add example with passing cmdline flags to the LAMMPS instance

test/lib_python/Makefile

@@ -10,8 +10,8 @@ default:
 test: $(LIB) $(OUTPUTS)
 
 log.%-$(MACH)$(TAG): in.%.py $(LIB)
-	$(MPICMD) python  $< $(LMPFLAGS)
-	mv log.lammps $@
+	$(MPICMD) python  $< $(LMPFLAGS) -log none -screen $@ -echo screen 
+	test -f log.lammps && mv log.lammps $@ || true
 
 clean:
 	-rm -f log.* lammps.py *.pyc liblammps*.so

test/lib_python/in.simple-001.py

@@ -1,16 +1,10 @@
 #!/usr/bin/env python -i
-# 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
 
 infile = 'in.simple'
 me = 0
 
 from lammps import lammps
-lmp = lammps(cmdargs=['-echo','screen'])
+lmp = lammps()
 
 # run infile one line at a time
 

test/lib_python/in.simple-002.py

@@ -0,0 +1,34 @@
+#!/usr/bin/env python -i
+# 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
+
+import sys
+
+infile = 'in.simple'
+me = 0
+
+from lammps import lammps
+lmp = lammps(cmdargs=sys.argv[1:])
+
+# run infile one line at a time
+
+lines = open(infile,'r').readlines()
+for line in lines: lmp.command(line)
+
+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]
+