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ltemplify.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.
"""
ltemplify.py
The "ltemplify.py" script can be used to convert existing LAMMPS
input script and data files into a single .lt file
(which includes both topology and force-field information
for a single molecule in your system).
Example:
ltemplify.py -name Mol file.in file.data > mol.lt
This creates a template for a new type of molecule (named "Mol"),
consisting of all the atoms in the lammps files you included,
and saves this data in a single ttree file ("mol.lt").
This file can be used with moltemplate (ttree) to
define large systems containing this molecule.
"""
import sys
from ttree_lex import *
from lttree_styles import *
def Intify(s):
if s.isdigit():
return int(s)
elif s[0:2] == 'id':
return int(s[2:])
elif s[0:4] == 'type':
return int(s[4:])
else:
return s
def IsNumber(s):
try:
float(s)
return True
except ValueError, TypeError:
return False
def StringToInterval(sel_str, slice_delim='*'):
# Split a string into 1-3 tokens using the slice_delim and convert to int.
# What a mess. I should rewrite this function
i_slice = sel_str.find(slice_delim)
if i_slice == -1:
a = sel_str
b = sel_str
c = ''
else:
a = sel_str[:i_slice]
bc = sel_str[i_slice+len(slice_delim):]
b = ''
c = ''
i_slice = bc.find(slice_delim)
if i_slice == -1:
b = bc
c = ''
else:
b = bc[:i_slice]
c = bc[i_slice+len(slice_delim):]
if a == '':
a = None
elif a.isdigit():
a = int(a)
else:
raise InputError('Error: invalid selection string \"'+
sel_str+'\"\n')
if b == '':
b = None
elif b.isdigit():
b = int(b)
else:
raise InputError('Error: invalid selection string \"'+
sel_str+'\"\n')
if c == '':
c = None
elif c.isdigit():
c = int(c)
else:
raise InputError('Error: invalid selection string \"'+
sel_str+'\"\n')
if c == None:
return (a,b)
else:
return (a,b,c)
# Selections are simply lists of 2-tuples (pairs)
def LammpsSelectToIntervals(sel_str, slice_delim='*', or_delim=', '):
"""
This function converts a string such as "1*4 6 9*12 50*70*10" into
a list of tuples, for example: [(1,4), (6,6), (9,12), (50,50), (60,60), (70,70)]
In general, the of intervals has the form:
[(a1,b1), (a2,b2), (a3,b3), ... ]
An atom is considered to belong to this selection
if it happens to lie within the closed interval [a,b]
for any pair of a,b values in the list of intervals.
If for a given pair a,b, either a or b is "None", then that a or b
value is not used to disqualify membership in the interval.
(Similar to -infinity or +infinity. In other words if a is set to None,
then to belong to the interval it is enough to be less than b.)
"""
selection_list = []
#tokens = sel_str.split(or_delim) <-- Not what we want when len(or_delim)>1
tokens = LineLex.TextBlock2Lines(sel_str, or_delim, keep_delim=False)
for token in tokens:
token = token.strip()
interval = StringToInterval(token, slice_delim)
if len(interval)==2:
# Normally, "interval" should be a tuple containing 2 entries
selection_list.append(interval)
else:
assert(len(interval)==3)
# Handle 1000:2000:10 notation
# (corresponding to 1000, 1010, 1020, 1030, ..., 1990, 2000)
a=interval[0]
b=interval[1]
incr=interval[2]
i=a
while i<=b:
selection_list.append((i,i))
i += incr
return selection_list
def IntervalListToMinMax(interval_list):
min_a = None
max_b = None
for (a,b) in interval_list:
if ((not (type(a) is int)) or (not (type(b) is int))):
return None,None #only integer min/max makes sense. otherwise skip
if (min_a == None) or (a < min_a):
min_a = a
if (max_b == None) or (b > max_b):
max_b = b
return min_a, max_b
def MergeIntervals(interval_list):
"""
A crude simple function that merges consecutive intervals in the list
whenever they overlap. (This function does not bother to compare
non-consecutive entries in the interval_list.)
"""
i = 1
while i < len(interval_list):
if ((interval_list[i-1][1] == None) or
(interval_list[i-1][1]+1 >= interval_list[i][0])):
interval_list[i-1] = (interval_list[i-1][0], interval_list[i][1])
del interval_list[i]
else:
i += 1
def BelongsToSel(i, sel):
if (i == None) or (sel == None) or (len(sel) == 0):
# If the user has not specified a selection for this category,
# then by default all objects are accepted
return True
elif (type(i) is str):
if i.isdigit():
i = int(i)
else:
return True
belongs = False
for interval in sel:
assert(len(interval) == 2)
if interval[0]:
if i >= interval[0]:
if (interval[1] == None) or (i <= interval[1]):
belongs = True
break
elif interval[1]:
if i <= interval[1]:
belongs = True
break
else:
# In that case, the user entered something like "*"
# which covers all possible numbers
belongs = True
break
return belongs
try:
g_program_name = __file__.split('/')[-1] # = 'ltemplify.py'
g_version_str = '0.51'
g_date_str = '2015-10-27'
sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+'\n')
non_empty_output = False
no_warnings = True
indent = 2
cindent = 0
atomid_selection = []
atomtype_selection = []
molid_selection = []
mol_name = ''
min_sel_atomid = None
min_sel_atomtype = None
min_sel_bondid = None
min_sel_bondtype = None
min_sel_angleid = None
min_sel_angletype = None
min_sel_dihedralid = None
min_sel_dihedraltype = None
min_sel_improperid = None
min_sel_impropertype = None
max_sel_atomid = None
max_sel_atomtype = None
max_sel_bondid = None
max_sel_bondtype = None
max_sel_angleid = None
max_sel_angletype = None
max_sel_dihedralid = None
max_sel_dihedraltype = None
max_sel_improperid = None
max_sel_impropertype = None
needed_atomids = set([])
needed_atomtypes = set([])
needed_molids = set([])
needed_bondids = set([])
needed_bondtypes = set([])
needed_angleids = set([])
needed_angletypes = set([])
needed_dihedralids = set([])
needed_dihedraltypes = set([])
needed_improperids = set([])
needed_impropertypes = set([])
min_needed_atomtype = None
max_needed_atomtype = None
min_needed_bondtype = None
max_needed_bondtype = None
min_needed_angletype = None
max_needed_angletype = None
min_needed_dihedraltype = None
max_needed_dihedraltype = None
min_needed_impropertype = None
max_needed_impropertype = None
min_needed_atomid = None
max_needed_atomid = None
min_needed_molid = None
max_needed_molid = None
min_needed_bondid = None
max_needed_bondid = None
min_needed_angleid = None
max_needed_angleid = None
min_needed_dihedralid = None
max_needed_dihedralid = None
min_needed_improperid = None
max_needed_improperid = None
# To process the selections, we need to know the atom style:
atom_style_undefined = True
i_atomid = None
i_atomtype = None
i_molid = None
i_x = None
i_y = None
i_z = None
l_in_init = []
l_in_settings = []
l_in_masses = []
l_in_pair_coeffs = []
l_in_bond_coeffs = []
l_in_angle_coeffs = []
l_in_dihedral_coeffs = []
l_in_improper_coeffs = []
l_in_group = []
l_in_fix_shake = []
l_in_fix_rigid = []
l_in_fix_poems = []
l_in_fix_qeq = []
l_in_fix_qmmm = []
l_data_masses = []
l_data_bond_coeffs = []
l_data_angle_coeffs = []
l_data_dihedral_coeffs = []
l_data_improper_coeffs = []
l_data_pair_coeffs = []
l_data_pairij_coeffs = []
l_data_atoms = []
l_data_velocities = []
l_data_bonds = []
l_data_angles = []
l_data_dihedrals = []
l_data_impropers = []
# class2 force fields
#l_in_bondbond_coeffs = [] <--not needed, included in l_in_angle_coeff
#l_in_bondangle_coeffs = [] <--not needed, included in l_in_angle_coeff
#l_in_middlebondtorsion_coeffs = [] not needed, included in l_in_dihedral_coeff
#l_in_endbondtorsion_coeffs = [] <--not needed, included in l_in_dihedral_coeff
#l_in_angletorsion_coeffs = [] <--not needed, included in l_in_dihedral_coeff
#l_in_angleangletorsion_coeffs = [] not needed, included in l_in_dihedral_coeff
#l_in_bondbond13_coeffs = [] <--not needed, included in l_in_dihedral_coeff
#l_in_angleangle_coeffs = [] <--not needed, included in l_in_improper_coeff
l_data_bondbond_coeffs = []
l_data_bondangle_coeffs = []
l_data_middlebondtorsion_coeffs = []
l_data_endbondtorsion_coeffs = []
l_data_angletorsion_coeffs = []
l_data_angleangletorsion_coeffs = []
l_data_bondbond13_coeffs = []
l_data_angleangle_coeffs = []
# non-point-like particles:
l_data_ellipsoids = []
l_data_lines = []
l_data_triangles = []
# automatic generation of bonded interactions by type:
l_data_angles_by_type = []
l_data_dihedrals_by_type = []
l_data_impropers_by_type = []
atoms_already_read = False
some_pair_coeffs_read = False
complained_atom_style_mismatch = False
infer_types_from_comments = False
remove_coeffs_from_data_file = True
argv = sys.argv
i = 1
while i < len(argv):
#sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n')
if argv[i] == '-columns':
if i+1 >= len(argv):
raise InputError('Error: the \"'+argv[i]+'\" argument should be followed by a quoted\n'
' string which contains a space-delimited list of the names of\n'
' of columns in the \"Atoms\" section of the LAMMPS data file.\n'
' If the list contains the symbols:\n'
' \"atom-ID\" or \"atomid\", they are interpreted\n'
' as unique atom ID numbers, and columns named\n'
' \"atom-type\" or \"atomtype\" are interpreted\n'
' as atom types. Finally, columns named\n'
' \"molecule-ID\", \"molecule\", or \"mol-ID\", or \"mol\"\n'
' are interpreted as unique molecule id numbers.\n'
'Example:\n'
' '+argv[i]+' \'atom-ID atom-type q polarizability molecule-ID x y z\'\n'
' defines a custom atom_style containing the properties\n'
' atom-ID atom-type q polarizability molecule-ID x y z\n'
' Make sure you enclose the entire list in quotes.\n');
column_names = argv[i+1].strip('\"\'').strip().split()
del argv[i:i+2]
elif (argv[i] == '-ignore-comments'):
infer_types_from_comments = False
del argv[i:i+1]
elif (argv[i] == '-infer-comments'):
infer_types_from_comments = True
del argv[i:i+1]
elif ((argv[i] == '-name') or
(argv[i] == '-molname') or
(argv[i] == '-molecule-name') or
(argv[i] == '-molecule_name')):
if i+1 >= len(argv):
raise InputError('Error: '+argv[i]+' flag should be followed by a a molecule type name.\n')
cindent = 2
indent += cindent
mol_name = argv[i+1]
del argv[i:i+2]
elif ((argv[i].lower() == '-atomstyle') or
(argv[i].lower() == '-atom_style') or
(argv[i].lower() == '-atom-style')):
if i+1 >= len(argv):
raise 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_undefined = False
column_names = AtomStyle2ColNames(argv[i+1])
if (argv[i+1].strip().split()[0] in g_style_map):
l_in_init.append((' '*indent) + 'atom_style ' + argv[i+1] + '\n')
sys.stderr.write('\n \"Atoms\" column format:\n')
sys.stderr.write(' '+(' '.join(column_names))+'\n')
i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names)
# Which columns contain the coordinates?
ii_coords = ColNames2Coords(column_names)
assert(len(ii_coords) == 1)
i_x = ii_coords[0][0]
i_y = ii_coords[0][1]
i_z = ii_coords[0][2]
if i_molid:
sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+', i_molid='+str(i_molid+1)+')\n\n')
else:
sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+')\n')
del argv[i:i+2]
elif ((argv[i].lower() == '-id') or
#(argv[i].lower() == '-a') or
#(argv[i].lower() == '-atoms') or
(argv[i].lower() == '-atomid') or
#(argv[i].lower() == '-atomids') or
(argv[i].lower() == '-atom-id')
#(argv[i].lower() == '-atom-ids') or
#(argv[i].lower() == '-$atom') or
#(argv[i].lower() == '-$atoms')
):
if i+1 >= len(argv):
raise InputError('Error: '+argv[i]+' flag should be followed by a list of integers\n'
' (or strings). These identify the group of atoms you want to\n'
' to include in the template you are creating.\n')
atomid_selection += LammpsSelectToIntervals(argv[i+1])
min_sel_atomid, max_sel_atomid = IntervalListToMinMax(atomid_selection)
del argv[i:i+2]
elif ((argv[i].lower() == '-datacoeffs') or
(argv[i].lower() == '-datacoeff') or
(argv[i].lower() == '-Coeff') or
(argv[i].lower() == '-Coeffs')):
remove_coeffs_from_data_file = False
del argv[i:i+1]
elif ((argv[i].lower() == '-type') or
#(argv[i].lower() == '-t') or
(argv[i].lower() == '-atomtype') or
(argv[i].lower() == '-atom-type')
#(argv[i].lower() == '-atomtypes') or
#(argv[i].lower() == '-atom-types') or
#(argv[i].lower() == '-@atom') or
#(argv[i].lower() == '-@atoms') or
#(argv[i].lower() == '-@atomtype') or
#(argv[i].lower() == '-@atomtypes')
):
if i+1 >= len(argv):
raise InputError('Error: '+argv[i]+' flag should be followed by a list of integers.\n'
' (or strings). These identify the group of atom types you want to\n'
' to include in the template you are creating.\n')
atomtype_selection += LammpsSelectToIntervals(argv[i+1])
min_sel_atomtype, max_sel_atomtype = IntervalListToMinMax(atomtype_selection)
del argv[i:i+2]
elif ((argv[i].lower() == '-mol') or
#(argv[i].lower() == '-m') or
(argv[i].lower() == '-molid') or
#(argv[i].lower() == '-molids') or
(argv[i].lower() == '-mol-id') or
#(argv[i].lower() == '-mol-ids') or
#(argv[i].lower() == '-molecule') or
(argv[i].lower() == '-moleculeid') or
(argv[i].lower() == '-molecule-id')
#(argv[i].lower() == '-molecules') or
#(argv[i].lower() == '-molecule-ids') or
#(argv[i].lower() == '-$mol') or
#(argv[i].lower() == '-$molecule')
):
if i+1 >= len(argv):
sys.stderr.write('Error: '+argv[i]+' flag should be followed by a list of integers.\n'
' (or strings). These identify the group of molecules you want to\n'
' include in the template you are creating.\n')
molid_selection += LammpsSelectToIntervals(argv[i+1])
del argv[i:i+2]
else:
i += 1
# We might need to parse the simulation boundary-box.
# If so, use these variables. (None means uninitialized.)
boundary_xlo = None
boundary_xhi = None
boundary_ylo = None
boundary_yhi = None
boundary_zlo = None
boundary_zhi = None
boundary_xy = None
boundary_yz = None
boundary_xz = None
# atom type names
atomtypes_name2int = {}
atomtypes_int2name = {}
#atomids_name2int = {} not needed
atomids_int2name = {}
atomids_by_type = {}
if atom_style_undefined:
# The default atom_style is "full"
column_names = AtomStyle2ColNames('full')
i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names)
# Which columns contain the coordinates?
ii_coords = ColNames2Coords(column_names)
assert(len(ii_coords) == 1)
i_x = ii_coords[0][0]
i_y = ii_coords[0][1]
i_z = ii_coords[0][2]
#---------------------------------------------------------
#-- The remaining arguments are files that the user wants
#-- us to read and convert. It is typical to have
#-- multiple input files, because LAMMPS users often
#-- store their force field parameters in either the LAMMPS
#-- data files and input script files, or both.
