permittivity_driver.py Command Help
Command: $SCHRODINGER/run permittivity_gui_dir/permittivity_driver.py
usage: $SCHRODINGER/run permittivity_gui_dir/permittivity_driver.py
[-h] [-any_inputfile_type] [-config_yaml YAML]
[-workflow_type WORKFLOW_TYPE] [-seed SEED] [-forcefield FORCE_FIELD]
[-enable_metal_force_field] [-replica_num REPLICA_NUM]
[-polymer_cru_num POLYMER_CRU_NUM]
[-max_oligomer_size MAX_OLIGOMER_SIZE]
[-jaguar_options KEYWORD=VALUE KEYWORD=VALUE [KEYWORD=VALUE KEYWORD=VALUE ...]]
[-jaguar_finer_options KEYWORD=VALUE KEYWORD=VALUE [KEYWORD=VALUE KEYWORD=VALUE ...]]
[-elec_polarizability KEYWORD=VALUE KEYWORD=VALUE [KEYWORD=VALUE KEYWORD=VALUE ...]]
[-abbe_number_wavelength NANOMETER,NANOMETER,NANOMETER]
[-refractive_index_wavelength START,END,NUM] [-parallel PARALLEL]
[-molecules NUMBER_OF_MOLECULES] [-initial_density DENSITY]
[-monomer_ff_q] [-md_ensemble MD_ENSEMBLE] [-md_temp KELVIN]
[-md_press BAR] [-md_time NANOSECOND] [-md_timestep FEMTOSECONDS]
[-relaxation_protocol PROTOCOL]
[-md_time_last_relaxation FLAG_MD_TIME_LAST_RELAXATION]
[-dipole_record_int DIPOLE_RECORD_INT] [-md_trj_int MD_TRJ_INT]
[-dipole_data_last_frac FRACTION] [-electric_polar ELECTRIC_POLAR]
[-cpu_host HOSTNAME:X] [-gpu_host HOSTNAME:X] [-HOST <hostname>] [-D]
[-VIEWNAME <viewname>] [-OPLSDIR OPLSDIR] [-JOBNAME JOBNAME]
input_file [input_file ...]
Permittivity workflow: 1) jaguar for polarizability; 2) homo-polymer builder,
amorphous cell builder, desmond system builder, relaxation, production run,
dipole calculation, auto-correlation, fitting, and nonuniform fourier
transform. Copyright Schrodinger, LLC. All rights reserved.
positional arguments:
input_file The structure file to run polymer builder, disorder
system builder, or directly molecular dynamics on.
(e.g., mae, maegz, cms)
options:
-h, -help Show this help message and exit.
-any_inputfile_type If True, the workflow accept any file types and runs
as is. (default: False)
-config_yaml YAML A YAML file contains information of the task configs.
If provided, use this file to set all command flags
and ignore any other command arguments. (default:
None)
-workflow_type WORKFLOW_TYPE
Please choose from refractive_index, abbe_number,
static_permittivity, complex_permittivity. If a config
yaml is explicitly provided using -config_yaml, ignore
this flag. (default: permittivity)
-seed SEED Seed for random number generator. (default: 1234)
-forcefield FORCE_FIELD
Force field to use. Valid force fields are OPLS_2005,
S-OPLS and SPFF (default: S-OPLS)
-enable_metal_force_field
Use the metal force field for metal atoms. This is
only relevant if using OPLS5, and if not specified
then the standard OPLS5 force field will be used for
all atoms including metals. (default: False)
-replica_num REPLICA_NUM
Number of replica for the molecular dynamics related
tasks. (default: None)
-dipole_data_last_frac FRACTION
The last this fraction of the molecular dynamics data
will be used for analysis. (default: 0.8)
-electric_polar ELECTRIC_POLAR
Average polarizability of input system (default: None)
-cpu_host HOSTNAME:X Specify the host, HOSTNAME, for CPU subjobs and the
number of allowed simultaneous CPU subjobs, X
(default: localhost:1)
-gpu_host HOSTNAME:X Specify the host, HOSTNAME, for GPU subjobs and the
number of allowed simultaneous GPU subjobs, X
(default: localhost:1)
Polymer Builder Settings:
-polymer_cru_num POLYMER_CRU_NUM
The number of constitutional repeat units (CRU) in
each polymer. (default: 25)
-max_oligomer_size MAX_OLIGOMER_SIZE
The number of constitutional repeat units (CRU) in the
largest oligomer that jaguar calculations are
performed on. (default: 2)
Jaguar Settings:
-jaguar_options KEYWORD=VALUE KEYWORD=VALUE [KEYWORD=VALUE KEYWORD=VALUE ...]
