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lammps/tools/moltemplate/src/bonds_by_type.py
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bonds_by_type.py
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#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2011, Regents of the University of California
# All rights reserved.
"""
bonds_by_type.py reads a LAMMPS data file (or an excerpt of a LAMMPS)
data file containing bonded many-body interactions by atom type
(and bond type), and generates a list of additional interactions
in LAMMPS format consistent with those type (to the standard out).
Typical Usage:
bonds_by_type.py -atoms atoms.data \\
-bonds bonds.data \\
-bondsbytype bonds_by_type.data \\
> new_bonds.data
"""
# -bonds-ids-atom-pairs bonds_ids_atom_pairs.data \\
import sys
#from extract_lammps_data import *
#from nbody_by_type_lib import GenInteractions_str
import ttree_lex
#from ttree_lex import *
from lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid
def LookupBondTypes(bond_types,
bond_ids,
bond_pairs,
lines_atoms,
lines_bonds,
lines_bondsbytype,
atom_style,
section_name,
prefix='',
suffix='',
bond_ids_offset=0):
#report_progress = False):
"""
LookupBondTypes() looks up bond types.
Output:
...It looks up the corresponding type of each bond and store it in the
"bond_types" list. (If the bond_ids were not specified by the user,
generate them and store them in the bond_ids list.)
Input (continued):
This function requires:
...a list of bonded pairs of atoms
stored in the lines_bonds variable (from the "Data Bond List"
or "Data Bonds AtomId AtomId" sections)
...and a list of atom types
stored in the lines_atoms variable (from the "Data Atoms" section)
...and a list of bond-types-as-a-function-of-atom-types
stored in the lines_bondsbytype (from the "Data Bonds By Type" section)
Generated bond_ids (if applicable) are of the form
prefix + str(number) + suffix
(where "number" begins at bond_ids_offset+1)
"""
column_names = AtomStyle2ColNames(atom_style)
i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names)
atomids = []
atomtypes = []
atomids2types = {}
for iv in range(0, len(lines_atoms)):
line = lines_atoms[iv].strip()
if '#' in line:
icomment = line.find('#')
line = (line[:icomment]).strip()
if len(line) > 0:
tokens = ttree_lex.SplitQuotedString(line)
if ((len(tokens) <= i_atomid) or (len(tokens) <= i_atomtype)):
sys.stderr.write("\""+line+"\"\n")
raise(ttree_lex.InputError('Error not enough columns on line '+str(iv+1)+' of \"Atoms\" section.'))
tokens = ttree_lex.SplitQuotedString(line)
atomid = ttree_lex.EscCharStrToChar(tokens[i_atomid])
atomids.append(atomid)
atomtype = ttree_lex.EscCharStrToChar(tokens[i_atomtype])
atomtypes.append(atomtype)
atomids2types[atomid] = atomtype
assert(isinstance(bond_ids, list))
assert(isinstance(bond_types, list))
assert(isinstance(bond_pairs, list))
del bond_ids[:]
del bond_types[:]
del bond_pairs[:]
for ie in range(0, len(lines_bonds)):
line = lines_bonds[ie].strip()
if '#' in line:
icomment = line.find('#')
line = (line[:icomment]).strip()
if len(line) == 0:
continue
tokens = ttree_lex.SplitQuotedString(line)
if section_name == "Data Bonds AtomId AtomId":
if len(tokens) == 2:
bondid_n = bond_ids_offset + len(bond_ids) + 1
bond_ids.append(prefix+str(bondid_n)+suffix)
bond_pairs.append( (ttree_lex.EscCharStrToChar(tokens[0]),
ttree_lex.EscCharStrToChar(tokens[1])) )
else:
raise(ttree_lex.InputError('Incorrect number of columns on line '+str(ie+1)+' of \"'+section_name+'\" section.'))
elif section_name == "Data Bond List":
if len(tokens) == 3:
bond_ids.append(ttree_lex.EscCharStrToChar(tokens[0]))
bond_pairs.append( (ttree_lex.EscCharStrToChar(tokens[1]),
ttree_lex.EscCharStrToChar(tokens[2])) )
else:
raise(ttree_lex.InputError('Incorrect number of columns on line '+str(ie+1)+' of \"'+section_name+'\" section.'))