#-- We want to search all of the LAMMPS input files in
#-- order to make sure we extracted all the force field
#-- parameters (coeff commands).
#---------------------------------------------------------
for i_arg in range(1,len(argv)):
fname = argv[i_arg]
try:
lammps_file = open(fname, 'r')
except IOError:
raise InputError('Error: unrecognized argument (\"'+fname+'\"),\n'
' OR unable to open file:\n'
'\n'
' \"'+fname+'\"\n'
' for reading.\n'
'\n'
' (If you were not trying to open a file with this name,\n'
' then there is a problem in your argument list.)\n')
sys.stderr.write('reading file \"'+fname+'\"\n')
atomid2type = {}
atomid2mol = {}
data_file_header_names = set(['LAMMPS Description',
'Atoms', 'Masses', 'Velocities', 'Bonds',
'Angles', 'Dihedrals', 'Impropers',
'Pair Coeffs',
'Bond Coeffs', 'Angle Coeffs',
'Dihedral Coeffs', 'Improper Coeffs',
#class2 force fields:
'BondBond Coeffs', 'BondAngle Coeffs',
'MiddleBondTorsion Coeffs', 'EndBondTorsion Coeffs',
'AngleTorsion Coeffs', 'AngleAngleTorsion Coeffs',
'BondBond13 Coeffs',
'AngleAngle Coeffs',
# non-point-like particles:
'Ellipsoids', 'Triangles', 'Lines',
#specifying bonded interactions by type:
'Angles By Type', 'Dihedrals By Type', 'Impropers By Type'
])
lex=LineLex(lammps_file, fname)
lex.source_triggers = set(['include','import'])
# set up lex to accept most characters in file names:
lex.wordterminators = '(){}' + lex.whitespace
# set up lex to understand the "include" statement:
lex.source = 'include'
lex.escape = '\\'
while lex:
infile = lex.infile
lineno = lex.lineno
line = lex.ReadLine()
if (lex.infile != infile):
infile = lex.infile
lineno = lex.lineno
#sys.stderr.write(' processing \"'+line.strip()+'\", (\"'+infile+'\":'+str(lineno)+')\n')
if line == '':
break
tokens = line.strip().split()
if (len(tokens) > 0):
if ((tokens[0] == 'atom_style') and
atom_style_undefined):
sys.stderr.write(' Atom Style found. Processing: \"'+line.strip()+'\"\n')
if atoms_already_read:
raise InputError('Error: The file containing the \"atom_style\" command must\n'
' come before the data file in the argument list.\n'
' (The templify program needs to know the atom style before reading\n'
' the data file. Either change the order of arguments so that the\n'
' LAMMPS input script file is processed before the data file, or use\n'
' the \"-atom_style\" command line argument to specify the atom_style.)\n')
column_names = AtomStyle2ColNames(line.split()[1])
i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names)
# Which columns contain the coordinates?
ii_coords = ColNames2Coords(column_names)
assert(len(ii_coords) == 1)
i_x = ii_coords[0][0]
i_y = ii_coords[0][1]
i_z = ii_coords[0][2]
sys.stderr.write('\n \"Atoms\" column format:\n')
sys.stderr.write(' '+(' '.join(column_names))+'\n')
if i_molid:
sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+', i_molid='+str(i_molid+1)+')\n\n')
else:
sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+')\n\n')
l_in_init.append((' '*indent)+line.lstrip())
elif (tokens[0] in set(['units',
'angle_style',
'bond_style',
'dihedral_style',
'improper_style',
'min_style',
'pair_style',
'pair_modify',
'special_bonds',
'kspace_style',
'kspace_modify'])):
l_in_init.append((' '*indent)+line.lstrip())
#if (line.strip() == 'LAMMPS Description'):
# sys.stderr.write(' reading \"'+line.strip()+'\"\n')
# # skip over this section
# while lex:
# line = lex.ReadLine()
# if line.strip() in data_file_header_names:
# lex.push_raw_text(line) # <- Save line for later
# break
elif (line.strip() == 'Atoms'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
atoms_already_read = True
# Before attempting to read atomic coordinates, first find
# the lattice vectors of the simulation's boundary box:
# Why do we care about the Simulation Boundary?
# Some LAMMPS data files store atomic coordinates in a
# complex format with 6 numbers, 3 floats, and 3 integers.
# The 3 floats are x,y,z coordinates. Any additional numbers
# following these are integers which tell LAMMPS which cell
# the particle belongs to, (in case it has wandered out of
# the original periodic boundary box). In order to find
# the true location of the particle, we need to offset that
# particle's position with the unit-cell lattice vectors:
# avec, bvec, cvec (or multiples thereof)
# avec, bvec, cvec are the axis of the parallelepiped which
# define the simulation's boundary. They are described here:
#http://lammps.sandia.gov/doc/Section_howto.html#howto-12
if ((boundary_xlo==None) or (boundary_xhi==None) or
(boundary_ylo==None) or (boundary_yhi==None) or
(boundary_zlo==None) or (boundary_zhi==None)):
raise InputError('Error: Either DATA file lacks a boundary-box header, or it is in the wrong\n'
' place. At the beginning of the file, you need to specify the box size:\n'
' xlo xhi ylo yhi zlo zhi (and xy xz yz if triclinic)\n'
' These numbers should appear BEFORE the other sections in the data file\n'
' (such as the \"Atoms\", \"Masses\", \"Bonds\", \"Pair Coeffs\" sections)\n'
'\n'
' Use this format (example):\n'
' -100.0 100.0 xhi xlo\n'
' 0.0 200.0 yhi ylo\n'
' -25.0 50.0 zhi zlo\n'
'\n'
'For details, see http://lammps.sandia.gov/doc/read_data.html\n'
'\n'
' (NOTE: If the atom coordinates are NOT followed by integers, then\n'
' these numbers are all ignored, however you must still specify\n'
' xlo, xhi, ylo, yhi, zlo, zhi. You can set them all to 0.0.)\n')
if not (boundary_xy and boundary_yz and boundary_xz):
# Then use a simple rectangular boundary box:
avec = (boundary_xhi-boundary_xlo, 0.0, 0.0)
bvec = (0.0, boundary_yhi-boundary_ylo, 0.0)
cvec = (0.0, 0.0, boundary_zhi-boundary_zlo)
else:
# Triclinic geometry in LAMMPS is explained here:
# http://lammps.sandia.gov/doc/Section_howto.html#howto-12
# http://lammps.sandia.gov/doc/read_data.html
avec = (boundary_xhi-boundary_xlo, 0.0, 0.0)
bvec = (boundary_xy, boundary_yhi-boundary_ylo, 0.0)
cvec = (boundary_xz, boundary_yz, boundary_zhi-boundary_zlo)
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
if ((len(tokens) <= i_atomid) or
(len(tokens) <= i_atomtype) or
((i_molid != None) and
(len(tokens) <= i_molid))):
raise InputError('Error: The number of columns in the \"Atoms\" section does\n'
' not match the atom_style (see column name list above).\n')
elif ((len(tokens) != len(column_names)) and
(len(tokens) != len(column_names)+3) and
(not complained_atom_style_mismatch)):
complained_atom_style_mismatch = True
sys.stderr.write('Warning: The number of columns in the \"Atoms\" section does\n'
' not match the atom_style (see column name list above).\n')
# this is not a very serious warning.
#no_warnings = False <--no need. commenting out
atomid = Intify(tokens[i_atomid])
atomtype = Intify(tokens[i_atomtype])
molid = None
if i_molid:
molid = Intify(tokens[i_molid])
atomid2type[atomid] = atomtype
if i_molid:
atomid2mol[atomid] = molid
if (BelongsToSel(atomid, atomid_selection) and
BelongsToSel(atomtype, atomtype_selection) and
BelongsToSel(molid, molid_selection)):
tokens[i_atomid] = '$atom:id'+tokens[i_atomid]
#tokens[i_atomid] = '$atom:'+atomids_int2name[atomid]
# fill atomtype_int2str[] with a default name (change later):
#tokens[i_atomtype] = '@atom:type'+tokens[i_atomtype]
atomtype_name = 'type'+tokens[i_atomtype]
atomtypes_int2name[atomtype] = atomtype_name
tokens[i_atomtype] = '@atom:'+atomtype_name
# Interpreting unit-cell counters
# If present, then unit-cell "flags" must be
# added to the x,y,z coordinates.
#
# For more details on unit-cell "flags", see:
# http://lammps.sandia.gov/doc/read_data.html
# "In the data file, atom lines (all lines or
# none of them) can optionally list 3 trailing
# integer values (nx,ny,nz), which are used to
# initialize the atom’s image flags.
# If nx,ny,nz values are not listed in the
# data file, LAMMPS initializes them to 0.
# Note that the image flags are immediately
# updated if an atom’s coordinates need to
# wrapped back into the simulation box."
if (len(tokens) == len(column_names)+3):
nx = int(tokens[-3])
ny = int(tokens[-2])
nz = int(tokens[-1])
x = float(tokens[i_x]) + nx*avec[0]+ny*bvec[0]+nz*cvec[0]
y = float(tokens[i_y]) + nx*avec[1]+ny*bvec[1]+nz*cvec[1]
z = float(tokens[i_z]) + nx*avec[2]+ny*bvec[2]+nz*cvec[2]
tokens[i_x] = str(x)
tokens[i_y] = str(y)
tokens[i_z] = str(z)
# Now get rid of them:
del tokens[-3:]
# I can't use atomids_int2name or atomtypes_int2name yet
# because they probably have not been defined yet.
# (Instead assign these names in a later pass.)
if i_molid:
tokens[i_molid] = '$mol:id'+tokens[i_molid]
l_data_atoms.append((' '*indent)+(' '.join(tokens)+'\n'))
needed_atomids.add(atomid)
needed_atomtypes.add(atomtype)
# Not all atom_styles have molids.
# Check for this before adding.
if molid != None:
needed_molids.add(molid)
for atomtype in needed_atomtypes:
assert(type(atomtype) is int)
if ((min_needed_atomtype == None) or
(min_needed_atomtype > atomtype)):
min_needed_atomtype = atomtype
if ((max_needed_atomtype == None) or
(max_needed_atomtype < atomtype)):
max_needed_atomtype = atomtype
for atomid in needed_atomids:
assert(type(atomid) is int)
if ((min_needed_atomid == None) or
(min_needed_atomid > atomid)):
min_needed_atomid = atomid
if ((max_needed_atomid == None) or
(max_needed_atomid < atomid)):
max_needed_atomid = atomid
for molid in needed_molids:
assert(type(molid) is int)
if ((min_needed_molid == None) or
(min_needed_molid > molid)):
min_needed_molid = molid
if ((max_needed_molid == None) or
(max_needed_molid < molid)):
max_needed_molid = molid
elif (line.strip() == 'Masses'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
# Read the next line of text but don't skip comments
comment_char_backup = lex.commenters
lex.commenters = ''
line = lex.ReadLine()
lex.commenters = comment_char_backup
comment_text = ''
ic = line.find('#')
if ic != -1:
line = line[:ic]
comment_text = line[ic+1:].strip()
line = line.rstrip()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
atomtype = Intify(tokens[0])
atomtype_name = str(atomtype)
if comment_text != '':
comment_tokens = comment_text.split()
# Assume the first word after the # is the atom type name
atomtype_name = comment_tokens[0]
if BelongsToSel(atomtype, atomtype_selection):
#tokens[0] = '@atom:type'+tokens[0]
l_data_masses.append((' '*indent)+(' '.join(tokens)+'\n'))
# infer atom type names from comment strings?
if infer_types_from_comments:
if atomtype_name in atomtypes_name2int:
raise InputError('Error: duplicate atom type names in mass section: \"'+atomtype_name+'\"\n'
' (By default '+g_program_name+' attempts to infer atom type names from\n'
' comments which appear in the \"Masses\" section of your data file.)\n'
' You can avoid this error by adding the \"-ignore-comments\" argument.\n')
atomtypes_name2int[atomtype_name] = atomtype
atomtypes_int2name[atomtype] = atomtype_name
else:
atomtypes_int2name[atomtype] = 'type'+str(atomtype)
elif (line.strip() == 'Velocities'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
atomid = Intify(tokens[0])
atomtype = None
if atomid in atomid2type:
atomtype = atomid2type[atomid]
moldid = None
if atomid in atomid2mol:
molid = atomid2mol[atomid]
if (BelongsToSel(atomid, atomid_selection) and
BelongsToSel(atomtype, atomtype_selection) and
BelongsToSel(molid, molid_selection)):
tokens[0] = '$atom:id'+tokens[0]
#tokens[0] = '$atom:'+atomids_int2name[atomid]
