-<LI>If you find a bug, <A HREF = "Section_errors.html#err_2">this section</A> describes
-how to report it.
+<LI>If you find a bug, <A HREF = "Section_errors.html#err_2">Section_errors 2</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
+details are given in <A HREF = "Section_tools.html">Section_tools</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 paper describe the basic parallel algorithms used in
LAMMPS. If you use LAMMPS results in your published work, please cite
this paper and include a pointer to the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>
(http://lammps.sandia.gov):
</P>
<P>S. J. Plimpton, <B>Fast Parallel Algorithms for Short-Range Molecular
Dynamics</B>, J Comp Phys, 117, 1-19 (1995).
</P>
<P>Other papers describing specific algorithms used in LAMMPS are listed
under the <A HREF = "http://lammps.sandia.gov/cite.html">Citing LAMMPS link</A> of
the LAMMPS WWW page.
</P>
<P>The <A HREF = "http://lammps.sandia.gov/papers.html">Publications link</A> on the
LAMMPS WWW page lists papers that have cited LAMMPS. If your paper is
not listed there for some reason, feel free to send us the info. If
the simulations in your paper produced cool pictures or animations,
we'll be pleased to add them to the
<A HREF = "http://lammps.sandia.gov/pictures.html">Pictures</A> or
<A HREF = "http://lammps.sandia.gov/movies.html">Movies</A> pages of the LAMMPS WWW
site.
</P>
<P>The core group of LAMMPS developers is at Sandia National Labs:
</P>
<UL><LI>Steve Plimpton, sjplimp at sandia.gov
<LI>Aidan Thompson, athomps at sandia.gov
<LI>Paul Crozier, pscrozi at sandia.gov
</UL>
<P>The following folks are responsible for significant contributions to
the code, or other aspects of the LAMMPS development effort. Many of
the packages they have written are somewhat unique to LAMMPS and the
code would not be as general-purpose as it is without their expertise
and efforts.
</P>
<UL><LI>Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM and USER-OMP packages
<LI>Roy Pollock (LLNL), Ewald and PPPM solvers
<LI>Mike Brown (ORNL), brownw at ornl.gov, GPU package
<LI>Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential
<LI>Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics
<LI>Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion
<LI>Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling
<LI>Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
<LI>Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA package
<LI>Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
<LI>Pieter in' t Veld (BASF), pieter.intveld at basf.com, USER-EWALDN package for 1/r^N long-range solvers
<LI>Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling
<LI>Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
<LI>Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SPH package
</UL>
-<P>As discussed in <A HREF = "Section_history.html">this section</A>, LAMMPS originated
-as a cooperative project between DOE labs and industrial
+<P>As discussed in <A HREF = "Section_history.html">Section_history</A>, LAMMPS
+originated as a cooperative project between DOE labs and industrial
partners. Folks involved in the design and testing of the original
version of LAMMPS were the following:
</P>
<UL><LI>John Carpenter (Mayo Clinic, formerly at Cray Research)
<LI>Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
<P>The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
</P>
<P>(1) The FLD package was created by Amit Kumar and Michael Bybee from
Jonathan Higdon's group at UIUC.
</P>
<P>(2) 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:
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 FLD package was created by Amit Kumar and Michael Bybee from
Jonathan Higdon's group at UIUC.
(2) 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
extract_fix(), and extract_variable() methods return values or
pointers to data structures internal to LAMMPS.
</P>
<P>For extract_global() see the src/library.cpp file for the list of
valid names. New names could easily be added. A double or integer is
returned. You need to specify the appropriate data type via the type
argument.
</P>
<P>For extract_atom(), a pointer to internal LAMMPS atom-based data is
returned, which you can use via normal Python subscripting. See the
extract() method in the src/atom.cpp file for a list of valid names.
Again, new names could easily be added. A pointer to a vector of
doubles or integers, or a pointer to an array of doubles (double **)
is returned. You need to specify the appropriate data type via the
type argument.
</P>
<P>For extract_compute() and extract_fix(), the global, per-atom, or
local data calulated by the compute or fix can be accessed. What is
returned depends on whether the compute or fix calculates a scalar or
vector or array. For a scalar, a single double value is returned. If
the compute or fix calculates a vector or array, a pointer to the
internal LAMMPS data is returned, which you can use via normal Python
subscripting. The one exception is that for a fix that calculates a
global vector or array, a single double value from the vector or array
is returned, indexed by I (vector) or I and J (array). I,J are
zero-based indices. The I,J arguments can be left out if not needed.
