2006-09-22 00:22:34 +08:00
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<HTML>
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<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>
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<HR>
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<H3>2. Getting Started
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</H3>
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<P>This section describes how to unpack, make, and run LAMMPS, for both
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new and experienced users.
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</P>
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2.1 <A HREF = "#2_1">What's in the LAMMPS distribution</A><BR>
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2.2 <A HREF = "#2_2">Making LAMMPS</A><BR>
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2007-02-10 05:37:30 +08:00
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2.3 <A HREF = "#2_3">Making LAMMPS with optional packages</A><BR>
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2.4 <A HREF = "#2_4">Building LAMMPS as a library</A><BR>
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2.5 <A HREF = "#2_5">Running LAMMPS</A><BR>
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2.6 <A HREF = "#2_6">Command-line options</A><BR>
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2.7 <A HREF = "#2_7">Screen output</A><BR>
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2.8 <A HREF = "#2_8">Tips for users of previous versions</A> <BR>
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2006-09-22 00:22:34 +08:00
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<HR>
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<H4><A NAME = "2_1"></A>2.1 What's in the LAMMPS distribution
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</H4>
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2007-06-04 23:32:50 +08:00
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<P>When you download LAMMPS you will need to unzip and untar the
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2006-09-22 00:22:34 +08:00
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downloaded file with the following commands, after placing the file in
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an appropriate directory.
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</P>
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<PRE>gunzip lammps*.tar.gz
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tar xvf lammps*.tar
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</PRE>
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<P>This will create a LAMMPS directory containing two files and several
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sub-directories:
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</P>
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2007-09-28 07:25:52 +08:00
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<DIV ALIGN=center><TABLE BORDER=1 >
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2006-09-22 00:22:34 +08:00
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<TR><TD >README</TD><TD > text file</TD></TR>
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<TR><TD >LICENSE</TD><TD > the GNU General Public License (GPL)</TD></TR>
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<TR><TD >bench</TD><TD > benchmark problems</TD></TR>
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<TR><TD >doc</TD><TD > documentation</TD></TR>
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<TR><TD >examples</TD><TD > simple test problems</TD></TR>
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<TR><TD >potentials</TD><TD > embedded atom method (EAM) potential files</TD></TR>
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<TR><TD >src</TD><TD > source files</TD></TR>
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<TR><TD >tools</TD><TD > pre- and post-processing tools
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</TD></TR></TABLE></DIV>
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<HR>
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<H4><A NAME = "2_2"></A>2.2 Making LAMMPS
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</H4>
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<P><B><I>Read this first:</I></B>
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</P>
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<P>Building LAMMPS can be non-trivial. You will likely need to edit a
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makefile, there are compiler options, additional libraries can be used
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(MPI, FFT), etc. Please read this section carefully. If you are not
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comfortable with makefiles, or building codes on a Unix platform, or
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running an MPI job on your machine, please find a local expert to help
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2007-05-01 08:14:45 +08:00
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you. Many compiling, linking, and run problems that users are not
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really LAMMPS issues - they are peculiar to the user's system,
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compilers, libraries, etc. Such questions are better answered by a
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local expert.
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2006-09-22 00:22:34 +08:00
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</P>
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<P>If you have a build problem that you are convinced is a LAMMPS issue
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(e.g. the compiler complains about a line of LAMMPS source code), then
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2006-09-26 23:44:28 +08:00
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please send an email to the
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2007-02-10 05:37:30 +08:00
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<A HREF = "http://lammps.sandia.gov/authors.html">developers</A>.
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2006-09-22 00:22:34 +08:00
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</P>
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2007-02-10 05:37:30 +08:00
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<P>If you succeed in building LAMMPS on a new kind of machine (which
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there isn't a similar Makefile for in the distribution), send it to
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the developers and we'll include it in future LAMMPS releases.
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2006-09-22 00:22:34 +08:00
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</P>
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<P><B><I>Building a LAMMPS executable:</I></B>
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</P>
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<P>The src directory contains the C++ source and header files for LAMMPS.
