
Generation of cube files¶
Code author: Robert M. Parrish and Francesco A. Evangelista
Section author: Francesco A. Evangelista
Introduction¶
Psi4 has the ability to export cube files that store information about basis functions, molecular orbitals, the electron density, and the electrostatic potential (ESP). Cube files store the value of a scalar quantity on a regular Cartesian grid, and can be visualized with several visualization programs, some of which are free, like VMD (http://www.ks.uiuc.edu/Research/vmd/).
An example utilization of the code is:
molecule h2o {
0 1
O
H 1 1.0
H 1 1.0 2 104.5
}
set basis cc-pvdz
set scf_type df
set freeze_core True
set cubeprop_tasks ['orbitals']
set cubeprop_orbitals [5,6,-5,-6]
energy('scf')
cubeprop()
In this example, the cubeprop()
call after the energy('scf')
command
executes the cubeprop code. The array CUBEPROP_TASKS
specifies which
tasks should be executed. In this case the task 'orbitals'
generates cube
files for orbitals. The CUBEPROP_ORBITALS
option specifies that cube files
should be generated only for alpha orbitals 5 (HOMO) and 6 (LUMO) and
beta orbitals 5 (indicated as -5) and 6.
If the option CUBEPROP_ORBITALS
is not provided, then cube files are
generated for all orbitals.
After running, the above input will generate four files: Psi_a_5.cube,
Psi_a_6.cube, Psi_b_5.cube, and Psi_b_6.cube.
Tip
If your cube plots are too coarse, try to decrease the grid spacing via
the option CUBIC_GRID_SPACING
. If the edges of your plot are cut then
increase the size of the grid via the option CUBIC_GRID_OVERAGE
.
Cubeprop Tasks¶
The cubeprop utility can be probided a list of tasks to perform.
Tasks are specified by the CUBEPROP_TASKS
option, which is a list of strings
that identify the tasks. Several tasks are available. These include:
- ORBITALS [Default if
CUBEPROP_TASKS
is not specified] - Produces cube representations of the molecular orbitals
. Orbitals are sorted according to increasing orbital energy ignoring symmetry.
- DENSITY
- This task can be used to obtain the alpha and beta electron densities,
and
, together with the total density
, and the spin density
.
- BASIS_FUNCTIONS
- This task is useful to produce cube files of the atomic orbital basis
functions
.
- ESP
- Calculates the total (nuclear + electronic) electrostatic potential
.
Note
The ESP
task requires the user to specify a density-fitting basis
via the DF_BASIS_SCF keyword.
Warning
It is important to specify the CUBEPROP_ORBITALS
option when
dealing with large molecules to avoid running out of disk space.
For example, using the default grid spacing of
0.2 Ångstroms, the size of a single cube file for a molecule like water
is of the order of 1.4 MB. For a molecule with 200 basis functions, the cube
files for all the orbitals occupy more than half a GB.
Cubeprop Options¶
- CUBEPROP_FILEPATH
- The directory in which to place the cube files. The default is the directory that contains the input file.
- CUBEPROP_ORBITALS
- A list of the orbitals for which cube files are generated. Alpha orbitals
are specified by positive integers, where the lowest orbital is 1.
Beta orbitals are indicated by prefixing the number with a minus sign.
Orbitals are ordered according to their energy.
Notice that if the
CUBEPROP_ORBITALS
list is empty then cubeprop will produce cube files for all alpha and beta orbitals. - CUBEPROP_BASIS_FUNCTIONS
- A list of basis functions for which cube files are generated. Basis functions are numbered starting from 1.
- CUBIC_GRID_SPACING
- A vector that specifies the grid spacing in the X, Y, and Z directions. The default value is [0.2,0.2,0.2] Ångstroms.
- CUBIC_GRID_OVERAGE
- A vector that controls the spatial extent of the grid in the X, Y, and Z directions. The default value is [4.0,4.0,4.0] Ångstroms.