openpathsampling.pathsimulator.PathSampling¶
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class
openpathsampling.pathsimulator.
PathSampling
(storage, move_scheme=None, sample_set=None, initialize=True)[source]¶ General path sampling code.
Takes a single move_scheme and generates samples from that, keeping one per replica after each move.
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__init__
(storage, move_scheme=None, sample_set=None, initialize=True)[source]¶ Parameters: - storage (
openpathsampling.storage.Storage
) – the storage where all results should be stored in - move_scheme (
openpathsampling.MoveScheme
) – the move scheme used for the pathsampling cycle - sample_set (
openpathsampling.SampleSet
) – the initial SampleSet for the Simulator - initialize (bool) – if False the new PathSimulator will continue at the step and not create a new SampleSet object to cut the connection to previous steps
- storage (
Methods
__init__
(storage[, move_scheme, sample_set, …])param storage: the storage where all results should be stored in :type storage: openpathsampling.storage.Storage
:param move_scheme: the move scheme used for the pathsampling cycle :type move_scheme:openpathsampling.MoveScheme
:param sample_set: the initial SampleSet for the Simulator :type sample_set:openpathsampling.SampleSet
:param initialize: if False the new PathSimulator will continue at the step and not create a new SampleSet object to cut the connection to previous steps :type initialize: boolargs
()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 from_step
(storage, step[, initialize])param storage: the storage to be used to hold the simulation results :type storage: openpathsampling.storage.Storage
:param step: the step used to fill the initial parameters :type step:openpathsampling.MCStep
:param initialize: if False the new PathSimulator will continue at the given step and not create a new SampleSet object to cut the connection to previous steps.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 restart_at_step
(step[, storage])Continue with a loaded pathsampling at a given step reverse_uuid
()run
(n_steps)Run the simulator for a number of steps run_until
(n_steps)ruuid
(uid)save_current_step
()Save the current step to the storage 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 current_step
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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classmethod
from_step
(storage, step, initialize=True)[source]¶ Parameters: - storage (
openpathsampling.storage.Storage
) – the storage to be used to hold the simulation results - step (
openpathsampling.MCStep
) – the step used to fill the initial parameters - initialize (bool) – if False the new PathSimulator will continue at the given step and not create a new SampleSet object to cut the connection to previous steps.
Returns: the new simulator object
Return type: openpathsampling.PathSampling
- storage (
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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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restart_at_step
(step, storage=None)[source]¶ Continue with a loaded pathsampling at a given step
Notes
You can only continue from a step that is compatible in the sense that it was previously generated from the pathsampling instance.
If you want to switch the move scheme you need to create a new pathsampling instance. You can do so with the constructor or using the classmethod from_step which simplifies the setup process
Parameters: - step (
MCStep
) – the step to be continued from. You are always free to chose any step which can be used to fork a simulation but for analysis you may only use one path of steps. - storage (
Storage
) – If given this will change the storage used to store the generated steps
- step (
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run
(n_steps)[source]¶ Run the simulator for a number of steps
Parameters: n_steps (int) – number of step to be run
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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
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