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### 2. Getting Started

This section describes how to build and run LAMMPS, for both new and experienced users.

2.1 What's in the LAMMPS distribution
2.2 Making LAMMPS
2.3 Making LAMMPS with optional packages
2.4 Building LAMMPS via the Make.py script
2.5 Building LAMMPS as a library
2.6 Running LAMMPS
2.7 Command-line options
2.8 Screen output
2.9 Tips for users of previous versions

#### 2.1 What's in the LAMMPS distribution

When you download LAMMPS you will need to unzip and untar the downloaded file with the following commands, after placing the file in an appropriate directory.

    gunzip lammps*.tar.gz
    tar xvf lammps*.tar

This will create a LAMMPS directory containing two files and several sub-directories:

README | text file
LICENSE | the GNU General Public License (GPL)
bench | benchmark problems
doc | documentation
examples | simple test problems
potentials | embedded atom method (EAM) potential files
src | source files
tools | pre- and post-processing tools

If you download one of the Windows executables from the download page, then you just get a single file:

    lmp_windows.exe

Skip to the Running LAMMPS sections for info on how to launch these executables on a Windows box.

The Windows executables for serial or parallel only include certain packages and bug-fixes/upgrades listed on this page up to a certain date, as stated on the download page. If you want something with more packages or that is more current, you'll have to download the source tarball and build it yourself from source code using Microsoft Visual Studio, as described in the next section.

#### 2.2 Making LAMMPS

This section has the following sub-sections:

- Read this first
- Steps to build a LAMMPS executable
- Common errors that can occur when making LAMMPS
- Additional build tips
- Building for a Mac
- Building for Windows

Read this first:

Building LAMMPS can be non-trivial. You may need to edit a makefile, there are compiler options to consider, additional libraries can be used (MPI, FFT, JPEG), LAMMPS packages may be included or excluded, some of these packages use auxiliary libraries which need to be pre-built, etc.

Please read this section 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 compiling, linking, and run problems that users have are often not LAMMPS issues - they are peculiar to the user's system, compilers, libraries, etc. Such questions are better answered by a local expert.

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 a question to the LAMMPS mail list.

If you succeed in building LAMMPS on a new kind of machine, for which there isn't a similar Makefile for in the src/MAKE directory, send it to the developers and we can include it in the LAMMPS distribution.

Steps to build a LAMMPS executable:

Step 0

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 machines. From within the src directory, type "make" or "gmake". You should see a list of available choices. If one of those is the machine and options you want, you can type a command like:

    make linux
    or
    gmake mac

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.

If you get no errors and an executable like lmp_linux or lmp_mac is produced, you're done; it's your lucky day.

Note that by default only a few of LAMMPS optional packages are installed. To build LAMMPS with optional packages, see this section below.

Step 1

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 src/MAKE/Makefile.* 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.

Step 2

Change the first line of src/MAKE/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".

Step 3

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 mpicc 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 commercial Intel icc compiler, which can be downloaded from Intel's compiler site.

If building a C++ code on your machine requires additional libraries, then you should list them as part of the LIB variable.

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++ 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.

Step 4

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).

The LMP_INC variable is used to include options that turn on ifdefs within the LAMMPS code. The options that are currently recogized are:

- -DLAMMPS_GZIP
- -DLAMMPS_JPEG
- -DLAMMPS_MEMALIGN
- -DLAMMPS_XDR
- -DLAMMPS_SMALLBIG
- -DLAMMPS_BIGBIG
- -DLAMMPS_SMALLSMALL
- -DLAMMPS_LONGLONG_TO_LONG
- -DPACK_ARRAY
- -DPACK_POINTER
- -DPACK_MEMCPY

The read_data and dump commands will read/write gzipped files if you compile with -DLAMMPS_GZIP. It requires that your Unix support the "popen" command.

If you use -DLAMMPS_JPEG, the dump image command will be able to write out JPEG image files. If not, it will only be able to write out text-based PPM image files. For JPEG files, you must also link LAMMPS with a JPEG library, as described below.

Using -DLAMMPS_MEMALIGN= 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.

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 dump command for details.

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 with more than 2 billion atoms or to allow moving atoms to wrap back through a periodic box more than 512 times. The only reason to use the SMALLSMALL setting is if your machine does not support 64-bit integers. See the Additional build tips section below for more details.