Jaguar keywords to include in generic Jaguar
calculations.Can be given multiple keywords, ex.
-jaguar_options dftname=b3lyp basis=6-31G*. If this is
the last flag before positional arguments, use -- to
terminate the list of keywords. (default:
basis=6-31G** dftname=B3LYP igeopt=1 nofail=1
nops_opt_switch=10 maxit=300 maxitg=300)
-jaguar_finer_options KEYWORD=VALUE KEYWORD=VALUE [KEYWORD=VALUE KEYWORD=VALUE ...]
Jaguar keywords to include in finer generic Jaguar
calculations.Can be given multiple keywords, ex.
-jaguar_options dftname=b3lyp basis=6-31G*. If this is
the last flag before positional arguments, use -- to
terminate the list of keywords. (default: )
-elec_polarizability KEYWORD=VALUE KEYWORD=VALUE [KEYWORD=VALUE KEYWORD=VALUE ...]
Jaguar keywords to include in Jaguar polarizability
calculations.Can be given multiple keywords, ex.
-elec_polarizability dftname=b3lyp basis=6-31G*. If
this is the last flag before positional arguments, use
-- to terminate the list of keywords. (default:
basis=cc-pVTZ-pp(-f)++ dftname=B3LYP nofail=1
maxit=300)
-abbe_number_wavelength NANOMETER,NANOMETER,NANOMETER
Abbe number is from the refractive indexes at these
three wavelengths. Defaults are the Fraunhofer C, D1,
and F spectral lines. (default: 656.3,589.3,486.1)
-refractive_index_wavelength START,END,NUM
Refrective indexes are calculated at NUM wavelengths
in the range of [START nm, END nm] (default: None)
-parallel PARALLEL Each Jaguar job uses this number of processors for
parallelization. (default: None)
Disorder System Builder Settings:
-molecules NUMBER_OF_MOLECULES
Number of molecules to place in the cell (default:
500)
-initial_density DENSITY
The initial density target for building the amorphous
cell. (default: 0.5)
-monomer_ff_q Use forcefield charges computed for the monomer for
the polymer. This option is particularly useful for
S-OPLS, which uses OPLS_2005 charges by default for
molecules larger than 100 heavy atoms. (default:
False)
Molecular Dynamics Simulation Setting:
-md_ensemble MD_ENSEMBLE
Molecular dynamics ensemble (NVE, NVT) for data
collection. (default: NVE)
-md_temp KELVIN Temperature (K) of molecular dynamics simulations.
(default: 300.0)
-md_press BAR Pressure (bar) of NPT molecular dynamics simulations
before the production run. (default: 1.01325)
-md_time NANOSECOND Time (ns) of molecular dynamics production
simulations. (default: 50.0)
-md_timestep FEMTOSECONDS
Timestep (fs) of molecular dynamics simulations.
(default: 2.0)
-relaxation_protocol PROTOCOL
The relaxation protocol before molecular dynamics
production run. The argument must be either a user
input file or a known protocol name (e.g.,
Hofmann,Compressive). (default: Hofmann)
-md_time_last_relaxation FLAG_MD_TIME_LAST_RELAXATION
The simulation time (ns) of the additional relaxation
stage after the molecular dynamics relaxation protocol
(-relaxation_protocol). (default: 10)
-dipole_record_int DIPOLE_RECORD_INT
Dipole recording interval (default: 0.1)
-md_trj_int MD_TRJ_INT
MD trajectory recording interval (in ps). (default:
500)
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)
-OPLSDIR OPLSDIR Specifies directory for custom forcefield parameters.
(default: None)
-JOBNAME JOBNAME Provide an explicit name for the job. (default: None)