thermal_conductivity_driver.py Command Help

Command: $SCHRODINGER/run thermal_conductivity_gui_dir/thermal_conductivity_driver.py

usage: $SCHRODINGER/run thermal_conductivity_gui_dir/thermal_conductivity_driver.py
       [-h] [-grad_direction {a,b,c}] [-nswap NSWAP] [-nbin NBIN]
       [-swap_freq SWAP_FREQ] [-temp_freq TEMP_FREQ] [-relaxation]
       [-add_post_relaxation] [-qm_corr] [-qm_corr_time QM_CORR_TIME]
       [-qm_corr_trj_int QM_CORR_TRJ_INT] [-md_time MD_TIME]
       [-md_timestep MD_TIMESTEP] [-md_trj_int MD_TRJ_INT] [-seed SEED]
       [-save_trj_data {none,cms,trj}] [-md_umbrella] [-md_ensemble ENSEMBLE]
       [-md_temp MD_TEMP] [-no_cms_ff_update] [-HOST <hostname>] [-D]
       [-VIEWNAME <viewname>] [-JOBNAME JOBNAME]
       input_file

Compute thermal conductivity using reverse non-equilibrium MD method Copyright
Schrodinger, LLC. All rights reserved.

positional arguments:
  input_file            Input file

options:
  -h, -help             Show this help message and exit.
  -grad_direction {a,b,c}
                        Direction to establish temperature gradient (default:
                        a)
  -nswap NSWAP          Number of swaps between hot and cold atoms to
                        establish gradient (default: 1)
  -nbin NBIN            Number of bins to compute local temperature (default:
                        10)
  -swap_freq SWAP_FREQ  Time interval for velocity swap between hot and cold
                        atom (in ps) (default: 0.6)
  -temp_freq TEMP_FREQ  Temperature recording interval (in ps) (default: 0.1)
  -relaxation           Add an MD relaxation step (default: False)
  -add_post_relaxation  Add a post-relaxation step before the MD (default:
                        False)
  -qm_corr              Apply frozen phonon correction to the thermal
                        conductivity calculation (default: False)
  -qm_corr_time QM_CORR_TIME
                        MD time (ps) used for the Density of states
                        calculation. (default: 100.0)
  -qm_corr_trj_int QM_CORR_TRJ_INT
                        Trajectory interval (in ps) used for the Density of
                        state calculation. (default: 0.004)
  -md_time MD_TIME      MD time (in ns) of the simulation. (default: 20.0)
  -md_timestep MD_TIMESTEP
                        MD time step (in fs) of the simulations. (default:
                        1.0)
  -md_trj_int MD_TRJ_INT
                        MD trajectory recording interval (in ps). (default:
                        100.0)
  -seed SEED            Seed for random number generator. (default: 1234)
  -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)
  -md_umbrella          Run desmond subjobs on the driver host. (default:
                        False)
  -md_ensemble ENSEMBLE
                        Desmond ensemble. Known values are: NVE, NVT, NPT
                        (default: NVE)
  -md_temp MD_TEMP      Temperature (in K) of the simulations. (default:
                        300.0)
  -no_cms_ff_update     Do not update the force field of an input CMS file to
                        the current version. (default: False)

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)