4. Modules

4.1. gen_mesh — Mesh generation

This module contains functions that are necessary to generate and optimize meshes by numerical error thresholds of the initial-guess density.

var_mesh.gen_mesh.atom_amount(mol)

Get the amount of atoms in a molecule.

Args:

mol :

Object of class Mole.

Returns: dict

Atom type identifiers as keys and amounts as values.

var_mesh.gen_mesh.atom_types(mol)

Get types of atoms in a molecule.

Args:

mol :

Object of class Mole.

Returns: set

Unique atom type identifiers.

var_mesh.gen_mesh.build_mesh(mesh, types, levels, mode)

Build mesh for given grid levels.

Args:

mesh :

Object of class Grids.

typeslist

Atom type identifiers.

levelslist

Grid levels per atom type.

modestr

Set the output format. If the code does not support different grids for different atom types, only the largest atom grid will be used in an optimization step. Can be one of 'pyscf', 'erkale' or 'gamess'.

Returns:

Object of class Grids.

var_mesh.gen_mesh.get_ang(symb, level)

Get angular grids.

Args:

symbstr

Atom type identifier.

levelint

Grid level of atom type.

Returns: int

Amount of angular grids.

var_mesh.gen_mesh.get_combs(mol, level)

Generate possible grid level combinations for a fine grid search.

Args:

mol :

Object of class Mole.

levelint

Grid level of the found match in the coarse grid search.

Returns: ndarray

Possible combinations of grid levels.

var_mesh.gen_mesh.get_rad(symb, level)

Get radial grids.

Args:

symbstr

Atom type identifier.

levelint

Grid level of atom type.

Returns: int

Amount of radial grids.

var_mesh.gen_mesh.get_steps()

Get the maximum number of optimization steps.

Returns: int

Largest grid level.

var_mesh.gen_mesh.mesh_error(mf)

Calculate the error per electron when integrating the electron density.

Args:

mol :

Object of class RKS or UKS.

Returns: float

Mesh error.

var_mesh.gen_mesh.var_mesh(mesh, thres=1e-06, precise=True, mode='pyscf')

Minimize grid points for a given error threshold for the initial density.

Args:

mesh :

Object of class Grids.

Kwargs:

thresfloat

Maximum error of the initial-guess density (normalized to one electron).

precisebool

Disable the coarse grid search when set to False. This will speed up the mesh generation but results in more grid points.

modestr

Set the output format. If the code does not support different grids for different atom types, only the largest atom grid will be used in an optimization step. Can be one of 'pyscf', 'erkale' or 'gamess'.

Returns:

Object of class Grids.

4.2. helpers — Mesh visualization

This module contains functions to visualize different meshes, but are not necessary to generate them.

var_mesh.helpers.plot_mesh_2d(mesh, weight=False, plane='xy')

Project atoms and grid points to a given plane in a 2d plot.

Args:

mesh :

Object of class Grids.

Kwargs:

weightbool or int

Scale grid points by their weights when set to True. Integers will scale grid points.

planestr

Contains the plane to project on to. Needs two elements of 'x', 'y', and 'z'.

var_mesh.helpers.plot_mesh_3d(mesh, weight=False, **kwargs)

Plot atoms and grid points in a 3d plot.

Args:

mesh :

Object of class Grids.

Kwargs:

weightbool or int

Scale grid points by their weights when set to True. Integers will scale grid points.