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.

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 kspace_style command for info about PPPM. See Step 6 below for info about building LAMMPS with an FFT library.

Step 5

The 3 MPI variables are used to specify an MPI library to build LAMMPS with.

If you want LAMMPS to run in parallel, you must have an MPI library installed on your platform. If you use an MPI-wrapped compiler, such as "mpicc" to build LAMMPS, you should be able to leave these 3 variables blank; the MPI wrapper knows where to find the needed files. If not, and MPI is installed on your system in the usual place (under /usr/local), you also may not need to specify these 3 variables. 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 MPI which the compiler has no trouble finding.

Failing this, with these 3 variables you can 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).

If you are installing MPI yourself, we recommend Argonne's MPICH2 or OpenMPI. MPICH can be downloaded from the Argonne MPI site. OpenMPI can be downloaded from the OpenMPI site. 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.

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 the src/MAKE/Makefile.serial file 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. To build from the src directory, type "make stubs", or from the 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.

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.

Step 6

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 kspace_style command.

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 KISS FFT library, 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.

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.

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.

FFTW is a fast, portable library that should also work on any platform. You can download it from www.fftw.org. 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.

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.

Step 7

The 3 JPG variables allow you to specify a JPEG library which LAMMPS uses when writing out JPEG files via the dump image command. These can be left blank if you do not use the -DLAMMPS_JPEG switch discussed above in Step 4, since in that case JPEG output will be disabled.

A standard JPEG library usually goes by the name libjpeg.a 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.

As before, if these header and library files are in the usual place on your machine, you may not need to set these variables.

Step 8

Note that by default only a few of LAMMPS optional packages are installed. To build LAMMPS with optional packages, see this section below, before proceeding to Step 9.

Step 9

That's it. Once you have a correct Makefile.foo, you have installed the optional LAMMPS packages you want to include in your build, and you have pre-built any other needed libraries (e.g. MPI, FFT, package libraries), all you need to do from the src directory is type something like this:

    make foo
    or
    gmake foo

You should get the executable lmp_foo when the build is complete.

Errors that can occur when making LAMMPS:

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.

Here are two non-obvious errors that can occur:

(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.

    make makelist
    make -f Makefile.list linux
    gmake -f Makefile.list mac

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.

(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.

Additional build tips:

(1) Building LAMMPS for multiple platforms.

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.

(2) Cleaning up.

Typing "make clean-all" or "make clean-foo" will delete *.o object files created when LAMMPS is built, for either all builds or for a particular machine.

(3) Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or -DLAMMPS_BIBIG or -DLAMMPS_SMALLSMALL

As explained above, any of these 3 settings can be specified on the LMP_INC line in your low-level src/MAKE/Makefile.foo.

The default is -DLAMMPS_SMALLBIG which allows for systems with up to 2^63 atoms and timesteps (about 9 billion billion). The atom limit is for atomic systems that do not require atom IDs. For molecular models, which require atom IDs, the limit is 2^31 atoms (about 2 billion). With this setting, image flags are stored in 32-bit integers, which means for 3 dimensions that atoms can only wrap around a periodic box at most 512 times. If atoms move through the periodic box more than this limit, 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 compute msd command, to be faulty.

To allow for larger molecular systems or larger image flags, compile with -DLAMMPS_BIGBIG. This enables molecular systems with up to 2^63 atoms (about 9 billion billion). And image flags will not "roll over" until they reach 2^20 = 1048576.

IMPORTANT NOTE: As of 6/2012, the BIGBIG setting does not yet enable molecular systems to grow as large as 2^63. Only the image flag roll over is currently affected by this compile option.

If your system does not support 8-byte integers, you will need to compile with the -DLAMMPS_SMALLSMALL setting. This will restrict your total number of atoms (for atomic or molecular models) and timesteps to 2^31 (about 2 billion). Image flags will roll over at 2^9 = 512.

Note that in src/lmptype.h there are also settings for the MPI data types associated with the integers that store atom IDs and total system sizes. These need to be consistent with the associated C data types, or else LAMMPS will generate a run-time error.

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 restriction 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.

Building for a Mac:

OS X is BSD Unix, so it should just work. See the src/MAKE/Makefile.mac file.

