solid_electrolyte_interphase_driver.py Command Help
Command: $SCHRODINGER/run solid_electrolyte_interphase_gui_dir/solid_electrolyte_interphase_driver.py
usage: $SCHRODINGER/run solid_electrolyte_interphase_gui_dir/solid_electrolyte_interphase_driver.py
[-h] [-reaction_config REACTION_CONFIG]
[-reactant_priority {min_distance,random}]
[-reaction_order {user_defined,random}]
[-charge_scaling_coeff CHARGE_SCALING_COEFF]
[-scale_neutral_mol_charge] [-relax] [-brownie_md_time BROWNIE_MD_TIME]
[-reduction_zone_width REDUCTION_ZONE_WIDTH]
[-custom_charge_method {xtb,user_defined,dft}]
[-qm_charge_method {mulliken,lowdin,stockholder,esp}]
[-keywords KEYWORDS] [-barrier_coord BARRIER_COORD]
[-unproductive_reaction_time UNPRODUCTIVE_REACTION_TIME]
[-keep_subjob_dir] [-electrode_asl ELECTRODE_ASL]
[-uniform_electrode_charge UNIFORM_ELECTRODE_CHARGE]
[-interface_electrode_asl INTERFACE_ELECTRODE_ASL]
[-interface_electrode_charge INTERFACE_ELECTRODE_CHARGE]
[-bulk_electrode_charge BULK_ELECTRODE_CHARGE]
[-electrolyte_atom_smile ELECTROLYTE_ATOM_SMILE]
[-num_electrolyte_atoms NUM_ELECTROLYTE_ATOMS]
[-electrolyte_vdw_radius ELECTROLYTE_VDW_RADIUS]
[-electrolyte_range ELECTROLYTE_RANGE ELECTROLYTE_RANGE]
[-electrolyte_add_interval ELECTROLYTE_ADD_INTERVAL]
[-split_components] [-md_temp MD_TEMP] [-md_time MD_TIME]
[-md_timestep MD_TIMESTEP] [-md_trj_int MD_TRJ_INT]
[-md_eneseq_int MD_ENESEQ_INT] [-save_trj_data {none,cms,trj}]
[-water_fftype WATER_TYPE] [-seed SEED] [-forcefield FORCE_FIELD]
[-md_umbrella] [-md_ensemble ENSEMBLE] [-cpu_host HOSTNAME:X]
[-gpu_host HOSTNAME:X] [-TPP TPP] [-HOST <hostname>] [-D]
[-VIEWNAME <viewname>] [-OPLSDIR OPLSDIR] [-JOBNAME JOBNAME]
input_file
Driver to perform electrolyte reaction at electrode. The difference between
polymer cross-link driver and solid_electrolyte_interface_driver. Copyright
Schrodinger, LLC. All rights reserved.
positional arguments:
input_file Input file
options:
-h, -help Show this help message and exit.
-reaction_config REACTION_CONFIG
Input configuration file containing instruction about
reaction (default: None)
-reactant_priority {min_distance,random}
Define the priority of selecting reactant.
min_distance option will return a sorted reactant list
reactant based on distance between the atoms defined
in match criteria. Thus, reactant with shortest
distance will have the highest priority. random option
will return a random list of reactant (default:
min_distance)
-reaction_order {user_defined,random}
Define the order of reactions. If user_defined is
selected, reactions will be performed in the order
defined in the reaction config file. If random option
is selected, order of the reaction will be randomized
and probability of the reaction will be set to 1.0.
(default: user_defined)
-charge_scaling_coeff CHARGE_SCALING_COEFF
Scale the atomic charges with given constant value.
Scaling will only be performed for atoms where charges
are defined by the custom charge property (default: 1)
-scale_neutral_mol_charge
Scale the charge of neutral molecule. This option is
only applicable if the charge is defined by custom
charge property (default: False)
-relax Apply Materials relaxation protocol on structure.
