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 Summary

Constructors

Constructor	Description
HarmonicOscillatorsTestCase(double[] O_k, double[] K_k, double beta)	Constructor for HarmonicOscillatorsTestCase

Method Summary

Modifier and Type	Method	Description
double[]	analyticalEntropies(int subtractComponent)
double[]	analyticalFreeEnergies()
double[]	analyticalMeans()
double[]	analyticalObservable(String observable)
double[]	analyticalStandardDeviations()
double[]	analyticalVariances()
static Object[]	evenlySpacedOscillators(int n_states, int n_samplesPerState, double lower_O_k, double upper_O_k, double lower_K_k, double upper_K_k, Long seed)
static void	main(String[] args)
Object[]	sample(int[] N_k, String mode, Long seed)	Sample from harmonic oscillator w/ gaussian invalid input: '&' std

Methods inherited from class java.lang.Object

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

Constructor Details

HarmonicOscillatorsTestCase

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

Constructor for HarmonicOscillatorsTestCase

Parameters:

O_k - array of equilibrium positions

K_k - array of spring constants

beta - inverse temperature

Method Details

analyticalMeans

public double[] analyticalMeans()

analyticalVariances

public double[] analyticalVariances()

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 w/ gaussian invalid input: '&' std

Parameters:

N_k - number of samples 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

evenlySpacedOscillators

public static Object[] evenlySpacedOscillators(int n_states,
 int n_samplesPerState,
 double lower_O_k,
 double upper_O_k,
 double lower_K_k,
 double upper_K_k,
 Long seed)

main

public static void main(String[] args)