(MPI, FFT), 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 users have do not

really have to do with LAMMPS - they are peculiar to the user's

system, compilers, libraries, etc.  Such questions are better answered

by a local expert.

you.  Many compiling, linking, and run problems that users are 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

<P><B><I>Building a LAMMPS executable:</I></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 directory with

It also contains a top-level Makefile and a MAKE sub-directory with

low-level Makefile.* files for several 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

</P>

<P>(2) Other errors typically occur because the low-level Makefile isn't

setup correctly for your machine.  If your platform is named "foo",

you need to create a Makefile.foo in the MAKE directory.  Use whatever

existing file is closest to your platform as a starting point.  See

the next section for more instructions.

you need to create a Makefile.foo in the MAKE sub-directory.  Use

whatever existing file is closest to your platform as a starting

point.  See the next section for more instructions.

</P>

<P><B><I>Editing a new low-level Makefile.foo:</I></B>

</P>

<P>(2) Set the paths and flags for your C++ compiler, including

optimization flags.  You can use g++, the open-source GNU compiler,

which is available on all Unix systems.  Vendor compilers often

produce faster code.  On boxes with Intel CPUs, I use the free Intel

icc compiler, which you can download from <A HREF = "http://www.intel.com/software/products/noncom">Intel's compiler

produce faster code.  On boxes with Intel CPUs, we suggest using the

free Intel icc compiler, which you can download from <A HREF = "http://www.intel.com/software/products/noncom">Intel's compiler

site</A>.

</P>

<P>(3) If you want LAMMPS to run in parallel, you must have an MPI

library installed on your platform.  Makefile.foo needs to specify

where the mpi.h file (-I switch) and the libmpi.a library (-L switch)

is found.  On my Linux box, I use Argonne's MPICH 1.2 which can be

downloaded from the <A HREF = "http://www-unix.mcs.anl.gov/mpi">Argonne MPI

library installed on your platform.  If you do not use "mpicc" as your

compiler/linker, then Makefile.foo needs to specify where the mpi.h

file (-I switch) and the libmpi.a library (-L switch) is found.  If

you are installing MPI yourself, we recommend Argonne's MPICH 1.2

which can be downloaded from the <A HREF = "http://www-unix.mcs.anl.gov/mpi">Argonne MPI

site</A>.  LAM MPI 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 will be

faster than MPICH or LAM, so find out how to link against it.  If you

use MPICH or LAM, 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

faster than MPICH or LAM, so find out how to build and link with it.

If you use MPICH or LAM, 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 may arise when linking LAMMPS to

the MPI library.

</P>

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 runs.

therefore insufficient for timing long LAMMPS simulations.

</P>

<P>(5) If you want to use the particle-particle particle-mesh (PPPM)

option in LAMMPS for long-range Coulombics, you must have a 1d FFT

but the last one are native vendor-provided libraries.  FFTW is a

fast, portable library that should work on any platform.  You can

download it from <A HREF = "http://www.fftw.org">www.fftw.org</A>.  Use version

2.1.X, not the newer 3.0.X.  Building FFTW for my box was as simple as

./configure; make.  Whichever FFT library you have on your platform,

you'll need to set the appropriate -I and -L switches in Makefile.foo.

2.1.X, not the newer 3.0.X.  Building FFTW for your box should be as

simple as ./configure; make.  Whichever FFT library you have on your

platform, you'll need to set the appropriate -I and -L switches in

Makefile.foo.

</P>

<P>If you examine fft3d.c and fft3d.h you'll see it's possible to add

other vendor FFT libraries via #ifdef statements in the appropriate

<P>(5) Building for MicroSoft Windows.

</P>

<P>I've never done this, but LAMMPS is just standard C++ with MPI and FFT

calls.  You should be able to use cygwin to build LAMMPS with a Unix

make.  Or you should be able to pull all the source files into Visual

C++ (ugh) or some similar development environment and build it.  In

the src/MAKE/Windows directory are some notes from users on how they

built LAMMPS under Windows, so you can look at their instructions for

tips.  Good luck - we can't help you on this one.

calls.  You can use cygwin to build LAMMPS with a Unix make; see

Makefile.cygwin.  Or you should be able to pull all the source files

into Visual C++ (ugh) or some similar development environment and

build it.  In the src/MAKE/Windows directory are some notes from users

on how they built LAMMPS under Windows, so you can look at their

instructions for tips.  Good luck - we can't help you on this one.

</P>

<H4><A NAME = "2_3"></A>2.3 Making LAMMPS with optional packages 

</H4>

The one exception is that to use the "opt" package, you must also be

using the "molecule" and "manybody" packages.  You may wish to exclude

certain packages if you will never run certain kinds of simulations.

This will produce a smaller executable which may run a bit faster.

This will keep you from having to build auxiliary libraries (see

below) and will produce a smaller executable which may run a bit

faster.

</P>

<P>By default, LAMMPS includes only the "kspace", "manybody", and

"molecule" packages.  As described below, some packages require LAMMPS

(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 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.

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

processors.

</P>

<P>The input script specifies what simulation is run on which partition;

see the <A HREF = "variable.html">variable</A> and <A HREF = "next.html">next</A> commands.

Simulations running on different partitions can also communicate with

each other; see the <A HREF = "temper.html">temper</A> command.

see the <A HREF = "variable.html">variable</A> and <A HREF = "next.html">next</A> commands.  <A HREF = "Section_howto.html#4_4">This

howto section</A> gives examples of how to use

these commands in this way.  Simulations running on different

partitions can also communicate with each other; see the

<A HREF = "temper.html">temper</A> command.

