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rLAMMPS lammps
basics.html
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
<HTML>
<HEAD>
<META
NAME=
"Generator"
CONTENT=
"Cosmo Create 1.0.3"
>
</HEAD>
<BODY>
<H2>
Basics of Using LAMMPS
</H2>
<P>
<A
HREF=
"README.html"
>
Return
</A>
to top-level of LAMMPS documentation.
</P>
<UL>
<LI>
<A
HREF=
"#_cch3_931273040"
>
Distribution
</A>
<LI>
<A
HREF=
"#_cch3_930327142"
>
Making LAMMPS
</A>
<LI>
<A
HREF=
"#_cch3_930327155"
>
Running LAMMPS
</A>
<LI>
<A
HREF=
"#_cch3_930759879"
>
Examples
</A>
<LI>
<A
HREF=
"#_cch3_931282515"
>
Other Tools
</A>
<LI>
<A
HREF=
"#_cch3_931282000"
>
Extending LAMMPS
</A>
</UL>
<HR>
<H3>
<A
NAME=
"_cch3_931273040"
>
Distribution
</A></H3>
<P>
When you unzip/untar the LAMMPS distribution you should have several
directories:
</P>
<UL>
<LI>
src = source files for LAMMPS
<LI>
doc = HTML documentation
<LI>
examples = sample problems with inputs and outputs
<LI>
tools = serial program for creating and massaging LAMMPS data files
<LI>
converters = msi2lmp, lmp2arc, amber = codes
&
scripts for converting
between MSI/Discover, AMBER, and LAMMPS formats
</UL>
<HR>
<H3>
<A
NAME=
"_cch3_930327142"
>
Making LAMMPS
</A></H3>
<P>
The src directory contains the F90 and C source files for LAMMPS as
well as several sample Makefiles for different machines. To make LAMMPS
for a specfic machine, you simply type
</P>
<P>
make machine
</P>
<P>
from within the src directoy. E.g. "make sgi" or "make t3e". This
should create an executable such as lmp_sgi or lmp_t3e. For optimal
performance you'll want to use a good F90 compiler to make LAMMPS; on
Linux boxes I've been told the Leahy F90 compiler is a good choice.
(If you don't have an F90 compiler, I can give you an older F77-based
version of LAMMPS 99, but you'll lose the dynamic memory and some
other new features in LAMMPS 2001.)
</P>
<P>
In the src directory, there is one top-level Makefile and several
low-level machine-specific files named Makefile.xxx where xxx = the
machine name. If a low-level Makefile exists for your platform, you do
not need to edit the top-level Makefile. However you should check the
system-specific section of the low-level Makefile to insure the
various paths are correct for your environment. If a low-level
Makefile does not exist for your platform, you will need to add a
suitable target to the top-level Makefile. You will also need to
create a new low-level Makefile using one of the existing ones as a
template. If you wish to make LAMMPS for a single-processor
workstation that doesn't have an installed MPI library, you can
specify the "serial" target which uses a directory of MPI stubs to
link against - e.g.
"
make serial
"
. You will need to make the
stub library (type
"
make
"
in STUBS directory) for your
workstation before doing this.
</P>
<P>
Note that the two-level Makefile system allows you to make LAMMPS for
multiple platforms. Each target creates its own object directory for
separate storage of its *.o files.
</P>
<P>
There are a few compiler switches of interest which can be specified
in the low-level Makefiles. If you use a F90FLAGS switch of -DSYNC
then synchronization calls will be made before the timing routines in
integrate.f. This may slow down the code slightly, but will make the
individual timings reported at the end of a run more accurate. The
F90FLAGS setting of -DSENDRECV will use MPI_Sendrecv calls for data
exchange between processors instead of MPI_Irecv, MPI_Send,
MPI_Wait. Sendrecv is often slower, but on some platforms can be
faster, so it is worth trying, particularly if your communication
timings seem slow.
</P>
<P>
The CCFLAGS setting in the low-level Makefiles requires a FFT setting,
for example -DFFT_SGI or -DFFT_T3E. This is for inclusion of the
appropriate machine-specific native 1-d FFT libraries on various
platforms. Currently, the supported machines and switches (used in
fft_3d.c) are FFT_SGI, FFT_DEC, FFT_INTEL, FFT_T3E, and FFT_FFTW. The
latter is a publicly available portable FFT library,
<A
HREF=
"http://www.fftw.org"
>
FFTW
</A>
, which you can install on any
machine. If none of these options is suitable for your machine, please
contact me, and we'll discuss how to add the capability to call your
machine's native FFT library. You can also use FFT_NONE if you have no
need to use the PPPM option in LAMMPS.
</P>
<P>
For Linux and T3E compilation, there is a also a CCFLAGS setting for KLUDGE
needed (see Makefile.linux and Makefile.t3e). This is to enable F90 to
call C with appropriate underscores added to C function names.
