openpathsampling.pathsimulator.CommittorSimulation¶
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class
openpathsampling.pathsimulator.
CommittorSimulation
(storage, engine=None, states=None, randomizer=None, initial_snapshots=None, direction=None)[source]¶ Committor simulations. What state do you hit from a given snapshot?
Parameters: - storage (
Storage
) – the file to store simulations in - engine (
DynamicsEngine
) – the dynamics engine to use to run the simulation - states (list of
Volume
) – the volumes representing the stable states - randomizer (
SnapshotModifier
) – the method used to modify the input snapshot before each shot - initial_snapshots (list of
Snapshot
) – initial snapshots to use - direction (int or None) – if direction > 0, only forward shooting is used, if direction < 0, only backward, and if direction is None, mix of forward and backward. Useful if using no modification on the randomizer.
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__init__
(storage, engine=None, states=None, randomizer=None, initial_snapshots=None, direction=None)[source]¶ x.__init__(…) initializes x; see help(type(x)) for signature
Methods
__init__
(storage[, engine, states, …])x.__init__(…) initializes x; see help(type(x)) for signature args
()Return a list of args of the __init__ function of a class base
()Return the most parent class actually derived from StorableObject count_weaks
()Return number of objects subclassed from StorableObject still in memory descendants
()Return a list of all subclassed objects 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
()run
(n_per_snapshot[, as_chain])Run the simulation. ruuid
(uid)save_initial_step
()Save the initial state as an MCStep to the storage set_observer
(active)(De-)Activate observing creation of storable objects sync_storage
()Will sync all collective variables and the storage to disk to_dict
()Convert object into a dictionary representation Attributes
ACTIVE_LONG
CREATION_COUNT
INSTANCE_UUID
base_cls
Return the base class base_cls_name
Return the name of the base class calc_name
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
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__delattr__
¶ x.__delattr__(‘name’) <==> del x.name
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__format__
()¶ default object formatter
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__getattribute__
¶ x.__getattribute__(‘name’) <==> x.name
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__reduce__
()¶ helper for pickle
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__reduce_ex__
()¶ helper for pickle
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__repr__
¶
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__setattr__
¶ x.__setattr__(‘name’, value) <==> x.name = value
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__sizeof__
() → int¶ size of object in memory, in bytes
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__str__
¶
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classmethod
args
()¶ Return a list of args of the __init__ function of a class
Returns: the list of argument names. No information about defaults is included. Return type: list of str
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classmethod
base
()¶ Return the most parent class actually derived from StorableObject
Important to determine which store should be used for storage
Returns: the base class Return type: type
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base_cls_name
¶ Return the name of the base class
Returns: the string representation of the base class Return type: str
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cls
¶ Return the class name as a string
Returns: the class name Return type: str
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static
count_weaks
()¶ Return number of objects subclassed from StorableObject still in memory
This includes objects not yet recycled by the garbage collector.
Returns: dict of str – the dictionary which assigns the base class name of each references objects the integer number of objects still present Return type: int
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default_name
¶ Return the default name.
Usually derived from the objects class
Returns: the default name Return type: str
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classmethod
descendants
()¶ Return a list of all subclassed objects
Returns: list of subclasses of a storable object Return type: list of type
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fix_name
()¶ Set the objects name to be immutable.
Usually called after load and save to fix the stored state.
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classmethod
from_dict
(dct)[source]¶ Reconstruct an object from a dictionary representaiton
Parameters: dct (dict) – the dictionary containing a state representaion of the class. Returns: the reconstructed storable object Return type: openpathsampling.netcdfplus.StorableObject
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idx
(store)¶ Return the index which is used for the object in the given store.
Once you store a storable object in a store it gets assigned a unique number that can be used to retrieve the object back from the store. This function will ask the given store if the object is stored if so what the used index is.
Parameters: store ( openpathsampling.netcdfplus.ObjectStore
) – the store in which to ask for the indexReturns: the integer index for the object of it exists or None else Return type: int or None
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is_named
¶ True if this object has a custom name.
This distinguishes default algorithmic names from assigned names.
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name
¶ Return the current name of the object.
If no name has been set a default generated name is returned.
Returns: the name of the object Return type: str
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named
(name)¶ Name an unnamed object.
This only renames the object if it does not yet have a name. It can be used to chain the naming onto the object creation. It should also be used when naming things algorithmically: directly setting the .name attribute could override a user-defined name.
Parameters: name (str) – the name to be used for the object. Can only be set once Examples
>>> import openpathsampling as p >>> full = p.FullVolume().named('myFullVolume')
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static
objects
()¶ Returns a dictionary of all storable objects
Returns: dict of str – a dictionary of all subclassed objects from StorableObject. The name points to the class Return type: type
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run
(n_per_snapshot, as_chain=False)¶ Run the simulation.
Parameters: - n_per_snapshot (int) – number of shots per snapshot
- as_chain (bool) – if as_chain is False (default), then the input to the modifier is always the original snapshot. If as_chain is True, then the input to the modifier is the previous (modified) snapshot. Useful for modifications that can’t cover the whole range from a given snapshot.
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save_initial_step
()¶ Save the initial state as an MCStep to the storage
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static
set_observer
(active)¶ (De-)Activate observing creation of storable objects
This can be used to track which storable objects are still alive and hence look for memory leaks and inspect caching. Use
openpathsampling.netcdfplus.base.StorableObject.count_weaks()
to get the current summary of created objectsParameters: active (bool) – if True then observing is enabled. False disables observing. Per default observing is disabled.
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sync_storage
()¶ Will sync all collective variables and the storage to disk
- storage (