Merge branch 'master' into lammps-icms

Resolved Conflicts:
	lib/meam/Makefile.gfortran
	lib/poems/Makefile.g++
	lib/reax/Makefile.gfortran
	python/lammps.py
	src/USER-CUDA/cuda.cpp

python/lammps.py

@@ -17,23 +17,15 @@ import types
 from ctypes import *
 import os.path
 
-LMPINT = 0
-LMPDOUBLE = 1
-LMPIPTR = 2
-LMPDPTR = 3
-LMPDPTRPTR = 4
-
-LOCATION = os.path.dirname(__file__)
-
 class lammps:
-  def __init__(self,name="",cmdlineargs=None):
+  def __init__(self,name="",cmdargs=None):
 
-    # load liblmp.so by default
-    # if name = "g++", load liblmp_g++.so
+    # load liblammps.so by default
+    # if name = "g++", load liblammps_g++.so
     
     try:
-      if not name: self.lib = CDLL("liblmp.so")
-      else: self.lib = CDLL("liblmp_%s.so" % name)
+      if not name: self.lib = CDLL("liblammps.so")
+      else: self.lib = CDLL("liblammps_%s.so" % name)
     except:
       raise OSError,"Could not load LAMMPS dynamic library"
 
@@ -42,10 +34,10 @@ class lammps:
     # no_mpi call lets LAMMPS use MPI_COMM_WORLD
     # cargs = array of C strings from args
     
-    if cmdlineargs:
-      cmdlineargs.insert(0,"lammps.py")
-      narg = len(cmdlineargs)
-      cargs = (c_char_p*narg)(*cmdlineargs)
+    if cmdargs:
+      cmdargs.insert(0,"lammps.py")
+      narg = len(cmdargs)
+      cargs = (c_char_p*narg)(*cmdargs)
       self.lmp = c_void_p()
       self.lib.lammps_open_no_mpi(narg,cargs,byref(self.lmp))
     else:
@@ -68,30 +60,26 @@ class lammps:
     self.lib.lammps_command(self.lmp,cmd)
 
   def extract_global(self,name,type):
-    if type == LMPDOUBLE:
-      self.lib.lammps_extract_global.restype = POINTER(c_double)
-      ptr = self.lib.lammps_extract_global(self.lmp,name)
-      return ptr[0]
-    if type == LMPINT:
+    if type == 0:
       self.lib.lammps_extract_global.restype = POINTER(c_int)
-      ptr = self.lib.lammps_extract_global(self.lmp,name)
-      return ptr[0]
-    return None
+    elif type == 1:
+      self.lib.lammps_extract_global.restype = POINTER(c_double)
+    else: return None
+    ptr = self.lib.lammps_extract_global(self.lmp,name)
+    return ptr[0]
 
   def extract_atom(self,name,type):
-    if type == LMPDPTRPTR:
-      self.lib.lammps_extract_atom.restype = POINTER(POINTER(c_double))
-      ptr = self.lib.lammps_extract_atom(self.lmp,name)
-      return ptr
-    if type == LMPDPTR:
-      self.lib.lammps_extract_atom.restype = POINTER(c_double)
-      ptr = self.lib.lammps_extract_atom(self.lmp,name)
-      return ptr
-    if type == LMPIPTR:
+    if type == 0:
       self.lib.lammps_extract_atom.restype = POINTER(c_int)
-      ptr = self.lib.lammps_extract_atom(self.lmp,name)
-      return ptr
-    return None
+    elif type == 1:
+      self.lib.lammps_extract_atom.restype = POINTER(POINTER(c_int))
+    elif type == 2:
+      self.lib.lammps_extract_atom.restype = POINTER(c_double)
+    elif type == 3:
+      self.lib.lammps_extract_atom.restype = POINTER(POINTER(c_double))
+    else: return None
+    ptr = self.lib.lammps_extract_atom(self.lmp,name)
+    return ptr
 
   def extract_compute(self,id,style,type):
     if type == 0:
@@ -153,18 +141,26 @@ class lammps:
       return result
     return None
 
+  # return total number of atoms in system
+  
   def get_natoms(self):
     return self.lib.lammps_get_natoms(self.lmp)
 
-  def get_coords(self):
-    nlen = 3 * self.lib.lammps_get_natoms(self.lmp)
-    coords = (c_double*nlen)()
-    self.lib.lammps_get_coords(self.lmp,coords)
-    return coords
+  # return vector of atom properties gathered across procs, ordered by atom ID
 
-  # assume coords is an array of c_double, as created by get_coords()
-  # could check if it is some other Python object and create c_double array?
-  # constructor for c_double array can take an arg to use to fill it?
-  
-  def put_coords(self,coords):
-    self.lib.lammps_put_coords(self.lmp,coords)
+  def gather_atoms(self,name,type,count):
+    natoms = self.lib.lammps_get_natoms(self.lmp)
+    if type == 0:
+      data = ((count*natoms)*c_double)()
+      self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
+    elif type == 1:
+      data = ((count*natoms)*c_double)()
+      self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
+    else: return None
+    return data
+
+  # scatter vector of atom properties across procs, ordered by atom ID
+  # assume vector is of correct type and length, as created by gather_atoms()
+
+  def scatter_atoms(self,name,type,count,data):
+    self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data)