kmc_compute_charge_mobility_driver.py Command Help
Command: $SCHRODINGER/run kmc_compute_charge_mobility_gui_dir/kmc_compute_charge_mobility_driver.py
usage: $SCHRODINGER/run kmc_compute_charge_mobility_gui_dir/kmc_compute_charge_mobility_driver.py
[-h] [-charge TYPE [TYPE ...]] [-db SQL_FILE] [-matsci] [-no_pairs]
[-dist ANGSTROMS] [-dist_type DISTANCE_TYPE] [-crystal]
[-rmsd ANGSTROMS] [-force_new_pairs] [-avg_jeff] [-no_qm]
[-apply_ml_models APPLY_ML_MODELS]
[-site_keys KEYWORD=VALUE KEYWORD=VALUE ...] [-TPP THREADS]
[-save_qm_files] [-fixdb] [-no_kmc] [-numq NUMBER_OF_CHARGES]
[-steps STEPS | -time MICROSECONDS] [-recint NANOSECONDS]
[-injection INJECTION_SITES] [-seed SEED] [-temp KELVIN] [-coulomb]
[-eff_charge EFF_CHARGE] [-e_rate E_RATE] [-h_rate H_RATE]
[-e_anni E_ANNI] [-h_anni H_ANNI] [-singlet_rad SINGLET_RAD]
[-singlet_nonrad SINGLET_NONRAD] [-triplet_rad TRIPLET_RAD]
[-triplet_nonrad TRIPLET_NONRAD] [-qint CARRIER_INTERACTION]
[-field [F1x,F1y,F1z F2x,F2y,F2z ...]] [-use_db_rates] [-write_trajs]
[-calc_msd] [-bin_t] [-n_t_bins N_T_BINS] [-acc_t_bin_width]
[-lags LAGS] [-lag_start LAG_START] [-lag_step LAG_STEP]
[-n_lags N_LAGS] [-all_lags] [-bin_sd] [-n_sd_bins N_SD_BINS]
[-bin_sd_idxs BIN_SD_IDXS] [-fit_bin_if FIT_BIN_IF]
[-fit_type {linear,quadratic}] [-HOST <hostname>] [-D]
[-VIEWNAME <viewname>] [-JOBNAME JOBNAME]
input_file output_file
Driver for the Votca setup calculations Copyright Schrodinger, LLC. All rights
reserved.
positional arguments:
input_file Input file structure file
output_file Output file structure file. The structure will have
the same atoms and coordinates as the input file.
options:
-h, -help Show this help message and exit.
-apply_ml_models APPLY_ML_MODELS
Filename of a *.pkl file containing machine learning
models to fill in hopping parameter table. If
supplied, these models will be used instead of DFT
calculations. (default: None)
-use_db_rates For KMC-only run, use rate from database file; do not
calculate rate from hopping parameters. (default:
False)
General options:
-charge TYPE [TYPE ...]
Type of charge. Either hole or electron or both (space
separated). (default: ['hole'])
-db SQL_FILE Existing database file to use instead of creating a
new one (default: None)
-matsci Use MatSci KMC engine instead of VOTCA. (default:
False)
Neighbor list options:
-no_pairs Do not find pairs (default: False)
-dist ANGSTROMS Nearest-neighbor distance (default: 4.0)
-dist_type DISTANCE_TYPE
Atoms to consider for finding molecular pairs. Must be
either heavy or all (default: heavy)
-crystal Find identical sites and pairs using symmetry (using
RMSD of atomic coordinates) and use that to reduce the
number of site energies and couplings computed
(default: False)
-rmsd ANGSTROMS Maximum RMSD in atom coordinates for sites and pairs
to be considered identical. Only used if -crystal is
given. (default: 0.1)
-force_new_pairs If pair data already exists in the database and
-no_pairs is not used, delete existing pair
information and recalculate, otherwise without
-force_new_pairs, the job will not start. (default:
False)
-avg_jeff Average forward and backward coupling energies for
internal KMC engine. (default: False)
QM options:
-no_qm Do not compute site energies or couplings (default:
False)
-site_keys KEYWORD=VALUE KEYWORD=VALUE ...
