Section_start.html
No OneTemporary
Actions

Subscribers

None

File Metadata

Created: Mon, Sep 9, 07:41

Section_start.html
View Options

	<HTML>
	<CENTER><A HREF = "Section_intro.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_commands.html">Next Section</A>
	</CENTER>






	<HR>

	<H3>2. Getting Started
	</H3>
	<P>This section describes how to build and run LAMMPS, for both new and
	experienced users.
	</P>
	2.1 <A HREF = "#start_1">What's in the LAMMPS distribution</A><BR>
	2.2 <A HREF = "#start_2">Making LAMMPS</A><BR>
	2.3 <A HREF = "#start_3">Making LAMMPS with optional packages</A><BR>
	2.4 <A HREF = "#start_4">Building LAMMPS via the Make.py script</A><BR>
	2.5 <A HREF = "#start_5">Building LAMMPS as a library</A><BR>
	2.6 <A HREF = "#start_6">Running LAMMPS</A><BR>
	2.7 <A HREF = "#start_7">Command-line options</A><BR>
	2.8 <A HREF = "#start_8">Screen output</A><BR>
	2.9 <A HREF = "#start_9">Tips for users of previous versions</A> <BR>

	<HR>

	<HR>

	<H4><A NAME = "start_1"></A>2.1 What's in the LAMMPS distribution
	</H4>
	<P>When you download a LAMMPS tarball you will need to unzip and untar
	the downloaded file with the following commands, after placing the
	tarball in an appropriate directory.
	</P>
	<PRE>gunzip lammps*.tar.gz
	tar xvf lammps*.tar
	</PRE>
	<P>This will create a LAMMPS directory containing two files and several
	sub-directories:
	</P>
	<DIV ALIGN=center><TABLE BORDER=1 >
	<TR><TD >README</TD><TD > text file</TD></TR>
	<TR><TD >LICENSE</TD><TD > the GNU General Public License (GPL)</TD></TR>
	<TR><TD >bench</TD><TD > benchmark problems</TD></TR>
	<TR><TD >doc</TD><TD > documentation</TD></TR>
	<TR><TD >examples</TD><TD > simple test problems</TD></TR>
	<TR><TD >potentials</TD><TD > embedded atom method (EAM) potential files</TD></TR>
	<TR><TD >src</TD><TD > source files</TD></TR>
	<TR><TD >tools</TD><TD > pre- and post-processing tools
	</TD></TR></TABLE></DIV>

	<P>Note that the <A HREF = "download">download page</A> also has links to download
	Windows exectubles and installers, as well as pre-built executables
	for a few specific Linux distributions. It also has instructions for
	how to download/install LAMMPS for Macs (via Homebrew), and to
	download and update LAMMPS from SVN and Git repositories, which gives
	you the same files that are in the download tarball.
	</P>
	<P>The Windows and Linux executables for serial or parallel only include
	certain packages and bug-fixes/upgrades listed on <A HREF = "http://lammps.sandia.gov/bug.html">this
	page</A> up to a certain date, as
	stated on the download page. If you want an executable with
	non-included packages or that is more current, then you'll need to
	build LAMMPS yourself, as discussed in the next section.
	</P>
	<P>Skip to the <A HREF = "#start_6">Running LAMMPS</A> sections for info on how to
	launch a LAMMPS Windows executable on a Windows box.
	</P>
	<HR>

	<H4><A NAME = "start_2"></A>2.2 Making LAMMPS
	</H4>
	<P>This section has the following sub-sections:
	</P>
	<UL><LI><A HREF = "#start_2_1">Read this first</A>
	<LI><A HREF = "#start_2_2">Steps to build a LAMMPS executable</A>
	<LI><A HREF = "#start_2_3">Common errors that can occur when making LAMMPS</A>
	<LI><A HREF = "#start_2_4">Additional build tips</A>
	<LI><A HREF = "#start_2_5">Building for a Mac</A>
	<LI><A HREF = "#start_2_6">Building for Windows</A>
	</UL>
	<HR>

	<A NAME = "start_2_1"></A><B><I>Read this first:</I></B>

	<P>If you want to avoid building LAMMPS yourself, read the preceeding
	section about options available for downloading and installing
	executables. Details are discussed on the <A HREF = "download">download</A> page.
	</P>
	<P>Building LAMMPS can be simple or not-so-simple. If all you need are
	the default packages installed in LAMMPS, and MPI is already installed
	on your machine, or you just want to run LAMMPS in serial, then you
	can typically use the Makefile.mpi or Makefile.serial files in
	src/MAKE by typing one of these lines (from the src dir):
	</P>
	<PRE>make mpi
	make serial
	</PRE>
	<P>Note that on a facility supercomputer, there are often "modules"
	loaded in your environment that provide the compilers and MPI you
	should use. In this case, the "mpicxx" compile/link command in
	Makefile.mpi should just work by accessing those modules.
	</P>
	<P>It may be the case that one of the other Makefile.machine files in the
	src/MAKE sub-directories is a better match to your system (type "make"
	to see a list), you can use it as-is by typing (for example):
	</P>
	<PRE>make stampede
	</PRE>
	<P>If any of these builds (with an existing Makefile.machine) works on
	your system, then you're done!
	</P>
	<P>If you want to do one of the following:
	</P>
	<UL><LI>use optional LAMMPS features that require additional libraries
	<LI>use optional packages that require additional libraries
	<LI>use optional accelerator packages that require special compiler/linker settings
	<LI>run on a specialized platform that has its own compilers, settings, or other libs to use
	</UL>
	<P>then building LAMMPS is more complicated. You may need to find where
	auxiliary libraries exist on your machine or install them if they
	don't. You may need to build additional libraries that are part of
	the LAMMPS package, before building LAMMPS. You may need to edit a
	Makefile.machine file to make it compatible with your system.
	</P>
	<P>Note that there is a Make.py tool in the src directory that automates
	several of these steps, but you still have to know what you are doing.
	<A HREF = "#start_4">Section 2.4</A> below describes the tool. It is a convenient
	way to work with installing/un-installing various packages, the
	Makefile.machine changes required by some packages, and the auxiliary
	libraries some of them use.
	</P>
	<P>Please read the following sections carefully. If you are not
	comfortable with makefiles, or building codes on a Unix platform, or
	running an MPI job on your machine, please find a local expert to help
	you. Many compilation, linking, and run problems that users have are
	often not really LAMMPS issues - they are peculiar to the user's
	system, compilers, libraries, etc. Such questions are better answered
	by a local expert.
	</P>
	<P>If you have a build problem that you are convinced is a LAMMPS issue
	(e.g. the compiler complains about a line of LAMMPS source code), then
	please post the issue to the <A HREF = "http://lammps.sandia.gov/mail.html">LAMMPS mail
	list</A>.
	</P>
	<P>If you succeed in building LAMMPS on a new kind of machine, for which
	there isn't a similar machine Makefile included in the
	src/MAKE/MACHINES directory, then send it to the developers and we can
	include it in the LAMMPS distribution.
	</P>
	<HR>

	<A NAME = "start_2_2"></A><B><I>Steps to build a LAMMPS executable:</I></B>

	<P><B>Step 0</B>
	</P>
	<P>The src directory contains the C++ source and header files for LAMMPS.
	It also contains a top-level Makefile and a MAKE sub-directory with
	low-level Makefile.* files for many systems and machines. See the
	src/MAKE/README file for a quick overview of what files are available
	and what sub-directories they are in.
	</P>
	<P>The src/MAKE dir has a few files that should work as-is on many
	platforms. The src/MAKE/OPTIONS dir has more that invoke additional
	compiler, MPI, and other setting options commonly used by LAMMPS, to
	illustrate their syntax. The src/MAKE/MACHINES dir has many more that
	have been tweaked or optimized for specific machines. These files are
	all good starting points if you find you need to change them for your
	machine. Put any file you edit into the src/MAKE/MINE directory and
	it will be never be touched by any LAMMPS updates.
	</P>
	<P>>From within the src directory, type "make" or "gmake". You should see
	a list of available choices from src/MAKE and all of its
	sub-directories. If one of those has the options you want or is the
	machine you want, you can type a command like:
	</P>
	<PRE>make mpi
	or
	make serial_icc
	or
	gmake mac
	</PRE>
	<P>Note that the corresponding Makefile.machine can exist in src/MAKE or
	any of its sub-directories. If a file with the same name appears in
	multiple places (not a good idea), the order they are used is as
	follows: src/MAKE/MINE, src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES.
	This gives preference to a file you have created/edited and put in
	src/MAKE/MINE.
	</P>
	<P>Note that on a multi-processor or multi-core platform you can launch a
	parallel make, by using the "-j" switch with the make command, which
	will build LAMMPS more quickly.
	</P>
	<P>If you get no errors and an executable like lmp_mpi or lmp_g++_serial
	or lmp_mac is produced, then you're done; it's your lucky day.
	</P>
	<P>Note that by default only a few of LAMMPS optional packages are
	installed. To build LAMMPS with optional packages, see <A HREF = "#start_3">this
	section</A> below.
	</P>
	<P><B>Step 1</B>
	</P>
	<P>If Step 0 did not work, you will need to create a low-level Makefile
	for your machine, like Makefile.foo. You should make a copy of an
	existing Makefile.* in src/MAKE or one of its sub-directories as a
	starting point. The only portions of the file you need to edit are
	the first line, the "compiler/linker settings" section, and the
	"LAMMPS-specific settings" section. When it works, put the edited
	file in src/MAKE/MINE and it will not be altered by any future LAMMPS
	updates.
	</P>
	<P><B>Step 2</B>
	</P>
	<P>Change the first line of Makefile.foo to list the word "foo" after the
	"#", and whatever other options it will set. This is the line you
	will see if you just type "make".
	</P>
	<P><B>Step 3</B>
	</P>
	<P>The "compiler/linker settings" section lists compiler and linker
	settings for your C++ compiler, including optimization flags. You can
	use g++, the open-source GNU compiler, which is available on all Unix
	systems. You can also use mpicxx which will typically be available if
	MPI is installed on your system, though you should check which actual
	compiler it wraps. Vendor compilers often produce faster code. On
	boxes with Intel CPUs, we suggest using the Intel icc compiler, which
	can be downloaded from <A HREF = "http://www.intel.com/software/products/noncom">Intel's compiler site</A>.
	</P>


