Clean up after renaming back to fix python/move (950bfb84) · Commits · 郑智淋 / lammps

examples/python/README.fix_python_move

+2 −2

Original line number	Diff line number	Diff line
		@@ -2,7 +2,7 @@ This folder contains several LAMMPS input scripts and a python module
		file py_nve.py to demonstrate the use of the fix style python/move
		to reimplement NVE using Python.

		in.fix_python_nve_melt:
		in.fix_python_move_nve_melt:
		This is a version of the melt example which replaces the default NVE integrator
		with a Python implementation. Fix python/move is used to create an
		instance of the py_nve.NVE class which implements the required interface.
		@@ -10,7 +10,7 @@ It demonstrates how to access LAMMPS data as numpy arrays. This gives direct
		access to memory owned by the C++ code, allows easy manipulation through numpy
		operations and avoids unnecessary copies.

		in.fix_python_nve_melt_opt:
		in.fix_python_move_nve_melt_opt:
		This version of melt example uses NVE_Opt instead of NVE. While this Python
		implementation is still much slower than the native version, it shows that
		simple code transformations can lead to speedups.

examples/python/in.fix_python_nve_melt→examples/python/in.fix_python_move_nve_melt

+0 −0

File moved.

View file

examples/python/in.fix_python_nve_melt_opt→examples/python/in.fix_python_move_nve_melt_opt

+0 −0

File moved.

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src/.gitignore

+2 −2

Original line number	Diff line number	Diff line
		@@ -908,8 +908,8 @@
		/python_impl.cpp
		/python_impl.h
		/python_compat.h
		/fix_move_python.cpp
		/fix_move_python.h
		/fix_python_move.cpp
		/fix_python_move.h
		/fix_python.cpp
		/fix_python.h
		/pair_python.cpp

src/PYTHON/fix_python_move.cpp

+19 −19

Original line number	Diff line number	Diff line
		@@ -42,7 +42,7 @@ FixPythonMove::FixPythonMove(LAMMPS lmp, int narg, char *arg) :

		python->init();

		py_integrator = NULL;
		py_move = NULL;

		PyGILState_STATE gstate = PyGILState_Ensure();

		@@ -80,8 +80,8 @@ FixPythonMove::FixPythonMove(LAMMPS lmp, int narg, char *arg) :
		// create LAMMPS atom type to potential file type mapping in python class
		// by calling 'lammps_pair_style.map_coeff(name,type)'

		PyObject *py_integrator_type = PyObject_GetAttrString(pModule, cls_name);
		if (!py_integrator_type) {
		PyObject *py_move_type = PyObject_GetAttrString(pModule, cls_name);
		if (!py_move_type) {
		PyErr_Print();
		PyErr_Clear();
		PyGILState_Release(gstate);
		@@ -93,10 +93,10 @@ FixPythonMove::FixPythonMove(LAMMPS lmp, int narg, char *arg) :

		PyObject * ptr = PY_VOID_POINTER(lmp);
		PyObject * arglist = Py_BuildValue("(O)", ptr);
		PyObject * py_integrator_obj = PyObject_CallObject(py_integrator_type, arglist);
		PyObject * py_move_obj = PyObject_CallObject(py_move_type, arglist);
		Py_DECREF(arglist);

		if (!py_integrator_obj) {
		if (!py_move_obj) {
		PyErr_Print();
		PyErr_Clear();
		PyGILState_Release(gstate);
		@@ -104,7 +104,7 @@ FixPythonMove::FixPythonMove(LAMMPS lmp, int narg, char *arg) :
		}

		// check object interface
		py_integrator = (void *) py_integrator_obj;
		py_move = (void *) py_move_obj;

		PyGILState_Release(gstate);
		}
		@@ -114,7 +114,7 @@ FixPythonMove::FixPythonMove(LAMMPS lmp, int narg, char *arg) :
		FixPythonMove::~FixPythonMove()
		{
		PyGILState_STATE gstate = PyGILState_Ensure();
		if(py_integrator) Py_DECREF((PyObject*) py_integrator);
		if(py_move) Py_DECREF((PyObject*) py_move);
		PyGILState_Release(gstate);
		}

