Merge pull request #374 from agiliopadua/master

# polarizer.py - add Drude oscillators to LAMMPS data file.

# Agilio Padua <agilio.padua@univ-bpclermont.fr>

# Alain Dequidt <alain.dequidt@univ-bpclermont.fr>

# version 2015/07/17

# version 2017/02/03

import sys

import argparse

        print("# Commands to include in the LAMMPS input script\n")

        print("# adapt the pair_style line as needed")

        print("pair_style hybrid/overlay ... coul/long {0:.1f} "\

        print("# adapt the pair_style command as needed")

        print("pair_style hybrid/overlay ... coul/long/cs {0:.1f} "\

              "thole {1:.3f} {0:.1f}\n".format(cutoff, thole))

        print("read_data {0}\n".format(outfile))

        print("# add interactions between any atoms and Drude particles")

        print("pair_coeff    *   {0}* coul/long".format(att['id']))

        print("# add interactions between atoms and Drude particles")

        print("pair_coeff    * {0:3d}* coul/long/cs".format(att['id']))

        # Thole parameters for I,J pairs

        print("# add Thole screening if more than 1 Drude per molecule")

        print("# add Thole damping if more than 1 Drude per molecule")

        ifound = False

        for atti in self.atomtypes:

            itype = atti['type'].split()[0]

                if ifound and jfound:

                    alphaij = (alphai * alphaj)**0.5

                    tholeij = (tholei + tholej) / 2.0

                    if tholeij == thole:

                        print("pair_coeff {0:4} {1:4} thole {2:7.3f}".format(

                            atti['id'], attj['id'], alphaij))

                    else:

                        print("pair_coeff {0:4} {1:4} thole {2:7.3f} "\

                              "{3:7.3f}".format(atti['id'],attj['id'],

                                                    alphaij, tholeij))

                jfound = False

            ifound = False

        print("")

        print("# ATTENTION!")

        print("#  * special_bonds may need 'extra' keyword, LAMMPS will exit "

              "with a message")

        print("#  * give all I<=J pair interactions, no mixing")

        print("#  * if using fix shake the group-ID must not include "

              "Drude particles")

        print("#    use group ATOMS for example")

              "with a message.")

        print("#  * If using fix shake the group-ID must not include "

              "Drude particles.")

        print("#    Use group ATOMS for example.")

        print("#  * Give all I<=J pair interactions, no mixing.")

        print("#  * Pair style coul/long/cs from CORESHELL package is used "\

              "for interactions")

        print("#    of Drude particles. Alternatively pair lj/cut/thole/long "\

              "could be used,")

        print("#    avoiding hybrid/overlay and allowing mixing. See doc "\

              "pages.")

# --------------------------------------