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Merge pull request #374 from agiliopadua/master 

Updated polarizer.py in USER-DRUDE to use coul/long/cs
This commit is contained in:
sjplimp 2017-02-10 09:22:22 -07:00 committed by GitHub
parent 207adc3968 27aca14094
commit fbb24c2406
1 changed files with 26 additions and 14 deletions
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40
tools/drude/polarizer.py
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@ -2,7 +2,7 @@
# 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
@ -560,17 +560,17 @@ class Data(object):
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]
@ -596,9 +596,14 @@ class Data(object):
if ifound and jfound:
alphaij = (alphai * alphaj)**0.5
tholeij = (tholei + tholej) / 2.0
print("pair_coeff {0:4} {1:4} thole {2:7.3f} "\
"{3:7.3f}".format(atti['id'], attj['id'],
alphaij, tholeij))
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("")
@ -627,11 +632,18 @@ class Data(object):
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.")
# --------------------------------------