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Rename fix python to fix python/invoke

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This commit is contained in:
Richard Berger
2017-12-15 13:53:04 -05:00
parent 950bfb84a9
commit bcc5f49d0b
11 changed files with 41 additions and 36 deletions
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4
doc/src/Section_commands.txt
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@ -585,7 +585,6 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"lineforce"_fix_lineforce.html, "lineforce"_fix_lineforce.html,
"momentum (k)"_fix_momentum.html, "momentum (k)"_fix_momentum.html,
"move"_fix_move.html, "move"_fix_move.html,
"move/python"_fix_move_python.html,
"mscg"_fix_mscg.html, "mscg"_fix_mscg.html,
"msst"_fix_msst.html, "msst"_fix_msst.html,
"neb"_fix_neb.html, "neb"_fix_neb.html,
@ -621,7 +620,8 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"press/berendsen"_fix_press_berendsen.html, "press/berendsen"_fix_press_berendsen.html,
"print"_fix_print.html, "print"_fix_print.html,
"property/atom"_fix_property_atom.html, "property/atom"_fix_property_atom.html,
"python"_fix_python.html, "python/invoke"_fix_python_invoke.html,
"python/move"_fix_python_move.html,
"qeq/comb (o)"_fix_qeq_comb.html, "qeq/comb (o)"_fix_qeq_comb.html,
"qeq/dynamic"_fix_qeq.html, "qeq/dynamic"_fix_qeq.html,
"qeq/fire"_fix_qeq.html, "qeq/fire"_fix_qeq.html,

4
doc/src/Section_python.txt
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@ -123,7 +123,7 @@ code directly from an input script:
"python"_python.html "python"_python.html
"variable python"_variable.html "variable python"_variable.html
"fix python"_fix_python.html "fix python/invoke"_fix_python_invoke.html
"pair_style python"_pair_python.html :ul "pair_style python"_pair_python.html :ul
The "python"_python.html command which can be used to define and The "python"_python.html command which can be used to define and
@ -165,7 +165,7 @@ doc page for its python-style variables for more info, including
examples of Python code you can write for both pure Python operations examples of Python code you can write for both pure Python operations
and callbacks to LAMMPS. and callbacks to LAMMPS.
The "fix python"_fix_python.html command can execute The "fix python/invoke"_fix_python_invoke.html command can execute
Python code at selected timesteps during a simulation run. Python code at selected timesteps during a simulation run.
The "pair_style python"_pair_python command allows you to define The "pair_style python"_pair_python command allows you to define

10
doc/src/fix_python.txt → doc/src/fix_python_invoke.txt
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@ -6,14 +6,14 @@
:line :line
fix python command :h3 fix python/invoke command :h3
[Syntax:] [Syntax:]
fix ID group-ID python N callback function_name :pre fix ID group-ID python/invoke N callback function_name :pre
ID, group-ID are ignored by this fix :ulb,l ID, group-ID are ignored by this fix :ulb,l
python = style name of this fix command :l python/invoke = style name of this fix command :l
N = execute every N steps :l N = execute every N steps :l
callback = {post_force} or {end_of_step} :l callback = {post_force} or {end_of_step} :l
{post_force} = callback after force computations on atoms every N time steps {post_force} = callback after force computations on atoms every N time steps
@ -36,8 +36,8 @@ def end_of_step_callback(lammps_ptr):
# access LAMMPS state using Python interface # access LAMMPS state using Python interface
""" :pre """ :pre
fix pf all python 50 post_force post_force_callback fix pf all python/invoke 50 post_force post_force_callback
fix eos all python 50 end_of_step end_of_step_callback :pre fix eos all python/invoke 50 end_of_step end_of_step_callback :pre
[Description:] [Description:]

12
doc/src/fix_move_python.txt → doc/src/fix_python_move.txt
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@ -6,22 +6,22 @@
:line :line
fix move/python command :h3 fix python/move command :h3
[Syntax:] [Syntax:]
fix move/python pymodule.CLASS :pre fix python/move pymodule.CLASS :pre
pymodule.CLASS = use class [CLASS] in module/file [pymodule] to compute how to move atoms pymodule.CLASS = use class [CLASS] in module/file [pymodule] to compute how to move atoms
[Examples:] [Examples:]
fix 1 all move/python py_nve.NVE fix 1 all python/move py_nve.NVE
fix 1 all move/python py_nve.NVE_OPT :pre fix 1 all python/move py_nve.NVE_OPT :pre
[Description:] [Description:]
The {move/python} fix style provides a way to define ways how particles The {python/move} fix style provides a way to define ways how particles
are moved during an MD run from python script code, that is loaded from are moved during an MD run from python script code, that is loaded from
a file into LAMMPS and executed at the various steps where other fixes a file into LAMMPS and executed at the various steps where other fixes
can be executed. This python script must contain specific python class can be executed. This python script must contain specific python class
@ -96,7 +96,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:] [Related commands:]
"fix nve"_fix_nve.html, "fix python"_fix_python.html "fix nve"_fix_nve.html, "fix python/invoke"_fix_python_invoke.html
[Default:] none [Default:] none

3
doc/src/lammps.book
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@ -245,7 +245,8 @@ fix_pour.html
fix_press_berendsen.html fix_press_berendsen.html
fix_print.html fix_print.html
fix_property_atom.html fix_property_atom.html
fix_python.html fix_python_invoke.html
fix_python_move.html
fix_qbmsst.html fix_qbmsst.html
fix_qeq.html fix_qeq.html
fix_qeq_comb.html fix_qeq_comb.html