-See <A HREF = "Section_howto.html#howto_15">this section</A> of the manual for a
+See <A HREF = "Section_howto.html#howto_15">Section_howto 15</A> of the manual for a
discussion of global, per-atom, and local data, and of scalar, vector,
and array data types. See the doc pages for individual
<A HREF = "compute.html">computes</A> and <A HREF = "fix.html">fixes</A> for a description of what
they calculate and store.
</P>
<P>For extract_variable(), an <A HREF = "variable.html">equal-style or atom-style
variable</A> is evaluated and its result returned.
</P>
<P>For equal-style variables a single double value is returned and the
group argument is ignored. For atom-style variables, a vector of
doubles is returned, one value per atom, which you can use via normal
Python subscripting. The values will be zero for atoms not in the
specified group.
</P>
<P>The get_natoms() method returns the total number of atoms in the
simulation, as an int. Note that extract_global("natoms") returns the
same value, but as a double, which is the way LAMMPS stores it to
allow for systems with more atoms than can be stored in an int (> 2
billion).
</P>
<P>The get_coords() method returns an ctypes vector of doubles of length
3*natoms, for the coordinates of all the atoms in the simulation,
ordered by x,y,z and then by atom ID (see code for put_coords()
below). The array can be used via normal Python subscripting. If
atom IDs are not consecutively ordered within LAMMPS, a None is
returned as indication of an error.
</P>
<P>Note that the data structure get_coords() returns is different from
the data structure returned by extract_atom("x") in four ways. (1)
Get_coords() returns a vector which you index as x[i];
extract_atom() returns an array which you index as x[i][j]. (2)
Get_coords() orders the atoms by atom ID while extract_atom() does
not. (3) Get_coords() returns a list of all atoms in the simulation;
extract_atoms() returns just the atoms local to each processor. (4)
Finally, the get_coords() data structure is a copy of the atom coords
stored internally in LAMMPS, whereas extract_atom returns an array
that points directly to the internal data. This means you can change
values inside LAMMPS from Python by assigning a new values to the
extract_atom() array. To do this with the get_atoms() vector, you
need to change values in the vector, then invoke the put_coords()
method.
</P>
<P>The put_coords() method takes a vector of coordinates for all atoms in
the simulation, assumed to be ordered by x,y,z and then by atom ID,
and uses the values to overwrite the corresponding coordinates for
each atom inside LAMMPS. This requires LAMMPS to have its "map"
option enabled; see the <A HREF = "atom_modify.html">atom_modify</A> command for
details. If it is not or if atom IDs are not consecutively ordered,
no coordinates are reset,
</P>
<P>The array of coordinates passed to put_coords() must be a ctypes
vector of doubles, allocated and initialized something like this:
</P>
<PRE>from ctypes import *
natoms = lmp.get_atoms()
n3 = 3*natoms
x = (c_double*n3)()
x<B>0</B> = x coord of atom with ID 1
x<B>1</B> = y coord of atom with ID 1
x<B>2</B> = z coord of atom with ID 1
x<B>3</B> = x coord of atom with ID 2
...
x<B>n3-1</B> = z coord of atom with ID natoms
lmp.put_coords(x)
</PRE>
<P>Alternatively, you can just change values in the vector returned by
get_coords(), since it is a ctypes vector of doubles.
</P>
<HR>
<P>As noted above, these Python class methods correspond one-to-one with
the functions in the LAMMPS library interface in src/library.cpp and
library.h. This means you can extend the Python wrapper via the
following steps:
</P>
<UL><LI>Add a new interface function to src/library.cpp and
src/library.h.
<LI>Verify the new function is syntactically correct by building LAMMPS as
-a library - see <A HREF = "Section_start.html#start_4">this section</A> of the
+a library - see <A HREF = "Section_start.html#start_4">Section_start 4</A> of the
manual.
<LI>Add a wrapper method in the Python LAMMPS module to python/lammps.py
for this interface function.
<LI>Rebuild the Python wrapper via python/setup_serial.py or
python/setup.py.
