add documentation for fix move/python

"lineforce"_fix_lineforce.html,

"momentum (k)"_fix_momentum.html,

"move"_fix_move.html,

"move/python"_fix_move_python.html,

"mscg"_fix_mscg.html,

"msst"_fix_msst.html,

"neb"_fix_neb.html,

"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)

:link(ld,Manual.html)

:link(lc,Section_commands.html#comm)

:line

fix move/python command :h3

[Syntax:]

fix move/python pymodule.CLASS :pre

pymodule.CLASS = use class [CLASS] in module/file [pymodule] to compute how to move atoms

[Examples:]

fix  1 all move/python py_nve.NVE

fix  1 all move/python py_nve.NVE_OPT :pre

[Description:]

The {move/python} fix style provides a way to define ways how particles

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

can be executed. This python script must contain specific python class

definitions.

This allows to implement complex position updates and also modified

time integration methods. Due to python being an interpreted language,

however, the performance of this fix can be moderately to significantly

slower than the corresponding C++ code. For specific cases, this

performance penalty can be limited through effective use of NumPy.

:line

The python module file has to start with the following code:

from __future__ import print_function

import lammps

import ctypes

import traceback

import numpy as np

#

class LAMMPSFix(object):

    def __init__(self, ptr, group_name="all"):

        self.lmp = lammps.lammps(ptr=ptr)

        self.group_name = group_name

#

class LAMMPSFixMove(LAMMPSFix):

    def __init__(self, ptr, group_name="all"):

        super(LAMMPSFixMove, self).__init__(ptr, group_name)

#

    def init(self):

        pass

#

    def initial_integrate(self, vflag):

        pass

#

    def final_integrate(self):

        pass

#

    def initial_integrate_respa(self, vflag, ilevel, iloop):

        pass

#

    def final_integrate_respa(self, ilevel, iloop):

        pass

#

    def reset_dt(self):

        pass :pre

Any classes implementing new atom motion functionality have to be

derived from the [LAMMPSFixMove] class, overriding the available

methods as needed.

Examples for how to do this are in the {examples/python} folder.

:line

[Restart, fix_modify, output, run start/stop, minimize info:]

No information about this fix is written to "binary restart

files"_restart.html.  None of the "fix_modify"_fix_modify.html options

are relevant to this fix.  No global or per-atom quantities are stored

by this fix for access by various "output

commands"_Section_howto.html#howto_15.  No parameter of this fix can

be used with the {start/stop} keywords of the "run"_run.html command.

This fix is not invoked during "energy minimization"_minimize.html.

[Restrictions:]

This pair style is part of the PYTHON package.  It is only enabled if

LAMMPS was built with that package.  See the "Making

LAMMPS"_Section_start.html#start_3 section for more info.

[Related commands:]

"fix nve"_fix_nve.html, "fix python"_fix_python.html

[Default:] none

   fix_meso_stationary

   fix_momentum

   fix_move

   fix_move_python

   fix_mscg

   fix_msst

   fix_mvv_dpd

fix_meso_stationary.html

fix_momentum.html

fix_move.html

fix_move_python.html

fix_mscg.html

fix_msst.html

fix_mvv_dpd.html

/python_impl.cpp

/python_impl.h

/python_compat.h

/fix_move_python.cpp

/fix_move_python.h

/fix_python.cpp

/fix_python.h

/fix_python_move.cpp

/fix_python_move.h

/pair_python.cpp

/pair_python.h

/reader_molfile.cpp