tinkerparm2lt.py
f037f89f5f4dlammm-devel

tinkerparm2lt.py
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			#! /usr/bin/env python
			#
			# The purpose of this script is to create a moltemplate lt file for the opls.
			# and oplsaa forcefields.

			__author__ = 'Jason Lambert and Andrew Jewett'
			# (some additional corrections by Miguel Gonzalez, Yue Chun Chiu and others)
			__version__ = '0.1'
			__date__ = '2016-11-20'



			import sys
			import os
			from sets import Set
			from operator import itemgetter


			g_program_name = __file__.split('/')[-1]


			doc_msg = \
			"Typical Usage:\n\n" + \
			" "+g_program_name+" -name OPLS < oplsaa.prm > oplsaa.lt\n\n" + \
			" where \"oplsaa.prm\" is a force-field file downloaded from the TINKER website,\n" + \
			" \"oplsaa.lt\" is the corresponding file converted into moltemplate (.lt) format.\n" + \
			" and \"OPLS\" is the name that future moltemplate users will use to refer to\n" + \
			" this force-field (optional).\n" + \
			"Optional Arguments\n" + \
			" -name FORCEFIELDNAME # Give the force-field a name\n" + \
			" -file FILE_NAME # Read force field parameters from a file\n" + \
			" -url URL # Read force field parameters from a file on the web\n" + \
			" -atoms \"QUOTED LIST\" # Restrict output to a subset of atom types\n"




			def SplitQuotedString(string,
			quotes='\'\"',
			delimiters=' \t\r\f\n',
			escape='\\',
			comment_char='#'):
			tokens = []
			token = ''
			reading_token = True
			escaped_state = False
			quote_state = None
			for c in string:

			if (c in comment_char) and (not escaped_state) and (quote_state==None):
			tokens.append(token)
			return tokens

			elif (c in delimiters) and (not escaped_state) and (quote_state==None):
			if reading_token:
			tokens.append(token)
			token = ''
			reading_token = False

			elif c in escape:
			if escaped_state:
			token += c
			reading_token = True
			escaped_state = False
			else:
			escaped_state = True
			# and leave c (the '\' character) out of token
			elif (c in quotes) and (not escaped_state):
			if (quote_state != None):
			if (c == quote_state):
			quote_state = None
			else:
			quote_state = c
			token += c
			reading_token = True
			else:
			if (c == 'n') and (escaped_state == True):
			c = '\n'
			elif (c == 't') and (escaped_state == True):
			c = '\t'
			elif (c == 'r') and (escaped_state == True):
			c = '\r'
			elif (c == 'f') and (escaped_state == True):
			c = '\f'
			token += c
			reading_token = True
			escaped_state = False

			if len(string) > 0:
			tokens.append(token)
			return tokens




			def RemoveOuterQuotes(text, quotes='\"\''):
			if ((len(text)>=2) and (text[0] in quotes) and (text[-1]==text[0])):
			return text[1:-1]
			else:
			return text






			try:
			sys.stderr.write(g_program_name+", version "+__version__+", "+__date__+"\n")
			if sys.version < '2.6':
			raise Exception('Error: Using python '+sys.version+'\n'+
			' Alas, your version of python is too old.\n'
			' You must upgrade to a newer version of python (2.6 or later).')

			if sys.version < '2.7':
			from ordereddict import OrderedDict
			else:
			from collections import OrderedDict

			if sys.version > '3':
			import io
			else:
			import cStringIO


			# defaults:
			ffname = "TINKER_FORCE_FIELD"
			type_subset = Set([])
			filename_in = ""
			file_in = sys.stdin
			dihedral_style_name = "fourier"
			special_bonds_command = "special_bonds lj/coul 0.0 0.0 0.5"
			mixing_style = "geometric"
			contains_united_atoms = False

			argv = [arg for arg in sys.argv]

			i = 1

			while i < len(argv):

