git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14326 f3b2605a-c512-4ea7-a41b-209d697bcdaa

python/examples/demo.py

@@ -15,21 +15,14 @@ if len(argv) != 1:
   print "Syntax: demo.py"
   sys.exit()
 
-me = 0
-# uncomment if running in parallel via Pypar
-#import pypar
-#me = pypar.rank()
-#nprocs = pypar.size()
-
 from lammps import lammps
-
 lmp = lammps()
 
 # test out various library functions after running in.demo
 
 lmp.file("in.demo")
 
-if me == 0: print "\nPython output:"
+print "\nPython output:"
 
 natoms = lmp.extract_global("natoms",0)
 mass = lmp.extract_atom("mass",2)
@@ -55,7 +48,3 @@ xc[0] = xc[0] + 1.0
 lmp.scatter_atoms("x",1,3,xc)
 
 print "Changed x[0][0] via scatter_atoms =",x[0][0]
-
-# uncomment if running in parallel via Pypar
-#print "Proc %d out of %d procs has" % (me,nprocs), lmp
-#pypar.finalize()

python/examples/simple.py

@@ -2,9 +2,24 @@
 # preceeding line should have path for Python on your machine
 
 # simple.py
-# Purpose: mimic operation of couple/simple/simple.cpp via Python
-# Syntax:  simple.py in.lammps
-#          in.lammps = LAMMPS input script
+# Purpose: mimic operation of examples/COUPLE/simple/simple.cpp via Python
+
+# Serial syntax: simple.py in.lammps
+#                in.lammps = LAMMPS input script
+
+# Parallel syntax: mpirun -np 4 simple.py in.lammps
+#                  in.lammps = LAMMPS input script
+
+# if run in parallel with script as-is:
+#   will invoke P instances of a one-processor run
+#   both Python and LAMMPS will run on single processors
+#   each will read same input file, write to same log.lammps file (bad)
+
+# if run in parallel after uncommening either Pypar or mpi4py sections below:
+#   will invoke 1 instance of a P-processor run
+#   both Python and LAMMPS will run in parallel
+#   see the split.py example for how to use multiple procs
+#     to run multiple LAMMPS jobs, each on a subset of procs
 
 import sys
 
@@ -19,11 +34,16 @@ infile = sys.argv[1]
 
 me = 0
 
-# uncomment if running in parallel via Pypar
+# uncomment this if running in parallel via Pypar
 #import pypar
 #me = pypar.rank()
 #nprocs = pypar.size()
 
+# uncomment this if running in parallel via mpi4py
+#from mpi4py import MPI
+#me = MPI.COMM_WORLD.Get_rank()
+#nprocs = MPI.COMM_WORLD.Get_size()
+
 from lammps import lammps
 lmp = lammps()
 
@@ -54,3 +74,7 @@ print "Force on 1 atom via extract_variable:",fx[0]
 # uncomment if running in parallel via Pypar
 #print "Proc %d out of %d procs has" % (me,nprocs), lmp
 #pypar.finalize()
+
+# uncomment if running in parallel via mpi4py
+#print "Proc %d out of %d procs has" % (me,nprocs), lmp
+#MPI.Finalize()

python/examples/split.py

@@ -0,0 +1,79 @@
+#!/usr/bin/env python -i
+# preceeding line should have path for Python on your machine
+
+# split.py
+# Purpose: similar to simple.py, but first the world communicator
+#   is split in two halves and LAMMPS is run only on one partition
+# Syntax:  split.py in.lammps
+#          in.lammps = LAMMPS input script
+
+import sys
+
+# parse command line
+
+argv = sys.argv
+if len(argv) != 2:
+  print "Syntax: simple.py in.lammps"
+  sys.exit()
+
+infile = sys.argv[1]
+
+me = 0
+
+# this example *only* works with mpi4py version 2.0.0 or later
+
+from mpi4py import MPI
+comm = MPI.COMM_WORLD
+me = comm.Get_rank()
+nprocs = comm.Get_size()
+
+# create two subcommunicators
+
+if me < nprocs // 2:  color = 0
+else: color = 1
+  
+split = comm.Split(color,key=0)
+
+if color == 0:
+  from lammps import lammps
+  lmp = lammps(comm=split)
+
+  # run infile one line at a time
+
+  lines = open(infile,'r').readlines()
+  for line in lines: lmp.command(line)
+
+  # run 10 more steps
+  # get coords from LAMMPS
+  # change coords of 1st atom
+  # put coords back into LAMMPS
+  # run a single step with changed coords
+
+  lmp.command("run 10")
+  x = lmp.gather_atoms("x",1,3)
+  epsilon = 0.1
+  x[0] += epsilon
+  lmp.scatter_atoms("x",1,3,x)
+  lmp.command("run 1");
+
+  f = lmp.extract_atom("f",3)
+  print "Force on 1 atom via extract_atom: ",f[0][0]
+
+  fx = lmp.extract_variable("fx","all",1)
+  print "Force on 1 atom via extract_variable:",fx[0]
+  print "Proc %d out of %d procs has" % (me,nprocs), lmp
+  print "Calculation on partition 0 complete"
+
+else:
+  # could run a 2nd calculation on second partition
+  #   with different LAMMPS instance or another code
+  # in this case, just sleep on second partition
+  
+  import time
+  time.sleep(2)
+  print "Calculation on partition 1 complete"
+
+# shutdown mpi4py
+  
+comm.Barrier()
+MPI.Finalize()

python/examples/trivial.py

@@ -17,12 +17,6 @@ if len(argv) != 2:
 
 infile = sys.argv[1]
 
-me = 0
-# uncomment if running in parallel via Pypar
-#import pypar
-#me = pypar.rank()
-#nprocs = pypar.size()
-
 from lammps import lammps
 lmp = lammps()
 
@@ -30,11 +24,7 @@ lmp = lammps()
 
 lmp.file(infile)
 
-# run infile one line at a time
+# or run infile one line at a time
 
 #lines = open(infile,'r').readlines()
 #for line in lines: lmp.command(line)
-
-# uncomment if running in parallel via Pypar
-#print "Proc %d out of %d procs has" % (me,nprocs), lmp
-#pypar.finalize()