rpsteele
commented
2 years ago Another use case to add to this ticket...
After performing a geometry optimization that properly returns to IQmol, addition of new atoms to the structure also is not propagated to the input file.
As an example from my class... The students optimize the structure of benzene (via a Q-Chem job). To the resultant structure, they then add a Li atom, in order to form the noncovalent Li+@benzene complex. When they go to Q-Chem setup, the job does not include the added Li atom.
When a user runs a geometry optimization, this structure correctly appears in the molecular viewer. However, if the user attempts to run a subsequent job, the correct coordinates are not translated into the new input file.
For example, let's say a user optimizes the structure in job 1. In job 2, they try to run a harmonic frequency calculation on this optimized structure. The coordinates populated in the input file for job 2 are the initial structure coordinates from job 1, not the optimized coordinates. Even if the user explicitly selects the last entry in the list of energies under the "Geometry" heading, the correct coordinates are still not used.