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Cube (.cub, .cube)

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

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Basic Examples  (3)

Import and plot the electronic density from a Cube file:

Wolfram Language code: Import["ExampleData/Pyridinecarbonitrile_DEN.cub", "Graphics3D"]

Import and plot a Cube file containing two orbitals:

Wolfram Language code: Import["ExampleData/Pyridinecarbonitrile_MO_25_29.cub", "Graphics3D"]

Import a molecule from a Cube file:

Wolfram Language code: mol = Import["ExampleData/Pyridinecarbonitrile_DEN.cub"]

Find a matching Entity for the molecule:

Wolfram Language code: ToEntity@mol

Find the volumetric data in the molecule's MetaInformation:

Wolfram Language code: mol["MetaInformation"]

Export the molecule to a Cube file:

Wolfram Language code: Export["test.cub", mol]

Import Elements  (1)

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

Wolfram Language code: volData = Import["ExampleData/Pyridinecarbonitrile_MO_25_29.cub", "VolumetricData"]
Wolfram Language code: ListDensityPlot3D[volData[["Data", 1]], DataRange -> volData["DataRange"], BoxRatios -> Automatic]

Export Elements  (1)

Export a molecule and data to a Cube file:

Wolfram Language code: mol = Molecule[{Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["N"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["C"], Atom["N"]}, {Bond[{1, 2}, "Aromatic"], Bond[{2, 3}, "Aromatic"], Bond[{3, 4}, "Aromatic"], Bond[{4, 5}, "Aromat ... 267874284}, {0., 2.167739145652817, 0.389417833298357}, {0., -2.167739145652817, 0.389417833298357}, {0., -2.077788538513299, -2.136138267874284}, {0., 0., 2.120315868129184}, {0., 0., 3.280315790471602}}, "Angstroms", {{1}, {2}}}]]]; volData = <|"Data" -> {NumericArray[{{{9.532699550618418*^-6, 0.000010906699571933132, 0.00001232249996974133, 0.000013743099771090783, 0.000015124000128707848, 0.000016414500350947492, 0.000017559099433128722, 0.000018499800717108883, 0.0000191787003132049, 0.000019 ... 632355*^-6, -1.5902099903541966*^-6, -1.4878800129736192*^-6, -1.366959963888803*^-6, -1.2345200275376556*^-6, -1.0970200037263567*^-6, -9.59980980042019*^-7, -8.278730092570186*^-7, -7.040640070954396*^-7, -5.908499929319078*^-7}}}, "Real32"]}, "DataRange" -> {{-3.44, 3.43}, {-4.65, 4.70}, {-5.14, 6.15}}|>;
Wolfram Language code: Export["test.cub", {mol, volData}, {{"Molecule", "VolumetricData"}}]

Import Options  (2)

Specify the value and style for the orbital isosurface:

Wolfram Language code: First@Import["ExampleData/Pyridinecarbonitrile_MO_25_29.cub", "Graphics3D", Contours -> {-0.04, 0.04}, ContourStyle -> {Red, Blue}]

Use textures for the surfaces:

Wolfram Language code: First@Import["ExampleData/Pyridinecarbonitrile_MO_25_29.cub", "Graphics3D", Contours -> {-0.04, 0.04}, ContourStyle -> {Texture[[image]], Texture[[image]]}]

When importing the "Graphics3D" element, it is possible pass in options for MoleculePlot3D or ListContourPlot3D.

Specify a specific PlotTheme:

Wolfram Language code: Import["ExampleData/Pyridinecarbonitrile_MO_25_29.cub", "Graphics3D", PlotTheme -> "Tubes"]

Control the display of the output with Graphics3D options:

Wolfram Language code: First@Import["ExampleData/Pyridinecarbonitrile_MO_25_29.cub", "Graphics3D", Boxed -> True, Axes -> True, ViewPoint -> {2, -2.4, 2.}]

Use a custom ColorFunction:

Wolfram Language code: First@Import["ExampleData/Pyridinecarbonitrile_MO_25_29.cub", "Graphics3D", ColorFunction -> Function[{x, y, z, f}, Hue[z + x y]], PlotTheme -> "Wireframe"]