<LI>You should now be able to invoke the new interface function from a
Python script. Isn't ctypes amazing?
</UL>
<HR>
<HR>
<A NAME = "py_7"></A><H4>11.7 Example Python scripts that use LAMMPS
</H4>
<P>These are the Python scripts included as demos in the python/examples
directory of the LAMMPS distribution, to illustrate the kinds of
things that are possible when Python wraps LAMMPS. If you create your
own scripts, send them to us and we can include them in the LAMMPS
distribution.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >trivial.py</TD><TD > read/run a LAMMPS input script thru Python</TD></TR>
<TR><TD >demo.py</TD><TD > invoke various LAMMPS library interface routines</TD></TR>
<TR><TD >simple.py</TD><TD > mimic operation of couple/simple/simple.cpp in Python</TD></TR>
<TR><TD >gui.py</TD><TD > GUI go/stop/temperature-slider to control LAMMPS</TD></TR>
<TR><TD >plot.py</TD><TD > real-time temeperature plot with GnuPlot via Pizza.py</TD></TR>
<TR><TD >viz_tool.py</TD><TD > real-time viz via some viz package</TD></TR>
<TR><TD >vizplotgui_tool.py</TD><TD > combination of viz_tool.py and plot.py and gui.py
</TD></TR></TABLE></DIV>
<HR>
<P>For the viz_tool.py and vizplotgui_tool.py commands, replace "tool"
with "gl" or "atomeye" or "pymol" or "vmd", depending on what
visualization package you have installed.
</P>
<P>Note that for GL, you need to be able to run the Pizza.py GL tool,
which is included in the pizza sub-directory. See the <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py doc
pages</A> for more info:
</P>
<P>Note that for AtomEye, you need version 3, and there is a line in the
scripts that specifies the path and name of the executable. See the
AtomEye WWW pages <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">here</A> or <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html">here</A> for more details:
<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.
+<A HREF = "Section_accelerate.html">Section_accelerate</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>
<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>See <A HREF = "Section_accelerate.html">Section_accelerate</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
<PRE>dump ID group-ID image N file color diameter keyword value ...
</PRE>
<UL><LI>ID = user-assigned name for the dump
<LI>group-ID = ID of the group of atoms to be imaged
<LI>image = style of dump command (other styles <I>atom</I> or <I>cfg</I> or <I>dcd</I> or <I>xtc</I> or <I>xyz</I> or <I>local</I> or <I>custom</I> are discussed on the <A HREF = "dump.html">dump</A> doc page)
<LI>N = dump every this many timesteps
<LI>file = name of file to write image to
<LI>color = atom attribute that determines color of each atom
<LI>diameter = atom attribute that determines size of each atom
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>adiam</I> or <I>atom</I> or <I>bond</I> or <I>size</I> or <I>view</I> or <I>center</I> or <I>up</I> or <I>zoom</I> or <I>persp</I> or <I>box</I> or <I>axes</I> or <I>shiny</I> or <I>ssao</I>
<PRE> <I>adiam</I> value = number = numeric value for atom diameter (distance units)
<I>atom</I> = yes/no = do or do not draw atoms
<I>bond</I> values = color width = color and width of bonds
color = <I>atom</I> or <I>type</I> or <I>none</I>
width = number or <I>atom</I> or <I>type</I> or <I>none</I>
number = numeric value for bond width (distance units)
<I>size</I> values = width height = size of images
width = width of image in # of pixels
height = height of image in # of pixels
<I>view</I> values = theta phi = view of simulation box
theta = view angle from +z axis (degrees)
phi = azimuthal view angle (degrees)
theta or phi can be a variable (see below)
<I>center</I> values = flag Cx Cy Cz = center point of image
flag = "s" for static, "d" for dynamic
Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box)
Cx,Cy,Cz can be variables (see below)
<I>up</I> values = Ux Uy Uz = direction that is "up" in image
Ux,Uy,Uz = components of up vector
Ux,Uy,Uz can be variables (see below)
<I>zoom</I> value = zfactor = size that simulation box appears in image
zfactor = scale image size by factor > 1 to enlarge, factor < 1 to shrink
zfactor can be a variable (see below)
<I>persp</I> value = pfactor = amount of "perspective" in image
dump ID group-ID image N file color diameter keyword value ... :pre
ID = user-assigned name for the dump :ulb,l
group-ID = ID of the group of atoms to be imaged :l
image = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
N = dump every this many timesteps :l
file = name of file to write image to :l
