10.5 Visualizing and Plotting Orbitals, Densities, and Other Volumetric Data

10.5.1 Visualizing Orbitals Using MolDen and MacMolPlt

(June 30, 2021)

Upon request, Q-Chem will generate an input file for MolDen, a freely-available molecular visualization program. 963 Schaftenaar G., Noordik J. H.
J. Comput.-Aided Mol. Design
(2000), 14, pp. 123.
Link
13 Albrecht A. C., Hutley M. C.
J. Chem. Phys.
(1971), 55, pp. 4438.
Link
MolDen can be used to view ball-and-stick molecular models (including stepwise visualization of a geometry optimization), molecular orbitals, vibrational normal modes, and vibrational spectra. MolDen also contains a powerful Z-matrix editor. In conjunction with Q-Chem, orbital visualization via MolDen is currently supported for s, p, and d functions (pure or Cartesian), as well as pure f functions. Upon setting MOLDEN_FORMAT to TRUE, Q-Chem will append a MolDen-formatted input file to the end of the Q-Chem log file. As some versions of MolDen have difficulty parsing the Q-Chem log file itself, we recommend that the user cut and paste the MolDen-formatted part of the Q-Chem log file into a separate file to be read by MolDen.

MOLDEN_FORMAT
       Requests a MolDen-formatted input file containing information from a Q-Chem job.
TYPE:
       LOGICAL
DEFAULT:
       FALSE
OPTIONS:
       TRUE Append MolDen input file at the end of the Q-Chem output file.
RECOMMENDATION:
       None.

MolDen-formatted files can also be read by MacMolPlt, another freely-available visualization program. 113 Bode B. M., Gordon M. S.
J. Mol. Graphics Mod.
(1998), 16, pp. 133.
Link
12 Albrecht A. C.
J. Chem. Phys.
(1961), 34, pp. 1476.
Link
MacMolPlt generates orbital iso-contour surfaces much more rapidly than MolDen, however, within MacMolPlt these surfaces are only available for Cartesian Gaussian basis functions, i.e., PURECART = 2222, which may not be the default.

Example 10.5  Generating a MolDen file for molecular orbital visualization.

$molecule
   0 1
   O
   H  1  0.95
   H  1  0.95  2  104.5
$end

$rem
   METHOD           hf
   BASIS            cc-pvtz
   PRINT_ORBITALS   true (default is to print 5 virtual orbitals)
   MOLDEN_FORMAT    true
$end

View output

For geometry optimizations and vibrational frequency calculations, one need only set MOLDEN_FORMAT to TRUE, and the relevant geometry or normal mode information will automatically appear in the MolDen section of the Q-Chem log file.

Example 10.6  Generating a MolDen file to step through a geometry optimization.

$molecule
   0  1
   O
   H  1  0.95
   H  1  0.95  2  104.5
$end

$rem
   JOBTYPE         opt
   METHOD          hf
   BASIS           6-31G*
   MOLDEN_FORMAT   true
$end

View output