From Jmol
Jump to navigation Jump to search

Jmol for Q-Chem

Q-Chem 3.2 is now also supported. Older versions may work too, but only the older 2.1 has been tested for structure reading only. Since the different options in Q-Chem can give quite different formatted output and has all kinds of output options for each, it is not guaranteed that the output from all types of calculations will be properly parsed. Most testing has been done with DFT and HF calculations for restricted, unrestricted and restricted open shell cases, with single point, geometry optimizations and frequency calculations.

Jmol reads the all structures sequentially where each Standard Nuclear Orientation results in a new atom set or model. Since this can result in a large amount of structures, they are collected into groups of atom sets based on the job number in the input file, most easily selected using the AtomSetChooser.

Multiple Jobs

Every Job is collected in its own branch.

Jobtype opt

In case of a geometry optimization, all structures associated with the optimization trajectory are read.

Jobtype freq

When the output of a frequency job is encountered, a new 'Frequencies' branch containing all the frequencies is generated in the job branch. Each of the vibrational modes will be associated with a new atom set and the title of that atomset reflects the frequency of that vibration.

Note that if the 2nd-order derivatives have to be evaluated numerically, a lot of structures may be calculated before the frequencies are found and the associated branch in the AtomSetChooser is created.

Mulliken Net Atomic Charges

When a Mulliken Net Atomic Charges analysis is encountered, the charge on the atoms are assigned too.

Molecular Orbitals

Currently only the 11.7.29 prerelease version is able to parse molecular orbitals.

If the output file contains the general basis set and molecular orbitals coefficients, i.e., by including in the rem block

print_general_basis true
print_orbitals true

The moleculare orbitals will be read in as well as their associated symmetry, if available, and occupancy. Since the occupancy of each orbital is properly interpreted, one can issue the script command 'mo homo'.

If both alpha and beta molecular orbitals are encountered, e.g. in unrestricted calculations, both sets of orbitals will be read. The Jmol numbering is sequential starting with the alpha orbitals followed by the beta orbitals. Since that Jmol numbering does not reflect the orbital number within only the beta orbitals, the latter info is provided between parentheses at the end of the symmetry label. The characters before the parentheses reflect the type of orbital: AB for a filled restricted, V for an empty restricted, A or B for a singly occupied restricted or unrestricted alpha or beta, respectively, and VA or VB for an empty restricted or unrestricted alpha or beta molecular orbital.