Printing orbital densities to cube files — BAGEL Manual

# Printing orbital densities to cube files

## Description

This module prints molecular orbital densities in the Gaussian Cube format. It can be used to view the shape and extent of relativistic or gauge-including molecular orbitals, which cannot be viewed in Molden due to the use of complex basis functions or the four-component framework.

A separate .cub file is generated for each printed orbital, plus one for the total electron density. The axis vectors are simply the Cartesian x, y, and z axes.

In addition, one can print the relaxed electron density in MP2, SA-CASSCF, and CASPT2 force calculations as well. See nuclear gradient and derivative coupling and the example below.

Command: `moprint`

## Keywords

`paired`

Description: Determined whether we plot spatial MOs (true) or spin MOs.
Datatype: bool
Default: True, unless we are printing 4-component orbitals generated with an external magnetic field.
Recommendation: Use the default.

`orbitals`

Description: Indices of the molecular orbitals to be printed.
Datatype: Vector of integers
Default: Prints the active orbitals from CASSCF, and the frontier orbitals from Hartree–Fock

`start_pos`

Description: Coordinates for one corner of the box within which densities are printed.
Datatype: Array of 3 doubles
Default: A position is chosen so that all atoms (except the dummy atoms) are at least \(4 a_0\) from the edges of the box.
Recommendation: Use the default.

`inc_size`

Description: Distances between adjacent gridpoints in each of the three dimensions.
Datatype: Array of 3 doubles
Default: \(0.25 a_0\) in each direction.
Recommendation: Use the default.

`angstrom`

Description: Unit of the “inc_size” parameter
Datatype: bool
Default: False (meaning Bohr; set to true for angstrom)

`mo_filename`

Description: Name of the MO cube file
Datatype: string
Default: “mo”

`density_filename`

Description: Name of the density cube file
Datatype: string
Default: “density”

## Example

### Sample input: Print MO

Write molecular orbitals:

    { "bagel" : [

    .... energy calculation....

    {
      "title" : "moprint",
      "inc_size" : [ 0.20, 0.20, 0.20 ],
      "orbitals" : [ 14, 15, 16, 17, 18, 19, 20, 21, 22 ]
    }

    ]}

### Sample input: Print relaxed density

Write relaxed density to the file `density_0.cub` from the XMS-CASPT2 force calculation:

    { "bagel" : [

    {
      "title" : "molecule",
      "basis" : "svp",
      "df_basis" : "svp-jkfit",
      "geometry" : [
        { "atom" : "Li", "xyz" : [ 0.000000, 0.000000, 6.000000] },
        { "atom" : "F",  "xyz" : [ 0.000000, 0.000000, 0.000000] }
      ]
    },

    {
      "title" : "force",
      "target" : 0,
      "density_print" : true,
      "moprint" : {
        "density_filename" : "density_0",
        "inc_size" : [ 0.20, 0.20, 0.20 ]
      },
      "method" : [ {
        "title" : "caspt2",
        "smith" : {
          "method" : "caspt2",
          "shift" : 0.2,
          "frozen" : true
        },
        "nstate" : 4,
        "nact" : 4,
        "nclosed" : 3
      } ]
    }

    ]}