Hello,
with the newest Avogadro 2, OpenBabel and xtb plugin on my Windows11 notebook I compute orbitals, but they do not show up in the “Molecular Orbitals” window. The MO window is empty - see the printscreen. Please help.
PS: I get the message about xtb calculated oribtals; likewise in the log.log file I see :
"main_:75: The following dictionary was passed back to Avogadro: {‘readProperties’: True, ‘moleculeFormat’: ‘molden’, ‘molden’: '[Molden Format]\n[Title]\n[Atoms] AU\nC 1 "
I’ll reply more thoroughly to you shortly, but to begin with you can look in the calculation directory (in the plugin’s submenu) and open the molden.input file manually with Avogadro. That should give you the results, at least.
I see the molden.input file in the deep xtb calculation subdirectory. But Avogadro 1.100 can not open this file (I am under Windows, and have no molden program )…
If you rename it to something like file.molden it will be fine.
Not entirely sure I want to enable .input as a recognized extension…
Thanks ! After renaming molden.input to file.molden and opening it I got the orbitals.
Only minor issue remains now: how to tell Avogadro to display orbitals around HOMO+/-10 ?
You can just click on other lines in the table. It will pre-compute +/- 5 around the HOMO/LUMO gap, but it doesn’t take long to click on another one and have it render.
Well, I can not get more lines with so desired orbitals upon mere clicking. Got only 100% status of each orbital, but no extra lines…
The “Molecular Orbitals” window has constant number of lines…
I looked carefully into file.molden. Is has 36 orbitals , roughly half of them is occupied.
Avogadro2 assigns wrong ordering.
The issue there is that xtb doesn’t print the full set of MOs, and Avogadro currently doesn’t really expect that the set of MOs will be incomplete.
I need to change the plugin slightly so that the MO indices are passed back to Avogadro, but I’m not sure whether that will entirely fix the issue.
Besides which, the interface between Avogadro and the plugin is clearly not working at the moment anyway, since the orbitals weren’t being loaded for you. Can you please reproduce the original issue (no MOs being displayed after running an orbital calc with the plugin) and send the log file, input file, and the various output files from the calculation folder? (As an archive e.g. .zip). Then I can take a look. Thanks!
I think the main thing is that parts of Avogadro assume electrons / 2 → HOMO, and there needs to be more code that sets the HOMO or orbital occupations. The latter is probably the better option to also handle other kinds of calculations.
Hello,
you can reproduce this issue with any small molecule.
For instance CH3Cl, optimize it using FF, and then calculate orbitals using xtB-as-plugin. Open the calculation files, rename molden.input to file.molden and open this file in Avogadro2.
In molden.input file there are all xtb calculated orbitals. But Avogadro2 does not properly counts the MOs, it wrongly assignes HOMO-x numbering…
This is the CH3Cl set of MOs.
This is content of file.molden:
[Molden Format]
[Title]
[Atoms] AU
C 1 6 -0.32225284938446E+01 0.10954114935358E+00 -0.19633106382764E+00
H 2 1 -0.49742369209648E+01 0.34268151953554E+00 -0.12626681597391E+01
Cl 3 17 -0.31584459800891E+01 0.23299476033206E+01 0.22965925517897E+01
H 4 1 -0.31310019661650E+01 -0.17949467532935E+01 0.59391560906370E+00
H 5 1 -0.16012695866399E+01 0.43486558373585E+00 -0.14314765127271E+01
[GTO]
1 0
s 4 1.00000000000000
51.0493630955799 -0.163120632101274
8.79112274068875 -0.199110245810007
0.706404222589298 0.318820477536558
0.269228134134116 0.127065041842404
p 4 1.00000000000000
5.82636561408000 0.737164515452096
1.51068960187200 0.682163716148503
0.532564832880000 0.357830539292537