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2007-05-01 08:14:45 +08:00
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It also contains a top-level Makefile and a MAKE sub-directory with
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2006-09-22 00:22:34 +08:00
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low-level Makefile.* files for several machines. From within the src
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directory, type "make" or "gmake". You should see a list of available
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choices. If one of those is the machine and options you want, you can
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type a command like:
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</P>
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<PRE>make linux
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gmake mac
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</PRE>
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<P>If you get no errors and an executable like lmp_linux or lmp_mac is
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2007-02-10 05:37:30 +08:00
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produced, you're done; it's your lucky day.
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2006-09-22 00:22:34 +08:00
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</P>
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2007-02-10 05:37:30 +08:00
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<P><B><I>Errors that can occur when making LAMMPS:</I></B>
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2006-09-22 00:22:34 +08:00
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</P>
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<P>(1) If the make command breaks immediately with errors that indicate
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it can't find files with a "*" in their names, this can be because
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your machine's make doesn't support wildcard expansion in a makefile.
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Try gmake instead of make. If that doesn't work, try using a -f
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switch with your make command to use Makefile.list which explicitly
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lists all the needed files, e.g.
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</P>
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<PRE>make makelist
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make -f Makefile.list linux
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gmake -f Makefile.list mac
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</PRE>
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<P>The first "make" command will create a current Makefile.list with all
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the file names in your src dir. The 2nd "make" command (make or
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gmake) will use it to build LAMMPS.
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</P>
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<P>(2) Other errors typically occur because the low-level Makefile isn't
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setup correctly for your machine. If your platform is named "foo",
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2007-05-01 08:14:45 +08:00
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you need to create a Makefile.foo in the MAKE sub-directory. Use
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whatever existing file is closest to your platform as a starting
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point. See the next section for more instructions.
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2006-09-22 00:22:34 +08:00
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</P>
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<P><B><I>Editing a new low-level Makefile.foo:</I></B>
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</P>
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<P>These are the issues you need to address when editing a low-level
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Makefile for your machine. With a couple exceptions, the only portion
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of the file you should need to edit is the "System-specific Settings"
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section.
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</P>
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<P>(1) Change the first line of Makefile.foo to include the word "foo"
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and whatever other options you set. This is the line you will see if
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you just type "make".
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</P>
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<P>(2) Set the paths and flags for your C++ compiler, including
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optimization flags. You can use g++, the open-source GNU compiler,
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which is available on all Unix systems. Vendor compilers often
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2007-05-01 08:14:45 +08:00
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produce faster code. On boxes with Intel CPUs, we suggest using the
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free Intel icc compiler, which you can download from <A HREF = "http://www.intel.com/software/products/noncom">Intel's compiler
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2006-09-22 00:22:34 +08:00
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site</A>.
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</P>
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<P>(3) If you want LAMMPS to run in parallel, you must have an MPI
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2007-05-01 08:14:45 +08:00
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library installed on your platform. If you do not use "mpicc" as your
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compiler/linker, then Makefile.foo needs to specify where the mpi.h
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file (-I switch) and the libmpi.a library (-L switch) is found. If
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you are installing MPI yourself, we recommend Argonne's MPICH 1.2
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which can be downloaded from the <A HREF = "http://www-unix.mcs.anl.gov/mpi">Argonne MPI
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2006-09-22 00:22:34 +08:00
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site</A>. LAM MPI should also work. If
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you are running on a big parallel platform, your system people or the
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vendor should have already installed a version of MPI, which will be
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2007-05-01 08:14:45 +08:00
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faster than MPICH or LAM, so find out how to build and link with it.
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If you use MPICH or LAM, you will have to configure and build it for
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your platform. The MPI configure script should have compiler options
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to enable you to use the same compiler you are using for the LAMMPS
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2006-09-22 00:22:34 +08:00
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build, which can avoid problems that may arise when linking LAMMPS to
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the MPI library.
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</P>
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<P>(4) If you just want LAMMPS to run on a single processor, you can use
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the STUBS library in place of MPI, since you don't need an MPI library
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installed on your system. See the Makefile.serial file for how to
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specify the -I and -L switches. You will also need to build the STUBS
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library for your platform before making LAMMPS itself. From the STUBS
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dir, type "make" and it will hopefully create a libmpi.a suitable for
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linking to LAMMPS. If the build fails, you will need to edit the
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STUBS/Makefile for your platform.
