sphractal.utils

Module Contents

Functions

estDuration(func)	Return time taken to run a function.
getMinMaxXYZ(atomsXYZ)	Return the minimum and maximum values of each dimension of a set of coordinates.
readInp(filePath[, radType])	Parse an xyz or a lmp file.
allDirVecs()	Return a list of vectors corresponding to the standard 26 directions from a point.
findNN(atomsRad, atomsXYZ, minXYZ, maxXYZ, maxAtomRad)	Compute the nearest neighbour list and average bond length for each atom.
findTetras(tetraVtxsIdxs, r, alpha)	Return tetrahedrons with their circumsphere radii smaller than a specified alpha value.
rmDupTris(tris)	Remove triangles that occur twice (internal triangles).
alphaShape(atomsXYZ, tetraVtxsIdxs, alpha)	Return points that form the surface using alpha shape algorithm.
findSurf(atomsXYZ, atomsNeighIdxs[, option, alpha, bulkCN])	Return the indices of surface atoms.
findAtomNeighs(neighIdxs, atomsSurfIdxs)	Divide a list of atomic neighbours into two based on whether they lie on the surface.
calcDist(p1, p2)	Return Euclidean distance between two points.
getOrdSurfNeighCombs(surfNeighDists, surfNeighIdxs)	Compute ID pairs of a set of neighbouring atoms, ordered by distance from a given point.
closestSurfAtoms(pointXYZ, surfNeighIdxs, atomsXYZ, ...)	Return two closest surface atom pairs from a given point, that are neighbour of each other.
oppositeInnerAtoms(pointXYZ, atom1XYZ, atomNeighIdxs, ...)	Return whether a point lies opposite of the average coordinates of neighbouring inner atoms of a given atom.

sphractal.utils.estDuration(func)

Return time taken to run a function.

sphractal.utils.getMinMaxXYZ(atomsXYZ)

Return the minimum and maximum values of each dimension of a set of coordinates.

sphractal.utils.readInp(filePath, radType='atomic')

Parse an xyz or a lmp file.

sphractal.utils.allDirVecs()

Return a list of vectors corresponding to the standard 26 directions from a point.

sphractal.utils.findNN(atomsRad, atomsXYZ, minXYZ, maxXYZ, maxAtomRad, radMult=1.2, calcBL=False)

Compute the nearest neighbour list and average bond length for each atom.

Parameters:

• atomsRad (1D ndarray of floats) – Radius of each atom.

• atomsXYZ (2D ndarray of floats) – Cartesian coordinates of each atom.

• minXYZ (1D ndarray of floats) – Minimum values of each dimension in the Cartesian space.

• maxXYZ (1D ndarray of floats) – Maximum values of each dimension in the Cartesian space.

• maxAtomRad (Union[int,float]) – Maximum value of atomic radius.

• radMult (Union[int,float]) – Multiplier to the atomic radii.

• calcBL (bool, optional) – Whether to compute the average bond length for each atom.

Returns:

• atomsNeighIdxsPadded (2D ndarray of ints) – Neighbour atoms indices of each atom, padded with -1 for fixed number of columns.

• atomsAvgBondLen (1D ndarray of floats) – Average bond lengths for each each.

sphractal.utils.findTetras(tetraVtxsIdxs, r, alpha)

Return tetrahedrons with their circumsphere radii smaller than a specified alpha value.

sphractal.utils.rmDupTris(tris)

Remove triangles that occur twice (internal triangles).

sphractal.utils.alphaShape(atomsXYZ, tetraVtxsIdxs, alpha)

Return points that form the surface using alpha shape algorithm.

Algorithm modified from https://stackoverflow.com/questions/26303878/alpha-shapes-in-3d Radius of the sphere fitting inside the tetrahedral < alpha (http://mathworld.wolfram.com/Circumsphere.html)

sphractal.utils.findSurf(atomsXYZ, atomsNeighIdxs, option='alphaShape', alpha=3.0, bulkCN=12)

Return the indices of surface atoms.

Parameters:

• atomsXYZ (2D ndarray of floats) – Cartesian coordinates of each atom.

• atomsNeighIdxs (2D ndarray of ints) – Neighbour atoms indices of each atom.

• option ({'alphaShape', 'convexHull', 'numNeigh'}, optional) – Algorithm to identify the spheres on the surface. ‘convexHull’ tends to identify less surface atoms; ‘numNeigh’ tends to identify more surface atoms. ‘alphaShape’ is a generalisation of ‘convexHull’.

• alpha (Union[int, float], optional) – ‘alpha’ for the alpha shape algorithm, only used if ‘option’ is ‘alphaShape’.

• bulkCN (int, optional) – Minimum number of neighbouring atoms for a non-surface atom.

Returns:

atomsSurfIdxs – Indices of surface atoms.

Return type:

1D ndarray of ints

Notes

Other alternatives include: - https://dl.acm.org/doi/abs/10.1145/2073304.2073339 - https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.25384 - https://www.jstage.jst.go.jp/article/tmrsj/45/4/45_115/_article

sphractal.utils.findAtomNeighs(neighIdxs, atomsSurfIdxs)

Divide a list of atomic neighbours into two based on whether they lie on the surface.

sphractal.utils.calcDist(p1, p2)

Return Euclidean distance between two points.

sphractal.utils.getOrdSurfNeighCombs(surfNeighDists, surfNeighIdxs)

Compute ID pairs of a set of neighbouring atoms, ordered by distance from a given point.

sphractal.utils.closestSurfAtoms(pointXYZ, surfNeighIdxs, atomsXYZ, atomsNeighIdxs)

Return two closest surface atom pairs from a given point, that are neighbour of each other.

sphractal.utils.oppositeInnerAtoms(pointXYZ, atom1XYZ, atomNeighIdxs, atomsSurfIdxs, atomsXYZ, atomsNeighIdxs)

Return whether a point lies opposite of the average coordinates of neighbouring inner atoms of a given atom.