0.212023236906000 5.398303027584788E-002
2 0
s 3 1.00000000000000
3.37022769753360 0.273591105889083
0.613891182214980 0.264605406538605
0.166142911484160 8.246594753408230E-002
3 0
s 4 1.00000000000000
9.34674866189868 -0.125552785052236
2.63274953955161 -0.254029831967196
0.472092932487140 0.305184566430756
0.232271649766237 8.559661830788402E-002
p 4 1.00000000000000
8.96653868620652 -0.317209215069455
0.926601749794952 0.357031126383567
0.418792332287928 0.280771537007085
0.202453454537036 4.152131922185704E-002
d 3 1.00000000000000
3.20597745654841 2.13231494102881
1.00523897559031 0.971375176087545
0.391565355448865 0.129419082352652
4 0
s 3 1.00000000000000
3.37022769753360 0.273591105889083
0.613891182214980 0.264605406538605
0.166142911484160 8.246594753408230E-002
5 0
s 3 1.00000000000000
3.37022769753360 0.273591105889083
0.613891182214980 0.264605406538605
0.166142911484160 8.246594753408230E-002
[MO]
Sym= 1a
Ene= -1.05282827011373
Spin= Alpha
Occup= 2.00000000
1 4.060378057440216E-002
2 1.083137419866094E-003
3 3.753179371156806E-002
4 4.213816284108944E-002
5 -6.561872048770307E-003
6 0.981151079699653
7 1.737781213602045E-004
8 6.023058061222195E-003
9 6.762146809090162E-003
10 1.700326422958499E-003
11 -5.559954279960332E-004
12 -1.144330994962465E-003
13 -7.524048527787518E-005
14 -8.449513511443549E-005
15 -2.927600500969232E-003
16 -6.561947641410705E-003
17 -6.561906973934917E-003
Sym= 2a
Ene= -0.621652236581656
Spin= Alpha
Occup= 2.00000000
1 0.576355003991025
2 -1.546781159781626E-003
3 -5.345621451673015E-002
4 -6.001999373856769E-002
5 0.228643662959873
6 -0.107845827688730
7 -3.914198832848628E-003
8 -0.135593938935599
9 -0.152236286230775
10 -5.404843958994873E-003
11 1.767370885540072E-003
12 3.637473073454801E-003
13 2.391677445571995E-004
14 2.685279621786108E-004
15 9.305945728503391E-003
16 0.228638173590808
17 0.228639723803956
Sym= 3a
Ene= -0.520809849667157
Spin= Alpha
Occup= 2.00000000
1 -1.632269756129727E-006
2 -0.311602879121982
3 -0.356752451811833
4 0.325765565413470
5 4.457401411989895E-002
6 -2.941122594719108E-007
7 -0.147802330928474
8 -0.169219247889594
9 0.154519433665390
10 -2.992943759817717E-004
11 1.413607186108324E-003
12 -1.114312810126552E-003
13 3.855726390160346E-004
14 9.084741786782867E-004
15 -4.070581216568523E-005
16 0.351199301493097
17 -0.395770781047725
Sym= 4a
Ene= -0.520806917425547
Spin= Alpha
Occup= 2.00000000
1 1.169960426699672E-005
2 0.482989302004463
3 -0.238885945815307
4 0.200381624197198
5 -0.431265746244052
6 -6.893174322232462E-006
7 0.229102075356092
8 -0.113339799545076
9 9.502117074226349E-002
10 -3.458828308435320E-004
11 9.795433310342044E-004
12 -6.336605001906724E-004
13 -6.538652855790988E-004
14 -1.334398299224526E-003
15 -3.698146329677654E-005
16 0.254227197646565
17 0.177024270583395
Sym= 5a
Ene= -0.505856737632911
Spin= Alpha
Occup= 2.00000000
1 -5.212692497792739E-002
2 -9.887880651135333E-003
3 -0.343306795898844
4 -0.385420430378048
5 0.129019115725025
6 0.140507997810290
7 1.300524057060689E-002
8 0.450220256409048
9 0.505489458954859
10 1.018494717232968E-003
11 -3.329006987212628E-004
12 -6.855940185117048E-004
13 -4.515205833103319E-005
14 -5.076025178975560E-005
15 -1.753673007931158E-003
16 0.129047482450587
17 0.129044617587618
Sym= 6a
Ene= -0.415015817891013
Spin= Alpha
Occup= 2.00000000
1 -5.883164454056881E-007
2 -9.527007326094829E-002
3 -0.100975051542177
4 9.238606649941593E-002
5 2.934561651725630E-002
6 -1.176075848567695E-007
7 0.549966539566645
8 0.582902911312226
9 -0.533318893776999
10 -3.537001616243145E-004
11 8.014823841436581E-003
12 -7.661123679812266E-003
13 3.855618150479437E-003
14 5.014011813926334E-003
15 6.007609047908154E-004
16 0.167968698821493
17 -0.197312271050848
Sym= 7a
Ene= -0.415015360521622
Spin= Alpha