Building for Windows:

The LAMMPS download page has an option to download both a serial and parallel pre-built Windows exeutable. See the Running LAMMPS section for instructions for running these executables on a Windows box.

The pre-built executables are built with a subset of the available pacakges; see the download page for the list. If you want a Windows version with specific packages included and excluded, you can build it yourself.

One way to do this is install and use cygwin to build LAMMPS with a standard Linus make, just as you would on any Linux box; see src/MAKE/Makefile.cygwin.

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.

#### 2.3 Making LAMMPS with optional packages

This section has the following sub-sections:

- Package basics
- Including/excluding packages
- Packages that require extra libraries
- Additional Makefile settings for extra libraries

Package basics:

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. You can see the list of all packages by typing "make package" from within the src directory of the LAMMPS distribution.

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

    lmp_machine -h

to run your executable with the optional -h command-line switch for "help", which will list the styles and commands known to your executable.

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 Section_packages of the manual. The difference between standard and user packages is as follows:

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.

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.

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 this section of the documentation.

Including/excluding packages:

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:

    make yes-colloid
    make g++

or

    make no-manybody
    make g++

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.

The reason to exclude packages is if you will never run certain kinds of simulations. 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.

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.

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-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.

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.

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.

Typing "make package-update" 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.

Typing "make package-status" 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.

Packages that require extra libraries:

A few of the standard and user packages require additional auxiliary libraries to be compiled first. If you get a LAMMPS build error about a missing library, this is likely the reason. The source code or hooks to these libraries is included in the LAMMPS distribution under the "lib" directory. Look at the lib/README file for a list of these or see Section_packages of the doc pages.

Each lib directory has a README file (e.g. lib/reax/README) with instructions on how to build that library. Typically this is done in this manner:

    make -f Makefile.g++

in the appropriate directory, e.g. in lib/reax. However, some of the libraries do not build this way. Again, see the libary README file for details.

If you are building the library, you will need to use a Makefile that is a match for your system. If one of the provided Makefiles is not appropriate for your system you will need to edit or add one. For example, in the case of Fortran-based libraries, your system must have a Fortran compiler, the settings for which will need to be listed in the Makefile.

When you have built one of these libraries, there are 2 things to check:

(1) The file libname.a should now exist in lib/name. E.g. lib/reax/libreax.a. This is the library file LAMMPS will link against. One exception is the lib/cuda library which produces the file liblammpscuda.a, because there is already a system library libcuda.a.

(2) The file Makefile.lammps should exist in lib/name. E.g. lib/cuda/Makefile.lammps. This file may be auto-generated by the build of the library, or you may need to make a copy of the appropriate provided file (e.g. lib/meam/Makefile.lammps.gfortran). Either way you should insure that the settings in this file are appropriate for your system.

There are typically 3 settings in the Makefile.lammps file (unless some are blank or not needed): a SYSINC, SYSPATH, and SYSLIB setting, specific to this package. These are settings the LAMMPS build will import when compiling the LAMMPS package files (not the library files), and linking to the auxiliary library. They typically list any other system libraries needed to support the package and where to find them. An example is the BLAS and LAPACK libraries needed by the USER-ATC package. Or the system libraries that support calling Fortran from C++, as the MEAM and REAX packages do.

(3) One exception to these rules is the lib/linalg directory, which is simply BLAS and LAPACK files used by the USER-ATC package (and possibly other packages in the future). If you do not have these libraries on your system, you can use one of the Makefiles in this directory (which you may need to modify) to build a dummy BLAS and LAPACK library. It can then be included in the lib/atc/Makefile.lammps file as part of the SYSPATH and SYSLIB lines so that LAMMPS will build properly with the USER-ATC package.

Note that if the Makefile.lammps settings are not correct for your box, the LAMMPS build will likely fail.

There are also a few packages, like KIM and USER-MOLFILE, that use additional auxiliary libraries which are not provided with LAMMPS. In these cases, there is no corresponding sub-directory under the lib directory. You are expected to download and install these libraries yourself before building LAMMPS with the package installed, if they are not already on your system.

However there is still a Makefile.lammps file with settings used when building LAMMPS with the package installed, as in (2) above. Is is found in the package directory itself, e.g. src/KIM/Makefile.lammps. This file contains the same 3 settings described above for SYSINC, SYSPATH, and SYSLIB. The Makefile.lammps file contains instructions on how to specify these settings for your system. You need to specify the settings before building LAMMPS with one of those packages installed, else the LAMMPS build will likely fail.