(default: False)
-brownie_md_time BROWNIE_MD_TIME
MD time (in ps) of the simulations. (default: 100)
-reduction_zone_width REDUCTION_ZONE_WIDTH
Width of reduction zone in Angstrom. (default: 50)
-custom_charge_method {xtb,user_defined,dft}
Define the method to assign custom charge on atoms. If
the forcefield option is selected, charges will be
assigned based on forcefield selected. (default: xtb)
-qm_charge_method {mulliken,lowdin,stockholder,esp}
Define the charge method to assign atomic charges on
atoms from the QM calculation. (default: mulliken)
-keywords KEYWORDS Specify Jaguar &gen section key-value pairs. Each key-
value pair should be separated from the next by
whitespace and each should be represented in terms of
a <key>=<value> pair. (default: dftname=B3LYP-D3
basis=6-31++G** igeopt=1 iaccg=3 maxit=100 nofail=1
isymm=0 nops_opt_switch=10 )
-barrier_coord BARRIER_COORD
Coordinate of the barrier in z direction. The flag
takes priority over barrier location provided in input
structure file. (default: None)
-unproductive_reaction_time UNPRODUCTIVE_REACTION_TIME
Maximum time of unproductive run. If no reaction is
performed in this time, the simulation will be
terminated. (default: 10000)
-keep_subjob_dir Keep compressed subjob directories after run.
(default: False)
-split_components Split system in components when Desmond system is
built. This can speed up the the force field
assignment for systems that contain multiple identical
molecules. (default: False)
-md_temp MD_TEMP Temperature (in K) of the simulations. (default:
300.0)
-md_time MD_TIME MD time (in ns) of the simulation. (default: 100.0)
-md_timestep MD_TIMESTEP
MD time step (in fs) of the simulations. (default:
2.0)
-md_trj_int MD_TRJ_INT
MD trajectory recording interval (in ps). (default:
10.0)
-md_eneseq_int MD_ENESEQ_INT
MD energy recording interval (in ps). (default: 10.0)
-save_trj_data {none,cms,trj}
Specify whether intermediate CMS or trajectory files
be included with the job output. Choices are none
(save no files), cms (save .cms files) and trj (save
.cms and trajectory files). Default is none. (default:
none)
-water_fftype WATER_TYPE
Force field type for water molecules. Must be used
with -split_components. If using "none", the Residue
Name atom property is used instead. (default: SPC)
-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: OPLS_2005)
-md_umbrella Run desmond subjobs on the driver host. (default:
False)
-md_ensemble ENSEMBLE
Desmond ensemble. Known values are: NVE, NVT, NPT
(default: NVT)
-cpu_host HOSTNAME:X Specify the host, HOSTNAME, for CPU subjobs and the
number of allowed simultaneous CPU subjobs, X
(default: None)
-gpu_host HOSTNAME:X Specify the host, HOSTNAME, for GPU subjobs and the
number of allowed simultaneous GPU subjobs, X
(default: None)
-TPP TPP Specify the number of threads to use for parallelizing
each subjob that supports threading. (default: 1)
Electrode options:
-electrode_asl ELECTRODE_ASL
Define ASL to select electrode atoms. (default: None)
-uniform_electrode_charge UNIFORM_ELECTRODE_CHARGE
Define the charge on electrode atom. If Charge is
specified, it will be applied uniformly to each atom
defined by electrode ASL. If electrode charge is not
specified, electrode charges will either be assigned
by interface electrode charges and bulk electrode
charges or keep the previously defined charges.
(default: None)
-interface_electrode_asl INTERFACE_ELECTRODE_ASL
Define ASL to select electrode atoms which are in
contact with electrolyte. (default: None)
-interface_electrode_charge INTERFACE_ELECTRODE_CHARGE
Define the charge on interface electrodeatom. If
Charge is specified, it will beapplied uniformly to
each atom definedby interface electrode ASL. (default:
None)
-bulk_electrode_charge BULK_ELECTRODE_CHARGE
Define the charge on bulk electrode atoms. If Charge
is specified, it will be applied uniformly to each
atom defined by bulk electrode ASL. (default: None)
Electrolyte options:
-electrolyte_atom_smile ELECTROLYTE_ATOM_SMILE
Add electrolyte atom in the system. (default: None)
-num_electrolyte_atoms NUM_ELECTROLYTE_ATOMS
Number of electrolyte atoms to add in the system.
(default: None)
-electrolyte_vdw_radius ELECTROLYTE_VDW_RADIUS
Van der Waals radius of electrolyte atom. (default:
2.0)
-electrolyte_range ELECTROLYTE_RANGE ELECTROLYTE_RANGE
Minimum and maximum coordinate of the system where the
electrolyte atoms will be added. (default: None)
-electrolyte_add_interval ELECTROLYTE_ADD_INTERVAL
Interval (in ps) between adding electrolyte atoms in
the system. (default: None)
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)