Abstract Collective Variables¶

Overview

`pysages.colvars.core.CollectiveVariable`(indices)	Abstract base class for defining collective variables
`pysages.colvars.core.AxisCV`(indices, axis[, ...])	Collective variable that specifies a Cartesian Axis in addition.
`pysages.colvars.core.TwoPointCV`(indices)	Collective variable that takes group of length 2.
`pysages.colvars.core.ThreePointCV`(indices)	Collective variable that takes group of length 3.
`pysages.colvars.core.FourPointCV`(indices)	Collective variable that takes group of length 4.

Details

Abstract base classes for collective variables.

class pysages.colvars.core.CollectiveVariable(indices, group_length=None)¶

Abstract base class for defining collective variables

When defining a new collective variable. Override the constructor if you need to enforce any invariant over the indices (it can otherwise be omitted).

Parameters:

indices (Union[list[int], list[tuple(int)]]) – Must be a list or tuple of atoms (integers or ranges) or groups of atoms. A group is specified as a nested list or tuple of atoms.
group_length (Optional[int]) – Specify if a fixed group length is expected.

property multicomponent¶: Indicates whether the collective variable is tensor valued or not.

abstract property function¶: Returns an external method that implements the actual computation of the collective variable.

class pysages.colvars.core.AxisCV(indices, axis, group_length=None)¶

Collective variable that specifies a Cartesian Axis in addition.

Parameters:

indices (list[int], list[tuple(int)]) – Must be a list or tuple of atoms (integers or ranges) or groups of atoms. A group is specified as a nested list or tuple of atoms.
axis (int) – Index of the Cartesian coordinate: 0 (X), 1 (Y), 2 (Z)
group_length (int, optional) – Specify if a fixed group length is expected.

class pysages.colvars.core.TwoPointCV(indices)¶

Collective variable that takes group of length 2.

Parameters:: indices (list[tuple(int)]) – Must be a group (size 2) of atoms. A group is specified as a nested list or tuple of atoms.

class pysages.colvars.core.ThreePointCV(indices)¶

Collective variable that takes group of length 3.

Parameters:: indices (list[tuple(int)]) – Must be a group (size 3) of atoms. A group is specified as a nested list or tuple of atoms.

class pysages.colvars.core.FourPointCV(indices)¶

Collective variable that takes group of length 4.

Parameters:: indices (list[tuple(int)]) – Must be a group (size 4) of atoms. A group is specified as a nested list or tuple of atoms.

pysages.colvars.core.multicomponent(cls)¶

Class decorator for multi-component (tensor-valued) collective variables. By default CVs are assumed to be scalar-valued functions, so multi-component ones have to be annotated as such.

Example

>>> from pysages.colvars.core import TwoPointCV, multicomponent
>>> @multicomponent
>>> class Displacement(TwoPointCV):
>>>     def function(self):
>>>         return lambda r1, r2: r2 - r1

pysages.colvars.core.build(cv: CollectiveVariable, *cvs: CollectiveVariable, differentiate: bool = True)¶

Jit compile and stack collective variables.

Parameters:

cv (CollectiveVariable) – Collective Variable object to jit compile.
cvs (list[CollectiveVariable]) – Sequence of Collective variables that get stacked on top of each other.
differentiate (bool = True) – Indicates whether to differentiate the collective variables.

Returns:

Jit compiled function, that takes a snapshot object, and access its positions and indices. With this information the collective variables (and their derivatives if differentiate is True) are computed and returned.

Return type:

Callable[Snapshot]