openpathsampling.collectivevariables.CollectiveVariable

class openpathsampling.collectivevariables.CollectiveVariable(name, cv_time_reversible=False)[source]

Wrapper for a function that acts on snapshots or iterables of snapshots

Parameters
  • name (string) – A descriptive name of the collectivevariable. It is used in the string representation.

  • cv_time_reversible (bool) – If True (default) the CV assumes that reversed snapshots have the same value. This is the default case when CVs do not depend on momenta reversal. This will speed up computation of CVs by about a factor of two. In rare cases you might want to set this to False

name
cv_time_reversible
_cache_dict

The ChainDict that will cache calculated values for fast access

Type

openpathsampling.chaindict.ChainDict

__init__(name, cv_time_reversible=False)[source]
Parameters

post (openpathsampling.chaindict.ChainDict) – the underlying chain dict to be used

Methods

__init__(name[, cv_time_reversible])

param post

the underlying chain dict to be used

args()

Return a list of args of the __init__ function of a class

base()

Return the most parent class actually derived from StorableObject

cache_all()

Sync this CV with attached storages

count_weaks()

Return number of objects subclassed from StorableObject still in memory

descendants()

Return a list of all subclassed objects

disable_diskcache()

enable_diskcache()

fix_name()

Set the objects name to be immutable.

from_dict(dct)

Reconstruct an object from a dictionary representaiton

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

reverse_uuid()

ruuid(uid)

set_cache_store(value_store)

Attach store variables to the collective variables.

set_observer(active)

(De-)Activate observing creation of storable objects

str_chain()

Return a string representation of the chain of dicts called.

sync()

Sync this CV with the attached storages

to_dict()

Convert object into a dictionary representation

with_diskcache([template, chunksize, …])

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

default_name

Return the default name.

is_named

True if this object has a custom name.

name

Return the current name of the object.

observe_objects

passing_chain

Return a list of chaindicts in order they will be tried.