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Detect correct integer type in lammps python interface

This commit is contained in:
Richard Berger 2017-07-15 14:52:08 -05:00
parent b9fd1156b2
commit 93be2d264e
2 changed files with 40 additions and 17 deletions
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15
examples/python/py_integrate.py
View File

@ -4,9 +4,14 @@ import ctypes
import traceback
import numpy as np
class LAMMPSIntegrator(object):
def __init__(self, ptr):
class LAMMPSFix(object):
def __init__(self, ptr, group_name="all"):
self.lmp = lammps.lammps(ptr=ptr)
self.group_name = group_name
class LAMMPSIntegrator(LAMMPSFix):
def __init__(self, ptr, group_name="all"):
super(LAMMPSIntegrator, self).__init__(ptr, group_name)
def init(self):
pass
@ -29,8 +34,9 @@ class LAMMPSIntegrator(object):
class NVE(LAMMPSIntegrator):
""" Python implementation of fix/nve """
def __init__(self, ptr):
def __init__(self, ptr, group_name="all"):
super(NVE, self).__init__(ptr)
assert(self.group_name == "all")
def init(self):
dt = self.lmp.extract_global("dt", 1)
@ -66,8 +72,9 @@ class NVE(LAMMPSIntegrator):
class NVE_Opt(LAMMPSIntegrator):
""" Tuned Python implementation of fix/nve """
def __init__(self, ptr):
def __init__(self, ptr, group_name="all"):
super(NVE_Opt, self).__init__(ptr)
assert(self.group_name == "all")
def init(self):
dt = self.lmp.extract_global("dt", 1)

42
python/lammps.py
View File

@ -37,7 +37,7 @@ def get_ctypes_int(size):
return c_int32
elif size == 8:
return c_int64
return c_int
return c_int
class MPIAbortException(Exception):
def __init__(self, message):
@ -266,25 +266,41 @@ class lammps(object):
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))
def _ctype_to_numpy_int(self, ctype_int):
if ctype_int == c_int32:
return np.int32
elif ctype_int == c_int64:
return np.int64
return np.intc
a = np.frombuffer(ptr.contents, dtype=np.intc)
def extract_atom_iarray(self, name, nelem, dim=1):
if name in ['id', 'molecule']:
c_int_type = self.lmp.c_tagint
elif name in ['image']:
c_int_type = self.lmp.c_imageint
else:
c_int_type = c_int
np_int_type = self._ctype_to_numpy_int(c_int_type)
if dim == 1:
tmp = self.lmp.extract_atom(name, 0)
ptr = cast(tmp, POINTER(c_int_type * nelem))
else:
tmp = self.lmp.extract_atom(name, 1)
ptr = cast(tmp[0], POINTER(c_int_type * nelem * dim))
a = np.frombuffer(ptr.contents, dtype=np_int_type)
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))
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))
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)