574e4067dc
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118 lines
3.0 KiB
ReStructuredText
118 lines
3.0 KiB
ReStructuredText
.. index:: fix python/move
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fix python/move command
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=======================
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Syntax
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""""""
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.. parsed-literal::
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fix python/move pymodule.CLASS
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pymodule.CLASS = use class **CLASS** in module/file **pymodule** to compute how to move atoms
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Examples
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""""""""
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.. parsed-literal::
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fix 1 all python/move py_nve.NVE
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fix 1 all python/move py_nve.NVE_OPT
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Description
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"""""""""""
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The *python/move* fix style provides a way to define ways how particles
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are moved during an MD run from python script code, that is loaded from
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a file into LAMMPS and executed at the various steps where other fixes
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can be executed. This python script must contain specific python class
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definitions.
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This allows to implement complex position updates and also modified
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time integration methods. Due to python being an interpreted language,
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however, the performance of this fix can be moderately to significantly
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slower than the corresponding C++ code. For specific cases, this
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performance penalty can be limited through effective use of NumPy.
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----------
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The python module file has to start with the following code:
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.. parsed-literal::
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from __future_\_ import print_function
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import lammps
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import ctypes
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import traceback
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import numpy as np
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#
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class LAMMPSFix(object):
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def __init__(self, ptr, group_name="all"):
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self.lmp = lammps.lammps(ptr=ptr)
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self.group_name = group_name
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#
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class LAMMPSFixMove(LAMMPSFix):
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def __init__(self, ptr, group_name="all"):
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super(LAMMPSFixMove, self).__init__(ptr, group_name)
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#
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def init(self):
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pass
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#
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def initial_integrate(self, vflag):
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pass
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#
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def final_integrate(self):
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pass
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#
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def initial_integrate_respa(self, vflag, ilevel, iloop):
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pass
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#
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def final_integrate_respa(self, ilevel, iloop):
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pass
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#
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def reset_dt(self):
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pass
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Any classes implementing new atom motion functionality have to be
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derived from the **LAMMPSFixMove** class, overriding the available
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methods as needed.
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Examples for how to do this are in the *examples/python* folder.
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----------
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**Restart, fix\_modify, output, run start/stop, minimize info:**
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No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix\_modify <fix_modify>` options
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are relevant to this fix. No global or per-atom quantities are stored
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by this fix for access by various :doc:`output commands <Howto_output>`.
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No parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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This pair style is part of the PYTHON package. It is only enabled if
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LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
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Related commands
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""""""""""""""""
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:doc:`fix nve <fix_nve>`, :doc:`fix python/invoke <fix_python_invoke>`
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**Default:** none
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Commands_all.html
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