Jaguar keywords to include in site energy
calculations. If this is the last flag before the
input/output file names, use -- to terminate the list
of keywords. (default: dftname=B3LYP basis=LACV3P**
maxit=500 vshift=0.0)
-TPP THREADS Number of threads to use per subjob (default: 1)
-save_qm_files Save QSite and Jaguar files for successful subjobs.
(default: False)
-fixdb Only run site energies and couplings to replace those
that are missing in the SQL database given by -db.
(default: False)
KMC options:
-no_kmc Do not compute KMC mobilities (default: False)
-numq NUMBER_OF_CHARGES
Number of charges to inject into the system (default:
1)
-steps STEPS The number of KMC steps to run, must be > 100.
(default: 10000000)
-time MICROSECONDS Time in microseconds for the KMC mobility simulation.
If used, this overrides the -steps value. (default:
None)
-recint NANOSECONDS Time interval in nanoseconds for recording the KMC
trajectory (default: 10)
-injection INJECTION_SITES
Injection site(s) for charges. Can be one of the
following: "random" to indicate that injection sites
are random, an integer to specify a specific molecule
(segment), any other string will be interpreted as a
molecule (segment) type and the injection site(s) will
be chosen randomly from molecules of that type.
Segment type names are given by the pdbres property of
the first atom in each molecule. Specifying a molecule
number is only allowed when there is a single charge.
(default: random)
-seed SEED Seed for random number generator. (default: 1234)
-temp KELVIN Temperature in Kelvin for the KMC mobility simulation
(default: 298.15)
-coulomb Consider Coulomb interactions between charges during
KMC. (default: False)
-eff_charge EFF_CHARGE
Effective charge for coulomb interactions. (default:
1)
-e_rate E_RATE The rate of electron injection in s^-1. (default:
None)
-h_rate H_RATE The rate of hole injection in s^-1. (default: None)
-e_anni E_ANNI The rate at which electrons annihilate on hole
injection sites, in s^-1. (default: None)
-h_anni H_ANNI The rate at which holes annihilate on electron
injection sites, in s^-1. (default: None)
-singlet_rad SINGLET_RAD
The rate at which singlet excitons decay with
radiation, in s^-1. (default: None)
-singlet_nonrad SINGLET_NONRAD
The rate at which singlet excitons decay without
radiation, in s^-1. (default: None)
-triplet_rad TRIPLET_RAD
The rate at which triplet excitons decay with
radiation, in s^-1. (default: None)
-triplet_nonrad TRIPLET_NONRAD
The rate at which triplet excitons decay without
radiation, in s^-1. (default: None)
-qint CARRIER_INTERACTION
"none": no explicit Coulomb interaction, "integer":
explicit raw Coulomb interaction using charges of
+/-1. (default: none)
-field [F1x,F1y,F1z F2x,F2y,F2z ...]
Sets of three comma-separated floats giving the field
strength (MV/m) in the X,Y,Z directions. For instance
{FLAG_FIELD} 0,0,10. To produce mobilities at multiple
fields, separate fields by spaces such as 10,0,0
0,10,0 0,0,10 to produce mobilities with the same
field in the x, y and then z direction. Fields with
negative values can be given directly without quoting
or escaping, such as -field -10,0,0 -15,0,0. If this
is the last argument before the input and output file
names, the list of fields must be terminated by two
dashes "--". (default: [(0, 0, 36)])
Mean Square Displacement:
-write_trajs Write a zipped csv of the trajectory for each charge.