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</P>
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<P>The file STUBS/mpi.cpp has a CPU timer function MPI_Wtime() that calls
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gettimeofday() . If your system doesn't support gettimeofday() ,
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you'll need to insert code to call another timer. Note that the
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ANSI-standard function clock() rolls over after an hour or so, and is
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2007-05-01 08:14:45 +08:00
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therefore insufficient for timing long LAMMPS simulations.
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2006-09-22 00:22:34 +08:00
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</P>
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<P>(5) If you want to use the particle-particle particle-mesh (PPPM)
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option in LAMMPS for long-range Coulombics, you must have a 1d FFT
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library installed on your platform. This is specified by a switch of
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the form -DFFT_XXX where XXX = INTEL, DEC, SGI, SCSL, or FFTW. All
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but the last one are native vendor-provided libraries. FFTW is a
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fast, portable library that should work on any platform. You can
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download it from <A HREF = "http://www.fftw.org">www.fftw.org</A>. Use version
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2007-05-01 08:14:45 +08:00
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2.1.X, not the newer 3.0.X. Building FFTW for your box should be as
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simple as ./configure; make. Whichever FFT library you have on your
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platform, you'll need to set the appropriate -I and -L switches in
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Makefile.foo.
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2006-09-22 00:22:34 +08:00
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</P>
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<P>If you examine fft3d.c and fft3d.h you'll see it's possible to add
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other vendor FFT libraries via #ifdef statements in the appropriate
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places. If you successfully add a new FFT option, like -DFFT_IBM,
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2006-09-26 23:44:28 +08:00
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please send the <A HREF = "http://lammps.sandia.gov">developers</A> an email; we'd
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like to add it to LAMMPS.
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2006-09-22 00:22:34 +08:00
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</P>
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<P>(6) If you don't plan to use PPPM, you don't need an FFT library. Use
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a -DFFT_NONE switch in the CCFLAGS setting of Makefile.foo, or exclude
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the KSPACE package (see below).
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</P>
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<P>(7) There are a few other -D compiler switches you can set as part of
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CCFLAGS. The read_data and dump commands will read/write gzipped
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files if you compile with -DGZIP. It requires that your Unix support
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the "popen" command. Using one of the -DPACK_ARRAY, -DPACK_POINTER,
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and -DPACK_MEMCPY options can make for faster parallel FFTs (in the
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PPPM solver) on some platforms. The -DPACK_ARRAY setting is the
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default.
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</P>
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<P>(8) The DEPFLAGS setting is how the C++ compiler creates a dependency
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file for each source file. This speeds re-compilation when source
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(*.cpp) or header (*.h) files are edited. Some compilers do not
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support dependency file creation, or may use a different switch than
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-D. GNU g++ works with -D. If your compiler can't create dependency
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files (a long list of errors involving *.d files), then you'll need to
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create a Makefile.foo patterned after Makefile.tflop, which uses
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different rules that do not involve dependency files.
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</P>
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<P>That's it. Once you have a correct Makefile.foo and you have
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pre-built the MPI and FFT libraries it will use, all you need to do
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from the src directory is type one of these 2 commands:
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</P>
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<PRE>make foo
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gmake foo
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</PRE>
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<P>You should get the executable lmp_foo when the build is complete.
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</P>
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2007-02-10 05:37:30 +08:00
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<P><B><I>Additional build tips:</I></B>
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</P>
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<P>(1) Building LAMMPS for multiple platforms.
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</P>
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<P>You can make LAMMPS for multiple platforms from the same src
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directory. Each target creates its own object sub-dir called Obj_name
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where it stores the system-specific *.o files.
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</P>
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<P>(2) Cleaning up.
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</P>
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<P>Typing "make clean" will delete all *.o object files created when
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LAMMPS is built.
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2006-09-22 00:22:34 +08:00
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</P>
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2007-03-09 23:44:22 +08:00
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<P>(3) On some machines with some compiler options, the Coulomb tabling
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option that is enabled by default for "long" <A HREF = "pair_style.html">pair
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styles</A> such as <I>lj/cut/coul/long</I> and
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<I>lj/charmm/coul/long</I> does not work. Tables are used by these styles
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since it can offer a 2x speed-up. A symptom of this problem is
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getting wildly large energies on timestep 0 of the examples/peptide
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simulation.