Occup= 2.00000000
1 2.449502190555221E-006
2 0.136831574868171
3 -7.290699983203944E-002
4 6.141696056757012E-002
5 -0.210900737601243
6 2.899725719242190E-008
7 -0.789847634936926
8 0.420843783517991
9 -0.354532461128978
10 -8.458527044942189E-004
11 5.845665383596215E-003
12 -4.999812679101995E-003
13 -5.430424782767317E-003
14 -7.256339034576671E-003
15 5.843623076717940E-004
16 0.130864605946324
17 8.003656917811719E-002
Sym= 8a
Ene= -0.153911372125390
Spin= Alpha
Occup= 0.00000000
1 -0.465727983721294
2 -1.192941683107127E-002
3 -0.413368021266989
4 -0.464099672481515
5 7.285653081003481E-002
6 0.229352749272059
7 -1.322894127233422E-002
8 -0.458367234475612
9 -0.514624485899203
10 0.218850936656401
11 -7.156304406982017E-002
12 -0.147287892586580
13 -9.686189006040584E-003
14 -1.087530085523286E-002
15 -0.376812887518600
16 7.285746850552403E-002
17 7.285901217073378E-002
Sym= 9a
Ene= 1.874228132921546E-002
Spin= Alpha
Occup= 0.00000000
1 1.092491883833390E-005
2 0.142233945288470
3 -8.347499253919249E-002
4 7.068340560490224E-002
5 0.248181274995035
6 1.450287680726883E-006
7 -5.705128556458195E-003
8 3.346484154922579E-003
9 -2.837047736652874E-003
10 0.132101759961116
11 0.414947567120836
12 -0.547049327081952
13 -0.612451945694890
14 -0.448228554047548
15 0.169847262895024
16 -0.164400869707003
17 -8.380115391172749E-002
Sym= 10a
Ene= 1.874306538773398E-002
Spin= Alpha
Occup= 0.00000000
1 3.091135732803551E-006
2 -0.109314472569050
3 -0.104827237934174
4 9.617522596459792E-002
5 -4.653288581309909E-002
6 4.370877308278831E-007
7 4.383661714545494E-003
8 4.203138672995425E-003
9 -3.857366608616293E-003
10 0.166185954789200
11 0.542242499523146
12 -0.708428454312346
13 0.521123726838030
14 0.291716731426442
15 0.158484807786484
16 -0.191657288262603
17 0.238182777950788
Sym= 11a
Ene= 2.597374522193683E-002
Spin= Alpha
Occup= 0.00000000
1 -1.255975815339636E-006
2 -5.228890929563994E-004
3 -4.784349549238519E-004
4 4.408057209068239E-004
5 6.143037252122521E-003
6 -1.794319913031395E-007
7 2.454585885487585E-003
8 2.249289812300419E-003
9 -2.066120340784853E-003
10 0.554939603312919
11 -0.492106179571796
12 -6.283342374112286E-002
13 0.420074098408988
14 -0.603612223009732
15 0.300172652660927
16 2.223691362868259E-002
17 -2.837746703538811E-002
Sym= 12a
Ene= 2.597376151458166E-002
Spin= Alpha
Occup= 0.00000000
1 -2.353998902210399E-006
2 -6.505983754305699E-004
3 4.001460677156161E-004
4 -3.372479728907400E-004
5 2.922462068035250E-002
6 -3.289621075088338E-007
7 3.053147958983096E-003
8 -1.872075448981004E-003
9 1.589546226917444E-003
10 -0.629092249175161
11 0.476180418374889
12 0.152911830800271
13 0.363124242888917
14 -0.569682915508623
15 -0.336611803486064
16 -1.992978490144780E-002
17 -9.290767832593246E-003
Sym= 13a
Ene= 0.116454799203979
Spin= Alpha
Occup= 0.00000000
1 0.721739083939067
2 -1.508474674132272E-002
3 -0.524288518779885
4 -0.588539805533957
5 -0.532884903550599
6 0.175389171153541
7 -5.843519230440831E-003
8 -0.202304930915654
9 -0.227143946649888
10 -0.215997599933138
11 7.060783180280464E-002
12 0.145389768130333
13 9.577333682413394E-003
14 1.074458682628438E-002
15 0.371882929205332
16 -0.533015156460101
17 -0.532966989842335
Sym= 14a
Ene= 0.155000530481417
Spin= Alpha
Occup= 0.00000000
1 0.851012052241254
2 4.144724395769097E-003
3 0.141678277799248
4 0.159153285131310
5 -0.306679763456326
6 -0.131576753861350
7 6.443529872055558E-003
8 0.223448979358121
9 0.250865535330479
10 0.415742654983732
11 -0.135960886400790
12 -0.279781768582942
13 -1.838614198092237E-002
14 -2.064818552998597E-002
15 -0.715827154266990
16 -0.306807115319624
17 -0.306769623928906
Sym= 15a
Ene= 0.190464472060312
Spin= Alpha
Occup= 0.00000000
1 1.295468417636367E-004
2 -0.814668965979834
3 0.510049752722796
4 -0.433418052781700