			#sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n')

			if argv[i] == '-atoms':
			if i+1 >= len(argv):
			raise Exception('Error: the \"'+argv[i]+'\" argument should be followed by a quoted string\n'
			' which contains a space-delimited list of of a subset of atom types\n'
			' you want to use from the original force-field.\n'
			' Make sure you enclose the entire list in quotes.\n');
			type_subset = Set(argv[i+1].strip('\"\'').strip().split())
			del argv[i:i+2]

			elif argv[i] == '-name':
			if i+1 >= len(argv):
			raise Exception('Error: '+argv[i]+' flag should be followed by the name of the force-field\n')
			ffname = argv[i+1]
			del argv[i:i+2]

			elif argv[i] in ('-file','-in-file'):
			if i+1 >= len(argv):
			raise Exception('Error: '+argv[i]+' flag should be followed by the name of a force-field file\n')
			filename_in = argv[i+1]
			try:
			file_in = open(filename_in, 'r')
			except IOError:
			sys.stderr.write('Error: Unable to open file\n'
			' \"'+filename_in+'\"\n'
			' for reading.\n')
			sys.exit(1)
			del argv[i:i+2]

			elif argv[i] == '-dihedral-style':
			if i+1 >= len(argv):
			raise Exception('Error: '+argv[i]+' flag should be followed by either \"opls\" or \"fourier\"\n')
			dihedral_style_name = argv[i+1]
			if dihedral_style_name not in ('fourier','opls'):
			raise Exception('Error: '+argv[i]+' '+dihedral_style_name+' not supported.\n')
			del argv[i:i+2]


			elif argv[i] in ('-url','-in-url'):
			import urllib2
			if i+1 >= len(argv):
			raise Exception('Error: '+argv[i]+' flag should be followed by the name of a force-field file.\n')
			url = argv[i+1]
			try:
			request = urllib2.Request(url)
			file_in = urllib2.urlopen(request)
			except urllib2.URLError:
			sys.stdout.write("Error: Unable to open link:\n"+url+"\n")
			sys.exit(1)
			del argv[i:i+2]

			elif argv[i] in ('-help','--help','-?','--?'):
			sys.stderr.write(doc_msg)
			sys.exit(0)
			del argv[i:i+1]

			else:
			i += 1

			if len(argv) != 1:
			raise Exception('Error: Unrecongized arguments: ' +' '.join(argv[1:]) +
			'\n\n'+ doc_msg)


			#sys.stderr.write("Reading parameter file...\n")


			lines = file_in.readlines()

			atom2charge = OrderedDict() # lookup charge from atom type
			atom2mass = OrderedDict() # lookup mass from atom type
			atom2vdw_e = OrderedDict() # lookup Lennard-Jones "epsilon" parameter
			atom2vdw_s = OrderedDict() # lookup Lennard-Jones "sigma" parameter
			atom2descr = OrderedDict()
			atom2ffid = OrderedDict() # lookup force-field-ID from atom type
			# force-field-ID is an id number/string used to assign
			# bonds, angles, dihedrals, and impropers.

			bonds_by_type = OrderedDict() # lookup bond parameters by force-field-ID
			angles_by_type = OrderedDict() # lookup angle parameters by force-field-ID
			dihedrals_by_type = OrderedDict() # lookup dihedral parameters by force-field-ID
			impropers_by_type = OrderedDict() # lookup improper parameters by force-field-ID
			lines_ureybrad = []
			lines_biotype = []


			for iline in range(0, len(lines)):
			line = lines[iline]
			tokens = SplitQuotedString(line.strip(),
			comment_char='#')

