hopping_driver.py Command Help
Command: $SCHRODINGER/run hopping_gui_dir/hopping_driver.py
usage: $SCHRODINGER/run hopping_gui_dir/hopping_driver.py [-h]
[-keywords KEYWORD=VALUE KEYWORD=VALUE [KEYWORD=VALUE KEYWORD=VALUE ...]]
[-splitting]
[-monomers]
[-electron] [-hole]
[-separation]
[-reorg_electron REORGANIZATION_ENERGY]
[-reorg_hole REORGANIZATION_ENERGY]
[-reorg_separation REORGANIZATION_ENERGY]
[-name NAME]
[-temp TEMPERATURE]
[-uhf] [-cluster]
[-dist DISTANCE]
[-heavy] [-com]
[-species_type MAESTRO_FILE]
[-species_crit CRITERION]
[-random #_OF_DIMERS]
[-seed SEED]
[-use_charges CHARGE_METHOD]
[-esp_basis BASIS_SET]
[-PARALLEL CPUS]
[-TPP THREADS]
[-delete_wfn_files]
[-use_zip_data PATH]
[-restart_proj PROJECT_NAME]
[-restart_disp INCORPORATION]
[-restart_viewname VIEWNAME]
[-restart_host HOSTNAME:PROCESSORS]
[-restart_jobname JOBNAME]
[-v]
[-HOST <hostname>]
[input_file]
[output_file]
Driver for the Marcus Hopping Rate script Copyright Schrodinger, LLC. All
rights reserved.
positional arguments:
input_file Input file. By default, each structure in the file
should be a dimer to run. If -cluster is used, then
each structure in the file is considered a cluster and
will be searched for dimers based on the Clustering
options. A hopping rate calculation will be run for
each dimer. (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.
-keywords KEYWORD=VALUE KEYWORD=VALUE [KEYWORD=VALUE KEYWORD=VALUE ...], -k KEYWORD=VALUE KEYWORD=VALUE [KEYWORD=VALUE KEYWORD=VALUE ...]
Jaguar keyword to include in calculations. Can be
given multiple times, ex. -k dftname=b3lyp -k
basis=midix. If this is the last flag before the
input/output file names, use --to terminate the list
of keywords. (default: )
-splitting, -s Compute the electron coupling as one half the
splitting of the frontier orbitals of the complex -
HOMO/HOMO-1 for holes or LUMO/LUMO+1 for electrons.
The default is a full quantum mechanical treatment of
the electron transfer, including computing the
wavefunctions before and after electron transfer and
the electron transfer coupling integral between the
two states. (default: False)
-monomers, -m Compute the wavefunctions with monomers using DFT. The
default is to compute the wavefunctions of the
complexes using CDFT. This keyword is not valid with
-splitting. (default: False)
-electron Compute the electron hopping rate. At least one of
-electron, -hole, or -separation must be used.
(default: False)
-hole Compute the hole hopping rate. At least one of
-electron, -hole, or -separation must be used.
(default: False)
-separation Compute the rate of charge separation - a neutral
dimer going to anion and cation.
{CHARGE_REQUIREMENTS}. (default: False)
-reorg_electron REORGANIZATION_ENERGY
Electron reorganization energy for the monomer.
Reorganization energies can be calculated with the
Optoelectronics panel. Value must be in eV and is
required if -electron is used. (default: None)
-reorg_hole REORGANIZATION_ENERGY
Hole reorganization energy for the monomer.
Reorganization energies can be calculated with the
Optoelectronics panel. Value must be in eV and is
required if -hole is used. (default: None)
-reorg_separation REORGANIZATION_ENERGY
Reorganization energy for the monomer. Reorganization
energies can be calculated with the Optoelectronics
panel. Value must be in eV and is required if -hole is
used. (default: None)
-name NAME 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: marcus)
-temp TEMPERATURE, -t TEMPERATURE
Temperature (Kelvin) to compute the hopping rate at.
(default: 298.15)
-uhf The default is to use ROHF for open shell
calculations. Use of this flag will result in UHF
being used instead. This keyword is not valid with
-splitting. (default: False)
-PARALLEL CPUS Number of CPUS to pass to jaguar run with the
-PARALLEL flag. The default value of 1 causes the flag
not to be used. -PARALLEL may not be used with -TPP.
(default: 1)
-TPP THREADS Number of threads to pass to jaguar run with the -TPP
flag. -TPP may not be used with -PARALLEL and is only
used if it has a value > 1. (default: 1)
-delete_wfn_files Do not keep Jaguar .01.in wavefunction files for each
job. Not keeping these files will substantially reduce
the amount of disk space a job takes, but means that
restart jobs may have to re-run some computations.
(default: False)
-v, -version Show the program's version number and exit.
Clustering options:
-cluster The input file actually contains structures from which
dimers should be extracted. (default: False)
-dist DISTANCE The intermolecular distance used to find dimers (if
-clusters is used) and nearest neighbors (if
-use_charges is used). Value is in Angstroms.
(default: 4.0)
-heavy Consider only heavy atom-heavy atom distances when
finding dimers and clusters. The default is to include
distances to H atoms. (default: False)
-com Consider only center-of-mass distances when finding
dimers and clusters. The default is to use atom
distances. -heavy is ignored if this flag is used
(default: False)
-species_type MAESTRO_FILE
If dimers should be restricted by molecule type, use
this flag to indicate the type of molecule that
-species_criteria applies to. The value passed with
this flag should be a Maestro (.mae, .maegz) file that
contains the structure of the species. This flag is
only used when -clusters is used. (default: None)
-species_crit CRITERION
Specify the number of -species_type molecules that
must be included in each dimer in -cluster mode.
Choices are: "none" - no such molecules, "only_one" -
one and only one such molecule, "one" - at least one
such molecule, or "two" - both dimer molecules must be
of this type. (default: none)
-random #_OF_DIMERS From all dimers found, randomly choose this number to
run. (default: None)
-seed SEED The seed to use if random dimer choice is specified.
(default: 1234)
-use_charges CHARGE_METHOD
For each dimer, find all nearest neighbor molecules
within -dist of either dimer molecule. In the quantum
calculations, place a partial charge at the XYZ
coordinates of each atom in each nearest neighbor. The
value of this flag determines how the partial charge
is obtained. The value should be either an atom
property of the form "r_m_property_name" or the
special value "esp". "esp" will cause electrostatic
potential charges to be computed for each unique
molecular species found in the input structures. The
ESP charges will then be used for the partial charges
in all molecules of that species. The ESP charges are
obtained using a B3LYP calculation with the basis set
specified by the -esp_basis flag. (default: None)
-esp_basis BASIS_SET If "-use_charges esp" is used, the basis set used in
the B3LYP electrostatic potential charge calculation
(default: MIDIX)
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)