#NOTE:I can't use "atomids_int2name" yet because
# they probably have not been defined yet.
# (Instead assign these names in a later pass.)
l_data_velocities.append((' '*indent)+(' '.join(tokens)+'\n'))
# non-point-like-particles:
elif (line.strip() == 'Ellipsoids'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
atomid = Intify(tokens[0])
atomtype = None
if atomid in atomid2type:
atomtype = atomid2type[atomid]
moldid = None
if atomid in atomid2mol:
molid = atomid2mol[atomid]
if (BelongsToSel(atomid, atomid_selection) and
BelongsToSel(atomtype, atomtype_selection) and
BelongsToSel(molid, molid_selection)):
tokens[0] = '$atom:id'+tokens[0]
#tokens[0] = '$atom:'+atomids_int2name[atomid]
#NOTE:I can't use "atomids_int2name" yet because
# they probably have not been defined yet.
# (Instead assign these names in a later pass.)
l_data_ellipsoids.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (line.strip() == 'Lines'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
atomid = Intify(tokens[0])
atomtype = None
if atomid in atomid2type:
atomtype = atomid2type[atomid]
moldid = None
if atomid in atomid2mol:
molid = atomid2mol[atomid]
if (BelongsToSel(atomid, atomid_selection) and
BelongsToSel(atomtype, atomtype_selection) and
BelongsToSel(molid, molid_selection)):
tokens[0] = '$atom:id'+tokens[0]
#tokens[0] = '$atom:'+atomids_int2name[atomid]
#NOTE:I can't use "atomids_int2name" yet because
# they probably have not been defined yet.
# (Instead assign these names in a later pass.)
l_data_lines.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (line.strip() == 'Triangles'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
atomid = Intify(tokens[0])
atomtype = None
if atomid in atomid2type:
atomtype = atomid2type[atomid]
moldid = None
if atomid in atomid2mol:
molid = atomid2mol[atomid]
if (BelongsToSel(atomid, atomid_selection) and
BelongsToSel(atomtype, atomtype_selection) and
BelongsToSel(molid, molid_selection)):
tokens[0] = '$atom:id'+tokens[0]
#tokens[0] = '$atom:'+atomids_int2name[atomid]
#NOTE:I can't use "atomids_int2name" yet because
# they probably have not been defined yet.
# (Instead assign these names in a later pass.)
l_data_triangles.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (line.strip() == 'Bonds'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
if (len(tokens) < 4):
raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
' Nonsensical line in Bonds section:\n'
' \"'+line.strip()+'\"\n')
#tokens[0] = '$bond:id'+tokens[0]
#tokens[1] = '@bond:type'+tokens[1]
atomids = [None, None]
atomtypes = [None, None]
molids = [None, None]
in_selections = True
some_in_selection = False
for n in range(0,2):
atomids[n] = Intify(tokens[2+n])
if atomids[n] in atomid2type:
atomtypes[n] = atomid2type[atomids[n]]
if atomids[n] in atomid2mol:
molids[n] = atomid2mol[atomids[n]]
if (BelongsToSel(atomids[n], atomid_selection) and
BelongsToSel(atomtypes[n], atomtype_selection) and
BelongsToSel(molids[n], molid_selection)):
#tokens[2+n] = '$atom:id'+tokens[2+n]
#tokens[2+n] = '$atom:'+atomids_int2name[atomids[n]]
some_in_selection = True
else:
in_selections = False
if in_selections:
l_data_bonds.append((' '*indent)+(' '.join(tokens)+'\n'))
elif some_in_selection:
sys.stderr.write('WARNING: SELECTION BREAKS BONDS\n')
sys.stderr.write(' (between atom ids: ')
for n in range(0,2):
sys.stderr.write(str(atomids[n])+' ')
sys.stderr.write(')\n'
' The atoms you selected are bonded\n'
' to other atoms you didn\'t select.\n'
' Are you sure you selected the correct atoms?\n')
no_warnings = False
elif (line.strip() == 'Angles'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line == '':
break
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
if (len(tokens) < 5):
raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
' Nonsensical line in Angles section:\n'
' \"'+line.strip()+'\"\n')
#tokens[0] = '$angle:id'+tokens[0]
#tokens[1] = '@angle:type'+tokens[1]
atomids = [None, None, None]
atomtypes = [None, None, None]
molids = [None, None, None]
in_selections = True
some_in_selection = False
for n in range(0,3):
atomids[n] = Intify(tokens[2+n])
if atomids[n] in atomid2type:
atomtypes[n] = atomid2type[atomids[n]]
if atomids[n] in atomid2mol:
molids[n] = atomid2mol[atomids[n]]
if (BelongsToSel(atomids[n], atomid_selection) and
BelongsToSel(atomtypes[n], atomtype_selection) and
BelongsToSel(molids[n], molid_selection)):
#tokens[2+n] = '$atom:id'+tokens[2+n]
#tokens[2+n] = '$atom:'+atomids_int2name[atomids[n]]
some_in_selection = True
else:
in_selections = False
if in_selections:
l_data_angles.append((' '*indent)+(' '.join(tokens)+'\n'))
elif some_in_selection:
sys.stderr.write('WARNING: SELECTION BREAKS ANGLES\n')
sys.stderr.write(' (between atom ids: ')
for n in range(0,3):
sys.stderr.write(str(atomids[n])+' ')
sys.stderr.write(')\n'
' The atoms you selected participate in 3-body \"Angle\"\n'
' interactions with other atoms you didn\'t select.\n'
' (They will be ignored.)\n'
' Are you sure you selected the correct atoms?\n')
no_warnings = False
elif (line.strip() == 'Dihedrals'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
if (len(tokens) < 6):
raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
' Nonsensical line in Dihedrals section:\n'
' \"'+line.strip()+'\"\n')
#tokens[0] = '$dihedral:id'+tokens[0]
#tokens[1] = '@dihedral:type'+tokens[1]
atomids = [None, None, None, None]
atomtypes = [None, None, None, None]
molids = [None, None, None, None]
in_selections = True
some_in_selection = False
for n in range(0,4):
atomids[n] = Intify(tokens[2+n])
if atomids[n] in atomid2type:
atomtypes[n] = atomid2type[atomids[n]]
if atomids[n] in atomid2mol:
molids[n] = atomid2mol[atomids[n]]
if (BelongsToSel(atomids[n], atomid_selection) and
BelongsToSel(atomtypes[n], atomtype_selection) and
BelongsToSel(molids[n], molid_selection)):
#tokens[2+n] = '$atom:id'+tokens[2+n]
#tokens[2+n] = '$atom:'+atomids_int2name[atomids[n]]
some_in_selection = True
else:
in_selections = False
if in_selections:
l_data_dihedrals.append((' '*indent)+(' '.join(tokens)+'\n'))
elif some_in_selection:
sys.stderr.write('WARNING: SELECTION BREAKS DIHEDRALS\n')
sys.stderr.write(' (between atom ids: ')
for n in range(0,4):
sys.stderr.write(str(atomids[n])+' ')
sys.stderr.write(')\n'
' The atoms you selected participate in 4-body \"Dihedral\"\n'
' interactions with other atoms you didn\'t select.\n'
' (They will be ignored.)\n'
' Are you sure you selected the correct atoms?\n')
no_warnings = False
elif (line.strip() == 'Impropers'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
if (len(tokens) < 6):
raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
' Nonsensical line in Impropers section:\n'
' \"'+line.strip()+'\"\n')
#tokens[0] = '$improper:id'+tokens[0]
#tokens[1] = '@improper:type'+tokens[1]
atomids = [None, None, None, None]
atomtypes = [None, None, None, None]
molids = [None, None, None, None]
in_selections = True
some_in_selection = False
for n in range(0,4):
atomids[n] = Intify(tokens[2+n])
if atomids[n] in atomid2type:
atomtypes[n] = atomid2type[atomids[n]]
if atomids[n] in atomid2mol:
molids[n] = atomid2mol[atomids[n]]
if (BelongsToSel(atomids[n], atomid_selection) and
BelongsToSel(atomtypes[n], atomtype_selection) and
BelongsToSel(molids[n], molid_selection)):
#tokens[2+n] = '$atom:id'+tokens[2+n]
#tokens[2+n] = '$atom:'+atomids_int2name[atomids[n]]
some_in_selection = True
else:
in_selections = False
if in_selections:
l_data_impropers.append((' '*indent)+(' '.join(tokens)+'\n'))
elif some_in_selection:
sys.stderr.write('WARNING: SELECTION BREAKS IMPROPERS\n')
sys.stderr.write(' (between atom ids: ')
for n in range(0,4):
sys.stderr.write(str(atomids[n])+' ')
sys.stderr.write(')\n'
' The atoms you selected participate in 4-body \"Improper\"\n'
' interactions with other atoms you didn\'t select.\n'
' (They will be ignored.)\n'
' Are you sure you selected the correct atoms?\n')
no_warnings = False
elif (line.strip() == 'Bond Coeffs'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
#tokens[0] = '@bond:type'+tokens[0]
l_data_bond_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (line.strip() == 'Angle Coeffs'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
#tokens[0] = '@angle:type'+tokens[0]
l_data_angle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (line.strip() == 'Dihedral Coeffs'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
#tokens[0] = '@dihedral:type'+tokens[0]
l_data_dihedral_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (line.strip() == 'Improper Coeffs'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
#tokens[0] = '@improper:type'+tokens[0]
l_data_improper_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (line.strip() == 'Pair Coeffs'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
some_pair_coeffs_read = True
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
if (len(tokens) < 2):
raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
' Nonsensical line in Pair Coeffs section:\n'
' \"'+line.strip()+'\"\n')
atomtype_i_str = tokens[0]
if '*' in atomtype_i_str:
raise InputError('PROBLEM near or before '+ErrorLeader(infile, lineno)+'\n'
' As of 2015-8, moltemplate forbids use of the "\*\" wildcard\n'
' character in the \"Pair Coeffs\" section.\n')
else:
i = int(atomtype_i_str)
if ((not i) or
BelongsToSel(i, atomtype_selection)):
i_str = '@atom:type'+str(i)
tokens[0] = i_str
l_data_pair_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (line.strip() == 'PairIJ Coeffs'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
some_pair_coeffs_read = True
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
if (len(tokens) < 2):
raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
' Nonsensical line in Pair Coeffs section:\n'
' \"'+line.strip()+'\"\n')
atomtype_i_str = tokens[0]
atomtype_j_str = tokens[1]
if (('*' in atomtype_i_str) or ('*' in atomtype_j_str)):
raise InputError('PROBLEM near or before '+ErrorLeader(infile, lineno)+'\n'
' As of 2015-8, moltemplate forbids use of the "\*\" wildcard\n'
' character in the \"PairIJ Coeffs\" section.\n')
else:
i = int(atomtype_i_str)
j = int(atomtype_j_str)
if (((not i) or BelongsToSel(i, atomtype_selection)) and
((not j) or BelongsToSel(j, atomtype_selection))):
i_str = '@atom:type'+str(i)
j_str = '@atom:type'+str(j)
tokens[0] = i_str
tokens[1] = j_str
l_data_pair_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (tokens[0] == 'pair_coeff'):
some_pair_coeffs_read = True
if (len(tokens) < 3):
raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
' Nonsensical pair_coeff command:\n'
' \"'+line.strip()+'\"\n')
l_in_pair_coeffs.append(' '*indent+line.strip())
elif (tokens[0] == 'mass'):
some_pair_coeffs_read = True
if (len(tokens) < 3):
raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
' Nonsensical \"mass\" command:\n'
' \"'+line.strip()+'\"\n')
l_in_masses.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (tokens[0] == 'bond_coeff'):
if (len(tokens) < 2):
raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
' Nonsensical bond_coeff command:\n'
' \"'+line.strip()+'\"\n')
#tokens[1] = '@bond:type'+tokens[1]
l_in_bond_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (tokens[0] == 'angle_coeff'):
if (len(tokens) < 2):
raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
' Nonsensical angle_coeff command:\n'
' \"'+line.strip()+'\"\n')
#tokens[1] = '@angle:type'+tokens[1]
l_in_angle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (tokens[0] == 'dihedral_coeff'):
if (len(tokens) < 2):
raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
' Nonsensical dihedral_coeff command:\n'
' \"'+line.strip()+'\"\n')
#tokens[1] = '@dihedral:type'+tokens[1]
l_in_dihedral_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (tokens[0] == 'improper_coeff'):
if (len(tokens) < 2):
raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
' Nonsensical improper_coeff command:\n'
' \"'+line.strip()+'\"\n')
#tokens[1] = '@improper:type'+tokens[1]
l_in_improper_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
# -- class2 force fields --
elif (line.strip() == 'BondBond Coeffs'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
#tokens[0] = '@angle:type'+tokens[0]
l_data_bondbond_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (line.strip() == 'BondAngle Coeffs'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
#tokens[0] = '@angle:type'+tokens[0]
l_data_bondangle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (line.strip() == 'MiddleBondTorsion Coeffs'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
