def is_complete(self, output_file: Path) -> bool:
"""
Determines if the given output file completed successfully.
:param output_file: a Path object pointing to the output file
:return: True if successful, False otherwise
:raises AttributeError: if this method doesn't support the current step program
"""
output_filepath = Path(output_file).resolve()
if self.step_program == "gaussian16":
num_matches = len(
find_string(output_filepath, "Normal termination"))
opt_freq = sum([
self.current_step_config["opt"],
self.current_step_config["freq"]
])
if opt_freq > 0:
return num_matches == opt_freq
elif self.current_step_config["single_point"]:
return num_matches == 1
elif self.step_program == "gamess":
num_matches = len(
find_string(output_filepath, "GAMESS TERMINATED NORMALLY"))
return num_matches == sum([self.current_step_config["opt"]])
else:
raise AttributeError("Unknown program: {}".format(
self.step_program))
def needs_restart(self):
normal_t_count = len(find_string(self.output_file, "Normal termination"))
if "opt" in self.route and "freq" in self.route:
return normal_t_count < 2
elif "opt" in self.route or "freq" in self.route or "# Restart" in self.route:
return normal_t_count < 1
return False
def get_route(input_file: Path) -> str:
"""
:return:
"""
matches = find_string(input_file, "#")
if len(matches) == 0:
raise AttributeError("Unable to find route in input file: {}".format(input_file))
else:
return matches[0].strip()
def get_energy(output_file: str, format: str, excited_state: bool = False) -> float:
"""
Returns the energy from the given output file in units of electronvolts (eV).
:param output_file: the path to the output file
:param format: the format of the output file
:param excited_state: whether to extract excited state energy
:return: an energy in eV
"""
if format == "gaussian16":
energy_line = find_string(Path(output_file).resolve(), "SCF Done")[-1]
energy = float(energy_line.split("A.U.")[0].split()[-1]) * 27.2113246
elif format == "gamess":
raise NotImplementedError("GAMESS get_energy not implemented")
else:
raise AttributeError("Unable to obtain energy from file format '{}'".format(format))
return energy
def get_new_route(self):
if not self.output_file.exists():
return None
if self.needs_restart() and not self.error_fail():
self.clear_gau_files()
normal_t_count = len(find_string(self.output_file, "Normal termination"))
if "opt" in self.route and "freq" in self.route:
if normal_t_count == 1:
return self.restart_freq()
elif normal_t_count == 0:
return self.restart_opt()
elif "opt" in self.route:
return self.restart_opt()
elif "freq" in self.route:
return self.restart_freq()
elif self.convergence_fail() or self.formbx_fail() or self.link_9999_fail():
self.clear_gau_files()
return self.restart_opt(additional_opt_options=["recalcfc=4"])
def formbx_fail(self):
return len(find_string(self.output_file, "FormBX had a problem.")) > 0
def convergence_fail(self):
return len(find_string(self.output_file, "Convergence failure -- run terminated.")) > 0
def link_9999_fail(self):
return len(find_string(self.output_file, "Error termination request processed by link 9999.")) > 0
def error_fail(self):
return len(find_string(self.output_file, "Error termination")) > 0
def get_scf_energies(self):
scf_energies = find_string(self.output_file, "SCF Done:")
energies = [float(line.split("=")[1].split('A.U.')[0].strip()) for line in scf_energies]
return energies