</P>

<PRE>-in file 

</PRE>

(MPI, FFT), 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 users have do not

really have to do with LAMMPS - they are peculiar to the user's

system, compilers, libraries, etc.  Such questions are better answered

by a local expert.

you.  Many compiling, linking, and run problems that users are not

really 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

[{Building a LAMMPS executable:}]

The src directory contains the C++ source and header files for LAMMPS.

It also contains a top-level Makefile and a MAKE directory with

It also contains a top-level Makefile and a MAKE sub-directory with

low-level Makefile.* files for several 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

(2) Other errors typically occur because the low-level Makefile isn't

setup correctly for your machine.  If your platform is named "foo",

you need to create a Makefile.foo in the MAKE directory.  Use whatever

existing file is closest to your platform as a starting point.  See

the next section for more instructions.

you need to create a Makefile.foo in the MAKE sub-directory.  Use

whatever existing file is closest to your platform as a starting

point.  See the next section for more instructions.

[{Editing a new low-level Makefile.foo:}]

(2) Set the paths and flags for your C++ compiler, including

optimization flags.  You can use g++, the open-source GNU compiler,

which is available on all Unix systems.  Vendor compilers often

produce faster code.  On boxes with Intel CPUs, I use the free Intel

icc compiler, which you can download from "Intel's compiler

produce faster code.  On boxes with Intel CPUs, we suggest using the

free Intel icc compiler, which you can download from "Intel's compiler

site"_intel.

:link(intel,http://www.intel.com/software/products/noncom)

(3) If you want LAMMPS to run in parallel, you must have an MPI

library installed on your platform.  Makefile.foo needs to specify

where the mpi.h file (-I switch) and the libmpi.a library (-L switch)

is found.  On my Linux box, I use Argonne's MPICH 1.2 which can be

downloaded from the "Argonne MPI

library installed on your platform.  If you do not use "mpicc" as your

compiler/linker, then Makefile.foo needs to specify where the mpi.h

file (-I switch) and the libmpi.a library (-L switch) is found.  If

you are installing MPI yourself, we recommend Argonne's MPICH 1.2

which can be downloaded from the "Argonne MPI

site"_http://www-unix.mcs.anl.gov/mpi.  LAM MPI 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 will be

faster than MPICH or LAM, so find out how to link against it.  If you

use MPICH or LAM, 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

faster than MPICH or LAM, so find out how to build and link with it.

If you use MPICH or LAM, 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 may arise when linking LAMMPS to

the MPI library.

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 runs.

therefore insufficient for timing long LAMMPS simulations.

(5) If you want to use the particle-particle particle-mesh (PPPM)

option in LAMMPS for long-range Coulombics, you must have a 1d FFT

but the last one are native vendor-provided libraries.  FFTW is a

fast, portable library that should work on any platform.  You can

download it from "www.fftw.org"_http://www.fftw.org.  Use version

2.1.X, not the newer 3.0.X.  Building FFTW for my box was as simple as

./configure; make.  Whichever FFT library you have on your platform,

you'll need to set the appropriate -I and -L switches in Makefile.foo.

2.1.X, not the newer 3.0.X.  Building FFTW for your box should be as

simple as ./configure; make.  Whichever FFT library you have on your

platform, you'll need to set the appropriate -I and -L switches in

Makefile.foo.

If you examine fft3d.c and fft3d.h you'll see it's possible to add

other vendor FFT libraries via #ifdef statements in the appropriate

(5) Building for MicroSoft Windows.

I've never done this, but LAMMPS is just standard C++ with MPI and FFT

calls.  You should be able to use cygwin to build LAMMPS with a Unix

make.  Or you should be able to pull all the source files into Visual

C++ (ugh) or some similar development environment and build it.  In

the src/MAKE/Windows directory are some notes from users on how they

built LAMMPS under Windows, so you can look at their instructions for

tips.  Good luck - we can't help you on this one.

calls.  You can use cygwin to build LAMMPS with a Unix make; see

Makefile.cygwin.  Or you should be able to pull all the source files

into Visual C++ (ugh) or some similar development environment and

build it.  In the src/MAKE/Windows directory are some notes from users

on how they built LAMMPS under Windows, so you can look at their

instructions for tips.  Good luck - we can't help you on this one.

2.3 Making LAMMPS with optional packages :h4,link(2_3)

The one exception is that to use the "opt" package, you must also be

using the "molecule" and "manybody" packages.  You may wish to exclude

certain packages if you will never run certain kinds of simulations.

This will produce a smaller executable which may run a bit faster.

This will keep you from having to build auxiliary libraries (see

below) and will produce a smaller executable which may run a bit

faster.

By default, LAMMPS includes only the "kspace", "manybody", and

"molecule" packages.  As described below, some packages require LAMMPS

(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 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.

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

processors.

The input script specifies what simulation is run on which partition;

see the "variable"_variable.html and "next"_next.html commands.

Simulations running on different partitions can also communicate with

each other; see the "temper"_temper.html command.

see the "variable"_variable.html and "next"_next.html commands.  "This

howto section"_Section_howto.html#4_4 gives examples of how to use

these commands in this way.  Simulations running on different

partitions can also communicate with each other; see the

"temper"_temper.html command.

-in file :pre