ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Fix memory leak

Browse Source
This commit is contained in:
Richard Berger
2019-08-22 10:41:35 -06:00
parent ce7c3e6864
commit 5d7ce839a1
1 changed files with 29 additions and 31 deletions
Download Patch File Download Diff File Expand all files Collapse all files

60
python/lammps.py
View File

@ -221,8 +221,8 @@ class lammps(object):
# add way to insert Python callback for fix external
self.callback = {}
self.FIX_EXTERNAL_CALLBACK_FUNC = CFUNCTYPE(None, c_void_p, self.c_bigint, c_int, POINTER(self.c_tagint), POINTER(POINTER(c_double)), POINTER(POINTER(c_double)))
self.lib.lammps_set_fix_external_callback.argtypes = [c_void_p, c_char_p, self.FIX_EXTERNAL_CALLBACK_FUNC, c_void_p]
self.FIX_EXTERNAL_CALLBACK_FUNC = CFUNCTYPE(None, py_object, self.c_bigint, c_int, POINTER(self.c_tagint), POINTER(POINTER(c_double)), POINTER(POINTER(c_double)))
self.lib.lammps_set_fix_external_callback.argtypes = [c_void_p, c_char_p, self.FIX_EXTERNAL_CALLBACK_FUNC, py_object]
self.lib.lammps_set_fix_external_callback.restype = None
# shut-down LAMMPS instance
@ -357,26 +357,38 @@ class lammps(object):
else:
c_int_type = c_int
if dim == 1:
raw_ptr = self.lmp.extract_atom(name, 0)
else:
raw_ptr = self.lmp.extract_atom(name, 1)
return self.iarray(c_int_type, raw_ptr, nelem, dim)
def extract_atom_darray(self, name, nelem, dim=1):
if dim == 1:
raw_ptr = self.lmp.extract_atom(name, 2)
else:
raw_ptr = self.lmp.extract_atom(name, 3)
return self.darray(raw_ptr, nelem, dim)
def iarray(self, c_int_type, raw_ptr, nelem, dim=1):
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))
ptr = cast(raw_ptr, POINTER(c_int_type * nelem))
else:
tmp = self.lmp.extract_atom(name, 1)
ptr = cast(tmp[0], POINTER(c_int_type * nelem * dim))
ptr = cast(raw_ptr[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):
def darray(self, raw_ptr, nelem, dim=1):
if dim == 1:
tmp = self.lmp.extract_atom(name, 2)
ptr = cast(tmp, POINTER(c_double * nelem))
ptr = cast(raw_ptr, POINTER(c_double * nelem))
else:
tmp = self.lmp.extract_atom(name, 3)
ptr = cast(tmp[0], POINTER(c_double * nelem * dim))
ptr = cast(raw_ptr[0], POINTER(c_double * nelem * dim))
a = np.frombuffer(ptr.contents)
a.shape = (nelem, dim)
@ -617,28 +629,14 @@ class lammps(object):
return np.int64
return np.intc
def callback_wrapper(caller_ptr, ntimestep, nlocal, tag_ptr, x_ptr, fext_ptr):
if cast(caller_ptr,POINTER(py_object)).contents:
pyCallerObj = cast(caller_ptr,POINTER(py_object)).contents.value
else:
pyCallerObj = None
tptr = cast(tag_ptr, POINTER(self.c_tagint * nlocal))
tag = np.frombuffer(tptr.contents, dtype=_ctype_to_numpy_int(self.c_tagint))
tag.shape = (nlocal)
xptr = cast(x_ptr[0], POINTER(c_double * nlocal * 3))
x = np.frombuffer(xptr.contents)
x.shape = (nlocal, 3)
fptr = cast(fext_ptr[0], POINTER(c_double * nlocal * 3))
f = np.frombuffer(fptr.contents)
f.shape = (nlocal, 3)
callback(pyCallerObj, ntimestep, nlocal, tag, x, f)
def callback_wrapper(caller, ntimestep, nlocal, tag_ptr, x_ptr, fext_ptr):
tag = self.numpy.iarray(self.c_tagint, tag_ptr, nlocal, 1)
x = self.numpy.darray(x_ptr, nlocal, 3)
f = self.numpy.darray(fext_ptr, nlocal, 3)
callback(caller, ntimestep, nlocal, tag, x, f)
cFunc = self.FIX_EXTERNAL_CALLBACK_FUNC(callback_wrapper)
cCaller = cast(pointer(py_object(caller)), c_void_p)
cCaller = caller
self.callback[fix_name] = { 'function': cFunc, 'caller': caller }