	<P>If building a C++ code on your machine requires additional libraries,
	then you should list them as part of the LIB variable. You should
	not need to do this if you use mpicxx.
	</P>
	<P>The DEPFLAGS setting is what triggers the C++ compiler to create a
	dependency list for a source file. This speeds re-compilation when
	source (.cpp) or header (.h) files are edited. Some compilers do
	not support dependency file creation, or may use a different switch
	than -D. GNU g++ and Intel icc works with -D. If your compiler can't
	create dependency files, then you'll need to create a Makefile.foo
	patterned after Makefile.storm, which uses different rules that do not
	involve dependency files. Note that when you build LAMMPS for the
	first time on a new platform, a long list of *.d files will be printed
	out rapidly. This is not an error; it is the Makefile doing its
	normal creation of dependencies.
	</P>
	<P><B>Step 4</B>
	</P>
	<P>The "system-specific settings" section has several parts. Note that
	if you change any -D setting in this section, you should do a full
	re-compile, after typing "make clean" (which will describe different
	clean options).
	</P>
	<P>The LMP_INC variable is used to include options that turn on ifdefs
	within the LAMMPS code. The options that are currently recogized are:
	</P>
	<UL><LI>-DLAMMPS_GZIP
	<LI>-DLAMMPS_JPEG
	<LI>-DLAMMPS_PNG
	<LI>-DLAMMPS_FFMPEG
	<LI>-DLAMMPS_MEMALIGN
	<LI>-DLAMMPS_XDR
	<LI>-DLAMMPS_SMALLBIG
	<LI>-DLAMMPS_BIGBIG
	<LI>-DLAMMPS_SMALLSMALL
	<LI>-DLAMMPS_LONGLONG_TO_LONG
	<LI>-DPACK_ARRAY
	<LI>-DPACK_POINTER
	<LI>-DPACK_MEMCPY
	</UL>
	<P>The read_data and dump commands will read/write gzipped files if you
	compile with -DLAMMPS_GZIP. It requires that your machine supports
	the "popen()" function in the standard runtime library and that a gzip
	executable can be found by LAMMPS during a run.
	</P>
	<P>IMPORTANT NOTE: on some clusters with high-speed networks, using the
	fork() library calls (required by popen()) can interfere with the fast
	communication library and lead to simulations using compressed output
	or input to hang or crash. For selected operations, compressed file
	I/O is also available using a compression library instead, which are
	provided in the COMPRESS package. From more details about compiling
	LAMMPS with packages, please see below.
	</P>
	<P>If you use -DLAMMPS_JPEG, the <A HREF = "dump_image.html">dump image</A> command
	will be able to write out JPEG image files. For JPEG files, you must
	also link LAMMPS with a JPEG library, as described below. If you use
	-DLAMMPS_PNG, the <A HREF = "dump.html">dump image</A> command will be able to write
	out PNG image files. For PNG files, you must also link LAMMPS with a
	PNG library, as described below. If neither of those two defines are
	used, LAMMPS will only be able to write out uncompressed PPM image
	files.
	</P>
	<P>If you use -DLAMMPS_FFMPEG, the <A HREF = "dump_image.html">dump movie</A> command
	will be available to support on-the-fly generation of rendered movies
	the need to store intermediate image files. It requires that your
	machines supports the "popen" function in the standard runtime library
	and that an FFmpeg executable can be found by LAMMPS during the run.
	</P>
	<P>IMPORTANT NOTE: Similar to the note above, this option can conflict
	with high-speed networks, because it uses popen().
	</P>
	<P>Using -DLAMMPS_MEMALIGN=<bytes> enables the use of the
	posix_memalign() call instead of malloc() when large chunks or memory
	are allocated by LAMMPS. This can help to make more efficient use of
	vector instructions of modern CPUS, since dynamically allocated memory
	has to be aligned on larger than default byte boundaries (e.g. 16
	bytes instead of 8 bytes on x86 type platforms) for optimal
	performance.
	</P>
	<P>If you use -DLAMMPS_XDR, the build will include XDR compatibility
	files for doing particle dumps in XTC format. This is only necessary
	if your platform does have its own XDR files available. See the
	Restrictions section of the <A HREF = "dump.html">dump</A> command for details.
	</P>
	<P>Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG, -D-
	DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG. These
	settings refer to use of 4-byte (small) vs 8-byte (big) integers
	within LAMMPS, as specified in src/lmptype.h. The only reason to use
	the BIGBIG setting is to enable simulation of huge molecular systems
	(which store bond topology info) with more than 2 billion atoms, or to
	track the image flags of moving atoms that wrap around a periodic box
	more than 512 times. Normally, the only reason to use SMALLSMALL is
	if your machine does not support 64-bit integers, though you can use
	SMALLSMALL setting if you are running in serial or on a desktop
	machine or small cluster where you will never run large systems or for
	long time (more than 2 billion atoms, more than 2 billion timesteps).
	See the <A HREF = "#start_2_4">Additional build tips</A> section below for more
	details on these settings.
	</P>
	<P>Note that two packages, USER-ATC and USER-CUDA are not currently
	compatible with -DLAMMPS_BIGBIG. Also the GPU package requires the
	lib/gpu library to be compiled with the same setting, or the link will
	fail.
	</P>
	<P>The -DLAMMPS_LONGLONG_TO_LONG setting may be needed if your system or
	MPI version does not recognize "long long" data types. In this case a
	"long" data type is likely already 64-bits, in which case this setting
	will convert to that data type.
	</P>
	<P>Using one of the -DPACK_ARRAY, -DPACK_POINTER, and -DPACK_MEMCPY
	options can make for faster parallel FFTs (in the PPPM solver) on some
	platforms. The -DPACK_ARRAY setting is the default. See the
	<A HREF = "kspace_style.html">kspace_style</A> command for info about PPPM. See
	Step 6 below for info about building LAMMPS with an FFT library.
	</P>
	<P><B>Step 5</B>
	</P>
	<P>The 3 MPI variables are used to specify an MPI library to build LAMMPS
	with. Note that you do not need to set these if you use the MPI
	compiler mpicxx for your CC and LINK setting in the section above.
	The MPI wrapper knows where to find the needed files.
	</P>
	<P>If you want LAMMPS to run in parallel, you must have an MPI library
	installed on your platform. If MPI is installed on your system in the
	usual place (under /usr/local), you also may not need to specify these
	3 variables, assuming /usr/local is in your path. On some large
	parallel machines which use "modules" for their compile/link
	environements, you may simply need to include the correct module in
	your build environment, before building LAMMPS. Or the parallel
	machine may have a vendor-provided MPI which the compiler has no
	trouble finding.
	</P>
	<P>Failing this, these 3 variables can be used to specify where the mpi.h
	file (MPI_INC) and the MPI library file (MPI_PATH) are found and the
	name of the library file (MPI_LIB).
	</P>
	<P>If you are installing MPI yourself, we recommend Argonne's MPICH2
	or OpenMPI. MPICH can be downloaded from the <A HREF = "http://www.mcs.anl.gov/research/projects/mpich2/">Argonne MPI
	site</A>. OpenMPI can
	be downloaded from the <A HREF = "http://www.open-mpi.org">OpenMPI site</A>.
	Other MPI packages should also work. If you are running on a big
	parallel platform, your system people or the vendor should have
	already installed a version of MPI, which is likely to be faster
	than a self-installed MPICH or OpenMPI, so find out how to build
	and link with it. If you use MPICH or OpenMPI, you will have to
	configure and build it for your platform. The MPI configure script
	should have compiler options to enable you to use the same compiler
	you are using for the LAMMPS build, which can avoid problems that can
	arise when linking LAMMPS to the MPI library.
	</P>
	<P>If you just want to run LAMMPS on a single processor, you can use the
	dummy MPI library provided in src/STUBS, since you don't need a true
	MPI library installed on your system. See src/MAKE/Makefile.serial
	for how to specify the 3 MPI variables in this case. You will also
	need to build the STUBS library for your platform before making LAMMPS
	itself. Note that if you are building with src/MAKE/Makefile.serial,
	e.g. by typing "make serial", then the STUBS library is built for you.
	</P>
	<P>To build the STUBS library from the src directory, type "make
	mpi-stubs", or from the src/STUBS dir, type "make". This should
	create a libmpi_stubs.a file suitable for linking to LAMMPS. If the
	build fails, you will need to edit the STUBS/Makefile for your
	platform.
	</P>
	<P>The file STUBS/mpi.c provides a CPU timer function called MPI_Wtime()
	that calls gettimeofday() . If your system doesn't support
	gettimeofday() , you'll need to insert code to call another timer.
	Note that the ANSI-standard function clock() rolls over after an hour
	or so, and is therefore insufficient for timing long LAMMPS
	simulations.
	</P>
	<P><B>Step 6</B>
	</P>
	<P>The 3 FFT variables allow you to specify an FFT library which LAMMPS
	uses (for performing 1d FFTs) when running the particle-particle
	particle-mesh (PPPM) option for long-range Coulombics via the
	<A HREF = "kspace_style.html">kspace_style</A> command.
	</P>
	<P>LAMMPS supports various open-source or vendor-supplied FFT libraries
	for this purpose. If you leave these 3 variables blank, LAMMPS will
	use the open-source <A HREF = "http://kissfft.sf.net">KISS FFT library</A>, which is
	included in the LAMMPS distribution. This library is portable to all
	platforms and for typical LAMMPS simulations is almost as fast as FFTW
	or vendor optimized libraries. If you are not including the KSPACE
	package in your build, you can also leave the 3 variables blank.
	</P>
	<P>Otherwise, select which kinds of FFTs to use as part of the FFT_INC
	setting by a switch of the form -DFFT_XXX. Recommended values for XXX
	are: MKL, SCSL, FFTW2, and FFTW3. Legacy options are: INTEL, SGI,
	ACML, and T3E. For backward compatability, using -DFFT_FFTW will use
	the FFTW2 library. Using -DFFT_NONE will use the KISS library
	described above.
	</P>
	<P>You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables,
	so the compiler and linker can find the needed FFT header and library
	files. Note that on some large parallel machines which use "modules"
	for their compile/link environements, you may simply need to include
	the correct module in your build environment. Or the parallel machine
	may have a vendor-provided FFT library which the compiler has no
	trouble finding.
	</P>
	<P>FFTW is a fast, portable library that should also work on any
	platform. You can download it from
	<A HREF = "http://www.fftw.org">www.fftw.org</A>. Both the legacy version 2.1.X and
	the newer 3.X versions are supported as -DFFT_FFTW2 or -DFFT_FFTW3.
	Building FFTW for your box should be as simple as ./configure; make.
	Note that on some platforms FFTW2 has been pre-installed, and uses
	renamed files indicating the precision it was compiled with,
	e.g. sfftw.h, or dfftw.h instead of fftw.h. In this case, you can
	specify an additional define variable for FFT_INC called -DFFTW_SIZE,
	which will select the correct include file. In this case, for FFT_LIB
	you must also manually specify the correct library, namely -lsfftw or
	-ldfftw.
	</P>
	<P>The FFT_INC variable also allows for a -DFFT_SINGLE setting that will
	use single-precision FFTs with PPPM, which can speed-up long-range
	calulations, particularly in parallel or on GPUs. Fourier transform
	and related PPPM operations are somewhat insensitive to floating point
	truncation errors and thus do not always need to be performed in
	double precision. Using the -DFFT_SINGLE setting trades off a little
	accuracy for reduced memory use and parallel communication costs for
	transposing 3d FFT data. Note that single precision FFTs have only
	been tested with the FFTW3, FFTW2, MKL, and KISS FFT options.
	</P>
	<P><B>Step 7</B>
	</P>
	<P>The 3 JPG variables allow you to specify a JPEG and/or PNG library
	which LAMMPS uses when writing out JPEG or PNG files via the <A HREF = "dump_image.html">dump
	image</A> command. These can be left blank if you do not
	use the -DLAMMPS_JPEG or -DLAMMPS_PNG switches discussed above in Step
	4, since in that case JPEG/PNG output will be disabled.
	</P>
	<P>A standard JPEG library usually goes by the name libjpeg.a or
	libjpeg.so and has an associated header file jpeglib.h. Whichever
	JPEG library you have on your platform, you'll need to set the
	appropriate JPG_INC, JPG_PATH, and JPG_LIB variables, so that the
	compiler and linker can find it.
	</P>
	<P>A standard PNG library usually goes by the name libpng.a or libpng.so
	and has an associated header file png.h. Whichever PNG library you
	have on your platform, you'll need to set the appropriate JPG_INC,
	JPG_PATH, and JPG_LIB variables, so that the compiler and linker can
	find it.
	</P>
	<P>As before, if these header and library files are in the usual place on
	your machine, you may not need to set these variables.
	</P>
	<P><B>Step 8</B>
	</P>
	<P>Note that by default only a few of LAMMPS optional packages are
	installed. To build LAMMPS with optional packages, see <A HREF = "#start_3">this
	section</A> below, before proceeding to Step 9.
	</P>
	<P><B>Step 9</B>
	</P>
	<P>That's it. Once you have a correct Makefile.foo, and you have
	pre-built any other needed libraries (e.g. MPI, FFT, etc) all you need
	to do from the src directory is type something like this:
	</P>
	<PRE>make foo
	or
	gmake foo
	</PRE>
	<P>You should get the executable lmp_foo when the build is complete.
	</P>
	<HR>

