Added optional numpy access to atom data

The library interface was extended to provide direct access to atom data using
numpy arrays. No data copies are made and numpy operations directly manipulate
memory of the native code.

To keep this numpy dependency optional, all functions are wrapped into the
lammps.numpy sub-object which is only loaded when accessed.

python/lammps.py

@@ -162,6 +162,9 @@ class lammps(object):
         pythonapi.PyCObject_AsVoidPtr.argtypes = [py_object]
         self.lmp = c_void_p(pythonapi.PyCObject_AsVoidPtr(ptr))
 
+      # optional numpy support (lazy loading)
+      self._numpy = None
+
   def __del__(self):
     if self.lmp and self.opened:
       self.lib.lammps_close(self.lmp)
@@ -236,6 +239,41 @@ class lammps(object):
     ptr = self.lib.lammps_extract_atom(self.lmp,name)
     return ptr
 
+  @property
+  def numpy(self):
+    if not self._numpy:
+      import numpy as np
+      class LammpsNumpyWrapper:
+        def __init__(self, lmp):
+          self.lmp = lmp
+
+        def extract_atom_iarray(self, name, nelem, dim=1):
+          if dim == 1:
+              tmp = self.lmp.extract_atom(name, 0)
+              ptr = cast(tmp, POINTER(c_int * nelem))
+          else:
+              tmp = self.lmp.extract_atom(name, 1)
+              ptr = cast(tmp[0], POINTER(c_int * nelem * dim))
+
+          a = np.frombuffer(ptr.contents, dtype=np.intc)
+          a.shape = (nelem, dim)
+          return a
+
+        def extract_atom_darray(self, name, nelem, dim=1):
+          if dim == 1:
+              tmp = self.lmp.extract_atom(name, 2)
+              ptr = cast(tmp, POINTER(c_double * nelem))
+          else:
+              tmp = self.lmp.extract_atom(name, 3)
+              ptr = cast(tmp[0], POINTER(c_double * nelem * dim))
+
+          a = np.frombuffer(ptr.contents)
+          a.shape = (nelem, dim)
+          return a
+
+      self._numpy = LammpsNumpyWrapper(self)
+    return self._numpy
+
   # extract compute info
   
   def extract_compute(self,id,style,type):