Posterior Sampling State¶
Class providing the state vector during Bayesian posterior sampling simulations—the current position of a Markov chain in parameter space, together with its chain index, step count, and parameter count. Implementations store and retrieve the parameter vector (via get/set), advance the step counter, and optionally maintain a history of chain positions for convergence diagnostics. The state is updated at each MCMC step and queried by the likelihood function to evaluate the model at the proposed parameter values.
Default implementation: posteriorSampleStateSimple
Methods¶
parameterCountSet→voidSet the number of active parameters that this state vector will track, allocating internal storage for the parameter vector of the given dimension.
integer, intent(in ) :: parameterCount
chainIndex→integerReturn the integer index (0-based) of the Markov chain that owns this state object, used to identify chains in multi-chain posterior sampling algorithms.
chainIndexSet→voidAssign the integer chain index to this state object, identifying which Markov chain it belongs to in a multi-chain ensemble sampler.
integer, intent(in ) :: chainIndex
count→integerReturns the total number of sampling steps that have been taken since the state was last reset, used for logging and convergence diagnostics.
dimension→integerReturns the number of active parameters (dimension of the state vector) for this sampling state, equal to the value previously set by
parameterCountSet.reset→voidReset the state object to its initial condition by zeroing the step counter and clearing any accumulated history, in preparation for a new sampling run.
get→double precision, dimension(self%parameterCount)Return the current parameter vector representing the position of this chain in the model parameter space at the most recently accepted sampling step.
update→voidAdvance the state to the new parameter vector
stateNew, optionally logging it to the chain history;isConvergedandoutlierMaskare used to track whether post-convergence steps should be recorded.double precision, intent(in ), dimension(:) :: stateNewlogical , intent(in ) :: logStatelogical , intent(in ) :: isConvergedlogical , intent(in ), dimension(:), optional :: outlierMask
mean→double precision, dimension(self%parameterCount)Return the mean parameter vector computed over all stored steps in the chain history, providing a point estimate of the posterior mode or mean.
variance→double precision, dimension(self%parameterCount)Return the per-parameter variance computed over all stored steps in the chain history, providing a measure of posterior width for each model parameter.
acceptanceRate→double precisionReturn the fraction of proposed moves that were accepted over the recent history of this chain, used to monitor and adaptively tune proposal distributions.
restore→voidReplay a previously recorded state vector into the state history one step at a time, used when resuming a sampling run from a saved log file;
firstsignals the start of the restoration sequence.double precision, intent(in ), dimension(:) :: stateVectorlogical , intent(in ) :: first
posteriorSampleStateCorrelation¶
An extension of the history state, this class also computes and stores the correlation length in each parameter (which is taken to be the median correlation length over all non-outlier chains).
Methods
correlationLength— Return the current correlation length in the chains.correlationLengthCompute— Compute correlation lengths in the chains.postConvergenceCorrelationCount— Return the number of post-convergence correlation lengths that have accrued.
Parameters
[acceptedStateCount](default100) — The number of states to use in acceptance rate statistics.[missingRootHalosAreFatal](default.true.) — If true, if a hosted root halo is not found then a fatal error occurs. Otherwise, such cases are ignored and will not contribute to the halo mass function.[massMinimum]— The minimum mass to consider counts.[massMaximum]— The maximum mass to consider.[massCountPerDecade]— The number of bins per decade of mass.[countBootstraps]— The number of bootstrap samples to perform.[description]— A description of this mass function.[simulationReference]— A reference for the simulation.[simulationURL]— A URL for the simulation.
posteriorSampleStateHistory¶
An extension of the simple state, this class also records the mean and variance of each parameter over the history of the simulation.
Methods
operator(+)— Addition operator.operator(-)— Subtraction operator.operator(/)— Division operator.operator(*)— Multiplication operator.isZero— Returns true if the history is entirely zero.create— Creates a history object with a specified range of times.builder— Build a history object from an XML definition.dump— Dump a history object.dumpRaw— Dump a history object in binary.readRaw— Read a history object in binary.clone— Clone a history object.destroy— Destroys a history object.trim— Removes any times in a history which have become outdated.trimForward— Removes any times in a history after the given time. Optionally returns a history object with the removed history.increment— Adds two histories, possibly with different time series.interpolatedIncrement— Adds two histories, possibly with different time series, by interpolating the second onto the times of the first and adding the interpolated values.extend— Extends the time range of a history to encompass the specified limits.reset— Resets all entries in a history to zero.setToUnity— Set all entries in a history to unity.exists— Returns true if the given history has been created.timeSteps— Returns an array with the timesteps (i.e. the intervals between successive times) in the given history.serializeCount— Return a count of the number of properties in a serialized history object.serialize— Serialize a history object to an array.deserialize— Deserialize a history object from an array.append— Append a history or single instant onto the end of a history.nonStaticSizeOf— Returns the size of any non-static components of the type.create— Creates a history object with a specified range of times.builder— Build a history object from an XML definition.dump— Dump a history object.dumpRaw— Dump a history object in binary.readRaw— Read a history object in binary.clone— Clone a history object.destroy— Destroys a history object.trim— Removes any times in a history which have become outdated.trimForward— Removes any times in a history after the given time. Optionally returns a history object with the removed history.reset— Resets all entries in a history to zero.exists— Returns true if the given history has been created.append— Append a history or single instant onto the end of a history.nonStaticSizeOf— Returns the size of any non-static components of the type.