4
doc/src/python.txt
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@ -406,7 +406,7 @@ cases, LAMMPS has no simple way to check that something illogical is
being attempted. being attempted.
The same applies to Python functions called during a simulation run at The same applies to Python functions called during a simulation run at
each time step using "fix python"_fix_python.html. each time step using "fix python/invoke"_fix_python_invoke.html.
:line :line
@ -493,6 +493,6 @@ different source files, problems may occur.
[Related commands:] [Related commands:]
"shell"_shell.html, "variable"_variable.html, "fix python"_fix_python.html "shell"_shell.html, "variable"_variable.html, "fix python/invoke"_fix_python_invoke.html
[Default:] none [Default:] none

4
examples/python/in.fix_python → examples/python/in.fix_python_invoke
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@ -33,8 +33,8 @@ def post_force_callback(lmp, v):
""" """
fix 1 all nve fix 1 all nve
fix 2 all python 50 end_of_step end_of_step_callback fix 2 all python/invoke 50 end_of_step end_of_step_callback
fix 3 all python 50 post_force post_force_callback fix 3 all python/invoke 50 post_force post_force_callback
#dump id all atom 50 dump.melt #dump id all atom 50 dump.melt

4
src/.gitignore vendored
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@ -910,8 +910,8 @@
/python_compat.h /python_compat.h
/fix_python_move.cpp /fix_python_move.cpp
/fix_python_move.h /fix_python_move.h
/fix_python.cpp /fix_python_invoke.cpp
/fix_python.h /fix_python_invoke.h
/pair_python.cpp /pair_python.cpp
/pair_python.h /pair_python.h
/reader_molfile.cpp /reader_molfile.cpp

16
src/PYTHON/fix_python.cpp → src/PYTHON/fix_python_invoke.cpp
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@ -18,7 +18,7 @@
#include <Python.h> #include <Python.h>
#include <stdio.h> #include <stdio.h>
#include <string.h> #include <string.h>
#include "fix_python.h" #include "fix_python_invoke.h"
#include "atom.h" #include "atom.h"
#include "force.h" #include "force.h"
#include "update.h" #include "update.h"
@ -32,13 +32,13 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
FixPython::FixPython(LAMMPS *lmp, int narg, char **arg) : FixPythonInvoke::FixPythonInvoke(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg) Fix(lmp, narg, arg)
{ {
if (narg != 6) error->all(FLERR,"Illegal fix python command"); if (narg != 6) error->all(FLERR,"Illegal fix python/invoke command");
nevery = force->inumeric(FLERR,arg[3]); nevery = force->inumeric(FLERR,arg[3]);
if (nevery <= 0) error->all(FLERR,"Illegal fix python command"); if (nevery <= 0) error->all(FLERR,"Illegal fix python/invoke command");
// ensure Python interpreter is initialized // ensure Python interpreter is initialized
python->init(); python->init();
@ -48,7 +48,7 @@ FixPython::FixPython(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[4],"end_of_step") == 0) { } else if (strcmp(arg[4],"end_of_step") == 0) {
selected_callback = END_OF_STEP; selected_callback = END_OF_STEP;
} else { } else {
error->all(FLERR,"Unsupported callback name for fix/python"); error->all(FLERR,"Unsupported callback name for fix python/invoke");
} }
// get Python function // get Python function
@ -74,14 +74,14 @@ FixPython::FixPython(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
int FixPython::setmask() int FixPythonInvoke::setmask()
{ {
return selected_callback; return selected_callback;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void FixPython::end_of_step() void FixPythonInvoke::end_of_step()
{ {
PyGILState_STATE gstate = PyGILState_Ensure(); PyGILState_STATE gstate = PyGILState_Ensure();
@ -96,7 +96,7 @@ void FixPython::end_of_step()
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
void FixPython::post_force(int vflag) void FixPythonInvoke::post_force(int vflag)
{ {
if (update->ntimestep % nevery != 0) return; if (update->ntimestep % nevery != 0) return;

13
src/PYTHON/fix_python.h → src/PYTHON/fix_python_invoke.h
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@ -13,21 +13,22 @@
#ifdef FIX_CLASS #ifdef FIX_CLASS
FixStyle(python,FixPython) FixStyle(python,FixPythonInvoke)
FixStyle(python/invoke,FixPythonInvoke)
#else #else
#ifndef LMP_FIX_PYTHON_H #ifndef LMP_FIX_PYTHON_INVOKE_H
#define LMP_FIX_PYTHON_H #define LMP_FIX_PYTHON_INVOKE_H
#include "fix.h" #include "fix.h"
namespace LAMMPS_NS { namespace LAMMPS_NS {
class FixPython : public Fix { class FixPythonInvoke : public Fix {
public: public:
FixPython(class LAMMPS *, int, char **); FixPythonInvoke(class LAMMPS *, int, char **);
virtual ~FixPython() {} virtual ~FixPythonInvoke() {}
int setmask(); int setmask();
virtual void end_of_step(); virtual void end_of_step();
virtual void post_force(int); virtual void post_force(int);

3
src/Purge.list
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@ -16,6 +16,9 @@ style_region.h
style_neigh_bin.h style_neigh_bin.h
style_neigh_pair.h style_neigh_pair.h
style_neigh_stencil.h style_neigh_stencil.h
# deleted on 15 December 2017
fix_python.cpp
fix_python.h
# deleted on 11 October 2017 # deleted on 11 October 2017
fix_shear_history_omp.cpp fix_shear_history_omp.cpp
fix_shear_history_omp.h fix_shear_history_omp.h