	<A NAME = "start_2_3"></A><B><I>Errors that can occur when making LAMMPS:</I></B>

	<P>IMPORTANT NOTE: If an error occurs when building LAMMPS, the compiler
	or linker will state very explicitly what the problem is. The error
	message should give you a hint as to which of the steps above has
	failed, and what you need to do in order to fix it. Building a code
	with a Makefile is a very logical process. The compiler and linker
	need to find the appropriate files and those files need to be
	compatible with LAMMPS source files. When a make fails, there is
	usually a very simple reason, which you or a local expert will need to
	fix.
	</P>
	<P>Here are two non-obvious errors that can occur:
	</P>
	<P>(1) If the make command breaks immediately with errors that indicate
	it can't find files with a "*" in their names, this can be because
	your machine's native make doesn't support wildcard expansion in a
	makefile. Try gmake instead of make. If that doesn't work, try using
	a -f switch with your make command to use a pre-generated
	Makefile.list which explicitly lists all the needed files, e.g.
	</P>
	<PRE>make makelist
	make -f Makefile.list linux
	gmake -f Makefile.list mac
	</PRE>
	<P>The first "make" command will create a current Makefile.list with all
	the file names in your src dir. The 2nd "make" command (make or
	gmake) will use it to build LAMMPS. Note that you should
	include/exclude any desired optional packages before using the "make
	makelist" command.
	</P>
	<P>(2) If you get an error that says something like 'identifier "atoll"
	is undefined', then your machine does not support "long long"
	integers. Try using the -DLAMMPS_LONGLONG_TO_LONG setting described
	above in Step 4.
	</P>
	<HR>

	<A NAME = "start_2_4"></A><B><I>Additional build tips:</I></B>

	<P>(1) Building LAMMPS for multiple platforms.
	</P>
	<P>You can make LAMMPS for multiple platforms from the same src
	directory. Each target creates its own object sub-directory called
	Obj_target where it stores the system-specific *.o files.
	</P>
	<P>(2) Cleaning up.
	</P>
	<P>Typing "make clean-all" or "make clean-machine" will delete *.o object
	files created when LAMMPS is built, for either all builds or for a
	particular machine.
	</P>
	<P>(3) Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or
	-DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
	</P>
	<P>As explained above, any of these 3 settings can be specified on the
	LMP_INC line in your low-level src/MAKE/Makefile.foo.
	</P>
	<P>The default is -DLAMMPS_SMALLBIG which allows for systems with up to
	2^63 atoms and 2^63 timesteps (about 9e18). The atom limit is for
	atomic systems which do not store bond topology info and thus do not
	require atom IDs. If you use atom IDs for atomic systems (which is
	the default) or if you use a molecular model, which stores bond
	topology info and thus requires atom IDs, the limit is 2^31 atoms
	(about 2 billion). This is because the IDs are stored in 32-bit
	integers.
	</P>
	<P>Likewise, with this setting, the 3 image flags for each atom (see the
	<A HREF = "dump.html">dump</A> doc page for a discussion) are stored in a 32-bit
	integer, which means the atoms can only wrap around a periodic box (in
	each dimension) at most 512 times. If atoms move through the periodic
	box more than this many times, the image flags will "roll over",
	e.g. from 511 to -512, which can cause diagnostics like the
	mean-squared displacement, as calculated by the <A HREF = "compute_msd.html">compute
	msd</A> command, to be faulty.
	</P>
	<P>To allow for larger atomic systems with atom IDs or larger molecular
	systems or larger image flags, compile with -DLAMMPS_BIGBIG. This
	stores atom IDs and image flags in 64-bit integers. This enables
	atomic or molecular systems with atom IDS of up to 2^63 atoms (about
	9e18). And image flags will not "roll over" until they reach 2^20 =
	1048576.
	</P>
	<P>If your system does not support 8-byte integers, you will need to
	compile with the -DLAMMPS_SMALLSMALL setting. This will restrict the
	total number of atoms (for atomic or molecular systems) and timesteps
	to 2^31 (about 2 billion). Image flags will roll over at 2^9 = 512.
	</P>
	<P>Note that in src/lmptype.h there are definitions of all these data
	types as well as the MPI data types associated with them. The MPI
	types need to be consistent with the associated C data types, or else
	LAMMPS will generate a run-time error. As far as we know, the
	settings defined in src/lmptype.h are portable and work on every
	current system.
	</P>
	<P>In all cases, the size of problem that can be run on a per-processor
	basis is limited by 4-byte integer storage to 2^31 atoms per processor
	(about 2 billion). This should not normally be a limitation since such
	a problem would have a huge per-processor memory footprint due to
	neighbor lists and would run very slowly in terms of CPU secs/timestep.
	</P>
	<HR>

	<A NAME = "start_2_5"></A><B><I>Building for a Mac:</I></B>

	<P>OS X is BSD Unix, so it should just work. See the
	src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files.
	</P>
	<HR>

	<A NAME = "start_2_6"></A><B><I>Building for Windows:</I></B>

	<P>The LAMMPS download page has an option to download both a serial and
	parallel pre-built Windows executable. See the <A HREF = "#start_6">Running
	LAMMPS</A> section for instructions on running these executables
	on a Windows box.
	</P>
	<P>The pre-built executables hosted on the <A HREF = "http://lammps.sandia.gov/download.html">LAMMPS download
	page</A> are built with a subset
	of the available packages; see the download page for the list. These
	are single executable files. No examples or documentation in
	included. You will need to download the full source code package to
	obtain those.
	</P>
	<P>As an alternative, you can download "daily builds" (and some older
	versions) of the installer packages from
	<A HREF = "http://rpm.lammps.org/windows.html">rpm.lammps.org/windows.html</A>.
	These executables are built with most optional packages and the
	download includes documentation, some tools and most examples.
	</P>
	<P>If you want a Windows version with specific packages included and
	excluded, you can build it yourself.
	</P>
	<P>One way to do this is install and use cygwin to build LAMMPS with a
	standard unix style make program, just as you would on a Linux box;
	see src/MAKE/MACHINES/Makefile.cygwin.
	</P>
	<P>The other way to do this is using Visual Studio and project files.
	See the src/WINDOWS directory and its README.txt file for instructions
	on both a basic build and a customized build with pacakges you select.
	</P>
	<HR>

	<H4><A NAME = "start_3"></A>2.3 Making LAMMPS with optional packages
	</H4>
	<P>This section has the following sub-sections:
	</P>
	<UL><LI><A HREF = "#start_3_1">Package basics</A>
	<LI><A HREF = "#start_3_2">Including/excluding packages</A>
	<LI><A HREF = "#start_3_3">Packages that require extra libraries</A>
	<LI><A HREF = "#start_3_4">Packages that require Makefile.machine settings</A>
	</UL>
	<P>Note that the following <A HREF = "#start_4">Section 2.4</A> describes the Make.py
	tool which can be used to install/un-install packages and build the
	auxiliary libraries which some of them use. It can also auto-edit a
	Makefile.machine to add settings needed by some packages.
	</P>
	<HR>

	<A NAME = "start_3_1"></A><B><I>Package basics:</I></B>

	<P>The source code for LAMMPS is structured as a set of core files which
	are always included, plus optional packages. Packages are groups of
	files that enable a specific set of features. For example, force
	fields for molecular systems or granular systems are in packages.
	</P>
	<P>You can see the list of all packages by typing "make package" from
	within the src directory of the LAMMPS distribution. This also lists
	various make commands that can be used to manipulate packages.
	</P>
	<P>If you use a command in a LAMMPS input script that is specific to a
	particular package, you must have built LAMMPS with that package, else
	you will get an error that the style is invalid or the command is
	unknown. Every command's doc page specfies if it is part of a
	package. You can also type
	</P>
	<PRE>lmp_machine -h
	</PRE>
	<P>to run your executable with the optional <A HREF = "#start_7">-h command-line
	switch</A> for "help", which will list the styles and commands
	known to your executable.
	</P>
	<P>There are two kinds of packages in LAMMPS, standard and user packages.
	More information about the contents of standard and user packages is
	given in <A HREF = "Section_packages.html">Section_packages</A> of the manual. The
	difference between standard and user packages is as follows:
	</P>
	<P>Standard packages are supported by the LAMMPS developers and are
	written in a syntax and style consistent with the rest of LAMMPS.
	This means we will answer questions about them, debug and fix them if
	necessary, and keep them compatible with future changes to LAMMPS.
	</P>
	<P>User packages have been contributed by users, and always begin with
	the user prefix. If they are a single command (single file), they are
	typically in the user-misc package. Otherwise, they are a a set of
	files grouped together which add a specific functionality to the code.
	</P>
	<P>User packages don't necessarily meet the requirements of the standard
	packages. If you have problems using a feature provided in a user
	package, you will likely need to contact the contributor directly to
	get help. Information on how to submit additions you make to LAMMPS
	as a user-contributed package is given in <A HREF = "Section_modify.html#mod_15">this
	section</A> of the documentation.
	</P>
	<P>Some packages (both standard and user) require additional libraries.
	See more details below.
	</P>
	<HR>

