From 4d725c315322f39bdf77db23a7cfe55d3c164a98 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Fri, 15 Dec 2017 13:17:12 -0500
Subject: [PATCH] Revert "Rename fix python/move to move/python"
This reverts commit 4d915dba08a9b77a560a2938ac155db3a5699455.
---
...fix_move_python => README.fix_python_move} | 8 +--
...python_nve_melt => in.fix_python_nve_melt} | 2 +-
...ve_melt_opt => in.fix_python_nve_melt_opt} | 2 +-
...ix_move_python.cpp => fix_python_move.cpp} | 71 ++++++++++---------
.../{fix_move_python.h => fix_python_move.h} | 14 ++--
5 files changed, 50 insertions(+), 47 deletions(-)
rename examples/python/{README.fix_move_python => README.fix_python_move} (77%)
rename examples/python/{in.fix_move_python_nve_melt => in.fix_python_nve_melt} (90%)
rename examples/python/{in.fix_move_python_nve_melt_opt => in.fix_python_nve_melt_opt} (89%)
rename src/PYTHON/{fix_move_python.cpp => fix_python_move.cpp} (73%)
rename src/PYTHON/{fix_move_python.h => fix_python_move.h} (87%)
diff --git a/examples/python/README.fix_move_python b/examples/python/README.fix_python_move
similarity index 77%
rename from examples/python/README.fix_move_python
rename to examples/python/README.fix_python_move
index 9ab15f0b67..308d154119 100644
--- a/examples/python/README.fix_move_python
+++ b/examples/python/README.fix_python_move
@@ -1,16 +1,16 @@
This folder contains several LAMMPS input scripts and a python module
-file py_nve.py to demonstrate the use of the fix style move/python
+file py_nve.py to demonstrate the use of the fix style python/move
to reimplement NVE using Python.
-in.fix_move_python_nve_melt:
+in.fix_python_nve_melt:
This is a version of the melt example which replaces the default NVE integrator
-with a Python implementation. Fix move/python is used to create an
+with a Python implementation. Fix python/move is used to create an
instance of the py_nve.NVE class which implements the required interface.
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_move_python_nve_melt_opt:
+in.fix_python_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.
diff --git a/examples/python/in.fix_move_python_nve_melt b/examples/python/in.fix_python_nve_melt
similarity index 90%
rename from examples/python/in.fix_move_python_nve_melt
rename to examples/python/in.fix_python_nve_melt
index 0274b8994d..24828d7445 100644
--- a/examples/python/in.fix_move_python_nve_melt
+++ b/examples/python/in.fix_python_nve_melt
@@ -17,7 +17,7 @@ pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
-fix 1 all move/python py_nve.NVE
+fix 1 all python/move py_nve.NVE
thermo 50
run 250
diff --git a/examples/python/in.fix_move_python_nve_melt_opt b/examples/python/in.fix_python_nve_melt_opt
similarity index 89%
rename from examples/python/in.fix_move_python_nve_melt_opt
rename to examples/python/in.fix_python_nve_melt_opt
index 5f7bca3096..9564ffa02e 100644
--- a/examples/python/in.fix_move_python_nve_melt_opt
+++ b/examples/python/in.fix_python_nve_melt_opt
@@ -17,7 +17,7 @@ pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
-fix 1 all move/python py_nve.NVE_Opt
+fix 1 all python/move py_nve.NVE_Opt
thermo 50
run 250
diff --git a/src/PYTHON/fix_move_python.cpp b/src/PYTHON/fix_python_move.cpp
similarity index 73%
rename from src/PYTHON/fix_move_python.cpp
rename to src/PYTHON/fix_python_move.cpp
index a910e13aee..2c216d8aad 100644
--- a/src/PYTHON/fix_move_python.cpp
+++ b/src/PYTHON/fix_python_move.cpp
@@ -19,7 +19,7 @@
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
-#include "fix_move_python.h"
+#include "fix_python_move.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
@@ -34,7 +34,7 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
