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Only process #653

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3bbe5f7
Added only_process to main and Scheduler
alongd May 10, 2023
403e414
Extended error type exceptions when saving thermo/transport libraries
alongd May 10, 2023
f8fe2cc
Save a species adjlist if given as an attribute of Species
alongd May 14, 2023
0de8145
Use the species adjlist if given when saving it in RMG libs
alongd May 10, 2023
c3d61c3
Tests: adjlist in Species dict
alongd May 14, 2023
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7 changes: 7 additions & 0 deletions arc/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -155,6 +155,7 @@
Only used for restarting.
running_jobs (dict, optional): A dictionary of jobs submitted in a precious ARC instance, used for restarting.
ts_adapters (list, optional): Entries represent different TS adapters.
only_process (bool, optional): Whether to only run statmech and process runs from a (restart) input file.

Attributes:
project (str): The project's name. Used for naming the working directory.
Expand Down Expand Up @@ -221,6 +222,7 @@
format (``True``) or classical two-parameter Arrhenius equation format (``False``).
trsh_ess_jobs (bool): Whether to attempt troubleshooting failed ESS jobs. Default is ``True``.
ts_adapters (list): Entries represent different TS adapters.
only_process (bool): Whether to only run statmech and process runs from a (restart) input file.
"""

def __init__(self,
Expand Down Expand Up @@ -249,6 +251,7 @@
level_of_theory: str = '',
max_job_time: Optional[float] = None,
n_confs: int = 10,
only_process: bool = False,
opt_level: Optional[Union[str, dict, Level]] = None,
orbitals_level: Optional[Union[str, dict, Level]] = None,
output: Optional[dict] = None,
Expand Down Expand Up @@ -323,6 +326,7 @@
for ts_adapter in self.ts_adapters or list():
if ts_adapter.lower() not in _registered_job_adapters.keys():
raise InputError(f'Unknown TS adapter: "{ts_adapter}"')
self.only_process = only_process

# attributes related to level of theory specifications
self.level_of_theory = level_of_theory
Expand Down Expand Up @@ -475,6 +479,8 @@
restart_dict['dont_gen_confs'] = self.dont_gen_confs
if self.ts_adapters:
restart_dict['ts_adapters'] = self.ts_adapters
if self.only_process:
restart_dict['only_process'] = self.only_process

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restart_dict['e_confs'] = self.e_confs
restart_dict['ess_settings'] = self.ess_settings
if self.freq_level is not None:
Expand Down Expand Up @@ -592,6 +598,7 @@
trsh_ess_jobs=self.trsh_ess_jobs,
fine_only=self.fine_only,
ts_adapters=self.ts_adapters,
only_process=self.only_process,
)

save_yaml_file(path=os.path.join(self.project_directory, 'output', 'status.yml'), content=self.scheduler.output)
Expand Down
8 changes: 4 additions & 4 deletions arc/plotter.py
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Expand Up @@ -777,11 +777,11 @@
try:
thermo_library.load_entry(index=i,
label=spc.label,
molecule=spc.mol_list[0].copy(deep=True).to_adjacency_list(),
molecule=spc.adjlist or spc.mol_list[0].copy(deep=True).to_adjacency_list(),
thermo=spc.thermo,
shortDesc=spc.thermo.comment,
longDesc=spc.long_thermo_description)
except (InvalidAdjacencyListError, DatabaseError, ValueError) as e:
except (InvalidAdjacencyListError, DatabaseError, ValueError, TypeError) as e:

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logger.error(f'Could not save species {spc.label} in the thermo library, got:')
logger.info(e)
else:
Expand All @@ -806,11 +806,11 @@
try:
transport_library.load_entry(index=i,
label=spc.label,
molecule=spc.mol_list[0].copy(deep=True).to_adjacency_list(),
molecule=spc.adjlist or spc.mol_list[0].copy(deep=True).to_adjacency_list(),
transport=spc.transport_data,
shortDesc=spc.thermo.comment,
longDesc=description)
except (InvalidAdjacencyListError, ValueError) as e:
except (InvalidAdjacencyListError, DatabaseError, ValueError, TypeError) as e:

