Fix memory leak (b49957c1) · Commits · 郑智淋 / lammps

python/lammps.py

+29 −31

Original line number	Diff line number	Diff line
		@@ -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 }

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