forte2.orbitals.cube_generator#
Module Contents#
- forte2.orbitals.cube_generator.write_orbital_cubes(system, C, indices=None, prefix='orbital', filepath='.', format=('cube',), spacing=0.2, padding=4.0)#
A convenience function to write cube files for molecular orbitals.
- Parameters:
- systemforte2.system.System
The system object containing the molecular information.
- CNDArray
The molecular orbital coefficients matrix.
- indicesList[int], optional, default=None
The indices (zero-based) of the orbitals to generate cube files for. By default all orbitals are generated.
- prefixstr, optional, default=”orbital”
The prefix for the cube file names.
- filepathstr, optional, default=”.”
The directory to save the cube files in.
- formatTuple[str, …] or str, optional, default=(“cube”,)
- Output formats to generate. Supported values:
“cube”: standard CUBE files. For two-component systems, writes separate alpha and beta magnitude files (“_a.cube” and “_b.cube”).
“2ccube”: two-component cube files (“.2ccube”). For two-component systems only, writes four datasets consecutively per orbital in the order: alpha real, alpha imag, beta real, beta imag.
Multiple formats can be requested at once, e.g., formats=(“cube”,”2ccube”).
- spacingfloat, optional, default=0.2
The spacing between grid points in the cube file (in bohr).
- paddingfloat, optional, default=4.0
The extra space (in bohr) added in all directions around the atoms when generating the grid.
- forte2.orbitals.cube_generator.simple_grid(atoms, spacing: tuple[float, float, float], padding: tuple[float, float, float])#
Create a simple cubic grid around the given atoms.
- Parameters:
- atomsList[Tuple[int, Tuple[float, float, float]]]
List of atoms, each represented as a tuple (Z, (x, y, z)).
- spacingTuple[float, float, float]
The spacing between grid points in the x, y, and z directions.
- paddingTuple[float, float, float]
The amount of padding (extra space) to add to the grid in the x, y, and z directions around the atoms when generating the grid.
- Returns:
- grid_originTuple[float, float, float]
The origin of the grid.
- npointsTuple[int, int, int]
The number of grid points in the x, y, and z directions.
- scaled_axesList[Tuple[float, float, float]]
The scaled axes for the grid.
- class forte2.orbitals.cube_generator.CubeGenerator(spacing=0.2, padding=4.0)#
Class to generate cube files from a given set of molecular orbitals.
- Parameters:
- spacingfloat, optional, default=0.2
The spacing between grid points in the cube file (in bohr).
- paddingfloat, optional, default=4.0
The extra space (in bohr) added in all directions around the atoms when generating the grid.
- spacing#
- padding#
- write_cubes(system, C, indices=None, prefix='orbital', filepath='.', formats=('cube',)) None#
Generate cube files for the given orbitals.
This method generates cube files for the specified molecular orbitals represented by the coefficient matrix C. The cube files are saved in the specified directory with the given prefix. The files are named as:
{prefix}_{index:0{number_of_digits}d}.cube
where index is the zero-based index of the orbital and number_of_digits is determined by the maximum index to ensure proper zero-padding.
- Parameters:
- systemforte2.system.System
The system object containing the molecular information.
- CNDArray
The molecular orbital coefficients matrix.
- indicesList[int], optional, default=None
The indices (zero-based) of the orbitals to generate cube files for. By default all orbitals are generated.
- prefixstr, optional, default=”orbital”
The prefix for the cube file names.
- filepathstr, optional, default=”.”
The directory to save the cube files in.
- formatsTuple[str, …], optional, default=(“cube”,)
- Output formats to generate. Supported values:
“cube”: standard CUBE files. For two-component systems, writes separate alpha and beta magnitude files (“_a.cube” and “_b.cube”).
“2ccube”: two-component cube files (“.2ccube”). For two-component systems only, writes four datasets consecutively per orbital in the order: alpha real, alpha imag, beta real, beta imag.
Multiple formats can be requested at once, e.g., formats=(“cube”,”2ccube”).