WOLFRAM

Wolfram Language & System Documentation Center

FCHK (.fchk)

  • Import supports the FCHK file format.

Background & Context

    • MIME type: chemical/x-gaussian-checkpointGaussian-formatted checkpoint file.
    • Plain-text version of the binary checkpoint file.
    • Used to store result of quantum chemistry calculation results.
    • Plain text format.
    • Maintained by Gaussian, Inc.

Import

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
    "Metadata"an Association containing results from the file
  • Results such as molecular-orbital energies and occupation are stored in the "Metadata".
  • The calculation results are also included in the "Molecule" element. Use mol["MetaInformation"] to retrieve them from the molecule mol.
  • Three-dimensional coordinates from the file are stored in the molecule in the AtomCoordinates option value.
  • Use mol["AtomCoordinates"] to retrieve the coordinates from the imported molecule mol.

Examples

open all close all

Basic Examples  (1)

Import an FCHK file as a molecule:

Wolfram Language code: mol = Import["ExampleData/bisCWdhpe2Cl_13benz_c1.fchk"]

Show the molecule in 3D:

Wolfram Language code: MoleculePlot3D[mol]

Dipole and orbital information is stored in the molecule's MetaInformation:

Wolfram Language code: mol["MetaInformation"]

Scope  (2)

Import the molecule and get the computed dipole moment:

Wolfram Language code: mol = Import["ExampleData/bisCWdhpe2Cl_13benz_c1.fchk"]; dipole = mol["MetaInformation"]["DipoleMoment"]

Show the dipole together with a 3D plot of the molecule:

Wolfram Language code: Show[ MoleculePlot3D[mol], Graphics3D[{Red, Arrow[{{0, 0, 0}, QuantityMagnitude@dipole}]}], ViewPoint -> Right ]

Find the wavelength of light corresponding to a molecule's band gap using the formula:

Wolfram Language code: FormulaData[{"PhotonEnergy", "Wavelength"}]

Import the molecule and get the computed dipole moment:

Wolfram Language code: mol = Import["ExampleData/bisCWdhpe2Cl_13benz_c1.fchk"];
Wolfram Language code: {occupation, energies} = Lookup[mol["MetaInformation"], {"AlphaOrbitalOccupations", "AlphaOrbitalEnergies"}]

Find the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO):

Wolfram Language code: {lumo} = FirstPosition[Normal@occupation, 0.0]
Wolfram Language code: homo = lumo - 1

Find the energy required to promote an electron from HOMO to LUMO:

Wolfram Language code: bandgap = energies[[lumo]] - energies[[homo]]

Use FormulaData to convert to wavelength:

Wolfram Language code: FormulaData[{"PhotonEnergy", "Wavelength"}, {"E" -> bandgap}]

Convert the result to nanometers:

Wolfram Language code: UnitConvert[%[[2]], "Nanometers"]

Visualize the result as a color:

Wolfram Language code: ColorData["VisibleSpectrum"][QuantityMagnitude[%]]