Merge pull request #742 from rbberger/fix_python_move

"press/berendsen"_fix_press_berendsen.html,

"print"_fix_print.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/dynamic"_fix_qeq.html,

"qeq/fire"_fix_qeq.html,

"python"_python.html

"variable python"_variable.html

"fix python"_fix_python.html

"fix python/invoke"_fix_python_invoke.html

"pair_style python"_pair_python.html :ul

The "python"_python.html command which can be used to define and

examples of Python code you can write for both pure Python operations

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.

The "pair_style python"_pair_python command allows you to define

:line

fix python command :h3

fix python/invoke command :h3

[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

python = style name of this fix command :l

python/invoke = style name of this fix command :l

N = execute every N steps :l

callback = {post_force} or {end_of_step} :l

  {post_force} = callback after force computations on atoms every N time steps

    # access LAMMPS state using Python interface

""" :pre

fix pf  all python 50 post_force post_force_callback

fix eos all python 50 end_of_step end_of_step_callback :pre

fix pf  all python/invoke 50 post_force post_force_callback

fix eos all python/invoke 50 end_of_step end_of_step_callback :pre

[Description:]

"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 python/move command :h3

[Syntax:]

fix python/move pymodule.CLASS :pre

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

[Examples:]

fix  1 all python/move py_nve.NVE

fix  1 all python/move py_nve.NVE_OPT :pre

[Description:]

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

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/invoke"_fix_python_invoke.html

[Default:] none

   fix_press_berendsen

   fix_print

   fix_property_atom

   fix_python

   fix_python_invoke

   fix_python_move

   fix_qbmsst

   fix_qeq

   fix_qeq_comb