WOLFRAM

Background & Context

    • MIME type: chemical/x-cubeGaussian cube file.
    • Used by electronic structure programs to store orbital or density values on a three-dimensional grid.
    • Plain-text format.
    • Can contain volumetric data for an arbitrary number of orbitals.
    • Maintained by Gaussian, Inc.

Import & Export

  • Import["file.cub"] imports a list of molecules from a Cube file.
  • Export["file.cub",expr] exports a molecule or list of molecules to a Cube file.
  • Import["file.cub",elem] imports the specified element from a Cube file.
  • Import["file.cub",{{elem1,elem2,}}] imports multiple elements.
  • The import format can be specified with Import["file","Cube"] or Import["file",{"Cube",elem,}].
  • Export["file.cub",mol] creates a Cube file from a molecule containing a "VolumetricData" key in its MetaInformation.
  • Export["file.cub",{expr1,expr2,},{{elem1,elem2,}}] treats each expri as specifying the corresponding elemi.
  • Export["file.cub",expr,opt1->val1,] exports expr with the specified option elements taken to have the specified values.
  • Export["file.cub",{elem1->expr1,elem2->expr2,},"Rules"] uses rules to specify the elements to be exported.
  • When creating a Cube file, volumetric data can be either in the molecule expression as MetaInformation or given to Export as a separate element.
  • See the following reference pages for full general information:
  • Import, Exportimport from or export to a file
    CloudImport, CloudExportimport from or export to a cloud object
    ImportString, ExportStringimport from or export to a string
    ImportByteArray, ExportByteArrayimport from or export to a byte array

Import Elements

  • General Import elements:
  • "Elements" list of elements and options available in this file
    "Summary"summary of the file
    "Rules"list of rules for all available elements
  • Data elements:
  • "Molecule"a symbolic representation of the molecule model
    "VolumetricData"an Association containing the electronic orbital information
    "Graphics3D"a 3D graphic containing a model of the molecule along with contours representing electronic isosurfaces
  • The "VolumetricData" element contains the following keys:
  • "DataRange"a list of bounding box coordinates {{xmin,xmax},{ymin,ymax},{zmin,zmax}}
    "Data"a list of three-dimensional arrays specifying the value of the orbital wavefunction or density on a grid
    "OrbitalNumber"an optional list specifying numerical values for the orbitals

Options

Examples

open allclose all

Basic Examples  (3)Summary of the most common use cases

Import and plot the electronic density from a Cube file:

Out[1]=1

Import and plot a Cube file containing two orbitals:

Out[1]=1

Import a molecule from a Cube file:

Out[1]=1

Find a matching Entity for the molecule:

Out[2]=2

Find the volumetric data in the molecule's MetaInformation:

Out[3]=3

Export the molecule to a Cube file:

Out[4]=4

Import Elements  (1)

Import the volumetric data for two molecular orbitals from a Cube file:

Out[1]=1
Out[2]=2

Export Elements  (1)

Export a molecule and data to a Cube file:

Out[3]=3

Import Options  (1)

Specify the value and style for the orbital isosurface:

Out[1]=1

Use textures for the surfaces:

Out[2]=2