Package ffx.numerics.estimator

Class MultistateBennettAcceptanceRatio.HarmonicOscillatorsTestCase

java.lang.Object
ffx.numerics.estimator.MultistateBennettAcceptanceRatio.HarmonicOscillatorsTestCase
Enclosing class:
MultistateBennettAcceptanceRatio
public static class MultistateBennettAcceptanceRatio.HarmonicOscillatorsTestCase extends Object
Harmonic oscillators test case generates data for testing the MBAR implementation

  • Constructor Details

    • HarmonicOscillatorsTestCase

      public HarmonicOscillatorsTestCase(double[] O_k, double[] K_k, double beta)

  • Method Details

    • analyticalMeans

      public double[] analyticalMeans()

    • analyticalStandardDeviations

      public double[] analyticalStandardDeviations()

    • analyticalObservable

      public double[] analyticalObservable(String observable)

    • analyticalFreeEnergies

      public double[] analyticalFreeEnergies()

    • analyticalEntropies

      public double[] analyticalEntropies(int subtractComponent)

    • sample

      public Object[] sample(int[] N_k, String mode, Long seed)
      Sample from harmonic oscillator with gaussian and standard deviation.
      Parameters:
      N_k - number of snaps per state
      mode - only u_kn -> return K x N_tot matrix where u_kn[k,n] is reduced potential of sample n evaluated at state k
      Returns:
      u_kn[k, n] is reduced potential of sample n evaluated at state k