
+
+ memory->create(rho0, n + 1, "pair:rho0");
+ memory->create(soundspeed, n + 1, "pair:soundspeed");
+ memory->create(B, n + 1, "pair:B");
+ memory->create(cut, n + 1, n + 1, "pair:cut");
+ memory->create(viscosity, n + 1, n + 1, "pair:viscosity");
+}
+
+/* ----------------------------------------------------------------------
+ global settings
+ ------------------------------------------------------------------------- */
+
+void PairSPHTaitwater::settings(int narg, char **arg) {
+ if (narg != 0)
+ error->all(
+ "Illegal number of setting arguments for pair_style sph/taitwater");
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs for one or more type pairs
+ ------------------------------------------------------------------------- */
+
+void PairSPHTaitwater::coeff(int narg, char **arg) {
+ if (narg != 6)
+ error->all(
+ "Incorrect args for pair_style sph/taitwater coefficients");
+ if (!allocated)
+ allocate();
+
+ int ilo, ihi, jlo, jhi;
+ force->bounds(arg[0], atom->ntypes, ilo, ihi);
+ force->bounds(arg[1], atom->ntypes, jlo, jhi);
+
+ double rho0_one = force->numeric(arg[2]);
+ double soundspeed_one = force->numeric(arg[3]);
+ double viscosity_one = force->numeric(arg[4]);
+ double cut_one = force->numeric(arg[5]);
+ double B_one = soundspeed_one * soundspeed_one * rho0_one / 7.0;
+
+ int count = 0;
+ for (int i = ilo; i <= ihi; i++) {
+ rho0[i] = rho0_one;
+ soundspeed[i] = soundspeed_one;
+ B[i] = B_one;
+ for (int j = MAX(jlo,i); j <= jhi; j++) {
+ viscosity[i][j] = viscosity_one;
+ //printf("setting cut[%d][%d] = %f\n", i, j, cut_one);
+ cut[i][j] = cut_one;
+
+ setflag[i][j] = 1;
+
+ //cut[j][i] = cut[i][j];
+ //viscosity[j][i] = viscosity[i][j];
+ //setflag[j][i] = 1;
+ count++;
+ }
+ }
+
+ if (count == 0)
+ error->all("Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+ init for one type pair i,j and corresponding j,i
+ ------------------------------------------------------------------------- */
+
+double PairSPHTaitwater::init_one(int i, int j) {
+
+ if (setflag[i][j] == 0) {
+ error->all("Not all pair sph/taitwater coeffs are set");
+ }
+
+ cut[j][i] = cut[i][j];
+ viscosity[j][i] = viscosity[i][j];
+
+ return cut[i][j];
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairSPHTaitwater::single(int i, int j, int itype, int jtype,
+ double rsq, double factor_coul, double factor_lj, double &fforce) {
+ fforce = 0.0;
+
+ return 0.0;
+}
diff --git a/src/verlet.h b/src/USER-SPH/pair_sph_taitwater.h
similarity index 56%
copy from src/verlet.h
copy to src/USER-SPH/pair_sph_taitwater.h
index 8b8c90b7a..de081aa54 100644
--- a/src/verlet.h
+++ b/src/USER-SPH/pair_sph_taitwater.h
@@ -1,48 +1,48 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#ifdef INTEGRATE_CLASS
+#ifdef PAIR_CLASS
-IntegrateStyle(verlet,Verlet)
+PairStyle(sph/taitwater,PairSPHTaitwater)
#else
-#ifndef LMP_VERLET_H
-#define LMP_VERLET_H
+#ifndef LMP_PAIR_TAITWATER_H
+#define LMP_PAIR_TAITWATER_H
-#include "integrate.h"
+#include "pair.h"
namespace LAMMPS_NS {
-class Verlet : public Integrate {
+class PairSPHTaitwater : public Pair {
public:
- Verlet(class LAMMPS *, int, char **);
- virtual ~Verlet() {}
- void init();
- void setup();
- void setup_minimal(int);
- void run(int);
- void cleanup();
+ PairSPHTaitwater(class LAMMPS *);
+ virtual ~PairSPHTaitwater();
+ virtual void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ virtual double init_one(int, int);
+ virtual double single(int, int, int, int, double, double, double, double &);
protected:
- int triclinic; // 0 if domain is orthog, 1 if triclinic
- int torqueflag; // zero out arrays every step
- int erforceflag;
+ double *rho0, *soundspeed, *B;
+ double **cut,**viscosity;
+ int first;
- void force_clear();
+ void allocate();
};
}
#endif
#endif
diff --git a/src/USER-SPH/pair_sph_taitwater_morris.cpp b/src/USER-SPH/pair_sph_taitwater_morris.cpp
new file mode 100644
index 000000000..5e5eb1d09
--- /dev/null
+++ b/src/USER-SPH/pair_sph_taitwater_morris.cpp
@@ -0,0 +1,300 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+ ------------------------------------------------------------------------- */
+
+#include "math.h"
+#include "stdlib.h"
+#include "pair_sph_taitwater_morris.h"
+#include "atom.h"
+#include "force.h"
+#include "comm.h"
+#include "neigh_list.h"
+#include "memory.h"
+#include "error.h"
+#include "domain.h"
+
+using namespace LAMMPS_NS;
+
+#define MIN(a,b) ((a) < (b) ? (a) : (b))
+#define MAX(a,b) ((a) > (b) ? (a) : (b))
+
+/* ---------------------------------------------------------------------- */
+
+PairSPHTaitwaterMorris::PairSPHTaitwaterMorris(LAMMPS *lmp) :
+ Pair(lmp) {
+
+ first = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairSPHTaitwaterMorris::~PairSPHTaitwaterMorris() {
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+
+ memory->destroy(cut);
+ memory->destroy(rho0);
+ memory->destroy(soundspeed);
+ memory->destroy(B);
+ memory->destroy(viscosity);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairSPHTaitwaterMorris::compute(int eflag, int vflag) {
+ int i, j, ii, jj, inum, jnum, itype, jtype;
+ double xtmp, ytmp, ztmp, delx, dely, delz, fpair;
+
+ int *ilist, *jlist, *numneigh, **firstneigh;
+ double vxtmp, vytmp, vztmp, imass, jmass, fi, fj, fvisc, h, ih, ihsq, velx, vely, velz;
+ double rsq, tmp, wfd, delVdotDelR, deltaE;
+
+ if (eflag || vflag)
+ ev_setup(eflag, vflag);
+ else
+ evflag = vflag_fdotr = 0;
+
+ double **v = atom->vest;
+ double **x = atom->x;
+ double **f = atom->f;
+ double *rho = atom->rho;
+ double *mass = atom->mass;
+ double *de = atom->de;
+ double *drho = atom->drho;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ int newton_pair = force->newton_pair;
+
+ // check consistency of pair coefficients
+
+ if (first) {
+ for (i = 1; i <= atom->ntypes; i++) {
+ for (j = 1; i <= atom->ntypes; i++) {
+ if (cutsq[i][j] > 1.e-32) {
+ if (!setflag[i][i] || !setflag[j][j]) {
+ if (comm->me == 0) {
+ printf(
+ "SPH particle types %d and %d interact with cutoff=%g, but not all of their single particle properties are set.\n",
+ i, j, sqrt(cutsq[i][j]));
+ }
+ }
+ }
+ }
+ }
+ first = 0;
+ }
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // loop over neighbors of my atoms
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ vxtmp = v[i][0];
+ vytmp = v[i][1];
+ vztmp = v[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ imass = mass[itype];
+
+ // compute pressure of atom i with Tait EOS
+ tmp = rho[i] / rho0[itype];
+ fi = tmp * tmp * tmp;
+ fi = B[itype] * (fi * fi * tmp - 1.0) / (rho[i] * rho[i]);
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx * delx + dely * dely + delz * delz;
+ jtype = type[j];
+ jmass = mass[jtype];
+
+ if (rsq < cutsq[itype][jtype]) {
+ h = cut[itype][jtype];
+ ih = 1.0 / h;
+ ihsq = ih * ih;
+
+ wfd = h - sqrt(rsq);
+ if (domain->dimension == 3) {
+ // Lucy Kernel, 3d
+ // Note that wfd, the derivative of the weight function with respect to r,
+ // is lacking a factor of r.
+ // The missing factor of r is recovered by
+ // (1) using delV . delX instead of delV . (delX/r) and
+ // (2) using f[i][0] += delx * fpair instead of f[i][0] += (delx/r) * fpair
+ wfd = -25.066903536973515383e0 * wfd * wfd * ihsq * ihsq * ihsq * ih;
+ } else {
+ // Lucy Kernel, 2d
+ wfd = -19.098593171027440292e0 * wfd * wfd * ihsq * ihsq * ihsq;
+ }
+
+ // compute pressure of atom j with Tait EOS
+ tmp = rho[j] / rho0[jtype];
+ fj = tmp * tmp * tmp;
+ fj = B[jtype] * (fj * fj * tmp - 1.0) / (rho[j] * rho[j]);
+
+ velx=vxtmp - v[j][0];
+ vely=vytmp - v[j][1];
+ velz=vztmp - v[j][2];
+
+ // dot product of velocity delta and distance vector
+ delVdotDelR = delx * velx + dely * vely + delz * velz;
+
+ // Morris Viscosity (Morris, 1996)
+
+ fvisc = 2 * viscosity[itype][jtype] / (rho[i] * rho[j]);
+
+ fvisc *= imass * jmass * wfd;
+
+ // total pair force & thermal energy increment
+ fpair = -imass * jmass * (fi + fj) * wfd;
+ deltaE = -0.5 *(fpair * delVdotDelR + fvisc * (velx*velx + vely*vely + velz*velz));
+
+ // printf("testvar= %f, %f \n", delx, dely);
+
+ f[i][0] += delx * fpair + velx * fvisc;
+ f[i][1] += dely * fpair + vely * fvisc;
+ f[i][2] += delz * fpair + velz * fvisc;
+
+ // and change in density
+ drho[i] += jmass * delVdotDelR * wfd;
+
+ // change in thermal energy
+ de[i] += deltaE;
+
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx * fpair + velx * fvisc;
+ f[j][1] -= dely * fpair + vely * fvisc;
+ f[j][2] -= delz * fpair + velz * fvisc;
+ de[j] += deltaE;
+ drho[j] += imass * delVdotDelR * wfd;
+ }
+
+ if (evflag)
+ ev_tally(i, j, nlocal, newton_pair, 0.0, 0.0, fpair, delx, dely, delz);
+ }
+ }
+ }
+
+ if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ----------------------------------------------------------------------
+ allocate all arrays
+ ------------------------------------------------------------------------- */
+
+void PairSPHTaitwaterMorris::allocate() {
+ allocated = 1;
+ int n = atom->ntypes;
+
+ memory->create(setflag, n + 1, n + 1, "pair:setflag");
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ setflag[i][j] = 0;
+
+ memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
+
+ memory->create(rho0, n + 1, "pair:rho0");
+ memory->create(soundspeed, n + 1, "pair:soundspeed");
+ memory->create(B, n + 1, "pair:B");
+ memory->create(cut, n + 1, n + 1, "pair:cut");
+ memory->create(viscosity, n + 1, n + 1, "pair:viscosity");
+}
+
+/* ----------------------------------------------------------------------
+ global settings
+ ------------------------------------------------------------------------- */
+
+void PairSPHTaitwaterMorris::settings(int narg, char **arg) {
+ if (narg != 0)
+ error->all(
+ "Illegal number of setting arguments for pair_style sph/taitwater/morris");
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs for one or more type pairs
+ ------------------------------------------------------------------------- */
+
+void PairSPHTaitwaterMorris::coeff(int narg, char **arg) {
+ if (narg != 6)
+ error->all(
+ "Incorrect args for pair_style sph/taitwater/morris coefficients");
+ if (!allocated)
+ allocate();
+
+ int ilo, ihi, jlo, jhi;
+ force->bounds(arg[0], atom->ntypes, ilo, ihi);
+ force->bounds(arg[1], atom->ntypes, jlo, jhi);
+
+ double rho0_one = force->numeric(arg[2]);
+ double soundspeed_one = force->numeric(arg[3]);
+ double viscosity_one = force->numeric(arg[4]);
+ double cut_one = force->numeric(arg[5]);
+ double B_one = soundspeed_one * soundspeed_one * rho0_one / 7.0;
+
+ int count = 0;
+ for (int i = ilo; i <= ihi; i++) {
+ rho0[i] = rho0_one;
+ soundspeed[i] = soundspeed_one;
+ B[i] = B_one;
+ for (int j = MAX(jlo,i); j <= jhi; j++) {
+ viscosity[i][j] = viscosity_one;
+ //printf("setting cut[%d][%d] = %f\n", i, j, cut_one);
+ cut[i][j] = cut_one;
+
+ setflag[i][j] = 1;
+ count++;
+ }
+ }
+
+ if (count == 0)
+ error->all("Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+ init for one type pair i,j and corresponding j,i
+ ------------------------------------------------------------------------- */
+
+double PairSPHTaitwaterMorris::init_one(int i, int j) {
+
+ if (setflag[i][j] == 0) {
+ error->all("Not all pair sph/taitwater/morris coeffs are not set");
+ }
+
+ cut[j][i] = cut[i][j];
+ viscosity[j][i] = viscosity[i][j];
+
+ return cut[i][j];
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairSPHTaitwaterMorris::single(int i, int j, int itype, int jtype,
+ double rsq, double factor_coul, double factor_lj, double &fforce) {
+ fforce = 0.0;
+
+ return 0.0;
+}
diff --git a/src/verlet.h b/src/USER-SPH/pair_sph_taitwater_morris.h
similarity index 54%
copy from src/verlet.h
copy to src/USER-SPH/pair_sph_taitwater_morris.h
index 8b8c90b7a..5390d73f0 100644
--- a/src/verlet.h
+++ b/src/USER-SPH/pair_sph_taitwater_morris.h
@@ -1,48 +1,48 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#ifdef INTEGRATE_CLASS
+#ifdef PAIR_CLASS
-IntegrateStyle(verlet,Verlet)
+PairStyle(sph/taitwater/morris,PairSPHTaitwaterMorris)
#else
-#ifndef LMP_VERLET_H
-#define LMP_VERLET_H
+#ifndef LMP_PAIR_TAITWATER_MORRIS_H
+#define LMP_PAIR_TAITWATER_MORRIS_H
-#include "integrate.h"
+#include "pair.h"
namespace LAMMPS_NS {
-class Verlet : public Integrate {
+class PairSPHTaitwaterMorris : public Pair {
public:
- Verlet(class LAMMPS *, int, char **);
- virtual ~Verlet() {}
- void init();
- void setup();
- void setup_minimal(int);
- void run(int);
- void cleanup();
+ PairSPHTaitwaterMorris(class LAMMPS *);
+ virtual ~PairSPHTaitwaterMorris();
+ virtual void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ virtual double init_one(int, int);
+ virtual double single(int, int, int, int, double, double, double, double &);
protected:
- int triclinic; // 0 if domain is orthog, 1 if triclinic
- int torqueflag; // zero out arrays every step
- int erforceflag;
+ double *rho0, *soundspeed, *B;
+ double **cut,**viscosity;
+ int first;
- void force_clear();
+ void allocate();
};
}
#endif
#endif
diff --git a/src/atom.cpp b/src/atom.cpp
index b9c9c3e70..a0f65365e 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -1,1663 +1,1668 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "limits.h"
#include "atom.h"
#include "style_atom.h"
#include "atom_vec.h"
#include "atom_vec_ellipsoid.h"
#include "comm.h"
#include "neighbor.h"
#include "force.h"
#include "modify.h"
#include "fix.h"
#include "output.h"
#include "thermo.h"
#include "update.h"
#include "domain.h"
#include "group.h"
#include "accelerator_cuda.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 1
#define DELTA_MEMSTR 1024
#define EPSILON 1.0e-6
#define CUDA_CHUNK 3000
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
{
natoms = 0;
nlocal = nghost = nmax = 0;
ntypes = 0;
nbondtypes = nangletypes = ndihedraltypes = nimpropertypes = 0;
nbonds = nangles = ndihedrals = nimpropers = 0;
bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
extra_bond_per_atom = 0;
firstgroupname = NULL;
sortfreq = 1000;
nextsort = 0;
userbinsize = 0.0;
maxbin = maxnext = 0;
binhead = NULL;
next = permute = NULL;
// initialize atom arrays
// customize by adding new array
tag = type = mask = image = NULL;
x = v = f = NULL;
molecule = NULL;
q = NULL;
mu = NULL;
omega = angmom = torque = NULL;
radius = rmass = NULL;
vfrac = s0 = NULL;
x0 = NULL;
ellipsoid = NULL;
spin = NULL;
eradius = ervel = erforce = NULL;
cs = csforce = vforce = ervelforce = NULL;
etag = NULL;
+ rho = drho = NULL;
+ e = de = NULL;
+ cv = NULL;
+ vest = NULL;
maxspecial = 1;
nspecial = NULL;
special = NULL;
num_bond = NULL;
bond_type = bond_atom = NULL;
num_angle = NULL;
angle_type = angle_atom1 = angle_atom2 = angle_atom3 = NULL;
num_dihedral = NULL;
dihedral_type = dihedral_atom1 = dihedral_atom2 = NULL;
dihedral_atom3 = dihedral_atom4 = NULL;
num_improper = NULL;
improper_type = improper_atom1 = improper_atom2 = NULL;
improper_atom3 = improper_atom4 = NULL;
// initialize atom style and array existence flags
// customize by adding new flag
sphere_flag = ellipsoid_flag = peri_flag = electron_flag = 0;
- wavepacket_flag = 0;
+ wavepacket_flag = sph_flag = 0;
molecule_flag = q_flag = mu_flag = 0;
rmass_flag = radius_flag = omega_flag = torque_flag = angmom_flag = 0;
vfrac_flag = spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;
cs_flag = csforce_flag = vforce_flag = ervelforce_flag= etag_flag = 0;
+ rho_flag = e_flag = cv_flag = vest_flag = 0;
// ntype-length arrays
mass = NULL;
mass_setflag = NULL;
// callback lists & extra restart info
nextra_grow = nextra_restart = 0;
extra_grow = extra_restart = NULL;
nextra_grow_max = nextra_restart_max = 0;
nextra_store = 0;
extra = NULL;
// default mapping values and hash table primes
tag_enable = 1;
map_style = 0;
map_tag_max = 0;
map_nhash = 0;
nprimes = 38;
primes = new int[nprimes];
int plist[] = {5041,10007,20011,30011,40009,50021,60013,70001,80021,
90001,100003,110017,120011,130003,140009,150001,160001,
170003,180001,190027,200003,210011,220009,230003,240007,
250007,260003,270001,280001,290011,300007,310019,320009,
330017,340007,350003,362881,3628801};
for (int i = 0; i < nprimes; i++) primes[i] = plist[i];
// default atom style = atomic
atom_style = NULL;
avec = NULL;
create_avec("atomic",0,NULL);
}
/* ---------------------------------------------------------------------- */
Atom::~Atom()
{
delete [] atom_style;
delete avec;
delete [] firstgroupname;
memory->destroy(binhead);
memory->destroy(next);
memory->destroy(permute);
// delete atom arrays
// customize by adding new array
memory->destroy(tag);
memory->destroy(type);
memory->destroy(mask);
memory->destroy(image);
memory->destroy(x);
memory->destroy(v);
memory->destroy(f);
memory->destroy(q);
memory->destroy(mu);
memory->destroy(omega);
memory->destroy(angmom);
memory->destroy(torque);
memory->destroy(radius);
memory->destroy(rmass);
memory->destroy(vfrac);
memory->destroy(s0);
memory->destroy(x0);
memory->destroy(ellipsoid);
memory->destroy(spin);
memory->destroy(eradius);
memory->destroy(ervel);
memory->destroy(erforce);
memory->destroy(molecule);
memory->destroy(nspecial);
memory->destroy(special);
memory->destroy(num_bond);
memory->destroy(bond_type);
memory->destroy(bond_atom);
memory->destroy(num_angle);
memory->destroy(angle_type);
memory->destroy(angle_atom1);
memory->destroy(angle_atom2);
memory->destroy(angle_atom3);
memory->destroy(num_dihedral);
memory->destroy(dihedral_type);
memory->destroy(dihedral_atom1);
memory->destroy(dihedral_atom2);
memory->destroy(dihedral_atom3);
memory->destroy(dihedral_atom4);
