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Output file notes

    Chemissian currently supports Gaussian, US-Gamess, Firefly/PC-Gamess, Q-Chem, Molpro (via molden format), Turbomole (via molden format), ORCA (via molden format), NWChem, and Spartan output files. Below are some specific requirements for each supported program's output files.

    Common note: Use only single-point output files (i.e., without geometry optimization)

  • Notes to Gaussian users:

    • Make sure that your Gaussian input file looks like, e.g.:

    "#P B3LYP/Lanl2dz pop=full GFInput"

    #P option enables extended printout, pop=full enables printout of all molecular orbital coefficients, and the GFInput keyword enables printout of basis set data.
    (B3LYP/Lanl2dz are just examples of a method and basis set; you can use any other DFT(HF) method and basis set).

    Chemissian uses the "EIGENVALUES" section from the Gaussian output file to build MO energy level diagrams. It is also needed to plot MOs or charge density maps and to describe the TDDFT/CIS spectrum peak nature. To plot electron density maps, basis set information is also needed. Therefore, the "GFInput" keyword should be included in the Gaussian input; otherwise, the "Analyze electronic density" menu item will be disabled.

    To visualize calculated TDDFT or CIS UV-VIS spectrum, the Gaussian input file should contain:

    #P B3LYP/Lanl2DZ TD(SINGLETS, NStates=45) Pop=Full GFInput IOp(9/40=7)

    B3LYP is just a DFT method, and Lanl2DZ is just a basis set (You may choose any other method and basis). Chemissian uses data about molecular orbitals to plot the MO diagram, so the "#P" and "pop=full" keywords are necessary. (Later, you will also see transitions corresponding to the selected peak (in the "Analyze spectrum" window) of the TDDFT-calculated spectrum on this diagram.) If you want to plot charge densities and MOs contour maps, Chemissian needs information about the basis set, so use the "GFInput" keyword (and Gaussian will print the basis set). "TD" is a keyword to calculate the spectrum, which will be shown when you load the Gaussian output into Chemissian.

    If you use the ONIOM feature of Gaussian, specify gfinput gfoldprint options in the Gaussian input

  • Notes to Q-Chem users:

    Specify the following keywords in the $rem section of the Q-Chem input file:
    $rem
       print_general_basis=true
       print_orbitals=99999
    $end
    These keywords will force Q-Chem to print the LCAO-MO matrix and basis set in its output file.

  • Notes to Spartan users:

    Spartan 8:

    • Use "directory based filesystem" mode in the Spartan program (not .spartan files).
    To enable this mode, configure Spartan as follows:

    1) Go to Options -> Preferences -> X-Platform
    Select "Directory Based" as the Document Style

    2) Go to Options -> Preferences -> Settings
    Select the "Keep Verbose" checkbox.
    Spartan will create a directory for the calculation.

    Spartan 14:

    1) Go to Options -> Preferences -> Miscellaneous
    Select "Directory Based" as the Document Style

    In "Data Compression Options," uncheck "Gzip text files" and "Use binary archive."

    2) Go to Options -> Preferences -> Settings
    Select the "Keep Verbose" checkbox.
    Spartan will create a directory for the calculation.

    When submitting a job via Setup->Calculations:
    Choose
    -"Calculate: energy"
    -"Print: Orbitals and energies; Charges and Bond Orders"
     

    Now, to load the Spartan output, you just need to click "File --> Open…" in Chemissian and select the (standard) "output" file. Chemissian will also try to load data from the "voutput" file (number of electrons, UV-VIS spectrum) and from the "archive" file (basis set data) in the directory where the "output" file is located. If these files are missing in the directory (or have other names), Chemissian will ask you to input their location.

  • Notes to Molpro users:

    • Use the MOLDEN file generated by Molpro (see Molpro manual).

  • Notes to NWChem users:

    • Use the print "final evals" "final vectors" option in the scf-section of the NWChem input file.

    E.g., correct SCF input should contain:
    scf
       print "final evals" "final vectors"
    end

    Correct DFT input should contain:
    dft
       print "final evals" "final vectors"
    end

    To get the EOM-CCSD spectrum with oscillator strengths, the dipole option should be included in the tce section of the NWChem input.

  • Notes to Turbomole users:

    There is partial support for Turbomole files via the MOLDEN format. To generate a MOLDEN file, you can use the tm2molden utility that is part of the Turbomole package.

  • Notes to ORCA users:

    There is partial support for ORCA files via the MOLDEN format. To generate a MOLDEN file, one can use the following command:

    "orca_2mkl yourfile -molden",
    where yourfile.gbw is generated by ORCA
    (see the ORCA manual for details)

    When you load a MOLDEN file generated by ORCA, Chemissian will also ask for an additional (main) ORCA output file. If that file contains TD-DFT/CIS data, Chemissian will load and display it.

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