optoelectronics_driver.py Command Help
Command: $SCHRODINGER/run optoelectronics_gui_dir/optoelectronics_driver.py
usage: $SCHRODINGER/run optoelectronics_gui_dir/optoelectronics_driver.py
[-h] [-mode MODE] [-properties PROPERTY [PROPERTY ...]]
[-koopmans POTENTIALS] [-oxidation_electrode_potential POTENTIAL_(V)]
[-reduction_electrode_potential POTENTIAL_(V)] [-cpus CPUs_PER_JOB]
[-tadf_gap_method METHOD] [-TPP THREADS] [-name JOBNAME]
[-nocheckpoint] [-settings PATH] [-write_settings PATH]
[-use_zip_data PATH] [-restart_proj PROJECT_NAME]
[-restart_disp INCORPORATION] [-restart_viewname VIEWNAME]
[-restart_host HOSTNAME:PROCESSORS] [-restart_jobname JOBNAME]
[-keywords KEYWORD=VALUE KEYWORD=VALUE ... [KEYWORD=VALUE KEYWORD=VALUE ... ...]]
[-triplet_slope SLOPE] [-triplet_intercept INTERCEPT]
[-oxidation_slope SLOPE] [-oxidation_intercept INTERCEPT]
[-oxidation_solvent_keywords [KEYWORD=VALUE KEYWORD=VALUE ... ...]]
[-reduction_slope SLOPE] [-reduction_intercept INTERCEPT]
[-reduction_solvent_keywords [KEYWORD=VALUE KEYWORD=VALUE ... ...]]
[-tddft_approximation APPROXIMATION] [-singlet_idxs 0,1,2,3,,...]
[-triplet_idxs 1,2,3,,...] [-compress_subjobs] [-HOST <hostname>]
[input_file] [output_file]
This is the driver script to run one or more optoelectronics jobs. For each
molecule, a Workflow object is established. The jobs the Workflow will run
depend on the options chosen. Some jobs depend on other jobs to finish before
starting. It is the job of the Workflow to submit jobs when all the required
dependencies have finished successfully. An internal JobDJ queue is
established that the Workflow objects submit jobs to. Actually running jobs
when processors become available is the job of the queue. Copyright
Schrodinger, LLC. All rights reserved.
positional arguments:
input_file Input file. (default: None)
output_file Output file. This file will contain structures with
the computed properties. (default: None)
options:
-h, -help Show this help message and exit.
-mode MODE Calculation mode. By default, "screening" uses a fast
QM calculation with post-QM empirical parameters for
redox potentials and triplet energies that have been
determined by comparing to experimental data. Also by
default, "custom1" uses a reasonable set of QM
parameters and no post-QM parameters. "custom2" has no
default settings. Parameters for all three methods can
be viewed and set using the GUI Advanced Options.
(default: None)
-properties PROPERTY [PROPERTY ...]
Properties to calculate. "oxidation" is oxidation
potential, "reduction" is reduction potential, "hole"
is hole reorganization energy, "electron" is electron
reorganization energy, "triplet" is triplet energy,
"triplet_reorg" is the triplet reorganization energy,
"spectrum" is absorption spectrum, "s1_t1_gap" is the
energy gap between T1 and S1, "fluorescence" is the
fluorescent emission spectrum, "isc_reorg" is the ISC
(inter-system crossing) reorganization energy, and
"risc_reorg" is the RISC (reverse inter-system
crossing) reorganization energy. Properties should be
given as a space-separated list (-properties hole
electron) and terminated with "--" if they are the
last argument before the input file. (default: None)
-koopmans POTENTIALS Which redox potentials to compute via Koopmans'
approximation. o=oxidation, r=reduction, or=oxidation
and reduction, none=neither potential. Those
potentials not calculated via Koopmans' approximation
will be computed using a full adiabatic cycle. The
default is "-koopmans or" for screening and "-koopmans
none" for other modes. (default: None)
-oxidation_electrode_potential POTENTIAL_(V)
The relative potential of the electrode in Volts for
the reference electrode. This value is used in
adiabatic oxidation potentials and for both adiabatic
and Koopmans-based potentials to convert oxidation
potentials back to a scaled HOMO energy. The default
is 0.0 (NHE electrode - which has an absolute
potential of -4.28). The sign convention is such that
SCE and Ferrocene electrodes should have negative
values for this flag. (default: None)
-reduction_electrode_potential POTENTIAL_(V)
The relative potential of the electrode in Volts for
the reference electrode. This value is used in
adiabatic reduction potentials and for both adiabatic
and Koopmans-based potentials to convert reduction
potentials back to a scaled LUMO energy. The default
is 0.0 (NHE electrode - which has an absolute
potential of -4.28). The sign convention is such that
SCE and Ferrocene electrodes should have negative
values for this flag. (default: None)
-cpus CPUs_PER_JOB DEPRECATED. Use -TPP instead. Number of cpus to run
each structure on. Selecting this option rather than
-TPP will result in Jaguar determining how to divide
this number of cpus between the available processors
and threads. (default: None)
-tadf_gap_method METHOD
Method for computing the S1-T1 gap used for Thermally
Activated Delayed Fluorescence. "at_s0" uses the S0
geometry and computes both T1 and S1 using TD-DFT with
S0 as the reference wavefunction. "at_t1" uses the T1
geometry and computes both T1 and S1 using TD-DFT with
S0 as the reference wavefunction. The default is
"at_t1". (default: None)
-TPP THREADS Number of threads per MPI processor to use for each
job. (default: None)
-name JOBNAME Base name of any files created for structures that do
not have an existing Title or have a Title that
contains characters that are invalid for job names.