			if (len(tokens)>1) and (tokens[0] == 'atom'):
			tokens = map(RemoveOuterQuotes,
			SplitQuotedString(line.strip(),
			comment_char=''))
			if (len(tokens) > 6):
			if ((len(type_subset) == 0) or (tokens[1] in type_subset)):
			atom2ffid[tokens[1]] = tokens[2]
			#atom2mass[tokens[1]] = float(tokens[6])
			#Some atoms in oplsaa.prm have zero mass. Unfortunately this
			#causes LAMMPS to crash, even if these atoms are never used,
			#so I give the mass a non-zero value instead.
			atom2mass[tokens[1]] = max(float(tokens[6]), 1e-30)
			atom2descr[tokens[1]] = tokens[4]
			if tokens[4].find('(UA)') != -1:
			contains_united_atoms = True
			else:
			raise Exception('Error: Invalid atom line:\n'+line)
			elif (len(tokens) > 2) and (tokens[0] == 'charge'):
			if ((len(type_subset) == 0) or (tokens[1] in type_subset)):
			atom2charge[tokens[1]] = float(tokens[2])
			elif (len(tokens) > 3) and (tokens[0] == 'vdw'):
			if ((len(type_subset) == 0) or (tokens[1] in type_subset)):
			atom2vdw_e[tokens[1]] = float(tokens[3]) # "epsilon"
			atom2vdw_s[tokens[1]] = float(tokens[2]) # "sigma"
			elif (len(tokens) > 4) and (tokens[0] == 'bond'):
			k = float(tokens[3])
			r0 = float(tokens[4])
			bonds_by_type[tokens[1],tokens[2]] = (k, r0)
			elif (len(tokens) > 5) and (tokens[0] == 'angle'):
			k = float(tokens[4])
			angle0 = float(tokens[5])
			angles_by_type[tokens[1],tokens[2],tokens[3]] = (k, angle0)
			elif (len(tokens) > 11) and (tokens[0] == 'torsion'):
			if dihedral_style_name == 'fourier':
			# http://lammps.sandia.gov/doc/dihedral_fourier.html
			m = (len(tokens) - 5) / 3
			K = [0.0 for i in range(0,m)]
			n = [0.0 for i in range(0,m)]
			d = [0.0 for i in range(0,m)]
			for i in range(0,m):
			K[i] = float(tokens[5+3*i])
			d[i] = float(tokens[5+3*i+1])
			n[i] = float(tokens[5+3*i+2])
			dihedrals_by_type[tokens[1],tokens[2],tokens[3],tokens[4]]=(K,n,d)
			elif dihedral_style_name == 'opls':
			# http://lammps.sandia.gov/doc/dihedral_opls.html
			K1 = float(tokens[5])
			K2 = float(tokens[8])
			K3 = float(tokens[11])
			K4 = 0.0
			if len(tokens) > 14:
			K4 = float(tokens[14])
			if ((float(tokens[6]) != 0.0) or (float(tokens[7]) != 1.0) or
			(float(tokens[9]) not in (180.0,-180.0)) or (float(tokens[10]) != 2.0) or
			(float(tokens[12]) != 0.0) or (float(tokens[13]) != 3.0) or
			((K4 != 0.0) and
			((len(tokens) <= 16) or
			(float(tokens[15]) not in (180.0,-180.0)) or
			(float(tokens[16]) != 4.0)))):
			raise Exception("Error: This parameter file is incompatible with -dihedral-style \""+dihedral_style_name+"\"\n"+
			" (See line number "+str(iline+1)+" of parameter file.)\n")
			dihedrals_by_type[tokens[1],tokens[2],tokens[3],tokens[4]]=(K1,K2,K3,K4)
			else:
			assert(False)

			elif (len(tokens) > 7) and (tokens[0] == 'imptors'):
			k = float(tokens[5])
			angle0 = float(tokens[6])
			multiplicity = float(tokens[7])
			impropers_by_type[tokens[1],tokens[2],tokens[3],tokens[4]] = (k/multiplicity, angle0)
			elif ((len(tokens) > 0) and (tokens[0] == 'biotype')):
			# I'm not sure what to do with these, so I'll store them for now and
			# append them as comments to the .lt file generated by the program.
			lines_biotype.append(line.rstrip())
			elif ((len(tokens) > 0) and (tokens[0] == 'ureybrad')):
			# I'm not sure what to do with these, so I'll store them for now and
			# append them as comments to the .lt file generated by the program.
			lines_ureybrad.append(line.rstrip())
			elif ((len(tokens) > 1) and (tokens[0] == 'radiusrule')):
			if tokens[1] == 'GEOMETRIC':
			mixing_style = 'geometric'
			elif tokens[1] == 'ARITHMETIC':
			mixing_style = 'arithmetic'
			else:
			raise Exception("Error: Unrecognized mixing style: "+tokens[1]+", found here:\n" +
			line)
			elif ((len(tokens) > 1) and (tokens[0] == 'epsilonrule')):
			if tokens[1] != 'GEOMETRIC':
			raise Exception("Error: As of 2016-9-21, LAMMPS only supports GEOMETRIC mixing of energies\n" +
			" This force field simply cannot be used with LAMMPS in a general way.\n" +
			" One way around this is to manually change the \"epsilonrule\" back to\n" +
			" GEOMETRIC, and limit the number of atom types considered by this\n" +
			" program by using the -atoms \"LIST OF ATOMS\" argument,\n" +
			" to only include the atoms you care about, and then explicitly\n" +
			" define pair_coeffs for all possible pairs of these atom types.\n" +
			" If this is a popular force-field, then lobby the LAMMPS developers\n" +
			" to consider alternate mixing rules.\n\n" +
			"The offending line from the file is line number "+str(iline)+":\n" +
			line+"\n")

			except Exception as err:
			sys.stderr.write('\n\n'+str(err)+'\n')
			sys.exit(1)








