Avogadro parsing of Gaussian output/log files which contain IR frequencies table but are continued as "Restart"

General Discussion Support
1

I believe this to be a bug with Avogadro

Environment Information

Avogadro version:1.2.0
Operating system and version: Windows 10 Enterprise (22H2) OS build 19045.4529

Expected Behavior

Parsing the frequency table contained in Gaussian G09, Revision E.01 output file (trying to animate the frequency modes)

Actual Behavior

but due to the fact that the output file is a continuation file (“Restart”) the Avogadro molecule editor indicates “error”

Steps to Reproduce

tried with different “Restart” output files with
malathion_Def2QZVPPD_200100_VeryTightOpt_Zmat_Freq.out (317.1 KB)
60437-30-1_Def2SVPD_200100_VeryTightOpt_Freq.out (704.4 KB)
1066-53-1_Def2QZVPPD_200100_VeryTightOpt_Freq.out (88.5 KB)
4253-91-2_Def2QZVPPD_200100_VeryTightOpt_Zmat_Freq.out (141.6 KB)
141-05-9_Def2QZVPPD_200100_VeryTightOpt_Freq.out (260.8 KB)
the frequency table contained in Gaussian G09, Revision E.01 output file (trying to animate the frequency modes)
Please upload files if appropriate here (or via file-sharing service like Dropbox or Pastebin)
950-35-6_NIST_Def2QZVPPD_200100_VeryTightOpt_Freq_Large.out (186.7 KB)
1611-31-0_Def2QZVPPD_200100_VeryTightOpt_Zmat_Freq.out (178.5 KB)
depp_Def2QZVPPD_200100_VeryTightOpt_Freq.out (377.5 KB)
dimp_Def2QZVPPD_200100_VeryTightOpt_Freq.out (380.9 KB)
decp_Def2QZVPPD_200100_VeryTightOpt_Freq.out (116.5 KB)

2

First off, Avogadro (and Open Babel) can read formatted checkpoints, so might be a workaround.

But my big suggestion is to move to the nightly builds / betas of Avogadro2 (https://two.avogadro.cc/) … We can’t provide fixes for Avogadro 1.2. – I literally can’t install the libraries needed to compile it. For example, I’m not sure if Avogadro 1.2 can read vibrations from fchk files … but I added that to Avo2.

The downside is that I can confirm the latest Avogadro2 / Open Babel don’t read your files either.

The plus side is that I’ve been working on a bunch of Gaussian parsing bugs including a few from my own students, so I’ll be able to put out a fix in a day or two.

3

I looked at these in more detail. It’ll be hard to handle because there’s not a clear set of coordinates in the restart calculations.

Normally, Gaussian prints the input atoms and coordinates and/or steps in the optimization.

Here, I can work out the atoms and order … and then the optimized z-matrix parameters. But I don’t see anywhere that determines the full z-matrix connectivity.

                       ----------------------------
                       !   Optimized Parameters   !
                       ! (Angstroms and Degrees)  !
 ----------------------                            ----------------------
 !      Name          Value   Derivative information (Atomic Units)     !
 ------------------------------------------------------------------------
 !       B1          1.8545   -DE/DX =    0.0                           !
 !       B2          1.5315   -DE/DX =    0.0                           !
 !       B3          1.5217   -DE/DX =    0.0                           !
…
 !       A1        108.3912   -DE/DX =    0.0                           !
 !       A2        111.1986   -DE/DX =    0.0                           !
 !       A3        103.9201   -DE/DX =    0.0                           !
 !       A4        113.1783   -DE/DX =    0.0                           !
 !       A5        111.8128   -DE/DX =    0.0                           !
…
 !       D1       -123.6548   -DE/DX =    0.0                           !
 !       D2        -87.174    -DE/DX =    0.0                           !
 !       D3        163.4145   -DE/DX =    0.0                           !
 !       D4         60.5825   -DE/DX =    0.0                           !

But I don’t know how to reconstruct B1 = atoms X and Y, A1 = angle between atoms ? and ? and ?, etc.

OTOH, the formatted checkpoints, I think should have everything and in Avogadro2 should support reading vibrations.

4

@Alex_Balboa, if there’s a way to reconstruct the coordinates or the full z-matrix from these output files, please let me know. I’m not seeing much to go on.

5

I am sending the files via the DoD SAFE sharing file system as a zipped file for review and consideration. Please note that the Gaussian route used did NOT include the save normal modes into the checkpoint file (not a default setting in Gaussian G09, but a default setting in Gaussian G16). Thanks a lot so far for all your assistance.

Sincerely,
alex

Should the following utility be used:
https://gaussian.com/gdiffs/
The freqchk utility can recover normal modes from the .chk or .fchk file, and can save the normal modes it generates to a .chk file (but cannot save to an .fchk file).

7

I used the following release of Avogadro to see if I could open the formatted checkpoint file:

Version 1.93.0 AvogadroLibs Verion 1.93.1 Qt Version 1.93.1

under Lubuntu (Linux kernel 5.11.0-50-generic #56-Ubuntu SMP Thu Jan 13 18:22:14 UTC 2022)

but the tab section under “Quantum” Vibrational modes is grayed out…

possibly meaning that unless the vibrational modes are saved within the checkpoint/formatted checkpoint, Avogadro 1.93.0 cannot parse the frequency table to animate the frequency modes?

8

Version 1.93 is really old. Looks like it was compiled in Jan 2022?

You’d want to try 1.99 for example.

I’ll take a look at the files you sent, thanks. Gaussian hasn’t documented the .chk file at all. The impression I’ve gotten is that they want programs to use the .fchk file. Too bad if G09 doesn’t save vibrations to .fchk files. (Though that explains why I never saw that until this year when folks sent me some examples.)

9

Installing the Linux download “Download Flatpak” (version 1.99) and that version worked so everything is good on the Linux side… will have my colleague try the Windows version and see how well that works… will keep you updated. but thanks for a great job on this latest release of Avogadro… extremely well laid out and intuitive to use.

2 Likes
10

We’re still missing some bits from 1.2, but hope to get there soon. :slight_smile: