Package ffx.algorithms.cli

Class BarostatOptions

java.lang.Object
ffx.algorithms.cli.BarostatOptions
public class BarostatOptions extends Object
Represents command line options for scripts that use a barostat/NPT.
Since:
1.0
Author:
Michael J. Schnieders, Hernan V. Bernabe

  • Field Details

    • DEFAULT_MAX_DENSITY

      public static final String DEFAULT_MAX_DENSITY
      Default maximum density constraint on the barostat that prevents reduction in unit cell (particularly at or near vapor states).
      See Also:

    • DEFAULT_MIN_DENSITY

      public static final String DEFAULT_MIN_DENSITY
      Default "tin box" constraint on the barostat that prevents expansion of the unit cell (particularly at or near vapor states).
      See Also:

    • DEFAULT_MAX_ANGLE_MOVE

      public static final String DEFAULT_MAX_ANGLE_MOVE
      Default width of proposed crystal angle moves (uniformly distributed) in degrees.
      See Also:

    • DEFAULT_MAX_VOLUME_MOVE

      public static final String DEFAULT_MAX_VOLUME_MOVE
      Default size of proposed unit cell volume moves (uniformly distributed) in Angstroms^3.
      See Also:

    • DEFAULT_BAROSTAT_INTERVAL

      public static final String DEFAULT_BAROSTAT_INTERVAL
      Default mean number of MD steps (Poisson distribution) between barostat move proposals.
      See Also:

    • DEFAULT_BAROSTAT_PRINT_INTERVAL

      public static final String DEFAULT_BAROSTAT_PRINT_INTERVAL
      Default number of Barostat moves between print statements.
      See Also:

  • Constructor Details

    • BarostatOptions

      public BarostatOptions()

  • Method Details

    • checkNPT

      public CrystalPotential checkNPT(MolecularAssembly molecularAssembly, CrystalPotential crystalPotential)
      If pressure has been set > 0, creates a Barostat around a CrystalPotential, else returns the original, unmodified CrystalPotential.
      Parameters:
      molecularAssembly - Primary molecularAssembly of the CrystalPotential.
      crystalPotential - A CrystalPotential.
      Returns:
      Either a Barostat (NPT enabled) or the CrystalPotential.

    • createBarostat

      public Barostat createBarostat(MolecularAssembly assembly, CrystalPotential crystalPotential) throws IllegalArgumentException
      Creates a Barostat around a CrystalPotential.
      Parameters:
      assembly - Primary assembly of the CrystalPotential.
      crystalPotential - A CrystalPotential.
      Returns:
      An NPT potential.
      Throws:
      IllegalArgumentException - If this BarostatOptions has pressure <= 0.

    • getPressure

      public double getPressure()
      -p or --npt Specify use of a Monte Carlo Barostat at the given pressure (default 0 = constant volume).
      Returns:
      Returns the pressure (atm).

    • setPressure

      public void setPressure(double pressure)

    • isIsotropic

      public boolean isIsotropic()
      Restrict the MC Barostat to isotropic moves. The lattice angles are * held fixed, and lattice lengths are scaled equally.
      Returns:
      Returns true if the Barostat is isotropic.

    • setIsotropic

      public void setIsotropic(boolean isotropic)

    • getMaxD

      public double getMaxD()
      The maximum density accepted by the MC Barostat (g/cc).
      Returns:
      Returns the maximum density.

    • setMaxD

      public void setMaxD(double maxD)

    • getMinD

      public double getMinD()
      The minimum density accepted by the MC Barostat (g/cc).
      Returns:
      Returns the minimum density.

    • setMinD

      public void setMinD(double minD)

    • getMaxV

      public double getMaxV()
      The volume of a proposed unit cell volume moves (uniformly distributed) in Angstroms^3.
      Returns:
      Returns the maximum volume move.

    • getMaxAM

      public double getMaxAM()
      The width of proposed crystal angle moves (uniformly distributed) in degrees.
      Returns:
      Returns the width of angle moves.

    • setMaxAM

      public void setMaxAM(double maxAM)

    • setMaxV

      public void setMaxV(double maxV)

    • getBarInt

      public int getBarInt()
      The mean number of MD steps (Poisson distribution) between barostat move proposals.
      Returns:
      Returns the mean number of MD steps between barostat MC trials.

    • setBarInt

      public void setBarInt(int barInt)

    • getPrintInt

      public int getPrintInt()
      --bpi or --barostatPrintInterval Sets the number of Barostat MC cycles between print statements.

    • setPrintInt

      public void setPrintInt(int printInterval)