memory->destroy(num_improper);
memory->destroy(improper_type);
memory->destroy(improper_atom1);
memory->destroy(improper_atom2);
memory->destroy(improper_atom3);
memory->destroy(improper_atom4);
// delete per-type arrays
delete [] mass;
delete [] mass_setflag;
// delete extra arrays
memory->destroy(extra_grow);
memory->destroy(extra_restart);
memory->destroy(extra);
// delete mapping data structures
map_delete();
delete [] primes;
}
/* ----------------------------------------------------------------------
copy modify settings from old Atom class to current Atom class
------------------------------------------------------------------------- */
void Atom::settings(Atom *old)
{
map_style = old->map_style;
}
/* ----------------------------------------------------------------------
create an AtomVec style
called from input script, restart file, replicate
------------------------------------------------------------------------- */
void Atom::create_avec(const char *style, int narg, char **arg, char *suffix)
{
delete [] atom_style;
if (avec) delete avec;
// unset atom style and array existence flags
// may have been set by old avec
// customize by adding new flag
sphere_flag = ellipsoid_flag = peri_flag = electron_flag = 0;
molecule_flag = q_flag = mu_flag = 0;
rmass_flag = radius_flag = omega_flag = torque_flag = angmom_flag = 0;
vfrac_flag = spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;
int sflag;
avec = new_avec(style,narg,arg,suffix,sflag);
if (sflag) {
char estyle[256];
sprintf(estyle,"%s/%s",style,suffix);
int n = strlen(estyle) + 1;
atom_style = new char[n];
strcpy(atom_style,estyle);
} else {
int n = strlen(style) + 1;
atom_style = new char[n];
strcpy(atom_style,style);
}
// if molecular system, default is to have array map
molecular = avec->molecular;
if (map_style == 0 && molecular) map_style = 1;
}
/* ----------------------------------------------------------------------
generate an AtomVec class, first with suffix appended
------------------------------------------------------------------------- */
AtomVec *Atom::new_avec(const char *style, int narg, char **arg,
char *suffix, int &sflag)
{
if (suffix && lmp->suffix_enable) {
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",style,suffix);
if (0) return NULL;
#define ATOM_CLASS
#define AtomStyle(key,Class) \
else if (strcmp(estyle,#key) == 0) return new Class(lmp,narg,arg);
#include "style_atom.h"
#undef AtomStyle
#undef ATOM_CLASS
}
sflag = 0;
if (0) return NULL;
#define ATOM_CLASS
#define AtomStyle(key,Class) \
else if (strcmp(style,#key) == 0) return new Class(lmp,narg,arg);
#include "style_atom.h"
#undef ATOM_CLASS
else error->all("Invalid atom style");
return NULL;
}
/* ---------------------------------------------------------------------- */
void Atom::init()
{
// delete extra array since it doesn't persist past first run
if (nextra_store) {
memory->destroy(extra);
extra = NULL;
nextra_store = 0;
}
// check arrays that are atom type in length
check_mass();
// setup of firstgroup
if (firstgroupname) {
firstgroup = group->find(firstgroupname);
if (firstgroup < 0)
error->all("Could not find atom_modify first group ID");
} else firstgroup = -1;
// init AtomVec
avec->init();
}
/* ---------------------------------------------------------------------- */
void Atom::setup()
{
// setup bins for sorting
// cannot do this in init() because uses neighbor cutoff
if (sortfreq > 0) setup_sort_bins();
}
/* ----------------------------------------------------------------------
return ptr to AtomVec class if matches style or to matching hybrid sub-class
return NULL if no match
------------------------------------------------------------------------- */
AtomVec *Atom::style_match(const char *style)
{
if (strcmp(atom_style,style) == 0) return avec;
else if (strcmp(atom_style,"hybrid") == 0) {
AtomVecHybrid *avec_hybrid = (AtomVecHybrid *) avec;
for (int i = 0; i < avec_hybrid->nstyles; i++)
if (strcmp(avec_hybrid->keywords[i],style) == 0)
return avec_hybrid->styles[i];
}
return NULL;
}
/* ----------------------------------------------------------------------
modify parameters of the atom style
some options can only be invoked before simulation box is defined
first and sort options cannot be used together
------------------------------------------------------------------------- */
void Atom::modify_params(int narg, char **arg)
{
if (narg == 0) error->all("Illegal atom_modify command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"map") == 0) {
if (iarg+2 > narg) error->all("Illegal atom_modify command");
if (strcmp(arg[iarg+1],"array") == 0) map_style = 1;
else if (strcmp(arg[iarg+1],"hash") == 0) map_style = 2;
else error->all("Illegal atom_modify command");
if (domain->box_exist)
error->all("Atom_modify map command after simulation box is defined");
iarg += 2;
} else if (strcmp(arg[iarg],"first") == 0) {
if (iarg+2 > narg) error->all("Illegal atom_modify command");
if (strcmp(arg[iarg+1],"all") == 0) {
delete [] firstgroupname;
firstgroupname = NULL;
} else {
int n = strlen(arg[iarg+1]) + 1;
firstgroupname = new char[n];
strcpy(firstgroupname,arg[iarg+1]);
sortfreq = 0;
}
iarg += 2;
} else if (strcmp(arg[iarg],"sort") == 0) {
if (iarg+3 > narg) error->all("Illegal atom_modify command");
sortfreq = atoi(arg[iarg+1]);
userbinsize = atof(arg[iarg+2]);
if (sortfreq < 0 || userbinsize < 0.0)
error->all("Illegal atom_modify command");
if (sortfreq >= 0 && firstgroupname)
error->all("Atom_modify sort and first options "
"cannot be used together");
iarg += 3;
} else error->all("Illegal atom_modify command");
}
}
/* ----------------------------------------------------------------------
allocate and initialize array or hash table for global -> local map
set map_tag_max = largest atom ID (may be larger than natoms)
for array option:
array length = 1 to largest tag of any atom
set entire array to -1 as initial values
for hash option:
map_nhash = length of hash table
map_nbucket = # of hash buckets, prime larger than map_nhash
so buckets will only be filled with 0 or 1 atoms on average
------------------------------------------------------------------------- */
void Atom::map_init()
{
map_delete();
if (tag_enable == 0)
error->all("Cannot create an atom map unless atoms have IDs");
int max = 0;
for (int i = 0; i < nlocal; i++) max = MAX(max,tag[i]);
MPI_Allreduce(&max,&map_tag_max,1,MPI_INT,MPI_MAX,world);
if (map_style == 1) {
memory->create(map_array,map_tag_max+1,"atom:map_array");
for (int i = 0; i <= map_tag_max; i++) map_array[i] = -1;
} else {
// map_nhash = max of atoms/proc or total atoms, times 2, at least 1000
int nper = static_cast<int> (natoms/comm->nprocs);
map_nhash = MAX(nper,nmax);
if (map_nhash > natoms) map_nhash = static_cast<int> (natoms);
if (comm->nprocs > 1) map_nhash *= 2;
map_nhash = MAX(map_nhash,1000);
// map_nbucket = prime just larger than map_nhash
int n = map_nhash/10000;
n = MIN(n,nprimes-1);
map_nbucket = primes[n];
if (map_nbucket < map_nhash && n < nprimes-1) map_nbucket = primes[n+1];
// set all buckets to empty
// set hash to map_nhash in length
// put all hash entries in free list and point them to each other
map_bucket = new int[map_nbucket];
for (int i = 0; i < map_nbucket; i++) map_bucket[i] = -1;
map_hash = new HashElem[map_nhash];
map_nused = 0;
map_free = 0;
for (int i = 0; i < map_nhash; i++) map_hash[i].next = i+1;
map_hash[map_nhash-1].next = -1;
}
}
/* ----------------------------------------------------------------------
clear global -> local map for all of my own and ghost atoms
for hash table option:
global ID may not be in table if image atom was already cleared
------------------------------------------------------------------------- */
void Atom::map_clear()
{
if (map_style == 1) {
int nall = nlocal + nghost;
for (int i = 0; i < nall; i++) map_array[tag[i]] = -1;
} else {
int previous,global,ibucket,index;
int nall = nlocal + nghost;
for (int i = 0; i < nall; i++) {
// search for key
// if don't find it, done
previous = -1;
global = tag[i];
ibucket = global % map_nbucket;
index = map_bucket[ibucket];
while (index > -1) {
if (map_hash[index].global == global) break;
previous = index;
index = map_hash[index].next;
}
if (index == -1) continue;
// delete the hash entry and add it to free list
// special logic if entry is 1st in the bucket
if (previous == -1) map_bucket[ibucket] = map_hash[index].next;
else map_hash[previous].next = map_hash[index].next;
map_hash[index].next = map_free;
map_free = index;
map_nused--;
}
}
}
/* ----------------------------------------------------------------------
set global -> local map for all of my own and ghost atoms
loop in reverse order so that nearby images take precedence over far ones
and owned atoms take precedence over images
this enables valid lookups of bond topology atoms
for hash table option:
if hash table too small, re-init
global ID may already be in table if image atom was set
------------------------------------------------------------------------- */
void Atom::map_set()
{
if (map_style == 1) {
int nall = nlocal + nghost;
for (int i = nall-1; i >= 0 ; i--) map_array[tag[i]] = i;
} else {
int previous,global,ibucket,index;
int nall = nlocal + nghost;
if (nall > map_nhash) map_init();
for (int i = nall-1; i >= 0 ; i--) {
// search for key
// if found it, just overwrite local value with index
previous = -1;
global = tag[i];
ibucket = global % map_nbucket;
index = map_bucket[ibucket];
while (index > -1) {
if (map_hash[index].global == global) break;
previous = index;
index = map_hash[index].next;
}
if (index > -1) {
map_hash[index].local = i;
continue;
}
// take one entry from free list
// add the new global/local pair as entry at end of bucket list
// special logic if this entry is 1st in bucket
index = map_free;
map_free = map_hash[map_free].next;
if (previous == -1) map_bucket[ibucket] = index;
else map_hash[previous].next = index;
map_hash[index].global = global;
map_hash[index].local = i;
map_hash[index].next = -1;
map_nused++;
}
}
}
/* ----------------------------------------------------------------------
set global to local map for one atom
for hash table option:
global ID may already be in table if atom was already set
------------------------------------------------------------------------- */
void Atom::map_one(int global, int local)
{
if (map_style == 1) map_array[global] = local;
else {
// search for key
// if found it, just overwrite local value with index
int previous = -1;
int ibucket = global % map_nbucket;
int index = map_bucket[ibucket];
while (index > -1) {
if (map_hash[index].global == global) break;
previous = index;
index = map_hash[index].next;
}
if (index > -1) {
map_hash[index].local = local;
return;
}
// take one entry from free list
// add the new global/local pair as entry at end of bucket list
// special logic if this entry is 1st in bucket
index = map_free;
map_free = map_hash[map_free].next;
if (previous == -1) map_bucket[ibucket] = index;
else map_hash[previous].next = index;
map_hash[index].global = global;
map_hash[index].local = local;
map_hash[index].next = -1;
map_nused++;
}
}
/* ----------------------------------------------------------------------
free the array or hash table for global to local mapping
------------------------------------------------------------------------- */
void Atom::map_delete()
{
if (map_style == 1) {
if (map_tag_max) memory->destroy(map_array);
} else {
if (map_nhash) {
delete [] map_bucket;
delete [] map_hash;
}
map_nhash = 0;
}
map_tag_max = 0;
}
/* ----------------------------------------------------------------------
lookup global ID in hash table, return local index
------------------------------------------------------------------------- */
int Atom::map_find_hash(int global)
{
int local = -1;
int index = map_bucket[global % map_nbucket];
while (index > -1) {
if (map_hash[index].global == global) {
local = map_hash[index].local;
break;
}
index = map_hash[index].next;
}
return local;
}
/* ----------------------------------------------------------------------
add unique tags to any atoms with tag = 0
new tags are grouped by proc and start after max current tag
called after creating new atoms
------------------------------------------------------------------------- */
void Atom::tag_extend()
{
// maxtag_all = max tag for all atoms
int maxtag = 0;
for (int i = 0; i < nlocal; i++) maxtag = MAX(maxtag,tag[i]);
int maxtag_all;
MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_INT,MPI_MAX,world);
// notag = # of atoms I own with no tag (tag = 0)
// notag_sum = # of total atoms on procs <= me with no tag
int notag = 0;
for (int i = 0; i < nlocal; i++) if (tag[i] == 0) notag++;
int notag_sum;
MPI_Scan(&notag,&notag_sum,1,MPI_INT,MPI_SUM,world);
// itag = 1st new tag that my untagged atoms should use
int itag = maxtag_all + notag_sum - notag + 1;
for (int i = 0; i < nlocal; i++) if (tag[i] == 0) tag[i] = itag++;
}
/* ----------------------------------------------------------------------
check that atom IDs span range from 1 to Natoms
return 0 if mintag != 1 or maxtag != Natoms
return 1 if OK
doesn't actually check if all tag values are used
------------------------------------------------------------------------- */
int Atom::tag_consecutive()
{
int idmin = MAXTAGINT;
int idmax = 0;
for (int i = 0; i < nlocal; i++) {
idmin = MIN(idmin,tag[i]);
idmax = MAX(idmax,tag[i]);
}
int idminall,idmaxall;
MPI_Allreduce(&idmin,&idminall,1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&idmax,&idmaxall,1,MPI_INT,MPI_MAX,world);
if (idminall != 1 || idmaxall != static_cast<int> (natoms)) return 0;
return 1;
}
/* ----------------------------------------------------------------------
count and return words in a single line
make copy of line before using strtok so as not to change line
trim anything from '#' onward
------------------------------------------------------------------------- */
int Atom::count_words(const char *line)
{
int n = strlen(line) + 1;
char *copy;
memory->create(copy,n,"atom:copy");
strcpy(copy,line);
char *ptr;
if (ptr = strchr(copy,'#')) *ptr = '\0';
if (strtok(copy," \t\n\r\f") == NULL) {
memory->destroy(copy);
return 0;
}
n = 1;
while (strtok(NULL," \t\n\r\f")) n++;
memory->destroy(copy);
return n;
}
/* ----------------------------------------------------------------------
unpack n lines from Atom section of data file
call style-specific routine to parse line
------------------------------------------------------------------------- */
void Atom::data_atoms(int n, char *buf)
{
int m,imagedata,xptr,iptr;
double xdata[3],lamda[3],sublo[3],subhi[3];
double *coord;
char *next;
next = strchr(buf,'\n');
*next = '\0';
int nwords = count_words(buf);
*next = '\n';
if (nwords != avec->size_data_atom && nwords != avec->size_data_atom + 3)
error->all("Incorrect atom format in data file");
char **values = new char*[nwords];
// set bounds for my proc
// if periodic and I am lo/hi proc, adjust bounds by EPSILON
// insures all data atoms will be owned even with round-off
int triclinic = domain->triclinic;
if (triclinic == 0) {
sublo[0] = domain->sublo[0]; subhi[0] = domain->subhi[0];
sublo[1] = domain->sublo[1]; subhi[1] = domain->subhi[1];
sublo[2] = domain->sublo[2]; subhi[2] = domain->subhi[2];
} else {
sublo[0] = domain->sublo_lamda[0]; subhi[0] = domain->subhi_lamda[0];
sublo[1] = domain->sublo_lamda[1]; subhi[1] = domain->subhi_lamda[1];
sublo[2] = domain->sublo_lamda[2]; subhi[2] = domain->subhi_lamda[2];
}
if (domain->xperiodic) {
if (comm->myloc[0] == 0) sublo[0] -= EPSILON;
if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] += EPSILON;
}
if (domain->yperiodic) {
if (comm->myloc[1] == 0) sublo[1] -= EPSILON;
if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] += EPSILON;
}
if (domain->zperiodic) {
if (comm->myloc[2] == 0) sublo[2] -= EPSILON;
if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] += EPSILON;
}
// xptr = which word in line starts xyz coords
// iptr = which word in line starts ix,iy,iz image flags
xptr = avec->xcol_data - 1;
int imageflag = 0;
if (nwords > avec->size_data_atom) imageflag = 1;
if (imageflag) iptr = nwords - 3;
// loop over lines of atom data
// tokenize the line into values
// extract xyz coords and image flags
// remap atom into simulation box
// if atom is in my sub-domain, unpack its values
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
values[0] = strtok(buf," \t\n\r\f");
if (values[0] == NULL) error->all("Incorrect atom format in data file");
for (m = 1; m < nwords; m++) {
values[m] = strtok(NULL," \t\n\r\f");
if (values[m] == NULL) error->all("Incorrect atom format in data file");
}
if (imageflag)
imagedata = ((atoi(values[iptr+2]) + 512 & 1023) << 20) |
((atoi(values[iptr+1]) + 512 & 1023) << 10) |
(atoi(values[iptr]) + 512 & 1023);
else imagedata = (512 << 20) | (512 << 10) | 512;
xdata[0] = atof(values[xptr]);
xdata[1] = atof(values[xptr+1]);
xdata[2] = atof(values[xptr+2]);
domain->remap(xdata,imagedata);
if (triclinic) {
domain->x2lamda(xdata,lamda);
coord = lamda;
} else coord = xdata;
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2])
avec->data_atom(xdata,imagedata,values);
buf = next + 1;
}
delete [] values;
}
/* ----------------------------------------------------------------------
unpack n lines from Velocity section of data file
check that atom IDs are > 0 and <= map_tag_max
call style-specific routine to parse line
------------------------------------------------------------------------- */