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</P>
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<P>Here are several work-arounds. Coulomb tables can be disabled by
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setting "table 0" in the <A HREF = "pair_modify.html">pair_modify</A> command.
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</P>
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<P>The associated files (e.g. pair_lj_cut_coul_long.cpp) can be compiled
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at a lower optimization level like -O2, or with the compiler flag
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<I>-fno-strict-aliasing</I>. The latter can be done by adding something
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like these lines in your Makefile.machine:
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</P>
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<PRE>NOALIAS = -fno-strict-aliasing
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</PRE>
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<PRE>pair_lj_cut_coul_long.o : pair_lj_cut_coul_long.cpp
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$(CC) $(CCFLAGS) $(NOALIAS) -c $<
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</PRE>
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<PRE>pair_lj_charmm_coul_long.o : pair_lj_charmm_coul_long.cpp
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$(CC) $(CCFLAGS) $(NOALIAS) -c $<
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</PRE>
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<P>On a Macintosh, try compiling the pair "long" files without the -fast
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compiler option.
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2007-02-10 05:37:30 +08:00
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</P>
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<P>(4) Building for a Macintosh.
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</P>
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<P>OS X is BSD Unix, so it already works. See the Makefile.mac file.
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</P>
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<P>(5) Building for MicroSoft Windows.
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|
|
|
|
</P>
|
|
|
|
|
<P>I've never done this, but LAMMPS is just standard C++ with MPI and FFT
|
2007-05-01 08:14:45 +08:00
|
|
|
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.
|
2007-02-10 05:37:30 +08:00
|
|
|
</P>
|
2007-10-03 05:55:02 +08:00
|
|
|
<HR>
|
|
|
|
|
|
2007-02-10 05:37:30 +08:00
|
|
|
<H4><A NAME = "2_3"></A>2.3 Making LAMMPS with optional packages
|
|
|
|
|
</H4>
|
2006-09-22 00:22:34 +08:00
|
|
|
<P>The source code for LAMMPS is structured as a large set of core files
|
2007-10-04 01:27:50 +08:00
|
|
|
which are always used, plus optional packages, which 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 both standard and user-contributed packages by
|
|
|
|
|
typing "make package".
|
2007-10-03 05:55:02 +08:00
|
|
|
</P>
|
|
|
|
|
<P>The current list of standard packages is as follows:
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2007-09-28 07:25:52 +08:00
|
|
|
<DIV ALIGN=center><TABLE BORDER=1 >
|
2007-06-23 07:41:35 +08:00
|
|
|
<TR><TD >asphere </TD><TD > aspherical particles and force fields</TD></TR>
|
2006-09-22 00:22:34 +08:00
|
|
|
<TR><TD >class2 </TD><TD > class 2 force fields</TD></TR>
|
2007-06-20 20:56:17 +08:00
|
|
|
<TR><TD >colloid </TD><TD > colloidal particle force fields</TD></TR>
|
2007-06-23 07:41:35 +08:00
|
|
|
<TR><TD >dipole </TD><TD > point dipole particles and force fields</TD></TR>
|
2006-09-22 00:22:34 +08:00
|
|
|
<TR><TD >dpd </TD><TD > dissipative particle dynamics (DPD) force field</TD></TR>
|
|
|
|
|
<TR><TD >granular </TD><TD > force fields and boundary conditions for granular systems</TD></TR>
|
|
|
|
|
<TR><TD >kspace </TD><TD > long-range Ewald and particle-mesh (PPPM) solvers</TD></TR>
|
2006-09-28 03:12:31 +08:00
|
|
|
<TR><TD >manybody </TD><TD > metal, 3-body, bond-order potentials</TD></TR>
|
2007-02-10 05:37:30 +08:00
|
|
|
<TR><TD >meam </TD><TD > modified embedded atom method (MEAM) potential</TD></TR>
|
2006-09-22 00:22:34 +08:00
|
|
|
<TR><TD >molecule </TD><TD > force fields for molecular systems</TD></TR>
|
2007-02-10 05:37:30 +08:00
|
|
|
<TR><TD >opt </TD><TD > optimized versions of a few pair potentials</TD></TR>
|
2006-09-22 00:22:34 +08:00
|
|
|
<TR><TD >poems </TD><TD > coupled rigid body motion</TD></TR>
|
|
|
|
|
<TR><TD >xtc </TD><TD > dump atom snapshots in XTC format
|
|
|
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
|
|
2007-10-03 05:55:02 +08:00
|
|
|
<P>There are also user-contributed packages which may be as simple as a
|
2007-10-04 01:27:50 +08:00
|
|
|
single additional file or many files grouped together which add a
|
|
|
|
|
specific functionality to the code. The difference between a
|
2007-10-03 05:55:02 +08:00
|
|
|
<I>standard</I> package versus a <I>user</I> package 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 don't necessarily meet these requirements. If you have
|
|
|
|
|
problems using a feature provided in a user package, you will likely
|
2007-10-04 01:27:50 +08:00
|
|
|
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#package">this section</A> of the
|
|
|
|
|
documentation.
