Q-Chem
Contents
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 derivative 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 (by including
print_general_basis true
print_orbitals true
The moleculare orbitals will be read in as well as their associated symmetry (from the wavefunction analysis) and occupancy. The occupancy is only reflected in the symmetry label for the molecular orbital, so information about HOMO and LUMO is not passed on to Jmol.
If both alpha and beta molecular orbitals are encountered, e.g. in unrestricted calculations, both sets of orbitals will be read. The numbering is sequential starting with the alpha orbitals followed by the beta orbitals.
In order to provide info of the orbital occupancy the symmetry labeling contains, where # refers to the MO number in the Q-Chem output file since that is not always the same as the MO number in Jmol when also beta orbitals are encountered:
- Restricted AB(#) for an occupied orbital or V(#) for a virtual one
- Restriced Open Shell AB(#) for a doubly occupied orbital, RO-1A(#) or RO-1B(#) for a singly occupied alpha or beta orbital, or V(#) for a virtual orbital
- Unrestriced A(#) or VA(#) for an occupied and virtual alpha orbital respectively, or B(#) or VB(#) for an occupied and virtual beta orbital respectively