void Atom::data_vels(int n, char *buf)
{
int j,m,tagdata;
char *next;
next = strchr(buf,'\n');
*next = '\0';
int nwords = count_words(buf);
*next = '\n';
if (nwords != avec->size_data_vel)
error->all("Incorrect velocity format in data file");
char **values = new char*[nwords];
// loop over lines of atom velocities
// tokenize the line into values
// if I own atom tag, unpack its values
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
values[0] = strtok(buf," \t\n\r\f");
for (j = 1; j < nwords; j++)
values[j] = strtok(NULL," \t\n\r\f");
tagdata = atoi(values[0]);
if (tagdata <= 0 || tagdata > map_tag_max)
error->one("Invalid atom ID in Velocities section of data file");
if ((m = map(tagdata)) >= 0) avec->data_vel(m,&values[1]);
buf = next + 1;
}
delete [] values;
}
/* ----------------------------------------------------------------------
unpack n lines from atom-style specific section of data file
check that atom IDs are > 0 and <= map_tag_max
call style-specific routine to parse line
------------------------------------------------------------------------- */
void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus)
{
int j,m,tagdata;
char *next;
next = strchr(buf,'\n');
*next = '\0';
int nwords = count_words(buf);
*next = '\n';
if (nwords != avec_bonus->size_data_bonus)
error->all("Incorrect bonus data format in data file");
char **values = new char*[nwords];
// loop over lines of bonus atom data
// tokenize the line into values
// if I own atom tag, unpack its values
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
values[0] = strtok(buf," \t\n\r\f");
for (j = 1; j < nwords; j++)
values[j] = strtok(NULL," \t\n\r\f");
tagdata = atoi(values[0]);
if (tagdata <= 0 || tagdata > map_tag_max)
error->one("Invalid atom ID in Bonus section of data file");
// ok to call child's data_atom_bonus() method thru parent avec_bonus,
// since data_bonus() was called with child ptr, and method is virtual
if ((m = map(tagdata)) >= 0) avec_bonus->data_atom_bonus(m,&values[1]);
buf = next + 1;
}
delete [] values;
}
/* ----------------------------------------------------------------------
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_bonds(int n, char *buf)
{
int m,tmp,itype,atom1,atom2;
char *next;
int newton_bond = force->newton_bond;
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
sscanf(buf,"%d %d %d %d",&tmp,&itype,&atom1,&atom2);
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max)
error->one("Invalid atom ID in Bonds section of data file");
if (itype <= 0 || itype > nbondtypes)
error->one("Invalid bond type in Bonds section of data file");
if ((m = map(atom1)) >= 0) {
bond_type[m][num_bond[m]] = itype;
bond_atom[m][num_bond[m]] = atom2;
num_bond[m]++;
}
if (newton_bond == 0) {
if ((m = map(atom2)) >= 0) {
bond_type[m][num_bond[m]] = itype;
bond_atom[m][num_bond[m]] = atom1;
num_bond[m]++;
}
}
buf = next + 1;
}
}
/* ----------------------------------------------------------------------
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_angles(int n, char *buf)
{
int m,tmp,itype,atom1,atom2,atom3;
char *next;
int newton_bond = force->newton_bond;
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
sscanf(buf,"%d %d %d %d %d",&tmp,&itype,&atom1,&atom2,&atom3);
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max ||
atom3 <= 0 || atom3 > map_tag_max)
error->one("Invalid atom ID in Angles section of data file");
if (itype <= 0 || itype > nangletypes)
error->one("Invalid angle type in Angles section of data file");
if ((m = map(atom2)) >= 0) {
angle_type[m][num_angle[m]] = itype;
angle_atom1[m][num_angle[m]] = atom1;
angle_atom2[m][num_angle[m]] = atom2;
angle_atom3[m][num_angle[m]] = atom3;
num_angle[m]++;
}
if (newton_bond == 0) {
if ((m = map(atom1)) >= 0) {
angle_type[m][num_angle[m]] = itype;
angle_atom1[m][num_angle[m]] = atom1;
angle_atom2[m][num_angle[m]] = atom2;
angle_atom3[m][num_angle[m]] = atom3;
num_angle[m]++;
}
if ((m = map(atom3)) >= 0) {
angle_type[m][num_angle[m]] = itype;
angle_atom1[m][num_angle[m]] = atom1;
angle_atom2[m][num_angle[m]] = atom2;
angle_atom3[m][num_angle[m]] = atom3;
num_angle[m]++;
}
}
buf = next + 1;
}
}
/* ----------------------------------------------------------------------
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_dihedrals(int n, char *buf)
{
int m,tmp,itype,atom1,atom2,atom3,atom4;
char *next;
int newton_bond = force->newton_bond;
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
sscanf(buf,"%d %d %d %d %d %d",&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max ||
atom3 <= 0 || atom3 > map_tag_max ||
atom4 <= 0 || atom4 > map_tag_max)
error->one("Invalid atom ID in Dihedrals section of data file");
if (itype <= 0 || itype > ndihedraltypes)
error->one("Invalid dihedral type in Dihedrals section of data file");
if ((m = map(atom2)) >= 0) {
dihedral_type[m][num_dihedral[m]] = itype;
dihedral_atom1[m][num_dihedral[m]] = atom1;
dihedral_atom2[m][num_dihedral[m]] = atom2;
dihedral_atom3[m][num_dihedral[m]] = atom3;
dihedral_atom4[m][num_dihedral[m]] = atom4;
num_dihedral[m]++;
}
if (newton_bond == 0) {
if ((m = map(atom1)) >= 0) {
dihedral_type[m][num_dihedral[m]] = itype;
dihedral_atom1[m][num_dihedral[m]] = atom1;
dihedral_atom2[m][num_dihedral[m]] = atom2;
dihedral_atom3[m][num_dihedral[m]] = atom3;
dihedral_atom4[m][num_dihedral[m]] = atom4;
num_dihedral[m]++;
}
if ((m = map(atom3)) >= 0) {
dihedral_type[m][num_dihedral[m]] = itype;
dihedral_atom1[m][num_dihedral[m]] = atom1;
dihedral_atom2[m][num_dihedral[m]] = atom2;
dihedral_atom3[m][num_dihedral[m]] = atom3;
dihedral_atom4[m][num_dihedral[m]] = atom4;
num_dihedral[m]++;
}
if ((m = map(atom4)) >= 0) {
dihedral_type[m][num_dihedral[m]] = itype;
dihedral_atom1[m][num_dihedral[m]] = atom1;
dihedral_atom2[m][num_dihedral[m]] = atom2;
dihedral_atom3[m][num_dihedral[m]] = atom3;
dihedral_atom4[m][num_dihedral[m]] = atom4;
num_dihedral[m]++;
}
}
buf = next + 1;
}
}
/* ----------------------------------------------------------------------
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_impropers(int n, char *buf)
{
int m,tmp,itype,atom1,atom2,atom3,atom4;
char *next;
int newton_bond = force->newton_bond;
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
sscanf(buf,"%d %d %d %d %d %d",&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max ||
atom3 <= 0 || atom3 > map_tag_max ||
atom4 <= 0 || atom4 > map_tag_max)
error->one("Invalid atom ID in Impropers section of data file");
if (itype <= 0 || itype > nimpropertypes)
error->one("Invalid improper type in Impropers section of data file");
if ((m = map(atom2)) >= 0) {
improper_type[m][num_improper[m]] = itype;
improper_atom1[m][num_improper[m]] = atom1;
improper_atom2[m][num_improper[m]] = atom2;
improper_atom3[m][num_improper[m]] = atom3;
improper_atom4[m][num_improper[m]] = atom4;
num_improper[m]++;
}
if (newton_bond == 0) {
if ((m = map(atom1)) >= 0) {
improper_type[m][num_improper[m]] = itype;
improper_atom1[m][num_improper[m]] = atom1;
improper_atom2[m][num_improper[m]] = atom2;
improper_atom3[m][num_improper[m]] = atom3;
improper_atom4[m][num_improper[m]] = atom4;
num_improper[m]++;
}
if ((m = map(atom3)) >= 0) {
improper_type[m][num_improper[m]] = itype;
improper_atom1[m][num_improper[m]] = atom1;
improper_atom2[m][num_improper[m]] = atom2;
improper_atom3[m][num_improper[m]] = atom3;
improper_atom4[m][num_improper[m]] = atom4;
num_improper[m]++;
}
if ((m = map(atom4)) >= 0) {
improper_type[m][num_improper[m]] = itype;
improper_atom1[m][num_improper[m]] = atom1;
improper_atom2[m][num_improper[m]] = atom2;
improper_atom3[m][num_improper[m]] = atom3;
improper_atom4[m][num_improper[m]] = atom4;
num_improper[m]++;
}
}
buf = next + 1;
}
}
/* ----------------------------------------------------------------------
allocate arrays of length ntypes
only done after ntypes is set
------------------------------------------------------------------------- */
void Atom::allocate_type_arrays()
{
if (avec->mass_type) {
mass = new double[ntypes+1];
mass_setflag = new int[ntypes+1];
for (int itype = 1; itype <= ntypes; itype++) mass_setflag[itype] = 0;
}
}
/* ----------------------------------------------------------------------
set a mass and flag it as set
called from reading of data file
------------------------------------------------------------------------- */
void Atom::set_mass(const char *str)
{
if (mass == NULL) error->all("Cannot set mass for this atom style");
int itype;
double mass_one;
int n = sscanf(str,"%d %lg",&itype,&mass_one);
if (n != 2) error->all("Invalid mass line in data file");
if (itype < 1 || itype > ntypes) error->all("Invalid type for mass set");
mass[itype] = mass_one;
mass_setflag[itype] = 1;
if (mass[itype] <= 0.0) error->all("Invalid mass value");
}
/* ----------------------------------------------------------------------
set a mass and flag it as set
called from EAM pair routine
------------------------------------------------------------------------- */
void Atom::set_mass(int itype, double value)
{
if (mass == NULL) error->all("Cannot set mass for this atom style");
if (itype < 1 || itype > ntypes) error->all("Invalid type for mass set");
mass[itype] = value;
mass_setflag[itype] = 1;
if (mass[itype] <= 0.0) error->all("Invalid mass value");
}
/* ----------------------------------------------------------------------
set one or more masses and flag them as set
called from reading of input script
------------------------------------------------------------------------- */
void Atom::set_mass(int narg, char **arg)
{
if (mass == NULL) error->all("Cannot set mass for this atom style");
int lo,hi;
force->bounds(arg[0],ntypes,lo,hi);
if (lo < 1 || hi > ntypes) error->all("Invalid type for mass set");
for (int itype = lo; itype <= hi; itype++) {
mass[itype] = atof(arg[1]);
mass_setflag[itype] = 1;
if (mass[itype] <= 0.0) error->all("Invalid mass value");
}
}
/* ----------------------------------------------------------------------
set all masses as read in from restart file
------------------------------------------------------------------------- */
void Atom::set_mass(double *values)
{
for (int itype = 1; itype <= ntypes; itype++) {
mass[itype] = values[itype];
mass_setflag[itype] = 1;
}
}
/* ----------------------------------------------------------------------
check that all masses have been set
------------------------------------------------------------------------- */
void Atom::check_mass()
{
if (mass == NULL) return;
for (int itype = 1; itype <= ntypes; itype++)
if (mass_setflag[itype] == 0) error->all("All masses are not set");
}
/* ----------------------------------------------------------------------
check that radii of all particles of itype are the same
return 1 if true, else return 0
also return the radius value for that type
------------------------------------------------------------------------- */
int Atom::radius_consistency(int itype, double &rad)
{
double value = -1.0;
int flag = 0;
for (int i = 0; i < nlocal; i++) {
if (type[i] != itype) continue;
if (value < 0.0) value = radius[i];
else if (value != radius[i]) flag = 1;
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall) return 0;
MPI_Allreduce(&value,&rad,1,MPI_DOUBLE,MPI_MAX,world);
return 1;
}
/* ----------------------------------------------------------------------
check that shape of all particles of itype are the same
return 1 if true, else return 0
also return the 3 shape params for itype
------------------------------------------------------------------------- */
int Atom::shape_consistency(int itype,
double &shapex, double &shapey, double &shapez)
{
double zero[3] = {0.0, 0.0, 0.0};
double one[3] = {-1.0, -1.0, -1.0};
double *shape;
AtomVecEllipsoid *avec_ellipsoid =
(AtomVecEllipsoid *) style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec_ellipsoid->bonus;
int flag = 0;
for (int i = 0; i < nlocal; i++) {
if (type[i] != itype) continue;
if (ellipsoid[i] < 0) shape = zero;
else shape = bonus[ellipsoid[i]].shape;
if (one[0] < 0.0) {
one[0] = shape[0];
one[1] = shape[1];
one[2] = shape[2];
} else if (one[0] != shape[0] || one[1] != shape[1] || one[2] != shape[2])
flag = 1;
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall) return 0;
double oneall[3];
MPI_Allreduce(one,oneall,3,MPI_DOUBLE,MPI_MAX,world);
shapex = oneall[0];
shapey = oneall[1];
shapez = oneall[2];
return 1;
}
/* ----------------------------------------------------------------------
reorder owned atoms so those in firstgroup appear first
called by comm->exchange() if atom_modify first group is set
only owned atoms exist at this point, no ghost atoms
------------------------------------------------------------------------- */
void Atom::first_reorder()
{
// insure there is one extra atom location at end of arrays for swaps
if (nlocal == nmax) avec->grow(0);
// loop over owned atoms
// nfirst = index of first atom not in firstgroup
// when find firstgroup atom out of place, swap it with atom nfirst
int bitmask = group->bitmask[firstgroup];
nfirst = 0;
while (nfirst < nlocal && mask[nfirst] & bitmask) nfirst++;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & bitmask && i > nfirst) {
avec->copy(i,nlocal,0);
avec->copy(nfirst,i,0);
avec->copy(nlocal,nfirst,0);
while (nfirst < nlocal && mask[nfirst] & bitmask) nfirst++;
}
}
}
/* ----------------------------------------------------------------------
perform spatial sort of atoms within my sub-domain
always called between comm->exchange() and comm->borders()
don't have to worry about clearing/setting atom->map since done in comm
------------------------------------------------------------------------- */
void Atom::sort()
{
int i,m,n,ix,iy,iz,ibin,empty;
// set next timestep for sorting to take place
nextsort = (update->ntimestep/sortfreq)*sortfreq + sortfreq;
// download data from GPU if necessary
if (lmp->cuda && !lmp->cuda->oncpu) lmp->cuda->downloadAll();
// re-setup sort bins if needed
if (domain->box_change) setup_sort_bins();
if (nbins == 1) return;
// reallocate per-atom vectors if needed
if (nlocal > maxnext) {
memory->destroy(next);
memory->destroy(permute);
maxnext = atom->nmax;
memory->create(next,maxnext,"atom:next");
memory->create(permute,maxnext,"atom:permute");
}
// insure there is one extra atom location at end of arrays for swaps
if (nlocal == nmax) avec->grow(0);
// bin atoms in reverse order so linked list will be in forward order
for (i = 0; i < nbins; i++) binhead[i] = -1;
for (i = nlocal-1; i >= 0; i--) {
ix = static_cast<int> ((x[i][0]-bboxlo[0])*bininvx);
iy = static_cast<int> ((x[i][1]-bboxlo[1])*bininvy);
iz = static_cast<int> ((x[i][2]-bboxlo[2])*bininvz);
ix = MAX(ix,0);
iy = MAX(iy,0);
iz = MAX(iz,0);
ix = MIN(ix,nbinx-1);
iy = MIN(iy,nbiny-1);
iz = MIN(iz,nbinz-1);
ibin = iz*nbiny*nbinx + iy*nbinx + ix;
next[i] = binhead[ibin];
binhead[ibin] = i;
}
// permute = desired permutation of atoms
// permute[I] = J means Ith new atom will be Jth old atom
n = 0;
for (m = 0; m < nbins; m++) {
i = binhead[m];
while (i >= 0) {
permute[n++] = i;
i = next[i];
}
}
// current = current permutation, just reuse next vector
// current[I] = J means Ith current atom is Jth old atom
int *current = next;
for (i = 0; i < nlocal; i++) current[i] = i;
// reorder local atom list, when done, current = permute
// perform "in place" using copy() to extra atom location at end of list
// inner while loop processes one cycle of the permutation
// copy before inner-loop moves an atom to end of atom list
// copy after inner-loop moves atom at end of list back into list
// empty = location in atom list that is currently empty
for (i = 0; i < nlocal; i++) {
if (current[i] == permute[i]) continue;
avec->copy(i,nlocal,0);
empty = i;
while (permute[empty] != i) {
avec->copy(permute[empty],empty,0);
empty = current[empty] = permute[empty];
}
avec->copy(nlocal,empty,0);
current[empty] = permute[empty];
}
// upload data back to GPU if necessary
if (lmp->cuda && !lmp->cuda->oncpu) lmp->cuda->uploadAll();
// sanity check that current = permute
//int flag = 0;
//for (i = 0; i < nlocal; i++)
// if (current[i] != permute[i]) flag = 1;
//int flagall;
//MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
//if (flagall) error->all("Atom sort did not operate correctly");
}
/* ----------------------------------------------------------------------
setup bins for spatial sorting of atoms
------------------------------------------------------------------------- */
void Atom::setup_sort_bins()
{
// binsize:
// user setting if explicitly set
// 1/2 of neighbor cutoff for non-CUDA
// CUDA_CHUNK atoms/proc for CUDA
// check if neighbor cutoff = 0.0
double binsize;
if (userbinsize > 0.0) binsize = userbinsize;
else if (!lmp->cuda) binsize = 0.5 * neighbor->cutneighmax;
else {
if (domain->dimension == 3) {
double vol = (domain->boxhi[0]-domain->boxlo[0]) *
(domain->boxhi[1]-domain->boxlo[1]) *
(domain->boxhi[2]-domain->boxlo[2]);
binsize = pow(1.0*CUDA_CHUNK/natoms*vol,1.0/3.0);
} else {
double area = (domain->boxhi[0]-domain->boxlo[0]) *
(domain->boxhi[1]-domain->boxlo[1]);
binsize = pow(1.0*CUDA_CHUNK/natoms*area,1.0/2.0);
}
}
if (binsize == 0.0) error->all("Atom sorting has bin size = 0.0");
double bininv = 1.0/binsize;
// nbin xyz = local bins
// bbox lo/hi = bounding box of my sub-domain
if (domain->triclinic)
domain->bbox(domain->sublo_lamda,domain->subhi_lamda,bboxlo,bboxhi);
else {
bboxlo[0] = domain->sublo[0];
bboxlo[1] = domain->sublo[1];
bboxlo[2] = domain->sublo[2];
bboxhi[0] = domain->subhi[0];
