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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>
		LAMMPS</H2>
		<P>
		LAMMPS = Large-scale Atomic/Molecular Massively Parallel Simulator</P>
		<P>
		This is the documentation for the LAMMPS 2001 version, written in F90,
		which has been superceded by more current versions. See the <A
		HREF="http://www.cs.sandia.gov/~sjplimp/lammps.html">LAMMPS WWW
		Site</A> for more information.
		<P>
		LAMMPS is a classical molecular dynamics code designed for simulating
		molecular and atomic systems on parallel computers using
		spatial-decomposition techniques. It runs on any parallel platform that
		supports F90 and the MPI message-passing library or on single-processor
		workstations.</P>
		<P>
		LAMMPS 2001 is copyrighted code that is distributed freely as
		open-source software under the GNU Public License (GPL). See the
		LICENSE file or <A HREF="http://www.gnu.org">www.gnu.org</A> for more
		details. Basically the GPL allows you as a user to use, modify, or
		distribute LAMMPS however you wish, so long as any software you
		distribute remains under the GPL.
		<P>
		Features of LAMMPS 2001 include:</P>
		<UL>
		<LI>
		short-range pairwise Lennard-Jones and Coulombic interactions
		<LI>
		long-range Coulombic interactions via Ewald or PPPM (particle-mesh
		Ewald)
		<LI>
		short-range harmonic bond potentials (bond, angle, torsion, improper)
		<LI>
		short-range class II (cross-term) molecular potentials
		<LI>
		NVE, NVT, NPT dynamics
		<LI>
		constraints on atoms or groups of atoms
		<LI>
		rRESPA long-timescale integrator
		<LI>
		energy minimizer (Hessian-free truncated Newton method)
		</UL>
		<P>
		For users of LAMMPS 99, this version is written in F90 to take
		advantage of dynamic memory allocation. This means the user does not
		have to fiddle with parameter settings and re-compile the code so
		often for different problems. This enhancment means there are new
		rules for the ordering of commands in a LAMMPS input script, as well
		as a few new commands to guide the memory allocator. Users should read
		the beginning sections of the <A
		HREF="input_commands.html">input_commands</A> file for an
		explanation.</P>
		<P>
		More details about the code can be found <A
		HREF="#_cch3_930958294">here</A>, in the HTML- or text-based
		documentation. The LAMMPS Web page is at <A
		HREF="http://www.cs.sandia.gov/~sjplimp/lammps.html">www.cs.sandia.gov/~sjplimp/lammps.html</A>
		, which includes benchmark timings and a list of papers written using
		LAMMPS results. They illustrate the kinds of scientific problems that
		can be modeled with LAMMPS. These two papers describe the parallel
		algorithms used in the code. Please cite these if you incorporate
		LAMMPS results in your work. And if you send me citations for your
		papers, I'll be pleased to add them to the LAMMPS WWW page.
		</P>
		<P>
		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.</P>
		<P>
		S. J. Plimpton, "Fast Parallel Algorithms for Short-Range Molecular Dynamics", J Comp Phys, 117, 1-19 (1995).</P>
		<P>
		LAMMPS was originally developed as part of a 5-way CRADA collaboration
		between 3 industrial partners (Cray Research, Bristol-Myers Squibb, and
		Dupont) and 2 DoE laboratories (Sandia National Laboratories and
		Lawrence Livermore National Laboratories).</P>
		<P>
		The primary author of LAMMPS is Steve Plimpton, but others have written
		or worked on significant portions of the code:</P>
		<UL>
		<LI>
		Roy Pollock (LLNL): Ewald, PPPM solvers
		<LI>
		Mark Stevens (Sandia): rRESPA, NPT integrators
		<LI>
		Eric Simon (Cray Research): class II force fields
		<LI>
		Todd Plantenga (Sandia): energy minimizer
		<LI>
		Steve Lustig (Dupont): msi2lmp tool
		<LI>
		Mike Peachey (Cray Research): msi2lmp tool
		</UL>
		<P>
		Other CRADA partners involved in the design and testing of LAMMPS are </P>
		<UL>
		<LI>
		John Carpenter (Cray Research)
		<LI>
		Terry Stouch (Bristol-Myers Squibb)
		<LI>
		Jim Belak (LLNL)
		</UL>
		<P>
		If you have questions about LAMMPS, please contact me:
		</P>
		<DL>
		<DT>
		Steve Plimpton
		<DD>
		sjplimp@sandia.gov
		<DD>
		www.cs.sandia.gov/~sjplimp
		<DD>
		Sandia National Labs
		<DD>
		Albuquerque, NM 87185
		</DL>
		<HR>
		<H3>
		<A NAME="_cch3_930958294">More Information about LAMMPS</A></H3>
		<DIR>
		<LI>
		<A HREF="basics.html">Basics</A>
		<DIR>
		<LI>
		how to make, run, and test LAMMPS with the example problems
		</DIR>
		<LI>
		<A HREF="input_commands.html">Input Commands</A>
		<DIR>
		<LI>
		a complete listing of input commands used by LAMMPS
		</DIR>
		<LI>
		<A HREF="data_format.html">Data Format</A>
		<DIR>
		<LI>
		the data file format used by LAMMPS
		</DIR>
		<LI>
		<A HREF="force_fields.html">Force Fields</A>
		<DIR>
		<LI>
		the equations LAMMPS uses to compute force-fields
		</DIR>
		<LI>
		<A HREF="units.html">Units</A>
		<DIR>
		<LI>
		the input/output and internal units for LAMMPS variables
		</DIR>
		<LI>
		<A HREF="history.html">History</A>
		<DIR>
		<LI>
		a brief timeline of features added to LAMMPS
		</DIR>
		<LI>
		<A HREF="deficiencies.html">Deficiencies</A>
		<DIR>
		<LI>
		features LAMMPS does not (yet) have
