lammps/doc/Section_start.txt

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:link(lws,http://lammps.sandia.gov)
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2. Getting Started :h3

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

2.1 "What's in the LAMMPS distribution"_#2_1
2.2 "Making LAMMPS"_#2_2
2.3 "Running LAMMPS"_#2_3
2.4 "Command-line options"_#2_4
2.5 "Screen output"_#2_5
2.6 "Tips for users of previous versions"_#2_6 :all(b)

:line

2.1 What's in the LAMMPS distribution :h4,link(2_1)

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 :pre

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 :tb(s=:)

:line

2.2 Making LAMMPS :h4,link(2_2)

[{Read this first:}]

Building LAMMPS can be non-trivial.  You will likely need to edit a
makefile, there are compiler options, additional libraries can be used
(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 of the emails we get about build and run problems are not
really about LAMMPS - 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 send an email to the developers.  Note that doesn't include
linking problems - that's a question for a local expert!

Also, if you succeed in building LAMMPS on a new kind of machine
(which there isn't a similar Makefile for in the distribution), send
it to the developers and we'll include it in future LAMMPS releases.

[{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
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
type a command like:

make linux
gmake mac :pre

If you get no errors and an executable like lmp_linux or lmp_mac is
produced, you're done; it's your lucky day.  The remainder of this
section addressed the following topics: errors that occur when making
LAMMPS, editing a new low-level Makefile.foo, how to make LAMMPS with
and without packages, and additional build tips.

[{Errors that occur when making LAMMPS:}]

(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 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 Makefile.list which explicitly
lists all the needed files, e.g.

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

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.

(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.

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

These are the issues you need to address when editing a low-level
Makefile for your machine.  With a couple exceptions, the only portion
of the file you should need to edit is the "System-specific Settings"
section.

(1) Change the first line of Makefile.foo to include the word "foo"
and whatever other options you set.  This is the line you will see if
you just type "make".

(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
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
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
build, which can avoid problems that may arise when linking LAMMPS to
the MPI library.

(4) If you just want LAMMPS to run on a single processor, you can use
the STUBS library in place of MPI, since you don't need an MPI library
installed on your system.  See the Makefile.serial file for how to
specify the -I and -L switches.  You will also need to build the STUBS
library for your platform before making LAMMPS itself.  From the STUBS
dir, type "make" and it will hopefully create a libmpi.a suitable for
linking to LAMMPS.  If the build fails, you will need to edit the
STUBS/Makefile for your platform.

The file STUBS/mpi.cpp has a CPU timer function 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 runs.

(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
library installed on your platform.  This is specified by a switch of
the form -DFFT_XXX where XXX = INTEL, DEC, SGI, SCSL, or FFTW.  All
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.

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
places.  If you successfully add a new FFT option, like -DFFT_IBM,
please send the developers an email; we'd like to add it to LAMMPS.

(6) If you don't plan to use PPPM, you don't need an FFT library.  Use
a -DFFT_NONE switch in the CCFLAGS setting of Makefile.foo, or exclude
the KSPACE package (see below).

(7) There are a few other -D compiler switches you can set as part of
CCFLAGS.  The read_data and dump commands will read/write gzipped
files if you compile with -DGZIP.  It requires that your Unix support
the "popen" command.  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.

(8) The DEPFLAGS setting is how the C++ compiler creates a dependency
file for each 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 (a long list of errors involving *.d files), then you'll need to
create a Makefile.foo patterned after Makefile.tflop, which uses
different rules that do not involve dependency files.

That's it.  Once you have a correct Makefile.foo and you have
pre-built the MPI and FFT libraries it will use, all you need to do
from the src directory is type one of these 2 commands:

make foo
gmake foo :pre

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

[{How to make LAMMPS with and without packages:}]

The source code for LAMMPS is structured as a large set of core files
that are always used plus additional 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 packages by typing "make package".  The current
list of packages is as follows:

class2 : class 2 force fields
dpd : dissipative particle dynamics (DPD) force field
granular : force fields and boundary conditions for granular systems
kspace : long-range Ewald and particle-mesh (PPPM) solvers
molecule : force fields for molecular systems
poems : coupled rigid body motion
xtc : dump atom snapshots in XTC format :tb(s=:)

Any or all of these packages can be included or excluded when LAMMPS
is built.  The default is to include only the kspace and molecule
packages.  You may wish to exclude certain packages if you will never
run certain kinds of simulations.  This will produce a smaller
executable which in some cases will also run a bit faster.

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
"make yes-all" or "make no-all" to include/exclude all optional
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 not seen when LAMMPS is built.  After you
have included or excluded a package, you must re-make LAMMPS.

Additional make options exist to help manage LAMMPS files that exist
in both the src directory and in package sub-directories.  Typing
"make package-update" will overwrite src files with files from the
package directories if the package has been included.  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.