color = atom attribute that determines color of each atom :l
diameter = atom attribute that determines size of each atom :l
zero or more keyword/value pairs may be appended :l
keyword = {adiam} or {atom} or {bond} or {size} or {view} or {center} or {up} or {zoom} or {persp} or {box} or {axes} or {shiny} or {ssao} :l
{adiam} value = number = numeric value for atom diameter (distance units)
{atom} = yes/no = do or do not draw atoms
{bond} values = color width = color and width of bonds
color = {atom} or {type} or {none}
width = number or {atom} or {type} or {none}
number = numeric value for bond width (distance units)
{size} values = width height = size of images
width = width of image in # of pixels
height = height of image in # of pixels
{view} values = theta phi = view of simulation box
theta = view angle from +z axis (degrees)
phi = azimuthal view angle (degrees)
theta or phi can be a variable (see below)
{center} values = flag Cx Cy Cz = center point of image
flag = "s" for static, "d" for dynamic
Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box)
Cx,Cy,Cz can be variables (see below)
{up} values = Ux Uy Uz = direction that is "up" in image
Ux,Uy,Uz = components of up vector
Ux,Uy,Uz can be variables (see below)
{zoom} value = zfactor = size that simulation box appears in image
zfactor = scale image size by factor > 1 to enlarge, factor < 1 to shrink
zfactor can be a variable (see below)
{persp} value = pfactor = amount of "perspective" in image
<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> or <I>scaleyz</I> or <I>scalexz</I> or <I>scalexy</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
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} or {scaleyz} or {scalexz} or {scalexy}
{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
<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> or <I>ewald/omp</I> or <I>pppm/omp</I> or <I>pppm/proxy</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
<I>ewald/omp</I> value = precision
precision = desired accuracy
<I>pppm/omp</I> value = precision
precision = desired accuracy
<I>pppm/proxy</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>The <I>pppm/proxy</I> style is a special variant for calculations
in hybrid OpenMP/MPI parallel mode. It is functionally equivalent
with <I>pppm</I>, but it its force computation is being executed
as a single thread concurrently with a multi-threaded non-bonded
calculation for a pair style with <I>pppm/omp</I> suffix. For calcuations
across many multi-core nodes, this can have a performance benefit
over performing the real and reciprocal space part separately,
specifically when otherwise the time spent on the pair style
would slightly less than in <I>pppm</I> without threading.
</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>, <I>omp</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
+<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</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">Section_accelerate</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, USER-OMP, 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>See <A HREF = "Section_accelerate.html">Section_accelerate</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
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
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
<LI><A HREF = "pair_lubricateU.html">pair_style lubricateU</A> - hydrodynamic lubrication forces for Fast Lubrication Dynamics
<LI><A HREF = "pair_lubricateU.html">pair_style lubricateU/poly</A> - hydrodynamic lubrication forces for Fast Lubrication Dynamics with polydispersity
<LI>style = <I>delete</I> or <I>block</I> or <I>cone</I> or <I>cylinder</I> or <I>plane</I> or <I>prism</I> or <I>sphere</I> or <I>union</I> or <I>intersect</I>
<PRE> <I>delete</I> = no args
<I>block</I> args = xlo xhi ylo yhi zlo zhi
xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all dimensions (distance units)
<I>cone</I> args = dim c1 c2 radlo radhi lo hi
dim = <I>x</I> or <I>y</I> or <I>z</I> = axis of cone
c1,c2 = coords of cone axis in other 2 dimensions (distance units)
radlo,radhi = cone radii at lo and hi end (distance units)
lo,hi = bounds of cone in dim (distance units)
<I>cylinder</I> args = dim c1 c2 radius lo hi
dim = <I>x</I> or <I>y</I> or <I>z</I> = axis of cylinder
c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
radius = cylinder radius (distance units)
lo,hi = bounds of cylinder in dim (distance units)
<I>plane</I> args = px py pz nx ny nz
px,py,pz = point on the plane (distance units)
nx,ny,nz = direction normal to plane (distance units)