Parameters
[acceptedStateCount](default100) — The number of states to use in acceptance rate statistics.[timeBegin](default0.05d0*ageUniverse) — The earliest time at which to tabulate the volume averaged history of galaxies (in Gyr).[timeEnd](defaultageUniverse) — The latest time at which to tabulate the volume averaged history of galaxies (in Gyr).[historyCount](default30) — The number of steps (spaced logarithmically in cosmic time) at which to tabulate the volume averaged history of galaxies.
posteriorSampleStateSimple¶
This class stores the current state but makes no attempt to record a history of the state and so cannot provide measures of the mean or variance of state over the simulation history. It does, however, maintain a running average of the state acceptance rate. The number of steps over which the acceptance rate should be computed is specified by the acceptedStateCount.
(Default implementation)
Methods
calculationReset— Reset memoized calculations.
Parameters
[efficiencyWind](default2.2157d-3) — The coupling efficiency of the black hole accretion-driven wind, defined as the fraction of the accreted rest-mass energy that is deposited as kinetic or thermal energy into the surrounding gas via AGN-driven outflows.[redshiftReionization](default9.97d0) — The redshift of reionization below which baryonic accretion onto halos is suppressed due to the ionizing background heating the intergalactic medium and preventing gas from accreting onto low-mass halos.[opticalDepthReionization]— The optical depth to electron scattering below which baryonic accretion is suppressed.[velocitySuppressionReionization](default35.0d0) — The velocity scale below which baryonic accretion is suppressed.[accretionNegativeAllowed](default.true.) — Specifies whether negative accretion (mass loss) is allowed in the simple halo accretion model.[accretionNewGrowthOnly](default.false.) — Specifies whether accretion from the IGM is allowed only when a halo is growing past its previous greatest mass.[acceptedStateCount](default100) — The number of states to use in acceptance rate statistics.[timeStepRelative](default0.1d0) — The maximum allowed relative change in time for a single step in the evolution of a node.[timeStepAbsolute](default1.0d0) — The maximum allowed absolute change in time (in Gyr) for a single step in the evolution of a node.[timeStepMinimum](default1.0d-6) — The smallest timestep to use in profiling ODE solver steps.[timeStepMaximum](default1.0d+1) — The largest timestep to use in profiling ODE solver steps.[timeStepPointsPerDecade](default3) — The number of bins per decade of timestep to use when profiling ODE solver steps.[wavelength](default1.0d4) — The wavelength of the photon packet (in AA).[wavelengthMinimum](default0.5d4) — The minimum wavelength of the photon packet (in AA).[wavelengthMaximum](default2.0d4) — The maximum wavelength of the photon packet (in AA).[luminosity](default1.0d0) — The luminosity of the photon packet (in \(L_\odot\)).[massRatioMajorMerger](default0.25d0) — The mass ratio above which mergers are considered to be “major”.[destinationGasMinorMerger](defaultvar_str('spheroid')) — The component to which satellite galaxy gas moves to as a result of a minor merger.[destinationStarsMinorMerger](defaultvar_str('spheroid')) — The component to which satellite galaxy stars move to as a result of a minor merger.[degreesOfFreedom](default3.0d0) — Number of degrees of freedom to assume when computing the energy density of cooling gas in the “simple” cooling time class.[timeScale](default1.0d0) — The timescale (in Gyr) for cooling in the simple cooling rate model.[reionizationRedshift](default9.97d0) — The redshift of reionization in the simple IGM state model.[reionizationTemperature](default1.0d4) — The post-reionization temperature (in units of Kelvin) in the simple IGM state model.[preReionizationTemperature](default10.0d0) — The pre-reionization temperature (in units of Kelvin) in the simple IGM state model.[useFormationHalo](default.false.) — Specifies whether or not the “formation halo” should be used when solving for the radii of galaxies.[solveForInactiveProperties](default.true.) — If true, galactic structure is solved for during evaluation of inactive property integrals. Otherwise, structure is not solved for during this phase—this should only be used if the inactive property integrands do not depend on galactic structure.[rateFractionalMaximum](default10.0d0) — The maximum fractional mass loss rate per dynamical time in the simple model of mass loss due to tidal stripping.[beta](default1.0d0) — The scaling factor which multiplies the tidal mass loss rate.[OmegaMatter](default0.3153d0) — The density of matter in the Universe in units of the critical density.[OmegaBaryon](default0.04930d0) — The density of baryons in the Universe in units of the critical density.[OmegaDarkEnergy](default0.6847d0) — The density of dark energy in the Universe in units of the critical density.[temperatureCMB](default2.72548d0) — The present day temperature of the CMB in units of Kelvin.[HubbleConstant](default67.36d0) — The present day value of the Hubble parameter in units of km/s/Mpc.