fix python/move command

Syntax

fix python/move pymodule.CLASS

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

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.


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

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.


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

No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.

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 for more info.