Package ffx.algorithms.commands

Class Minimize

java.lang.Object
ffx.utilities.FFXCommand
ffx.algorithms.cli.AlgorithmsCommand
ffx.algorithms.commands.Minimize
public class Minimize extends AlgorithmsCommand
The Minimize script uses a limited-memory BFGS algorithm to minimize the energy of a molecular system.
Usage:
ffxc Minimize [options] <filename> [file2...]

  • Constructor Details

    • Minimize

      public Minimize()
      Minimize Constructor.

    • Minimize

      public Minimize(FFXBinding binding)
      Minimize Constructor.
      Parameters:
      binding - The Binding to use.

    • Minimize

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

  • Method Details

    • run

      public Minimize run()
      Execute this Command.
      Overrides:
      run in class FFXCommand
      Returns:
      The current FFXCommand.

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • getEnergyList

      public List<Double> getEnergyList()
      Get the list of energies recorded during minimization.
      Returns:
      A List of Double energies, or null if minimization was not run.

    • getRMSGradient

      public double getRMSGradient()
      Get the final RMS gradient after minimization.
      Returns:
      The final RMS gradient or NaN if minimization was not run.

    • getEnergy

      public double getEnergy()
      Get the final energy after minimization.
      Returns:
      The final energy or NaN if minimization was not run.

    • getPotentials

      public List<Potential> getPotentials()
      Returns a List of all Potential objects associated with this script.
      Overrides:
      getPotentials in class AlgorithmsCommand
      Returns:
      All Potentials. Sometimes empty, never null.