Merge pull request #12 from schrummy14/master

Commits to have LIGGGHTS work with Python3

python/examples/in.simpExample

@@ -0,0 +1,53 @@
+# Simple example based on contactModels/in.newModels
+
+variable density equal 2500
+
+# Contact model example
+atom_style granular
+atom_modify map array
+boundary f f f
+newton off
+
+communicate single vel yes
+
+units si
+
+region reg block -0.05 0.05 -0.05 0.05 0.0 0.15 units box
+create_box 1 reg
+
+neighbor 0.002 bin
+neigh_modify delay 0
+
+# Material properties required for new pair styles
+fix m1 all property/global youngsModulus peratomtype 5.0e6
+fix m2 all property/global poissonsRatio peratomtype 0.3
+fix m3 all property/global coefficientRestitution peratomtypepair 1 0.95
+fix m4 all property/global coefficientFriction peratomtypepair 1 0.05
+fix m5 all property/global characteristicVelocity scalar 2.0
+
+# Pair Style
+pair_style gran model hertz tangential history
+pair_coeff * *
+
+timestep 1.0e-5
+
+fix grav all gravity 9.81 vector 0.0 0.0 -1.0
+
+# Region for Particle Insertion
+region bc cylinder z 0.0 0.0 0.045 0.00 0.15 units box
+
+fix pts1 all particletemplate/sphere 15485863 atom_type 1 density constant ${density} radius constant 0.0025
+fix pdd1 all particledistribution/discrete 15485867 1 pts1 1.0
+fix ins all insert/pack seed 32452843 distributiontemplate pdd1 vel constant 0.0 0.0 -0.5 &
+    insert_every once overlapcheck yes all_in yes particles_in_region 18 region bc
+
+fix integr all nve/sphere
+
+compute rke all erotate/sphere update_on_run_end yes
+thermo_style custom step time atoms ke c_rke cpu cpuremain
+thermo 1000
+thermo_modify lost ignore norm no
+
+run 500
+
+fix z0 all store/state 0 z

python/examples/simpExample.py

@@ -0,0 +1,60 @@
+from liggghts import liggghts
+
+# Try loading in liggghts
+lmp = liggghts()
+
+# Try reading in an input file
+lmp.file("in.simpExample")
+
+
+# Try performing a command
+print("")
+print("Attempting to run simulation another 500 steps")
+lmp.command("run 500")
+
+# Try extracting a global value
+print("")
+print("Attempting to get the number of atoms in simulation")
+numAtoms = lmp.extract_global("natoms", 0)
+print("natoms =", numAtoms)
+
+# Try extracting atom's positions
+print("")
+print("Attempting to get the atom's positions")
+pos = lmp.extract_atom("x",3)
+for k in range(0,numAtoms):
+    print("Pos[%i] = [%f, %f, %f]" % (k, pos[k][0], pos[k][1], pos[k][2]))
+
+# Try extracting a compute
+print("")
+print("Attempting to get the rotational KE")
+rke = lmp.extract_compute("rke",0,0)
+print("rke = %f" % rke)
+
+# Try extracting a fix
+print("")
+print("Attempting to get the pos_z before python ran another 500 steps")
+z0 = lmp.extract_fix("z0",1,1)
+print("z0[0] = %f" % z0[0])
+
+# Try extracting a variable
+print("")
+print("Attempting to get the density variable used in simulation")
+density = lmp.extract_variable("density","all",0)
+print("density = %f" % density)
+
+# Testing get_natoms
+print("")
+print("Testing get_natoms")
+natoms = lmp.get_natoms()
+print("natoms = %i" % natoms)
+
+# Testing gather_atoms
+print("")
+print("Testing gather_atoms (NOTICE THAT IDS ARE DIFFERENT!!!)")
+x_gather_atoms = lmp.gather_atoms("x",1,3)
+for k in range(natoms):
+    x = x_gather_atoms[3*k+0]
+    y = x_gather_atoms[3*k+1]
+    z = x_gather_atoms[3*k+2]
+    print("x[%i] = [%f, %f, %f]" % (k, x, y, z))