	<A NAME = "start_3_2"></A><B><I>Including/excluding packages:</I></B>

	<P>To use or not use a package you must include or exclude it before
	building LAMMPS. From the src directory, this is typically as simple
	as:
	</P>
	<PRE>make yes-colloid
	make g++
	</PRE>
	<P>or
	</P>
	<PRE>make no-manybody
	make g++
	</PRE>
	<P>IMPORTANT NOTE: You should NOT include/exclude packages and build
	LAMMPS in a single make command by using multiple targets, e.g. make
	yes-colloid g++. This is because the make procedure creates a list of
	source files that will be out-of-date for the build if the package
	configuration changes during the same command.
	</P>
	<P>Some packages have individual files that depend on other packages
	being included. LAMMPS checks for this and does the right thing.
	I.e. individual files are only included if their dependencies are
	already included. Likewise, if a package is excluded, other files
	dependent on that package are also excluded.
	</P>
	<P>If you will never run simulations that use the features in a
	particular packages, there is no reason to include it in your build.
	For some packages, this will keep you from having to build auxiliary
	libraries (see below), and will also produce a smaller executable
	which may run a bit faster.
	</P>
	<P>When you download a LAMMPS tarball, these packages are pre-installed
	in the src directory: KSPACE, MANYBODY,MOLECULE. When you download
	LAMMPS source files from the SVN or Git repositories, no packages are
	pre-installed.
	</P>
	<P>Packages are included or excluded by typing "make yes-name" or "make
	no-name", where "name" is the name of the package in lower-case, e.g.
	name = kspace for the KSPACE package or name = user-atc for the
	USER-ATC package. You can also type "make yes-standard", "make
	no-standard", "make yes-std", "make no-std", "make yes-user", "make
	no-user", "make yes-all" or "make no-all" to include/exclude various
	sets of packages. Type "make package" to see the all of the
	package-related make options.
	</P>
	<P>IMPORTANT NOTE: Inclusion/exclusion of a package works by simply
	moving files back and forth between the main src directory and
	sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
	so that the files are seen or not seen when LAMMPS is built. After
	you have included or excluded a package, you must re-build LAMMPS.
	</P>
	<P>Additional package-related make options exist to help manage LAMMPS
	files that exist in both the src directory and in package
	sub-directories. You do not normally need to use these commands
	unless you are editing LAMMPS files or have downloaded a patch from
	the LAMMPS WWW site.
	</P>
	<P>Typing "make package-update" or "make pu" will overwrite src files
	with files from the package sub-directories if the package has been
	included. It should be used after a patch is installed, since patches
	only update the files in the package sub-directory, but not the src
	files. Typing "make package-overwrite" will overwrite files in the
	package sub-directories with src files.
	</P>
	<P>Typing "make package-status" or "make ps" will show which packages are
	currently included. Of those that are included, it will list files
	that are different in the src directory and package sub-directory.
	Typing "make package-diff" lists all differences between these files.
	Again, type "make package" to see all of the package-related make
	options.
	</P>
	<HR>

	<A NAME = "start_3_3"></A><B><I>Packages that require extra libraries:</I></B>

	<P>A few of the standard and user packages require additional auxiliary
	libraries. Most of them are provided with LAMMPS, in which case they
	must be compiled first, before LAMMPS is built if you wish to include
	that package. If you get a LAMMPS build error about a missing
	library, this is likely the reason. See the
	<A HREF = "Section_packages.html">Section_packages</A> doc page for a list of
	packages that have these kinds of auxiliary libraries.
	</P>
	<P>The lib directory in the distribution has sub-directories with package
	names that correspond to the needed auxiliary libs, e.g. lib/reax.
	Each sub-directory has a README file that gives more details. Code
	for most of the auxiliary libraries is included in that directory.
	Examples are the USER-ATC and MEAM packages.
	</P>
	<P>A few of the lib sub-directories do not include code, but do include
	instructions and sometimes scripts that automate the process of
	downloading the auxiliary library and installing it so LAMMPS can link
	to it. Examples are the KIM and VORONOI and USER-MOLFILE and USER-SMD
	packages.
	</P>
	<P>The lib/python directory (for the PYTHON package) contains only a
	choice of Makefile.lammps.* files. This is because no auxiliary code
	or libraries are needed, only the Python library and other system libs
	that already available on your system. However, the Makefile.lammps
	file is needed to tell the LAMMPS build which libs to use and where to
	find them.
	</P>
	<P>For libraries with provided code, the sub-directory README file
	(e.g. lib/reax/README) has instructions on how to build that library.
	Typically this is done by typing something like:
	</P>
	<PRE>make -f Makefile.g++
	</PRE>
	<P>If one of the provided Makefiles is not appropriate for your system
	you will need to edit or add one. Note that all the Makefiles have a
	setting for EXTRAMAKE at the top that specifies a Makefile.lammps.*
	file.
	</P>
	<P>If the library build is successful, it will produce 2 files in the lib
	directory:
	</P>
	<PRE>libpackage.a
	Makefile.lammps
	</PRE>
	<P>The Makefile.lammps file will be a copy of the EXTRAMAKE file setting
	specified in the library Makefile.* you used.
	</P>
	<P>Note that you must insure that the settings in Makefile.lammps are
	appropriate for your system. If they are not, the LAMMPS build will
	fail.
	</P>
	<P>As explained in the lib/package/README files, the settings in
	Makefile.lammps are used to specify additional system libraries and
	their locations so that LAMMPS can build with the auxiliary library.
	For example, if the MEAM or REAX packages are used, the auxiliary
	libraries consist of F90 code, built with a Fortran complier. To link
	that library with LAMMPS (a C++ code) via whatever C++ compiler LAMMPS
	is built with, typically requires additional Fortran-to-C libraries be
	included in the link. Another example are the BLAS and LAPACK
	libraries needed to use the USER-ATC or USER-AWPMD packages.
	</P>
	<P>For libraries without provided code, the sub-directory README file has
	information on where to download the library and how to build it,
	e.g. lib/voronoi/README and lib/smd/README. The README files also
	describe how you must either (a) create soft links, via the "ln"
	command, in those directories to point to where you built or installed
	the packages, or (b) check or edit the Makefile.lammps file in the
	same directory to provide that information.
	</P>
	<P>Some of the sub-directories, e.g. lib/voronoi, also have an install.py
	script which can be used to automate the process of
	downloading/building/installing the auxiliary library, and setting the
	needed soft links. Type "python install.py" for further instructions.
	</P>
	<P>As with the sub-directories containing library code, if the soft links
	or settings in the lib/package/Makefile.lammps files are not correct,
	the LAMMPS build will typically fail.
	</P>
	<HR>

	<A NAME = "start_3_4"></A><B><I>Packages that require Makefile.machine settings</I></B>

	<P>A few packages require specific settings in Makefile.machine, to
	either build or use the package effectively. These are the
	USER-INTEL, KOKKOS, USER-OMP, and OPT packages. The details of what
	flags to add or what variables to define are given on the doc pages
	that describe each of these accelerator packages in detail:
	</P>
	<UL><LI><A HREF = "accelerate_intel.html">USER-INTEL package</A>
	<LI><A HREF = "accelerate_kokkos.html">KOKKOS package</A>
	<LI><A HREF = "accelerate_omp.html">USER-OMP package</A>
	<LI><A HREF = "accelerate_opt.html">OPT package</A>
	</UL>
	<P>Here is a brief summary of what Makefile.machine changes are needed.
	Note that the Make.py tool, described in the next <A HREF = "#start_4">Section
	2.4</A> can automatically add the needed info to an existing
	machine Makefile, using simple command-line arguments.
	</P>
	<P>In src/MAKE/OPTIONS see the following Makefiles for examples of the
	changes described below:
	</P>
	<UL><LI>Makefile.intel_cpu
	<LI>Makefile.intel_phi
	<LI>Makefile.kokkos_omp
	<LI>Makefile.kokkos_cuda
	<LI>Makefile.kokkos_phi
	<LI>Makefile.omp
	</UL>
	<P>For the USER-INTEL package, you have 2 choices when building. You can
	build with CPU or Phi support. The latter uses Xeon Phi chips in
	"offload" mode. Each of these modes requires additional settings in
	your Makefile.machine for CCFLAGS and LINKFLAGS.
	</P>
	<P>For CPU mode (if using an Intel compiler):
	</P>
	<UL><LI>CCFLAGS: add -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits
	<LI>LINKFLAGS: add -fopenmp
	</UL>
	<P>For Phi mode add the following in addition to the CPU mode flags:
	</P>
	<UL><LI>CCFLAGS: add -DLMP_INTEL_OFFLOAD and
	<LI>LINKFLAGS: add -offload
	</UL>
	<P>And also add this to CCFLAGS:
	</P>
	<PRE>-offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\""
	</PRE>
	<P>For the KOKKOS package, you have 3 choices when building. You can
	build with OMP or Cuda or Phi support. Phi support uses Xeon Phi
	chips in "native" mode. This can be done by setting the following
	variables in your Makefile.machine:
	</P>
	<UL><LI>for OMP support, set OMP = yes
	<LI>for Cuda support, set OMP = yes and CUDA = yes
	<LI>for Phi support, set OMP = yes and MIC = yes
	</UL>
	<P>These can also be set as additional arguments to the make command, e.g.
	</P>
	<PRE>make g++ OMP=yes MIC=yes
	</PRE>
	<P>Building the KOKKOS package with CUDA support requires a Makefile
	machine that uses the NVIDIA "nvcc" compiler, as well as an
	appropriate "arch" setting appropriate to the GPU hardware and NVIDIA
	software you have on your machine. See
	src/MAKE/OPTIONS/Makefile.kokkos_cuda for an example of such a machine
	Makefile.
	</P>
	<P>For the USER-OMP package, your Makefile.machine needs additional
	settings for CCFLAGS and LINKFLAGS.
	</P>
	<UL><LI>CCFLAGS: add -fopenmp and -restrict
	<LI>LINKFLAGS: add -fopenmp
	</UL>
	<P>For the OPT package, your Makefile.machine needs an additional
	settings for CCFLAGS.
	</P>
	<UL><LI>CCFLAGS: add -restrict
	</UL>
	<HR>

	<H4><A NAME = "start_4"></A>2.4 Building LAMMPS via the Make.py script
	</H4>
	<P>The src directory includes a Make.py script, written in Python, which
	can be used to automate various steps of the build process. It is
	particularly useful for working with the accelerator packages, as well
	as other packages which require auxiliary libraries to be built.
	</P>
	<P>The goal of the Make.py tool is to allow any complex multi-step LAMMPS
	build to be performed as a single Make.py command. And you can
	archive the commands, so they can be re-invoked later via the -r
	(redo) switch. If you find some LAMMPS build procedure that can't be
	done in a single Make.py command, let the developers know, and we'll
	see if we can augment the tool.
	</P>
	<P>You can run Make.py from the src directory by typing either:
	</P>
	<PRE>Make.py -h
	python Make.py -h
	</PRE>
	<P>which will give you help info about the tool. For the former to work,
	you may need to edit the first line of Make.py to point to your local
	Python. And you may need to insure the script is executable:
	</P>
	<PRE>chmod +x Make.py
	</PRE>
	<P>Here are examples of build tasks you can perform with Make.py:
	</P>
	<DIV ALIGN=center><TABLE BORDER=1 >
	<TR><TD >Install/uninstall packages</TD><TD > Make.py -p no-lib kokkos omp intel</TD></TR>
	<TR><TD >Build specific auxiliary libs</TD><TD > Make.py -a lib-atc lib-meam</TD></TR>
	<TR><TD >Build libs for all installed packages</TD><TD > Make.py -p cuda gpu -gpu mode=double arch=31 -a lib-all</TD></TR>
	<TR><TD >Create a Makefile from scratch with compiler and MPI settings</TD><TD > Make.py -m none -cc g++ -mpi mpich -a file</TD></TR>
	<TR><TD >Augment Makefile.serial with settings for installed packages</TD><TD > Make.py -p intel -intel cpu -m serial -a file</TD></TR>
	<TR><TD >Add JPG and FFTW support to Makefile.mpi</TD><TD > Make.py -m mpi -jpg -fft fftw -a file</TD></TR>
	<TR><TD >Build LAMMPS with a parallel make using Makefile.mpi</TD><TD > Make.py -j 16 -m mpi -a exe</TD></TR>
	<TR><TD >Build LAMMPS and libs it needs using Makefile.serial with accelerator settings</TD><TD > Make.py -p gpu intel -intel cpu -a lib-all file serial
	</TD></TR></TABLE></DIV>