To use the poems package you must build LAMMPS with the POEMS library,
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).
It is included in the LAMMPS distribution.  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 in the LAMMPS
distribution.  By default this uses Makefile which uses the gcc
compiler.  If you need to use another compiler (so that the POEMS
library and LAMMPS are consistent), use another poems/Makefile.* or
create your own and invoke it as "make -f Makefile.*".

[{Building LAMMPS as a library:}]

LAMMPS can be built as a library, which can then be called from
another application or a scripting language.  See "this
section"_Section_howto.html#4_10 for more info on coupling LAMMPS to
other codes.  Building LAMMPS as a library is done by typing

make makelib
make -f Makefile.lib foo :pre

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
another application can link to.  The callable functions in the
library are listed in library.h, but you can add as many functions as
you wish to library.h and library.cpp, which can access LAMMPS data
and return it to the caller or set LAMMPS data values as specified by
the caller. These 3 functions are included in the library:

void lammps_open(int, char **, MPI_Comm);
void lammps_close();
int lammps_command(char *); :pre

The lammps_open() function is used to initialize LAMMPS, passing in a
list of strings as if they were "command-line arguments"_#2_4 when
LAMMPS is run from the command line and a MPI communicator for LAMMPS
to run under.  The lammps_close() function is used to shut down LAMMPS
and free all its memory.  The lammps_command() function is used to
pass a string to LAMMPS as if it were an input command read from an
input script.  See the library.h file for more information about the
arguments and return values for these 3 functions.

[{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-dir called Obj_name
where it stores the system-specific *.o files.

(2) Cleaning up.

Typing "make clean" will delete all *.o object files created when
LAMMPS is built.

(3) On some 64-bit machines, compiling with -O3 appears to break the
Coulombic tabling option used by the "pair_style"_pair_style.html
{lj/cut/coul/long} and {lj/charmm/coul/long} styles.  By default,
tabling is used by these styles since it can offer a 2x speed-up.  It
can be disabled via the "pair_modify"_pair_modify.html command.
Alternatively, the associated files (e.g. pair_lj_cut_coul_long.cpp)
can be compiled with -O2, or with the compiler flag
{-fno-strict-aliasing}.  Either of those build changes seems to fix
the problem.

(4) Building for a Macintosh.

OS X is BSD Unix, so it already works.  See the Makefile.mac file.

(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 - I can't help you on this one.

:line

2.3 Running LAMMPS :h4,link(2_3)

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"_Section_commands.html
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 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 one of the Lennard-Jones tests on a Linux
box, using mpirun to launch a parallel job:

cd src
make linux
cp lmp_linux ../examples/lj
cd ../examples/lj
mpirun -np 4 lmp_linux < in.lj.nve :pre

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 copied the LAMMPS executable
(lmp_linux) to the directory with the input files.  If you don't do
this, LAMMPS may look for input files or create output files in the
directory where the executable is, rather than where you run it from.

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 "this section"_Section_errors.html 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.

:line

2.4 Command-line options :h4,link(2_4)

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:

mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none < in.alloy :pre

These are the command-line options:

-echo style :pre

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"_echo.html command in the input script itself.

-partition 8x2 4 5 ... :pre

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.

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.

-in file :pre

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.

-log file :pre

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"_log.html command in the input script will override this setting.

-screen file :pre

Specify a file for LAMMPS to write it's 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.

-var name value :pre

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
name index value" at the beginning of the input script.  See the
"variable"_variable.html command for more info on defining variables
and "this section"_Section_commands.html#3_2 for more info on using
variables in scripts.

:line

2.5 LAMMPS screen output :h4,link(2_5)

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 :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

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

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

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"_special_bonds.html 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"_neigh_modify.html 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"_minimize.html 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 :pre

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 evalulations
are typically done at each iteration to perform a 1d line minimization
in the search direction.

If a "kspace_style"_kspace_style.html 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 :pre

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.

:line

2.6 Tips for users of previous LAMMPS versions :h4,link(2_6)

LAMMPS 2003 is a complete C++ rewrite of LAMMPS 2001, which was
written in F90.  Features of earlier versions of LAMMPS are listed in
"this section"_Section_history.html.  The F90 and F77 versions (2001
and 99) are also freely distributed as open-source codes; check the
"LAMMPS WWW Site"_lws 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.

If you are a previous user of LAMMPS 2001, these are the most
significant changes you will notice in LAMMPS 2003:

(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 LAMMPS 2003,
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"_read_data.html command for details.  The data file
section "Nonbond Coeff" has been renamed to "Pair Coeff" in LAMMPS
2003.

(4) Binary restart files written by LAMMPS 2001 cannot be read by
LAMMPS 2003 with a "read_restart"_read_restart.html 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
LAMMPS 2003 "read_data"_read_data.html command to read it in.

(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.