bboxhi[1] = domain->subhi[1];
bboxhi[2] = domain->subhi[2];
}
nbinx = static_cast<int> ((bboxhi[0]-bboxlo[0]) * bininv);
nbiny = static_cast<int> ((bboxhi[1]-bboxlo[1]) * bininv);
nbinz = static_cast<int> ((bboxhi[2]-bboxlo[2]) * bininv);
if (domain->dimension == 2) nbinz = 1;
if (nbinx == 0) nbinx = 1;
if (nbiny == 0) nbiny = 1;
if (nbinz == 0) nbinz = 1;
bininvx = nbinx / (bboxhi[0]-bboxlo[0]);
bininvy = nbiny / (bboxhi[1]-bboxlo[1]);
bininvz = nbinz / (bboxhi[2]-bboxlo[2]);
if (1.0*nbinx*nbiny*nbinz > INT_MAX)
error->one("Too many atom sorting bins");
nbins = nbinx*nbiny*nbinz;
// reallocate per-bin memory if needed
if (nbins > maxbin) {
memory->destroy(binhead);
maxbin = nbins;
memory->create(binhead,maxbin,"atom:binhead");
}
}
/* ----------------------------------------------------------------------
register a callback to a fix so it can manage atom-based arrays
happens when fix is created
flag = 0 for grow, 1 for restart
------------------------------------------------------------------------- */
void Atom::add_callback(int flag)
{
int ifix;
// find the fix
// if find NULL ptr:
// it's this one, since it is being replaced and has just been deleted
// at this point in re-creation
// if don't find NULL ptr:
// i is set to nfix = new one currently being added at end of list
for (ifix = 0; ifix < modify->nfix; ifix++)
if (modify->fix[ifix] == NULL) break;
// add callback to lists, reallocating if necessary
if (flag == 0) {
if (nextra_grow == nextra_grow_max) {
nextra_grow_max += DELTA;
memory->grow(extra_grow,nextra_grow_max,"atom:extra_grow");
}
extra_grow[nextra_grow] = ifix;
nextra_grow++;
} else if (flag == 1) {
if (nextra_restart == nextra_restart_max) {
nextra_restart_max += DELTA;
memory->grow(extra_restart,nextra_restart_max,"atom:extra_restart");
}
extra_restart[nextra_restart] = ifix;
nextra_restart++;
}
}
/* ----------------------------------------------------------------------
unregister a callback to a fix
happens when fix is deleted, called by its destructor
flag = 0 for grow, 1 for restart
------------------------------------------------------------------------- */
void Atom::delete_callback(const char *id, int flag)
{
int ifix;
for (ifix = 0; ifix < modify->nfix; ifix++)
if (strcmp(id,modify->fix[ifix]->id) == 0) break;
// compact the list of callbacks
if (flag == 0) {
int match;
for (match = 0; match < nextra_grow; match++)
if (extra_grow[match] == ifix) break;
for (int i = match; i < nextra_grow-1; i++)
extra_grow[i] = extra_grow[i+1];
nextra_grow--;
} else if (flag == 1) {
int match;
for (match = 0; match < nextra_grow; match++)
if (extra_restart[match] == ifix) break;
for (int i = ifix; i < nextra_restart-1; i++)
extra_restart[i] = extra_restart[i+1];
nextra_restart--;
}
}
/* ----------------------------------------------------------------------
decrement ptrs in callback lists to fixes beyond the deleted ifix
happens after fix is deleted
------------------------------------------------------------------------- */
void Atom::update_callback(int ifix)
{
for (int i = 0; i < nextra_grow; i++)
if (extra_grow[i] > ifix) extra_grow[i]--;
for (int i = 0; i < nextra_restart; i++)
if (extra_restart[i] > ifix) extra_restart[i]--;
}
/* ----------------------------------------------------------------------
return a pointer to a named internal variable
if don't recognize name, return NULL
customize by adding names
------------------------------------------------------------------------- */
void *Atom::extract(char *name)
{
if (strcmp(name,"id") == 0) return (void *) tag;
if (strcmp(name,"type") == 0) return (void *) type;
if (strcmp(name,"x") == 0) return (void *) x;
if (strcmp(name,"v") == 0) return (void *) v;
if (strcmp(name,"f") == 0) return (void *) f;
if (strcmp(name,"mass") == 0) return (void *) mass;
if (strcmp(name,"rmass") == 0) return (void *) rmass;
return NULL;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
call to avec tallies per-atom vectors
add in global to local mapping storage
------------------------------------------------------------------------- */
bigint Atom::memory_usage()
{
memlength = DELTA_MEMSTR;
memory->create(memstr,memlength,"atom:memstr");
memstr[0] = '\0';
bigint bytes = avec->memory_usage();
memory->destroy(memstr);
if (map_style == 1)
bytes += memory->usage(map_array,map_tag_max+1);
else if (map_style == 2) {
bytes += map_nbucket*sizeof(int);
bytes += map_nhash*sizeof(HashElem);
}
if (maxnext) {
bytes += memory->usage(next,maxnext);
bytes += memory->usage(permute,maxnext);
}
return bytes;
}
/* ----------------------------------------------------------------------
accumulate per-atom vec names in memstr, padded by spaces
return 1 if padded str is not already in memlist, else 0
------------------------------------------------------------------------- */
int Atom::memcheck(const char *str)
{
int n = strlen(str) + 3;
char *padded = new char[n];
strcpy(padded," ");
strcat(padded,str);
strcat(padded," ");
if (strstr(memstr,padded)) {
delete [] padded;
return 0;
}
if (strlen(memstr) + n >= memlength) {
memlength += DELTA_MEMSTR;
memory->grow(memstr,memlength,"atom:memstr");
}
strcat(memstr,padded);
delete [] padded;
return 1;
}
diff --git a/src/atom.h b/src/atom.h
index 9b56510ca..98b687ec9 100644
--- a/src/atom.h
+++ b/src/atom.h
@@ -1,225 +1,230 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_ATOM_H
#define LMP_ATOM_H
#include "pointers.h"
namespace LAMMPS_NS {
class Atom : protected Pointers {
public:
char *atom_style;
class AtomVec *avec;
// atom counts
bigint natoms; // total # of atoms in system, could be 0
int nlocal,nghost; // # of owned and ghost atoms on this proc
int nmax; // max # of owned+ghost in arrays on this proc
int tag_enable; // 0/1 if atom ID tags are defined
int molecular; // 0 = atomic, 1 = molecular system
bigint nbonds,nangles,ndihedrals,nimpropers;
int ntypes,nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
int bond_per_atom,angle_per_atom,dihedral_per_atom,improper_per_atom;
int extra_bond_per_atom;
int firstgroup; // store atoms in this group first, -1 if unset
int nfirst; // # of atoms in first group on this proc
char *firstgroupname; // group-ID to store first, NULL if unset
// per-atom arrays
// customize by adding new array
int *tag,*type,*mask,*image;
double **x,**v,**f;
int *molecule;
double *q,**mu;
double **omega,**angmom,**torque;
double *radius,*rmass,*vfrac,*s0;
double **x0;
int *ellipsoid;
int *spin;
double *eradius,*ervel,*erforce,*ervelforce;
double *cs,*csforce,*vforce;
int *etag;
+ double *rho, *drho;
+ double *e, *de;
+ double **vest;
+ double *cv;
int **nspecial; // 0,1,2 = cummulative # of 1-2,1-3,1-4 neighs
int **special; // IDs of 1-2,1-3,1-4 neighs of each atom
int maxspecial; // special[nlocal][maxspecial]
int *num_bond;
int **bond_type;
int **bond_atom;
int *num_angle;
int **angle_type;
int **angle_atom1,**angle_atom2,**angle_atom3;
int *num_dihedral;
int **dihedral_type;
int **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4;
int *num_improper;
int **improper_type;
int **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
// atom style and per-atom array existence flags
// customize by adding new flag
int sphere_flag,ellipsoid_flag,peri_flag,electron_flag;
- int wavepacket_flag;
+ int wavepacket_flag,sph_flag;
int molecule_flag,q_flag,mu_flag;
int rmass_flag,radius_flag,omega_flag,torque_flag,angmom_flag;
int vfrac_flag,spin_flag,eradius_flag,ervel_flag,erforce_flag;
int cs_flag,csforce_flag,vforce_flag,ervelforce_flag,etag_flag;
+ int rho_flag,e_flag,cv_flag,vest_flag;
// extra peratom info in restart file destined for fix & diag
double **extra;
// per-type arrays
double *mass;
int *mass_setflag;
// callback ptrs for atom arrays managed by fix classes
int nextra_grow,nextra_restart; // # of callbacks of each type
int *extra_grow,*extra_restart; // index of fix to callback to
int nextra_grow_max,nextra_restart_max; // size of callback lists
int nextra_store;
int map_style; // default or user-specified style of map
// 0 = none, 1 = array, 2 = hash
// spatial sorting of atoms
int sortfreq; // sort atoms every this many steps, 0 = off
bigint nextsort; // next timestep to sort on
// functions
Atom(class LAMMPS *);
~Atom();
void settings(class Atom *);
void create_avec(const char *, int, char **, char *suffix = NULL);
class AtomVec *new_avec(const char *, int, char **, char *, int &);
void init();
void setup();
class AtomVec *style_match(const char *);
void modify_params(int, char **);
void tag_extend();
int tag_consecutive();
int parse_data(const char *);
int count_words(const char *);
void data_atoms(int, char *);
void data_vels(int, char *);
void data_bonus(int, char *, class AtomVec *);
void data_bonds(int, char *);
void data_angles(int, char *);
void data_dihedrals(int, char *);
void data_impropers(int, char *);
void allocate_type_arrays();
void set_mass(const char *);
void set_mass(int, double);
void set_mass(int, char **);
void set_mass(double *);
void check_mass();
int radius_consistency(int, double &);
int shape_consistency(int, double &, double &, double &);
void first_reorder();
void sort();
void add_callback(int);
void delete_callback(const char *, int);
void update_callback(int);
void *extract(char *);
inline int* get_map_array() {return map_array;};
inline int get_map_size() {return map_tag_max+1;};
bigint memory_usage();
int memcheck(const char *);
// functions for global to local ID mapping
// map lookup function inlined for efficiency
inline int map(int global) {
if (map_style == 1) return map_array[global];
else return map_find_hash(global);
};
void map_init();
void map_clear();
void map_set();
void map_one(int, int);
void map_delete();
int map_find_hash(int);
private:
// global to local ID mapping
int map_tag_max;
int *map_array;
struct HashElem {
int global; // key to search on = global ID
int local; // value associated with key = local index
int next; // next entry in this bucket, -1 if last
};
int map_nhash; // # of entries hash table can hold
int map_nused; // # of actual entries in hash table
int map_free; // ptr to 1st unused entry in hash table
int map_nbucket; // # of hash buckets
int *map_bucket; // ptr to 1st entry in each bucket
HashElem *map_hash; // hash table
int *primes; // table of prime #s for hashing
int nprimes; // # of primes
// spatial sorting of atoms
int nbins; // # of sorting bins
int nbinx,nbiny,nbinz; // bins in each dimension
int maxbin; // max # of bins
int maxnext; // max size of next,permute
int *binhead; // 1st atom in each bin
int *next; // next atom in bin
int *permute; // permutation vector
double userbinsize; // requested sort bin size
double bininvx,bininvy,bininvz; // inverse actual bin sizes
double bboxlo[3],bboxhi[3]; // bounding box of my sub-domain
int memlength; // allocated size of memstr
char *memstr; // string of array names already counted
void setup_sort_bins();
};
}
#endif
diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp
index 7c25edf76..e3d2ae8ea 100644
--- a/src/fix_gravity.cpp
+++ b/src/fix_gravity.cpp
@@ -1,190 +1,218 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "fix_gravity.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "respa.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{CHUTE,SPHERICAL,GRADIENT,VECTOR};
/* ---------------------------------------------------------------------- */
FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 5) error->all("Illegal fix gravity command");
time_depend = 1;
+ scalar_flag = 1;
+ global_freq = 1;
+ extscalar = 1;
magnitude = atof(arg[3]);
if (strcmp(arg[4],"chute") == 0) {
if (narg != 6) error->all("Illegal fix gravity command");
style = CHUTE;
phi = 0.0;
theta = 180.0 - atof(arg[5]);
} else if (strcmp(arg[4],"spherical") == 0) {
if (narg != 7) error->all("Illegal fix gravity command");
style = SPHERICAL;
phi = atof(arg[5]);
theta = atof(arg[6]);
} else if (strcmp(arg[4],"gradient") == 0) {
if (narg != 9) error->all("Illegal fix gravity command");
style = GRADIENT;
phi = atof(arg[5]);
theta = atof(arg[6]);
phigrad = atof(arg[7]);
thetagrad = atof(arg[8]);
} else if (strcmp(arg[4],"vector") == 0) {
if (narg != 8) error->all("Illegal fix gravity command");
style = VECTOR;
xdir = atof(arg[5]);
ydir = atof(arg[6]);
zdir = atof(arg[7]);
} else error->all("Illegal fix gravity command");
double PI = 4.0*atan(1.0);
degree2rad = PI/180.0;
if (style == CHUTE || style == SPHERICAL || style == GRADIENT) {
if (domain->dimension == 3) {
xgrav = sin(degree2rad * theta) * cos(degree2rad * phi);
ygrav = sin(degree2rad * theta) * sin(degree2rad * phi);
zgrav = cos(degree2rad * theta);
} else {
xgrav = sin(degree2rad * theta);
ygrav = cos(degree2rad * theta);
zgrav = 0.0;
}
} else if (style == VECTOR) {
if (domain->dimension == 3) {
double length = sqrt(xdir*xdir + ydir*ydir + zdir*zdir);
xgrav = xdir/length;
ygrav = ydir/length;
zgrav = zdir/length;
} else {
double length = sqrt(xdir*xdir + ydir*ydir);
xgrav = xdir/length;
ygrav = ydir/length;
zgrav = 0.0;
}
}
time_origin = update->ntimestep;
+
+ eflag = 0;
+ egrav = 0.0;
}
/* ---------------------------------------------------------------------- */
int FixGravity::setmask()
{
int mask = 0;
mask |= POST_FORCE;
+ mask |= THERMO_ENERGY;
mask |= POST_FORCE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixGravity::init()
{
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
dt = update->dt;
xacc = magnitude*xgrav;
yacc = magnitude*ygrav;
zacc = magnitude*zgrav;
}
/* ---------------------------------------------------------------------- */
void FixGravity::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
}
}
/* ---------------------------------------------------------------------- */
void FixGravity::post_force(int vflag)
{
// update direction of gravity vector if gradient style
if (style == GRADIENT) {
if (domain->dimension == 3) {
double phi_current = degree2rad *
(phi + (update->ntimestep - time_origin)*dt*phigrad*360.0);
double theta_current = degree2rad *
(theta + (update->ntimestep - time_origin)*dt*thetagrad*360.0);
xgrav = sin(theta_current) * cos(phi_current);
ygrav = sin(theta_current) * sin(phi_current);
zgrav = cos(theta_current);
} else {
double theta_current = degree2rad *
(theta + (update->ntimestep - time_origin)*dt*thetagrad*360.0);
xgrav = sin(theta_current);
ygrav = cos(theta_current);
}
xacc = magnitude*xgrav;
yacc = magnitude*ygrav;
zacc = magnitude*zgrav;
}
+ double **x = atom->x;
double **f = atom->f;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *mask = atom->mask;
int *type = atom->type;
int nlocal = atom->nlocal;
double massone;
+ eflag = 0;
+ egrav = 0.0;
+
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
massone = rmass[i];
f[i][0] += massone*xacc;
f[i][1] += massone*yacc;
f[i][2] += massone*zacc;
+ egrav -= massone * (xacc*x[i][0] + yacc*x[i][1] + zacc*x[i][2]);
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
massone = mass[type[i]];
f[i][0] += massone*xacc;
f[i][1] += massone*yacc;
f[i][2] += massone*zacc;
+ egrav -= massone * (xacc*x[i][0] + yacc*x[i][1] + zacc*x[i][2]);
}
}
}
/* ---------------------------------------------------------------------- */
void FixGravity::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
+
+/* ----------------------------------------------------------------------
+ potential energy in gravity field
+------------------------------------------------------------------------- */
+
+double FixGravity::compute_scalar()
+{
+ // only sum across procs one time
+
+ if (eflag == 0) {
+ MPI_Allreduce(&egrav,&egrav_all,1,MPI_DOUBLE,MPI_SUM,world);
+ eflag = 1;
+ }
+ return egrav_all;
+}
diff --git a/src/fix_gravity.h b/src/fix_gravity.h
index 248a9ffa1..3f82d6c7f 100644
--- a/src/fix_gravity.h
+++ b/src/fix_gravity.h
@@ -1,52 +1,55 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(gravity,FixGravity)
#else
#ifndef LMP_FIX_GRAVITY_H
#define LMP_FIX_GRAVITY_H
#include "fix.h"
namespace LAMMPS_NS {
class FixGravity : public Fix {
friend class FixPour;
public:
FixGravity(class LAMMPS *, int, char **);
int setmask();
void init();
void setup(int);
void post_force(int);
void post_force_respa(int, int, int);
+ double compute_scalar();
private:
int style;
double magnitude,dt;
double phi,theta,phigrad,thetagrad;
double xdir,ydir,zdir;
double xgrav,ygrav,zgrav,xacc,yacc,zacc;
double degree2rad;
int nlevels_respa;
int time_origin;
+ int eflag;
+ double egrav,egrav_all;
};
}
#endif
#endif
diff --git a/src/min.cpp b/src/min.cpp
index 1a507de0d..2d66eb8c0 100644
--- a/src/min.cpp
+++ b/src/min.cpp
@@ -1,773 +1,787 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Aidan Thompson (SNL)
improved CG and backtrack ls, added quadratic ls
Sources: Numerical Recipes frprmn routine
"Conjugate Gradient Method Without the Agonizing Pain" by
JR Shewchuk, http://www-2.cs.cmu.edu/~jrs/jrspapers.html#cg
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "min.h"
#include "atom.h"
#include "domain.h"
#include "comm.h"
#include "update.h"
#include "modify.h"
#include "fix_minimize.h"
#include "compute.h"
#include "neighbor.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "kspace.h"
#include "output.h"
#include "thermo.h"
#include "timer.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
Min::Min(LAMMPS *lmp) : Pointers(lmp)
{
dmax = 0.1;
searchflag = 0;
linestyle = 0;
elist_global = elist_atom = NULL;
vlist_global = vlist_atom = NULL;
nextra_global = 0;
fextra = NULL;
nextra_atom = 0;
xextra_atom = fextra_atom = NULL;
extra_peratom = extra_nlen = NULL;
