atom keywords

System descriptors

atom.element

Point every atoms to an element defined in element. Generated automatically if atom.xyz is a string pointing to an xyz file.

type: array

size: [inf,1]

example: atom.element = [1;1]

atom.fracxyz

Direct coordinates of every atoms; atom.fracxyz may be an array passed from MATLAB, in which case atom.element must be provided by the user; atom.fracxyz may be a string containing the path to an xyz file, in which case atom.element is extracted from the first column.

type: array, string

example: atom.fracxyz = [0 0 0; 0.25 0.25 0.25]; atom.fracxyz = 'si.xyz'

atom.magmom

Initial magnetic moment of every atom if doing a non-collinear spin calculation. The moment is expressed in spherical coordinates (r,polar,azimuth). The units are Bohr magneton and radiant. If atom.magmom is a char array, then the string must be the path of an XZY file. The fifth column of the XYZ file is the spin in collinear spin calculations, and the fifth, sixth and seventh columns of the XYZ file are the spin coordinates (r,polar,azimuth) in non-collinear spin calculations.

type: array, string

size: [inf 1]

example: atom.magmom = [5 pi/2 pi;5 pi/4 0;5 7*pi/12 0];

atom.magmomd

Initial magnetic moment of every atom if doing a non-collinear spin calculation. The moment is expressed in spherical coordinates (r,polar,azimuth). The units are Bohr magneton and degree. If atom.magmomd is a char array, then the string must be the path of an XZY file. The fifth column of the XYZ file is the spin in collinear spin calculations, and the fifth, sixth and seventh columns of the XYZ file are the spin coordinates (r,polar,azimuth) in non-collinear spin calculations.

type: array

size: [inf 1]

example: atom.magmomd = [5 90 179.9;5 45 0.1;5 135 0.1];

atom.magmomcart

Initial magnetic moment of every atom if doing a non-collinear spin calculation. The moment is expressed in Cartesian coordinates (x,y,z). The units are Bohr magneton. If atom.magmomcart is a char array, then the string must be the path of an XZY file. The fifth column of the XYZ file is the spin in collinear spin calculations, and the fifth, sixth and seventh columns of the XYZ file are the spin coordinates (x,y,z) in non-collinear spin calculations.

type: array

size: [inf 1]

example: atom.magmomcart = [2.3766 0.1071 2.0362; 2.8785 2.5474 2.2732; 1.9672 2.8020 2.2294];

atom.nvalence

atom.nvalence determines the number of valence electrons in self-consistent calculations. The valence is intrinsically linked to the density. By default, atom.nvalence is determined such that the system is charge neutral. It is however possible to choose a value whereby the system is non-neutral.

type: scalar

example: atom.nvalence = 63

atom.xyz

Cartesian coordinates of every atoms; atom.xyz may be an array passed from MATLAB, in which case atom.element must be provided by the user; atom.xyz may be a string containing the path to an xyz file, in which case atom.element is extracted from the first column.

type: array, string

example: atom.xyz = [0 0 0; 0.25 0.25 0.25]; atom.xyz = 'si.xyz'