			#sys.stderr.write(" done.\n")
			#sys.stderr.write("Converting to moltemplate format...\n")







			system_is_charged = False
			for atom_type in atom2charge:
			if atom2charge[atom_type] != 0.0:
			system_is_charged = True

			if system_is_charged:
			pair_style_name = "lj/cut/coul/long"
			pair_style_params = "10.0 10.0"
			kspace_style = " kspace_style pppm 0.0001\n"
			else:
			pair_style_name = "lj/cut"
			pair_style_params = "10.0"
			kspace_style = ""

			pair_style_command = " pair_style hybrid "+pair_style_name+" "+pair_style_params+"\n"

			bond_style_name = "harmonic"
			angle_style_name = "harmonic"
			improper_style_name = "harmonic"







			sys.stdout.write("# This file was generated automatically using:\n")
			sys.stdout.write("# "+g_program_name+" "+" ".join(sys.argv[1:])+"\n")
			if contains_united_atoms:
			sys.stdout.write("#\n"
			"# WARNING: Many of these atoms are probably UNITED-ATOM (UA) atoms.\n"
			"# The hydrogen atoms have been absorbed into the heavy atoms, and the\n"
			"# force-field modified accordingly. Do not mix with ordinary atoms.\n")
			sys.stdout.write("#\n"
			"# WARNING: The following 1-2, 1-3, and 1-4 weighting parameters were ASSUMED:\n")
			sys.stdout.write("# "+special_bonds_command+"\n")
			sys.stdout.write("# (See http://lammps.sandia.gov/doc/special_bonds.html for details)\n")
			if len(lines_ureybrad) > 0:
			sys.stdout.write("#\n"
			"# WARNING: All Urey-Bradley interactions have been IGNORED including:\n")
			sys.stdout.write("# ffid1 ffid2 ffid3 K r0\n# ")
			sys.stdout.write("\n# ".join(lines_ureybrad))
			sys.stdout.write("\n\n")
			sys.stdout.write("\n\n")
			sys.stdout.write(ffname+" {\n\n")


			sys.stdout.write(" write_once(\"In Charges\") {\n")
			for atype in atom2mass:
			assert(atype in atom2descr)
			sys.stdout.write(" set type @atom:" + atype + " charge " + str(atom2charge[atype]) +
			" # \"" + atom2descr[atype] + "\"\n")
			sys.stdout.write(" } #(end of atom partial charges)\n\n\n")


			sys.stdout.write(" write_once(\"Data Masses\") {\n")
			for atype in atom2mass:
			sys.stdout.write(" @atom:" + atype + " " + str(atom2mass[atype]) + "\n")
			sys.stdout.write(" } #(end of atom masses)\n\n\n")


			sys.stdout.write(" write_once(\"In Settings\") {\n")
			for atype in atom2vdw_e:
			assert(atype in atom2vdw_s)
			assert(atype in atom2ffid)

			sys.stdout.write(" pair_coeff " +
			"@atom:"+atype+"_b"+atom2ffid[atype]+"_a"+atom2ffid[atype]+"_d"+atom2ffid[atype]+"_i"+atom2ffid[atype]+" "
			"@atom:"+atype+"_b"+atom2ffid[atype]+"_a"+atom2ffid[atype]+"_d"+atom2ffid[atype]+"_i"+atom2ffid[atype]+" "+
			pair_style_name +
			" " + str(atom2vdw_e[atype]) +
			" " + str(atom2vdw_s[atype]) + "\n")
			sys.stdout.write(" } #(end of pair_coeffs)\n\n\n")



			sys.stdout.write(" # ------- force-field-IDs for bonded interaction lookup -------\n")
			sys.stdout.write(" # (First append the \"force-field-ID\" to the atom type name.\n")
			sys.stdout.write(" # Later use these expanded names for force-field lookup.)\n")
			for atype in atom2ffid:
			ffid = atype + "_ffid" + atom2ffid[atype]
			sys.stdout.write(" replace{ @atom:" + atype +
			" @atom:"+atype+"_b"+atom2ffid[atype]+"_a"+atom2ffid[atype]+"_d"+atom2ffid[atype]+"_i"+atom2ffid[atype]+" }\n")
			sys.stdout.write(" #(end of force-field-IDs)\n\n\n")



