stress_strain_driver.py Command Help
Command: $SCHRODINGER/run stress_strain_gui_dir/stress_strain_driver.py
usage: $SCHRODINGER/run stress_strain_gui_dir/stress_strain_driver.py
[-h] [-eta ETA] [-deformation_step_size DEFORMATION_STEP_SIZE]
[-max_strain_step MAX_STRAIN_STEP] [-num_cycle NUM_CYCLE] [-cyclic]
[-deformation_steps DEFORMATION_STEPS]
[-deformation_dir {a,b,c} [{a,b,c} ...]]
[-cyclic_type {sawtooth,sinusoidal}] [-ptensor_avg PTENSOR_AVG]
[-residual_strain RESIDUAL_STRAIN] [-md_enegrp_int MD_ENEGRP_INT]
[-react] [-smarts SMARTS] [-smarts_index SMARTS_INDEX]
[-smarts_method {internal,canvas,rdkit}]
[-max_reactive_bond MAX_REACTIVE_BOND]
[-bond_cutoff_percent BOND_CUTOFF_PERCENT]
[-brownie_relax_time BROWNIE_RELAX_TIME] [-md_time MD_TIME]
[-md_temp MD_TEMP] [-md_press MD_PRESS] [-md_timestep MD_TIMESTEP]
[-md_trj_int MD_TRJ_INT] [-md_ptensor_int MD_PTENSOR_INT] [-seed SEED]
[-md_ensemble ENSEMBLE] [-save_trj_data {none,cms,trj}] [-combine_trj]
[-md_umbrella] [-no_cms_ff_update] [-D] [-OPLSDIR OPLSDIR]
input_file
Driver for the Stress Strain simulations. Copyright Schrodinger, LLC. All
rights reserved.
positional arguments:
input_file Input file.
options:
-h, -help Show this help message and exit.
-eta ETA Eta of the deformation. Allowed values are between
-1.00 and 0.50. (default: 0.5)
-deformation_step_size DEFORMATION_STEP_SIZE
Deformation step size in the deformation direction.
(default: 0.015)
-max_strain_step MAX_STRAIN_STEP
Maximum number of steps in the deformation direction
for the initial step in cyclic stress strain
simulation. (default: 80)
-num_cycle NUM_CYCLE Number of stress strain loading cycles. (default: 10)
-cyclic Enable cyclic stress strain simulation. (default:
False)
-deformation_steps DEFORMATION_STEPS
Number of deformation steps. (default: 40)
-deformation_dir {a,b,c} [{a,b,c} ...]
List of main deformation directions. (default: a)
-cyclic_type {sawtooth,sinusoidal}
Type of cyclic stress strain simulation. (default:
sawtooth)
-ptensor_avg PTENSOR_AVG
Percentage of the the total trajectory to use when
computing pressure tensor. (default: 20.0)
-residual_strain RESIDUAL_STRAIN
Perform residual strain calculations. Percentage of
the the total trajectory to use when computing NPT
cell dimensions. (default: None)
-md_enegrp_int MD_ENEGRP_INT
Removed in 2022-2, use -md_ptensor_int instead to set
pressure tensor interval. (default: None)
-md_time MD_TIME MD time (in ns) of the simulation. (default: 100.0)
-md_temp MD_TEMP Temperature (in K) of the simulations. (default:
300.0)
-md_press MD_PRESS Pressure (in bar) of the simulations. (default:
1.01325)
-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_ptensor_int MD_PTENSOR_INT
MD pressure tensor recording interval (in ps).
(default: 1.0)
-seed SEED Seed for random number generator. (default: 1234)
-md_ensemble ENSEMBLE
Desmond ensemble. Known values are: NVE, NVT, NPT
(default: NVT)
-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)
-combine_trj Merge all trajectories into a single one. (default:
False)
-md_umbrella Run desmond subjobs on the driver host. (default:
False)
-no_cms_ff_update Do not update the force field of an input CMS file to
the current version. (default: False)
Setting for bond scission.:
-react Allow bond breaking during simulation. (default:
False)
-smarts SMARTS Define SMARTS for reactive species. Add multiple
-SMARTS flags to define multiple reactive species.
(default: None)
-smarts_index SMARTS_INDEX
Define two integers (comma separated) to determine the
reactive bond. SMARTS indices must be defined for each
SMARTS entry. (default: None)
-smarts_method {internal,canvas,rdkit}
SMARTS matching method. (default: internal)
-max_reactive_bond MAX_REACTIVE_BOND
Maximum number of bond scissions allowed per strain
step. (default: 5)
-bond_cutoff_percent BOND_CUTOFF_PERCENT
Define reactive bond criteria in terms of percentage
increase from the equilibrium value. For example,
-bond_cutoff_percent 20 means any bond above 1.20
times the equilibrium length is a candidate for
reaction. (default: 20)
-brownie_relax_time BROWNIE_RELAX_TIME
Time (in ps) for brownian MD. (default: 100)
Job Control Options:
-D, -DEBUG Show details of Job Control operation. (default:
False)
-OPLSDIR OPLSDIR Specifies directory for custom forcefield parameters.
(default: None)