Package ffx.potential.commands

Class PhEnergy

java.lang.Object
ffx.utilities.FFXCommand
ffx.potential.cli.PotentialCommand
ffx.potential.commands.PhEnergy
public class PhEnergy extends PotentialCommand
The Energy script evaluates the energy of a system.
Usage:
ffxc PhEnergy <filename>

  • Field Details

  • Constructor Details

    • PhEnergy

      public PhEnergy()
      Energy constructor.

    • PhEnergy

      public PhEnergy(FFXBinding binding)
      Energy constructor.
      Parameters:
      binding - The Binding to use.

    • PhEnergy

      public PhEnergy(String[] args)
      PhEnergy constructor that sets the command line arguments.
      Parameters:
      args - Command line arguments.

  • Method Details

    • run

      public PhEnergy run()
      Execute the script.
      Overrides:
      run in class FFXCommand
      Returns:
      The current FFXCommand.

    • getPotentials

      public List<Potential> getPotentials()
      Description copied from class: PotentialCommand
      Returns a List of all Potential objects associated with this script. Should be written to tolerate nulls, as many tests run help() and exit without instantiating their Potentials.
      Overrides:
      getPotentials in class PotentialCommand
      Returns:
      All Potentials. Sometimes empty, never null.

    • setESVLambda

      public static void setESVLambda(double lambda, ExtendedSystem extendedSystem)
      Sets lambda values for the extended system. Note that it is expected that the tautomer is set correctly from dynamics.
      Parameters:
      lambda -
      extendedSystem -

    • setESVTautomer

      public static void setESVTautomer(double tautomer, ExtendedSystem extendedSystem)
      Sets tautomer values for the extended system. Note that it is expected that the lambda is set correctly from dynamics.
      Parameters:
      tautomer -
      extendedSystem -