|
2007-10-03 05:55:02 +08:00
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
2007-02-10 05:37:30 +08:00
|
|
|
<P>Any or all packages can be included or excluded when LAMMPS is built.
|
2007-10-03 05:55:02 +08:00
|
|
|
The one exception is that to use the standard "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 keep you from having to build auxiliary
|
|
|
|
|
libraries (see below) and will produce a smaller executable which may
|
|
|
|
|
run a bit faster.
|
2007-02-10 05:37:30 +08:00
|
|
|
</P>
|
|
|
|
|
<P>By default, LAMMPS includes only the "kspace", "manybody", and
|
2007-10-03 05:55:02 +08:00
|
|
|
"molecule" packages. As described below, some standard packages
|
|
|
|
|
require LAMMPS be linked to separately built library files, which will
|
|
|
|
|
require editing of your src/MAKE/Makefile.machine.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<P>Packages are included or excluded by typing "make yes-name" or "make
|
|
|
|
|
no-name", where "name" is the name of the package. You can also type
|
2007-10-03 05:55:02 +08:00
|
|
|
"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. These commands work by simply moving files back and
|
|
|
|
|
forth between the main src directory and sub-directories with the
|
|
|
|
|
package name, 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.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<P>Additional make options exist to help manage LAMMPS files that exist
|
2007-02-10 05:37:30 +08:00
|
|
|
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
|
2006-09-22 00:22:34 +08:00
|
|
|
"make package-update" will overwrite src files with files from the
|
2007-02-10 05:37:30 +08:00
|
|
|
package directories if the package has been included. It should be
|
|
|
|
|
used after a patch is installed, since patches only update the master
|
|
|
|
|
package version of a file. Typing "make package-overwrite" will
|
|
|
|
|
overwrite files in the package directories with src files. Typing
|
|
|
|
|
"make package-check" will list differences between src and package
|
|
|
|
|
versions of the same files.
|
|
|
|
|
</P>
|
2007-04-20 07:25:27 +08:00
|
|
|
<P>To use the "meam" package you must build LAMMPS with the MEAM library
|
|
|
|
|
in lib/meam, which computes the modified embedded atom method
|
|
|
|
|
potential, which is a generalization of EAM potentials that can be
|
|
|
|
|
used to model a wider variety of materials. This MEAM implementation
|
|
|
|
|
was written by Greg Wagner at Sandia. To build LAMMPS with MEAM, you
|
|
|
|
|
must use a low-level LAMMPS Makefile that includes the MEAM directory
|
|
|
|
|
in its paths. See Makefile.linux_meam as an example. You must also
|
|
|
|
|
build MEAM itself as a library before building LAMMPS, so that LAMMPS
|
|
|
|
|
can link against it. This requires a F90 compiler. The library is
|
|
|
|
|
built by typing "make" from within the meam directory with the
|
|
|
|
|
appropriate Makefile, e.g. "make -f Makefile.icc". If one of the
|
|
|
|
|
provided Makefiles is not appropriate for your system you can edit or
|
|
|
|
|
add one as needed.
|
2007-02-10 05:37:30 +08:00
|
|
|
</P>
|
2007-03-07 22:32:28 +08:00
|
|
|
<P>Note that linking a Fortran library to a C++ code can be problematic
|
|
|
|
|
(e.g. Fortran routine names can't be found due to non-standard
|
|
|
|
|
underscore rules) and typically requires additional C++ or F90
|
|
|
|
|
libraries be included in the link. You may need to read documentation
|
|
|
|
|
for your compiler about how to do this correctly.
