openmmtools.multistate.ParallelTemperingAnalyzer¶
- class openmmtools.multistate.ParallelTemperingAnalyzer(*args, unbias_restraint=True, restraint_energy_cutoff='auto', restraint_distance_cutoff='auto', n_equilibration_iterations=None, statistical_inefficiency=None, max_subset=100, **kwargs)[source]¶
The ParallelTemperingAnalyzer is the analyzer for a simulation generated from a Parallel Tempering sampler simulation, implemented as an instance of the
ReplicaExchangeAnalyzer
as the sampler is a subclass of theyank.multistate.ReplicaExchangeSampler
See also
PhaseAnalyzer
ReplicaExchangeAnalyzer
- Attributes
has_log_weights
Return True if the storage has log weights, False otherwise
kT
Quantity of boltzmann constant times temperature of the phase in units of energy per mol
- max_n_iterations
- mbar
n_equilibration_iterations
int: The number of equilibration iterations.
n_iterations
int: The total number of iterations of the phase.
n_replicas
int: Number of replicas.
n_states
int: Number of sampled thermodynamic states.
name
User-readable string name of the phase
observables
List of observables that the instanced analyzer can compute/fetch.
reference_states
Tuple of reference states
i
andj
forMultiPhaseAnalyzer
instancesreporter
Sampler Reporter tied to this object.
- restraint_distance_cutoff
- restraint_energy_cutoff
statistical_inefficiency
float: The statistical inefficiency of the sampler.
- unbias_restraint
- use_full_trajectory
use_online_data
Get the online data flag
Methods
clear
()Reset all cached objects.
generate_mixing_statistics
([number_equilibrated])Compute and return replica mixing statistics.
get_effective_energy_timeseries
([energies, ...])Generate the effective energy (negative log deviance) timeseries that is generated for this phase.
get_enthalpy
()Compute the difference in enthalpy and error in that estimate from the MBAR object
get_entropy
()Compute the difference in entropy and error in that estimate from the MBAR object
get_free_energy
()Compute the free energy and error in free energy from the MBAR object
read_energies
()Extract energies from the ncfile and order them by replica, state, iteration.
read_logZ
([iteration])Extract logZ estimates from the ncfile, if present.
read_log_weights
()Extract log weights from the ncfile, if present.
reformat_energies_for_mbar
(u_kln[, n_k])Convert [replica, state, iteration] data into [state, total_iteration] data
show_mixing_statistics
([cutoff, ...])Print summary of mixing statistics.
- __init__(*args, unbias_restraint=True, restraint_energy_cutoff='auto', restraint_distance_cutoff='auto', n_equilibration_iterations=None, statistical_inefficiency=None, max_subset=100, **kwargs)¶
The reporter provides the hook into how to read the data, all other options control where differences are measured from and how each phase interfaces with other phases.
Methods
__init__
(*args[, unbias_restraint, ...])The reporter provides the hook into how to read the data, all other options control where differences are measured from and how each phase interfaces with other phases.
clear
()Reset all cached objects.
generate_mixing_statistics
([number_equilibrated])Compute and return replica mixing statistics.
get_effective_energy_timeseries
([energies, ...])Generate the effective energy (negative log deviance) timeseries that is generated for this phase.
get_enthalpy
()Compute the difference in enthalpy and error in that estimate from the MBAR object
get_entropy
()Compute the difference in entropy and error in that estimate from the MBAR object
get_free_energy
()Compute the free energy and error in free energy from the MBAR object
read_energies
()Extract energies from the ncfile and order them by replica, state, iteration.
read_logZ
([iteration])Extract logZ estimates from the ncfile, if present.
read_log_weights
()Extract log weights from the ncfile, if present.
reformat_energies_for_mbar
(u_kln[, n_k])Convert [replica, state, iteration] data into [state, total_iteration] data
show_mixing_statistics
([cutoff, ...])Print summary of mixing statistics.
Attributes
has_log_weights
Return True if the storage has log weights, False otherwise
kT
Quantity of boltzmann constant times temperature of the phase in units of energy per mol
max_n_iterations
Analyzer helper descriptor of a cached value with a dependency graph.
mbar
Analyzer helper descriptor of a cached value with a dependency graph.
n_equilibration_iterations
int: The number of equilibration iterations.
n_iterations
int: The total number of iterations of the phase.
n_replicas
int: Number of replicas.
n_states
int: Number of sampled thermodynamic states.
name
User-readable string name of the phase
observables
List of observables that the instanced analyzer can compute/fetch.
reference_states
Tuple of reference states
i
andj
forMultiPhaseAnalyzer
instancesreporter
Sampler Reporter tied to this object.
restraint_distance_cutoff
Analyzer helper descriptor of a cached value with a dependency graph.
restraint_energy_cutoff
Analyzer helper descriptor of a cached value with a dependency graph.
statistical_inefficiency
float: The statistical inefficiency of the sampler.
unbias_restraint
Analyzer helper descriptor of a cached value with a dependency graph.
use_full_trajectory
Analyzer helper descriptor of a cached value with a dependency graph.
use_online_data
Get the online data flag