2.6.4. prismatique.sample.check_atomic_coords_file_format

check_atomic_coords_file_format(atomic_coords_filename)

Check whether a given atomic coordinates file is of the correct format.

An exception is raised if the file is invalid.

Parameters:

atomic_coords_filenamestr

See the documentation for the classes prismatique.discretization.Params and prismatique.thermal.Params for context: the former discusses sample unit cells and supercells; and the latter discusses the effective root-mean-squared displacements of atoms, which we denote by \(u_{i,\text{rms}}\).

atomic_coords_filename is a relative or absolute path to a file that specifies the zero-temperature expectation value of the atomic coordinates for each atom in the unit cell of the sample, along with \(\frac{1}{\sqrt{3}}u_{i,\text{rms}}\) for each atom, where \(u_{i,\text{rms}}\) was introduced in Eq. (2.9.1.11). The file must be encoded as ASCII text (UTF-8). The file should be formatted as follows: the first line can be whatever header the user desires, i.e. the first line is treated as a comment; the second line is of the form “a b c”, where “a”, “b”, and “c” are the \(x\)-, \(y\)-, and \(z\)-dimensions of the unit cell in angstroms; each subsequent line except for the last specifies attributes of an atom and is of the form “Z x y z’ occ u_x_rms”, where “Z” is the atomic number of said atom, “x”, “y” and “z’” are the \(x\)-, \(y\)-, and \(z^{\prime}\)-coordinates respectively of said atom in angstroms [the \(z^{\prime}\)-coordinate of an atom is related to the \(z\)-coordinate of the same atom by \(z=-z^{\prime}+\Delta Z\), with \(\Delta Z\) being the \(z\)-dimension of the sample’s supercell], “occ” is the likelihood that said atom exists, and “u_x_rms” is \(\frac{1}{\sqrt{3}}u_{i,\text{rms}}\) for said atom in angstroms; and the last line in the file should be “-1”. Example files can be found in the examples directory of the prismatique repository. Note that “occ” is ignored in prismatique.

Returns: