Package ffx.algorithms.optimize.anneal

Class FlatEndAnnealSchedule

java.lang.Object
ffx.algorithms.optimize.anneal.FlatEndAnnealSchedule
All Implemented Interfaces:
AnnealingSchedule
public class FlatEndAnnealSchedule extends Object implements AnnealingSchedule
Composite annealing schedule with flat ends (i.e. spends extra time at the low and high temperatures).
Since:
1.0
Author:
Jacob M. Litman, Michael J. Schnieders

  • Constructor Summary

    Constructors
    Constructor
    Description
    FlatEndAnnealSchedule(AnnealingSchedule middle, double tLow, double tHigh, double lengthBefore, double lengthAfter)
    Creates a flat-ended annealing schedule based on a provided schedule for the middle, which is flat for some number of steps at the ends.

  • Method Summary

    Modifier and Type
    Method
    Description
    double
    getHighTemp()
    Gets the starting temperature.
    double
    getLowTemp()
    Gets the final temperature.
    int
    getNumWindows()
    Gets the number of annealing windows (including repeat windows).
    double
    getTemperature(int i)
    Get the temperature for annealing step i.
    double[]
    getTemperatures()
    Get all temperatures this schedule specifies.
    double
    maxWindowLength()
    Returns the longest window to be used (normalized to the number of MD steps in a "regular" window).
    double
    minWindowLength()
    Returns the shortest window to be used (normalized to the number of MD steps in a "regular" window).
    String
    toString()
     
    double
    totalWindowLength()
    Returns the sum of window lengths to be used (normalized to the number of MD steps in a "regular" window).
    double
    windowLength(int window)
    Get the relative size of a window (normalized to the number of MD steps in a "regular" window).

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

  • Constructor Details

    • FlatEndAnnealSchedule

      public FlatEndAnnealSchedule(AnnealingSchedule middle, double tLow, double tHigh, double lengthBefore, double lengthAfter)
      Creates a flat-ended annealing schedule based on a provided schedule for the middle, which is flat for some number of steps at the ends.
      Parameters:
      middle - Annealing schedule to use in the middle.
      tLow - Low temperature to use at the last window.
      tHigh - High temperature to use at the first window.
      lengthBefore - Relative length of the first ("flat") tempering window at the high temperature. 0 disables this end.
      lengthAfter - Relative length of the last ("flat") tempering window at the low temperature. 0 disables this end.

  • Method Details

    • getHighTemp

      public double getHighTemp()
      Description copied from interface: AnnealingSchedule
      Gets the starting temperature.
      Specified by:
      getHighTemp in interface AnnealingSchedule
      Returns:
      Starting temperature in Kelvin.

    • getLowTemp

      public double getLowTemp()
      Description copied from interface: AnnealingSchedule
      Gets the final temperature.
      Specified by:
      getLowTemp in interface AnnealingSchedule
      Returns:
      Final temperature in Kelvin.

    • getNumWindows

      public int getNumWindows()
      Description copied from interface: AnnealingSchedule
      Gets the number of annealing windows (including repeat windows).
      Specified by:
      getNumWindows in interface AnnealingSchedule
      Returns:
      Number of annealing windows.

    • getTemperature

      public double getTemperature(int i)
      Description copied from interface: AnnealingSchedule
      Get the temperature for annealing step i.
      Specified by:
      getTemperature in interface AnnealingSchedule
      Parameters:
      i - An annealing step [0-nWindows)
      Returns:
      Associated temperature.

    • getTemperatures

      public double[] getTemperatures()
      Description copied from interface: AnnealingSchedule
      Get all temperatures this schedule specifies.
      Specified by:
      getTemperatures in interface AnnealingSchedule
      Returns:
      An array of temperatures specified.

    • maxWindowLength

      public double maxWindowLength()
      Description copied from interface: AnnealingSchedule
      Returns the longest window to be used (normalized to the number of MD steps in a "regular" window).
      Specified by:
      maxWindowLength in interface AnnealingSchedule
      Returns:
      Maximum normalized window length.

    • minWindowLength

      public double minWindowLength()
      Description copied from interface: AnnealingSchedule
      Returns the shortest window to be used (normalized to the number of MD steps in a "regular" window).
      Specified by:
      minWindowLength in interface AnnealingSchedule
      Returns:
      Minimum normalized window length.

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • totalWindowLength

      public double totalWindowLength()
      Description copied from interface: AnnealingSchedule
      Returns the sum of window lengths to be used (normalized to the number of MD steps in a "regular" window).
      Specified by:
      totalWindowLength in interface AnnealingSchedule
      Returns:
      Total normalized window length.

    • windowLength

      public double windowLength(int window)
      Description copied from interface: AnnealingSchedule
      Get the relative size of a window (normalized to the number of MD steps in a "regular" window).
      Specified by:
      windowLength in interface AnnealingSchedule
      Parameters:
      window - Window to check.
      Returns:
      Normalized length of the window.