extra_max = NULL;
requestor = NULL;
}
/* ---------------------------------------------------------------------- */
Min::~Min()
{
delete [] elist_global;
delete [] elist_atom;
delete [] vlist_global;
delete [] vlist_atom;
delete [] fextra;
memory->sfree(xextra_atom);
memory->sfree(fextra_atom);
memory->destroy(extra_peratom);
memory->destroy(extra_nlen);
memory->destroy(extra_max);
memory->sfree(requestor);
}
/* ---------------------------------------------------------------------- */
void Min::init()
{
// create fix needed for storing atom-based quantities
// will delete it at end of run
char **fixarg = new char*[3];
fixarg[0] = (char *) "MINIMIZE";
fixarg[1] = (char *) "all";
fixarg[2] = (char *) "MINIMIZE";
modify->add_fix(3,fixarg);
delete [] fixarg;
fix_minimize = (FixMinimize *) modify->fix[modify->nfix-1];
// clear out extra global and per-atom dof
// will receive requests for new per-atom dof during pair init()
// can then add vectors to fix_minimize in setup()
nextra_global = 0;
delete [] fextra;
fextra = NULL;
nextra_atom = 0;
memory->sfree(xextra_atom);
memory->sfree(fextra_atom);
memory->destroy(extra_peratom);
memory->destroy(extra_nlen);
memory->destroy(extra_max);
memory->sfree(requestor);
xextra_atom = fextra_atom = NULL;
extra_peratom = extra_nlen = NULL;
extra_max = NULL;
requestor = NULL;
// virial_style:
// 1 if computed explicitly by pair->compute via sum over pair interactions
// 2 if computed implicitly by pair->virial_compute via sum over ghost atoms
if (force->newton_pair) virial_style = 2;
else virial_style = 1;
// setup lists of computes for global and per-atom PE and pressure
ev_setup();
// set flags for what arrays to clear in force_clear()
- // need to clear torques,erforce if arrays exists
+ // need to clear additionals arrays if they exist
torqueflag = 0;
if (atom->torque_flag) torqueflag = 1;
erforceflag = 0;
if (atom->erforce_flag) erforceflag = 1;
+ e_flag = 0;
+ if (atom->e_flag) e_flag = 1;
+ rho_flag = 0;
+ if (atom->rho_flag) rho_flag = 1;
// orthogonal vs triclinic simulation box
triclinic = domain->triclinic;
// reset reneighboring criteria if necessary
neigh_every = neighbor->every;
neigh_delay = neighbor->delay;
neigh_dist_check = neighbor->dist_check;
if (neigh_every != 1 || neigh_delay != 0 || neigh_dist_check != 1) {
if (comm->me == 0)
error->warning("Resetting reneighboring criteria during minimization");
}
neighbor->every = 1;
neighbor->delay = 0;
neighbor->dist_check = 1;
niter = neval = 0;
// style-specific initialization
init_style();
}
/* ----------------------------------------------------------------------
setup before run
------------------------------------------------------------------------- */
void Min::setup()
{
if (comm->me == 0 && screen) fprintf(screen,"Setting up minimization ...\n");
// setup extra global dof due to fixes
// cannot be done in init() b/c update init() is before modify init()
nextra_global = modify->min_dof();
if (nextra_global) fextra = new double[nextra_global];
// compute for potential energy
int id = modify->find_compute("thermo_pe");
if (id < 0) error->all("Minimization could not find thermo_pe compute");
pe_compute = modify->compute[id];
// style-specific setup does two tasks
// setup extra global dof vectors
// setup extra per-atom dof vectors due to requests from Pair classes
// cannot be done in init() b/c update init() is before modify/pair init()
setup_style();
// ndoftotal = total dof for entire minimization problem
// dof for atoms, extra per-atom, extra global
bigint ndofme = 3*atom->nlocal;
for (int m = 0; m < nextra_atom; m++)
ndofme += extra_peratom[m]*atom->nlocal;
MPI_Allreduce(&ndofme,&ndoftotal,1,MPI_LMP_BIGINT,MPI_SUM,world);
ndoftotal += nextra_global;
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
atom->setup();
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
if (atom->sortfreq > 0) atom->sort();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
neighbor->build();
neighbor->ncalls = 0;
// remove these restriction eventually
if (nextra_global && searchflag == 0)
error->all("Cannot use a damped dynamics min style with fix box/relax");
if (nextra_atom && searchflag == 0)
error->all("Cannot use a damped dynamics min style with per-atom DOF");
// atoms may have migrated in comm->exchange()
reset_vectors();
// compute all forces
ev_set(update->ntimestep);
force_clear();
modify->setup_pre_force(vflag);
if (force->pair) force->pair->compute(eflag,vflag);
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);
if (force->improper) force->improper->compute(eflag,vflag);
}
if (force->kspace) {
force->kspace->setup();
force->kspace->compute(eflag,vflag);
}
if (force->newton) comm->reverse_comm();
// update per-atom minimization variables stored by pair styles
if (nextra_atom)
for (int m = 0; m < nextra_atom; m++)
requestor[m]->min_xf_get(m);
modify->setup(vflag);
output->setup(1);
// stats for Finish to print
ecurrent = pe_compute->compute_scalar();
if (nextra_global) ecurrent += modify->min_energy(fextra);
if (output->thermo->normflag) ecurrent /= atom->natoms;
einitial = ecurrent;
fnorm2_init = sqrt(fnorm_sqr());
fnorminf_init = fnorm_inf();
}
/* ----------------------------------------------------------------------
setup without output or one-time post-init setup
flag = 0 = just force calculation
flag = 1 = reneighbor and force calculation
------------------------------------------------------------------------- */
void Min::setup_minimal(int flag)
{
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
if (flag) {
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
neighbor->build();
neighbor->ncalls = 0;
}
// atoms may have migrated in comm->exchange()
reset_vectors();
// compute all forces
ev_set(update->ntimestep);
force_clear();
modify->setup_pre_force(vflag);
if (force->pair) force->pair->compute(eflag,vflag);
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);
if (force->improper) force->improper->compute(eflag,vflag);
}
if (force->kspace) {
force->kspace->setup();
force->kspace->compute(eflag,vflag);
}
if (force->newton) comm->reverse_comm();
// update per-atom minimization variables stored by pair styles
if (nextra_atom)
for (int m = 0; m < nextra_atom; m++)
requestor[m]->min_xf_get(m);
modify->setup(vflag);
// stats for Finish to print
ecurrent = pe_compute->compute_scalar();
if (nextra_global) ecurrent += modify->min_energy(fextra);
if (output->thermo->normflag) ecurrent /= atom->natoms;
einitial = ecurrent;
fnorm2_init = sqrt(fnorm_sqr());
fnorminf_init = fnorm_inf();
}
/* ----------------------------------------------------------------------
perform minimization, calling iterate() for N steps
------------------------------------------------------------------------- */
void Min::run(int n)
{
// minimizer iterations
stop_condition = iterate(n);
stopstr = stopstrings(stop_condition);
// if early exit from iterate loop:
// set update->nsteps to niter for Finish stats to print
// set output->next values to this timestep
// call energy_force() to insure vflag is set when forces computed
// output->write does final output for thermo, dump, restart files
// add ntimestep to all computes that store invocation times
// since are hardwiring call to thermo/dumps and computes may not be ready
if (stop_condition) {
update->nsteps = niter;
if (update->restrict_output == 0) {
for (int idump = 0; idump < output->ndump; idump++)
output->next_dump[idump] = update->ntimestep;
output->next_dump_any = update->ntimestep;
if (output->restart_every) output->next_restart = update->ntimestep;
}
output->next_thermo = update->ntimestep;
modify->addstep_compute_all(update->ntimestep);
ecurrent = energy_force(0);
output->write(update->ntimestep);
}
}
/* ---------------------------------------------------------------------- */
void Min::cleanup()
{
// stats for Finish to print
efinal = ecurrent;
fnorm2_final = sqrt(fnorm_sqr());
fnorminf_final = fnorm_inf();
// reset reneighboring criteria
neighbor->every = neigh_every;
neighbor->delay = neigh_delay;
neighbor->dist_check = neigh_dist_check;
// delete fix at end of run, so its atom arrays won't persist
modify->delete_fix("MINIMIZE");
}
/* ----------------------------------------------------------------------
evaluate potential energy and forces
may migrate atoms due to reneighboring
return new energy, which should include nextra_global dof
return negative gradient stored in atom->f
return negative gradient for nextra_global dof in fextra
------------------------------------------------------------------------- */
double Min::energy_force(int resetflag)
{
// check for reneighboring
// always communicate since minimizer moved atoms
int nflag = neighbor->decide();
if (nflag == 0) {
timer->stamp();
comm->forward_comm();
timer->stamp(Timer::COMM);
} else {
if (modify->n_min_pre_exchange) {
timer->stamp();
modify->min_pre_exchange();
timer->stamp(Timer::MODIFY);
}
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
if (domain->box_change) {
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
}
timer->stamp();
comm->exchange();
if (atom->sortfreq > 0 &&
update->ntimestep >= atom->nextsort) atom->sort();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
timer->stamp(Timer::COMM);
neighbor->build();
timer->stamp(Timer::NEIGHBOR);
}
ev_set(update->ntimestep);
force_clear();
timer->stamp();
if (modify->n_min_pre_force) {
modify->min_pre_force(vflag);
timer->stamp(Timer::MODIFY);
}
if (force->pair) {
force->pair->compute(eflag,vflag);
timer->stamp(Timer::PAIR);
}
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);
if (force->improper) force->improper->compute(eflag,vflag);
timer->stamp(Timer::BOND);
}
if (force->kspace) {
force->kspace->compute(eflag,vflag);
timer->stamp(Timer::KSPACE);
}
if (force->newton) {
comm->reverse_comm();
timer->stamp(Timer::COMM);
}
// update per-atom minimization variables stored by pair styles
if (nextra_atom)
for (int m = 0; m < nextra_atom; m++)
requestor[m]->min_xf_get(m);
// fixes that affect minimization
if (modify->n_min_post_force) {
timer->stamp();
modify->min_post_force(vflag);
timer->stamp(Timer::MODIFY);
}
// compute potential energy of system
// normalize if thermo PE does
double energy = pe_compute->compute_scalar();
if (nextra_global) energy += modify->min_energy(fextra);
if (output->thermo->normflag) energy /= atom->natoms;
// if reneighbored, atoms migrated
// if resetflag = 1, update x0 of atoms crossing PBC
// reset vectors used by lo-level minimizer
if (nflag) {
if (resetflag) fix_minimize->reset_coords();
reset_vectors();
}
return energy;
}
/* ----------------------------------------------------------------------
clear force on own & ghost atoms
setup and clear other arrays as needed
------------------------------------------------------------------------- */
void Min::force_clear()
{
int i;
// clear global force array
// nall includes ghosts only if either newton flag is set
int nall;
if (force->newton) nall = atom->nlocal + atom->nghost;
else nall = atom->nlocal;
int ntot = nall * comm->nthreads;
double **f = atom->f;
for (i = 0; i < ntot; i++) {
f[i][0] = 0.0;
f[i][1] = 0.0;
f[i][2] = 0.0;
}
if (torqueflag) {
double **torque = atom->torque;
for (i = 0; i < nall; i++) {
torque[i][0] = 0.0;
torque[i][1] = 0.0;
torque[i][2] = 0.0;
}
}
if (erforceflag) {
double *erforce = atom->erforce;
for (i = 0; i < nall; i++) erforce[i] = 0.0;
}
+
+ if (e_flag) {
+ double *de = atom->de;
+ for (i = 0; i < nall; i++) de[i] = 0.0;
+ }
+
+ if (rho_flag) {
+ double *drho = atom->drho;
+ for (i = 0; i < nall; i++) drho[i] = 0.0;
+ }
}
/* ----------------------------------------------------------------------
pair style makes request to add a per-atom variables to minimization
requestor stores callback to pair class to invoke during min
to get current variable and forces on it and to update the variable
return flag that pair can use if it registers multiple variables
------------------------------------------------------------------------- */
int Min::request(Pair *pair, int peratom, double maxvalue)
{
int n = nextra_atom + 1;
xextra_atom = (double **) memory->srealloc(xextra_atom,n*sizeof(double *),
"min:xextra_atom");
fextra_atom = (double **) memory->srealloc(fextra_atom,n*sizeof(double *),
"min:fextra_atom");
memory->grow(extra_peratom,n,"min:extra_peratom");
memory->grow(extra_nlen,n,"min:extra_nlen");
memory->grow(extra_max,n,"min:extra_max");
requestor = (Pair **) memory->srealloc(requestor,n*sizeof(Pair *),
"min:requestor");
requestor[nextra_atom] = pair;
extra_peratom[nextra_atom] = peratom;
extra_max[nextra_atom] = maxvalue;
nextra_atom++;
return nextra_atom-1;
}
/* ---------------------------------------------------------------------- */
void Min::modify_params(int narg, char **arg)
{
if (narg == 0) error->all("Illegal min_modify command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"dmax") == 0) {
if (iarg+2 > narg) error->all("Illegal min_modify command");
dmax = atof(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"line") == 0) {
if (iarg+2 > narg) error->all("Illegal min_modify command");
if (strcmp(arg[iarg+1],"backtrack") == 0) linestyle = 0;
else if (strcmp(arg[iarg+1],"quadratic") == 0) linestyle = 1;
else error->all("Illegal min_modify command");
iarg += 2;
} else error->all("Illegal min_modify command");
}
}
/* ----------------------------------------------------------------------
setup lists of computes for global and per-atom PE and pressure
------------------------------------------------------------------------- */
void Min::ev_setup()
{
delete [] elist_global;
delete [] elist_atom;
delete [] vlist_global;
delete [] vlist_atom;
elist_global = elist_atom = NULL;
vlist_global = vlist_atom = NULL;
nelist_global = nelist_atom = 0;
nvlist_global = nvlist_atom = 0;
for (int i = 0; i < modify->ncompute; i++) {
if (modify->compute[i]->peflag) nelist_global++;
if (modify->compute[i]->peatomflag) nelist_atom++;
if (modify->compute[i]->pressflag) nvlist_global++;
if (modify->compute[i]->pressatomflag) nvlist_atom++;
}
if (nelist_global) elist_global = new Compute*[nelist_global];
if (nelist_atom) elist_atom = new Compute*[nelist_atom];
if (nvlist_global) vlist_global = new Compute*[nvlist_global];
if (nvlist_atom) vlist_atom = new Compute*[nvlist_atom];
nelist_global = nelist_atom = 0;
nvlist_global = nvlist_atom = 0;
for (int i = 0; i < modify->ncompute; i++) {
if (modify->compute[i]->peflag)
elist_global[nelist_global++] = modify->compute[i];
if (modify->compute[i]->peatomflag)
elist_atom[nelist_atom++] = modify->compute[i];
if (modify->compute[i]->pressflag)
vlist_global[nvlist_global++] = modify->compute[i];
if (modify->compute[i]->pressatomflag)
vlist_atom[nvlist_atom++] = modify->compute[i];
}
}
/* ----------------------------------------------------------------------
set eflag,vflag for current iteration
invoke matchstep() on all timestep-dependent computes to clear their arrays
eflag/vflag based on computes that need info on this ntimestep
always set eflag_global = 1, since need energy every iteration
eflag = 0 = no energy computation
eflag = 1 = global energy only
eflag = 2 = per-atom energy only
eflag = 3 = both global and per-atom energy
vflag = 0 = no virial computation (pressure)
vflag = 1 = global virial with pair portion via sum of pairwise interactions
vflag = 2 = global virial with pair portion via F dot r including ghosts
vflag = 4 = per-atom virial only
vflag = 5 or 6 = both global and per-atom virial
------------------------------------------------------------------------- */
void Min::ev_set(bigint ntimestep)
{
int i,flag;
int eflag_global = 1;
for (i = 0; i < nelist_global; i++)
elist_global[i]->matchstep(ntimestep);
flag = 0;
int eflag_atom = 0;
for (i = 0; i < nelist_atom; i++)
if (elist_atom[i]->matchstep(ntimestep)) flag = 1;
if (flag) eflag_atom = 2;
if (eflag_global) update->eflag_global = update->ntimestep;
if (eflag_atom) update->eflag_atom = update->ntimestep;
eflag = eflag_global + eflag_atom;
flag = 0;
int vflag_global = 0;
for (i = 0; i < nvlist_global; i++)
if (vlist_global[i]->matchstep(ntimestep)) flag = 1;
if (flag) vflag_global = virial_style;
flag = 0;
int vflag_atom = 0;
for (i = 0; i < nvlist_atom; i++)
if (vlist_atom[i]->matchstep(ntimestep)) flag = 1;
if (flag) vflag_atom = 4;
if (vflag_global) update->vflag_global = update->ntimestep;
if (vflag_atom) update->vflag_atom = update->ntimestep;
vflag = vflag_global + vflag_atom;
}
/* ----------------------------------------------------------------------
compute and return ||force||_2^2
------------------------------------------------------------------------- */
double Min::fnorm_sqr()
{
int i,n;
double *fatom;
double local_norm2_sqr = 0.0;
for (i = 0; i < nvec; i++) local_norm2_sqr += fvec[i]*fvec[i];
if (nextra_atom) {
for (int m = 0; m < nextra_atom; m++) {
fatom = fextra_atom[m];
n = extra_nlen[m];
for (i = 0; i < n; i++)
local_norm2_sqr += fatom[i]*fatom[i];
}
}
double norm2_sqr = 0.0;
MPI_Allreduce(&local_norm2_sqr,&norm2_sqr,1,MPI_DOUBLE,MPI_SUM,world);
if (nextra_global)
for (i = 0; i < nextra_global; i++)
norm2_sqr += fextra[i]*fextra[i];
return norm2_sqr;
}
/* ----------------------------------------------------------------------
compute and return ||force||_inf
------------------------------------------------------------------------- */
double Min::fnorm_inf()
{
int i,n;
double *fatom;
double local_norm_inf = 0.0;
for (i = 0; i < nvec; i++)
local_norm_inf = MAX(fabs(fvec[i]),local_norm_inf);
