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Remove mentions of Pypar

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This commit is contained in:
Richard Berger
2021-06-01 17:51:06 -04:00
parent 232ae5e856
commit 400b55e6d5
4 changed files with 22 additions and 31 deletions
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25
python/README
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@ -38,13 +38,14 @@ Once you have successfully wrapped LAMMPS, you can run the Python
scripts in the examples sub-directory: scripts in the examples sub-directory:
trivial.py read/run a LAMMPS input script thru Python trivial.py read/run a LAMMPS input script thru Python
demo.py invoke various LAMMPS library interface routines demo.py invoke various LAMMPS library interface routines
simple.py parallel example, mimicing examples/COUPLE/simple/simple.cpp simple.py parallel example, mimicing examples/COUPLE/simple/simple.cpp
split.py parallel example split.py parallel example
mc.py Monte Carlo energy relaxation wrapper on LAMMPS mc.py Monte Carlo energy relaxation wrapper on LAMMPS
gui.py GUI go/stop/temperature-slider to control LAMMPS gui.py GUI go/stop/temperature-slider to control LAMMPS
plot.py real-time temperature plot with GnuPlot via Pizza.py plot.py real-time temperature plot with GnuPlot via Pizza.py
viz_tool.py real-time viz via some viz package matplotlib_plot.py real-time temperature plot with Matplotlib via Pizza.py
viz_tool.py real-time viz via some viz package
vizplotgui_tool.py combination of viz.py and plot.py and gui.py vizplotgui_tool.py combination of viz.py and plot.py and gui.py
For the viz_tool.py and vizplotgui_tool.py commands, replace "tool" For the viz_tool.py and vizplotgui_tool.py commands, replace "tool"
@ -100,24 +101,24 @@ split.py in.simple # can run in parallel (see below)
gui.py in.gui 100 gui.py in.gui 100
plot.py in.plot 10 1000 thermo_temp plot.py in.plot 10 1000 thermo_temp
matplotlib_plot.py in.plot 10 1000 thermo_temp
viz_tool.py in.viz 100 5000 viz_tool.py in.viz 100 5000
vizplotgui_tool.py in.viz 100 thermo_temp vizplotgui_tool.py in.viz 100 thermo_temp
To run LAMMPS in parallel from Python, so something like this: To run LAMMPS in parallel from Python, so something like this:
% mpirun -np 4 simple.py in.simple % mpirun -np P simple.py in.simple
% mpirun -np 4 python split.py in.simple % mpirun -np P python split.py in.simple
If you run simple.py as-is, this will invoke P instances of a If you run simple.py as-is, this will invoke P instances of a
one-processor run, where both Python and LAMMPS will run on single one-processor run, where both Python and LAMMPS will run on single
processors. Each running job will read the same input file, and write processors. Each running job will read the same input file, and write
to same log.lammps file, which isn't too useful. to same log.lammps file, which isn't too useful.
However, if you have either the Pypar or mpi4py packages installed in However, if you have the mpi4py Python package installed and uncomment mpi4py
your Python, and uncomment the Pypar or mpi4py code in simple.py, then code in simple.py, then the above commands will invoke 1 instance of a
the above commands will invoke 1 instance of a P-processor run. Both P-processor run. Both Python and LAMMPS will run on P processors. The job will
Python and LAMMPS will run on P processors. The job will read the read the input file and write a single log.lammps file.
input file and write a single log.lammps file.
The split.py script can also be run in parallel. It uses mpi4py The split.py script can also be run in parallel. It uses mpi4py
version 2.0.0 (or later), which makes it possible to pass a version 2.0.0 (or later), which makes it possible to pass a

1
python/examples/.gitignore vendored Normal file
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@ -0,0 +1 @@
/tmp*

17
python/examples/matplotlib_plot.py
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@ -28,10 +28,10 @@ nsteps = int(sys.argv[3])
compute = sys.argv[4] compute = sys.argv[4]
me = 0 me = 0
# uncomment if running in parallel via Pypar # uncomment this if running in parallel via mpi4py
#import pypar #from mpi4py import MPI
#me = pypar.rank() #me = MPI.COMM_WORLD.Get_rank()
#nprocs = pypar.size() #nprocs = MPI.COMM_WORLD.Get_size()
from lammps import lammps from lammps import lammps
lmp = lammps() lmp = lammps()
@ -82,11 +82,8 @@ while ntimestep < nsteps:
lmp.command("run 0 pre no post yes") lmp.command("run 0 pre no post yes")
# uncomment if running in parallel via Pypar # uncomment if running in parallel via mpi4py
#print("Proc %d out of %d procs has" % (me,nprocs), lmp) #print("Proc %d out of %d procs has" % (me,nprocs), lmp)
#pypar.finalize()
if sys.version_info[0] == 3: if me == 0:
input("Press Enter to exit...") input("Press Enter to exit...")
else:
raw_input("Press Enter to exit...")

10
python/examples/simple.py
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@ -9,7 +9,7 @@
# Parallel syntax: mpirun -np 4 simple.py in.lammps # Parallel syntax: mpirun -np 4 simple.py in.lammps
# in.lammps = LAMMPS input script # in.lammps = LAMMPS input script
# also need to uncomment either Pypar or mpi4py sections below # also need to uncomment mpi4py sections below
from __future__ import print_function from __future__ import print_function
import sys import sys
@ -27,11 +27,6 @@ infile = sys.argv[1]
me = 0 me = 0
# uncomment this if running in parallel via Pypar
#import pypar
#me = pypar.rank()
#nprocs = pypar.size()
# uncomment this if running in parallel via mpi4py # uncomment this if running in parallel via mpi4py
#from mpi4py import MPI #from mpi4py import MPI
#me = MPI.COMM_WORLD.Get_rank() #me = MPI.COMM_WORLD.Get_rank()
@ -133,8 +128,5 @@ lmp.reset_box([0,0,0],[10,10,8],0,0,0)
boxlo,boxhi,xy,yz,xz,periodicity,box_change = lmp.extract_box() boxlo,boxhi,xy,yz,xz,periodicity,box_change = lmp.extract_box()
if me == 0: print("Box info",boxlo,boxhi,xy,yz,xz,periodicity,box_change) if me == 0: print("Box info",boxlo,boxhi,xy,yz,xz,periodicity,box_change)
# uncomment if running in parallel via Pypar
#print("Proc %d out of %d procs has" % (me,nprocs), lmp)
# uncomment if running in parallel via mpi4py # uncomment if running in parallel via mpi4py
#print("Proc %d out of %d procs has" % (me,nprocs), lmp) #print("Proc %d out of %d procs has" % (me,nprocs), lmp)