python/install.py

@@ -1,17 +1,21 @@
 #!/usr/bin/env python
 
-# copy LAMMPS src/libliggghts.so and liggghts.py to system dirs
+# copy LIGGGHTS src/libliggghts.so and liggghts.py to system dirs
 
 instructions = """
 Syntax: python install.py [-h] [libdir] [pydir]
         libdir = target dir for src/libliggghts.so, default = /usr/local/lib
         pydir = target dir for liggghts.py, default = Python site-packages dir
 """
 
-import sys,os,commands
+import sys,os # ,commands
+if sys.version_info[0] == 3:
+  import subprocess as commands
+else:
+  import commands
 
 if (len(sys.argv) > 1 and sys.argv[1] == "-h") or len(sys.argv) > 3:
-  print instructions
+  print(instructions)
   sys.exit()
 
 if len(sys.argv) >= 2: libdir = sys.argv[1]
@@ -24,35 +28,35 @@
 # warn if not in LD_LIBRARY_PATH or LD_LIBRARY_PATH is undefined
 
 if not os.path.isdir(libdir):
-  print "ERROR: libdir %s does not exist" % libdir
+  print("ERROR: libdir %s does not exist" % libdir)
   sys.exit()
 
 if "LD_LIBRARY_PATH" not in os.environ:
-  print "WARNING: LD_LIBRARY_PATH undefined, cannot check libdir %s" % libdir
+  print("WARNING: LD_LIBRARY_PATH undefined, cannot check libdir %s" % libdir)
 else:
   libpaths = os.environ['LD_LIBRARY_PATH'].split(':')
   if libdir not in libpaths:
-    print "WARNING: libdir %s not in LD_LIBRARY_PATH" % libdir
+    print("WARNING: libdir %s not in LD_LIBRARY_PATH" % libdir)
 
 str = "cp ../src/libliggghts.so %s" % libdir
-print str
+print(str)
 outstr = commands.getoutput(str)
-if len(outstr.strip()): print outstr
+if len(outstr.strip()): print(outstr)
 
 # copy liggghts.py to pydir if it exists
 # if pydir not specified, install in site-packages via distutils setup()
 
 if pydir:
   if not os.path.isdir(pydir):
-    print "ERROR: pydir %s does not exist" % pydir
+    print("ERROR: pydir %s does not exist" % pydir)
     sys.exit()
   str = "cp ../python/liggghts.py %s" % pydir
-  print str
+  print(str)
   outstr = commands.getoutput(str)
-  if len(outstr.strip()): print outstr
+  if len(outstr.strip()): print(outstr)
   sys.exit()
 
-print "installing liggghts.py in Python site-packages dir"
+print("installing liggghts.py in Python site-packages dir")
 
 os.chdir('../python')                # in case invoked via make in src dir
 

python/liggghts.py

@@ -18,6 +18,9 @@
 
 class liggghts:
   def __init__(self,name="",cmdargs=None):
+
+    # Check which python version is being used
+    self.pyVersion = sys.version_info
 
     # load libliggghts.so by default
     # if name = "g++", load libliggghts_g++.so
@@ -28,7 +31,7 @@ def __init__(self,name="",cmdargs=None):
     except:
       type,value,tb = sys.exc_info()
       traceback.print_exception(type,value,tb)
-      raise OSError,"Could not load LIGGGHTS dynamic library"
+      raise OSError("Could not load LIGGGHTS dynamic library")
 