		</DIR>
		</DIR>
		</BODY>
		</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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		<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
		<HTML>
		<HEAD>
		<META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
		</HEAD>
		<BODY>
		<H2>
		LAMMPS Data Format</H2>
		<P>
		<A HREF="README.html">Return</A> to top-level of LAMMPS documentation</P>
		<P>
		This file describes the format of the data file read into LAMMPS with
		the "read data" command. The data file contains basic
		information about the size of the problem to be run, the initial atomic
		coordinates, molecular topology, and (optionally) force-field
		coefficients. It will be easiest to understand this file if you read it
		while looking at a sample data file from the examples.</P>
		<P>
		This page has 2 sections:</P>
		<UL>
		<LI>
		<A HREF="#_cch3_930958962">Rules for formatting the Data File</A>
		<LI>
		<A HREF="#_cch3_930958969">Sample file with Annotations</A>
		</UL>
		<HR>
		<H3>
		<A NAME="_cch3_930958962">Rules for formatting the Data File: </A></H3>
		<P>
		Blank lines are important. After the header section, new entries are
		separated by blank lines. </P>
		<P>
		Indentation and space between words/numbers on one line is not
		important except that keywords (e.g. Masses, Bond Coeffs) must be
		left-justified and capitalized as shown. </P>
		<P>
		The header section (thru box bounds) must appear first in the file, the
		remaining entries (Masses, various Coeffs, Atoms, Bonds, etc) can come
		in any order. </P>
		<P>
		These entries must be in the file: header section, Masses, Atoms. </P>
		<P>
		These entries must be in the file if there are a non-zero number of
		them: Bonds, Angles, Dihedrals, Impropers. Force field coefficients
		can be specified in the input script, so do not have to appear in the
		data file. The one exception to this is class 2 force field
		coefficients which can only be specified in the data file.
		<P>
		The Nonbond Coeffs entry contains one line for each atom type. These
		are the coefficients for an interaction between 2 atoms of the same
		type. The cross-type coeffs are computed by the appropriate class I or
		class II mixing rules, or can be specified explicitly using the
		"nonbond coeff" command in the input command script. See the <A
		HREF="force_fields.html">force_fields</A> page for more information. </P>
		<P>
		In the Atoms entry, the atoms can be in any order so long as there are
		N entries. The 1st number on the line is the atom-tag (number from 1 to
		N) which is used to identify the atom throughout the simulation. The
		molecule-tag is a second identifier which is attached to the atom; it
		can be 0, or a counter for the molecule the atom is part of, or any
		other number you wish. The q value is the charge of the atom in
		electron units (e.g. +1 for a proton). The xyz values are the initial
		position of the atom. For 2-d simulations specify z as 0.0.</P>
		<P>
		The final 3 nx,ny,nz values on a line of the Atoms entry are optional.
		LAMMPS only reads them if the "true flag" command is
		specified in the input command script. Otherwise they are initialized
		to 0 by LAMMPS. Their meaning, for each dimension, is that
		"n" box-lengths are added to xyz to get the atom's
		"true" un-remapped position. This can be useful in pre- or
		post-processing to enable the unwrapping of long-chained molecules
		which wind thru the periodic box one or more times. The value of
		"n" can be positive, negative, or zero. For 2-d simulations
		specify nz as 0. </P>
		<P>
		Atom velocities are initialized to 0.0 if there is no Velocities entry.
		In the Velocities entry, the atoms can be in any order so long as there
		are N entries. The 1st number on the line is the atom-tag (number from
		1 to N) which is used to identify the atom which the given velocity
		will be assigned to.</P>
		<P>
		Entries for Velocities, Bonds, Angles, Dihedrals, Impropers must appear
		in the file after an Atoms entry.</P>
		<P>
		For simulations with periodic boundary conditions, xyz coords are
		remapped into the periodic box (from as far away as needed), so the
		initial coordinates need not be inside the box. The nx,ny,nz values
		(as read in or as set to zero by LAMMPS) are appropriately adjusted by
		this remapping. </P>
		<P>
		The number of coefficients specified on each line of coefficient
		entries (Nonbond Coeffs, Bond Coeffs, etc) depends on the
		"style" of interaction. This must be specified in the input
		command script before the "read data" command is issued, unless the
		default is used. See the <A
		HREF="input_commands.html">input_commands</A> page for a description
		of the various style options. The <A HREF="input_commands.html">input_commands</A>
		and <A HREF="force_fields.html">force_fields</A> pages explain the
		meaning and valid values for each of the coefficients. </P>
		<HR>
		<H3>
		<A NAME="_cch3_930958969">Sample file with Annotations</A></H3>
		<P>
		Here is a sample file with annotations in parenthesis and lengthy
		sections replaced by dots (...). Note that the blank lines are
		important in this example.</P>
		<PRE>

