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lttree_styles.py
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Thu, Oct 10, 16:00

lttree_styles.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2012, Regents of the University of California
# All rights reserved.
from ttree_lex import InputError
# Users of lttree typically generate the following files:
# The variable below refer to file names generated by
# write() and write_once() commands in a lttree-file.
# (I keep changing my mind what I want these names to be.)
data_prefix="Data "
data_prefix_no_space="Data"
data_atoms="Data Atoms"
data_masses="Data Masses"
data_velocities="Data Velocities"
data_bonds="Data Bonds"
data_bond_list="Data Bond List"
data_angles="Data Angles"
data_dihedrals="Data Dihedrals"
data_impropers="Data Impropers"
data_bond_coeffs="Data Bond Coeffs"
data_angle_coeffs="Data Angle Coeffs"
data_dihedral_coeffs="Data Dihedral Coeffs"
data_improper_coeffs="Data Improper Coeffs"
data_pair_coeffs="Data Pair Coeffs"
# interactions-by-type (not id. This is not part of the LAMMPS standard.)
data_bonds_by_type="Data Bonds By Type"
data_angles_by_type="Data Angles By Type"
data_dihedrals_by_type="Data Dihedrals By Type"
data_impropers_by_type="Data Impropers By Type"
# class2 data sections
data_bondbond_coeffs="Data BondBond Coeffs"
data_bondangle_coeffs="Data BondAngle Coeffs"
data_middlebondtorsion_coeffs="Data MiddleBondTorsion Coeffs"
data_endbondtorsion_coeffs="Data EndBondTorsion Coeffs"
data_angletorsion_coeffs="Data AngleTorsion Coeffs"
data_angleangletorsion_coeffs="Data AngleAngleTorsion Coeffs"
data_bondbond13_coeffs="Data BondBond13 Coeffs"
data_angleangle_coeffs="Data AngleAngle Coeffs"
# sections for non-point-like particles:
data_ellipsoids="Data Ellipsoids"
data_lines="Data Lines"
data_triangles="Data Triangles"
# periodic boundary conditions
data_boundary="Data Boundary"
# (for backward compatibility), an older version of this file was named:
data_pbc="Data PBC"
# The files are fragments of a LAMMPS data file (see "read_data").
# In addition, moltemplate may also generate the following files:
in_prefix="In "
in_prefix_no_space="In"
in_init="In Init"
in_settings="In Settings"
in_coords="In Coords"
# These files represent different sections of the LAMMPS input script.
# Atom Styles in LAMMPS as of 2011-7-29
g_style_map = {'angle': ['atom-ID','molecule-ID','atom-type','x','y','z'],
'atomic': ['atom-ID','atom-type','x','y','z'],
'bond': ['atom-ID','molecule-ID','atom-type','x','y','z'],
'charge': ['atom-ID','atom-type','q','x','y','z'],
'dipole': ['atom-ID','atom-type','q','x','y','z','mux','muy','muz'],
'electron': ['atom-ID','atom-type','q','spin','eradius','x','y','z'],
'ellipsoid': ['atom-ID','atom-type','x','y','z','quatw','quati','quatj','quatk'],
'full': ['atom-ID','molecule-ID','atom-type','q','x','y','z'],
'line': ['atom-ID','molecule-ID','atom-type','lineflag','density','x','y','z'],
'meso': ['atom-ID','atom-type','rho','e','cv','x','y','z'],
'molecular': ['atom-ID','molecule-ID','atom-type','x','y','z'],
'peri': ['atom-ID','atom-type','volume','density','x','y','z'],
'sphere': ['atom-ID','atom-type','diameter','density','x','y','z'],
'tri': ['atom-ID','molecule-ID','atom-type','triangleflag','density','x','y','z'],
'wavepacket':['atom-ID','atom-type','charge','spin','eradius','etag','cs_re','cs_im','x','y','z'],
'hybrid': ['atom-ID','atom-type','x','y','z'],
# The following styles were removed from LAMMPS as of 2012-3
'colloid': ['atom-ID','atom-type','x','y','z'],
'granular': ['atom-ID','atom-type','diameter','density','x','y','z']}
def AtomStyle2ColNames(atom_style_string):
atom_style_string = atom_style_string.strip()
if len(atom_style_string) == 0:
raise InputError('Error: Invalid atom_style\n'
' (The atom_style command was followed by an empty string.)\n')
atom_style_args = atom_style_string.split()
atom_style = atom_style_args[0]
hybrid_args = atom_style_args[1:]
if (atom_style not in g_style_map):
if (len(atom_style_args) >= 2):
# If the atom_style_string includes at least 2 words, then we
# interpret this as a list of the individual column names
return atom_style_args
else:
raise InputError('Error: Unrecognized atom_style: \"'+atom_style+'\"\n')
if (atom_style != 'hybrid'):
return g_style_map[atom_style]
else:
column_names = ['atom-ID','atom-type','x','y','z']
if (len(hybrid_args)==0):
raise InputError('Error: atom_style hybrid must be followed by a sub_style.\n')
for sub_style in hybrid_args:
if (sub_style not in g_style_map):
raise InputError('Error: Unrecognized atom_style: \"'+sub_style+'\"\n')
for cname in g_style_map[sub_style]:
if cname not in column_names:
column_names.append(cname)
return column_names
def ColNames2AidAtypeMolid(column_names):