#elif section_name == "Data Bonds BondType AtomId AtomId":
# if len(tokens) == 3:
# bondid_n = bond_ids_offset + len(bond_ids) + 1
# bond_ids.append(prefix+str(bondid_n)+suffix)
# bond_types.append(ttree_lex.EscCharStrToChar(tokens[0]))
# bond_pairs.append( (ttree_lex.EscCharStrToChar(tokens[1]),
# ttree_lex.EscCharStrToChar(tokens[2])) )
# else:
# raise(ttree_lex.InputError('Incorrect number of columns on line '+str(ie+1)+' of \"'+section_name+'\" section.'))
else:
raise(ttree_lex.InputError('Internal Error ('+g_program_name+'): Unknown section name: \"'+section_name+'\"'))
assert(len(bond_types) == 0)
typepattern_to_coefftypes = []
for i in range(0, len(lines_bondsbytype)):
line = lines_bondsbytype[i].strip()
if '#' in line:
icomment = line.find('#')
line = (line[:icomment]).strip()
if len(line) > 0:
tokens = ttree_lex.SplitQuotedString(line)
if (len(tokens) != 3):
raise(ttree_lex.InputError('Error: Wrong number of columns in the \"Bonds By Type\" section of data file.\n'
'Offending line:\n'+
'\"'+line+'\"\n'
'Expected 3 columns\n'))
coefftype = ttree_lex.EscCharStrToChar(tokens[0])
typepattern = []
for typestr in tokens[1:]:
if ((len(typestr) >= 2) and
(typestr[0] == '/') and (typestr[-1] == '/')):
regex_str = typestr[1:-1]
typepattern.append( re.compile(regex_str) )
else:
typepattern.append(ttree_lex.EscCharStrToChar(typestr))
typepattern_to_coefftypes.append([typepattern, coefftype])
assert(len(bond_ids) == len(bond_pairs))
for ie in range(0,len(bond_ids)):
bond_types.append(None)
for ie in range(0, len(bond_ids)):
bondid = bond_ids[ie]
(atomid1, atomid2) = bond_pairs[ie]
if atomid1 not in atomids2types:
raise ttree_lex.InputError('Error: atom \"'+atomid1+'\" not defined in \"Data Atoms\".\n'
' This usually happens when the user mistypes one of the names of the\n'
' $atoms in either a \"Data Atoms\" or \"Data Bond List\" section.\n'
' To find out where the mistake occured, search the \n'
' \"ttree_assignments.txt\" file for:\n'
' \"'+atomid1+'\"\n')
if atomid2 not in atomids2types:
raise ttree_lex.InputError('Error: atom \"'+atomid2+'\" not defined in \"Data Atoms\".\n'
' This usually happens when the user mistypes one of the names of the\n'
' $atoms in either a \"Data Atoms\" or \"Data Bond List\" section.\n'
' To find out where the mistake occured, search the \n'
' \"ttree_assignments.txt\" file for:\n'
' \"'+atomid2+'\"\n')
atomtype1 = atomids2types[atomid1]
atomtype2 = atomids2types[atomid2]
#for n in range(0, len(typepattern_to_coefftypes)):
for typepattern, coefftype in typepattern_to_coefftypes:
# use string comparisons to check if atom types match the pattern
if (ttree_lex.MatchesAll((atomtype1, atomtype2), typepattern) or
ttree_lex.MatchesAll((atomtype2, atomtype1), typepattern)):
# ("MatchesAll()" defined in "ttree_lex.py")
bond_types[ie] = coefftype
for ie in range(0, len(bond_ids)):
if not bond_types[ie]:
(atomid1, atomid2) = bond_pairs[ie]
atomtype1 = atomids2types[atomid1]
atomtype2 = atomids2types[atomid2]
raise ttree_lex.InputError('Error: No bond types defined for the bond between\n'
' atoms '+atomid1+' (type '+atomtype1+')\n'
' and '+atomid2+' (type '+atomtype2+')\n')
if __name__ == "__main__":
g_program_name = __file__.split('/')[-1] # = 'nbody_by_type.py'
g_date_str = '2015-11-09'
g_version_str = '0.11'
####### Main Code Below: #######
sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+' ')
if sys.version < '3':
sys.stderr.write(' (python version < 3)\n')
else:
sys.stderr.write('\n')
try:
fname_atoms = None
fname_bonds = None
fname_bondsbytype = None
section_name = 'Data Bond List' # (This will be replaced later.)