if (nextra_atom) {
for (int m = 0; m < nextra_atom; m++) {
fatom = fextra_atom[m];
n = extra_nlen[m];
for (i = 0; i < n; i++)
local_norm_inf = MAX(fabs(fatom[i]),local_norm_inf);
}
}
double norm_inf = 0.0;
MPI_Allreduce(&local_norm_inf,&norm_inf,1,MPI_DOUBLE,MPI_MAX,world);
if (nextra_global)
for (i = 0; i < nextra_global; i++)
norm_inf = MAX(fabs(fextra[i]),norm_inf);
return norm_inf;
}
/* ----------------------------------------------------------------------
possible stop conditions
------------------------------------------------------------------------- */
char *Min::stopstrings(int n)
{
char *strings[] = {"max iterations",
"max force evaluations",
"energy tolerance",
"force tolerance",
"search direction is not downhill",
"linesearch alpha is zero",
"forces are zero",
"quadratic factors are zero",
"trust region too small",
"HFTN minimizer error"};
return strings[n];
}
diff --git a/src/min.h b/src/min.h
index db9590b1b..f367fa7b9 100644
--- a/src/min.h
+++ b/src/min.h
@@ -1,107 +1,108 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_MIN_H
#define LMP_MIN_H
#include "pointers.h"
namespace LAMMPS_NS {
class Min : protected Pointers {
public:
double einitial,efinal,eprevious;
double fnorm2_init,fnorminf_init,fnorm2_final,fnorminf_final;
double alpha_final;
int niter,neval;
int stop_condition;
char *stopstr;
int searchflag; // 0 if damped dynamics, 1 if sub-cycles on local search
Min(class LAMMPS *);
virtual ~Min();
void init();
void setup();
void setup_minimal(int);
void run(int);
void cleanup();
int request(class Pair *, int, double);
virtual bigint memory_usage() {return 0;}
void modify_params(int, char **);
double fnorm_sqr();
double fnorm_inf();
virtual void init_style() {}
virtual void setup_style() = 0;
virtual void reset_vectors() = 0;
virtual int iterate(int) = 0;
protected:
int eflag,vflag; // flags for energy/virial computation
int virial_style; // compute virial explicitly or implicitly
double dmax; // max dist to move any atom in one step
int linestyle; // 0 = backtrack, 1 = quadratic
int nelist_global,nelist_atom; // # of PE,virial computes to check
int nvlist_global,nvlist_atom;
class Compute **elist_global; // lists of PE,virial Computes
class Compute **elist_atom;
class Compute **vlist_global;
class Compute **vlist_atom;
+ int triclinic; // 0 if domain is orthog, 1 if triclinic
int pairflag;
int torqueflag,erforceflag;
- int triclinic; // 0 if domain is orthog, 1 if triclinic
+ int e_flag,rho_flag;
int narray; // # of arrays stored by fix_minimize
class FixMinimize *fix_minimize; // fix that stores auxiliary data
class Compute *pe_compute; // compute for potential energy
double ecurrent; // current potential energy
bigint ndoftotal; // total dof for entire problem
int nvec; // local atomic dof = length of xvec
double *xvec; // variables for atomic dof, as 1d vector
double *fvec; // force vector for atomic dof, as 1d vector
int nextra_global; // # of extra global dof due to fixes
double *fextra; // force vector for extra global dof
// xextra is stored by fix
int nextra_atom; // # of extra per-atom variables
double **xextra_atom; // ptr to the variable
double **fextra_atom; // ptr to the force on the variable
int *extra_peratom; // # of values in variable, e.g. 3 in x
int *extra_nlen; // total local length of variable, e.g 3*nlocal
double *extra_max; // max allowed change per iter for atom's var
class Pair **requestor; // Pair that stores/manipulates the variable
int neigh_every,neigh_delay,neigh_dist_check; // neighboring params
double energy_force(int);
void force_clear();
double compute_force_norm_sqr();
double compute_force_norm_inf();
void ev_setup();
void ev_set(bigint);
char *stopstrings(int);
};
}
#endif
diff --git a/src/respa.cpp b/src/respa.cpp
index 76fd20fc6..829fe1dfb 100644
--- a/src/respa.cpp
+++ b/src/respa.cpp
@@ -1,699 +1,713 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include "stdlib.h"
#include "string.h"
#include "respa.h"
#include "neighbor.h"
#include "atom.h"
#include "domain.h"
#include "comm.h"
#include "atom.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "kspace.h"
#include "output.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "fix_respa.h"
#include "timer.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
Respa::Respa(LAMMPS *lmp, int narg, char **arg) : Integrate(lmp, narg, arg)
{
if (narg < 1) error->all("Illegal run_style respa command");
nlevels = atoi(arg[0]);
if (nlevels < 1) error->all("Respa levels must be >= 1");
if (narg < nlevels) error->all("Illegal run_style respa command");
loop = new int[nlevels];
for (int iarg = 1; iarg < nlevels; iarg++) {
loop[iarg-1] = atoi(arg[iarg]);
if (loop[iarg-1] <= 0) error->all("Illegal run_style respa command");
}
loop[nlevels-1] = 1;
// set level at which each force is computed
// argument settings override defaults
level_bond = level_angle = level_dihedral = level_improper = -1;
level_pair = level_kspace = -1;
level_inner = level_middle = level_outer = -1;
int iarg = nlevels;
while (iarg < narg) {
if (strcmp(arg[iarg],"bond") == 0) {
if (iarg+2 > narg) error->all("Illegal run_style respa command");
level_bond = atoi(arg[iarg+1]) - 1;
iarg += 2;
} else if (strcmp(arg[iarg],"angle") == 0) {
if (iarg+2 > narg) error->all("Illegal run_style respa command");
level_angle = atoi(arg[iarg+1]) - 1;
iarg += 2;
} else if (strcmp(arg[iarg],"dihedral") == 0) {
if (iarg+2 > narg) error->all("Illegal run_style respa command");
level_dihedral = atoi(arg[iarg+1]) - 1;
iarg += 2;
} else if (strcmp(arg[iarg],"improper") == 0) {
if (iarg+2 > narg) error->all("Illegal run_style respa command");
level_improper = atoi(arg[iarg+1]) - 1;
iarg += 2;
} else if (strcmp(arg[iarg],"pair") == 0) {
if (iarg+2 > narg) error->all("Illegal run_style respa command");
level_pair = atoi(arg[iarg+1]) - 1;
iarg += 2;
} else if (strcmp(arg[iarg],"inner") == 0) {
if (iarg+4 > narg) error->all("Illegal run_style respa command");
level_inner = atoi(arg[iarg+1]) - 1;
cutoff[0] = atof(arg[iarg+2]);
cutoff[1] = atof(arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"middle") == 0) {
if (iarg+4 > narg) error->all("Illegal run_style respa command");
level_middle = atoi(arg[iarg+1]) - 1;
cutoff[2] = atof(arg[iarg+2]);
cutoff[3] = atof(arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"outer") == 0) {
if (iarg+2 > narg) error->all("Illegal run_style respa command");
level_outer = atoi(arg[iarg+1]) - 1;
iarg += 2;
} else if (strcmp(arg[iarg],"kspace") == 0) {
if (iarg+2 > narg) error->all("Illegal run_style respa command");
level_kspace = atoi(arg[iarg+1]) - 1;
iarg += 2;
} else error->all("Illegal run_style respa command");
}
// cannot specify both pair and inner/middle/outer
if (level_pair >= 0 &&
(level_inner >= 0 || level_middle >= 0 || level_outer >= 0))
error->all("Cannot set both respa pair and inner/middle/outer");
// if either inner and outer is specified, then both must be
if ((level_inner >= 0 && level_outer == -1) ||
(level_outer >= 0 && level_inner == -1))
error->all("Must set both respa inner and outer");
// middle cannot be set without inner/outer
if (level_middle >= 0 && level_inner == -1)
error->all("Cannot set respa middle without inner/outer");
// set defaults if user did not specify level
// bond to innermost level
// angle same as bond, dihedral same as angle, improper same as dihedral
// pair to outermost level if no inner/middle/outer
// inner/middle/outer have no defaults
// kspace same as pair or outer
if (level_bond == -1) level_bond = 0;
if (level_angle == -1) level_angle = level_bond;
if (level_dihedral == -1) level_dihedral = level_angle;
if (level_improper == -1) level_improper = level_dihedral;
if (level_pair == -1 && level_inner == -1) level_pair = nlevels-1;
if (level_kspace == -1 && level_pair >= 0) level_kspace = level_pair;
if (level_kspace == -1 && level_pair == -1) level_kspace = level_outer;
// print respa levels
if (comm->me == 0) {
if (screen) {
fprintf(screen,"Respa levels:\n");
for (int i = 0; i < nlevels; i++) {
fprintf(screen," %d =",i);
if (level_bond == i) fprintf(screen," bond");
if (level_angle == i) fprintf(screen," angle");
if (level_dihedral == i) fprintf(screen," dihedral");
if (level_improper == i) fprintf(screen," improper");
if (level_pair == i) fprintf(screen," pair");
if (level_inner == i) fprintf(screen," pair-inner");
if (level_middle == i) fprintf(screen," pair-middle");
if (level_outer == i) fprintf(screen," pair-outer");
if (level_kspace == i) fprintf(screen," kspace");
fprintf(screen,"\n");
}
}
if (logfile) {
fprintf(logfile,"Respa levels:\n");
for (int i = 0; i < nlevels; i++) {
fprintf(logfile," %d =",i);
if (level_bond == i) fprintf(logfile," bond");
if (level_angle == i) fprintf(logfile," angle");
if (level_dihedral == i) fprintf(logfile," dihedral");
if (level_improper == i) fprintf(logfile," improper");
if (level_pair == i) fprintf(logfile," pair");
if (level_inner == i) fprintf(logfile," pair-inner");
if (level_middle == i) fprintf(logfile," pair-middle");
if (level_outer == i) fprintf(logfile," pair-outer");
if (level_kspace == i) fprintf(logfile," kspace");
fprintf(logfile,"\n");
}
}
}
// check that levels are in correct order
if (level_angle < level_bond || level_dihedral < level_angle ||
level_improper < level_dihedral)
error->all("Invalid order of forces within respa levels");
if (level_pair >= 0) {
if (level_pair < level_improper || level_kspace < level_pair)
error->all("Invalid order of forces within respa levels");
}
if (level_pair == -1 && level_middle == -1) {
if (level_inner < level_improper || level_outer < level_inner ||
level_kspace != level_outer)
error->all("Invalid order of forces within respa levels");
}
if (level_pair == -1 && level_middle >= 0) {
if (level_inner < level_improper || level_middle < level_inner ||
level_outer < level_inner || level_kspace != level_outer)
error->all("Invalid order of forces within respa levels");
}
// warn if any levels are devoid of forces
int flag = 0;
for (int i = 0; i < nlevels; i++)
if (level_bond != i && level_angle != i && level_dihedral != i &&
level_improper != i && level_pair != i && level_inner != i &&
level_middle != i && level_outer != i && level_kspace != i) flag = 1;
if (flag && comm->me == 0)
error->warning("One or more respa levels compute no forces");
// check cutoff consistency if inner/middle/outer are enabled
if (level_inner >= 0 && cutoff[1] < cutoff[0])
error->all("Respa inner cutoffs are invalid");
if (level_middle >= 0 && (cutoff[3] < cutoff[2] || cutoff[2] < cutoff[1]))
error->all("Respa middle cutoffs are invalid");
// set outer pair of cutoffs to inner pair if middle is not enabled
if (level_inner >= 0 && level_middle < 0) {
cutoff[2] = cutoff[0];
cutoff[3] = cutoff[1];
}
// allocate other needed arrays
newton = new int[nlevels];
step = new double[nlevels];
}
/* ---------------------------------------------------------------------- */
Respa::~Respa()
{
delete [] loop;
delete [] newton;
delete [] step;
}
/* ----------------------------------------------------------------------
initialization before run
------------------------------------------------------------------------- */
void Respa::init()
{
// warn if no fixes
if (modify->nfix == 0 && comm->me == 0)
error->warning("No fixes defined, atoms won't move");
// create fix needed for storing atom-based respa level forces
// will delete it at end of run
char **fixarg = new char*[4];
fixarg[0] = (char *) "RESPA";
fixarg[1] = (char *) "all";
fixarg[2] = (char *) "RESPA";
fixarg[3] = new char[8];
sprintf(fixarg[3],"%d",nlevels);
modify->add_fix(4,fixarg);
delete [] fixarg[3];
delete [] fixarg;
fix_respa = (FixRespa *) modify->fix[modify->nfix-1];
// insure respa inner/middle/outer is using Pair class that supports it
if (level_inner >= 0)
if (force->pair && force->pair->respa_enable == 0)
error->all("Pair style does not support rRESPA inner/middle/outer");
// virial_style = 1 (explicit) since never computed implicitly like Verlet
virial_style = 1;
// setup lists of computes for global and per-atom PE and pressure
ev_setup();
// set flags for what arrays to clear in force_clear()
- // need to clear torques,erforce if arrays exists
+ // need to clear additionals arrays if they exist
torqueflag = 0;
if (atom->torque_flag) torqueflag = 1;
erforceflag = 0;
if (atom->erforce_flag) erforceflag = 1;
+ e_flag = 0;
+ if (atom->e_flag) e_flag = 1;
+ rho_flag = 0;
+ if (atom->rho_flag) rho_flag = 1;
// step[] = timestep for each level
step[nlevels-1] = update->dt;
for (int ilevel = nlevels-2; ilevel >= 0; ilevel--)
step[ilevel] = step[ilevel+1]/loop[ilevel];
// set newton flag for each level
for (int ilevel = 0; ilevel < nlevels; ilevel++) {
newton[ilevel] = 0;
if (force->newton_bond) {
if (level_bond == ilevel || level_angle == ilevel ||
level_dihedral == ilevel || level_improper == ilevel)
newton[ilevel] = 1;
}
if (force->newton_pair) {
if (level_pair == ilevel || level_inner == ilevel ||
level_middle == ilevel || level_outer == ilevel)
newton[ilevel] = 1;
}
}
// orthogonal vs triclinic simulation box
triclinic = domain->triclinic;
}
/* ----------------------------------------------------------------------
setup before run
------------------------------------------------------------------------- */
void Respa::setup()
{
if (comm->me == 0 && screen) fprintf(screen,"Setting up run ...\n");
update->setupflag = 1;
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
atom->setup();
modify->setup_pre_exchange();
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
if (atom->sortfreq > 0) atom->sort();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
neighbor->build();
neighbor->ncalls = 0;
// compute all forces
ev_set(update->ntimestep);
for (int ilevel = 0; ilevel < nlevels; ilevel++) {
force_clear(newton[ilevel]);
modify->setup_pre_force_respa(vflag,ilevel);
if (level_bond == ilevel && force->bond)
force->bond->compute(eflag,vflag);
if (level_angle == ilevel && force->angle)
force->angle->compute(eflag,vflag);
if (level_dihedral == ilevel && force->dihedral)
force->dihedral->compute(eflag,vflag);
if (level_improper == ilevel && force->improper)
force->improper->compute(eflag,vflag);
if (level_pair == ilevel && force->pair)
force->pair->compute(eflag,vflag);
if (level_inner == ilevel && force->pair)
force->pair->compute_inner();
if (level_middle == ilevel && force->pair)
force->pair->compute_middle();
if (level_outer == ilevel && force->pair)
force->pair->compute_outer(eflag,vflag);
if (level_kspace == ilevel && force->kspace) {
force->kspace->setup();
force->kspace->compute(eflag,vflag);
}
if (newton[ilevel]) comm->reverse_comm();
copy_f_flevel(ilevel);
}
modify->setup(vflag);
sum_flevel_f();
output->setup(1);
update->setupflag = 0;
}
/* ----------------------------------------------------------------------
setup without output
flag = 0 = just force calculation
flag = 1 = reneighbor and force calculation
------------------------------------------------------------------------- */
void Respa::setup_minimal(int flag)
{
update->setupflag = 1;
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
if (flag) {
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
neighbor->build();
neighbor->ncalls = 0;
}
// compute all forces
ev_set(update->ntimestep);
for (int ilevel = 0; ilevel < nlevels; ilevel++) {
force_clear(newton[ilevel]);
modify->setup_pre_force_respa(vflag,ilevel);
if (level_bond == ilevel && force->bond)
force->bond->compute(eflag,vflag);
if (level_angle == ilevel && force->angle)
force->angle->compute(eflag,vflag);
if (level_dihedral == ilevel && force->dihedral)
force->dihedral->compute(eflag,vflag);
if (level_improper == ilevel && force->improper)
force->improper->compute(eflag,vflag);
if (level_pair == ilevel && force->pair)
force->pair->compute(eflag,vflag);
if (level_inner == ilevel && force->pair)
force->pair->compute_inner();
if (level_middle == ilevel && force->pair)
force->pair->compute_middle();
if (level_outer == ilevel && force->pair)
force->pair->compute_outer(eflag,vflag);
if (level_kspace == ilevel && force->kspace) {
force->kspace->setup();
force->kspace->compute(eflag,vflag);
}
if (newton[ilevel]) comm->reverse_comm();
copy_f_flevel(ilevel);
}
modify->setup(vflag);
sum_flevel_f();
update->setupflag = 0;
}
/* ----------------------------------------------------------------------
run for N steps
------------------------------------------------------------------------- */
void Respa::run(int n)
{
bigint ntimestep;
for (int i = 0; i < n; i++) {
ntimestep = ++update->ntimestep;
ev_set(ntimestep);
recurse(nlevels-1);
if (modify->n_end_of_step) {
timer->stamp();
modify->end_of_step();
timer->stamp(Timer::MODIFY);
}
if (ntimestep == output->next) {
timer->stamp();
sum_flevel_f();
output->write(update->ntimestep);
timer->stamp(Timer::OUTPUT);
}
}
}
/* ----------------------------------------------------------------------
delete rRESPA fix at end of run, so its atom arrays won't persist
------------------------------------------------------------------------- */
void Respa::cleanup()
{
modify->post_run();
modify->delete_fix("RESPA");
}
/* ---------------------------------------------------------------------- */
void Respa::reset_dt()
{
step[nlevels-1] = update->dt;
for (int ilevel = nlevels-2; ilevel >= 0; ilevel--)
step[ilevel] = step[ilevel+1]/loop[ilevel];
}
/* ---------------------------------------------------------------------- */
void Respa::recurse(int ilevel)
{
copy_flevel_f(ilevel);
