I am using Avogadro 1.2.0 and I saw (while opening a new file) that
Avogadro can read NWchem output files. I have a frequency calculation
output file (my log file, a text file) from NWChem 6.6 that makes
Avogadro crash when I try to open it.
NWChem also prints 20 xyz files for each mode and a single file that
includes all 20 xyz geometries. I have been able to use Avogadro to
read that single file with the 20 xyz geometries to make a movie of
the vibrational mode but I have not found a way to make a figure that
displays the molecule and arrows to display the vibrational mode.
My questions:
1) Can I use Avogadro to read NWChem output files? Perhaps I am asking
Avogadro to read the wrong output file?
2) Is there a way to use Avogadro to make a figure to illustrate the
vibrational modes?
Avogadro reads all files through Open Babel which supports a wide range of formats, but it’s entirely possible that the NWChem support in OB has not kept up with recent versions. (Many comp. chem programs make subtle but problematic changes in their output files.)
The vibrational mode arrows are read from the output, so it would be a bit tricky to work that backwards from the XYZ files.
I know that Open Babel does read Molden vibrations - if it’s possible to save a Molden file from NWChem, it should have the vibrational results.
@Miroslav_Ilias Would it be possible how NWChem records the results underwent a reorganization?
Though I’m not a user of NWChem, after downloading the file you shared as ...out (i.e. without the additional _SAVED), I attempted to read it with an Avogadro AppImage for Linux from here. Avogadro recognizes it is about the results by NWChem, however reports «Could not find any atomic coordinates. Are you sure this is an NWChem output file?» and stops here.
I then turned to Jmol (version 16.1.11 2023-04-19 20:17). This program reports line 11294 as problematic
NWChem is not in Jmol’s list of programs here, and one potential pitfall to test/compare with the test files of the project (e.g. Jmol’s file H2O_1.nwo from here) is their age (NWChem 4.6 vs version 7.2.0 you shared).
