Rename fix python/integrate to python/move

This folder contains several LAMMPS input scripts and a python module

file py_integrate.py to demonstrate the use of the fix style python/integrate.

file py_nve.py to demonstrate the use of the fix style python/move

to reimplement NVE using Python.

in.fix_python_integrate_melt:

in.fix_python_nve_melt:

This is a version of the melt example which replaces the default NVE integrator

with a Python implementation. Fix python/integrate is used to create an

instance of the py_integrate.NVE class which implements the required interface.

with a Python implementation. Fix python/move is used to create an

instance of the py_nve.NVE class which implements the required interface.

It demonstrates how to access LAMMPS data as numpy arrays. This gives direct

access to memory owned by the C++ code, allows easy manipulation through numpy

operations and avoids unnecessary copies.

in.fix_python_integrate_melt_opt:

in.fix_python_nve_melt_opt:

This version of melt example uses NVE_Opt instead of NVE. While this Python

implementation is still much slower than the native version, it shows that

simple code transformations can lead to speedups.

neighbor	0.3 bin

neigh_modify	every 20 delay 0 check no

fix		1 all python/integrate py_integrate.NVE

fix		1 all python/move py_nve.NVE

thermo		50

run		250

neighbor	0.3 bin

neigh_modify	every 20 delay 0 check no

fix		1 all python/integrate py_integrate.NVE_Opt

fix		1 all python/move py_nve.NVE_Opt

thermo		50

run		250

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

        self.group_name = group_name

class LAMMPSIntegrator(LAMMPSFix):

class LAMMPSFixMove(LAMMPSFix):

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

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

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

    def init(self):

        pass

        pass

class NVE(LAMMPSIntegrator):

class NVE(LAMMPSFixMove):

    """ Python implementation of fix/nve """

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

        super(NVE, self).__init__(ptr)

            v[i,:] += dtfm * f[i,:]

class NVE_Opt(LAMMPSIntegrator):

class NVE_Opt(LAMMPSFixMove):

    """ Performance-optimized Python implementation of fix/nve """

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

        super(NVE_Opt, self).__init__(ptr)

/python_compat.h

/fix_python.cpp

/fix_python.h

/fix_python_integrate.cpp

/fix_python_integrate.h

/fix_python_move.cpp

/fix_python_move.h

/pair_python.cpp

/pair_python.h

/reader_molfile.cpp