for (int iloop = 0; iloop < loop[ilevel]; iloop++) {
timer->stamp();
modify->initial_integrate_respa(vflag,ilevel,iloop);
if (modify->n_post_integrate_respa)
modify->post_integrate_respa(ilevel,iloop);
timer->stamp(Timer::MODIFY);
if (ilevel) recurse(ilevel-1);
// at outermost level, check on rebuilding neighbor list
// at innermost level, communicate
// at middle levels, do nothing
if (ilevel == nlevels-1) {
int nflag = neighbor->decide();
if (nflag) {
if (modify->n_pre_exchange) {
timer->stamp();
modify->pre_exchange();
timer->stamp(Timer::MODIFY);
}
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
if (domain->box_change) {
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
}
timer->stamp();
comm->exchange();
if (atom->sortfreq > 0 &&
update->ntimestep >= atom->nextsort) atom->sort();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
timer->stamp(Timer::COMM);
if (modify->n_pre_neighbor) {
modify->pre_neighbor();
timer->stamp(Timer::MODIFY);
}
neighbor->build();
timer->stamp(Timer::NEIGHBOR);
}
} else if (ilevel == 0) {
timer->stamp();
comm->forward_comm();
timer->stamp(Timer::COMM);
}
force_clear(newton[ilevel]);
if (modify->n_pre_force_respa) {
timer->stamp();
modify->pre_force_respa(vflag,ilevel,iloop);
timer->stamp(Timer::MODIFY);
}
timer->stamp();
if (level_bond == ilevel && force->bond) {
force->bond->compute(eflag,vflag);
timer->stamp(Timer::BOND);
}
if (level_angle == ilevel && force->angle) {
force->angle->compute(eflag,vflag);
timer->stamp(Timer::BOND);
}
if (level_dihedral == ilevel && force->dihedral) {
force->dihedral->compute(eflag,vflag);
timer->stamp(Timer::BOND);
}
if (level_improper == ilevel && force->improper) {
force->improper->compute(eflag,vflag);
timer->stamp(Timer::BOND);
}
if (level_pair == ilevel && force->pair) {
force->pair->compute(eflag,vflag);
timer->stamp(Timer::PAIR);
}
if (level_inner == ilevel && force->pair) {
force->pair->compute_inner();
timer->stamp(Timer::PAIR);
}
if (level_middle == ilevel && force->pair) {
force->pair->compute_middle();
timer->stamp(Timer::PAIR);
}
if (level_outer == ilevel && force->pair) {
force->pair->compute_outer(eflag,vflag);
timer->stamp(Timer::PAIR);
}
if (level_kspace == ilevel && force->kspace) {
force->kspace->compute(eflag,vflag);
timer->stamp(Timer::KSPACE);
}
if (newton[ilevel]) {
comm->reverse_comm();
timer->stamp(Timer::COMM);
}
timer->stamp();
if (modify->n_post_force_respa)
modify->post_force_respa(vflag,ilevel,iloop);
modify->final_integrate_respa(ilevel,iloop);
timer->stamp(Timer::MODIFY);
}
copy_f_flevel(ilevel);
}
/* ----------------------------------------------------------------------
clear force on own & ghost atoms
------------------------------------------------------------------------- */
void Respa::force_clear(int newtonflag)
{
int i;
// clear global force array
// nall includes ghosts only if newton flag is set
int nall;
if (newtonflag) nall = atom->nlocal + atom->nghost;
else nall = atom->nlocal;
int ntot = nall * comm->nthreads;
double **f = atom->f;
for (i = 0; i < ntot; i++) {
f[i][0] = 0.0;
f[i][1] = 0.0;
f[i][2] = 0.0;
}
if (torqueflag) {
double **torque = atom->torque;
for (i = 0; i < nall; i++) {
torque[i][0] = 0.0;
torque[i][1] = 0.0;
torque[i][2] = 0.0;
}
}
if (erforceflag) {
double *erforce = atom->erforce;
for (i = 0; i < nall; i++) erforce[i] = 0.0;
}
+
+ if (e_flag) {
+ double *de = atom->de;
+ for (i = 0; i < nall; i++) de[i] = 0.0;
+ }
+
+ if (rho_flag) {
+ double *drho = atom->drho;
+ for (i = 0; i < nall; i++) drho[i] = 0.0;
+ }
}
/* ----------------------------------------------------------------------
copy force components from atom->f to FixRespa->f_level
------------------------------------------------------------------------- */
void Respa::copy_f_flevel(int ilevel)
{
double ***f_level = fix_respa->f_level;
double **f = atom->f;
int n = atom->nlocal;
for (int i = 0; i < n; i++) {
f_level[i][ilevel][0] = f[i][0];
f_level[i][ilevel][1] = f[i][1];
f_level[i][ilevel][2] = f[i][2];
}
}
/* ----------------------------------------------------------------------
copy force components from FixRespa->f_level to atom->f
------------------------------------------------------------------------- */
void Respa::copy_flevel_f(int ilevel)
{
double ***f_level = fix_respa->f_level;
double **f = atom->f;
int n = atom->nlocal;
for (int i = 0; i < n; i++) {
f[i][0] = f_level[i][ilevel][0];
f[i][1] = f_level[i][ilevel][1];
f[i][2] = f_level[i][ilevel][2];
}
}
/* ----------------------------------------------------------------------
sum all force components from FixRespa->f_level to create full atom->f
------------------------------------------------------------------------- */
void Respa::sum_flevel_f()
{
copy_flevel_f(0);
double ***f_level = fix_respa->f_level;
double **f = atom->f;
int n = atom->nlocal;
for (int ilevel = 1; ilevel < nlevels; ilevel++) {
for (int i = 0; i < n; i++) {
f[i][0] += f_level[i][ilevel][0];
f[i][1] += f_level[i][ilevel][1];
f[i][2] += f_level[i][ilevel][2];
}
}
}
diff --git a/src/respa.h b/src/respa.h
index e0981c764..409184c73 100644
--- a/src/respa.h
+++ b/src/respa.h
@@ -1,70 +1,70 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef INTEGRATE_CLASS
IntegrateStyle(respa,Respa)
#else
#ifndef LMP_RESPA_H
#define LMP_RESPA_H
#include "integrate.h"
namespace LAMMPS_NS {
class Respa : public Integrate {
public:
// public so Fixes, Pairs, Neighbor can see them
int nlevels; // number of rRESPA levels
// 0 = innermost level, nlevels-1 = outermost level
double *step; // timestep at each level
int *loop; // sub-cycling factor at each level
double cutoff[4]; // cutoff[0] and cutoff[1] = between inner and middle
// cutoff[2] and cutoff[3] = between middle and outer
// if no middle then 0,1 = 2,3
int level_bond,level_angle,level_dihedral; // level to compute forces at
int level_improper,level_pair,level_kspace;
int level_inner,level_middle,level_outer;
Respa(class LAMMPS *, int, char **);
~Respa();
void init();
void setup();
void setup_minimal(int);
void run(int);
void cleanup();
void reset_dt();
void copy_f_flevel(int);
void copy_flevel_f(int);
private:
int triclinic; // 0 if domain is orthog, 1 if triclinic
- int torqueflag; // zero out arrays every step
- int erforceflag;
+ int torqueflag,erforceflag;
+ int e_flag,rho_flag;
int *newton; // newton flag at each level
class FixRespa *fix_respa; // Fix to store the force level array
void recurse(int);
void force_clear(int);
void sum_flevel_f();
};
}
#endif
#endif
diff --git a/src/set.cpp b/src/set.cpp
index 941a57db7..a541fcca9 100644
--- a/src/set.cpp
+++ b/src/set.cpp
@@ -1,659 +1,684 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "set.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_ellipsoid.h"
#include "domain.h"
#include "region.h"
#include "group.h"
#include "comm.h"
#include "neighbor.h"
#include "force.h"
#include "pair.h"
#include "random_park.h"
#include "math_extra.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{ATOM_SELECT,MOL_SELECT,TYPE_SELECT,GROUP_SELECT,REGION_SELECT};
enum{TYPE,TYPE_FRACTION,MOLECULE,X,Y,Z,CHARGE,MASS,SHAPE,
DIPOLE,DIPOLE_RANDOM,QUAT,QUAT_RANDOM,
- DIAMETER,DENSITY,VOLUME,IMAGE,BOND,ANGLE,DIHEDRAL,IMPROPER};
+ DIAMETER,DENSITY,VOLUME,IMAGE,BOND,ANGLE,DIHEDRAL,IMPROPER,
+ MESO_E,MESO_CV,MESO_RHO};
#define BIG INT_MAX
/* ---------------------------------------------------------------------- */
Set::Set(LAMMPS *lmp) : Pointers(lmp)
{
PI = 4.0*atan(1.0);
}
/* ---------------------------------------------------------------------- */
void Set::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all("Set command before simulation box is defined");
if (atom->natoms == 0)
error->all("Set command with no atoms existing");
if (narg < 3) error->all("Illegal set command");
// style and ID info
if (strcmp(arg[0],"atom") == 0) style = ATOM_SELECT;
else if (strcmp(arg[0],"mol") == 0) style = MOL_SELECT;
else if (strcmp(arg[0],"type") == 0) style = TYPE_SELECT;
else if (strcmp(arg[0],"group") == 0) style = GROUP_SELECT;
else if (strcmp(arg[0],"region") == 0) style = REGION_SELECT;
else error->all("Illegal set command");
int n = strlen(arg[1]) + 1;
id = new char[n];
strcpy(id,arg[1]);
select = NULL;
// loop over keyword/value pairs
// call appropriate routine to reset attributes
if (comm->me == 0 && screen) fprintf(screen,"Setting atom values ...\n");
int allcount,origarg;
int iarg = 2;
while (iarg < narg) {
count = 0;
origarg = iarg;
if (strcmp(arg[iarg],"type") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (ivalue <= 0 || ivalue > atom->ntypes)
error->all("Invalid value in set command");
set(TYPE);
iarg += 2;
} else if (strcmp(arg[iarg],"type/fraction") == 0) {
if (iarg+4 > narg) error->all("Illegal set command");
newtype = atoi(arg[iarg+1]);
fraction = atof(arg[iarg+2]);
ivalue = atoi(arg[iarg+3]);
if (newtype <= 0 || newtype > atom->ntypes)
error->all("Invalid value in set command");
if (fraction < 0.0 || fraction > 1.0)
error->all("Invalid value in set command");
if (ivalue <= 0) error->all("Invalid random number seed in set command");
setrandom(TYPE_FRACTION);
iarg += 4;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (!atom->molecule_flag)
error->all("Cannot set this attribute for this atom style");
set(MOLECULE);
iarg += 2;
} else if (strcmp(arg[iarg],"x") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
dvalue = atof(arg[iarg+1]);
set(X);
iarg += 2;
} else if (strcmp(arg[iarg],"y") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
dvalue = atof(arg[iarg+1]);
set(Y);
iarg += 2;
} else if (strcmp(arg[iarg],"z") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
dvalue = atof(arg[iarg+1]);
set(Z);
iarg += 2;
} else if (strcmp(arg[iarg],"charge") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->q_flag)
error->all("Cannot set this attribute for this atom style");
set(CHARGE);
iarg += 2;
} else if (strcmp(arg[iarg],"mass") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->rmass_flag)
error->all("Cannot set this attribute for this atom style");
if (dvalue <= 0.0) error->all("Invalid mass in set command");
set(MASS);
iarg += 2;
} else if (strcmp(arg[iarg],"shape") == 0) {
if (iarg+4 > narg) error->all("Illegal set command");
xvalue = atof(arg[iarg+1]);
yvalue = atof(arg[iarg+2]);
zvalue = atof(arg[iarg+3]);
if (!atom->ellipsoid_flag)
error->all("Cannot set this attribute for this atom style");
if (xvalue < 0.0 || yvalue < 0.0 || zvalue < 0.0)
error->all("Invalid shape in set command");
if (xvalue > 0.0 || yvalue > 0.0 || zvalue > 0.0) {
if (xvalue == 0.0 || yvalue == 0.0 || zvalue == 0.0)
error->one("Invalid shape in set command");
}
set(SHAPE);
iarg += 4;
} else if (strcmp(arg[iarg],"dipole") == 0) {
if (iarg+4 > narg) error->all("Illegal set command");
xvalue = atof(arg[iarg+1]);
yvalue = atof(arg[iarg+2]);
zvalue = atof(arg[iarg+3]);
if (!atom->mu_flag)
error->all("Cannot set this attribute for this atom style");
set(DIPOLE);
iarg += 4;
} else if (strcmp(arg[iarg],"dipole/random") == 0) {
if (iarg+3 > narg) error->all("Illegal set command");
ivalue = atoi(arg[iarg+1]);
dvalue = atof(arg[iarg+2]);
if (!atom->mu_flag)
error->all("Cannot set this attribute for this atom style");
if (ivalue <= 0) error->all("Invalid random number seed in set command");
if (dvalue <= 0.0) error->all("Invalid dipole length in set command");
setrandom(DIPOLE_RANDOM);
iarg += 3;
} else if (strcmp(arg[iarg],"quat") == 0) {
if (iarg+5 > narg) error->all("Illegal set command");
xvalue = atof(arg[iarg+1]);
yvalue = atof(arg[iarg+2]);
zvalue = atof(arg[iarg+3]);
wvalue = atof(arg[iarg+4]);
if (!atom->ellipsoid_flag)
error->all("Cannot set this attribute for this atom style");
set(QUAT);
iarg += 5;
} else if (strcmp(arg[iarg],"quat/random") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (!atom->ellipsoid_flag)
error->all("Cannot set this attribute for this atom style");
if (ivalue <= 0) error->all("Invalid random number seed in set command");
setrandom(QUAT_RANDOM);
iarg += 2;
} else if (strcmp(arg[iarg],"diameter") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->radius_flag)
error->all("Cannot set this attribute for this atom style");
if (dvalue < 0.0) error->all("Invalid diameter in set command");
set(DIAMETER);
iarg += 2;
} else if (strcmp(arg[iarg],"density") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->rmass_flag)
error->all("Cannot set this attribute for this atom style");
set(DENSITY);
iarg += 2;
} else if (strcmp(arg[iarg],"volume") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->vfrac_flag)
error->all("Cannot set this attribute for this atom style");
set(VOLUME);
iarg += 2;
} else if (strcmp(arg[iarg],"image") == 0) {
if (iarg+4 > narg) error->all("Illegal set command");
ximageflag = yimageflag = zimageflag = 0;
if (strcmp(arg[iarg+1],"NULL") != 0) {
ximageflag = 1;
ximage = atoi(arg[iarg+1]);
}
if (strcmp(arg[iarg+2],"NULL") != 0) {
yimageflag = 1;
yimage = atoi(arg[iarg+2]);
}
if (strcmp(arg[iarg+3],"NULL") != 0) {
zimageflag = 1;
zimage = atoi(arg[iarg+3]);
}
if (ximageflag && ximage && !domain->xperiodic)
error->all("Cannot set non-zero image flag for non-periodic dimension");
if (yimageflag && yimage && !domain->yperiodic)
error->all("Cannot set non-zero image flag for non-periodic dimension");
if (zimageflag && zimage && !domain->zperiodic)
error->all("Cannot set non-zero image flag for non-periodic dimension");
set(IMAGE);
iarg += 4;
} else if (strcmp(arg[iarg],"bond") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (atom->avec->bonds_allow == 0)
error->all("Cannot set this attribute for this atom style");
if (ivalue <= 0 || ivalue > atom->nbondtypes)
error->all("Invalid value in set command");
topology(BOND);
iarg += 2;
} else if (strcmp(arg[iarg],"angle") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (atom->avec->angles_allow == 0)
error->all("Cannot set this attribute for this atom style");
if (ivalue <= 0 || ivalue > atom->nangletypes)
error->all("Invalid value in set command");
topology(ANGLE);
iarg += 2;
} else if (strcmp(arg[iarg],"dihedral") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (atom->avec->dihedrals_allow == 0)
error->all("Cannot set this attribute for this atom style");
if (ivalue <= 0 || ivalue > atom->ndihedraltypes)
error->all("Invalid value in set command");
topology(DIHEDRAL);
iarg += 2;
} else if (strcmp(arg[iarg],"improper") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (atom->avec->impropers_allow == 0)
error->all("Cannot set this attribute for this atom style");
if (ivalue <= 0 || ivalue > atom->nimpropertypes)
error->all("Invalid value in set command");
topology(IMPROPER);
iarg += 2;
+ } else if (strcmp(arg[iarg],"meso_e") == 0) {
+ if (iarg+2 > narg) error->all("Illegal set command");
+ dvalue = atof(arg[iarg+1]);
+ if (!atom->e_flag)
+ error->all("Cannot set this attribute for this atom style");
+ set(MESO_E);
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"meso_cv") == 0) {
+ if (iarg+2 > narg) error->all("Illegal set command");
+ dvalue = atof(arg[iarg+1]);
+ if (!atom->cv_flag)
+ error->all("Cannot set this attribute for this atom style");
+ set(MESO_CV);
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"meso_rho") == 0) {
+ if (iarg+2 > narg) error->all("Illegal set command");
+ dvalue = atof(arg[iarg+1]);
+ if (!atom->rho_flag)
+ error->all("Cannot set meso_rho for this atom style");
+ set(MESO_RHO);
+ iarg += 2;
} else error->all("Illegal set command");
// statistics
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
if (comm->me == 0) {
if (screen) fprintf(screen," %d settings made for %s\n",
allcount,arg[origarg]);
if (logfile) fprintf(logfile," %d settings made for %s\n",
allcount,arg[origarg]);
}
}
// free local memory
delete [] id;
delete [] select;
}
/* ----------------------------------------------------------------------
select atoms according to ATOM, MOLECULE, TYPE, GROUP, REGION style
n = nlocal or nlocal+nghost depending on keyword
------------------------------------------------------------------------- */
void Set::selection(int n)
{
delete [] select;
select = new int[n];
int nlo,nhi;
if (style == ATOM_SELECT) {
if (atom->tag_enable == 0)
error->all("Cannot use set atom with no atom IDs defined");
force->bounds(id,BIG,nlo,nhi);
int *tag = atom->tag;
for (int i = 0; i < n; i++)
if (tag[i] >= nlo && tag[i] <= nhi) select[i] = 1;
else select[i] = 0;
} else if (style == MOL_SELECT) {
if (atom->molecule_flag == 0)
error->all("Cannot use set mol with no molecule IDs defined");
if (strcmp(id,"0") == 0) nlo = nhi = 0;
else force->bounds(id,BIG,nlo,nhi);
int *molecule = atom->molecule;
for (int i = 0; i < n; i++)
if (molecule[i] >= nlo && molecule[i] <= nhi) select[i] = 1;
else select[i] = 0;
} else if (style == TYPE_SELECT) {
force->bounds(id,atom->ntypes,nlo,nhi);
int *type = atom->type;
for (int i = 0; i < n; i++)
if (type[i] >= nlo && type[i] <= nhi) select[i] = 1;
else select[i] = 0;
} else if (style == GROUP_SELECT) {
int igroup = group->find(id);
if (igroup == -1) error->all("Could not find set group ID");
int groupbit = group->bitmask[igroup];
int *mask = atom->mask;
for (int i = 0; i < n; i++)
if (mask[i] & groupbit) select[i] = 1;
else select[i] = 0;
} else if (style == REGION_SELECT) {
int iregion = domain->find_region(id);
if (iregion == -1) error->all("Set region ID does not exist");
double **x = atom->x;
for (int i = 0; i < n; i++)
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
select[i] = 1;
else select[i] = 0;
}
}
/* ----------------------------------------------------------------------
