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doc/Section_python.txt
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@ -304,13 +304,12 @@ if some of the packages are still being actively developed and
supported.
The packages Pypar and mpi4py have both been successfully tested with
LAMMPS. Both are widely used. Pypar is simpler and easy to set up
and use, but supports only a subset of MPI. Mpi4py is more
MPI-feature complete, but also a bit more complex to use. As of
version 2.0.0, mpi4py is the only python MPI wrapper that allows
passing a custom MPI communicator to the LAMMPS constructor, which
means one can easily run one or more LAMMPS instances on subsets of
the total MPI ranks.
LAMMPS. Pypar is simpler and easy to set up and use, but supports
only a subset of MPI. Mpi4py is more MPI-feature complete, but also a
bit more complex to use. As of version 2.0.0, mpi4py is the only
python MPI wrapper that allows passing a custom MPI communicator to
the LAMMPS constructor, which means one can easily run one or more
LAMMPS instances on subsets of the total MPI ranks.
:line
@ -380,7 +379,7 @@ Again, the "sudo" is only needed if required to copy mpi4py files into
your Python distribution's site-packages directory. To install with
user privilege into the user local directory type
python setup.py install --user
python setup.py install --user :pre
If you have successully installed mpi4py, you should be able to run
Python and type
@ -467,8 +466,8 @@ lmp_g++ -in in.lj :pre
[Test LAMMPS and Python in parallel:] :h5
To run LAMMPS in parallel, assuming you have installed the
"Pypar"_http://datamining.anu.edu.au/~ole/pypar package as discussed
above, create a test.py file containing these lines:
"Pypar"_Pypar package as discussed above, create a test.py file
containing these lines:
import pypar
from lammps import lammps
@ -477,7 +476,20 @@ lmp.file("in.lj")
print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()),lmp
pypar.finalize() :pre
You can then run it in parallel as:
To run LAMMPS in parallel, assuming you have installed the
"mpi4py"_mpi4py package as discussed above, create a test.py file
containing these lines:
from mpi4py import MPI
from lammps import lammps
lmp = lammps()
lmp.file("in.lj")
me = MPI.COMM_WORLD.Get_rank()
nprocs = MPI.COMM_WORLD.Get_size()
print "Proc %d out of %d procs has" % (me,nprocs),lmp
MPI.Finalize() :pre
You can either script in parallel as:
% mpirun -np 4 python test.py :pre
@ -547,7 +559,7 @@ from a C++ or C or Fortran program.
lmp = lammps() # create a LAMMPS object using the default liblammps.so library
4 optional args are allowed: name, cmdargs, ptr, comm
lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator. Requires mpi4py 2.0.0 or later
lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later
lmp = lammps(name="g++") # create a LAMMPS object using the liblammps_g++.so library
lmp = lammps(name="g++",cmdargs=list) # add LAMMPS command-line args, e.g. list = \["-echo","screen"\] :pre
@ -772,7 +784,8 @@ distribution.
trivial.py, read/run a LAMMPS input script thru Python,
demo.py, invoke various LAMMPS library interface routines,
simple.py, mimic operation of couple/simple/simple.cpp in Python,
simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp,
split.py, same as simple.py but running in parallel on a subset of procs,
gui.py, GUI go/stop/temperature-slider to control LAMMPS,
plot.py, real-time temeperature plot with GnuPlot via Pizza.py,
viz_tool.py, real-time viz via some viz package,