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logger.error(f'Could not save species {spc.label} in the transport library, got:')
logger.info(e)
logger.info(f'\n\nTransport properties for {spc.label}:')
Expand Down
34 changes: 24 additions & 10 deletions arc/reaction_test.py
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Expand Up @@ -121,20 +121,22 @@ def setUpClass(cls):
r_species=[ARCSpecies(label='NH2', smiles='[NH2]'),
ARCSpecies(label='N2H3', smiles='N[NH]')],
p_species=[ARCSpecies(label='NH3', smiles='N'),
ARCSpecies(label='H2NN(S)', adjlist="""multiplicity 1
1 N u0 p0 c+1 {2,D} {3,S} {4,S}
2 N u0 p2 c-1 {1,D}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}""")])
ARCSpecies(label='H2NN(S)',
adjlist="""multiplicity 1
1 N u0 p0 c+1 {2,D} {3,S} {4,S}
2 N u0 p2 c-1 {1,D}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}""")])
cls.rxn7 = ARCReaction(reactants=['NH2', 'N2H3'], products=['NH3', 'H2NN(T)'],
r_species=[ARCSpecies(label='NH2', smiles='[NH2]'),
ARCSpecies(label='N2H3', smiles='N[NH]')],
p_species=[ARCSpecies(label='NH3', smiles='N'),
ARCSpecies(label='H2NN(T)', adjlist="""multiplicity 3
1 N u0 p1 c0 {2,S} {3,S} {4,S}
2 N u2 p1 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}""")])
ARCSpecies(label='H2NN(T)',
adjlist="""multiplicity 3
1 N u0 p1 c0 {2,S} {3,S} {4,S}
2 N u2 p1 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}""")])
cls.rxn8 = ARCReaction(r_species=[ARCSpecies(label='CH4', smiles='C', xyz=cls.ch4_xyz),
ARCSpecies(label='OH', smiles='[OH]', xyz=cls.oh_xyz)],
p_species=[ARCSpecies(label='CH3', smiles='[CH3]', xyz=cls.ch3_xyz),
Expand Down Expand Up @@ -278,6 +280,11 @@ def test_as_dict(self):
'multiplicity': 1,
'number_of_rotors': 0},
{'arkane_file': None,
'adjlist': """multiplicity 1
1 N u0 p0 c+1 {2,D} {3,S} {4,S}
2 N u0 p2 c-1 {1,D}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}""",
'bond_corrections': {'H-N': 2, 'N=N': 1},
'charge': 0,
'cheap_conformer': 'N -0.08201544 0.01567102 0.28740725\n'
Expand Down Expand Up @@ -341,6 +348,13 @@ def test_as_dict(self):
'ts_xyz_guess': []}
self.assertEqual(rxn_dict_6, expected_dict_6)

rxn_7_dict = self.rxn7.as_dict()
self.assertEqual(rxn_7_dict['p_species'][1]['adjlist'], """multiplicity 3
1 N u0 p1 c0 {2,S} {3,S} {4,S}
2 N u2 p1 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}""")

def test_from_dict(self):
"""Test ARCReaction.from_dict()"""
rxn_dict = self.rxn1.as_dict()
Expand Down
8 changes: 6 additions & 2 deletions arc/scheduler.py
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Expand Up @@ -160,6 +160,7 @@
freq_scale_factor (float, optional): The harmonic frequencies scaling factor.
trsh_ess_jobs (bool, optional): Whether to attempt troubleshooting failed ESS jobs. Default is ``True``.
ts_adapters (list, optional): Entries represent different TS adapters.
only_process (bool, optional): Whether to only run statmech and process runs from a (restart) input file.

Attributes:
project (str): The project's name. Used for naming the working directory.
Expand Down Expand Up @@ -248,6 +249,7 @@
kinetics_adapter: str = 'arkane',
freq_scale_factor: float = 1.0,
ts_adapters: List[str] = None,
only_process: bool = False,
) -> None:

self.project = project
Expand Down Expand Up @@ -409,7 +411,9 @@
species.initial_xyz = species.conformers[0]
if species.label not in self.running_jobs:
self.running_jobs[species.label] = list() # initialize before running the first job
if species.is_monoatomic():
if only_process:
pass

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elif species.is_monoatomic():
if not self.output[species.label]['job_types']['sp'] \
and not self.output[species.label]['job_types']['composite'] \
and 'sp' not in list(self.job_dict[species.label].keys()) \
Expand Down Expand Up @@ -485,7 +489,7 @@
species.ts_conf_spawned = True
self.save_restart = True
self.timer = True
if not self.testing:
if not self.testing and not only_process:
self.schedule_jobs()

def schedule_jobs(self):
Expand Down
4 changes: 4 additions & 0 deletions arc/species/species.py
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Expand Up @@ -342,6 +342,7 @@ def __init__(self,
self._radius = None
self.mol = mol
self.mol_list = None
self.adjlist = adjlist
self.multiplicity = multiplicity
self.number_of_radicals = number_of_radicals
self.external_symmetry = external_symmetry
Expand Down Expand Up @@ -642,6 +643,8 @@ def as_dict(self,
species_dict['number_of_rotors'] = self.number_of_rotors
if self.external_symmetry is not None:
species_dict['external_symmetry'] = self.external_symmetry
if self.adjlist:
species_dict['adjlist'] = self.adjlist
if self.irc_label is not None:
species_dict['irc_label'] = self.irc_label
if self.optical_isomers is not None:
Expand Down Expand Up @@ -783,6 +786,7 @@ def from_dict(self, species_dict):
self.is_ts = species_dict['is_ts'] if 'is_ts' in species_dict else False
self.ts_conf_spawned = species_dict['ts_conf_spawned'] if 'ts_conf_spawned' in species_dict \
else False if self.is_ts else None
self.adjlist = species_dict['adjlist'] if 'adjlist' in species_dict else None
if self.is_ts:
self.ts_number = species_dict['ts_number'] if 'ts_number' in species_dict else None
self.ts_guesses_exhausted = species_dict['ts_guesses_exhausted'] if 'ts_guesses_exhausted' in species_dict else False
Expand Down