adsorption_energy_driver.py Command Help

Command: $SCHRODINGER/run adsorption_energy_gui_dir/adsorption_energy_driver.py

usage: $SCHRODINGER/run adsorption_energy_gui_dir/adsorption_energy_driver.py
       [-h] [-periodic] [-cfg FILE_NAME] [-mlff]
       [-mlff_keywords KEYWORD=VALUE KEYWORD=VALUE ...] [-mlff_preopt]
       [-keywords KEYWORD=VALUE KEYWORD=VALUE ...] [-free_energy]
       [-free_energy_loss FREE_ENERGY_LOSS] [-frozen] [-temp_start KELVIN]
       [-temp_points POINTS] [-temp_stepsize KELVIN] [-pressure_start KELVIN]
       [-pressure_points POINTS] [-pressure_stepmult MULTIPLIER]
       [-TPP THREADS] [-nimage NIMAGE] [-npools NPOOLS]
       [-ntg NTG | -nband NBAND] [-fraginput] [-include_kj]
       [-use_zip_data TARFILE] [-HOST <hostname>] [-D] [-VIEWNAME <viewname>]
       [-JOBNAME JOBNAME]
       input_file

Driver to compute energies for Gas-Surface -> Adsorbate reactions Copyright
Schrodinger, LLC. All rights reserved.

positional arguments:
  input_file            Input file

options:
  -h, -help             Show this help message and exit.
  -TPP THREADS          Number of threads per Jaguar or QE subjob (default: 1)
  -fraginput            Input file contains all reactants and fragments rather
                        than just reactants. (default: False)
  -include_kj           Include kJ/mol energy properties. (default: False)
  -use_zip_data TARFILE
                        The data in the specified archive from a previous job
                        will be used instead of running those steps again.
                        (default: None)

QM treatment:
  -periodic             Treat all structures as periodic using Quantum
                        ESPRESSO. The substrate will use the same PBC as the
                        adsorbate, the gas molecule get a PBC that provides a
                        buffer around the molecule. Free energy corrections
                        will still be computed using Jaguar on a non-periodic
                        gas molecule. (default: False)
  -cfg FILE_NAME        File name of the Quantum ESPRESSO cfg file. (default:
                        None)
  -mlff                 Compute adsorption energy with the given machine
                        learning force field. Structures can be periodic or
                        non-periodic. This flag does not affect the free
                        energy calculation performed by -free_energy (default:
                        False)
  -mlff_keywords KEYWORD=VALUE KEYWORD=VALUE ...
                        Jaguar keywords for the -mlff calculation, given as
                        space-separated keyword=value pairs (default:
                        mlff=Hybrid_MPNICE mlff_use_pbc=1)
  -mlff_preopt          Perform a Jaguar MLFF optimization of each structure
                        before running DFT. The keywords provided by
                        -mlff_keywords are used for the calculation. (default:
                        False)
  -keywords KEYWORD=VALUE KEYWORD=VALUE ...
                        Jaguar keywords given as a space-separated
                        keyword=value pairs (default: dftname=B3LYP
                        basis=MIDIXL)
  -free_energy          Compute free energies using non-periodic entropy
                        calculations and pressure contributions. (default:
                        False)
  -free_energy_loss FREE_ENERGY_LOSS
                        Percent of free energy lost by the gas molecule when
                        going from gas phase to adsorbed. (default: 30)
  -frozen               Use geometries frozen at the input geometry. For
                        Quantum ESPRESSO calculations, this requires a .cfg
                        file consistent with an SCF-only calculation. This
                        flag is ignored for any entropy calculations because
                        they must do a geometry optimization. This flag may
                        not be used with -free_energy when -periodic is not
                        also used. (default: False)

Temperature and pressure:
  -temp_start KELVIN    Starting temperature for the free energy calculations.
                        To compute free energy at several temperatures,
                        additionally specify the number of temperatures with
                        -temp_points and the step size with -temp_stepsize
                        (default: 298.15)
  -temp_points POINTS   Number of temperature points. (default: 1)
  -temp_stepsize KELVIN
                        Size of each temperature step. (default: 50.0)
  -pressure_start KELVIN
                        Starting pressure for the free energy calculations. To
                        compute free energy at several pressures, additionally
                        specify the number of pressures with -pressure_points
                        and the step multiplier with {FLAG_PRESSURE_STEPMULT}
                        (default: 0.13)
  -pressure_points POINTS
                        Number of pressure points. (default: 1)
  -pressure_stepmult MULTIPLIER
                        Multiplier for each pressure step. (default: 10.0)

Quantum ESPRESSO parallel options:
  -nimage NIMAGE        Number of images (points in the configuration space)
                        (default: None)
  -npools NPOOLS        Number of K-point groups to run in parallel (default:
                        None)
  -ntg NTG              Number of task groups to run in parallel (default:
                        None)
  -nband NBAND          Number of bands to run in parallel (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)
  -JOBNAME JOBNAME      Provide an explicit name for the job. (default: None)