#tokens[0] = '@dihedral:type'+tokens[0]
l_data_middlebondtorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (line.strip() == 'EndBondTorsion Coeffs'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
#tokens[0] = '@dihedral:type'+tokens[0]
l_data_endbondtorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (line.strip() == 'AngleTorsion Coeffs'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
#tokens[0] = '@dihedral:type'+tokens[0]
l_data_angletorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (line.strip() == 'AngleAngleTorsion Coeffs'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
#tokens[0] = '@dihedral:type'+tokens[0]
l_data_angleangletorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (line.strip() == 'BondBond13 Coeffs'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
#tokens[0] = '@dihedral:type'+tokens[0]
l_data_bondbond13_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (line.strip() == 'AngleAngle Coeffs'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
#tokens[0] = '@improper:type'+tokens[0]
l_data_angleangle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (line.strip() == 'Angles By Type'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
tokens[0] = '@angle:type'+tokens[0]
l_data_angles_by_type.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (line.strip() == 'Dihedrals By Type'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
tokens[0] = '@dihedral:type'+tokens[0]
l_data_dihedrals_by_type.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (line.strip() == 'Impropers By Type'):
sys.stderr.write(' reading \"'+line.strip()+'\"\n')
while lex:
line = lex.ReadLine()
if line.strip() in data_file_header_names:
lex.push_raw_text(line) # <- Save line for later
break
tokens = line.strip().split()
if len(tokens) > 0:
tokens[0] = '@improper:type'+tokens[0]
l_data_impropers_by_type.append((' '*indent)+(' '.join(tokens)+'\n'))
# Figure out the size of the simulation box boundary:
elif ((len(tokens)==4) and
(tokens[2] == 'xlo') and
(tokens[3] == 'xhi') and
IsNumber(tokens[0]) and
IsNumber(tokens[1])):
boundary_xlo = float(tokens[0])
boundary_xhi = float(tokens[1])
elif ((len(tokens)==4) and
(tokens[2] == 'ylo') and
(tokens[3] == 'yhi') and
IsNumber(tokens[0]) and
IsNumber(tokens[1])):
boundary_ylo = float(tokens[0])
boundary_yhi = float(tokens[1])
elif ((len(tokens)==4) and
(tokens[2] == 'zlo') and
(tokens[3] == 'zhi') and
IsNumber(tokens[0]) and
IsNumber(tokens[1])):
boundary_zlo = float(tokens[0])
boundary_zhi = float(tokens[1])
elif ((len(tokens)==6) and
(tokens[3] == 'xy') and
(tokens[4] == 'xz') and
(tokens[5] == 'yz') and
IsNumber(tokens[0]) and
IsNumber(tokens[1]) and
IsNumber(tokens[2])):
boundary_xy = float(tokens[0])
boundary_xz = float(tokens[1])
boundary_yz = float(tokens[2])
elif (tokens[0] == 'group'):
if (len(tokens) < 3):
raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
' Nonsensical group command:\n'
' \"'+line.strip()+'\"\n')
l_in_group.append((' '*indent)+(' '.join(tokens)+'\n'))
elif ((tokens[0] == 'fix') and (len(tokens) >= 4)):
if (tokens[3].find('rigid') == 0):
if (len(tokens) < 6):
raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
' Nonsensical '+tokens[0]+' '+tokens[3]+' command:\n'
' \"'+line.strip()+'\"\n')
l_in_fix_rigid.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (tokens[3].find('shake') == 0):
if (len(tokens) < 7):
raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
' Nonsensical '+tokens[0]+' '+tokens[3]+' command:\n'
' \"'+line.strip()+'\"\n')
l_in_fix_shake.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (tokens[3].find('poems') == 0):
if (len(tokens) < 4):
raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
' Nonsensical '+tokens[0]+' '+tokens[3]+' command:\n'
' \"'+line.strip()+'\"\n')
l_in_fix_poems.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (tokens[3].find('qeq') == 0):
if (len(tokens) < 8):
raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
' Nonsensical '+tokens[0]+' '+tokens[3]+' command:\n'
' \"'+line.strip()+'\"\n')
l_in_fix_qeq.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (tokens[3].find('qmmm') == 0):
if (len(tokens) < 8):
raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n'
' Nonsensical '+tokens[0]+' '+tokens[3]+' command:\n'
' \"'+line.strip()+'\"\n')
l_in_fix_qmmm.append((' '*indent)+(' '.join(tokens)+'\n'))
elif (tokens[3].find('restrain') == 0):
sys.stderr('WARNING: fix \"'+tokens[3]+'\" commands are NOT understood by '+g_program_name+'.\n'
' If you need restraints, add them to your final .LT file (eg. \"system.lt\"),\n'
' (And be sure to use unique (full, long) moltemplate names for each $atom:.)\n'
' Ignoring line \"'+line.strip()+'\"\n')
else:
sys.stderr.write(' Ignoring line \"'+line.strip()+'\"\n')
sys.stderr.write('\n\n')
sys.stderr.write(' processing \"Atoms\" section (')
# post-processing:
if len(l_data_masses) == 0:
infer_types_from_comments = False
# Pass 1 through l_data_atoms:
# Now do a second-pass throught the "l_data_atoms" section, and
# finish dealing with "infer_types_from_comments".
# During this pass, peplace the atomtype names and atomid names with
# atom type names which were inferred from comments read earlier.
sys.stderr.write('pass1')
for i in range(0, len(l_data_atoms)):
tokens = l_data_atoms[i].split()
atomid = tokens[i_atomid]
if atomid.find('$atom:') == 0:
atomid = atomid[6:]
# convert to an integer
atomid = Intify(atomid)
if infer_types_from_comments:
atomtype = tokens[i_atomtype]
# remove the "@atom:" prefix (we will put it back later)
if atomtype.find('@atom:') == 0:
atomtype = atomtype[6:]
# convert to an integer
atomtype = Intify(atomtype)
atomtype_name = atomtypes_int2name[atomtype]
if atomtype in atomids_by_type:
l_atomids = atomids_by_type[atomtype]
prev_count = len(l_atomids)
# lookup the most recently added atom of this type:
#prev_atomid_name = l_atomids[-1]
#ic = prev_atomid_name.rfind('_')
#prev_count = int(prev_atomid_name[ic+1:])
atomid_name = atomtype_name+'_'+str(prev_count+1)
atomids_by_type[atomtype].append(atomid)
else:
atomids_by_type[atomtype] = [atomid]
atomid_name = atomtype_name+'_1'
atomids_int2name[atomid] = atomid_name
#atomids_name2str[atomid_name] = atomid
else:
atomids_int2name[atomid] = 'id'+str(atomid)
sys.stderr.write(', pass2')
# Pass 2: If any atom types only appear once, simplify their atomid names.
for i in range(0, len(l_data_atoms)):
tokens = l_data_atoms[i].split()
# remove the "@atom:" prefix (we will put it back later)
atomtype = tokens[i_atomtype]
if atomtype.find('@atom:') == 0:
atomtype = atomtype[6:]
atomtype = Intify(atomtype)
if infer_types_from_comments:
if len(atomids_by_type[atomtype]) == 1:
atomid = tokens[i_atomid]
if atomid.find('$atom:') == 0:
atomid = atomid[6:]
atomid = Intify(atomid)
atomtype_name = atomtypes_int2name[atomtype]
atomids_int2name[atomid] = atomtype_name
sys.stderr.write(', pass3')
# Pass 3: substitute the atomid names and atom type names into l_data_atoms
for i in range(0, len(l_data_atoms)):
tokens = l_data_atoms[i].split()
atomid = tokens[i_atomid]
if atomid.find('$atom:') == 0:
atomid = atomid[6:]
# convert to an integer
atomid = Intify(atomid)
atomtype = tokens[i_atomtype]
if atomtype.find('@atom:') == 0:
atomtype = atomtype[6:]
atomtype = Intify(atomtype)
tokens = l_data_atoms[i].split()
tokens[i_atomid] = '$atom:'+atomids_int2name[atomid]
tokens[i_atomtype] = '@atom:'+atomtypes_int2name[atomtype]
l_data_atoms[i] = (' '*indent)+(' '.join(tokens)+'\n')
sys.stderr.write(')\n')
if len(l_data_atoms) == 0:
raise InputError('Error('+g_program_name+'): You have no atoms in you selection!\n'
'\n'
' Either you have chosen a set of atoms, molecules, or atom types which\n'
' does not exist, or there is a problem with (the format of) your\n'
' arguments. Check the documentation and examples.\n')
# --- Now delete items that were not selected from the other lists ---
# --- MASSES ---
# delete masses for atom types we don't care about anymore:
i_line = 0
while i_line < len(l_data_masses):
line = l_data_masses[i_line]
tokens = line.strip().split()
atomtype = Intify(tokens[0])
if ((not (atomtype in needed_atomtypes)) and
(not ((len(atomtype_selection) > 0) and
BelongsToSel(atomtype, atomtype_selection)))):
del l_data_masses[i_line]
else:
atomtype_name = atomtypes_int2name[atomtype]
tokens[0] = '@atom:'+atomtype_name
l_data_masses[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
# --- PAIR COEFFS ---
# delete data_pair_coeffs for atom types we don't care about anymore:
i_line = 0
while i_line < len(l_data_pair_coeffs):
line = l_data_pair_coeffs[i_line]
tokens = line.strip().split()
assert(len(tokens) > 0)
split_colon = tokens[0].split(':')
assert(len(split_colon) == 2)
atomtype = Intify(split_colon[1])
if ((not (atomtype in needed_atomtypes)) and
(not ((len(atomtype_selection) > 0) and
BelongsToSel(atomtype, atomtype_selection)))):
del l_data_pair_coeffs[i_line]
else:
i_line += 1
# delete data_pairij_coeffs for atom types we don't care about anymore:
i_line = 0
while i_line < len(l_data_pairij_coeffs):
line = l_data_pairij_coeffs[i_line]
tokens = line.strip().split()
assert(len(tokens) > 0)
split_colon_I = tokens[0].split(':')
assert(len(split_colon_I) == 2)
atomtype_I = Intify(split_colon_I[1])
split_colon_J = tokens[1].split(':')
assert(len(split_colon_J) == 2)
atomtype_J = Intify(split_colon_J[1])
if (((not (atomtype_I in needed_atomtypes)) and
(not ((len(atomtype_selection) > 0) and
BelongsToSel(atomtype_I, atomtype_selection))))
or
((not (atomtype_J in needed_atomtypes)) and
(not ((len(atomtype_selection) > 0) and
BelongsToSel(atomtype_J, atomtype_selection))))):
del l_data_pairij_coeffs[i_line]
else:
i_line += 1
# delete in_pair_coeffs for atom we don't care about anymore:
i_line = 0
while i_line < len(l_in_pair_coeffs):
line = l_in_pair_coeffs[i_line]
tokens = line.strip().split()
atomtype_i_str = tokens[1]
atomtype_j_str = tokens[2]
#if (('*' in atomtype_i_str) or
# ('*' in atomtype_j_str)):
# sys.stderr.write('WARNING: near or before '+ErrorLeader(infile, lineno)+'\n'
# ' pair_coeff command contains a \"*\" character.\n'
# ' Keep in mind that using moltemplate.sh you can manually change the\n'
# ' numbers assigned to each atom type (when using -a or -b). Make sure\n'
# ' nor to accidentally change the order of atom types in one of these\n'
# ' pair_coeff commands. For example, commands like\n'
# ' pair_coeff 10*4 20*10 0.15 3.6\n'
# ' can be generated by moltemplate.sh, however\n'
# ' they may be rejected by LAMMPS (because LAMMPS prefers this\n'
# ' pair_coeff 4*10 10*20 0.15 3.6)\n'
# ' Later on, you may want to check to make sure moltemplate.sh\n'
# ' is not doing this. (Fortunately you never have to worry unless\n'
# ' you are using the -a or -b arguments with moltemplate.sh)\n')
if ('*' in atomtype_i_str):
atomtype_i_tokens = atomtype_i_str.split('*')
if atomtype_i_tokens[0] == '':
if (min_sel_atomtype and
(min_sel_atomtype < min_needed_atomtype)):
i_a = min_sel_atomtype
else:
i_a = min_needed_atomtype
else:
i_a = Intify(atomtype_i_tokens[0])
if atomtype_i_tokens[1] == '':
if (max_sel_atomtype and
(max_sel_atomtype > max_needed_atomtype)):
i_b = max_sel_atomtype
else:
i_b = max_needed_atomtype
else:
i_b = Intify(atomtype_i_tokens[1])
else:
i_a = i_b = Intify(atomtype_i_str)
i_a_final = None
i_b_final = None
for i in range(i_a, i_b+1):
if ((i in needed_atomtypes) or (min_sel_atomtype <= i)):
i_a_final = i
break
for i in reversed(range(i_a, i_b+1)):
if ((i in needed_atomtypes) or (max_sel_atomtype >= i)):
i_b_final = i
break
#if i_a_final and i_b_final:
# if i_a_final == i_b_final:
# i_str = '@atom:type'+str(i_a_final)
# tokens[1] = i_str
# else:
# i_str = '@{atom:type'+str(i_a_final)+'}*@{atom:type'+str(i_b_final)+'}'
if ('*' in atomtype_j_str):
atomtype_j_tokens = atomtype_j_str.split('*')
if atomtype_j_tokens[0] == '':
if (min_sel_atomtype and
(min_sel_atomtype < min_needed_atomtype)):
j_a = min_sel_atomtype
else:
j_a = min_needed_atomtype
else:
j_a = Intify(atomtype_j_tokens[0])
if atomtype_j_tokens[1] == '':
if (max_sel_atomtype and
(max_sel_atomtype > max_needed_atomtype)):
j_b = max_sel_atomtype
else:
j_b = max_needed_atomtype
else:
j_b = Intify(atomtype_j_tokens[1])
else:
j_a = j_b = Intify(atomtype_j_str)
j_a_final = None
j_b_final = None
for j in range(j_a, j_b+1):
if ((j in needed_atomtypes) or (min_sel_atomtype <= j)):
j_a_final = j
break
for j in reversed(range(j_a, j_b+1)):
if ((j in needed_atomtypes) or (max_sel_atomtype >= j)):
j_b_final = j
break
#if j_a_final and j_b_final:
# if j_a_final == j_b_final:
# j_str = '@atom:type'+str(j_a_final)
# tokens[1] = j_str
# else:
# j_str = '@{atom:type'+str(j_a_final)+'}*@{atom:type'+str(j_b_final)+'}'
if not (i_a_final and i_b_final and j_a_final and j_b_final):
del l_in_pair_coeffs[i_line]
elif (('*' in atomtype_i_str) or ('*' in atomtype_j_str)):
del l_in_pair_coeffs[i_line]
for i in range(i_a_final, i_b_final+1):
for j in range(j_a_final, j_b_final+1):
if j >= i:
#tokens[1] = '@atom:type'+str(i)
#tokens[2] = '@atom:type'+str(j)
tokens[1] = '@atom:'+atomtypes_int2name[i]
tokens[2] = '@atom:'+atomtypes_int2name[j]
l_in_pair_coeffs.insert(i_line,
(' '*indent)+(' '.join(tokens)+'\n'))
i_line += 1
else:
#tokens[1] = '@atom:type'+tokens[1]
#tokens[2] = '@atom:type'+tokens[2]
tokens[1] = '@atom:'+atomtypes_int2name[int(tokens[1])]
tokens[2] = '@atom:'+atomtypes_int2name[int(tokens[2])]
l_in_pair_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
# delete mass commands for atom types we don't care about anymore:
i_line = 0
while i_line < len(l_in_masses):
line = l_in_masses[i_line]
tokens = line.strip().split()
atomtype_i_str = tokens[1]
#if (('*' in atomtype_i_str) or
# ('*' in atomtype_j_str)):
# sys.stderr.write('WARNING: near or before '+ErrorLeader(infile, lineno)+'\n'
# ' pair_coeff command contains a \"*\" character.\n'
# ' Keep in mind that using moltemplate.sh you can manually change the\n'
# ' numbers assigned to each atom type (when using -a or -b). Make sure\n'
# ' nor to accidentally change the order of atom types in one of these\n'
# ' pair_coeff commands. For example, commands like\n'
# ' pair_coeff 10*4 20*10 0.15 3.6\n'
# ' can be generated by moltemplate.sh, however\n'
# ' they may be rejected by LAMMPS (because LAMMPS prefers this\n'
# ' pair_coeff 4*10 10*20 0.15 3.6)\n'
# ' Later on, you may want to check to make sure moltemplate.sh\n'
# ' is not doing this. (Fortunately you never have to worry unless\n'
# ' you are using the -a or -b arguments with moltemplate.sh)\n')
if ('*' in atomtype_i_str):
atomtype_i_tokens = atomtype_i_str.split('*')
if atomtype_i_tokens[0] == '':
if (min_sel_atomtype and
(min_sel_atomtype < min_needed_atomtype)):
i_a = min_sel_atomtype
else:
i_a = min_needed_atomtype
else:
i_a = Intify(atomtype_i_tokens[0])
if atomtype_i_tokens[1] == '':
if (max_sel_atomtype and
(max_sel_atomtype > max_needed_atomtype)):
i_b = max_sel_atomtype
else:
i_b = max_needed_atomtype
else:
i_b = Intify(atomtype_i_tokens[1])
else:
i_a = i_b = Intify(atomtype_i_str)
i_a_final = None
i_b_final = None
for i in range(i_a, i_b+1):
if ((i in needed_atomtypes) or (min_sel_atomtype <= i)):
i_a_final = i
break
for i in reversed(range(i_a, i_b+1)):
if ((i in needed_atomtypes) or (max_sel_atomtype >= i)):
i_b_final = i
break
#if i_a_final and i_b_final:
# if i_a_final == i_b_final:
# i_str = '@atom:type'+str(i_a_final)
# tokens[1] = i_str
# else:
# i_str = '@{atom:type'+str(i_a_final)+'}*@{atom:type'+str(i_b_final)+'}'
if not (i_a_final and i_b_final and j_a_final and j_b_final):
del l_in_masses[i_line]
elif ('*' in atomtype_i_str):
del l_in_masses[i_line]
for i in range(i_a_final, i_b_final+1):
#tokens[1] = '@atom:type'+str(i)
tokens[1] = '@atom:'+atomtypes_int2name[i]
# CONTINUEHERE: CHECK THAT THIS IS WORKING
l_in_masses.insert(i_line, (' '*indent)+(' '.join(tokens)+'\n'))
i_line += 1
else:
assert(i_a == i_b)
#tokens[1] = '@atom:type'+str(i_a)
tokens[1] = '@atom:'+atomtypes_int2name[i_a]
# CONTINUEHERE: CHECK THAT THIS IS WORKING
l_in_masses[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
# --- BONDS AND BOND COEFFS ---
# delete lines from data_bonds if they involve atoms we don't care about
i_line = 0
while i_line < len(l_data_bonds):
line = l_data_bonds[i_line]
tokens = line.strip().split()
assert(len(tokens) == 4)
bondid = Intify(tokens[0])
bondtype = Intify(tokens[1])
atomid1 = Intify(tokens[2])
atomid2 = Intify(tokens[3])
#if ((atomid1 in needed_atomids) and
# (atomid2 in needed_atomids)):
tokens[0] = '$bond:id'+str(bondid)
tokens[1] = '@bond:type'+str(bondtype)
#tokens[2] = '$atom:id'+str(atomid1)
#tokens[3] = '$atom:id'+str(atomid2)
tokens[2] = '$atom:'+atomids_int2name[atomid1]
tokens[3] = '$atom:'+atomids_int2name[atomid2]
needed_bondids.add(bondid)
needed_bondtypes.add(bondtype)
l_data_bonds[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
#else:
# del l_data_bonds[i_line]
# delete data_bond_coeffs for bondtypes we don't care about anymore:
i_line = 0
while i_line < len(l_data_bond_coeffs):
line = l_data_bond_coeffs[i_line]
tokens = line.strip().split()
bondtype = Intify(tokens[0])
if (not (bondtype in needed_bondtypes)):
del l_data_bond_coeffs[i_line]
else:
tokens[0] = '@bond:type'+str(bondtype)
l_data_bond_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
# delete in_bond_coeffs for bondtypes we don't care about anymore:
for bondtype in needed_bondtypes:
assert(type(bondtype) is int)
if ((min_needed_bondtype == None) or
(min_needed_bondtype > bondtype)):
min_needed_bondtype = bondtype
if ((max_needed_bondtype == None) or
(max_needed_bondtype < bondtype)):
max_needed_bondtype = bondtype
for bondid in needed_bondids:
assert(type(bondid) is int)
if ((min_needed_bondid == None) or
(min_needed_bondid > bondid)):
min_needed_bondid = bondid
if ((max_needed_bondid == None) or
(max_needed_bondid < bondid)):
max_needed_bondid = bondid
i_line = 0
while i_line < len(l_in_bond_coeffs):
line = l_in_bond_coeffs[i_line]
tokens = line.strip().split()
bondtype_str = tokens[1]
if ('*' in bondtype_str):
bondtype_tokens = bondtype_str.split('*')
if bondtype_tokens[0] == '':
i_a = min_needed_bondtype
else:
i_a = Intify(bondtype_tokens[0])
if bondtype_tokens[1] == '':
i_b = max_needed_bondtype
else:
i_b = Intify(bondtype_tokens[1])
else:
i_a = Intify(bondtype_str)
i_b = i_a
if i_a < min_needed_bondtype:
i_a = min_needed_bondtype
if i_b > max_needed_bondtype:
i_b = max_needed_bondtype
#if i_a == i_b:
# i_str = '@bond:type'+str(i_a)
# tokens[1] = i_str
#else:
# i_str = '@{bond:type'+str(j_a)+'}*@{bond:type'+str(j_b)+'}'
if ('*' in bondtype_str):
del l_in_bond_coeffs[i_line]
for i in range(i_a, i_b+1):
if (i in needed_bondtypes):
tokens[1] = '@bond:type'+str(i)
l_in_bond_coeffs.insert(i_line,
(' '*indent)+(' '.join(tokens)+'\n'))
i_line += 1
else:
if i_a < i_b:
raise InputError('Error: number of bond types in data file is not consistent with the\n'
' number of bond types you have define bond_coeffs for.\n')
if (i_a == i_b) and (i_a in needed_bondtypes):
tokens[1] = '@bond:type'+str(i_a)
l_in_bond_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
else:
del l_in_bond_coeffs[i_line]
# --- ANGLES AND ANGLE COEFFS ---
# delete lines from data_angles if they involve atoms we don't care about
i_line = 0
while i_line < len(l_data_angles):
line = l_data_angles[i_line]
tokens = line.strip().split()
assert(len(tokens) == 5)
angleid = Intify(tokens[0])
angletype = Intify(tokens[1])
atomid1 = Intify(tokens[2])
atomid2 = Intify(tokens[3])
atomid3 = Intify(tokens[4])
#if ((atomid1 in needed_atomids) and
# (atomid2 in needed_atomids)):
tokens[0] = '$angle:id'+str(angleid)
tokens[1] = '@angle:type'+str(angletype)
#tokens[2] = '$atom:id'+str(atomid1)
#tokens[3] = '$atom:id'+str(atomid2)
#tokens[4] = '$atom:id'+str(atomid3)
tokens[2] = '$atom:'+atomids_int2name[atomid1]
tokens[3] = '$atom:'+atomids_int2name[atomid2]
tokens[4] = '$atom:'+atomids_int2name[atomid3]
needed_angleids.add(angleid)
needed_angletypes.add(angletype)
l_data_angles[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
#else:
# del l_data_angles[i_line]
# delete data_angle_coeffs for angletypes we don't care about anymore:
i_line = 0
while i_line < len(l_data_angle_coeffs):
line = l_data_angle_coeffs[i_line]
tokens = line.strip().split()
angletype = Intify(tokens[0])
if (not (angletype in needed_angletypes)):
del l_data_angle_coeffs[i_line]
else:
tokens[0] = '@angle:type'+str(angletype)
l_data_angle_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
# --- class2specific ----
# Do the same for BondBond and BondAngle Coeffs:
# NOTE: LAMMPS INPUT SCRIPTS, ALL CLASS2 COEFFS are represented by:
# angle_coeff, dihedral_coeff, and improper_coeff commands.
# THERE ARE NO bondbond_coeff commands, or bondangle_coeff commands,
# etc..., so we dont have to worry about l_in_bondbond_coeffs,...
# delete data_bondbond_coeffs for angletypes we don't care about anymore:
i_line = 0
while i_line < len(l_data_bondbond_coeffs):
line = l_data_bondbond_coeffs[i_line]
tokens = line.strip().split()
angletype = Intify(tokens[0])
if (not (angletype in needed_angletypes)):
del l_data_bondbond_coeffs[i_line]
else:
tokens[0] = '@angle:type'+str(angletype)
l_data_bondbond_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
# delete data_bondangle_coeffs for angletypes we don't care about anymore:
i_line = 0
while i_line < len(l_data_bondangle_coeffs):
line = l_data_bondangle_coeffs[i_line]
tokens = line.strip().split()
angletype = Intify(tokens[0])
if (not (angletype in needed_angletypes)):
del l_data_bondangle_coeffs[i_line]
else:
tokens[0] = '@angle:type'+str(angletype)
l_data_bondangle_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
# --- end of class2specific ----
# delete in_angle_coeffs for angletypes we don't care about anymore:
for angletype in needed_angletypes:
assert(type(angletype) is int)
if ((min_needed_angletype == None) or
(min_needed_angletype > angletype)):
min_needed_angletype = angletype
if ((max_needed_angletype == None) or
(max_needed_angletype < angletype)):
max_needed_angletype = angletype
for angleid in needed_angleids:
assert(type(angleid) is int)
if ((min_needed_angleid == None) or
(min_needed_angleid > angleid)):
min_needed_angleid = angleid
if ((max_needed_angleid == None) or
(max_needed_angleid < angleid)):
max_needed_angleid = angleid
i_line = 0
while i_line < len(l_in_angle_coeffs):
line = l_in_angle_coeffs[i_line]
tokens = line.strip().split()
angletype_str = tokens[1]
if ('*' in angletype_str):
angletype_tokens = angletype_str.split('*')
if angletype_tokens[0] == '':
i_a = min_needed_angletype
else:
i_a = Intify(angletype_tokens[0])
if angletype_tokens[1] == '':
i_b = max_needed_angletype
else:
i_b = Intify(angletype_tokens[1])
else:
i_a = i_b = Intify(angletype_str)
if i_a < min_needed_angletype:
i_a = min_needed_angletype
if i_b > max_needed_angletype:
i_b = max_needed_angletype
#if i_a == i_b:
# i_str = '@angle:type'+str(i_a)
# tokens[1] = i_str
#else:
# i_str = '@{angle:type'+str(j_a)+'}*@{angle:type'+str(j_b)+'}'
if ('*' in angletype_str):
del l_in_angle_coeffs[i_line]
for i in range(i_a, i_b+1):
if (i in needed_angletypes):
tokens[1] = '@angle:type'+str(i)
l_in_angle_coeffs.insert(i_line,
(' '*indent)+(' '.join(tokens)+'\n'))
i_line += 1
else:
if i_a < i_b:
raise InputError('Error: number of angle types in data file is not consistent with the\n'
' number of angle types you have define angle_coeffs for.\n')
if (i_a == i_b) and (i_a in needed_angletypes):
tokens[1] = '@angle:type'+str(i_a)
l_in_angle_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
else:
del l_in_angle_coeffs[i_line]
# --- DIHEDRALS AND DIHEDRAL COEFFS ---
# delete lines from data_dihedrals if they involve atoms we don't care about
i_line = 0
while i_line < len(l_data_dihedrals):
line = l_data_dihedrals[i_line]
tokens = line.strip().split()
assert(len(tokens) == 6)
dihedralid = Intify(tokens[0])
dihedraltype = Intify(tokens[1])
atomid1 = Intify(tokens[2])
atomid2 = Intify(tokens[3])
atomid3 = Intify(tokens[4])
atomid4 = Intify(tokens[5])
#if ((atomid1 in needed_atomids) and
# (atomid2 in needed_atomids)):
tokens[0] = '$dihedral:id'+str(dihedralid)
tokens[1] = '@dihedral:type'+str(dihedraltype)
#tokens[2] = '$atom:id'+str(atomid1)
#tokens[3] = '$atom:id'+str(atomid2)
#tokens[4] = '$atom:id'+str(atomid3)
#tokens[5] = '$atom:id'+str(atomid4)
tokens[2] = '$atom:'+atomids_int2name[atomid1]
tokens[3] = '$atom:'+atomids_int2name[atomid2]
tokens[4] = '$atom:'+atomids_int2name[atomid3]
tokens[5] = '$atom:'+atomids_int2name[atomid4]
needed_dihedralids.add(dihedralid)
needed_dihedraltypes.add(dihedraltype)
l_data_dihedrals[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
#else:
# del l_data_dihedrals[i_line]
# delete data_dihedral_coeffs for dihedraltypes we don't care about anymore:
i_line = 0
while i_line < len(l_data_dihedral_coeffs):
line = l_data_dihedral_coeffs[i_line]
tokens = line.strip().split()
dihedraltype = Intify(tokens[0])
if (not (dihedraltype in needed_dihedraltypes)):
del l_data_dihedral_coeffs[i_line]
else:
tokens[0] = '@dihedral:type'+str(dihedraltype)
