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]
[-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)
-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)