|
2007-02-10 05:37:30 +08:00
|
|
|
</P>
|
2007-04-20 07:25:27 +08:00
|
|
|
<P>To use the "poems" package you must build LAMMPS with the POEMS
|
|
|
|
|
library in lib/poems, which computes the constrained rigid-body motion
|
|
|
|
|
of articulated (jointed) multibody systems. POEMS was written and is
|
|
|
|
|
distributed by Prof Kurt Anderson's group at Rensselaer Polytechnic
|
|
|
|
|
Institute (RPI). To build LAMMPS with POEMS, you must use a low-level
|
|
|
|
|
LAMMPS Makefile that includes the POEMS directory in its paths. See
|
|
|
|
|
Makefile.g++_poems as an example. You must also build POEMS itself as
|
|
|
|
|
a library before building LAMMPS, so that LAMMPS can link against it.
|
|
|
|
|
The POEMS library is built by typing "make" from within the poems
|
|
|
|
|
directory with the appropriate Makefile, e.g. "make -f Makefile.g++".
|
|
|
|
|
If one of the provided Makefiles is not appropriate for your system
|
|
|
|
|
you can edit or add one as needed.
|
|
|
|
|
</P>
|
2007-10-03 05:55:02 +08:00
|
|
|
<HR>
|
|
|
|
|
|
2007-02-10 05:37:30 +08:00
|
|
|
<H4><A NAME = "2_4"></A>2.4 Building LAMMPS as a library
|
|
|
|
|
</H4>
|
2006-09-22 00:22:34 +08:00
|
|
|
<P>LAMMPS can be built as a library, which can then be called from
|
|
|
|
|
another application or a scripting language. See <A HREF = "Section_howto.html#4_10">this
|
|
|
|
|
section</A> for more info on coupling LAMMPS to
|
|
|
|
|
other codes. Building LAMMPS as a library is done by typing
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>make makelib
|
|
|
|
|
make -f Makefile.lib foo
|
|
|
|
|
</PRE>
|
|
|
|
|
<P>where foo is the machine name. The first "make" command will create a
|
|
|
|
|
current Makefile.lib with all the file names in your src dir. The 2nd
|
|
|
|
|
"make" command will use it to build LAMMPS as a library. This
|
|
|
|
|
requires that Makefile.foo have a library target (lib) and
|
|
|
|
|
system-specific settings for ARCHIVE and ARFLAGS. See Makefile.linux
|
|
|
|
|
for an example. The build will create the file liblmp_foo.a which
|
2007-02-10 05:37:30 +08:00
|
|
|
another application can link to.
|
|
|
|
|
</P>
|
|
|
|
|
<P>When used from a C++ program, the library allows one or more LAMMPS
|
|
|
|
|
objects to be instantiated. All of LAMMPS is wrapped in a LAMMPS_NS
|
|
|
|
|
namespace; you can safely use any of its classes and methods from
|
|
|
|
|
within your application code, as needed. See the sample code
|
|
|
|
|
examples/couple/c++_driver.cpp as an example.
|
|
|
|
|
</P>
|
|
|
|
|
<P>When used from a C or Fortran program or a scripting language, the
|
|
|
|
|
library has a simple function-style interface, provided in library.cpp
|
|
|
|
|
and library.h. See the sample code examples/couple/c_driver.cpp as an
|
|
|
|
|
example.