#### 2.4 Building LAMMPS via the Make.py script

The src directory includes a Make.py script, written in Python, which can be used to automate various steps of the build process.

You can run the script from the src directory by typing either:

    Make.py
    python Make.py

which will give you info about the tool. For the former to work, you may need to edit the 1st line of the script to point to your local Python. And you may need to insure the script is executable:

    chmod +x Make.py

The following options are supported as switches:

- -i file1 file2 ...
- -p package1 package2 ...
- -u package1 package2 ...
- -e package1 arg1 arg2 package2 ...
- -o dir
- -b machine
- -s suffix1 suffix2 ...
- -l dir
- -j N
- -h switch1 switch2 ...

Help on any switch can be listed by using -h, e.g.

    Make.py -h -i -p

At a hi-level, these are the kinds of package management and build tasks that can be performed easily, using the Make.py tool:

- install/uninstall packages and build the associated external libs (use -p and -u and -e)
- install packages needed for one or more input scripts (use -i and -p)
- build LAMMPS, either in the src dir or new dir (use -b)
- create a new dir with only the source code needed for one or more input scripts (use -i and -o)

The last bullet can be useful when you wish to build a stripped-down version of LAMMPS to run a specific script(s). Or when you wish to move the minimal amount of files to another platform for a remote LAMMPS build.

Note that using Make.py is not a substitute for insuring you have a valid src/MAKE/Makefile.foo for your system, or that external library Makefiles in any lib/* directories you use are also valid for your system. But once you have done that, you can use Make.py to quickly include/exclude the packages and external libraries needed by your input scripts.

#### 2.5 Building LAMMPS as a library

LAMMPS can be built as either a static or shared library, which can then be called from another application or a scripting language. See this section for more info on coupling LAMMPS to other codes. See this section for more info on wrapping and running LAMMPS from Python.

##### Static library:

To build LAMMPS as a static library (*.a file on Linux), type

    make makelib
    make -f Makefile.lib foo

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. Note that inclusion or exclusion of any desired optional packages should be done before typing "make makelib". The first "make" command will create a current Makefile.lib with all the file names in your src dir. The second "make" command will use it to build LAMMPS as a static library, using 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.

##### Shared library:

To build LAMMPS as a shared library (*.so file on Linux), which can be dynamically loaded, e.g. from Python, type

    make makeshlib
    make -f Makefile.shlib foo

where foo is the machine name. This kind of library is required when wrapping LAMMPS with Python; see Section_python for details. Again, note that inclusion or exclusion of any desired optional packages should be done before typing "make makelib". The first "make" command will create a current Makefile.shlib with all the file names in your src dir. The second "make" command will use it to build LAMMPS as a shared library, using the SHFLAGS and SHLIBFLAGS settings in src/MAKE/Makefile.foo. 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 the Python wrapper uses by default.

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/packges, since they are always built as shared libraries with the -fPIC switch. However, if a library like MPI or FFTW does not exist as a shared library, the second make command will generate an error. This means you will need to install a shared library version of the package. The build instructions for the library should tell you how to do this.

As an example, here is how to build and install the MPICH library, a popular open-source version of MPI, distributed by Argonne National Labs, as a shared library in the default /usr/local/lib location:

    ./configure --enable-shared
    make
    make install

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.

##### Additional requirement for using a shared library:

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.

For the csh or tcsh shells, you would add something like this to your ~/.cshrc file:

    setenv LD_LIBRARY_PATH $LD_LIBRARY_PATH:/home/sjplimp/lammps/src

##### Calling the LAMMPS library:

Either flavor of library (static or shared0 allows one or more LAMMPS objects to be instantiated from the calling program.

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.

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.

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 Section_howto 10 of the manual. See Section_python of the manual for a description of the Python wrapper provided with LAMMPS that operates through the LAMMPS library interface.

The files src/library.cpp and library.h define the C-style API for using LAMMPS as a library. See Section_howto 19 of the manual for a description of the interface and how to extend it for your needs.

