sphractal.surfExact

Module Contents

Functions

getNearFarCoord(scanBoxIdx, boxLen, lowBound, atomCoord)	Find the nearest and furthest point of a given box from a given atom.
scanBox(minXYZ, scanBoxIdxs, scanBoxNearFarXYZs, ...)	Find the nearest and furthest point of a given box from a given atom.
scanAtom(args)	Count the number of boxes that cover the outer spherical surface of a given atom.
scanAtomsForLoop(atomsIdxs, magn, boxLen, minXYZ, ...)	Serialised loop to scan the atoms for timing comparison with the parallelised version.
scanAllAtoms(args)	Count the number of boxes that cover the outer spherical surface of a set of atoms for a given box size.
writeBoxCoords(atomsEle, atomsXYZ, allSurfBoxs, ...)	Write out coordinates of scanned boxes.
findAtomsWithSurfNeighs(atomsNeighIdxs, atomsSurfIdxs)	Find atoms with neighbours that are on the surface.
exactBoxCnts(atomsEle, atomsRad, atomsSurfIdxs, ...[, ...])	Count the boxes that cover the outer surface of a set of overlapping spheres represented as exact spheres for different box sizes.

sphractal.surfExact.getNearFarCoord(scanBoxIdx, boxLen, lowBound, atomCoord, bufferDist=5.0)

Find the nearest and furthest point of a given box from a given atom.

sphractal.surfExact.scanBox(minXYZ, scanBoxIdxs, scanBoxNearFarXYZs, boxLen, atomIdx, atomRad, atomXYZ, atomNeighIdxs, atomsSurfIdxs, atomsXYZ, atomsNeighIdxs, bufferDist=5.0, rmInSurf=True)

Find the nearest and furthest point of a given box from a given atom.

sphractal.surfExact.scanAtom(args)

Count the number of boxes that cover the outer spherical surface of a given atom.

sphractal.surfExact.scanAtomsForLoop(atomsIdxs, magn, boxLen, minXYZ, atomsRad, atomsSurfIdxs, atomsXYZ, atomsNeighIdxs, bufferDist=5.0, rmInSurf=True)

Serialised loop to scan the atoms for timing comparison with the parallelised version.

sphractal.surfExact.scanAllAtoms(args)

Count the number of boxes that cover the outer spherical surface of a set of atoms for a given box size.

sphractal.surfExact.writeBoxCoords(atomsEle, atomsXYZ, allSurfBoxs, allBulkBoxs, minXYZ, boxLens, bufferDist, outDir, npName)

Write out coordinates of scanned boxes.

sphractal.surfExact.findAtomsWithSurfNeighs(atomsNeighIdxs, atomsSurfIdxs)

Find atoms with neighbours that are on the surface.

sphractal.surfExact.exactBoxCnts(atomsEle, atomsRad, atomsSurfIdxs, atomsXYZ, atomsNeighIdxs, maxRange, minMaxBoxLens, minXYZ, npName, outDir='outputs', numCPUs=None, numBoxLen=10, bufferDist=5.0, rmInSurf=True, writeBox=True, verbose=False)

Count the boxes that cover the outer surface of a set of overlapping spheres represented as exact spheres for different box sizes.

Parameters:

• atomsEle (1D ndarray of strs) – Element type of each atom.

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

• atomsSurfIdxs (1D ndarray of ints) – Indices of surface atoms.

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

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

• maxRange (float) – Maximum range among all dimensions of the Cartesian space, defines the borders of the largest box.

• minMaxBoxLens (tuple of floats) – Minimum and maximum box lengths.

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

• npName (str) – Identifier of the measured object, which forms part of the output file name, ideally unique.

• outDir (str, optional) – Path to the directory to store the output files.

• numCPUs (int, optional) – Number of CPUs to be used for parallelisation of tasks.

• numBoxLen (int, optional) – Number of box lengths to use for the collection of the box count data, spaced evenly on logarithmic scale.

• bufferDist (Union[int,float]) – Buffer distance from the borders of the largest box in Angstrom.

• rmInSurf (bool, optional) – Whether to remove the surface points on the inner surface.

• writeBox (bool, optional) – Whether to generate output files for visualisation.

• verbose (bool, optional) – Whether to display the details.

Returns:

• scales (list of floats) – Box lengths.

• counts (list of floats) – Number of boxes that cover the exact spherical surface of interest.

Examples

>>> eles, rads, xyzs, _, minxyz, maxxyz = readInp('example.xyz')
>>> neighs, _ = findNN(rads, xyzs, minxyz, maxxyz, 1.2)
>>> surfs = findSurf(xyzs, neighs, 'alphaShape', 5.0)
>>> scalesES, countsES = exactBoxCnts(eles, rads, surfs, xyzs, neighs, 100, (0.2, 1), minxyz, 'example')