def main(argv):
args = process_command_line(argv)
min_dic = {}
for_dic = {}
with open(args.catalyst, 'rb') as f:
catalyst_txt = f.read()
OH_down_catalyst = make_OH_down_catalyst(catalyst_txt)
for mol in args.molecule:
name = fileutil.get_filename(mol) + '+' + fileutil.get_filename(
os.path.basename(args.catalyst)) + '_' + args.solvent
if fileutil.remove_path(mol) in OH_DOWN:
pymol = create_molecule_with_cat(mol, args.format, args.mult,
OH_down_catalyst, name,
args.localopt, args.no_opt)
else:
pymol = create_molecule_with_cat(mol, args.format, args.mult,
catalyst_txt, name, args.localopt,
args.no_opt)
if 'min' in mol:
mol_type = os.path.basename(mol).split('_min')[0]
min_dic[mol_type] = pymol, name
if 'for' in mol:
mol_type = os.path.basename(mol).split('for_')[1].split('_TS')[0]
for_dic[mol_type] = pymol, name
write_input_files(min_dic, for_dic, args)
def main(argv):
args = process_command_line(argv)
output_dir = os.path.realpath(args.output_dir)
for mol in args.input:
name = fileutil.get_filename(mol) + '_' + args.solvent
if 'TS' in mol:
handle_TS(args, mol, name, output_dir)
else:
handle_normal(args, mol, name, output_dir)
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 main(argv):
args = process_command_line(argv)
cwd = os.getcwd()
for molec in args.input:
name = fileutil.get_filename(molec)
if molec[-4:] == ".com":
move_to_home(molec, args)
else:
print "Molecule " + molec + " doesn't have .com extension and will be ignored."
write_script_and_start_calculation(name, cwd, args)
with open(START_CALCS_LOG, 'ab') as f:
f.write(name + ';' + cwd + ';' + get_datetime() + '\n')
def handle_normal(mol_lst, args):
""" Writes replaced input files"""
inp = gaussian.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 = atom_replace(inp.descript, args)
inp.geom = atom_replace(inp.geom, args)
inp.add_custom_basis_from_dic(CUSTOM_BASIS_LOCATION)
with open(new_mol_name, 'wb') as f:
inp.write(f)
def handle_TS(mol_name, args):
"""Accepts path to gaussian input TS molecule."""
with open(mol_name, 'rb') as f:
input = gaussian.Input()
input.provide_existing_input_file(f.read())
new_name = fileutil.add_to_name_but_keep_ext(mol_name, args.name)
input.set_chk(fileutil.get_filename(new_name))
if args.kwards:
kwrds = args.kwards
else:
kwrds = TS_KWRDS.format(args.solvent)
if args.ECP:
kwrds += ' pseudo=read'
input.set_kwards(kwrds)
input.add_custom_basis_from_dic(args.basis)
with open(os.path.realpath(args.dir) + '/' + new_name, 'wb') as f:
input.write(f)
def create_new_normal_input(mol, args, name):
"""Returns new input file."""
inp = gaussian.Input()
with open(mol, 'rb') as f:
inp.provide_existing_input_file(f.read())
inp.kwards = replace(args, inp.kwards)
if 'chkbas' not in inp.kwards:
inp.kwards += " chkbas"
if "geom=allcheck" not in inp.kwards:
inp.kwards += " geom=allcheck"
inp.kwards = stringutil.case_insensitive_replace(inp.kwards, ' gen ',
' genchk ')
inp.set_chk(fileutil.get_filename(name))
inp.set_geometry('')
inp.set_charge('')
inp.set_mult('')
inp.custom_basis = ''
print inp.kwards
return inp.write()
def main(argv):
args = process_command_line(argv)
cwd = os.getcwd()
for molec in args.input:
name = fileutil.get_filename(molec)
if molec[-4:] == ".com":
shutil.copy(molec, args.folder)
#Check point file copying
if args.chk:
shutil.copy(args.chk, args.folder)
try:
shutil.copy(molec[:-4] + ".chk", args.folder)
except IOError:
pass
else:
print "Molecule " + molec + " doesn't have .com extension and will be ignored."
exec_script = EXEC_SCRIPT.format(args.folder, name, cwd)
f = open(args.folder + name, "wb")
f.write(exec_script)
f.close()
subprocess.call(["qsub", f.name])
def handle_mol(mol_name, args):
"""Accepts path to mol."""
if args.format != 'gau':
pymol = pybel.readfile(args.format, mol_name).next()
mol_txt = pymol.write('gau')
else:
with open(mol_name, 'rb') as f:
mol_txt = f.read()
mol_name_sans_ext = fileutil.get_filename(mol_name)
new_name = mol_name_sans_ext + args.suffix
std_input = gaussian.Input()
std_input.provide_existing_input_file(mol_txt)
std_input.set_chk(new_name)
std_input.set_proc(args.proc)
std_input.set_memory(args.memory)
std_input.set_charge(1)
kwards = create_kwards(pymol, args)
std_input.set_kwards(kwards)
#std_input.add_custom_basis_from_dic(BASIS[args.basis])
with open(new_name + '.com', 'wb') as f:
std_input.write(f)
def handle_mol(mol_name, args):
"""Accepts path to mol."""
if args.format != 'gau':
pymol = pybel.readfile(args.format, mol_name).next()
mol_txt = pymol.write('gau')
else:
with open(mol_name, 'rb') as f:
mol_txt = f.read()
mol_name_sans_ext = fileutil.get_filename(mol_name)
new_name = mol_name_sans_ext + args.name
std_input = gaussian.Input()
std_input.provide_existing_input_file(mol_txt)
std_input.set_chk(new_name)
if args.kwards:
kwrds = args.kwards
else:
kwrds = DEFAULT_KWRDS.format(args.solvent)
if args.ECP:
kwrds += ' pseudo=read'
std_input.set_kwards(kwrds)
std_input.add_custom_basis_from_dic(args.basis)
with open(os.path.realpath(args.dir) + '/' + new_name + '.com', 'wb') as f:
std_input.write(f)
def provide_pymol(self, pymol):
"""Class will use pymol to extract chkpoint name, multiplicity, charge and geometry."""
self.set_chk(fileutil.get_filename(pymol.title))
gaus_str = pymol.write('gau')
gaus_lst = gaus_str.split('\n\n')
self.provide_chrg_mult_geom(gaus_lst[2])