Any existing value Title property will be used in
preference to the value specified by this flag.
(default: None)
-nocheckpoint By default, if a Jaguar output file from a successful
run exists with the same name as would be produced by
a job, the job is not run and that output file is used
instead. This allows a partially successful run to be
restarted without re-running already completed steps.
Using this flag will result in all steps being run
regardless of existing Jaguar output. (default: False)
-settings PATH Path to a file that contains a list of settings. Each
line of the file should be in the format: -flag=value,
where -flag is a command line flag and value is the
value for that flag. Flags that do not take a value,
such as -nocheckpoint, can either be included with an
explicit =True or =False to indicate the presence or
absence of the flag or may be included without any
explicit =value just like on the command line. Leaving
such a flag out of the settings file is the same as
not using it on the command line. Parameters values
are taken in the following order of decreasing
preference: command line values, settings file values,
preferences set by the Advanced Options panel in the
Optoelectronics GUI on the machine launching the
driver, script defaults. See also the -write_settings
flag. (default: None)
-write_settings PATH Write out all settings to a file that can be read with
-settings. (default: None)
-keywords KEYWORD=VALUE KEYWORD=VALUE ... [KEYWORD=VALUE KEYWORD=VALUE ... ...]
Jaguar keywords to include in calculations. If this is
the last flag before the input/output file names, use
--to terminate the list of keywords. The default value
is taken from the Advanced Options of the
Optoelectronics Calculation panel for -mode. (default:
None)
-triplet_slope SLOPE The slope applied to the raw Jaguar triplet energy.
The default value is taken from the Advanced Options
of the Optoelectronics Calculation panel for -mode.
(default: None)
-triplet_intercept INTERCEPT
The intercept applied to the raw Jaguar triplet
energy. The default value is taken from the Advanced
Options of the Optoelectronics Calculation panel for
-mode. (default: None)
-oxidation_slope SLOPE
The slope applied to the raw Jaguar HOMO energy to
compute the oxidation potential. The default value is
taken from the Advanced Options of the Optoelectronics
Calculation panel for -mode. (default: None)
-oxidation_intercept INTERCEPT
The intercept applied to the raw Jaguar HOMO energy to
compute the oxidation potential. The default value is
taken from the Advanced Options of the Optoelectronics
Calculation panel for -mode. (default: None)
-oxidation_solvent_keywords [KEYWORD=VALUE KEYWORD=VALUE ... ...]
The additional solvent-related Jaguar keywords to use
when computing energies in solution. These are only
used for single-point energy calculations for
adiabatic oxidation potentials. The default value is
taken from the Advanced Options of the Optoelectronics
Calculation panel for -mode. (default: None)
-reduction_slope SLOPE
The slope applied to the raw Jaguar LUMO energy to
compute the reduction potential. The default value is
taken from the Advanced Options of the Optoelectronics
Calculation panel for -mode. (default: None)
-reduction_intercept INTERCEPT
The intercept applied to the raw Jaguar LUMO energy to
compute the reduction potential. The default value is
taken from the Advanced Options of the Optoelectronics
Calculation panel for -mode. (default: None)
-reduction_solvent_keywords [KEYWORD=VALUE KEYWORD=VALUE ... ...]
The additional solvent-related Jaguar keywords to use
when computing energies in solution. These are only
used for single-point energy calculations for
adiabatic reduction potentials. The default value is
taken from the Advanced Options of the Optoelectronics
Calculation panel for -mode. (default: None)
-tddft_approximation APPROXIMATION
The approximation to apply when performing TD-DFT
calculations. Must be either "Tamm-Dancoff" or
"Full_linear_response". The default value is taken
from the Advanced Options of the Optoelectronics
Calculation panel for -mode. (default: None)
-singlet_idxs 0,1,2,3,,...
The singlet excited states (0-based) for which to
calculate the properties isc_reorg and/or risc_reorg
using TD-DFT. The default is 1. (default: None)
-triplet_idxs 1,2,3,,...
The triplet excited states (1-based) for which to
calculate the properties isc_reorg and/or risc_reorg
using TD-DFT. The default is 1. (default: None)
-compress_subjobs Compress files from successful subjobs. The default
value is taken from the Advanced Options of the
Optoelectronics Calculation panel for -mode. (default:
False)
Restart options:
-use_zip_data PATH Extract the archive before running. Any completed
files in the archive will be used instead of
submitting new jobs. (default: None)
-restart_proj PROJECT_NAME
Project name the restart job is associated with.
(default: None)
-restart_disp INCORPORATION
Incorporation state for the restart job. Should be one
of: append, ignore. (default: None)
-restart_viewname VIEWNAME
Viewname for the panel submitting the restart job.
Leave blank if running from the command line.
(default: None)
-restart_host HOSTNAME:PROCESSORS
Host for restart in the form of "hostname:cpus".
(default: None)
-restart_jobname JOBNAME
Jobname for restart. (default: None)
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
(default: localhost)