LnProbability

class LnProbability

Natural logarithm of a probability distribution.

Public Functions

LnProbability(const std::vector<double> &values)

Construct with given values.

double value(const int bin) const

Return the value of the bin.

void set_value(const int bin, const double value)

Set the value of the bin.

void add(const int bin, const double value_to_add)

Add to the value of the bin.

void resize(const int size)

Set the number of macrostates.

const std::vector<double> values() const

Return the values.

int size() const

Return the size of the distribution.

double sum_probability(const int min, const int max) const

Return the sum of the probability from min to max indices.

double sum_probability() const

Return the sum of the probability of all values.

void normalize()

Normalize such that the sum of the probability is unity.

std::vector<int> minima(const int num_smooth = 10) const

Return the local minimum indices which are canditates for phase boundary. The returned indices must be global minimum between +/- num_smooth.

double equilibrium_objective(const int num_smooth = 10) const

Parameters

• num_smooth: Number of macrostates which define ‘local’ region for finding the minimum.

Return the objective function to minimize in order to obtain equilibrium between phases. If no phase boundaries, return the squared difference between the minimum and maximum values. If more than one, no current implementation. If exactly one, use objective function below.

double equilibrium_objective_boundary(int phase_boundary) const

Parameters

• phase_boundary: Index which is the boundary between phases. The exact index value is included in the second phase.

Return the objective function to minimize in order to obtain equilibrium between phases. The objective is the squared difference between the natural logs of the probabilities of the two phases.

LnProbability reduce(const int keep_every, const int start = 0) const

Return a reduced lnpi by keeping every this many macrostates.

Parameters

• keep_every: for keep_every == 2, return macrostates 0, 2, 4, 6…

• start: start from this value (default: 0). If negative, increment by keep_every