read_structure(filepath, outpath='.')[source]

Read the structure of the polyatomic system from a file and returns a list with the symbols of the atoms in the molecule and a 1D array with their positions $$[x_1, y_1, z_1, x_2, y_2, z_2, \dots]$$ in atomic units (Bohr radius = 1).

The atomic coordinates in the file must be in Angstroms. The xyz format is supported. Additionally, the new file structure.xyz, containing the input geometry, is created in a directory with path given by outpath.

Parameters
• filepath (str) – name of the molecular structure file in the working directory or the absolute path to the file if it is located in a different folder

• outpath (str) – path to the output directory

Returns

symbols of the atoms in the molecule and a 1D array with their positions in atomic units.

Return type

tuple[list, array]

Example

>>> symbols, coordinates = read_structure('h2.xyz')
>>> print(symbols, coordinates)
['H', 'H'] [0.    0.   -0.66140414    0.    0.    0.66140414]


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