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