l_data_dihedral_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
# --- class2specific ----
# Do the same for MiddleBondTorsion, EndBondTorsion, AngleTorsion,
# AngleAngleTorsion, and BondBond13 Coeffs
# NOTE: LAMMPS INPUT SCRIPTS, ALL CLASS2 COEFFS are represented by:
# angle_coeff, dihedral_coeff, and improper_coeff commands.
# THERE ARE NO "middlebondtorsion_coeff" commands, etc...so we don't
# have to worry about dealing with "l_in_middlebondtorsion_coeffs",...
# delete data_middlebondtorsion_coeffs for dihedraltypes we don't care about anymore:
i_line = 0
while i_line < len(l_data_middlebondtorsion_coeffs):
line = l_data_middlebondtorsion_coeffs[i_line]
tokens = line.strip().split()
dihedraltype = Intify(tokens[0])
if (not (dihedraltype in needed_dihedraltypes)):
del l_data_middlebondtorsion_coeffs[i_line]
else:
tokens[0] = '@dihedral:type'+str(dihedraltype)
l_data_middlebondtorsion_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
# delete data_endbondtorsion_coeffs for dihedraltypes we don't care about anymore:
i_line = 0
while i_line < len(l_data_endbondtorsion_coeffs):
line = l_data_endbondtorsion_coeffs[i_line]
tokens = line.strip().split()
dihedraltype = Intify(tokens[0])
if (not (dihedraltype in needed_dihedraltypes)):
del l_data_endbondtorsion_coeffs[i_line]
else:
tokens[0] = '@dihedral:type'+str(dihedraltype)
l_data_endbondtorsion_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
# delete data_angletorsion_coeffs for dihedraltypes we don't care about anymore:
i_line = 0
while i_line < len(l_data_angletorsion_coeffs):
line = l_data_angletorsion_coeffs[i_line]
tokens = line.strip().split()
dihedraltype = Intify(tokens[0])
if (not (dihedraltype in needed_dihedraltypes)):
del l_data_angletorsion_coeffs[i_line]
else:
tokens[0] = '@dihedral:type'+str(dihedraltype)
l_data_angletorsion_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
# delete data_angleangletorsion_coeffs for dihedraltypes we don't care about anymore:
i_line = 0
while i_line < len(l_data_angleangletorsion_coeffs):
line = l_data_angleangletorsion_coeffs[i_line]
tokens = line.strip().split()
dihedraltype = Intify(tokens[0])
if (not (dihedraltype in needed_dihedraltypes)):
del l_data_angleangletorsion_coeffs[i_line]
else:
tokens[0] = '@dihedral:type'+str(dihedraltype)
l_data_angleangletorsion_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
# delete data_bondbond13_coeffs for dihedraltypes we don't care about anymore:
i_line = 0
while i_line < len(l_data_bondbond13_coeffs):
line = l_data_bondbond13_coeffs[i_line]
tokens = line.strip().split()
dihedraltype = Intify(tokens[0])
if (not (dihedraltype in needed_dihedraltypes)):
del l_data_bondbond13_coeffs[i_line]
else:
tokens[0] = '@dihedral:type'+str(dihedraltype)
l_data_bondbond13_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
# --- end of class2specific ----
# delete in_dihedral_coeffs for dihedraltypes we don't care about anymore:
for dihedraltype in needed_dihedraltypes:
assert(type(dihedraltype) is int)
if ((min_needed_dihedraltype == None) or
(min_needed_dihedraltype > dihedraltype)):
min_needed_dihedraltype = dihedraltype
if ((max_needed_dihedraltype == None) or
(max_needed_dihedraltype < dihedraltype)):
max_needed_dihedraltype = dihedraltype
for dihedralid in needed_dihedralids:
assert(type(dihedralid) is int)
if ((min_needed_dihedralid == None) or
(min_needed_dihedralid > dihedralid)):
min_needed_dihedralid = dihedralid
if ((max_needed_dihedralid == None) or
(max_needed_dihedralid < dihedralid)):
max_needed_dihedralid = dihedralid
i_line = 0
while i_line < len(l_in_dihedral_coeffs):
line = l_in_dihedral_coeffs[i_line]
tokens = line.strip().split()
dihedraltype_str = tokens[1]
if ('*' in dihedraltype_str):
dihedraltype_tokens = dihedraltype_str.split('*')
if dihedraltype_tokens[0] == '':
i_a = min_needed_dihedraltype
else:
i_a = Intify(dihedraltype_tokens[0])
if dihedraltype_tokens[1] == '':
i_b = max_needed_dihedraltype
else:
i_b = Intify(dihedraltype_tokens[1])
else:
i_a = i_b = Intify(dihedraltype_str)
if i_a < min_needed_dihedraltype:
i_a = min_needed_dihedraltype
if i_b > max_needed_dihedraltype:
i_b = max_needed_dihedraltype
#if i_a == i_b:
# i_str = '@dihedral:type'+str(i_a)
# tokens[1] = i_str
#else:
# i_str = '@{dihedral:type'+str(j_a)+'}*@{dihedral:type'+str(j_b)+'}'
if ('*' in dihedraltype_str):
del l_in_dihedral_coeffs[i_line]
for i in range(i_a, i_b+1):
if (i in needed_dihedraltypes):
tokens[1] = '@dihedral:type'+str(i)
l_in_dihedral_coeffs.insert(i_line,
(' '*indent)+(' '.join(tokens)+'\n'))
i_line += 1
else:
if i_a < i_b:
raise InputError('Error: number of dihedral types in data file is not consistent with the\n'
' number of dihedral types you have define dihedral_coeffs for.\n')
if (i_a == i_b) and (i_a in needed_dihedraltypes):
tokens[1] = '@dihedral:type'+str(i_a)
l_in_dihedral_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
else:
del l_in_dihedral_coeffs[i_line]
# --- IMPROPERS AND IMPROPER COEFFS ---
# delete lines from data_impropers if they involve atoms we don't care about
i_line = 0
while i_line < len(l_data_impropers):
line = l_data_impropers[i_line]
tokens = line.strip().split()
assert(len(tokens) == 6)
improperid = Intify(tokens[0])
impropertype = Intify(tokens[1])
atomid1 = Intify(tokens[2])
atomid2 = Intify(tokens[3])
atomid3 = Intify(tokens[4])
atomid4 = Intify(tokens[5])
#if ((atomid1 in needed_atomids) and
# (atomid2 in needed_atomids)):
tokens[0] = '$improper:id'+str(improperid)
tokens[1] = '@improper:type'+str(impropertype)
#tokens[2] = '$atom:id'+str(atomid1)
#tokens[3] = '$atom:id'+str(atomid2)
#tokens[4] = '$atom:id'+str(atomid3)
#tokens[5] = '$atom:id'+str(atomid4)
tokens[2] = '$atom:'+atomids_int2name[atomid1]
tokens[3] = '$atom:'+atomids_int2name[atomid2]
tokens[4] = '$atom:'+atomids_int2name[atomid3]
tokens[5] = '$atom:'+atomids_int2name[atomid4]
needed_improperids.add(improperid)
needed_impropertypes.add(impropertype)
l_data_impropers[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
#else:
# del l_data_impropers[i_line]
# delete data_improper_coeffs for impropertypes we don't care about anymore:
i_line = 0
while i_line < len(l_data_improper_coeffs):
line = l_data_improper_coeffs[i_line]
tokens = line.strip().split()
impropertype = Intify(tokens[0])
if (not (impropertype in needed_impropertypes)):
del l_data_improper_coeffs[i_line]
else:
tokens[0] = '@improper:type'+str(impropertype)
l_data_improper_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
# --- class2specific ----
# Do the same for AngleAngle Coeffs
# NOTE: LAMMPS INPUT SCRIPTS, ALL CLASS2 COEFFS are represented by:
# angle_coeff, dihedral_coeff, and improper_coeff commands.
# THERE ARE NO "angleangle_coeff" commands, etc...so we don't
# have to worry about dealing with "l_in_angleangle_coeffs",...
# delete data_middlebondtorsion_coeffs for dihedraltypes we don't care about anymore:
# delete data_angleangle_coeffs for impropertypes we don't care about anymore:
i_line = 0
while i_line < len(l_data_angleangle_coeffs):
line = l_data_angleangle_coeffs[i_line]
tokens = line.strip().split()
impropertype = Intify(tokens[0])
if (not (impropertype in needed_impropertypes)):
del l_data_angleangle_coeffs[i_line]
else:
tokens[0] = '@improper:type'+str(impropertype)
l_data_angleangle_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
# --- end of class2specific ----
# delete in_improper_coeffs for impropertypes we don't care about anymore:
for impropertype in needed_impropertypes:
assert(type(impropertype) is int)
if ((min_needed_impropertype == None) or
(min_needed_impropertype > impropertype)):
min_needed_impropertype = impropertype
if ((max_needed_impropertype == None) or
(max_needed_impropertype < impropertype)):
max_needed_impropertype = impropertype
for improperid in needed_improperids:
assert(type(improperid) is int)
if ((min_needed_improperid == None) or
(min_needed_improperid > improperid)):
min_needed_improperid = improperid
if ((max_needed_improperid == None) or
(max_needed_improperid < improperid)):
max_needed_improperid = improperid
i_line = 0
while i_line < len(l_in_improper_coeffs):
line = l_in_improper_coeffs[i_line]
tokens = line.strip().split()
impropertype_str = tokens[1]
if ('*' in impropertype_str):
impropertype_tokens = impropertype_str.split('*')
if impropertype_tokens[0] == '':
i_a = min_needed_impropertype
else:
i_a = Intify(impropertype_tokens[0])
if impropertype_tokens[1] == '':
i_b = max_needed_impropertype
else:
i_b = Intify(impropertype_tokens[1])
else:
i_a = i_b = Intify(impropertype_str)
if i_a < min_needed_impropertype:
i_a = min_needed_impropertype
if i_b > max_needed_impropertype:
i_b = max_needed_impropertype
#if i_a == i_b:
# i_str = '@improper:type'+str(i_a)
# tokens[1] = i_str
#else:
# i_str = '@{improper:type'+str(j_a)+'}*@{improper:type'+str(j_b)+'}'
if ('*' in impropertype_str):
del l_in_improper_coeffs[i_line]
for i in range(i_a, i_b+1):
if (i in needed_impropertypes):
tokens[1] = '@improper:type'+str(i)
l_in_improper_coeffs.insert(i_line,
(' '*indent)+(' '.join(tokens)+'\n'))
i_line += 1
else:
if i_a < i_b:
raise InputError('Error: number of improper types in data file is not consistent with the\n'
' number of improper types you have define improper_coeffs for.\n')
if (i_a == i_b) and (i_a in needed_impropertypes):
tokens[1] = '@improper:type'+str(i_a)
l_in_improper_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n')
i_line += 1
else:
del l_in_improper_coeffs[i_line]
