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Minor: Updated docstrings in Scheduler
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And some updates in Job
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@alongd
alongd committed Aug 5, 2019
1 parent 6b4c635 commit 146bca0
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Showing 2 changed files with 156 additions and 31 deletions.
32 changes: 16 additions & 16 deletions arc/job/job.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,18 +46,18 @@ class Job(object):
software (str, optional): The electronic structure software to be used.
is_ts (bool, optional): Whether this species represents a transition structure.
scan (list, optional): A list representing atom labels for the dihedral scan
(e.g., "2 1 3 5" as a string or [2, 1, 3, 5] as a list of integers).
(e.g., "2 1 3 5" as a string or [2, 1, 3, 5] as a list of integers).
pivots (list, optional): The rotor scan pivots, if the job type is scan. Not used directly in these methods,
but used to identify the rotor.
but used to identify the rotor.
memory (int, optional): The total job allocated memory in GB.
comments (str, optional): Job comments (archived, not used).
trsh (str, optional): A troubleshooting keyword to be used in input files.
scan_trsh (str, optional): A troubleshooting method for rotor scans.
ess_trsh_methods (list, optional): A list of troubleshooting methods already tried out for ESS convergence.
bath_gas (str, optional): A bath gas. Currently used in OneDMin to calc L-J parameters.
Allowed values are He, Ne, Ar, Kr, H2, N2, O2
Allowed values are He, Ne, Ar, Kr, H2, N2, O2
initial_trsh (dict, optional): Troubleshooting methods to try by default. Keys are ESS software,
values are trshs.
values are trshs.
job_num (int, optional): Used as the entry number in the database, as well as the job name on the server.
job_server_name (str, optional): Job's name on the server (e.g., 'a103').
job_name (str, optional): Job's name for internal usage (e.g., 'opt_a103').
Expand All @@ -69,9 +69,9 @@ class Job(object):
scan_res (int, optional): The rotor scan resolution in degrees.
checkfile (str, optional): The path to a previous Gaussian checkfile to be used in the current job.
number_of_radicals (int, optional): The number of radicals (inputted by the user, ARC won't attempt to
determine it). Defaults to None. Important, e.g., if a Species is a bi-rad
singlet, in which case the job should be unrestricted with
multiplicity = 1.
determine it). Defaults to None. Important, e.g., if a Species is a bi-rad
singlet, in which case the job should be unrestricted with
multiplicity = 1.
conformers (str, optional): A path to the YAML file conformer coordinates for a Gromacs MD job.
radius (float, optional): The species radius in Angstrom.
testing (bool, optional): Whether the object is generated for testing purposes, True if it is.
Expand All @@ -83,8 +83,8 @@ class Job(object):
charge (int): The species net charge. Default is 0.
multiplicity (int): The species multiplicity.
number_of_radicals (int): The number of radicals (inputted by the user, ARC won't attempt to determine it).
Defaults to None. Important, e.g., if a Species is a bi-rad singlet, in which case
the job should be unrestricted with multiplicity = 1.
Defaults to None. Important, e.g., if a Species is a bi-rad singlet, in which case
the job should be unrestricted with multiplicity = 1.
spin (int): The spin. automatically derived from the multiplicity.
xyz (str): The xyz geometry. Used for the calculation.
radius (float): The species radius in Angstrom.
Expand All @@ -95,9 +95,9 @@ class Job(object):
level_of_theory (str): Level of theory, e.g. 'CBS-QB3', 'CCSD(T)-F12a/aug-cc-pVTZ', 'B3LYP/6-311++G(3df,3pd)'...
job_type (str): The job's type.
scan (list): A list representing atom labels for the dihedral scan
(e.g., "2 1 3 5" as a string or [2, 1, 3, 5] as a list of integers).
(e.g., "2 1 3 5" as a string or [2, 1, 3, 5] as a list of integers).
pivots (list): The rotor scan pivots, if the job type is scan. Not used directly in these methods,
but used to identify the rotor.
but used to identify the rotor.
scan_res (int): The rotor scan resolution in degrees.
software (str): The electronic structure software to be used.
server_nodes (list): A list of nodes this job was submitted to (for troubleshooting).
Expand All @@ -112,10 +112,10 @@ class Job(object):
final_time (datetime): The date-time this job was initiated.
run_time (timedelta): Job execution time.
job_status (list): The job's server and ESS statuses.
The job server status is in job.job_status[0] and can be either 'initializing' / 'running'
/ 'errored' / 'done'. The job ess (electronic structure software calculation) status is in
job.job_status[1] and can be either `initializing` / `running` / `errored:
{error type / message}` / `unconverged` / `done`.
The job server status is in job.job_status[0] and can be either 'initializing' / 'running'
/ 'errored' / 'done'. The job ess (electronic structure software calculation) status is in
job.job_status[1] and can be either `initializing` / `running` / `errored:
{error type / message}` / `unconverged` / `done`.
job_server_name (str): Job's name on the server (e.g., 'a103').
job_name (str): Job's name for internal usage (e.g., 'opt_a103').
job_id (int): The job's ID determined by the server.
Expand All @@ -138,7 +138,7 @@ class Job(object):
project_directory (str): The path to the project directory.
max_job_time (int): The maximal allowed job time on the server in hours.
bath_gas (str): A bath gas. Currently used in OneDMin to calc L-J parameters.
Allowed values are He, Ne, Ar, Kr, H2, N2, O2
Allowed values are He, Ne, Ar, Kr, H2, N2, O2
"""
def __init__(self, project, ess_settings, species_name, xyz, job_type, level_of_theory, multiplicity,
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