openpathsampling.collectivevariables.PLUMEDCV

class openpathsampling.collectivevariables.PLUMEDCV(name, plmd, definition, components=None, cv_requires_lists=True, cv_wrap_numpy_array=True, cv_scalarize_numpy_singletons=True, **kwargs)

Make CollectiveVariable computed by PLUMED [PLU2a] according to the command name: definition, where name is a PLUMED label and definition contains all PLUMED keywords. Takes an openpathsampling.engines.trajectory.Trajectory as input.

References

[PLU2a]

G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni, G. Bussi, PLUMED2: New feathers for an old bird, Comp. Phys. Comm. 185, 604 (2014); https://doi.org/10.1016/j.cpc.2013.09.018

Examples

>>> # To create a `CollectiveVariable` which calculates the dihedral psi
>>> # formed by the atoms [7,9,15,17] in Ala dipeptide:
>>> from openpathsampling import PLUMEDCV, PLUMEDInterface
>>> plmd = PLUMEDInterface(top)
>>> # top is an `openpathsampling.engines.topology.MDTrajTopology`
>>> psi_plumed = PLUMEDCV("psi",plmd,"TORSION ATOMS=7,9,15,17")
>>> print psi_plumed(traj)  # returns psi values for the trajectory

__init__(name, plmd, definition, components=None, cv_requires_lists=True, cv_wrap_numpy_array=True, cv_scalarize_numpy_singletons=True, **kwargs)

Parameters:

• name (string) – A descriptive name of the PLUMED collective variable, equivalent to a label in a PLUMED input file.

• plmd (openpathsampling.collectivevariable.PLUMEDInterface) – An interface to the Cython PLUMED wrapper. If the PLUMED collective variable is a function of previously defined ones, or if it is defined based on group/virtual atoms, the plmd interface must be the same one that was used for the preceding instantiantions.

• definition (string) – The PLUMED keywords that define the collective variable (see http://www.plumed.org/documentation).

• components (list of string) – The components (either default of customized) of the PLUMED collective variable (see http://www.plumed.org/documentation).

• cv_requires_lists

• cv_wrap_numpy_array

• cv_scalarize_numpy_singletons

• kwargs

Methods

__init__(name, plmd, definition[, ...])
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
compute_cv(trajectory)	Compute a PLUMED collective variable.
count_weaks()	Return number of objects subclassed from StorableObject still in memory
create_plumed_var(name, definition)	Create a PLUMED collective variable.
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.
f
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.