atom_style = 'full'
prefix=''
suffix=''
bond_lack_types = False
argv = [arg for arg in sys.argv]
# Loop over the remaining arguments not processed yet.
# These arguments are specific to the lttree.py program
# and are not understood by ttree.py:
i = 1
while i < len(argv):
#sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n')
if ((argv[i].lower() == '-?') or
(argv[i].lower() == '--?') or
(argv[i].lower() == '-help') or
(argv[i].lower() == '-help')):
if i+1 >= len(argv):
sys.stdout.write(man_page_text+'\n')
sys.exit(0)
elif argv[i].lower() == '-atoms':
if i+1 >= len(argv):
raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n'
' text which might appear in the "Atoms" section of a LAMMPS data file.\n')
fname_atoms = argv[i+1]
del(argv[i:i+2])
elif argv[i].lower() == '-bonds':
if i+1 >= len(argv):
raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n'
' text which might appear in the "Bonds" section of a LAMMPS data file.\n')
fname_bonds = argv[i+1]
del(argv[i:i+2])
elif argv[i].lower() == '-bond-list':
if i+1 >= len(argv):
raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name\n')
#raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n'
# ' text which might appear in the "Bonds No Types" section of a LAMMPS data file.\n')
fname_bonds = argv[i+1]
section_name = "Data Bond List"
del(argv[i:i+2])
elif argv[i].lower() == '-bondsbytype':
if i+1 >= len(argv):
raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name\n')
#raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing\n'
# ' text which might appear in the "'+section_name+' By Type" section\n'
# ' of a LAMMPS data file.\n')
fname_bondsbytype = argv[i+1]
del(argv[i:i+2])
elif ((argv[i].lower() == '-atom-style') or
(argv[i].lower() == '-atom_style')):
if i+1 >= len(argv):
raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a an atom_style name.\n'
' (Or single quoted string which includes a space-separated\n'
' list of column names.)\n')
atom_style = argv[i+1]
del(argv[i:i+2])
elif argv[i].lower() == '-prefix':
if i+1 >= len(argv):
raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a prefix string\n'
' (a string you want to appear to the left of the integer\n'
' which counts the bonded interactions you have generated.)\n')
prefix = argv[i+1]
del(argv[i:i+2])
elif argv[i].lower() == '-suffix':
if i+1 >= len(argv):
raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a suffix string\n'
' (a string you want to appear to the right of the integer\n'
' which counts the bonded interactions you have generated.)\n')
prefix = argv[i+1]
del(argv[i:i+2])
elif argv[i][0] == '-':
raise ttree_lex.InputError('Error('+g_program_name+'):\n'
'Unrecogized command line argument \"'+argv[i]+'\"\n')
else:
i += 1
if len(argv) != 1:
# if there are more than 2 remaining arguments,
problem_args = ['\"'+arg+'\"' for arg in argv[1:]]
raise ttree_lex.InputError('Syntax Error('+g_program_name+'):\n\n'
' Problem with argument list.\n'
' The remaining arguments are:\n\n'
' '+(' '.join(problem_args))+'\n\n'
' (The actual problem may be earlier in the argument list.)\n')
bond_types = []
bond_ids = []
bond_pairs = []
fatoms = open(fname_atoms, 'r')
fbonds = open(fname_bonds, 'r')
fbondsbytype = open(fname_bondsbytype, 'r')
lines_atoms = fatoms.readlines()
lines_bonds = fbonds.readlines()
lines_bondsbytype = fbondsbytype.readlines()
fatoms.close()
fbonds.close()
fbondsbytype.close()
LookupBondTypes(bond_types,
bond_ids,
bond_pairs,
lines_atoms,
lines_bonds,
lines_bondsbytype,
atom_style,
section_name,
prefix='',
suffix='')
assert(len(bond_types) == len(bond_ids) == len(bond_pairs))
ie=0
N = len(bond_types)
for ie in range(0, N):
sys.stdout.write(bond_ids[ie] + ' ' +
bond_types[ie] + ' ' +
bond_pairs[ie][0] + ' ' +
bond_pairs[ie][1] + '\n')
except (ValueError, ttree_lex.InputError) as err:
sys.stderr.write('\n'+str(err)+'\n')
sys.exit(-1)
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