def geodesic_ts_hess_irc_newtonnet(
reactant: Atoms,
product: Atoms,
calc_kwargs1: Dict[str, Any],
calc_kwargs2: Dict[str, Any],
logger: logging.Logger,
clean_up: bool = True,
) -> List[Dict[str, Any]]:
"""
Perform geodesic, transition state, and intrinsic reaction coordinate (IRC) calculations using NewtonNet.
Parameters
----------
reactant : Atoms
The reactant structure.
product : Atoms
The product structure.
calc_kwargs1 : dict
Keyword arguments for the ASE calculator for the geodesic and IRC jobs.
calc_kwargs2 : dict
Keyword arguments for the ASE calculator for the TS job with custom Hessian.
logger : logging.Logger
Logger for logging information.
clean_up : bool, optional
Whether to clean up raw files after completion, by default True.
Returns
-------
List[Dict[str, Any]]
List containing results from geodesic, TS, and IRC jobs.
"""
# Create NEB job
job1 = strip_decorator(geodesic_job)(reactant, product, calc_kwargs=calc_kwargs1)
logger.info("Created Geodesic job.")
# Create TS job with custom Hessian
job2 = strip_decorator(ts_job)(job1['highest_e_atoms'], use_custom_hessian=True, **calc_kwargs2)
logger.info("Created TS job with custom Hessian.")
# Create IRC job in forward direction
job3 = strip_decorator(irc_job)(job2['atoms'], direction='forward', **calc_kwargs1)
logger.info("Created IRC job in forward direction.")
# Create IRC job in reverse direction
job4 = strip_decorator(irc_job)(job2['atoms'], direction='reverse', **calc_kwargs1)
logger.info("Created IRC job in reverse direction.")
logger.info("All jobs executed successfully.")
if clean_up:
# Delete the raw files
directory_patterns = ["quacc-*", "tmp*"]
# Delete directories matching patterns
for pattern in directory_patterns:
for dir_path in glob.glob(pattern):
if os.path.isdir(dir_path):
shutil.rmtree(dir_path)
return [job1, job2, job3, job4]