	<P>The bench and examples directories give Make.py commands that can be
	used to build LAMMPS with the various packages and options needed to
	run all the benchmark and example input scripts. See these files for
	more details:
	</P>
	<UL><LI>bench/README
	<LI>bench/FERMI/README
	<LI>bench/KEPLER/README
	<LI>bench/PHI/README
	<LI>examples/README
	<LI>examples/accelerate/README
	<LI>examples/accelerate/make.list
	</UL>
	<P>All of the Make.py options and syntax help can be accessed by using
	the "-h" switch.
	</P>
	<P>E.g. typing "Make.py -h" gives
	</P>
	<PRE>Syntax: Make.py switch args ...
	switches can be listed in any order
	help switch:
	-h prints help and syntax for all other specified switches
	switch for actions:
	-a lib-all, lib-dir, clean, file, exe or machine
	list one or more actions, in any order
	machine is a Makefile.machine suffix, must be last if used
	one-letter switches:
	-d (dir), -j (jmake), -m (makefile), -o (output),
	-p (packages), -r (redo), -s (settings), -v (verbose)
	switches for libs:
	-atc, -awpmd, -colvars, -cuda
	-gpu, -meam, -poems, -qmmm, -reax
	switches for build and makefile options:
	-intel, -kokkos, -cc, -mpi, -fft, -jpg, -png
	</PRE>
	<P>Using the "-h" switch with other switches and actions gives additional
	info on all the other specified switches or actions. The "-h" can be
	anywhere in the command-line and the other switches do not need their
	arguments. E.g. type "Make.py -h -d -atc -intel" will print:
	</P>
	<PRE>-d dir
	dir = LAMMPS home dir
	if -d not specified, working dir must be lammps/src
	</PRE>
	<PRE>-atc make=suffix lammps=suffix2
	all args are optional and can be in any order
	make = use Makefile.suffix (def = g++)
	lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile)
	</PRE>
	<PRE>-intel mode
	mode = cpu or phi (def = cpu)
	build Intel package for CPU or Xeon Phi
	</PRE>
	<P>Note that Make.py never overwrites an existing Makefile.machine.
	Instead, it creates src/MAKE/MINE/Makefile.auto, which you can save or
	rename if desired. Likewise it creates an executable named
	src/lmp_auto, which you can rename using the -o switch if desired.
	</P>
	<P>The most recently executed Make.py commmand is saved in
	src/Make.py.last. You can use the "-r" switch (for redo) to re-invoke
	the last command, or you can save a sequence of one or more Make.py
	commands to a file and invoke the file of commands using "-r". You
	can also label the commands in the file and invoke one or more of them
	by name.
	</P>
	<P>A typical use of Make.py is to start with a valid Makefile.machine for
	your system, that works for a vanilla LAMMPS build, i.e. when optional
	packages are not installed. You can then use Make.py to add various
	settings (FFT, JPG, PNG) to the Makefile.machine as well as change its
	compiler and MPI options. You can also add additional packages to the
	build, as well as build the needed supporting libraries.
	</P>
	<P>You can also use Make.py to create a new Makefile.machine from
	scratch, using the "-m none" switch, if you also specify what compiler
	and MPI options to use, via the "-cc" and "-mpi" switches.
	</P>
	<HR>

	<H4><A NAME = "start_5"></A>2.5 Building LAMMPS as a library
	</H4>
	<P>LAMMPS can be built as either a static or shared library, which can
	then be called from another application or a scripting language. See
	<A HREF = "Section_howto.html#howto_10">this section</A> for more info on coupling
	LAMMPS to other codes. See <A HREF = "Section_python.html">this section</A> for
	more info on wrapping and running LAMMPS from Python.
	</P>
	<H5><B>Static library:</B>
	</H5>
	<P>To build LAMMPS as a static library (*.a file on Linux), type
	</P>
	<PRE>make foo mode=lib
	</PRE>
	<P>where foo is the machine name. This kind of library is typically used
	to statically link a driver application to LAMMPS, so that you can
	insure all dependencies are satisfied at compile time. This will use
	the ARCHIVE and ARFLAGS settings in src/MAKE/Makefile.foo. The build
	will create the file liblammps_foo.a which another application can
	link to. It will also create a soft link liblammps.a, which will
	point to the most recently built static library.
	</P>
	<H5><B>Shared library:</B>
	</H5>
	<P>To build LAMMPS as a shared library (*.so file on Linux), which can be
	dynamically loaded, e.g. from Python, type
	</P>
	<PRE>make foo mode=shlib
	</PRE>
	<P>where foo is the machine name. This kind of library is required when
	wrapping LAMMPS with Python; see <A HREF = "Section_python.html">Section_python</A>
	for details. This will use the SHFLAGS and SHLIBFLAGS settings in
	src/MAKE/Makefile.foo and perform the build in the directory
	Obj_shared_foo. This is so that each file can be compiled with the
	-fPIC flag which is required for inclusion in a shared library. The
	build will create the file liblammps_foo.so which another application
	can link to dyamically. It will also create a soft link liblammps.so,
	which will point to the most recently built shared library. This is
	the file the Python wrapper loads by default.
	</P>
	<P>Note that for a shared library to be usable by a calling program, all
	the auxiliary libraries it depends on must also exist as shared
	libraries. This will be the case for libraries included with LAMMPS,
	such as the dummy MPI library in src/STUBS or any package libraries in
	lib/packages, since they are always built as shared libraries using
	the -fPIC switch. However, if a library like MPI or FFTW does not
	exist as a shared library, the shared library build will generate an
	error. This means you will need to install a shared library version
	of the auxiliary library. The build instructions for the library
	should tell you how to do this.
	</P>
	<P>Here is an example of such errors when the system FFTW or provided
	lib/colvars library have not been built as shared libraries:
	</P>
	<PRE>/usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation
	R_X86_64_32 against `.rodata' can not be used when making a shared
	object; recompile with -fPIC
	/usr/local/lib/libfftw3.a: could not read symbols: Bad value
	</PRE>
	<PRE>/usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o):
	relocation R_X86_64_32 against `__pthread_key_create' can not be used
	when making a shared object; recompile with -fPIC
	../../lib/colvars/libcolvars.a: error adding symbols: Bad value
	</PRE>
	<P>As an example, here is how to build and install the <A HREF = "http://www-unix.mcs.anl.gov/mpi">MPICH
	library</A>, a popular open-source version of MPI, distributed by
	Argonne National Labs, as a shared library in the default
	/usr/local/lib location:
	</P>


	<PRE>./configure --enable-shared
	make
	make install
	</PRE>
	<P>You may need to use "sudo make install" in place of the last line if
	you do not have write privileges for /usr/local/lib. The end result
	should be the file /usr/local/lib/libmpich.so.
	</P>
	<H5><B>Additional requirement for using a shared library:</B>
	</H5>
	<P>The operating system finds shared libraries to load at run-time using
	the environment variable LD_LIBRARY_PATH. So you may wish to copy the
	file src/liblammps.so or src/liblammps_g++.so (for example) to a place
	the system can find it by default, such as /usr/local/lib, or you may
	wish to add the LAMMPS src directory to LD_LIBRARY_PATH, so that the
	current version of the shared library is always available to programs
	that use it.
	</P>
	<P>For the csh or tcsh shells, you would add something like this to your
	~/.cshrc file:
	</P>
	<PRE>setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
	</PRE>
	<H5><B>Calling the LAMMPS library:</B>
	</H5>
	<P>Either flavor of library (static or shared) allows one or more LAMMPS
	objects to be instantiated from the calling program.
	</P>
	<P>When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS
	namespace; you can safely use any of its classes and methods from
	within the calling code, as needed.
	</P>
	<P>When used from a C or Fortran program or a scripting language like
	Python, the library has a simple function-style interface, provided in
	src/library.cpp and src/library.h.
	</P>
	<P>See the sample codes in examples/COUPLE/simple for examples of C++ and
	C and Fortran codes that invoke LAMMPS thru its library interface.
	There are other examples as well in the COUPLE directory which are
	discussed in <A HREF = "Section_howto.html#howto_10">Section_howto 10</A> of the
	manual. See <A HREF = "Section_python.html">Section_python</A> of the manual for a
	description of the Python wrapper provided with LAMMPS that operates
	through the LAMMPS library interface.
	</P>
	<P>The files src/library.cpp and library.h define the C-style API for
	using LAMMPS as a library. See <A HREF = "Section_howto.html#howto_19">Section_howto
	19</A> of the manual for a description of the
	interface and how to extend it for your needs.
	</P>
	<HR>

	<H4><A NAME = "start_6"></A>2.6 Running LAMMPS
	</H4>
	<P>By default, LAMMPS runs by reading commands from standard input. Thus
	if you run the LAMMPS executable by itself, e.g.
	</P>
	<PRE>lmp_linux
	</PRE>
	<P>it will simply wait, expecting commands from the keyboard. Typically
	you should put commands in an input script and use I/O redirection,
	e.g.
	</P>
	<PRE>lmp_linux < in.file
	</PRE>
	<P>For parallel environments this should also work. If it does not, use
	the '-in' command-line switch, e.g.
	</P>
	<PRE>lmp_linux -in in.file
	</PRE>
	<P><A HREF = "Section_commands.html">This section</A> describes how input scripts are
	structured and what commands they contain.
	</P>
	<P>You can test LAMMPS on any of the sample inputs provided in the
	examples or bench directory. Input scripts are named in.* and sample
	outputs are named log.*.name.P where name is a machine and P is the
	number of processors it was run on.
	</P>
	<P>Here is how you might run a standard Lennard-Jones benchmark on a
	Linux box, using mpirun to launch a parallel job:
	</P>
	<PRE>cd src
	make linux
	cp lmp_linux ../bench
	cd ../bench
	mpirun -np 4 lmp_linux -in in.lj
	</PRE>
	<P>See <A HREF = "http://lammps.sandia.gov/bench.html">this page</A> for timings for this and the other benchmarks on
	various platforms. Note that some of the example scripts require
	LAMMPS to be built with one or more of its optional packages.
	</P>


	<HR>

	<P>On a Windows box, you can skip making LAMMPS and simply download an
	executable, as described above, though the pre-packaged executables
	include only certain packages.
	</P>
	<P>To run a LAMMPS executable on a Windows machine, first decide whether
	you want to download the non-MPI (serial) or the MPI (parallel)
	version of the executable. Download and save the version you have
	chosen.
	</P>
	<P>For the non-MPI version, follow these steps:
	</P>
	<UL><LI>Get a command prompt by going to Start->Run... ,
	then typing "cmd".

