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)[source]

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)[source]
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[, ...])

param name

A descriptive name of the PLUMED collective variable,

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.