# Because of the diversity of ways that these
# numbers are referred to in the LAMMPS documentation,
# we have to be flexible and allow the user to refer
# to these quantities in a variety of ways.
# Hopefully this covers everything:
if 'atom-ID' in column_names:
i_atomid = column_names.index('atom-ID')
elif 'atom−ID' in column_names: # (− is the character used in the manual)
i_atomid = column_names.index('atom−ID')
elif 'atomID' in column_names:
i_atomid = column_names.index('atomID')
elif 'atomid' in column_names:
i_atomid = column_names.index('atomid')
elif 'id' in column_names:
i_atomid = column_names.index('id')
elif 'atom' in column_names:
i_atomid = column_names.index('atom')
elif '$atom' in column_names:
i_atomid = column_names.index('$atom')
else:
raise InputError('Error: List of column names lacks an \"atom-ID\"\n')
if 'atom-type' in column_names:
i_atomtype = column_names.index('atom-type')
elif 'atom−type' in column_names: # (− hyphen character used in manual)
i_atomtype = column_names.index('atom−type')
elif 'atomtype' in column_names:
i_atomtype = column_names.index('atomtype')
elif 'type' in column_names:
i_atomtype = column_names.index('type')
elif '@atom' in column_names:
i_atomtype = column_names.index('@atom')
else:
raise InputError('Error: List of column names lacks an \"atom-type\"\n')
i_molid = None
if 'molecule-ID' in column_names:
i_molid = column_names.index('molecule-ID')
elif 'molecule−ID' in column_names: # (− hyphen character used in manual)
i_molid = column_names.index('molecule−ID')
elif 'moleculeID' in column_names:
i_molid = column_names.index('moleculeID')
elif 'moleculeid' in column_names:
i_molid = column_names.index('moleculeid')
elif 'molecule' in column_names:
i_molid = column_names.index('molecule')
elif 'molID' in column_names:
i_molid = column_names.index('molID')
elif 'molid' in column_names:
i_molid = column_names.index('molid')
elif 'mol' in column_names:
i_molid = column_names.index('mol')
elif '$mol' in column_names:
i_molid = column_names.index('$mol')
else:
pass # some atom_types do not have a valid molecule-ID
return i_atomid, i_atomtype, i_molid
def ColNames2Coords(column_names):
""" Which of the columns correspond to coordinates
which must be transformed using rigid-body
(affine: rotation + translation) transformations?
This function outputs a list of lists of triplets of integers.
"""
i_x = None
i_y = None
i_z = None
if 'x' in column_names:
i_x = column_names.index('x')
if 'y' in column_names:
i_y = column_names.index('y')
if 'z' in column_names:
i_z = column_names.index('z')
if (((i_x != None) != (i_y != None)) or
((i_y != None) != (i_z != None)) or
((i_z != None) != (i_x != None))):
raise InputError('Error: custom atom_style list must define x, y, and z.\n')
return [[i_x, i_y, i_z]]
def ColNames2Vects(column_names):
""" Which of the columns correspond to coordinates
which must be transformed using rotations?
Some coordinates like dipole moments and
ellipsoid orientations should only be rotated
(not translated).
This function outputs a list of lists of triplets of integers.
"""
vects = []
i_mux = None
i_muy = None
i_muz = None
if 'mux' in column_names:
i_mux = column_names.index('mux')
if 'muy' in column_names:
i_muy = column_names.index('muy')
if 'muz' in column_names:
i_muz = column_names.index('muz')
if (((i_mux != None) != (i_muy != None)) or
((i_muy != None) != (i_muz != None)) or
((i_muz != None) != (i_mux != None))):
raise InputError('Error: custom atom_style list must define mux, muy, and muz or none.\n')
if i_mux != None:
vects.append([i_mux, i_muy, i_muz])
return vects

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