			sys.stdout.write(" write_once(\"In Settings\") {\n")
			for btype in bonds_by_type:
			ffid1 = btype[0] if btype[0] != "0" else "X"
			ffid2 = btype[1] if btype[1] != "0" else "X"
			(k,r0) = bonds_by_type[btype]
			sys.stdout.write(" bond_coeff @bond:" + ffid1 + "-" + ffid2 + " " +
			bond_style_name +" "+ str(k) + " " +str(r0) + "\n")
			sys.stdout.write(" } #(end of bond_coeffs)\n\n")

			sys.stdout.write(" write_once(\"Data Bonds By Type\") {\n")
			for btype in bonds_by_type:
			ffid1 = btype[0] if btype[0] != "0" else "X"
			ffid2 = btype[1] if btype[1] != "0" else "X"
			sys.stdout.write(" @bond:" + ffid1 + "-" + ffid2)
			ffid1 = "@atom:_b"+btype[0]+"_a_d_i" if btype[0] != "0" else "@atom:*"
			ffid2 = "@atom:_b"+btype[1]+"_a_d_i" if btype[1] != "0" else "@atom:*"
			sys.stdout.write(" " + ffid1 + " " + ffid2 + "\n")
			sys.stdout.write(" } #(end of bonds by type)\n\n\n")



			sys.stdout.write(" write_once(\"In Settings\") {\n")
			for atype in angles_by_type:
			ffid1 = atype[0] if atype[0] != "0" else "X"
			ffid2 = atype[1] if atype[1] != "0" else "X"
			ffid3 = atype[2] if atype[2] != "0" else "X"
			(k,angle0) = angles_by_type[atype]
			sys.stdout.write(" angle_coeff @angle:"+ffid1+"-"+ffid2+"-"+ffid3+" "+
			angle_style_name +" "+ str(k) + " " +str(angle0) + "\n")
			sys.stdout.write(" } #(end of angle_coeffs)\n\n")

			sys.stdout.write(" write_once(\"Data Angles By Type\") {\n")
			for atype in angles_by_type:
			ffid1 = atype[0] if atype[0] != "0" else "X"
			ffid2 = atype[1] if atype[1] != "0" else "X"
			ffid3 = atype[2] if atype[2] != "0" else "X"
			sys.stdout.write(" @angle:" + ffid1 + "-" + ffid2 + "-" + ffid3)
			ffid1 = "@atom:_b_a"+atype[0]+"_d_i" if atype[0] != "0" else "@atom:*"
			ffid2 = "@atom:_b_a"+atype[1]+"_d_i" if atype[1] != "0" else "@atom:*"
			ffid3 = "@atom:_b_a"+atype[2]+"_d_i" if atype[2] != "0" else "@atom:*"
			sys.stdout.write(" " + ffid1 + " " + ffid2 + " " + ffid3 + "\n")
			sys.stdout.write(" } #(end of angles by type)\n\n\n")



			sys.stdout.write(" write_once(\"In Settings\") {\n")
			for dtype in dihedrals_by_type:
			ffid1 = dtype[0] if dtype[0] != "0" else "X"
			ffid2 = dtype[1] if dtype[1] != "0" else "X"
			ffid3 = dtype[2] if dtype[2] != "0" else "X"
			ffid4 = dtype[3] if dtype[3] != "0" else "X"
			sys.stdout.write(" dihedral_coeff @dihedral:"+
			ffid1 + "-" + ffid2 + "-" + ffid3 + "-" + ffid4 + " " +
			dihedral_style_name +" ")
			if dihedral_style_name == 'fourier':
			# http://lammps.sandia.gov/doc/dihedral_fourier.html
			(K,n,d) = dihedrals_by_type[dtype]
			m = len(K)
			assert((m == len(n)) and (m == len(d)))
			sys.stdout.write(str(m))
			for i in range(0,m):
			sys.stdout.write(" " + str(K[i]) + " " + str(n[i]) + " " + str(d[i]))
			sys.stdout.write("\n")
			elif dihedral_style_name == 'opls':
			# http://lammps.sandia.gov/doc/dihedral_opls.html
			(K1,K2,K3,K4) = dihedrals_by_type[dtype]
			sys.stdout.write(str(K1) +" "+ str(K2) +" "+ str(K3) +" "+ str(K4)+"\n")
			else:
			assert(False)
			sys.stdout.write(" } #(end of dihedral_coeffs)\n\n")