5 -0.920897320970216
6 4.144554179308006E-006
7 7.461827907174744E-002
8 -4.671872736007503E-002
9 3.969584568635467E-002
10 2.587416935275271E-002
11 0.138503438972377
12 -0.164377608325130
13 -0.167226838559814
14 -0.142287755756499
15 4.368591103583472E-002
16 0.636637325552574
17 0.284049589296266
Sym= 16a
Ene= 0.190481523724368
Spin= Alpha
Occup= 0.00000000
1 2.070849734516045E-005
2 0.669035190552722
3 0.599921302388524
4 -0.551558030210488
5 0.203559397254443
6 2.371497530914950E-006
7 -6.127757875596089E-002
8 -5.494982979703820E-002
9 5.051395979279643E-002
10 3.505792806665642E-002
11 0.167044747169808
12 -0.202102675236464
13 0.149571378902318
14 0.104257997954123
15 3.823654352356507E-002
16 0.695669923830042
17 -0.899262561448701
Having a look at it briefly, what happens for me is the same as you, that I run the orbitals calculation, and the MO dialog then opens but is empty, so I can confirm the bug.
However, if I then switch to another molecule in the Molecules Pane and back again, the dialog is then populated. So the information is being passed back correctly, there’s just something weird going on on the Avogadro side.
I know that’s a bit inconvenient, but at least that’s a bit of a work-around so you can see the orbitals without having to load the file manually. 
I’ll also note @ghutchis that some MOs seem to render the same even when they ought to be different (and are verifiably different by checking the file).
ethylene.molden.txt (8.4 KB)
Here, for example, orbitals 6 to 12 (by Avogadro’s reckoning) are displayed uniquely, but 1 to 5 all display the same, with s-type symmetry.
acetone.molden.txt (23.0 KB)
Acetone also shows a similar issue, but here not only do the five lowest energy orbitals all render identically, so do 17-20.
ch3cl.molden.txt (13.2 KB)
For CH3Cl, orbitals 1-5 all render identically, 14-17 render identically, and actually 11-13 don’t render at all.
Changing the render quality has no impact.
Yeah – looking at the files, the orbital numbering does actually match up with the scheme that xtb uses (i.e. even though it only looks at the valence orbitals, it just ignores the core orbitals for the purpose of the numbering).
So it’s the occupations that are needed really.
The occupancies are actually included in the .molden file, but unfortunately Avogadro doesn’t currently parse them.
Edit: I also just had a go at having the plugin pass the occupations back to Avogadro within the output JSON e.g.
example.json.txt (11.5 KB) and it doesn’t seem like the occupations are registered, as if I run an orbitals calculation and then save to CJSON the occupation data doesn’t appear. So it’s not a simple fix that can be done from the plugin.
Avogadro of course has to act appropriately for the given occupations, but getting the occupation data into Avogadro is a pre-requisite for that. The easiest way to get that to happen for now will be to add support for parsing occupation data from .molden files. I guess that’s not a huge undertaking and something that I can look at.
FYI: looking into the corresponding tutorial, Viewing Molecular Orbitals — Avogadro 1.100.0 documentation , I guess this is shown from the previous Avogadro version…
Yep, that’s one of the many parts of the manual that need updating before the 2.0 release.
Yep. Help updating the manual is most welcome.
Coming back to this … is it a problem with the MO window? In other words, if you use “Create Surfaces” does it show the same issue?
While in principle, the occupations are tracked, in practice the code for handling basis sets does not do a great job with that - I noticed as I was working on the MO window itself. (e.g., it assumes it can get the HOMO number as electrons / 2 which is problematic).
Yes, parsing occupation from molden would be great.