|
|
|
|
|
</P>
|
|
|
|
|
<P>You can add as many functions as you wish to library.cpp and
|
|
|
|
|
library.h. In a general sense, those functions can access LAMMPS data
|
2006-09-22 00:22:34 +08:00
|
|
|
and return it to the caller or set LAMMPS data values as specified by
|
2007-02-10 05:37:30 +08:00
|
|
|
the caller. These 4 functions are currently included in library.cpp:
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2007-02-10 05:37:30 +08:00
|
|
|
<PRE>void lammps_open(int, char **, MPI_Comm, void **ptr);
|
|
|
|
|
void lammps_close(void *ptr);
|
|
|
|
|
int lammps_file(void *ptr, char *);
|
|
|
|
|
int lammps_command(void *ptr, char *);
|
2006-09-22 00:22:34 +08:00
|
|
|
</PRE>
|
|
|
|
|
<P>The lammps_open() function is used to initialize LAMMPS, passing in a
|
2007-02-10 05:37:30 +08:00
|
|
|
list of strings as if they were <A HREF = "#2_6">command-line arguments</A> when
|
2006-09-22 00:22:34 +08:00
|
|
|
LAMMPS is run from the command line and a MPI communicator for LAMMPS
|
2007-02-10 05:37:30 +08:00
|
|
|
to run under. It returns a ptr to the LAMMPS object that is created,
|
|
|
|
|
and which should be used in subsequent library calls. Note that
|
|
|
|
|
lammps_open() can be called multiple times to create multiple LAMMPS
|
|
|
|
|
objects.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2007-02-10 05:37:30 +08:00
|
|
|
<P>The lammps_close() function is used to shut down LAMMPS and free all
|
|
|
|
|
its memory. The lammps_file() and lammps_command() functions are used
|
|
|
|
|
to pass a file or string to LAMMPS as if it were an input file or
|
|
|
|
|
single command read from an input script.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
2007-02-10 05:37:30 +08:00
|
|
|
<H4><A NAME = "2_5"></A>2.5 Running LAMMPS
|
2006-09-22 00:22:34 +08:00
|
|
|
</H4>
|
|
|
|
|
<P>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. <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 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 one of the Lennard-Jones tests on a Linux
|
|
|
|
|
box, using mpirun to launch a parallel job:
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>cd src
|
|
|
|
|
make linux
|
|
|
|
|
cp lmp_linux ../examples/lj
|
|
|
|
|
cd ../examples/lj
|
|
|
|
|
mpirun -np 4 lmp_linux < in.lj.nve
|
|
|
|
|
</PRE>
|
|
|
|
|
<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.
|
2007-04-02 22:26:01 +08:00
|
|
|
</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
|
2007-05-01 08:14:45 +08:00
|
|
|
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.
|
2006-09-22 00:22:34 +08:00
|
|
|
</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">this section</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>
|
|
|
|
|
|
2007-02-10 05:37:30 +08:00
|
|
|
<H4><A NAME = "2_6"></A>2.6 Command-line options
|
2006-09-22 00:22:34 +08:00
|
|
|
</H4>
|
|
|
|
|
<P>At run time, LAMMPS recognizes several optional command-line switches
|
|
|
|
|
which may be used in any order. For example, lmp_ibm might be
|
|
|
|
|
launched as follows:
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none < in.alloy
|
|
|
|
|
</PRE>
|
|
|
|
|
<P>These are the command-line options:
|
|
|
|
|
</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.
|
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|
</P>
|
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|
<PRE>-partition 8x2 4 5 ...
|
|
|
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|
</PRE>
|
|
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|
<P>Invoke LAMMPS in multi-partition mode. When LAMMPS is run on P
|
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|
|
|
processors and this switch is not used, LAMMPS runs in one partition,
|
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|
i.e. all P processors run a single simulation. If this switch is
|
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|
|
used, the P processors are split into separate partitions and each
|
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|
|
|
partition runs its own simulation. The arguments to the switch
|
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|
|
|
specify the number of processors in each partition. Arguments of the
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|
form MxN mean M partitions, each with N processors. Arguments of the
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|
|
form N mean a single partition with N processors. The sum of
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|
|
|
processors in all partitions must equal P. Thus the command
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|
|
|
"-partition 8x2 4 5" has 10 partitions and runs on a total of 25
|
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|
|
|
processors.
|
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|
|
|
</P>
|
|
|
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|
<P>The input script specifies what simulation is run on which partition;
|
2007-06-04 23:32:50 +08:00
|
|
|
see the <A HREF = "variable.html">variable</A> and <A HREF = "next.html">next</A> commands. This
|
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|
<A HREF = "Section_howto.html#4_4">howto section</A> gives examples of how to use
|
2007-05-01 08:14:45 +08:00
|
|
|
these commands in this way. Simulations running on different
|
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|
|
|
partitions can also communicate with each other; see the
|
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|
<A HREF = "temper.html">temper</A> command.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
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|
<PRE>-in file
|
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|
|
</PRE>
|
|
|
|
|
<P>Specify a file to use as an input script. This is an optional switch
|
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|
|
when running LAMMPS in one-partition mode. If it is not specified,
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|
|
LAMMPS reads its input script from stdin - e.g. lmp_linux < in.run.
|
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|
|
|
This is a required switch when running LAMMPS in multi-partition mode,
|
|
|
|
|
since multiple processors cannot all read from stdin.
|
|
|
|
|
</P>
|
|
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|
|
<PRE>-log file
|
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|
|
|
</PRE>
|
|
|
|
|
<P>Specify a log file for LAMMPS to write status information to. In
|
|
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|
|
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.