			sys.stdout.write(" write_once(\"Data Dihedrals By Type\") {\n")
			for dtype in dihedrals_by_type:
			ffid1 = dtype[0] if dtype[0] != "0" else "X"
			ffid2 = dtype[1] if dtype[1] != "0" else "X"
			ffid3 = dtype[2] if dtype[2] != "0" else "X"
			ffid4 = dtype[3] if dtype[3] != "0" else "X"
			sys.stdout.write(" @dihedral:"+ffid1+"-"+ffid2+"-"+ffid3+"-"+ffid4)
			ffid1 = "@atom:_b_a_d"+dtype[0]+"_i" if dtype[0] != "0" else "@atom:*"
			ffid2 = "@atom:_b_a_d"+dtype[1]+"_i" if dtype[1] != "0" else "@atom:*"
			ffid3 = "@atom:_b_a_d"+dtype[2]+"_i" if dtype[2] != "0" else "@atom:*"
			ffid4 = "@atom:_b_a_d"+dtype[3]+"_i" if dtype[3] != "0" else "@atom:*"
			sys.stdout.write(" "+ffid1+" "+ffid2+" "+ffid3+" "+ffid4+"\n")
			sys.stdout.write(" } #(end of dihedrals by type)\n\n\n")



			sys.stdout.write(" write_once(\"In Settings\") {\n")
			for itype in impropers_by_type:
			ffid1 = itype[0] if itype[0] != "0" else "X"
			ffid2 = itype[1] if itype[1] != "0" else "X"
			ffid3 = itype[2] if itype[2] != "0" else "X"
			ffid4 = itype[3] if itype[3] != "0" else "X"
			(k,angle0) = impropers_by_type[itype]
			sys.stdout.write(" improper_coeff @improper:"+
			ffid1 + "-" + ffid2 + "-" + ffid3 + "-" + ffid4 + " " +
			improper_style_name +" "+ str(k) +" "+ str(angle0) +"\n")
			sys.stdout.write(" } #(end of improper_coeffs)\n\n")

			sys.stdout.write(" write_once(\"Data Impropers By Type (opls_imp.py)\") {\n")
			for itype in impropers_by_type:
			ffid1 = itype[0] if itype[0] != "0" else "X"
			ffid2 = itype[1] if itype[1] != "0" else "X"
			ffid3 = itype[2] if itype[2] != "0" else "X"
			ffid4 = itype[3] if itype[3] != "0" else "X"
			sys.stdout.write(" @improper:"+ffid1+"-"+ffid2+"-"+ffid3+"-"+ffid4)
			ffid1 = "@atom:_b_a_d_i"+itype[0] if itype[0] != "0" else "@atom:*"
			ffid2 = "@atom:_b_a_d_i"+itype[1] if itype[1] != "0" else "@atom:*"
			ffid3 = "@atom:_b_a_d_i"+itype[2] if itype[2] != "0" else "@atom:*"
			ffid4 = "@atom:_b_a_d_i"+itype[3] if itype[3] != "0" else "@atom:*"
			sys.stdout.write(" "+ffid1+" "+ffid2+" "+ffid3+" "+ffid4+"\n")
			sys.stdout.write(" } #(end of impropers by type)\n\n\n")

			sys.stdout.write(" # -------- (descriptive comment) --------\n")
			sys.stdout.write(" # ---- biologically relevant atom types: ----\n # ")
			sys.stdout.write("\n # ".join(lines_biotype))
			sys.stdout.write("\n # ---------- (end of comment) ----------\n")
			sys.stdout.write("\n\n")

			sys.stdout.write(" write_once(\"In Init\") {\n")
			sys.stdout.write(" units real\n")
			sys.stdout.write(" atom_style full\n")
			sys.stdout.write(" bond_style hybrid "+bond_style_name+"\n")
			sys.stdout.write(" angle_style hybrid "+angle_style_name+"\n")
			sys.stdout.write(" dihedral_style hybrid "+dihedral_style_name+"\n")
			sys.stdout.write(" improper_style hybrid "+improper_style_name+"\n")
			sys.stdout.write(pair_style_command)
			sys.stdout.write(" pair_modify mix "+mixing_style+"\n")
			sys.stdout.write(" "+special_bonds_command+"\n")
			sys.stdout.write(kspace_style)
			sys.stdout.write(" } #end of init parameters\n\n")

			sys.stdout.write("} # "+ffname+"\n\n")




			#sys.stderr.write(" done.\n")

			if filename_in != "":
			file_in.close()

lammps/tools/moltemplate/src/tinkerparm2lt.pyf037f89f5f4dlammm-devel

tinkerparm2lt.pyView Options

lammps/tools/moltemplate/src/tinkerparm2lt.py
f037f89f5f4dlammm-devel

tinkerparm2lt.py
View Options