polymerist.mdtools.openfftools.boxvectors

For obtaining, scaling, and manipulating box vectors for Topologies

Attributes

`Vector`
`VectorQuantity`
`BoxVectors`
`BoxVectorsQuantity`

Exceptions

BoxVectorError

Raised when a provided set of box vectors is invalid (for whatever reason)

Functions

`xyz_to_box_vectors`(→ BoxVectorsQuantity)	Convert 3-vector of XYZ box dimensions into monoclinic box vectors in 3x3 diagonal reduced form
`get_topology_bbox`(→ BoxVectorsQuantity)	Get the tight bounding box of an OpenFF Topology
`pad_box_vectors`(→ BoxVectorsQuantity)	Pad an array of box vectors by some fixed distance from each face
`pad_box_vectors_uniform`(→ BoxVectorsQuantity)	Pad an array of box vectors by a fixed distance from each face of the box
`box_vectors_flexible`(→ BoxVectorsQuantity)	Allows for passing XYZ box dimensions
`get_box_volume`(→ openmm.unit.Quantity)	Compute volume of a box given a set of 3x3 box vectors
`encloses_box_vectors`(→ bool)	Check whether the unit cell defined by the inner box vectors is completely contained within the outer box vectors

Module Contents

polymerist.mdtools.openfftools.boxvectors.Vector

polymerist.mdtools.openfftools.boxvectors.VectorQuantity

polymerist.mdtools.openfftools.boxvectors.BoxVectors

polymerist.mdtools.openfftools.boxvectors.BoxVectorsQuantity

exception polymerist.mdtools.openfftools.boxvectors.BoxVectorError[source]

Bases: Exception

Raised when a provided set of box vectors is invalid (for whatever reason)

polymerist.mdtools.openfftools.boxvectors.xyz_to_box_vectors(xyz: VectorQuantity) → BoxVectorsQuantity

Convert 3-vector of XYZ box dimensions into monoclinic box vectors in 3x3 diagonal reduced form

Parameters:: xyz (VectorQuantity) – 3-element vector with associated units whose components indicate the length of the box in the x, y, and z directions
Returns:: box_vectors – A 3x3 matrix with associated units (same units as input vector) representing the monoclinic box vectors in reduced form
Return type:: BoxVectorsQuantity

polymerist.mdtools.openfftools.boxvectors.get_topology_bbox(offtop: openff.toolkit.Topology) → BoxVectorsQuantity[source]

Get the tight bounding box of an OpenFF Topology

Parameters:: offtop (Topology) – An OpenFF Topology
Returns:: box_vectors – The unit-aware box vectors representing the smallest monoclinic bounding box which contains all atoms in the Topology
Return type:: BoxVectorsQuantity

polymerist.mdtools.openfftools.boxvectors.pad_box_vectors(box_vectors: BoxVectorsQuantity, pad_vec: VectorQuantity) → BoxVectorsQuantity

Pad an array of box vectors by some fixed distance from each face Padding amount is set for each axis separately (i.e. x, y, and z)

Parameters:

box_vectors (BoxVectorsQuantity) – The unit-aware box vectors array to pad
pad_vec (VectorQuantity) – The padding vector specifying the amount to pad each pair of faces along each axis

E.g. a vector of np.array([1, 2, 3])*nanometer would pad the faces perpendicular to the x axis by 1 nm, perpendicular to the y axis by 2 nm, and the z-axis by 3 nm The lengths of the edges of the box would increase by 2, 4, and 6 nm along the x, y, and z axes, respectively

Returns:

box_vectors – The padded box vectors

Return type:

BoxVectorsQuantity

polymerist.mdtools.openfftools.boxvectors.pad_box_vectors_uniform(box_vectors: BoxVectorsQuantity, pad_amount: openmm.unit.Quantity) → BoxVectorsQuantity[source]

Pad an array of box vectors by a fixed distance from each face of the box

Parameters:

box_vectors (BoxVectorsQuantity) – The unit-aware box vectors array to pad
pad_amount (Quantity) – The distance to pad out from each face of the box

For a box with initial dimensions (Lx, Ly, Lz), the dimensions of the box returned after padding here will be (Lx + 2*pad_amount, Ly + 2*pad_amount, Lz + 2*pad_amount)

Returns:

box_vectors – The padded box vectors

Return type:

BoxVectorsQuantity

polymerist.mdtools.openfftools.boxvectors.box_vectors_flexible(box_vecs: VectorQuantity | BoxVectorsQuantity) → BoxVectorsQuantity: Allows for passing XYZ box dimensions

polymerist.mdtools.openfftools.boxvectors.get_box_volume(box_vectors: BoxVectorsQuantity, units_as_openm: bool = True) → openmm.unit.Quantity[source]: Compute volume of a box given a set of 3x3 box vectors

polymerist.mdtools.openfftools.boxvectors.encloses_box_vectors(outer_box_vectors: BoxVectorsQuantity, inner_box_vectors: BoxVectorsQuantity) → bool[source]: Check whether the unit cell defined by the inner box vectors is completely contained within the outer box vectors