<HR>
<H3>
<A
NAME=
"_cch3_930327155"
>
Running LAMMPS
</A></H3>
<P>
LAMMPS is run by redirecting a text file (script) of input commands into it.
</P>
<P>
lmp_sgi
<
in.lj
</P>
<P>
lmp_t3e
<
in.lj
</P>
<P>
The script file contains commands that specify the parameters for the
simulation as well as to read other necessary files such as a data file
that describes the initial atom positions, molecular topology, and
force-field parameters. The
<A
HREF=
"input_commands.html"
>
input_commands
</A>
page describes all the possible commands that can be used. The
<A
HREF=
"data_format.html"
>
data_format
</A>
page describes the format of
the data file.
</P>
<P>
LAMMPS can be run on any number of processors, including a single
processor. In principle 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 dynamical
trajectories.
</P>
<P>
When LAMMPS runs, it estimates the array sizes it should allocate based
on the problem you are simulating and the number of processors you
are running on. If you run out of physical memory, you will get a F90
allocation error and the code should hang or crash. The only thing you
can do about this is run on more processors or run a smaller problem. If
you get an error message to the screen about
"
boosting
"
something, it means LAMMPS under-estimated the size needed for one (or
more) data arrays. The
"
extra memory
"
command can be used in
the input script to augment these sizes at run time. A few arrays are
hard-wired to sizes that should be sufficient for most users. These are
specified with parameter settings in the global.f file. If you get a
message to
"
boost
"
one of these parameters you will have to
change it and re-compile LAMMPS.
</P>
<P>
Some LAMMPS errors are detected at setup; others like neighbor list
overflow may not occur until the middle of a run. Except for F90
allocation errors which may cause the code to hang (with an error
message) since only one processor may incur the error, LAMMPS should
always print a message to the screen and exit gracefully when it
encounters a fatal error. If the code ever crashes or hangs without
spitting out an error message first, it's probably a bug, so let me
know about it. Of course this applies to algorithmic or parallelism
issues, not to physics mistakes, like specifying too big a timestep or
putting 2 atoms on top of each other! One exception is that different
MPI implementations handle buffering of messages differently. If the
code hangs without an error message, it may be that you need to
specify an MPI setting or two (usually via an environment variable) to
enable buffering or boost the sizes of messages that can be
buffered.
</P>
<HR>
<H3>
<A
NAME=
"_cch3_930759879"
>
Examples
</A></H3>
<P>
There are several directories of sample problems in the examples
directory. All of them use an input file (in.*) of commands and a data
file (data.*) of initial atomic coordinates and produce one or more
output files. Sample outputs on different machines and numbers of
processors are included to compare your answers to. See the README
file in the examples sub-directory for more information on what LAMMPS
features the examples illustrate.
</P>
<P>
(1) lj = atomic simulations of Lennard-Jones systems.
<P>
(2) class2 = phenyalanine molecule using the DISCOVER cff95 class 2
force field.
<P>
(3) lc = liquid crystal molecules with various Coulombic options and
periodicity settings.
<P>
(4) flow = 2d flow of Lennard-Jones atoms in a channel using various
constraint options.
<P>
(5) polymer = bead-spring polymer models with one or two chain types.
</P>
<HR>
<H3>
<A
NAME=
"_cch3_931282515"
>
Other Tools
</A></H3>
<P>
The converters directory has source code and scripts for tools that
perform input/output file conversions between MSI Discover, AMBER, and
LAMMPS formats. See the README files for the individual tools for
additional information.
<P>
The tools directory has several serial programs that create and
massage LAMMPS data files.
<P>
(1) setup_chain.f = create a data file of polymer bead-spring chains
<P>
(2) setup_lj.f = create a data file of an atomic LJ mixture of species
<P>
(3) setup_flow_2d.f = create a 2d data file of LJ particles with walls for
a flow simulation
<P>
(4) replicate.c = replicate or scale an existing data file into a new one
<P>
(5) peek_restart.f = print-out info from a binary LAMMPS restart file
<P>
(6) restart2data.f = convert a binary LAMMPS restart file into a text data file
<P>
See the comments at the top of each source file for information on how
to use the tool.
<HR>
<H3>
<A
NAME=
"_cch3_931282000"
>
Extending LAMMPS
</A></H3>
<P>
User-written routines can be compiled and linked with LAMMPS, then
invoked with the "diagnostic" command as LAMMPS runs. These routines
can be used for on-the-fly diagnostics or a variety of other purposes.
The examples/lc directory shows an example of using the diagnostic
command with the in.lc.big.fixes input script. A sample diagnostic
routine is given there also: diagnostic_temp_molecules.f.
</BODY>
</HTML>
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