# --- GROUPS ---
# Now parse through all of the "group" commands and try and figure
# out if any of these groups contain any of the atoms we are keeping.
# If so, then save the group and write it out.
# (I hate trying to parse this kind of text.)
#if len(l_in_group) > 0:
# sys.stderr.write('\n'
# ' --groups-- Attempting to parse \"group\" commands.\n'
# ' This may cause '+g_program_name+' to crash.\n'
# ' If so, comment out all group commands in your input script(s), and\n'
# ' try again. (And please report the error. -Andrew 2014-10-30)\n')
i_line = 0
groups_needed = set(['all'])
while i_line < len(l_in_group):
line = l_in_group[i_line]
tokens = line.strip().split()
delete_this_command = False
explicit_definition = False
if len(tokens) < 3:
delete_this_command = True
group_name = tokens[1]
specifier_style = tokens[2]
str_logical = ''
str_selection = ''
if specifier_style[0:4] == 'type':
str_logical+=specifier_style[4:]
explicit_definition = True
specifier_style = 'type'
elif specifier_style == 'id':
str_logical+=specifier_style[2:]
explicit_definition = True
specifier_style = 'id'
elif specifier_style == 'molecule':
str_logical+=specifier_style[8:]
specifier_style = 'molecule'
explicit_definition = True
if explicit_definition:
i_token_sel_min = 3
if len(tokens) <= i_token_sel_min:
sys.stderr.write('WARNING: possible syntax error on this line:\n'
+' '+l_in_group[i_line]+'\n')
delete_this_command = True
if str_logical == '':
str_logical = tokens[i_token_sel_min]
if not str_logical[0].isdigit():
i_token_sel_min += 1
if len(tokens) <= i_token_sel_min:
tokens.append('')
else:
tokens.insert(i_token_sel_min, str_logical)
i_token_sel_max = len(tokens)-1
for i in range(i_token_sel_min, len(tokens)):
if tokens[i].isdigit():
break
else:
i_token_sel_max = i
assert(len(tokens) > i_token_sel_min)
if str_logical[0:2] in ('<=','>=','==','!=','<>'):
tokens[i_token_sel_min] = str_logical[2:] + tokens[i_token_sel_min]
str_logical = str_logical[0:2]
if str_logical == '<=':
l_group_selection = [ (None,int(tokens[i_token_sel_min])) ]
elif str_logical == '>=':
l_group_selection = [ (int(tokens[i_token_sel_min]),None) ]
elif str_logical == '==':
l_group_selection = [ (int(tokens[i_token_sel_min]),
int(tokens[i_token_sel_min])) ]
elif str_logical == '!=':
l_group_selection = [ (None,int(tokens[i_token_sel_min])-1),
(int(tokens[i_token_sel_min])+1,None)]
elif str_logical == '<>':
l_group_selection = [ (int(tokens[i_token_sel_min]),
int(tokens[i_token_sel_max])) ]
elif str_logical[0:1] in ('<','>'):
tokens[i_token_sel_min] = str_logical[1:] + tokens[i_token_sel_min]
str_logical = str_logical[0:1]
if str_logical == '<':
l_group_selection = [(None,int(tokens[i_token_sel_min])-1)]
elif str_logical == '>':
l_group_selection = [(int(tokens[i_token_sel_min])+1,None)]
else:
str_selection = ' '.join(tokens[i_token_sel_min:i_token_sel_max+1])
l_group_selection = LammpsSelectToIntervals(str_selection,
slice_delim=':',
or_delim=' ')
mn, mx = IntervalListToMinMax(l_group_selection)
if mn == None:
mn = 1
filtered_selection=[]
if specifier_style == 'type':
if mx == None:
mx = max_needed_atomtype
for i in range(mn, mx+1):
if (BelongsToSel(i, l_group_selection)
and (i in needed_atomtypes)):
filtered_selection.append((i,i))
elif specifier_style == 'id':
if mx == None:
mx = max_needed_atomid
for i in range(mn, mx+1):
if (BelongsToSel(i, l_group_selection)
and (i in needed_atomids)):
filtered_selection.append((i,i))
elif specifier_style == 'molecule':
if mx == None:
mx = max_needed_molid
for i in range(mn, mx+1):
if (BelongsToSel(i, l_group_selection)
and (i in needed_molids)):
filtered_selection.append((i,i))
MergeIntervals(filtered_selection)
if len(filtered_selection) > 0:
tokens = ['group', group_name, specifier_style]
for interval in filtered_selection:
a = interval[0]
b = interval[1]
if specifier_style == 'type':
if a == b:
tokens.append('@atom:type'+str(a))
else:
tokens.append('@{atom:type'+str(a)+
'}:@{atom:type'+str(b)+'}')
if specifier_style == 'id':
if a == b:
tokens.append('$atom:id'+str(a))
else:
tokens.append('${atom:id'+str(a)
+'}:${atom:id'+str(b)+'}')
if specifier_style == 'molecule':
if a == b:
tokens.append('$mol:id'+str(a))
else:
tokens.append('${mol:id'+str(a)+
'}:${mol:id'+str(b)+'}')
# Commenting out next two lines. (This is handled later.)
#l_in_group[i_line] = ' '.join(tokens)
#groups_needed.add(group_name)
else:
delete_this_command = True
else:
if len(tokens) > 3:
if tokens[2] == 'union':
i_token = 3
while i_token < len(tokens):
if not (tokens[i_token] in groups_needed):
del tokens[i_token]
else:
i_token += 1
# if none of the groups contain atoms we need,
# then delete the entire command
if len(tokens) <= 3:
delete_this_command = True
elif tokens[2] == 'intersect':
i_token = 3
while i_token < len(tokens):
if not (tokens[i_token] in groups_needed):
# if any of the groups we need are empty
# then delete the command
delete_this_command = True
break
i_token += 1
elif (tokens[2] == 'subtract') and (len(tokens) >= 5):
if not (tokens[3] in groups_needed):
delete_this_command = True
i_token = 4
while i_token < len(tokens):
if not (tokens[i_token] in groups_needed):
del tokens[i_token]
else:
i_token += 1
else:
# Otherwise I don't recongize the syntax of this
# group command. In that case, I just delete it.
delete_this_command = True
elif tokens[2] == 'clear':
pass
elif tokens[2] == 'delete':
pass
else:
delete_this_command = True
if delete_this_command:
sys.stderr.write('WARNING: Ignoring line \n\"'+l_in_group[i_line].rstrip()+'\"\n')
del l_in_group[i_line]
else:
groups_needed.add(group_name)
l_in_group[i_line] = (' '*indent) + ' '.join(tokens) + '\n'
i_line += 1
# --- fix rigid ---
i_line = 0
while i_line < len(l_in_fix_rigid):
line = l_in_fix_rigid[i_line]
tokens = line.strip().split()
if len(tokens) < 4:
break
fixid = tokens[1]
group_name = tokens[2]
delete_this_command = True
assert(tokens[3].find('rigid') == 0)
if group_name in groups_needed:
delete_this_command = False
if delete_this_command:
sys.stderr.write('WARNING: Ignoring line \n\"'+l_in_fix_rigid[i_line].rstrip()+'\"\n')
del l_in_fix_rigid[i_line]
else:
l_in_fix_rigid[i_line] = (' '*indent) + ' '.join(tokens) + '\n'
i_line += 1
# --- fix shake ---
i_line = 0
while i_line < len(l_in_fix_shake):
line = l_in_fix_shake[i_line]
tokens = line.strip().split()
if len(tokens) < 4:
break
fixid = tokens[1]
group_name = tokens[2]
delete_this_command = True
assert(tokens[3].find('shake') == 0)
# parse the list of angle types
#i_token = tokens.index('a')
for i_token in range(0, len(tokens)):
if tokens[i_token] == 'a':
break
if i_token != len(tokens):
i_token += 1
while (i_token < len(tokens)) and tokens[i_token].isdigit():
# delete angle types from the list which
# do not belong to the selection
btype=int(tokens[i_token])
if int(tokens[i_token]) in needed_angletypes:
tokens[i_token] = '@angle:type'+tokens[i_token]
i_token += 1
delete_this_command = False
else:
del tokens[i_token]
# parse the list of bond types
#i_token = tokens.index('b')
for i_token in range(0, len(tokens)):
if tokens[i_token] == 'b':
break
if i_token != len(tokens):
i_token += 1
while (i_token < len(tokens)) and tokens[i_token].isdigit():
# delete bond types from the list which
# do not belong to the selection
btype=int(tokens[i_token])
if int(tokens[i_token]) in needed_bondtypes:
tokens[i_token] = '@bond:type'+tokens[i_token]
i_token += 1
delete_this_command = False
else:
del tokens[i_token]
# parse the list of atom types
# i_token = tokens.index('t')
for i_token in range(0, len(tokens)):
if tokens[i_token] == 't':
break
if i_token != len(tokens):
i_token += 1
while (i_token < len(tokens)) and tokens[i_token].isdigit():
# delete atom types from the list which
# do not belong to the selection
btype=int(tokens[i_token])
if int(tokens[i_token]) in needed_atomtypes:
tokens[i_token] = '@atom:type'+tokens[i_token]
i_token += 1
delete_this_command = False
else:
del tokens[i_token]
# Selecting atoms by mass feature should still work, so we
# don't need to delete or ignore these kinds of commands.
#for i_token in range(0, len(tokens)):
# if tokens[i_token] == 'm':
# break
#if i_token != len(tokens):
# delete_this_command = True
if 'mol' in tokens:
delete_this_command = True
if not (group_name in groups_needed):
delete_this_command = True
if delete_this_command:
sys.stderr.write('WARNING: Ignoring line \n\"'+l_in_fix_shake[i_line].rstrip()+'\"\n')
del l_in_fix_shake[i_line]
else:
l_in_fix_shake[i_line] = (' '*indent) + ' '.join(tokens) + '\n'
i_line += 1
# --- fix poems ---
i_line = 0
while i_line < len(l_in_fix_poems):
line = l_in_fix_poems[i_line]
tokens = line.strip().split()
if len(tokens) < 4:
break
fixid = tokens[1]
group_name = tokens[2]
delete_this_command = True
assert(tokens[3].find('poems') == 0)
if group_name in groups_needed:
delete_this_command = False
if tokens[4] != 'molecule':
delete_this_command = True
sys.stderr.write('WARNING: '+g_program_name+' ONLY supports \"fix poems\" commands\n'
' which use the \"molecule\" keyword.\n')
if tokens[4] == 'file':
sys.stderr.write(' If you want use external files with fix poems, then you will have to\n'
' generate the file yourself. You ask use moltemplate to generate\n'
' this file for you, by manually adding a section at the end of your\n'
' final .LT file (eg. \"system.lt\") which resembles the following:\n\n'
'write(\"poems_file.txt\") {\n'
' 1 1 $atom:idname1a $atom:idname2a $atom:idname3a ...\n'
' 2 1 $atom:idname1b $atom:idname2b $atom:idname3b ...\n'
' 3 1 $atom:idname1c $atom:idname2c $atom:idname3c ...\n'
' : : etc...\n'
'}\n\n'
' ...where $atom:idname1a, $atom:idname2a, ... are moltemplate-compatible\n'
' unique (full,long) id-names for the atoms in each rigid body.\n'
' This will insure the atom-id numbers in this file are correct.\n'
' See the documentation for fix poems for details.\n')
if delete_this_command:
sys.stderr.write('WARNING: Ignoring line \n\"'+l_in_fix_poems[i_line].rstrip()+'\"\n')
del l_in_fix_poems[i_line]
else:
l_in_fix_poems[i_line] = (' '*indent) + ' '.join(tokens) + '\n'
i_line += 1
# --- fix qeq ---
i_line = 0
while i_line < len(l_in_fix_qeq):
line = l_in_fix_qeq[i_line]
tokens = line.strip().split()
if len(tokens) < 4:
break
fixid = tokens[1]
group_name = tokens[2]
delete_this_command = True
assert(tokens[3].find('qeq') == 0)
if group_name in groups_needed:
delete_this_command = False
if delete_this_command:
sys.stderr.write('WARNING: Ignoring line \n\"'+l_in_fix_qeq[i_line].rstrip()+'\"\n')
del l_in_fix_qeq[i_line]
else:
l_in_fix_qeq[i_line] = (' '*indent) + ' '.join(tokens) + '\n'
i_line += 1
# --- fix qmmm ---
i_line = 0
while i_line < len(l_in_fix_qmmm):
line = l_in_fix_qmmm[i_line]
tokens = line.strip().split()
if len(tokens) < 4:
break
fixid = tokens[1]
group_name = tokens[2]
delete_this_command = True
assert(tokens[3].find('qmmm') == 0)
if group_name in groups_needed:
delete_this_command = False
if delete_this_command:
sys.stderr.write('WARNING: Ignoring line \n\"'+l_in_fix_qmmm[i_line].rstrip()+'\"\n')
del l_in_fix_qmmm[i_line]
else:
l_in_fix_qmmm[i_line] = (' '*indent) + ' '.join(tokens) + '\n'
i_line += 1
########################################
### Now begin writing the template. ###
########################################
if not some_pair_coeffs_read:
sys.stderr.write('Warning: No \"pair coeffs\" set.\n'
' (No interactions between non-bonded atoms defined.)\n')
no_warnings = False
#sys.stderr.write('Writing ttree data to standard out.\n'
# ' You can redirect this to a file using:\n'+
# ' '+' '.join(sys.argv)+' > filename.ttree\n'
# ' ----------------------\n')
if mol_name != '':
sys.stdout.write(mol_name + ' {\n')
if len(l_in_init) > 0:
sys.stdout.write('\n### LAMMPS commands for initialization\n'
'### (These can be overridden later.)\n\n')
l_in_init.insert(0, (' '*cindent)+'write_once(\"'+in_init+'\") {\n')
l_in_init.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_in_init))
if len(l_in_settings) > 0:
sys.stdout.write('\n### LAMMPS commands for settings\n'
'### (These can be overridden later.)\n\n')
l_in_settings.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n')
l_in_settings.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_in_settings))
non_empty_output = True
if len(l_in_masses) > 0:
l_in_masses.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n')
l_in_masses.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_in_masses))
non_empty_output = True
if remove_coeffs_from_data_file:
if len(l_data_pair_coeffs) > 0:
for line in l_data_pair_coeffs:
tokens = line.strip().split()
atomtype_str = tokens[0]
l_in_pair_coeffs.append((' '*cindent)+' pair_coeff '+atomtype_str+' '+atomtype_str+' '+' '.join(tokens[1:])+'\n')
l_data_pair_coeffs = []
if len(l_data_pairij_coeffs) > 0:
for line in l_data_pairij_coeffs:
l_in_pair_coeffs.append((' '*cindent)+' pair_coeff '+line.strip()+'\n')
l_data_pairij_coeffs = []
if len(l_in_pair_coeffs) > 0:
l_in_pair_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n')
l_in_pair_coeffs.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_in_pair_coeffs))
non_empty_output = True
if (remove_coeffs_from_data_file and (len(l_data_bond_coeffs) > 0)):
for line in l_data_bond_coeffs:
l_in_bond_coeffs.append((' '*cindent)+' bond_coeff '+line.strip()+'\n')
l_data_bond_coeffs = []
if len(l_in_bond_coeffs) > 0:
l_in_bond_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n')
l_in_bond_coeffs.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_in_bond_coeffs))
non_empty_output = True
if (remove_coeffs_from_data_file and (len(l_data_angle_coeffs) > 0)):
for line in l_data_angle_coeffs:
l_in_angle_coeffs.append((' '*cindent)+' angle_coeff '+line.strip()+'\n')
l_data_angle_coeffs = []
for line in l_data_bondbond_coeffs:
tokens = line.strip().split()
l_in_angle_coeffs.append((' '*cindent)+' angle_coeff '+tokens[0]+' bb '+' '.join(tokens[1:])+'\n')
l_data_bondbond_coeffs = []
for line in l_data_bondangle_coeffs:
tokens = line.strip().split()
l_in_angle_coeffs.append((' '*cindent)+' angle_coeff '+tokens[0]+' ba '+' '.join(tokens[1:])+'\n')
l_data_bondangle_coeffs = []
if len(l_in_angle_coeffs) > 0:
l_in_angle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n')
l_in_angle_coeffs.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_in_angle_coeffs))
non_empty_output = True
if (remove_coeffs_from_data_file and (len(l_data_dihedral_coeffs) > 0)):
for line in l_data_dihedral_coeffs:
l_in_dihedral_coeffs.append((' '*cindent)+' dihedral_coeff '+line.strip()+'\n')
l_data_dihedral_coeffs = []
for line in l_data_middlebondtorsion_coeffs:
tokens = line.strip().split()
l_in_dihedral_coeffs.append((' '*cindent)+' dihedral_coeff '+tokens[0]+' mbt '+' '.join(tokens[1:])+'\n')
l_data_middlebondtorsion_coeffs = []
for line in l_data_endbondtorsion_coeffs:
tokens = line.strip().split()
l_in_dihedral_coeffs.append((' '*cindent)+' dihedral_coeff '+tokens[0]+' ebt '+' '.join(tokens[1:])+'\n')
l_data_endbondtorsion_coeffs = []
for line in l_data_angletorsion_coeffs:
tokens = line.strip().split()
l_in_dihedral_coeffs.append((' '*cindent)+' dihedral_coeff '+tokens[0]+' at '+' '.join(tokens[1:])+'\n')
l_data_angletorsion_coeffs = []
for line in l_data_angleangletorsion_coeffs:
tokens = line.strip().split()
l_in_dihedral_coeffs.append((' '*cindent)+' dihedral_coeff '+tokens[0]+' aat '+' '.join(tokens[1:])+'\n')
l_data_angleangletorsion_coeffs = []
for line in l_data_bondbond13_coeffs:
tokens = line.strip().split()
l_in_dihedral_coeffs.append((' '*cindent)+' dihedral_coeff '+tokens[0]+' bb13 '+' '.join(tokens[1:])+'\n')
l_data_bondbond13_coeffs = []
if len(l_in_dihedral_coeffs) > 0:
l_in_dihedral_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n')
l_in_dihedral_coeffs.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_in_dihedral_coeffs))
non_empty_output = True
if (remove_coeffs_from_data_file and (len(l_data_improper_coeffs) > 0)):
for line in l_data_improper_coeffs:
l_in_improper_coeffs.append((' '*cindent)+' improper_coeff '+line.strip()+'\n')
l_data_improper_coeffs = []
for line in l_data_angleangle_coeffs:
tokens = line.strip().split()
l_in_improper_coeffs.append((' '*cindent)+' improper_coeff '+tokens[0]+' aa '+' '.join(tokens[1:])+'\n')
l_data_angleangle_coeffs = []
if len(l_in_improper_coeffs) > 0:
l_in_improper_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n')
l_in_improper_coeffs.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_in_improper_coeffs))
non_empty_output = True
if non_empty_output:
sys.stdout.write('\n\n### DATA sections\n\n')
if len(l_data_masses) > 0:
l_data_masses.insert(0, (' '*cindent)+'write_once(\"'+data_masses+'\") {\n')
l_data_masses.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_masses))
non_empty_output = True
if len(l_data_bond_coeffs) > 0:
l_data_bond_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bond_coeffs+'\") {\n')
l_data_bond_coeffs.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_bond_coeffs))
non_empty_output = True
if len(l_data_angle_coeffs) > 0:
l_data_angle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angle_coeffs+'\") {\n')
l_data_angle_coeffs.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_angle_coeffs))
non_empty_output = True
if len(l_data_dihedral_coeffs) > 0:
l_data_dihedral_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_dihedral_coeffs+'\") {\n')
l_data_dihedral_coeffs.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_dihedral_coeffs))
non_empty_output = True
if len(l_data_improper_coeffs) > 0:
l_data_improper_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_improper_coeffs+'\") {\n')
l_data_improper_coeffs.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_improper_coeffs))
non_empty_output = True
if len(l_data_pair_coeffs) > 0:
l_data_pair_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_pair_coeffs+'\") {\n')
l_data_pair_coeffs.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_pair_coeffs))
non_empty_output = True
if len(l_data_pairij_coeffs) > 0:
l_data_pairij_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_pairij_coeffs+'\") {\n')
l_data_pairij_coeffs.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_pairij_coeffs))
non_empty_output = True
# class2 force fields:
if len(l_data_bondbond_coeffs) > 0:
l_data_bondbond_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bondbond_coeffs+'\") {\n')
l_data_bondbond_coeffs.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_bondbond_coeffs))
non_empty_output = True
if len(l_data_bondangle_coeffs) > 0:
l_data_bondangle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bondangle_coeffs+'\") {\n')
l_data_bondangle_coeffs.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_bondangle_coeffs))
non_empty_output = True
if len(l_data_middlebondtorsion_coeffs) > 0:
l_data_middlebondtorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_middlebondtorsion_coeffs+'\") {\n')
l_data_middlebondtorsion_coeffs.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_middlebondtorsion_coeffs))
non_empty_output = True
if len(l_data_endbondtorsion_coeffs) > 0:
l_data_endbondtorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_endbondtorsion_coeffs+'\") {\n')
l_data_endbondtorsion_coeffs.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_endbondtorsion_coeffs))
non_empty_output = True
if len(l_data_angletorsion_coeffs) > 0:
l_data_angletorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angletorsion_coeffs+'\") {\n')
l_data_angletorsion_coeffs.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_angletorsion_coeffs))
non_empty_output = True
if len(l_data_angleangletorsion_coeffs) > 0:
l_data_angleangletorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angleangletorsion_coeffs+'\") {\n')
l_data_angleangletorsion_coeffs.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_angleangletorsion_coeffs))
non_empty_output = True
if len(l_data_bondbond13_coeffs) > 0:
l_data_bondbond13_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bondbond13_coeffs+'\") {\n')
l_data_bondbond13_coeffs.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_bondbond13_coeffs))
non_empty_output = True
if len(l_data_angleangle_coeffs) > 0:
l_data_angleangle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angleangle_coeffs+'\") {\n')
l_data_angleangle_coeffs.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_angleangle_coeffs))
non_empty_output = True
# automatic generation of bonded interactions by type:
if len(l_data_angles_by_type) > 0:
l_data_angles_by_type.insert(0, (' '*cindent)+'write_once(\"'+data_angles_by_type+'\") {\n')
l_data_angles_by_type.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_angles_by_type))
non_empty_output = True
if len(l_data_dihedrals_by_type) > 0:
l_data_dihedrals_by_type.insert(0, (' '*cindent)+'write_once(\"'+data_dihedrals_by_type+'\") {\n')
l_data_dihedrals_by_type.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_dihedrals_by_type))
non_empty_output = True
if len(l_data_impropers_by_type) > 0:
l_data_impropers_by_type.insert(0, (' '*cindent)+'write_once(\"'+data_impropers_by_type+'\") {\n')
l_data_impropers_by_type.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_impropers_by_type))
non_empty_output = True
if len(l_data_atoms) > 0:
l_data_atoms.insert(0, (' '*cindent)+'write(\"'+data_atoms+'\") {\n')
l_data_atoms.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_atoms))
non_empty_output = True
else:
sys.stderr.write('Warning: missing \"Atoms\" section.\n'
' (Did you include a LAMMPS data file in your argument list?)\n')
no_warnings = False
# non-point-like particles
if len(l_data_ellipsoids) > 0:
l_data_ellipsoids.insert(0, (' '*cindent)+'write(\"'+data_ellipsoids+'\") {\n')
l_data_ellipsoids.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_ellipsoids))
if len(l_data_lines) > 0:
l_data_lines.insert(0, (' '*cindent)+'write(\"'+data_lines+'\") {\n')
l_data_lines.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_lines))
if len(l_data_triangles) > 0:
l_data_triangles.insert(0, (' '*cindent)+'write(\"'+data_triangles+'\") {\n')
l_data_triangles.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_triangles))
# DO NOT WRITE OUT VELOCITY DATA
# (Why: because it makes it difficult to combine this molecular template
# with molecule templates from other sources which lack velocity data.
# LAMMPS (and topotools) will crash if the number of entries in the
# Velocities section of a data file does not match the number of atoms.)
# COMMENTING OUT:
#if len(l_data_velocities) > 0:
# l_data_velocities.insert(0, (' '*cindent)+'write(\"'+data_velocities+'\") {\n')
# l_data_velocities.append((' '*cindent)+'}\n')
# sys.stdout.write('\n')
# sys.stdout.write(''.join(l_data_velocities))
if len(l_data_bonds) > 0:
l_data_bonds.insert(0, (' '*cindent)+'write(\"'+data_bonds+'\") {\n')
l_data_bonds.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_bonds))
non_empty_output = True
if len(l_data_angles) > 0:
l_data_angles.insert(0, (' '*cindent)+'write(\"'+data_angles+'\") {\n')
l_data_angles.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_angles))
non_empty_output = True
if len(l_data_dihedrals) > 0:
l_data_dihedrals.insert(0, (' '*cindent)+'write(\"'+data_dihedrals+'\") {\n')
l_data_dihedrals.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_dihedrals))
non_empty_output = True
if len(l_data_impropers) > 0:
l_data_impropers.insert(0, (' '*cindent)+'write(\"'+data_impropers+'\") {\n')
l_data_impropers.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_data_impropers))
non_empty_output = True
if len(l_in_group) > 0:
no_warnings = False
l_in_group.insert(0, (' '*cindent)+'write(\"'+in_settings+'\") {\n')
l_in_group.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_in_group))
#sys.stderr.write('######################################################\n'
# 'WARNING: One or more \"group\" commands appear to refer to relevant atoms.\n'
# ' Please check to make sure that the group(s) generated by\n'
# ' '+g_program_name+' contain the correct atoms. (-Andrew 2014-10-30)\n'
# '######################################################\n')
assert(non_empty_output)
if len(l_in_fix_rigid) > 0:
no_warnings = False
l_in_fix_rigid.insert(0, (' '*cindent)+'write(\"'+in_settings+'\") {\n')
l_in_fix_rigid.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_in_fix_rigid))
sys.stderr.write('WARNING: \"fix rigid\" style command(s) applied to selected atoms.\n'
' Please make sure that the fix group(s) are defined correctly.\n'
'######################################################\n')
assert(non_empty_output)
if len(l_in_fix_shake) > 0:
no_warnings = False
l_in_fix_shake.insert(0, (' '*cindent)+'write(\"'+in_settings+'\") {\n')
l_in_fix_shake.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_in_fix_shake))
sys.stderr.write('WARNING: \"fix shake\" style command(s) applied to selected atoms.\n'
' Please check to make sure that the fix group(s) are defined correctly,\n'
' and also check that the atom, bond, and angle types are correct.\n'
'######################################################\n')
assert(non_empty_output)
if len(l_in_fix_poems) > 0:
no_warnings = False
l_in_fix_poems.insert(0, (' '*cindent)+'write(\"'+in_settings+'\") {\n')
l_in_fix_poems.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_in_fix_poems))
sys.stderr.write('WARNING: \"fix poems\" style command(s) applied to selected atoms.\n'
' Please make sure that the fix group(s) are defined correctly.\n'
'######################################################\n')
assert(non_empty_output)
if len(l_in_fix_qeq) > 0:
no_warnings = False
l_in_fix_qeq.insert(0, (' '*cindent)+'write(\"'+in_settings+'\") {\n')
l_in_fix_qeq.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_in_fix_qeq))
sys.stderr.write('WARNING: \"fix qeq\" style command(s) applied to selected atoms.\n'
' Please make sure that the fix group(s) are defined correctly.\n'
'######################################################\n')
assert(non_empty_output)
if len(l_in_fix_qmmm) > 0:
no_warnings = False
l_in_fix_qmmm.insert(0, (' '*cindent)+'write(\"'+in_settings+'\") {\n')
l_in_fix_qmmm.append((' '*cindent)+'}\n')
sys.stdout.write('\n')
sys.stdout.write(''.join(l_in_fix_qmmm))
sys.stderr.write('WARNING: \"fix qmmm\" style command(s) applied to selected atoms.\n'
' Please make sure that the fix group(s) are defined correctly.\n'
'######################################################\n')
assert(non_empty_output)
if mol_name != '':
sys.stdout.write('\n} # end of \"'+mol_name+'\" type definition\n')
#if non_empty_output and no_warnings:
if non_empty_output:
sys.stderr.write('WARNING: The '+g_program_name+' script has not been rigorously tested.\n'
' Exotic (many-body) pair-styles and pair-styles with\n'
' unusual syntax (such hbond/dreiding) are not understood\n'
' by '+g_program_name+' (...although they are supported by moltemplate).\n'
' Please look over the resulting LT file and check for errors.\n'
' Convert any remaining atom, bond, angle, dihedral, or improper id\n'
' or type numbers to the corresponding $ or @-style counter variables.\n'
' Feel free to report any bugs you find. (-Andrew Jewett 2015-8-02)\n')
except (ValueError, InputError) as err:
sys.stderr.write('\n'+str(err)+'\n')
sys.exit(-1)

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