#### 2.6 Running LAMMPS

By default, LAMMPS runs by reading commands from stdin; e.g. lmp_linux < in.file. This means you first create an input script (e.g. in.file) containing the desired commands. This section describes how input scripts are structured and what commands they contain.

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.

Here is how you might run a standard Lennard-Jones benchmark on a Linux box, using mpirun to launch a parallel job:

    cd src
    make linux
    cp lmp_linux ../bench
    cd ../bench
    mpirun -np 4 lmp_linux < in.lj

See this page for timings for this and the other benchmarks on various platforms.

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.

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.

For the non-MPI version, follow these steps:

- Get a command prompt by going to Start->Run... , then typing "cmd".
- Move to the directory where you have saved lmp_win_no-mpi.exe (e.g. by typing: cd "Documents").
- At the command prompt, type "lmp_win_no-mpi -in in.lj", replacing in.lj with the name of your LAMMPS input script.

For the MPI version, which allows you to run LAMMPS under Windows on multiple processors, follow these steps:

- Download and install MPICH2 for Windows.
- 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.
- Get a command prompt by going to Start->Run... , then typing "cmd".
- Move to the directory where you have saved lmp_win_mpi.exe (e.g. by typing: cd "Documents").
- Then type something like this: "mpiexec -np 4 -localonly lmp_win_mpi -in in.lj", replacing in.lj with the name of your LAMMPS input script.
- Note that you may need to provide smpd with a passphrase --- it doesn't matter what you type.
- 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.
- Alternatively, you can still use this executable to run on a single processor by typing something like: "lmp_win_mpi -in in.lj".

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.

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.

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 Section_errors 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.

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.

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.

#### 2.7 Command-line options

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:

- -c or -cuda
- -e or -echo
- -i or -in
- -h or -help
- -l or -log
- -p or -partition
- -pl or -plog
- -ps or -pscreen
- -r or -reorder
- -sc or -screen
- -sf or -suffix
- -v or -var

For example, lmp_ibm might be launched as follows:

    mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none < in.alloy
    mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none < in.alloy

Here are the details on the options:

    -cuda on/off

Explicitly enable or disable CUDA support, as provided by the USER-CUDA package. If LAMMPS is built with this package, as described above in Section 2.3, then by default LAMMPS will run in CUDA mode. If this switch is set to "off", then it will not, even if it was built with the USER-CUDA package, which means you can run standard LAMMPS or with the GPU package for testing or benchmarking purposes. The only reason to set the switch to "on", is to check if LAMMPS was built with the USER-CUDA package, since an error will be generated if it was not.

    -echo style

Set the style of command echoing. The style can be none or screen or log or both. 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 log. The echo style can also be set by using the echo command in the input script itself.

    -in file

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 input script from stdin - e.g. lmp_linux < in.run. This is a required switch when running LAMMPS in multi-partition mode, since multiple processors cannot all read from stdin.

    -help

Print a list of options compiled into this executable for each LAMMPS style (atom_style, fix, compute, pair_style, bond_style, etc). This can help you know if the command you want to use was included via the appropriate package. LAMMPS will print the info and immediately exit if this switch is used.

    -log file

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 log command in the input script will override this setting. Option -plog will override the name of the partition log files file.N.

    -partition 8x2 4 5 ...

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.

Running with multiple partitions can e useful for running multi-replica simulations, 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.

To run multiple independent simulatoins from one input script, using multiple partitions, see Section_howto 4 of the manual. World- and universe-style variables are useful in this context.

    -plog file

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.

    -pscreen file

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.

    -reorder nth N
    -reorder custom filename

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 run_style verlet/split 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 Section_accelerate doc pages for more details.

If the keyword nth is used with a setting N, then it means every Nth processor will be moved to the end of the ranking. This is useful when using the run_style verlet/split 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

    0 1 2 3 4 5 6 7 8 9 10 11

to

    0 1 2 4 5 6 8 9 10 3 7 11

so that the processors in each partition will be

    0 1 2 4 5 6 8 9 10
    3 7 11

See the "processors" command for how to insure processors from each partition could then be grouped optimally for quad-core nodes.

If the keyword is custom", 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:

    I J

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.

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 processors out command for how to output info on the final assignment of physical processors to the LAMMPS simulation domain.

    -screen file

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.

