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)