openpathsampling.analysis.tis.StandardTISAnalysis
- class openpathsampling.analysis.tis.StandardTISAnalysis(network, steps=None, flux_method=None, scheme=None, ctp_method=None, max_lambda_calcs=None, combiners=None)[source]
Standard TIS analysis: flux, TCP, CTP.
This is what we call the “standard” TIS analysis. It splits the rate equation into a flux, a total crossing probability (calculated using ensemble crossing probability functions), and a conditional transition probability from the outermost interface.
Whenever possible, this code allows you to use default values.
For the flux, you must provide either a flux method or a move scheme (which will use the
MinusMoveFlux
).For the conditional transition probability, you may optionally provide a
ConditionalTransitionProbability
object, otherwise the code will create one for the outermost interfaces of each transition.For the total crossing probability, you must provide a dictionary for the
max_lambda_calcs
. The keys of this dictionary are the sampling transitions; the values can either be anEnsembleHistogrammer
(such as aFullHistogramMaxLambdas
) or a dictionary of histogram parameters, in which case the histogram parameters will be passed toFullHistogramMaxLambdas
. In addition, you may optionally provide a dictionary forcombiners
, which maps the interface set within the sampling transitions to a combining function, such asWHAM
. The default is to useWHAM
.- Parameters:
network (
TISNetwork
) – the network to analyzesteps (iterable of
MCStep
) – if given, the analysis is performed immediately using these steps; otherwise, the analysis can be performed later withcalculate()
flux_method (flux calculation method) – the method to use to calculate the flux; typical classes are
MinusMoveFlux
andDictFlux
. Optional, but if not given thenscheme
must be given.scheme (
MoveScheme
) – used to create aMinusMoveFlux
ifflux_method
is not provided. Not used ifflux_method
is given.ctp_method (
ConditionalTransitionProbability
) – object for calculating the conditional transition probability (optional)max_lambda_calcs (dict) – determines how the ensemble crossing probability histograms are build. Keys are sampling transitions, and values can be either
EnsembleHistogrammer
subclasses, or a list of histogram parameters to pass toFullHistogramMaxLambdas
.combiners (dict {
InterfaceSet
: combination method}) – links the interface set to the method that will be used to combine individual ensembles into the total crossing probability function. Default is to useWHAM
.
- __init__(network, steps=None, flux_method=None, scheme=None, ctp_method=None, max_lambda_calcs=None, combiners=None)[source]
Methods
__init__
(network[, steps, flux_method, ...])args
()Return a list of args of the __init__ function of a class
base
()Return the most parent class actually derived from StorableObject
calculate
(steps)Perform the analysis, using steps as input.
count_weaks
()Return number of objects subclassed from StorableObject still in memory
crossing_probability
(ensemble)Crossing probability function for a given ensemble
descendants
()Return a list of all subclassed objects
fix_name
()Set the objects name to be immutable.
flux
(from_state[, through_interface])Flux from a volume and through and interface.
from_dict
(dct)Reconstruct an object from a dictionary representaiton
from_weighted_trajectories
(input_dict)Calculate results from weighted trajectories dictionary.
get_uuid
()idx
(store)Return the index which is used for the object in the given store.
named
(name)Name an unnamed object.
objects
()Returns a dictionary of all storable objects
rate
(from_state, to_state)Rate for the transition between two states
rate_matrix
([steps])Calculate the rate matrix.
reverse_uuid
()ruuid
(uid)set_observer
(active)(De-)Activate observing creation of storable objects
state_fluxes
(from_state)All fluxes associated with a given initial state.
to_dict
()Convert object into a dictionary representation
transition_probability
(from_state, to_state)Transition probability between two states.
Attributes
ACTIVE_LONG
CREATION_COUNT
INSTANCE_UUID
base_cls
Return the base class
base_cls_name
Return the name of the base class
cls
Return the class name as a string
conditional_transition_probability
conditional transition probabilities
default_name
Return the default name.
flux_matrix
float}: keys are (state, interface); values are the associated flux
is_named
True if this object has a custom name.
name
Return the current name of the object.
observe_objects
progress
total_crossing_probability
total crossing probability
transition_probability_matrix
matrix of transition probabilities