    -suffix style

Use variants of various styles if they exist. The specified style can be opt, omp, gpu, or cuda. These refer to optional packages that LAMMPS can be built with, as described above in Section 2.3. The "opt" style corrsponds to the OPT package, the "omp" style to the USER-OMP package, the "gpu" style to the GPU package, and the "cuda" style to the USER-CUDA package.

As an example, all of the packages provide a pair_style lj/cut variant, with style names lj/cut/opt, lj/cut/omp, lj/cut/gpu, or lj/cut/cuda. A variant styles can be specified explicitly in your input script, e.g. pair_style lj/cut/gpu. If the -suffix switch is used, you do not need to modify your input script. The specified suffix (opt,omp,gpu,cuda) is automatically appended whenever your input script command creates a new atom, pair, fix, compute, or run style. If the variant version does not exist, the standard version is created.

For the GPU package, using this command-line switch also invokes the default GPU settings, as if the command "package gpu force/neigh 0 0 1" were used at the top of your input script. These settings can be changed by using the package gpu command in your script if desired.

For the OMP package, using this command-line switch also invokes the default OMP settings, as if the command "package omp *" were used at the top of your input script. These settings can be changed by using the package omp command in your script if desired.

The suffix command can also set a suffix and it can also turn off/on any suffix setting made via the command line.

    -var name value1 value2 ...

Specify a variable that will be defined for substitution purposes when the input script is read. "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 index-style variable 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 variable command for more info on defining index and other kinds of variables and this section for more info on using variables in input scripts.

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.

#### 2.8 LAMMPS screen output

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:

    Loop time of 49.002 on 2 procs for 2004 atoms

    Pair   time (%) = 35.0495 (71.5267)
    Bond   time (%) = 0.092046 (0.187841)
    Kspce  time (%) = 6.42073 (13.103)
    Neigh  time (%) = 2.73485 (5.5811)
    Comm   time (%) = 1.50291 (3.06703)
    Outpt  time (%) = 0.013799 (0.0281601)
    Other  time (%) = 2.13669 (4.36041)

    Nlocal:    1002 ave, 1015 max, 989 min
    Histogram: 1 0 0 0 0 0 0 0 0 1
    Nghost:    8720 ave, 8724 max, 8716 min
    Histogram: 1 0 0 0 0 0 0 0 0 1
    Neighs:    354141 ave, 361422 max, 346860 min
    Histogram: 1 0 0 0 0 0 0 0 0 1

    Total # of neighbors = 708282
    Ave neighs/atom = 353.434
    Ave special neighs/atom = 2.34032
    Number of reneighborings = 42
    Dangerous reneighborings = 2

The first section gives the breakdown of the CPU run time (in seconds) into major categories. The second 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.

The last section gives aggregate statistics for pair-wise neighbors and special neighbors that LAMMPS keeps track of (see the special_bonds 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 neigh_modify 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.

If an energy minimization was performed via the minimize command, additional information is printed, e.g.

    Minimization stats:
      E initial, next-to-last, final = -0.895962 -2.94193 -2.94342
      Gradient 2-norm init/final= 1920.78 20.9992
      Gradient inf-norm init/final= 304.283 9.61216
      Iterations = 36
      Force evaluations = 177

The first 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. The last 2 lines are 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.

If a kspace_style long-range Coulombics solve was performed during the run (PPPM, Ewald), then additional information is printed, e.g.

    FFT time (% of Kspce) = 0.200313 (8.34477)
    FFT Gflps 3d 1d-only = 2.31074 9.19989

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.

#### 2.9 Tips for users of previous LAMMPS versions

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 Section_history. The F90 and F77 versions (2001 and 99) are also freely distributed as open-source codes; check the LAMMPS WWW Site 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.

If you are a previous user of LAMMPS 2001, these are the most significant changes you will notice in C++ LAMMPS:

(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).

(2) All the functionality of LAMMPS 2001 is included in C++ LAMMPS, but you may need to specify the relevant commands in different ways.

(3) The format of the data file can be streamlined for some problems. See the read_data command for details. The data file section "Nonbond Coeff" has been renamed to "Pair Coeff" in C++ LAMMPS.

(4) Binary restart files written by LAMMPS 2001 cannot be read by C++ LAMMPS with a read_restart 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 restart2data 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 read_data command to read it in.

(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.