-FixMovePython::FixMovePython(LAMMPS *lmp, int narg, char **arg) :
+FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
dynamic_group_allow = 1;
@@ -42,7 +42,7 @@ FixMovePython::FixMovePython(LAMMPS *lmp, int narg, char **arg) :
python->init();
- py_move = NULL;
+ py_integrator = NULL;
PyGILState_STATE gstate = PyGILState_Ensure();
@@ -51,12 +51,12 @@ FixMovePython::FixMovePython(LAMMPS *lmp, int narg, char **arg) :
PyList_Append(py_path, PY_STRING_FROM_STRING("."));
- // create move instance
+ // create integrator instance
char * full_cls_name = arg[3];
char * lastpos = strrchr(full_cls_name, '.');
if (lastpos == NULL) {
- error->all(FLERR,"Fix move/python requires fully qualified class name");
+ error->all(FLERR,"Fix python/integrate requires fully qualified class name");
}
size_t module_name_length = strlen(full_cls_name) - strlen(lastpos);
@@ -74,15 +74,18 @@ FixMovePython::FixMovePython(LAMMPS *lmp, int narg, char **arg) :
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
- error->all(FLERR,"Loading python move module failure");
+ error->all(FLERR,"Loading python integrator module failure");
}
- PyObject *py_move_type = PyObject_GetAttrString(pModule, cls_name);
- if (!py_move_type) {
+ // 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) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
- error->all(FLERR,"Could not find move class in module'");
+ error->all(FLERR,"Could not find integrator class in module'");
}
delete [] module_name;
@@ -90,34 +93,34 @@ FixMovePython::FixMovePython(LAMMPS *lmp, int narg, char **arg) :
PyObject * ptr = PY_VOID_POINTER(lmp);
PyObject * arglist = Py_BuildValue("(O)", ptr);
- PyObject * py_move_obj = PyObject_CallObject(py_move_type, arglist);
+ PyObject * py_integrator_obj = PyObject_CallObject(py_integrator_type, arglist);
Py_DECREF(arglist);
- if (!py_move_obj) {
+ if (!py_integrator_obj) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
- error->all(FLERR,"Could not instantiate instance of move class'");
+ error->all(FLERR,"Could not instantiate instance of integrator class'");
}
// check object interface
- py_move = (void *) py_move_obj;
+ py_integrator = (void *) py_integrator_obj;
PyGILState_Release(gstate);
}
/* ---------------------------------------------------------------------- */
-FixMovePython::~FixMovePython()
+FixPythonMove::~FixPythonMove()
{
PyGILState_STATE gstate = PyGILState_Ensure();
- if(py_move) Py_DECREF((PyObject*) py_move);
+ if(py_integrator) Py_DECREF((PyObject*) py_integrator);
PyGILState_Release(gstate);
}
/* ---------------------------------------------------------------------- */
-int FixMovePython::setmask()
+int FixPythonMove::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
@@ -129,11 +132,11 @@ int FixMovePython::setmask()
/* ---------------------------------------------------------------------- */
-void FixMovePython::init()
+void FixPythonMove::init()
{
PyGILState_STATE gstate = PyGILState_Ensure();
- PyObject *py_move_obj = (PyObject *) py_move;
- PyObject *py_init = PyObject_GetAttrString(py_move_obj,"init");
+ PyObject *py_integrator_obj = (PyObject *) py_integrator;
+ PyObject *py_init = PyObject_GetAttrString(py_integrator_obj,"init");
if (!py_init) {
PyErr_Print();
PyErr_Clear();
@@ -146,11 +149,11 @@ void FixMovePython::init()
/* ---------------------------------------------------------------------- */
-void FixMovePython::initial_integrate(int vflag)
+void FixPythonMove::initial_integrate(int vflag)
{
PyGILState_STATE gstate = PyGILState_Ensure();
- PyObject *py_move_obj = (PyObject *) py_move;
- PyObject *py_initial_integrate = PyObject_GetAttrString(py_move_obj,"initial_integrate");
+ PyObject *py_integrator_obj = (PyObject *) py_integrator;