		@@ -135,8 +135,8 @@ int FixPythonMove::setmask()
		void FixPythonMove::init()
		{
		PyGILState_STATE gstate = PyGILState_Ensure();
		PyObject py_integrator_obj = (PyObject ) py_integrator;
		PyObject *py_init = PyObject_GetAttrString(py_integrator_obj,"init");
		PyObject py_move_obj = (PyObject ) py_move;
		PyObject *py_init = PyObject_GetAttrString(py_move_obj,"init");
		if (!py_init) {
		PyErr_Print();
		PyErr_Clear();
		@@ -152,8 +152,8 @@ void FixPythonMove::init()
		void FixPythonMove::initial_integrate(int vflag)
		{
		PyGILState_STATE gstate = PyGILState_Ensure();
		PyObject py_integrator_obj = (PyObject ) py_integrator;
		PyObject *py_initial_integrate = PyObject_GetAttrString(py_integrator_obj,"initial_integrate");
		PyObject py_move_obj = (PyObject ) py_move;
		PyObject *py_initial_integrate = PyObject_GetAttrString(py_move_obj,"initial_integrate");
		if (!py_initial_integrate) {
		PyErr_Print();
		PyErr_Clear();
		@@ -171,8 +171,8 @@ void FixPythonMove::initial_integrate(int vflag)
		void FixPythonMove::final_integrate()
		{
		PyGILState_STATE gstate = PyGILState_Ensure();
		PyObject py_integrator_obj = (PyObject ) py_integrator;
		PyObject *py_final_integrate = PyObject_GetAttrString(py_integrator_obj,"final_integrate");
		PyObject py_move_obj = (PyObject ) py_move;
		PyObject *py_final_integrate = PyObject_GetAttrString(py_move_obj,"final_integrate");
		if (!py_final_integrate) {
		PyErr_Print();
		PyErr_Clear();
		@@ -188,8 +188,8 @@ void FixPythonMove::final_integrate()
		void FixPythonMove::initial_integrate_respa(int vflag, int ilevel, int iloop)
		{
		PyGILState_STATE gstate = PyGILState_Ensure();
		PyObject py_integrator_obj = (PyObject ) py_integrator;
		PyObject *py_initial_integrate_respa = PyObject_GetAttrString(py_integrator_obj,"initial_integrate_respa");
		PyObject py_move_obj = (PyObject ) py_move;
		PyObject *py_initial_integrate_respa = PyObject_GetAttrString(py_move_obj,"initial_integrate_respa");
		if (!py_initial_integrate_respa) {
		PyErr_Print();
		PyErr_Clear();
		@@ -207,8 +207,8 @@ void FixPythonMove::initial_integrate_respa(int vflag, int ilevel, int iloop)
		void FixPythonMove::final_integrate_respa(int ilevel, int iloop)
		{
		PyGILState_STATE gstate = PyGILState_Ensure();
		PyObject py_integrator_obj = (PyObject ) py_integrator;
		PyObject *py_final_integrate_respa = PyObject_GetAttrString(py_integrator_obj,"final_integrate_respa");
		PyObject py_move_obj = (PyObject ) py_move;
		PyObject *py_final_integrate_respa = PyObject_GetAttrString(py_move_obj,"final_integrate_respa");
		if (!py_final_integrate_respa) {
		PyErr_Print();
		PyErr_Clear();
		@@ -226,8 +226,8 @@ void FixPythonMove::final_integrate_respa(int ilevel, int iloop)
		void FixPythonMove::reset_dt()
		{
		PyGILState_STATE gstate = PyGILState_Ensure();
		PyObject py_integrator_obj = (PyObject ) py_integrator;
		PyObject *py_reset_dt = PyObject_GetAttrString(py_integrator_obj,"reset_dt");
		PyObject py_move_obj = (PyObject ) py_move;
		PyObject *py_reset_dt = PyObject_GetAttrString(py_move_obj,"reset_dt");
		if (!py_reset_dt) {
		PyErr_Print();
		PyErr_Clear();

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