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>-screen file
|
|
|
|
|
</PRE>
|
2006-09-28 07:20:16 +08:00
|
|
|
<P>Specify a file for LAMMPS to write its screen information to. In
|
2006-09-22 00:22:34 +08:00
|
|
|
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.
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>-var name value
|
|
|
|
|
</PRE>
|
|
|
|
|
<P>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}). The value can be any string. Using
|
|
|
|
|
this command-line option is equivalent to putting the line "variable
|
2007-05-01 07:58:40 +08:00
|
|
|
name index value" at the beginning of the input script. Defining a
|
|
|
|
|
variable as a command-line argument overrides any setting for the same
|
|
|
|
|
variable in the input script, since variables cannot be re-defined.
|
|
|
|
|
See the <A HREF = "variable.html">variable</A> command for more info on defining
|
|
|
|
|
variables and <A HREF = "Section_commands.html#3_2">this section</A> for more info
|
|
|
|
|
on using variables in input scripts.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
2007-02-10 05:37:30 +08:00
|
|
|
<H4><A NAME = "2_7"></A>2.7 LAMMPS screen output
|
2006-09-22 00:22:34 +08:00
|
|
|
</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>
|
|
|
|
|
<PRE>Loop time of 49.002 on 2 procs for 2004 atoms
|
|
|
|
|
</PRE>
|
|
|
|
|
<PRE>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)
|
|
|
|
|
</PRE>
|
|
|
|
|
<PRE>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
|
|
|
|
|
</PRE>
|
|
|
|
|
<PRE>Total # of neighbors = 708282
|
|
|
|
|
Ave neighs/atom = 353.434
|
|
|
|
|
Ave special neighs/atom = 2.34032
|
|
|
|
|
Number of reneighborings = 42
|
|
|
|
|
Dangerous reneighborings = 2
|
|
|
|
|
</PRE>
|
|
|
|
|
<P>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.
|
|
|
|
|
</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:
|
|
|
|
|
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
|
|
|
|
|
</PRE>
|
|
|
|
|
<P>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
|
2006-09-28 07:20:16 +08:00
|
|
|
force-evaluations the minimizer required. Multiple force evaluations
|
2006-09-22 00:22:34 +08:00
|
|
|
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>
|
|
|
|
|
|
2007-02-10 05:37:30 +08:00
|
|
|
<H4><A NAME = "2_8"></A>2.8 Tips for users of previous LAMMPS versions
|
2006-09-22 00:22:34 +08:00
|
|
|
</H4>
|
|
|
|
|
<P>LAMMPS 2003 is a complete C++ rewrite of LAMMPS 2001, which was
|
|
|
|
|
written in F90. Features of earlier versions of LAMMPS are listed in
|
|
|
|
|
<A HREF = "Section_history.html">this section</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 LAMMPS 2003.
|
|
|
|
|
</P>
|
|
|
|
|
<P>If you are a previous user of LAMMPS 2001, these are the most
|
|
|
|
|
significant changes you will notice in LAMMPS 2003:
|
|
|
|
|
</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 LAMMPS 2003,
|
|
|
|
|
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 LAMMPS
|
|
|
|
|
2003.
|
|
|
|
|
</P>
|
|
|
|
|
<P>(4) Binary restart files written by LAMMPS 2001 cannot be read by
|
|
|
|
|
LAMMPS 2003 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
|
|
|
|
|
LAMMPS 2003 <A HREF = "read_data.html">read_data</A> command to read it in.
|
|
|
|
|
</P>
|
|
|
|
|
<P>(5) There are numerous small numerical changes in LAMMPS 2003 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>
|