		LAMMPS Description (1st line of file)

		100 atoms (this must be the 3rd line, 1st 2 lines are ignored)
		95 bonds (# of bonds to be simulated)
		50 angles (include these lines even if number = 0)
		30 dihedrals
		20 impropers

		5 atom types (# of nonbond atom types)
		10 bond types (# of bond types = sets of bond coefficients)
		18 angle types
		20 dihedral types (do not include a bond,angle,dihedral,improper type
		2 improper types line if number of bonds,angles,etc is 0)

		-0.5 0.5 xlo xhi (for periodic systems this is box size,
		-0.5 0.5 ylo yhi for non-periodic it is min/max extent of atoms)
		-0.5 0.5 zlo zhi (do not include this line for 2-d simulations)

		Masses

		1 mass
		...
		N mass (N = # of atom types)

		Nonbond Coeffs

		1 coeff1 coeff2 ...
		...
		N coeff1 coeff2 ... (N = # of atom types)

		Bond Coeffs

		1 coeff1 coeff2 ...
		...
		N coeff1 coeff2 ... (N = # of bond types)

		Angle Coeffs

		1 coeff1 coeff2 ...
		...
		N coeff1 coeff2 ... (N = # of angle types)

		Dihedral Coeffs

		1 coeff1 coeff2 ...
		...
		N coeff1 coeff2 ... (N = # of dihedral types)

		Improper Coeffs

		1 coeff1 coeff2 ...
		...
		N coeff1 coeff2 ... (N = # of improper types)

		BondBond Coeffs

		1 coeff1 coeff2 ...
		...
		N coeff1 coeff2 ... (N = # of angle types)

		BondAngle Coeffs

		1 coeff1 coeff2 ...
		...
		N coeff1 coeff2 ... (N = # of angle types)

		MiddleBondTorsion Coeffs

		1 coeff1 coeff2 ...
		...
		N coeff1 coeff2 ... (N = # of dihedral types)

		EndBondTorsion Coeffs

		1 coeff1 coeff2 ...
		...
		N coeff1 coeff2 ... (N = # of dihedral types)

		AngleTorsion Coeffs

		1 coeff1 coeff2 ...
		...
		N coeff1 coeff2 ... (N = # of dihedral types)

		AngleAngleTorsion Coeffs

		1 coeff1 coeff2 ...
		...
		N coeff1 coeff2 ... (N = # of dihedral types)

		BondBond13 Coeffs

		1 coeff1 coeff2 ...
		...
		N coeff1 coeff2 ... (N = # of dihedral types)

		AngleAngle Coeffs

		1 coeff1 coeff2 ...
		...
		N coeff1 coeff2 ... (N = # of improper types)

		Atoms

		1 molecule-tag atom-type q x y z nx ny nz (nx,ny,nz are optional -
		... see "true flag" input command)
		...
		N molecule-tag atom-type q x y z nx ny nz (N = # of atoms)

		Velocities

		1 vx vy vz
		...
		...
		N vx vy vz (N = # of atoms)

		Bonds

		1 bond-type atom-1 atom-2
		...
		N bond-type atom-1 atom-2 (N = # of bonds)

		Angles

		1 angle-type atom-1 atom-2 atom-3 (atom-2 is the center atom in angle)
		...
		N angle-type atom-1 atom-2 atom-3 (N = # of angles)

		Dihedrals

		1 dihedral-type atom-1 atom-2 atom-3 atom-4 (atoms 2-3 form central bond)
		...
		N dihedral-type atom-1 atom-2 atom-3 atom-4 (N = # of dihedrals)

		Impropers

		1 improper-type atom-1 atom-2 atom-3 atom-4 (atom-2 is central atom)
		...
		N improper-type atom-1 atom-2 atom-3 atom-4 (N = # of impropers)
		</PRE>
		</BODY>
		</HTML>

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