I’d like to try and test some other molecules for Vibronic Spectrum calculations, and also hopefully submit to an actual device later for testing purposes. How would I go about creating the .data file with the .npz that’s required for the molecule. I’d appreciate any support on the general process.
Meanwhile I’ve figured out the way to do it from scratch is to run DFT for my desired molecule, preferably with GAMESS. I’d like to know if there’s a guide on how to do this optimally for to be implemented in GBS.
I’ve run DFT calculations for some weeks, for a proposed-topological material before (so crystal, not molecule), however only with QuantumEspresso; suffice to say I’m also rusty on it. I only remember there were layers to it like scf → bands & dos → symkpoints etc. I am unsure how it’s done for a molecule in GAMESS and at what step is the geometry optimised and normal modes reported for example. Is this outlined somewhere?
Also preferably, maybe there is a database where this data is already reported for many given molecules? I’d really appreciate if someone could share such a database (if it exists).
Update: I managed to run DFT with RUNTYP=HESSIAN, and DFTTYP=B3LYP for neutral formic acid. The Formic Acid has been created in Avogadro, geometry optimized and then fed into gamess for the hessian type calculation.
I also used read_gamess to read the file in which works; however, the data.Formic() and what I am getting is quite different. First of all I am getting neither 7 nor 9 entries. I have 15. I don’t know if this is because GAMESS have forced me to do NOSYM=1.
I’d appreciate some guidance. Here are my input and output files - as well as the comparison of arrays for neutral frequencies.
formic_acid_input.txt (508 Bytes)
formic_acid_results.txt (273.5 KB)
Hi @Bartu_Bisgin thank you for your questions! We’re looking into your questions and will come back soon with an answer.
Hi @CatalinaAlbornoz, thank you!
Meanwhile I again found some other things. Indeed I believe because of NOSYM=1 (which is required for the ANALYTIC method). I assume I get 3M = 15 (for M= 5 atoms in formic acid) modes without the -6(5) constant for non-linear(linear) molecules. It actually seems the values are close. However, I don’t see the general framework to select which frequencies if I didn’t already have the answers at hand, the ordering of the read_gamess() output seems arbitrary (maybe it isn’t, only my 2nd day with GAMESS). Long story short, this calculation was done with C1 ie. no symmetry.
On the other hand, when I do SEMINUM, it allows me to give the CS symmetry, however due to my general lack of knowledge/experience of molecular DFT and Group Theory for Molecules, I don’t know how to specify the symmetry axes for Formic acid or other molecules in general. Thus, I can’t directly get to the 9 → 7 compact elements for representations.
Thus, at this point, the questions are → how to use GAMESS for other molecules to feed into the GBS by:
a) using the molecule’s respective point symmetry group (and how do we find + specify the symmetry points/axes into the gamess.inp file).
b) using C1, ie. completely ignorant to the internal symmetries and no irreducible representations (meaning, how can I choose right frequencies, is there a logical way in terms of read_gamess output)
Hi @Bartu_Bisgin and thanks for the questions.
Yes, you are right: formic acid has 3N - 6 vibrational modes and since N = 5 here, we have 9 vibrational modes. The
read_gamess function is an utility function to extract the data from the GAMESS output and it does not select the vibrational modes automatically. You can simply look at the modes or maybe visualise the GAMESS output with a program such as Jmole to find the 6 translation/rotation modes and discard them.
Please note that depending on the method you use to perform the electronic structure calculations, you might get slightly different numbers for the atomic displacements and the vibrational frequencies.
About using symmetries other than C1 (no symmetry), you might find more information in the GAMESS documentation and also here.
Please feel free to let us know if you have any other questions.