	<LI>Move to the directory where you have saved lmp_win_no-mpi.exe
	(e.g. by typing: cd "Documents").

	<LI>At the command prompt, type "lmp_win_no-mpi -in in.lj", replacing in.lj
	with the name of your LAMMPS input script.
	</UL>
	<P>For the MPI version, which allows you to run LAMMPS under Windows on
	multiple processors, follow these steps:
	</P>
	<UL><LI>Download and install
	<A HREF = "http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downloads">MPICH2</A>
	for Windows.

	<LI>You'll need to use the mpiexec.exe and smpd.exe files from the MPICH2
	package. Put them in same directory (or path) as the LAMMPS Windows
	executable.

	<LI>Get a command prompt by going to Start->Run... ,
	then typing "cmd".

	<LI>Move to the directory where you have saved lmp_win_mpi.exe
	(e.g. by typing: cd "Documents").

	<LI>Then type something like this: "mpiexec -localonly 4 lmp_win_mpi -in
	in.lj", replacing in.lj with the name of your LAMMPS input script.

	<LI>Note that you may need to provide smpd with a passphrase (it doesn't
	matter what you type).

	<LI>In this mode, output may not immediately show up on the screen, so if
	your input script takes a long time to execute, you may need to be
	patient before the output shows up. :l Alternatively, you can still
	use this executable to run on a single processor by typing something
	like: "lmp_win_mpi -in in.lj".
	</UL>
	<HR>

	<P>The screen output from LAMMPS is described in the next section. As it
	runs, LAMMPS also writes a log.lammps file with the same information.
	</P>
	<P>Note that this sequence of commands copies the LAMMPS executable
	(lmp_linux) to the directory with the input files. This may not be
	necessary, but some versions of MPI reset the working directory to
	where the executable is, rather than leave it as the directory where
	you launch mpirun from (if you launch lmp_linux on its own and not
	under mpirun). If that happens, LAMMPS will look for additional input
	files and write its output files to the executable directory, rather
	than your working directory, which is probably not what you want.
	</P>
	<P>If LAMMPS encounters errors in the input script or while running a
	simulation it will print an ERROR message and stop or a WARNING
	message and continue. See <A HREF = "Section_errors.html">Section_errors</A> for a
	discussion of the various kinds of errors LAMMPS can or can't detect,
	a list of all ERROR and WARNING messages, and what to do about them.
	</P>
	<P>LAMMPS can run a problem on any number of processors, including a
	single processor. In theory you should get identical answers on any
	number of processors and on any machine. In practice, numerical
	round-off can cause slight differences and eventual divergence of
	molecular dynamics phase space trajectories.
	</P>
	<P>LAMMPS can run as large a problem as will fit in the physical memory
	of one or more processors. If you run out of memory, you must run on
	more processors or setup a smaller problem.
	</P>
	<HR>