set an owned atom property directly
------------------------------------------------------------------------- */
void Set::set(int keyword)
{
AtomVecEllipsoid *avec_ellipsoid =
(AtomVecEllipsoid *) atom->style_match("ellipsoid");
selection(atom->nlocal);
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (!select[i]) continue;
if (keyword == TYPE) atom->type[i] = ivalue;
else if (keyword == MOLECULE) atom->molecule[i] = ivalue;
else if (keyword == X) atom->x[i][0] = dvalue;
else if (keyword == Y) atom->x[i][1] = dvalue;
else if (keyword == Z) atom->x[i][2] = dvalue;
else if (keyword == CHARGE) atom->q[i] = dvalue;
else if (keyword == MASS) atom->rmass[i] = dvalue;
else if (keyword == DIAMETER) atom->radius[i] = 0.5 * dvalue;
else if (keyword == VOLUME) atom->vfrac[i] = dvalue;
-
+ else if (keyword == MESO_E) atom->e[i] = dvalue;
+ else if (keyword == MESO_CV) atom->cv[i] = dvalue;
+ else if (keyword == MESO_RHO) atom->rho[i] = dvalue;
+
// set shape
else if (keyword == SHAPE)
avec_ellipsoid->set_shape(i,0.5*xvalue,0.5*yvalue,0.5*zvalue);
// set rmass via density
// if radius > 0.0, treat as sphere
// if shape > 0.0, treat as ellipsoid
// else set rmass to density directly
else if (keyword == DENSITY) {
if (atom->radius_flag && atom->radius[i] > 0.0)
atom->rmass[i] = 4.0*PI/3.0 *
atom->radius[i]*atom->radius[i]*atom->radius[i] * dvalue;
else if (atom->ellipsoid_flag && atom->ellipsoid[i] >= 0) {
double *shape = avec_ellipsoid->bonus[atom->ellipsoid[i]].shape;
atom->rmass[i] = 4.0*PI/3.0 * shape[0]*shape[1]*shape[2] * dvalue;
} else atom->rmass[i] = dvalue;
// reset any or all of 3 image flags
} else if (keyword == IMAGE) {
int xbox = (atom->image[i] & 1023) - 512;
int ybox = (atom->image[i] >> 10 & 1023) - 512;
int zbox = (atom->image[i] >> 20) - 512;
if (ximageflag) xbox = ximage;
if (yimageflag) ybox = yimage;
if (zimageflag) zbox = zimage;
atom->image[i] = ((zbox + 512 & 1023) << 20) |
((ybox + 512 & 1023) << 10) | (xbox + 512 & 1023);
// set dipole moment
} else if (keyword == DIPOLE) {
double **mu = atom->mu;
mu[i][0] = xvalue;
mu[i][1] = yvalue;
mu[i][2] = zvalue;
mu[i][3] = sqrt(mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] +
mu[i][2]*mu[i][2]);
// set quaternion orientation
} else if (keyword == QUAT) {
if (atom->ellipsoid[i] < 0)
error->one("Cannot set quaternion for atom that is not an ellipsoid");
double *quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
double theta2 = 0.5 * PI * wvalue/180.0;
double sintheta2 = sin(theta2);
quat[0] = cos(theta2);
quat[1] = xvalue * sintheta2;
quat[2] = yvalue * sintheta2;
quat[3] = zvalue * sintheta2;
MathExtra::qnormalize(quat);
}
count++;
}
}
/* ----------------------------------------------------------------------
set an owned atom property randomly
set seed based on atom tag
make atom result independent of what proc owns it
------------------------------------------------------------------------- */
void Set::setrandom(int keyword)
{
int i;
selection(atom->nlocal);
RanPark *random = new RanPark(lmp,1);
double **x = atom->x;
int seed = ivalue;
// set fraction of atom types to newtype
if (keyword == TYPE_FRACTION) {
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (select[i]) {
random->reset(seed,x[i]);
if (random->uniform() > fraction) continue;
atom->type[i] = newtype;
count++;
}
// set dipole moments to random orientations in 3d or 2d
// dipole length is determined by dipole type array
} else if (keyword == DIPOLE_RANDOM) {
double **mu = atom->mu;
int nlocal = atom->nlocal;
double msq,scale;
if (domain->dimension == 3) {
for (i = 0; i < nlocal; i++)
if (select[i]) {
random->reset(seed,x[i]);
mu[i][0] = random->uniform() - 0.5;
mu[i][1] = random->uniform() - 0.5;
mu[i][2] = random->uniform() - 0.5;
msq = mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2];
scale = dvalue/sqrt(msq);
mu[i][0] *= scale;
mu[i][1] *= scale;
mu[i][2] *= scale;
mu[i][3] = dvalue;
count++;
}
} else {
for (i = 0; i < nlocal; i++)
if (select[i]) {
random->reset(seed,x[i]);
mu[i][0] = random->uniform() - 0.5;
mu[i][1] = random->uniform() - 0.5;
mu[i][2] = 0.0;
msq = mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1];
scale = dvalue/sqrt(msq);
mu[i][0] *= scale;
mu[i][1] *= scale;
mu[i][3] = dvalue;
count++;
}
}
// set quaternions to random orientations in 3d or 2d
// no need to normalize quats since creations algorithms already do
} else if (keyword == QUAT_RANDOM) {
AtomVecEllipsoid *avec_ellipsoid =
(AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec_ellipsoid->bonus;
int *ellipsoid = atom->ellipsoid;
int nlocal = atom->nlocal;
double *quat;
if (domain->dimension == 3) {
double s,t1,t2,theta1,theta2;
for (i = 0; i < nlocal; i++)
if (select[i]) {
if (ellipsoid[i] < 0)
error->one("Cannot set quaternion for atom "
"that is not an ellipsoid");
quat = bonus[ellipsoid[i]].quat;
random->reset(seed,x[i]);
s = random->uniform();
t1 = sqrt(1.0-s);
t2 = sqrt(s);
theta1 = 2.0*PI*random->uniform();
theta2 = 2.0*PI*random->uniform();
quat[0] = cos(theta2)*t2;
quat[1] = sin(theta1)*t1;
quat[2] = cos(theta1)*t1;
quat[3] = sin(theta2)*t2;
count++;
}
} else {
double theta2;
for (i = 0; i < nlocal; i++)
if (select[i]) {
if (ellipsoid[i] < 0)
error->one("Cannot set quaternion for atom "
"that is not an ellipsoid");
quat = bonus[ellipsoid[i]].quat;
random->reset(seed,x[i]);
theta2 = PI*random->uniform();
quat[0] = cos(theta2);
quat[1] = 0.0;
quat[2] = 0.0;
quat[3] = sin(theta2);
count++;
}
}
}
delete random;
}
/* ---------------------------------------------------------------------- */
void Set::topology(int keyword)
{
int m,atom1,atom2,atom3,atom4;
// border swap to acquire ghost atom info
// enforce PBC before in case atoms are outside box
// init entire system since comm->exchange is done
// comm::init needs neighbor::init needs pair::init needs kspace::init, etc
if (comm->me == 0 && screen) fprintf(screen," system init for set ...\n");
lmp->init();
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
comm->exchange();
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
// select both owned and ghost atoms
selection(atom->nlocal + atom->nghost);
// for BOND, each of 2 atoms must be in group
if (keyword == BOND) {
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_bond[i]; m++) {
atom1 = atom->map(atom->bond_atom[i][m]);
if (atom1 == -1) error->one("Bond atom missing in set command");
if (select[i] && select[atom1]) {
atom->bond_type[i][m] = ivalue;
count++;
}
}
}
// for ANGLE, each of 3 atoms must be in group
if (keyword == ANGLE) {
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_angle[i]; m++) {
atom1 = atom->map(atom->angle_atom1[i][m]);
atom2 = atom->map(atom->angle_atom2[i][m]);
atom3 = atom->map(atom->angle_atom3[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1)
error->one("Angle atom missing in set command");
if (select[atom1] && select[atom2] && select[atom3]) {
atom->angle_type[i][m] = ivalue;
count++;
}
}
}
// for DIHEDRAL, each of 4 atoms must be in group
if (keyword == DIHEDRAL) {
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_dihedral[i]; m++) {
atom1 = atom->map(atom->dihedral_atom1[i][m]);
atom2 = atom->map(atom->dihedral_atom2[i][m]);
atom3 = atom->map(atom->dihedral_atom3[i][m]);
atom4 = atom->map(atom->dihedral_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1)
error->one("Dihedral atom missing in set command");
if (select[atom1] && select[atom2] && select[atom3] && select[atom4]) {
atom->dihedral_type[i][m] = ivalue;
count++;
}
}
}
// for IMPROPER, each of 4 atoms must be in group
if (keyword == IMPROPER) {
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_improper[i]; m++) {
atom1 = atom->map(atom->improper_atom1[i][m]);
atom2 = atom->map(atom->improper_atom2[i][m]);
atom3 = atom->map(atom->improper_atom3[i][m]);
atom4 = atom->map(atom->improper_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1)
error->one("Improper atom missing in set command");
if (select[atom1] && select[atom2] && select[atom3] && select[atom4]) {
atom->improper_type[i][m] = ivalue;
count++;
}
}
}
}
diff --git a/src/verlet.cpp b/src/verlet.cpp
index 1a0b9cbd2..680407434 100644
--- a/src/verlet.cpp
+++ b/src/verlet.cpp
@@ -1,404 +1,438 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "string.h"
#include "verlet.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "atom.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "kspace.h"
#include "output.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "fix.h"
#include "timer.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
Verlet::Verlet(LAMMPS *lmp, int narg, char **arg) :
Integrate(lmp, narg, arg) {}
/* ----------------------------------------------------------------------
initialization before run
------------------------------------------------------------------------- */
void Verlet::init()
{
// warn if no fixes
if (modify->nfix == 0 && comm->me == 0)
error->warning("No fixes defined, atoms won't move");
// virial_style:
// 1 if computed explicitly by pair->compute via sum over pair interactions
// 2 if computed implicitly by pair->virial_fdotr_compute via sum over ghosts
if (force->newton_pair) virial_style = 2;
else virial_style = 1;
// setup lists of computes for global and per-atom PE and pressure
ev_setup();
// set flags for what arrays to clear in force_clear()
- // need to clear torques,erforce if arrays exists
+ // need to clear additionals arrays if they exist
torqueflag = 0;
if (atom->torque_flag) torqueflag = 1;
erforceflag = 0;
if (atom->erforce_flag) erforceflag = 1;
+ e_flag = 0;
+ if (atom->e_flag) e_flag = 1;
+ rho_flag = 0;
+ if (atom->rho_flag) rho_flag = 1;
// orthogonal vs triclinic simulation box
triclinic = domain->triclinic;
}
/* ----------------------------------------------------------------------
setup before run
------------------------------------------------------------------------- */
void Verlet::setup()
{
if (comm->me == 0 && screen) fprintf(screen,"Setting up run ...\n");
update->setupflag = 1;
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
atom->setup();
modify->setup_pre_exchange();
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
if (atom->sortfreq > 0) atom->sort();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
neighbor->build();
neighbor->ncalls = 0;
// compute all forces
ev_set(update->ntimestep);
force_clear();
modify->setup_pre_force(vflag);
if (force->pair) force->pair->compute(eflag,vflag);
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);
if (force->improper) force->improper->compute(eflag,vflag);
}
if (force->kspace) {
force->kspace->setup();
force->kspace->compute(eflag,vflag);
}
if (force->newton) comm->reverse_comm();
modify->setup(vflag);
output->setup(1);
update->setupflag = 0;
}
/* ----------------------------------------------------------------------
setup without output
flag = 0 = just force calculation
flag = 1 = reneighbor and force calculation
------------------------------------------------------------------------- */
void Verlet::setup_minimal(int flag)
{
update->setupflag = 1;
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
if (flag) {
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
neighbor->build();
neighbor->ncalls = 0;
}
// compute all forces
ev_set(update->ntimestep);
force_clear();
modify->setup_pre_force(vflag);
if (force->pair) force->pair->compute(eflag,vflag);
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);
if (force->improper) force->improper->compute(eflag,vflag);
}
if (force->kspace) {
force->kspace->setup();
force->kspace->compute(eflag,vflag);
}
if (force->newton) comm->reverse_comm();
modify->setup(vflag);
update->setupflag = 0;
}
/* ----------------------------------------------------------------------
run for N steps
------------------------------------------------------------------------- */
void Verlet::run(int n)
{
bigint ntimestep;
int nflag,sortflag;
int n_post_integrate = modify->n_post_integrate;
int n_pre_exchange = modify->n_pre_exchange;
int n_pre_neighbor = modify->n_pre_neighbor;
int n_pre_force = modify->n_pre_force;
int n_post_force = modify->n_post_force;
int n_end_of_step = modify->n_end_of_step;
if (atom->sortfreq > 0) sortflag = 1;
else sortflag = 0;
for (int i = 0; i < n; i++) {
ntimestep = ++update->ntimestep;
ev_set(ntimestep);
// initial time integration
timer->stamp();
modify->initial_integrate(vflag);
if (n_post_integrate) modify->post_integrate();
timer->stamp(Timer::MODIFY);
// regular communication vs neighbor list rebuild
nflag = neighbor->decide();
if (nflag == 0) {
timer->stamp();
comm->forward_comm();
timer->stamp(Timer::COMM);
} else {
if (n_pre_exchange) {
timer->stamp();
modify->pre_exchange();
timer->stamp(Timer::MODIFY);
}
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
if (domain->box_change) {
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
}
timer->stamp();
comm->exchange();
if (sortflag && ntimestep >= atom->nextsort) atom->sort();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
timer->stamp(Timer::COMM);
if (n_pre_neighbor) {
modify->pre_neighbor();
timer->stamp(Timer::MODIFY);
}
neighbor->build();
timer->stamp(Timer::NEIGHBOR);
}
// force computations
force_clear();
timer->stamp();
if (n_pre_force) {
modify->pre_force(vflag);
timer->stamp(Timer::MODIFY);
}
if (force->pair) {
force->pair->compute(eflag,vflag);
timer->stamp(Timer::PAIR);
}
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);
if (force->improper) force->improper->compute(eflag,vflag);
timer->stamp(Timer::BOND);
}
if (force->kspace) {
force->kspace->compute(eflag,vflag);
timer->stamp(Timer::KSPACE);
}
// reverse communication of forces
if (force->newton) {
comm->reverse_comm();
timer->stamp(Timer::COMM);
}
// force modifications, final time integration, diagnostics
if (n_post_force) modify->post_force(vflag);
modify->final_integrate();
if (n_end_of_step) modify->end_of_step();
timer->stamp(Timer::MODIFY);
// all output
if (ntimestep == output->next) {
timer->stamp();
output->write(ntimestep);
timer->stamp(Timer::OUTPUT);
}
}
}
/* ---------------------------------------------------------------------- */
void Verlet::cleanup()
{
modify->post_run();
}
/* ----------------------------------------------------------------------
clear force on own & ghost atoms
setup and clear other arrays as needed
------------------------------------------------------------------------- */
void Verlet::force_clear()
{
int i;
// clear force on all particles
// if either newton flag is set, also include ghosts
if (neighbor->includegroup == 0) {
int nall;
if (force->newton) nall = atom->nlocal + atom->nghost;
else nall = atom->nlocal;
int ntot = nall * comm->nthreads;
double **f = atom->f;
for (i = 0; i < ntot; i++) {
f[i][0] = 0.0;
f[i][1] = 0.0;
f[i][2] = 0.0;
}
if (torqueflag) {
double **torque = atom->torque;
for (i = 0; i < nall; i++) {
torque[i][0] = 0.0;
torque[i][1] = 0.0;
torque[i][2] = 0.0;
}
}
if (erforceflag) {
double *erforce = atom->erforce;
for (i = 0; i < nall; i++) erforce[i] = 0.0;
}
+ if (e_flag) {
+ double *de = atom->de;
+ for (i = 0; i < nall; i++) de[i] = 0.0;
+ }
+
+ if (rho_flag) {
+ double *drho = atom->drho;
+ for (i = 0; i < nall; i++) drho[i] = 0.0;
+ }
+
// neighbor includegroup flag is set
// clear force only on initial nfirst particles
// if either newton flag is set, also include ghosts
} else {
int nall = atom->nfirst;
double **f = atom->f;
for (i = 0; i < nall; i++) {
f[i][0] = 0.0;
f[i][1] = 0.0;
f[i][2] = 0.0;
}
if (torqueflag) {
double **torque = atom->torque;
for (i = 0; i < nall; i++) {
torque[i][0] = 0.0;
torque[i][1] = 0.0;
torque[i][2] = 0.0;
}
}
if (erforceflag) {
double *erforce = atom->erforce;
for (i = 0; i < nall; i++) erforce[i] = 0.0;
}
+ if (e_flag) {
+ double *de = atom->de;
+ for (i = 0; i < nall; i++) de[i] = 0.0;
+ }
+
+ if (rho_flag) {
+ double *drho = atom->drho;
+ for (i = 0; i < nall; i++) drho[i] = 0.0;
+ }
+
if (force->newton) {
nall = atom->nlocal + atom->nghost;
for (i = atom->nlocal; i < nall; i++) {
f[i][0] = 0.0;
f[i][1] = 0.0;
f[i][2] = 0.0;
}
if (torqueflag) {
double **torque = atom->torque;
for (i = atom->nlocal; i < nall; i++) {
torque[i][0] = 0.0;
torque[i][1] = 0.0;
torque[i][2] = 0.0;
}
}
if (erforceflag) {
double *erforce = atom->erforce;
for (i = atom->nlocal; i < nall; i++) erforce[i] = 0.0;
}
+
+ if (e_flag) {
+ double *de = atom->de;
+ for (i = 0; i < nall; i++) de[i] = 0.0;
+ }
+
+ if (rho_flag) {
+ double *drho = atom->drho;
+ for (i = 0; i < nall; i++) drho[i] = 0.0;
+ }
}
}
}
diff --git a/src/verlet.h b/src/verlet.h
index 8b8c90b7a..327f72b83 100644
--- a/src/verlet.h
+++ b/src/verlet.h
@@ -1,48 +1,48 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef INTEGRATE_CLASS
IntegrateStyle(verlet,Verlet)
#else
#ifndef LMP_VERLET_H
#define LMP_VERLET_H
#include "integrate.h"
namespace LAMMPS_NS {
class Verlet : public Integrate {
public:
Verlet(class LAMMPS *, int, char **);
virtual ~Verlet() {}
void init();
void setup();
void setup_minimal(int);
void run(int);
void cleanup();
protected:
int triclinic; // 0 if domain is orthog, 1 if triclinic
- int torqueflag; // zero out arrays every step
- int erforceflag;
+ int torqueflag,erforceflag;
+ int e_flag,rho_flag;
void force_clear();
};
}
#endif
#endif
diff --git a/src/version.h b/src/version.h
index e8ed62630..e41eb3ca2 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "25 Aug 2011"
+#define LAMMPS_VERSION "27 Aug 2011"

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