I believe I have identified an unusual behavior in Avogadro while attempting to plot the orbitals. Attached are images illustrating the discrepancy. Despite using the same parameters: orbital number (in this case, 29) and isovalue (0.03), the orbitals generated by both Avogadro and Molden softwares exhibit different shapes. The expected output should resemble the one produced by Molden.
I have notmade any modifications to this part of the Avogadro code, leading me to suspect that this variation might be a bug. Is this am issue that you have encountered previously?
HF.molden.out (1.4 MB)
Weird. It renders just fine with Avogadro 1.x …
And when I ran it with
g09 as HF/6-31G(d) and read the
fchk file, it was fine:
So it seems to be an issue reading Molden files.
Just to be sure, can you tell me how you generated the file (e.g, program, method, basis set, etc.)
I used Orca to perform the following operations. Here is the input I employed:
! RHF cc-pvdz xyzfile useSym sp LARGEPRINT
%PAL NPROCS 16 END
%output print[p_mos] true
*xyz 0 1
C -0.023139979512 0.009866959807 0.000387294396
O -1.405150484480 -0.063110479358 0.021203426227
H -1.761493658243 0.836575801106 0.029781040012
C 0.680507462673 1.226200108684 -0.006089800865
C 2.089432991794 1.225361444018 -0.027574297645
C 2.791502556965 0.008191540350 -0.042532772891
O 4.173417358408 -0.066431128777 -0.063863328817
H 4.530926965115 0.832830229934 -0.066171150384
C 2.084939028295 -1.208008445580 -0.036010751303
C 0.681845842578 -1.207173252623 -0.014615191064
H 0.121924279060 -2.145928355622 -0.009359276877
H 2.643642787362 -2.147429411688 -0.047812589031
H 2.631584954124 2.177277883396 -0.032513282051
H 0.139590358623 2.178761246266 0.005486774558
Subsequently, I used the command
orca_2mkl HF -molden to generate the appropriate output for Avogadro.
Well, here’s an important question … does the Orca output itself generate the correct orbitals (vs. the molden, which is showing a bug).
I am not entirely certain I understand your question, but when I use
orca_plot HF.gbw -i with the gbw file obtained directly after my Orca calculation, my orbitals are correct while using VMD.
I think that the problem might lie in how Avogadro reads the molden file, as the Molden software has no trouble plotting them accurately.
Yes, I understand, Can you post the
.log file from Orca? You should be able to read the output file directly in Avogadro because you used the
Here are the Orca and Molden outputs. Personally, I do not find anything surprising in the basis set output from the Orca file, but I could have overlooked something
HF.out (1.4 MB)
HF.molden.out (512.4 KB)
Right. That was my question. So the bug is somewhere in the Molden reader. Thanks.