def create_new_TS_input(mol, args, name):
"""Returns new input file with right kwards."""
TS_inp = gaussian.TS_input()
with open(mol, 'rb') as f:
TS_inp.provide_existing_input_file(f.read())
TS_inp.kwards = replace(args, TS_inp.kwards)
TS_inp.set_chk(fileutil.get_filename(name))
print TS_inp.kwards
return TS_inp.write()
def handle_TS(mol_lst, args):
""" Writes replaced TS input files"""
inp = gaussian.TS_input()
for mol in mol_lst:
with open(mol, 'rb') as f:
old_input = f.read()
new_mol_name = atom_replace(mol, args)
inp.provide_existing_input_file(old_input)
inp.set_chk(fileutil.get_filename(new_mol_name))
inp.descript[0] = atom_replace(inp.descript[0], args)
inp.descript[1] = atom_replace(inp.descript[1], args)
inp.geom[0] = atom_replace(inp.geom[0], args)
inp.geom[1] = atom_replace(inp.geom[1], args)
inp.add_custom_basis_from_dic(CUSTOM_BASIS_LOCATION)
with open(new_mol_name, 'wb') as f:
inp.write(f)
def handle_TS(args, mol, name, output_dir):
input_ = gaussian.TS_input()
with open(mol, 'rb') as f:
input_txt = f.read()
input_.provide_existing_input_file(input_txt)
if args.kwards:
kwards = args.kwards
else:
kwards = TS_KWRDS.format(args.solvent)
if args.ECP:
kwards += ' pseudo=read'
input_.set_kwards(kwards)
descrip = input_.descript[0] + ' ' + args.descrip.format(args.solvent)
input_.set_description(descrip, 1)
input_.set_chk(name)
with open(output_dir + '/' + name + '.com', 'wb') as f:
input_.write(f)
def write_gau_TS_file(folder_name, pypair, name, ts_kwards, args):
"""Writes gaussian input TS file"""
inp = gaussian.TS_input()
inp.provide_pymol(pypair[0], 1)
inp.provide_pymol(pypair[1], 2)
inp.set_proc(args.proc)
inp.set_memory(args.memory)
inp.set_chk(name)
inp.set_kwards(ts_kwards)
inp.set_description(name, 1)
inp.set_description(name, 2)
inp.set_charge(args.charge, 1)
inp.set_charge(args.charge, 2)
inp.set_mult(args.mult, 1)
inp.set_mult(args.mult, 2)
inp.add_custom_basis_from_dic(BASIS[args.basis])
with open(folder_name + '/' + name + '.com', 'wb') as f:
inp.write(f)
def write_TS_mol(pymol1, pymol2, args, name):
inp = gaussian.TS_input()
inp.provide_pymol(pymol1, 1)
inp.provide_pymol(pymol2, 2)
inp.set_proc(8)
inp.set_memory(4000)
inp.set_chk(name)
kwards = TS_KWRDS.format(args.solvent)
if args.ECP:
kwards += ' pseudo=read'
inp.set_kwards(kwards)
inp.set_description(name, 1)
inp.set_description(name, 2)
inp.set_charge('0', 1)
inp.set_charge('0', 2)
inp.set_mult(args.mult, 1)
inp.set_mult(args.mult, 2)
inp.add_custom_basis_from_dic(args.basis)
with open(name + '.com', 'wb') as f:
inp.write(f)
def write_gau_file(pypair, name, args):
"""Writes gaussian input TS file"""
inp = gaussian.TS_input()
inp.provide_pymol(pypair[0], 1)
inp.provide_pymol(pypair[1], 2)
inp.set_proc(args.proc)
inp.set_memory(4000)
inp.set_chk(name)
kwards = TS_KWRDS.format(args.solvent)
if gaussian.is_ECP(args.catalyst[:-1]):
kwards += ' pseudo=read'
inp.set_kwards(kwards)
inp.set_description(name, 1)
inp.set_description(name, 2)
inp.set_charge(args.charge, 1)
inp.set_charge(args.charge, 2)
inp.set_mult(args.mult, 1)
inp.set_mult(args.mult, 2)
inp.add_custom_basis_from_dic(DEFAULT_BASIS)
with open(name + '.com', 'wb') as f:
inp.write(f)