     # create an instance of LAMMPS
     # don't know how to pass an MPI communicator from PyPar
@@ -55,12 +58,18 @@ def close(self):
     self.lmp = None
 
   def file(self,file):
+    if self.pyVersion[0] == 3:
+      file = file.encode()
     self.lib.lammps_file(self.lmp,file)
 
   def command(self,cmd):
+    if self.pyVersion[0] == 3:
+      cmd = cmd.encode()
     self.lib.lammps_command(self.lmp,cmd)
 
   def extract_global(self,name,type):
+    if self.pyVersion[0] == 3:
+      name = name.encode()
     if type == 0:
       self.lib.lammps_extract_global.restype = POINTER(c_int)
     elif type == 1:
@@ -70,6 +79,8 @@ def extract_global(self,name,type):
     return ptr[0]
 
   def extract_atom(self,name,type):
+    if self.pyVersion[0] == 3:
+      name = name.encode()
     if type == 0:
       self.lib.lammps_extract_atom.restype = POINTER(c_int)
     elif type == 1:
@@ -82,40 +93,44 @@ def extract_atom(self,name,type):
     ptr = self.lib.lammps_extract_atom(self.lmp,name)
     return ptr
 
-  def extract_compute(self,id,style,type):
+  def extract_compute(self,c_id,style,type):
+    if self.pyVersion[0] == 3:
+      c_id = c_id.encode()
     if type == 0:
       if style > 0: return None
       self.lib.lammps_extract_compute.restype = POINTER(c_double)
-      ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
+      ptr = self.lib.lammps_extract_compute(self.lmp,c_id,style,type)
       return ptr[0]
     if type == 1:
       self.lib.lammps_extract_compute.restype = POINTER(c_double)
-      ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
+      ptr = self.lib.lammps_extract_compute(self.lmp,c_id,style,type)
       return ptr
     if type == 2:
       self.lib.lammps_extract_compute.restype = POINTER(POINTER(c_double))
-      ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
+      ptr = self.lib.lammps_extract_compute(self.lmp,c_id,style,type)
       return ptr
     return None
 
   # in case of global datum, free memory for 1 double via lammps_free()
   # double was allocated by library interface function
 
-  def extract_fix(self,id,style,type,i=0,j=0):
+  def extract_fix(self,f_id,style,type,i=0,j=0):
+    if self.pyVersion[0] == 3:
+      f_id = f_id.encode()
     if type == 0:
       if style > 0: return None
       self.lib.lammps_extract_fix.restype = POINTER(c_double)
-      ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
+      ptr = self.lib.lammps_extract_fix(self.lmp,f_id,style,type,i,j)
       result = ptr[0]
       self.lib.lammps_free(ptr)
       return result
     if type == 1:
       self.lib.lammps_extract_fix.restype = POINTER(c_double)
-      ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
+      ptr = self.lib.lammps_extract_fix(self.lmp,f_id,style,type,i,j)
       return ptr
     if type == 2:
       self.lib.lammps_extract_fix.restype = POINTER(POINTER(c_double))
-      ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
+      ptr = self.lib.lammps_extract_fix(self.lmp,f_id,style,type,i,j)
       return ptr
     return None
 
@@ -124,6 +139,9 @@ def extract_fix(self,id,style,type,i=0,j=0):
   # memory was allocated by library interface function
 
   def extract_variable(self,name,group,type):
+    if self.pyVersion[0] == 3:
+      name = name.encode()
+      group = group.encode()
     if type == 0:
       self.lib.lammps_extract_variable.restype = POINTER(c_double)
       ptr = self.lib.lammps_extract_variable(self.lmp,name,group)
@@ -150,6 +168,8 @@ def get_natoms(self):
   # return vector of atom properties gathered across procs, ordered by atom ID
 
   def gather_atoms(self,name,type,count):
+    if self.pyVersion[0] == 3:
+      name = name.encode()
     natoms = self.lib.lammps_get_natoms(self.lmp)
     if type == 0:
       data = ((count*natoms)*c_int)()
@@ -164,4 +184,6 @@ def gather_atoms(self,name,type,count):
   # assume vector is of correct type and length, as created by gather_atoms()
 
   def scatter_atoms(self,name,type,count,data):
+    if self.pyVersion[0] == 3:
+      name = name.encode()
     self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data)