+ PyObject *py_initial_integrate = PyObject_GetAttrString(py_integrator_obj,"initial_integrate");
if (!py_initial_integrate) {
PyErr_Print();
PyErr_Clear();
@@ -165,11 +168,11 @@ void FixMovePython::initial_integrate(int vflag)
/* ---------------------------------------------------------------------- */
-void FixMovePython::final_integrate()
+void FixPythonMove::final_integrate()
{
PyGILState_STATE gstate = PyGILState_Ensure();
- PyObject *py_move_obj = (PyObject *) py_move;
- PyObject *py_final_integrate = PyObject_GetAttrString(py_move_obj,"final_integrate");
+ PyObject *py_integrator_obj = (PyObject *) py_integrator;
+ PyObject *py_final_integrate = PyObject_GetAttrString(py_integrator_obj,"final_integrate");
if (!py_final_integrate) {
PyErr_Print();
PyErr_Clear();
@@ -182,11 +185,11 @@ void FixMovePython::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixMovePython::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixPythonMove::initial_integrate_respa(int vflag, int ilevel, int iloop)
{
PyGILState_STATE gstate = PyGILState_Ensure();
- PyObject *py_move_obj = (PyObject *) py_move;
- PyObject *py_initial_integrate_respa = PyObject_GetAttrString(py_move_obj,"initial_integrate_respa");
+ PyObject *py_integrator_obj = (PyObject *) py_integrator;
+ PyObject *py_initial_integrate_respa = PyObject_GetAttrString(py_integrator_obj,"initial_integrate_respa");
if (!py_initial_integrate_respa) {
PyErr_Print();
PyErr_Clear();
@@ -201,11 +204,11 @@ void FixMovePython::initial_integrate_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-void FixMovePython::final_integrate_respa(int ilevel, int iloop)
+void FixPythonMove::final_integrate_respa(int ilevel, int iloop)
{
PyGILState_STATE gstate = PyGILState_Ensure();
- PyObject *py_move_obj = (PyObject *) py_move;
- PyObject *py_final_integrate_respa = PyObject_GetAttrString(py_move_obj,"final_integrate_respa");
+ PyObject *py_integrator_obj = (PyObject *) py_integrator;
+ PyObject *py_final_integrate_respa = PyObject_GetAttrString(py_integrator_obj,"final_integrate_respa");
if (!py_final_integrate_respa) {
PyErr_Print();
PyErr_Clear();
@@ -220,11 +223,11 @@ void FixMovePython::final_integrate_respa(int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-void FixMovePython::reset_dt()
+void FixPythonMove::reset_dt()
{
PyGILState_STATE gstate = PyGILState_Ensure();
- PyObject *py_move_obj = (PyObject *) py_move;
- PyObject *py_reset_dt = PyObject_GetAttrString(py_move_obj,"reset_dt");
+ PyObject *py_integrator_obj = (PyObject *) py_integrator;
+ PyObject *py_reset_dt = PyObject_GetAttrString(py_integrator_obj,"reset_dt");
if (!py_reset_dt) {
PyErr_Print();
PyErr_Clear();
diff --git a/src/PYTHON/fix_move_python.h b/src/PYTHON/fix_python_move.h
similarity index 87%
rename from src/PYTHON/fix_move_python.h
rename to src/PYTHON/fix_python_move.h
index 0573ea5062..0d06305fb9 100644
--- a/src/PYTHON/fix_move_python.h
+++ b/src/PYTHON/fix_python_move.h
@@ -23,21 +23,21 @@
#ifdef FIX_CLASS
-FixStyle(move/python,FixMovePython)
+FixStyle(python/move,FixPythonMove)
#else
-#ifndef LMP_FIX_MOVE_PYTHON_H
-#define LMP_FIX_MOVE_PYTHON_H
+#ifndef LMP_FIX_PYTHON_MOVE_H
+#define LMP_FIX_PYTHON_MOVE_H
#include "fix.h"
namespace LAMMPS_NS {
-class FixMovePython : public Fix {
+class FixPythonMove : public Fix {
public:
- FixMovePython(LAMMPS *lmp, int narg, char **arg);
- virtual ~FixMovePython();
+ FixPythonMove(LAMMPS *lmp, int narg, char **arg);
+ virtual ~FixPythonMove();
int setmask();
virtual void init();
@@ -48,7 +48,7 @@ class FixMovePython : public Fix {
virtual void reset_dt();
protected:
- void * py_move;
+ void * py_integrator;
};
}
--
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