Columns are time in seconds and the x, y, and z
components of the displacement in meters. (default:
False)
-calc_msd Calculate the mean-square displacement components as a
function of time (MSD(t)) for each charge, and from
those, their self-diffusion constants and, if using
the drift-diffusion model (see flag -fit_type), drift
velocities. At zero-field, it is automatically
calculated in order to get the mobility. Note that if
also using the flag -bin_t then the calculation time
can significantly increase. (default: False)
-bin_t Compute the MSD(t) by time binning where its accuracy
is controlled by the total number of frames, either
the given lags (-lags) or the lag start and step
(-lag_start and -lag_step), and some other parameters.
If not specified then compute the MSD(t) simply using
the first and last frame which is less accurate but
takes less compute time. (default: False)
-n_t_bins N_T_BINS The number of time bins used to calculate the MSD(t).
(default: 100)
-acc_t_bin_width Calculate the time bin width using the minimum and
maximum difference in times over all sampled (time,
displacement vector) pairs. If not given then
calculate the time bin width using only times from the
first and last frames. (default: False)
-lags LAGS The MSD(t) components are calculated by pair-wise
resampling of the trajectory. A pair is an initial
(time, displacement vector) point and a final (time,
displacement vector) point separated by some number of
frames N which is called the lag. All pairs for a
given N are sampled. This parameter (-lags) sets the
values of N. See also -lag_start, -lag_step, -n_lags,
and -all_lags. This parameter takes precedence.
(default: None)
-lag_start LAG_START The MSD(t) components are calculated by pair-wise
resampling of the trajectory. A pair is an initial
(time, displacement vector) point and a final (time,
displacement vector) point separated by some number of
frames N which is called the lag. All pairs for a
given N are sampled. This parameter (-lag_start) sets
the initial value of N. (default: 1000)
-lag_step LAG_STEP The MSD(t) components are calculated by pair-wise
resampling of the trajectory. A pair is an initial
(time, displacement vector) point and a final (time,
displacement vector) point separated by some number of
frames N which is called the lag. All pairs for a
given N are sampled. This parameter (-lag_step)
together with the initial value of N (see -lag_start)
define subsequent lag values over which to sample
pairs. (default: 1000)
-n_lags N_LAGS The MSD(t) components are calculated by pair-wise
resampling of the trajectory. A pair is an initial
(time, displacement vector) point and a final (time,
displacement vector) point separated by some number of
frames N which is called the lag. All pairs for a
given N are sampled. This parameter (-n_lags) sets the
number of lags to consider when using the options
-lag_start and -lag_step. (default: 100)
-all_lags The MSD(t) components are calculated by pair-wise
resampling of the trajectory. A pair is an initial
(time, displacement vector) point and a final (time,
displacement vector) point separated by some number of
frames N which is called the lag. All pairs for a
given N are sampled. This parameter (-all_lags) allows
using all possible lags given the number of points in
the trajectory, -lag_start, and -lag_step. The
parameter takes precendence over -n_lags. (default:
False)
-bin_sd Bin square displacement components per time bin. This
is used for analysis purposes only, and significantly
increases calculation time. (default: False)
-n_sd_bins N_SD_BINS The number of square displacement bins per time bin.
(default: 20)
-bin_sd_idxs BIN_SD_IDXS
Bin square displacement components only for these
specific time bins instead of all time bins. The
latter significantly increases compute time but
requires little memory, and vice versa for the former.
(default: None)
-fit_bin_if FIT_BIN_IF
Initial and final time bin indices over which to
linear fit the MSD(t) in order to calculate the self-
diffusion constants. If not given, the initial and
final values are 1/5 and 4/5 of the number of time
bins so that the middle 3/5 of the values are used in
the fit. (default: None)
-fit_type {linear,quadratic}
If "linear" then fit the MSD(t) to the equation
derived from the diffusion model. If "quadratic" then
fit to that from the drift-diffusion model. (default:
linear)
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
(default: localhost)
-D, -DEBUG Show details of Job Control operation. (default:
False)
-VIEWNAME <viewname> Specifies viewname used in job filtering in maestro.
(default: False)
-JOBNAME JOBNAME Provide an explicit name for the job. (default: None)