Hi, as per the subject I am trying to do QTAIM with Avogadro2 1.100 on Apple Silicon Mac.
In particular the analysis does not produce RCPs (3,+1), even though I made sure that they are present with Multiwfn.
The other thing is about atomic charges: when it calculates them it crashes.
What can I do?
Thanks for the help.
Riccardo
Can you provide me with an example file? That I can definitely fix.
The implementation was contributed by a Bader group alumnus - I’m not sure if it has ring / cage critical points.
What I would like to support is reading analysis from Multiwfn or other programs for visualization. If you have ideas on that, please let me know. The basic idea is to start with adding support for QTAIM properties to the CJSON file format. Since I don’t use it very much, it would help to have some suggestions on key features.
Given the extension I can’t attach it, but it is available at the following link:
Another suggestion is to add the possibility of displaying the density of CPs.
Finally, an example of multiwfn output is:
Just to interpret the multiwfn output…
REMARK C=(3,-3) N=(3,-1) O=(3,+1) F=(3,+3)
So if I remember my QTAIM:
I can certainly think of some good ways to read this and translate to the Avogadro QTAIM properties for visualization. As I said, I don’t remember if ring / cage points are implemented or not.
What you wrote is right.
I only add that in rare cases the CPs (3, -3) could be non-nuclear.
I understand that as far as QTAIM is concerned, the algorithm is rightly managed by Bader’s student.
As for the atomic charges, is it possible to patch the crash that occurs during the calculation?
Then as far as the visualization of the densities or the Laplacian of the densities in the critical points is concerned, it would be interesting to understand if they are ionic, covalent bonds, etc…
It should be. There were two challenges. First off, I’ve been using a development version using Qt6 and the QTAIM code wasn’t updated yet. Secondly, running QTAIM in Debug mode is really slow.
I should be able to find the crash today.
For that, I think it would help to either recruit some QTAIM experts to write up a concise plan for how that code should work (i.e., since I don’t use QTAIM in my research) or cases like the Multiwfn file in which case Avogadro can read the separate output for visualization.
I would really like to help, but I’m just a thesis student. I reached out because I’m currently working with QTAIM, and integration with Avogadro2 would be very interesting for what I’m doing.
In addition to that, I’d like to make two more suggestions:
• It would be great if Avogadro2 could visualize the energies from ORCA’s file_trj.xyz output, showing the energy associated with each conformer as written in the file.
• Also, support for reading .allxyz files would be helpful. Right now, I rely on gMolden for that. The format is similar to file_trj.xyz, where each structure has an associated energy.
If you’d like, I can send some example files.
You’re already helping. 
Yes. It’s on the roadmap and should be fairly easy to do - you should already be able to see the relative energies in the Analysis => Conformers dialog.
Oh dear god. What program decided to make up a new format / extension?
Sure, if you want to open a new topic for that, it shouldn’t be hard to support.
Edit: Just realized there’s another post where this was already explained… Feel free to ignore
ORCA will make a .allxyz file for some calculations, such as a relaxed surface scan. All the file contains is the final optimized XYZ coordinates from each step in the surface scan. The only difference between this and a regular XYZ file with multiple molecules in it is that there is a line between each set of XYZ coordinates with a single > character.
This is a snippet from a relaxed surface scan calculation I ran not too long ago with ORCA 6.0.1, and below that is the .allxyz file. (I added .txt to the end because the forum disallows files without approved extensions)
14
Coordinates from ORCA-job 000-Rot Relaxed Surface Scan Step 1 E -321.114733867234
C 0.713383 0.511963 0.009344
C 1.948366 -0.321913 -0.078878
N 0.773971 1.874787 0.090827
N -0.420294 2.356347 0.156841
N -1.262836 1.322272 0.119290
C -0.606475 0.139375 0.026842
C -1.296479 -1.181166 -0.032678
H 2.530923 -0.055397 -0.963384
H 2.582267 -0.165106 0.796512
H 1.703351 -1.383703 -0.138089
H -2.253666 1.491860 0.159965
H -1.899357 -1.357473 0.862074
H -1.952262 -1.249888 -0.904722
H -0.560890 -1.981956 -0.103943
>
14
Coordinates from ORCA-job 000-Rot Relaxed Surface Scan Step 2 E -321.114533060295
C 0.714997 0.512892 0.034642
C 1.940577 -0.322326 -0.134410
N 0.780211 1.867903 0.188467
N -0.412562 2.347299 0.302596
N -1.257071 1.317474 0.223412
C -0.605452 0.141029 0.059525
C -1.292797 -1.174757 -0.084995
H 2.300996 -0.292367 -1.166094
H 2.738704 0.050754 0.509031
H 1.745247 -1.365208 0.123908
H -2.246363 1.483207 0.302120
H -2.221912 -1.201972 0.489145
H -1.533019 -1.387171 -1.130124
H -0.651557 -1.976756 0.282779
000-Rot.allxyz.txt (8.7 KB)