	<H4><A NAME = "start_7"></A>2.7 Command-line options
	</H4>
	<P>At run time, LAMMPS recognizes several optional command-line switches
	which may be used in any order. Either the full word or a one-or-two
	letter abbreviation can be used:
	</P>
	<UL><LI>-c or -cuda
	<LI>-e or -echo
	<LI>-h or -help
	<LI>-i or -in
	<LI>-k or -kokkos
	<LI>-l or -log
	<LI>-nc or -nocite
	<LI>-pk or -package
	<LI>-p or -partition
	<LI>-pl or -plog
	<LI>-ps or -pscreen
	<LI>-r or -restart
	<LI>-ro or -reorder
	<LI>-sc or -screen
	<LI>-sf or -suffix
	<LI>-v or -var
	</UL>
	<P>For example, lmp_ibm might be launched as follows:
	</P>
	<PRE>mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none -in in.alloy
	mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none -in in.alloy
	</PRE>
	<P>Here are the details on the options:
	</P>
	<PRE>-cuda on/off
	</PRE>
	<P>Explicitly enable or disable CUDA support, as provided by the
	USER-CUDA package. Even if LAMMPS is built with this package, as
	described above in <A HREF = "#start_3">Section 2.3</A>, this switch must be set to
	enable running with the CUDA-enabled styles the package provides. If
	the switch is not set (the default), LAMMPS will operate as if the
	USER-CUDA package were not installed; i.e. you can run standard LAMMPS
	or with the GPU package, for testing or benchmarking purposes.
	</P>
	<PRE>-echo style
	</PRE>
	<P>Set the style of command echoing. The style can be <I>none</I> or <I>screen</I>
	or <I>log</I> or <I>both</I>. Depending on the style, each command read from
	the input script will be echoed to the screen and/or logfile. This
	can be useful to figure out which line of your script is causing an
	input error. The default value is <I>log</I>. The echo style can also be
	set by using the <A HREF = "echo.html">echo</A> command in the input script itself.
	</P>
	<PRE>-help
	</PRE>
	<P>Print a brief help summary and a list of options compiled into this
	executable for each LAMMPS style (atom_style, fix, compute,
	pair_style, bond_style, etc). This can tell you if the command you
	want to use was included via the appropriate package at compile time.
	LAMMPS will print the info and immediately exit if this switch is
	used.
	</P>
	<PRE>-in file
	</PRE>
	<P>Specify a file to use as an input script. This is an optional switch
	when running LAMMPS in one-partition mode. If it is not specified,
	LAMMPS reads its script from standard input, typically from a script
	via I/O redirection; e.g. lmp_linux < in.run. I/O redirection should
	also work in parallel, but if it does not (in the unlikely case that
	an MPI implementation does not support it), then use the -in flag.
	Note that this is a required switch when running LAMMPS in
	multi-partition mode, since multiple processors cannot all read from
	stdin.
	</P>
	<PRE>-kokkos on/off keyword/value ...
	</PRE>
	<P>Explicitly enable or disable KOKKOS support, as provided by the KOKKOS
	package. Even if LAMMPS is built with this package, as described
	above in <A HREF = "#start_3">Section 2.3</A>, this switch must be set to enable
	running with the KOKKOS-enabled styles the package provides. If the
	switch is not set (the default), LAMMPS will operate as if the KOKKOS
	package were not installed; i.e. you can run standard LAMMPS or with
	the GPU or USER-CUDA or USER-OMP packages, for testing or benchmarking
	purposes.
	</P>
	<P>Additional optional keyword/value pairs can be specified which
	determine how Kokkos will use the underlying hardware on your
	platform. These settings apply to each MPI task you launch via the
	"mpirun" or "mpiexec" command. You may choose to run one or more MPI
	tasks per physical node. Note that if you are running on a desktop
	machine, you typically have one physical node. On a cluster or
	supercomputer there may be dozens or 1000s of physical nodes.
	</P>
	<P>Either the full word or an abbreviation can be used for the keywords.
	Note that the keywords do not use a leading minus sign. I.e. the
	keyword is "t", not "-t". Also note that each of the keywords has a
	default setting. Example of when to use these options and what
	settings to use on different platforms is given in <A HREF = "Section_accelerate.html#acc_8">Section
	5.8</A>.
	</P>
	<UL><LI>d or device
	<LI>g or gpus
	<LI>t or threads
	<LI>n or numa
	</UL>
	<PRE>device Nd
	</PRE>
	<P>This option is only relevant if you built LAMMPS with CUDA=yes, you
	have more than one GPU per node, and if you are running with only one
	MPI task per node. The Nd setting is the ID of the GPU on the node to
	run on. By default Nd = 0. If you have multiple GPUs per node, they
	have consecutive IDs numbered as 0,1,2,etc. This setting allows you
	to launch multiple independent jobs on the node, each with a single
	MPI task per node, and assign each job to run on a different GPU.
	</P>
	<PRE>gpus Ng Ns
	</PRE>
	<P>This option is only relevant if you built LAMMPS with CUDA=yes, you
	have more than one GPU per node, and you are running with multiple MPI
	tasks per node (up to one per GPU). The Ng setting is how many GPUs
	you will use. The Ns setting is optional. If set, it is the ID of a
	GPU to skip when assigning MPI tasks to GPUs. This may be useful if
	your desktop system reserves one GPU to drive the screen and the rest
	are intended for computational work like running LAMMPS. By default
	Ng = 1 and Ns is not set.
	</P>
	<P>Depending on which flavor of MPI you are running, LAMMPS will look for
	one of these 3 environment variables
	</P>
	<PRE>SLURM_LOCALID (various MPI variants compiled with SLURM support)
	MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
	OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI)
	</PRE>
	<P>which are initialized by the "srun", "mpirun" or "mpiexec" commands.
	The environment variable setting for each MPI rank is used to assign a
	unique GPU ID to the MPI task.
	</P>
	<PRE>threads Nt
	</PRE>
	<P>This option assigns Nt number of threads to each MPI task for
	performing work when Kokkos is executing in OpenMP or pthreads mode.
	The default is Nt = 1, which essentially runs in MPI-only mode. If
	there are Np MPI tasks per physical node, you generally want Np*Nt =
	the number of physical cores per node, to use your available hardware
	optimally. This also sets the number of threads used by the host when
	LAMMPS is compiled with CUDA=yes.
	</P>
	<PRE>numa Nm
	</PRE>
	<P>This option is only relevant when using pthreads with hwloc support.
	In this case Nm defines the number of NUMA regions (typicaly sockets)
	on a node which will be utilizied by a single MPI rank. By default Nm
	= 1. If this option is used the total number of worker-threads per
	MPI rank is threads*numa. Currently it is always almost better to
	assign at least one MPI rank per NUMA region, and leave numa set to
	its default value of 1. This is because letting a single process span
	multiple NUMA regions induces a significant amount of cross NUMA data
	traffic which is slow.
	</P>
	<PRE>-log file
	</PRE>
	<P>Specify a log file for LAMMPS to write status information to. In
	one-partition mode, if the switch is not used, LAMMPS writes to the
	file log.lammps. If this switch is used, LAMMPS writes to the
	specified file. In multi-partition mode, if the switch is not used, a
	log.lammps file is created with hi-level status information. Each
	partition also writes to a log.lammps.N file where N is the partition
	ID. If the switch is specified in multi-partition mode, the hi-level
	logfile is named "file" and each partition also logs information to a
	file.N. For both one-partition and multi-partition mode, if the
	specified file is "none", then no log files are created. Using a
	<A HREF = "log.html">log</A> command in the input script will override this setting.
	Option -plog will override the name of the partition log files file.N.
	</P>
	<PRE>-nocite
	</PRE>
	<P>Disable writing the log.cite file which is normally written to list
	references for specific cite-able features used during a LAMMPS run.
	See the <A HREF = "http://lammps.sandia.gov/cite.html">citation page</A> for more
	details.
	</P>
	<PRE>-package style args ....
	</PRE>
	<P>Invoke the <A HREF = "package.html">package</A> command with style and args. The
	syntax is the same as if the command appeared at the top of the input
	script. For example "-package gpu 2" or "-pk gpu 2" is the same as
	<A HREF = "package.html">package gpu 2</A> in the input script. The possible styles
	and args are documented on the <A HREF = "package.html">package</A> doc page. This
	switch can be used multiple times, e.g. to set options for the
	USER-INTEL and USER-OMP packages which can be used together.
	</P>
	<P>Along with the "-suffix" command-line switch, this is a convenient
	mechanism for invoking accelerator packages and their options without
	having to edit an input script.
	</P>
	<PRE>-partition 8x2 4 5 ...
	</PRE>
	<P>Invoke LAMMPS in multi-partition mode. When LAMMPS is run on P
	processors and this switch is not used, LAMMPS runs in one partition,
	i.e. all P processors run a single simulation. If this switch is
	used, the P processors are split into separate partitions and each
	partition runs its own simulation. The arguments to the switch
	specify the number of processors in each partition. Arguments of the
	form MxN mean M partitions, each with N processors. Arguments of the
	form N mean a single partition with N processors. The sum of
	processors in all partitions must equal P. Thus the command
	"-partition 8x2 4 5" has 10 partitions and runs on a total of 25
	processors.
	</P>
	<P>Running with multiple partitions can e useful for running
	<A HREF = "Section_howto.html#howto_5">multi-replica simulations</A>, where each
	replica runs on on one or a few processors. Note that with MPI
	installed on a machine (e.g. your desktop), you can run on more
	(virtual) processors than you have physical processors.
	</P>
	<P>To run multiple independent simulatoins from one input script, using
	multiple partitions, see <A HREF = "Section_howto.html#howto_4">Section_howto 4</A>
	of the manual. World- and universe-style <A HREF = "variable.html">variables</A>
	are useful in this context.
	</P>
	<PRE>-plog file
	</PRE>
	<P>Specify the base name for the partition log files, so partition N
	writes log information to file.N. If file is none, then no partition
	log files are created. This overrides the filename specified in the
	-log command-line option. This option is useful when working with
	large numbers of partitions, allowing the partition log files to be
	suppressed (-plog none) or placed in a sub-directory (-plog
	replica_files/log.lammps) If this option is not used the log file for
	partition N is log.lammps.N or whatever is specified by the -log
	command-line option.
	</P>
	<PRE>-pscreen file
	</PRE>
	<P>Specify the base name for the partition screen file, so partition N
	writes screen information to file.N. If file is none, then no
	partition screen files are created. This overrides the filename
	specified in the -screen command-line option. This option is useful
	when working with large numbers of partitions, allowing the partition
	screen files to be suppressed (-pscreen none) or placed in a
	sub-directory (-pscreen replica_files/screen). If this option is not
	used the screen file for partition N is screen.N or whatever is
	specified by the -screen command-line option.
	</P>
	<PRE>-restart restartfile <I>remap</I> datafile keyword value ...
	</PRE>
	<P>Convert the restart file into a data file and immediately exit. This
	is the same operation as if the following 2-line input script were
	run:
	</P>
	<PRE>read_restart restartfile <I>remap</I>
	write_data datafile keyword value ...
	</PRE>
	<P>Note that the specified restartfile and datafile can have wild-card
	characters ("*",%") as described by the
	<A HREF = "read_restart.html">read_restart</A> and <A HREF = "write_data.html">write_data</A>
	commands. But a filename such as file.* will need to be enclosed in
	quotes to avoid shell expansion of the "*" character.
	</P>
	<P>Note that following restartfile, the optional flag <I>remap</I> can be
	used. This has the same effect as adding it to the
	<A HREF = "read_restart.html">read_restart</A> command, as explained on its doc
	page. This is only useful if the reading of the restart file triggers
	an error that atoms have been lost. In that case, use of the remap
	flag should allow the data file to still be produced.
	</P>
	<P>Also note that following datafile, the same optional keyword/value
	pairs can be listed as used by the <A HREF = "write_data.html">write_data</A>
	command.
	</P>
	<PRE>-reorder nth N
	-reorder custom filename
	</PRE>
	<P>Reorder the processors in the MPI communicator used to instantiate
	LAMMPS, in one of several ways. The original MPI communicator ranks
	all P processors from 0 to P-1. The mapping of these ranks to
	physical processors is done by MPI before LAMMPS begins. It may be
	useful in some cases to alter the rank order. E.g. to insure that
	cores within each node are ranked in a desired order. Or when using
	the <A HREF = "run_style.html">run_style verlet/split</A> command with 2 partitions
	to insure that a specific Kspace processor (in the 2nd partition) is
	matched up with a specific set of processors in the 1st partition.
	See the <A HREF = "Section_accelerate.html">Section_accelerate</A> doc pages for
	more details.
	</P>
	<P>If the keyword <I>nth</I> is used with a setting <I>N</I>, then it means every
	Nth processor will be moved to the end of the ranking. This is useful
	when using the <A HREF = "run_style.html">run_style verlet/split</A> command with 2
	partitions via the -partition command-line switch. The first set of
	processors will be in the first partition, the 2nd set in the 2nd
	partition. The -reorder command-line switch can alter this so that
	the 1st N procs in the 1st partition and one proc in the 2nd partition
	will be ordered consecutively, e.g. as the cores on one physical node.
	This can boost performance. For example, if you use "-reorder nth 4"
	and "-partition 9 3" and you are running on 12 processors, the
	processors will be reordered from
	</P>
	<PRE>0 1 2 3 4 5 6 7 8 9 10 11
	</PRE>
	<P>to
	</P>
	<PRE>0 1 2 4 5 6 8 9 10 3 7 11
	</PRE>
	<P>so that the processors in each partition will be
	</P>
	<PRE>0 1 2 4 5 6 8 9 10
	3 7 11
	</PRE>
	<P>See the "processors" command for how to insure processors from each
	partition could then be grouped optimally for quad-core nodes.
	</P>
	<P>If the keyword is <I>custom</I>, then a file that specifies a permutation
	of the processor ranks is also specified. The format of the reorder
	file is as follows. Any number of initial blank or comment lines
	(starting with a "#" character) can be present. These should be
	followed by P lines of the form:
	</P>
	<PRE>I J
	</PRE>
	<P>where P is the number of processors LAMMPS was launched with. Note
	that if running in multi-partition mode (see the -partition switch
	above) P is the total number of processors in all partitions. The I
	and J values describe a permutation of the P processors. Every I and
	J should be values from 0 to P-1 inclusive. In the set of P I values,
	every proc ID should appear exactly once. Ditto for the set of P J
	values. A single I,J pairing means that the physical processor with
	rank I in the original MPI communicator will have rank J in the
	reordered communicator.
	</P>
	<P>Note that rank ordering can also be specified by many MPI
	implementations, either by environment variables that specify how to
	order physical processors, or by config files that specify what
	physical processors to assign to each MPI rank. The -reorder switch
	simply gives you a portable way to do this without relying on MPI
	itself. See the <A HREF = "processors">processors out</A> command for how to output
	info on the final assignment of physical processors to the LAMMPS
	simulation domain.
	</P>
	<PRE>-screen file
	</PRE>
	<P>Specify a file for LAMMPS to write its screen information to. In
	one-partition mode, if the switch is not used, LAMMPS writes to the
	screen. If this switch is used, LAMMPS writes to the specified file
	instead and you will see no screen output. In multi-partition mode,
	if the switch is not used, hi-level status information is written to
	the screen. Each partition also writes to a screen.N file where N is
	the partition ID. If the switch is specified in multi-partition mode,
	the hi-level screen dump is named "file" and each partition also
	writes screen information to a file.N. For both one-partition and
	multi-partition mode, if the specified file is "none", then no screen
	output is performed. Option -pscreen will override the name of the
	partition screen files file.N.
	</P>
	<PRE>-suffix style
	</PRE>
	<P>Use variants of various styles if they exist. The specified style can
	be <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I>. These refer to
	optional packages that LAMMPS can be built with, as described above in
	<A HREF = "#start_3">Section 2.3</A>. The "cuda" style corresponds to the USER-CUDA
	package, the "gpu" style to the GPU package, the "intel" style to the
	USER-INTEL package, the "kk" style to the KOKKOS package, the "opt"
	style to the OPT package, and the "omp" style to the USER-OMP package.
	</P>
	<P>Along with the "-package" command-line switch, this is a convenient
	mechanism for invoking accelerator packages and their options without
	having to edit an input script.
	</P>
	<P>As an example, all of the packages provide a <A HREF = "pair_lj.html">pair_style
	lj/cut</A> variant, with style names lj/cut/cuda,
	lj/cut/gpu, lj/cut/intel, lj/cut/kk, lj/cut/omp, and lj/cut/opt. A
	variant style can be specified explicitly in your input script,
	e.g. pair_style lj/cut/gpu. If the -suffix switch is used the
	specified suffix (cuda,gpu,intel,kk,omp,opt) is automatically appended
	whenever your input script command creates a new
	<A HREF = "atom_style.html">atom</A>, <A HREF = "pair_style.html">pair</A>, <A HREF = "fix.html">fix</A>,
	<A HREF = "compute.html">compute</A>, or <A HREF = "run_style.html">run</A> style. If the variant
	version does not exist, the standard version is created.
	</P>
	<P>For the GPU package, using this command-line switch also invokes the
	default GPU settings, as if the command "package gpu 1" were used at
	the top of your input script. These settings can be changed by using
	the "-package gpu" command-line switch or the <A HREF = "package.html">package
	gpu</A> command in your script.
	</P>
	<P>For the USER-INTEL package, using this command-line switch also
	invokes the default USER-INTEL settings, as if the command "package
	intel 1" were used at the top of your input script. These settings
	can be changed by using the "-package intel" command-line switch or
	the <A HREF = "package.html">package intel</A> command in your script. If the
	USER-OMP package is also installed, the intel suffix will make the omp
	suffix a second choice, if a requested style is not available in the
	USER-INTEL package. It will also invoke the default USER-OMP
	settings, as if the command "package omp 0" were used at the top of
	your input script. These settings can be changed by using the
	"-package omp" command-line switch or the <A HREF = "package.html">package omp</A>
	command in your script.
	</P>
	<P>For the KOKKOS package, using this command-line switch also invokes
	the default KOKKOS settings, as if the command "package kokkos" were
	used at the top of your input script. These settings can be changed
	by using the "-package kokkos" command-line switch or the <A HREF = "package.html">package
	kokkos</A> command in your script.
	</P>
	<P>For the OMP package, using this command-line switch also invokes the
	default OMP settings, as if the command "package omp 0" were used at
	the top of your input script. These settings can be changed by using
	the "-package omp" command-line switch or the <A HREF = "package.html">package
	omp</A> command in your script.
	</P>
	<P>The <A HREF = "suffix.html">suffix</A> command can also be used within an input
	script to set a suffix, or to turn off or back on any suffix setting
	made via the command line.
	</P>
	<PRE>-var name value1 value2 ...
	</PRE>
	<P>Specify a variable that will be defined for substitution purposes when
	the input script is read. This switch can be used multiple times to
	define multiple variables. "Name" is the variable name which can be a
	single character (referenced as $x in the input script) or a full
	string (referenced as ${abc}). An <A HREF = "variable.html">index-style
	variable</A> will be created and populated with the
	subsequent values, e.g. a set of filenames. Using this command-line
	option is equivalent to putting the line "variable name index value1
	value2 ..." at the beginning of the input script. Defining an index
	variable as a command-line argument overrides any setting for the same
	index variable in the input script, since index variables cannot be
	re-defined. See the <A HREF = "variable.html">variable</A> command for more info on
	defining index and other kinds of variables and <A HREF = "Section_commands.html#cmd_2">this
	section</A> for more info on using variables
	in input scripts.
	</P>
	<P>NOTE: Currently, the command-line parser looks for arguments that
	start with "-" to indicate new switches. Thus you cannot specify
	multiple variable values if any of they start with a "-", e.g. a
	negative numeric value. It is OK if the first value1 starts with a
	"-", since it is automatically skipped.
	</P>
	<HR>

	<H4><A NAME = "start_8"></A>2.8 LAMMPS screen output
	</H4>
	<P>As LAMMPS reads an input script, it prints information to both the
	screen and a log file about significant actions it takes to setup a
	simulation. When the simulation is ready to begin, LAMMPS performs
	various initializations and prints the amount of memory (in MBytes per
	processor) that the simulation requires. It also prints details of
	the initial thermodynamic state of the system. During the run itself,
	thermodynamic information is printed periodically, every few
	timesteps. When the run concludes, LAMMPS prints the final
	thermodynamic state and a total run time for the simulation. It then
	appends statistics about the CPU time and storage requirements for the
	simulation. An example set of statistics is shown here:
	</P>
	<P>Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
	</P>
	<PRE>Performance: 18.436 ns/day 1.302 hours/ns 106.689 timesteps/s
	97.0% CPU use with 4 MPI tasks x no OpenMP threads
	</PRE>
	<PRE>MPI task timings breakdown:
	Section \| min time \| avg time \| max time \|%varavg\| %total
	---------------------------------------------------------------
	Pair \| 1.9808 \| 2.0134 \| 2.0318 \| 1.4 \| 71.60
	Bond \| 0.0021894 \| 0.0060319 \| 0.010058 \| 4.7 \| 0.21
	Kspace \| 0.3207 \| 0.3366 \| 0.36616 \| 3.1 \| 11.97
	Neigh \| 0.28411 \| 0.28464 \| 0.28516 \| 0.1 \| 10.12
	Comm \| 0.075732 \| 0.077018 \| 0.07883 \| 0.4 \| 2.74
	Output \| 0.00030518 \| 0.00042665 \| 0.00078821 \| 1.0 \| 0.02
	Modify \| 0.086606 \| 0.086631 \| 0.086668 \| 0.0 \| 3.08
	Other \| \| 0.007178 \| \| \| 0.26
	</PRE>
	<PRE>Nlocal: 501 ave 508 max 490 min
	Histogram: 1 0 0 0 0 0 1 1 0 1
	Nghost: 6586.25 ave 6628 max 6548 min
	Histogram: 1 0 1 0 0 0 1 0 0 1
	Neighs: 177007 ave 180562 max 170212 min
	Histogram: 1 0 0 0 0 0 0 1 1 1
	</PRE>
	<PRE>Total # of neighbors = 708028
	Ave neighs/atom = 353.307
	Ave special neighs/atom = 2.34032
	Neighbor list builds = 26
	Dangerous builds = 0
	</PRE>
	<P>The first section provides a global loop timing summary. The loop time
	is the total wall time for the section. The <I>Performance</I> line is
	provided for convenience to help predicting the number of loop
	continuations required and for comparing performance with other
	similar MD codes. The CPU use line provides the CPU utilzation per
	MPI task; it should be close to 100% times the number of OpenMP
	threads (or 1). Lower numbers correspond to delays due to file I/O or
	insufficient thread utilization.
	</P>
	<P>The MPI task section gives the breakdown of the CPU run time (in
	seconds) into major categories:
	</P>
	<UL><LI><I>Pair</I> stands for all non-bonded force computation
	<LI><I>Bond</I> stands for bonded interactions: bonds, angles, dihedrals, impropers
	<LI><I>Kspace</I> stands for reciprocal space interactions: Ewald, PPPM, MSM
	<LI><I>Neigh</I> stands for neighbor list construction
	<LI><I>Comm</I> stands for communicating atoms and their properties
	<LI><I>Output</I> stands for writing dumps and thermo output
	<LI><I>Modify</I> stands for fixes and computes called by them
	<LI><I>Other</I> is the remaining time
	</UL>
	<P>For each category, there is a breakdown of the least, average and most
	amount of wall time a processor spent on this section. Also you have the
	variation from the average time. Together these numbers allow to gauge
	the amount of load imbalance in this segment of the calculation. Ideally
	the difference between minimum, maximum and average is small and thus
	the variation from the average close to zero. The final column shows
	the percentage of the total loop time is spent in this section.
	</P>
	<P>When using the <A HREF = "timers.html">timers full</A> setting, an additional column
	is present that also prints the CPU utilization in percent. In
	addition, when using <I>timers full</I> and the <A HREF = "package.html">package omp</A>
	command are active, a similar timing summary of time spent in threaded
	regions to monitor thread utilization and load balance is provided. A
	new entry is the <I>Reduce</I> section, which lists the time spend in
	reducing the per-thread data elements to the storage for non-threaded
	computation. These thread timings are taking from the first MPI rank
	only and and thus, as the breakdown for MPI tasks can change from MPI
	rank to MPI rank, this breakdown can be very different for individual
	ranks. Here is an example output for this section:
	</P>
	<P>Thread timings breakdown (MPI rank 0):
	Total threaded time 0.6846 / 90.6%
	Section \| min time \| avg time \| max time \|%varavg\| %total
	---------------------------------------------------------------
	Pair \| 0.5127 \| 0.5147 \| 0.5167 \| 0.3 \| 75.18
	Bond \| 0.0043139 \| 0.0046779 \| 0.0050418 \| 0.5 \| 0.68
	Kspace \| 0.070572 \| 0.074541 \| 0.07851 \| 1.5 \| 10.89
	Neigh \| 0.084778 \| 0.086969 \| 0.089161 \| 0.7 \| 12.70
	Reduce \| 0.0036485 \| 0.003737 \| 0.0038254 \| 0.1 \| 0.55
	</P>
	<P>The third section lists the number of owned atoms (Nlocal), ghost atoms
	(Nghost), and pair-wise neighbors stored per processor. The max and min
	values give the spread of these values across processors with a 10-bin
	histogram showing the distribution. The total number of histogram counts
	is equal to the number of processors.
	</P>
	<P>The last section gives aggregate statistics for pair-wise neighbors
	and special neighbors that LAMMPS keeps track of (see the
	<A HREF = "special_bonds.html">special_bonds</A> command). The number of times
	neighbor lists were rebuilt during the run is given as well as the
	number of potentially "dangerous" rebuilds. If atom movement
	triggered neighbor list rebuilding (see the
	<A HREF = "neigh_modify.html">neigh_modify</A> command), then dangerous
	reneighborings are those that were triggered on the first timestep
	atom movement was checked for. If this count is non-zero you may wish
	to reduce the delay factor to insure no force interactions are missed
	by atoms moving beyond the neighbor skin distance before a rebuild
	takes place.
	</P>
	<P>If an energy minimization was performed via the
	<A HREF = "minimize.html">minimize</A> command, additional information is printed,
	e.g.
	</P>
	<PRE>Minimization stats:
	Stopping criterion = linesearch alpha is zero
	Energy initial, next-to-last, final =
	-6372.3765206 -8328.46998942 -8328.46998942
	Force two-norm initial, final = 1059.36 5.36874
	Force max component initial, final = 58.6026 1.46872
	Final line search alpha, max atom move = 2.7842e-10 4.0892e-10
	Iterations, force evaluations = 701 1516
	</PRE>
	<P>The first line prints the criterion that determined the minimization
	to be completed. The third line lists the initial and final energy,
	as well as the energy on the next-to-last iteration. The next 2 lines
	give a measure of the gradient of the energy (force on all atoms).
	The 2-norm is the "length" of this force vector; the inf-norm is the
	largest component. Then some information about the line search and
	statistics on how many iterations and force-evaluations the minimizer
	required. Multiple force evaluations are typically done at each
	iteration to perform a 1d line minimization in the search direction.
	</P>
	<P>If a <A HREF = "kspace_style.html">kspace_style</A> long-range Coulombics solve was
	performed during the run (PPPM, Ewald), then additional information is
	printed, e.g.
	</P>
	<PRE>FFT time (% of Kspce) = 0.200313 (8.34477)
	FFT Gflps 3d 1d-only = 2.31074 9.19989
	</PRE>
	<P>The first line gives the time spent doing 3d FFTs (4 per timestep) and
	the fraction it represents of the total KSpace time (listed above).
	Each 3d FFT requires computation (3 sets of 1d FFTs) and communication
	(transposes). The total flops performed is 5Nlog_2(N), where N is the
	number of points in the 3d grid. The FFTs are timed with and without
	the communication and a Gflop rate is computed. The 3d rate is with
	communication; the 1d rate is without (just the 1d FFTs). Thus you
	can estimate what fraction of your FFT time was spent in
	communication, roughly 75% in the example above.
	</P>
	<HR>

	<H4><A NAME = "start_9"></A>2.9 Tips for users of previous LAMMPS versions
	</H4>
	<P>The current C++ began with a complete rewrite of LAMMPS 2001, which
	was written in F90. Features of earlier versions of LAMMPS are listed
	in <A HREF = "Section_history.html">Section_history</A>. The F90 and F77 versions
	(2001 and 99) are also freely distributed as open-source codes; check
	the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> for distribution information if you prefer
	those versions. The 99 and 2001 versions are no longer under active
	development; they do not have all the features of C++ LAMMPS.
	</P>
	<P>If you are a previous user of LAMMPS 2001, these are the most
	significant changes you will notice in C++ LAMMPS:
	</P>
	<P>(1) The names and arguments of many input script commands have
	changed. All commands are now a single word (e.g. read_data instead
	of read data).
	</P>
	<P>(2) All the functionality of LAMMPS 2001 is included in C++ LAMMPS,
	but you may need to specify the relevant commands in different ways.
	</P>
	<P>(3) The format of the data file can be streamlined for some problems.
	See the <A HREF = "read_data.html">read_data</A> command for details. The data file
	section "Nonbond Coeff" has been renamed to "Pair Coeff" in C++ LAMMPS.
	</P>
	<P>(4) Binary restart files written by LAMMPS 2001 cannot be read by C++
	LAMMPS with a <A HREF = "read_restart.html">read_restart</A> command. This is
	because they were output by F90 which writes in a different binary
	format than C or C++ writes or reads. Use the <I>restart2data</I> tool
	provided with LAMMPS 2001 to convert the 2001 restart file to a text
	data file. Then edit the data file as necessary before using the C++
	LAMMPS <A HREF = "read_data.html">read_data</A> command to read it in.
	</P>
	<P>(5) There are numerous small numerical changes in C++ LAMMPS that mean
	you will not get identical answers when comparing to a 2001 run.
	However, your initial thermodynamic energy and MD trajectory should be
	close if you have setup the problem for both codes the same.
	</P>
	</HTML>

Section_start.htmlNo OneTemporaryActions

File Metadata

Section_start.htmlView Options

Event Timeline

Section_start.html
No OneTemporary
Actions

Section_start.html
View Options