Package ffx.algorithms.thermodynamics

Class OrthogonalSpaceTempering.Histogram

java.lang.Object
ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram
Enclosing class:
OrthogonalSpaceTempering
public class OrthogonalSpaceTempering.Histogram extends Object
Store and operate on a 2D Histogram of (Lambda, dU/dL) observations to produce an OST bias.
Since:
1.0
Author:
Michael J. Schnieders

  • Field Details

    • world

      protected final Comm world
      Parallel Java world communicator.

    • rank

      protected final int rank
      Rank of this process.

  • Method Details

    • disableResetStatistics

      public void disableResetStatistics()

    • evaluateTotalOSTBias

      public StringBuffer evaluateTotalOSTBias(boolean bias)
      evaluateTotalBias.
      Parameters:
      bias - If false, return the negative of the Total OST bias.
      Returns:
      A StringBuffer The total OST Bias.

    • evaluate2DOSTBias

      public StringBuffer evaluate2DOSTBias(boolean bias)
      evaluate2DOSTBias.
      Parameters:
      bias - If false, return the negative of the 2D OST bias.
      Returns:
      A StringBuffer with the 2D OST bias.

    • getIndependentWalkers

      public boolean getIndependentWalkers()
      For MPI parallel jobs, returns true if the walkers are independent (i.e. contribute to only their own histogram).
      Returns:
      True if the walkers are independent.

    • getLambdaResetValue

      public double getLambdaResetValue()

    • getRank

      public int getRank()
      For MPI parallel jobs, return the rank of this process.
      Returns:
      The rank of this process.

    • getResetStatistics

      public boolean getResetStatistics()

    • getSynchronousSend

      public Optional<SendSynchronous> getSynchronousSend()
      Return the SynchronousSend associated with this Histogram, if any.
      Returns:
      The SynchronousSend, if any.

    • setLastReceiveddUdL

      public void setLastReceiveddUdL(double lastReceiveddUdL)

    • updateFreeEnergyDifference

      public double updateFreeEnergyDifference(boolean print, boolean save)

    • updateMetaDynamicsFreeEnergyDifference

      public double updateMetaDynamicsFreeEnergyDifference(boolean print, boolean save)
      Update the free energy estimate for Meta Dynamics.
      Parameters:
      print - Whether to write the histogram to screen.
      save - Whether to write the histogram to disk.
      Returns:
      Free energy (via integration of ensemble-average dU/dL)

    • updateOSTFreeEnergyDifference

      public double updateOSTFreeEnergyDifference(boolean print, boolean save)
      Eqs. 7 and 8 from the 2012 Crystal Thermodynamics paper.
      Parameters:
      print - Whether to write the histogram to screen.
      save - Whether to write the histogram to disk.
      Returns:
      Free energy (via integration of ensemble-average dU/dL)

    • setLastReceivedLambda

      public void setLastReceivedLambda(double lastReceivedLambda)