Hello!
I believe this to be a bug with Avogadro… Actually am I the only person with Avogadro2 (1.97.0 AppImage) dumping the core after the QTAIM calculations, probably, in attempt to visualize their results?
Environment Information. Operating system and version:
Avogadro version: 1.97.0 (AppImage), Ubuntu 22.04
Expected Behavior
Eh… Expect to see results of the AIM analysis: CPs and Bond Paths, and some IAS of course.
Actual Behavior
Core dumped
Steps to Reproduce
Load any decent WFN file after any choice of the menu “QTAIM”.
See several calculation progress windows.
Wait for the progress bars to change.
Find the main window disappeared.
???
Is the QTAIM plugin finally dead or could it be revived?
Can you post a WFN that causes the problem? The files I have here are fine.
One of the simplest files tested. Core dumped again.
It is generated by ORCA 5.0.3 from MP2 / cc-pVTZ calculations and readily accepted by AIMAll 19.10.12.
Name BH3-cpv3 Run Type GeometryOpt Method MP2 Basis Set Gauss
GTO 4 MOL ORBITALS 106 PRIMITIVES 4 NUCLEI
B 1 (CENTRE 1) 0.00009672 0.00000002 0.00000006 CHARGE = 5.0
H 2 (CENTRE 2) 2.24275563 -0.00000006 -0.00000002 CHARGE = 1.0
H 3 (CENTRE 3) -1.12142622 1.94218225 -0.00000002 CHARGE = 1.0
H 4 (CENTRE 4) -1.12142613 -1.94218222 -0.00000002 CHARGE = 1.0
CENTRE ASSIGNMENTS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
CENTRE ASSIGNMENTS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
CENTRE ASSIGNMENTS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2
CENTRE ASSIGNMENTS 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3
CENTRE ASSIGNMENTS 3 3 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4 4 4 4
CENTRE ASSIGNMENTS 4 4 4 4 4 4
TYPE ASSIGNMENTS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 4 2
TYPE ASSIGNMENTS 3 4 2 3 4 2 3 4 2 3 4 2 3 5 6 7 8 9 10 5
TYPE ASSIGNMENTS 6 7 8 9 10 11 12 13 14 15 17 16 18 19 20 1 1 1 1 1
TYPE ASSIGNMENTS 4 2 3 4 2 3 5 6 7 8 9 10 1 1 1 1 1 4 2 3
TYPE ASSIGNMENTS 4 2 3 5 6 7 8 9 10 1 1 1 1 1 4 2 3 4 2 3
TYPE ASSIGNMENTS 5 6 7 8 9 10
EXPONENTS 5.4730000E+03 8.2090000E+02 1.8680000E+02 5.2830000E+01 1.7080000E+01
EXPONENTS 5.9990000E+00 2.2080000E+00 2.4150000E-01 5.4730000E+03 8.2090000E+02
EXPONENTS 1.8680000E+02 5.2830000E+01 1.7080000E+01 5.9990000E+00 2.2080000E+00
EXPONENTS 2.4150000E-01 5.8790000E-01 8.6100000E-02 1.2050000E+01 1.2050000E+01
EXPONENTS 1.2050000E+01 2.6130000E+00 2.6130000E+00 2.6130000E+00 7.4750000E-01
EXPONENTS 7.4750000E-01 7.4750000E-01 2.3850000E-01 2.3850000E-01 2.3850000E-01
EXPONENTS 7.6980000E-02 7.6980000E-02 7.6980000E-02 6.6100000E-01 6.6100000E-01
EXPONENTS 6.6100000E-01 6.6100000E-01 6.6100000E-01 6.6100000E-01 1.9900000E-01
EXPONENTS 1.9900000E-01 1.9900000E-01 1.9900000E-01 1.9900000E-01 1.9900000E-01
EXPONENTS 4.9000000E-01 4.9000000E-01 4.9000000E-01 4.9000000E-01 4.9000000E-01
EXPONENTS 4.9000000E-01 4.9000000E-01 4.9000000E-01 4.9000000E-01 4.9000000E-01
EXPONENTS 3.3870000E+01 5.0950000E+00 1.1590000E+00 3.2580000E-01 1.0270000E-01
EXPONENTS 1.4070000E+00 1.4070000E+00 1.4070000E+00 3.8800000E-01 3.8800000E-01
EXPONENTS 3.8800000E-01 1.0570000E+00 1.0570000E+00 1.0570000E+00 1.0570000E+00
EXPONENTS 1.0570000E+00 1.0570000E+00 3.3870000E+01 5.0950000E+00 1.1590000E+00
EXPONENTS 3.2580000E-01 1.0270000E-01 1.4070000E+00 1.4070000E+00 1.4070000E+00
EXPONENTS 3.8800000E-01 3.8800000E-01 3.8800000E-01 1.0570000E+00 1.0570000E+00
EXPONENTS 1.0570000E+00 1.0570000E+00 1.0570000E+00 1.0570000E+00 3.3870000E+01
EXPONENTS 5.0950000E+00 1.1590000E+00 3.2580000E-01 1.0270000E-01 1.4070000E+00
EXPONENTS 1.4070000E+00 1.4070000E+00 3.8800000E-01 3.8800000E-01 3.8800000E-01
EXPONENTS 1.0570000E+00 1.0570000E+00 1.0570000E+00 1.0570000E+00 1.0570000E+00
EXPONENTS 1.0570000E+00
MO 1 OCC NO = 2.00000000 ORB. ENERGY = -7.61061501
2.51696120E-01 4.69019238E-01 7.90427139E-01 1.17931080E+00 1.42847458E+00
1.18859728E+00 4.41451209E-01 -2.34357164E-03 -2.84918921E-04 -5.32195992E-04
-9.05800258E-04 -1.38532154E-03 -1.80169285E-03 -1.82372158E-03 -1.20082818E-03
8.20832320E-04 1.88256847E-02 9.51879140E-04 4.09658548E-10 -1.76961733E-05
0.00000000E+00 3.69206965E-10 -1.59487712E-05 0.00000000E+00 2.68068199E-10
-1.15798421E-05 0.00000000E+00 -1.71447766E-10 -9.21495354E-04 -8.87392685E-10
0.00000000E+00 -4.11650364E-05 0.00000000E+00 8.27417383E-05 6.50585290E-04
-7.33327028E-04 0.00000000E+00 0.00000000E+00 0.00000000E+00 -7.84663702E-05
2.33954729E-04 -1.55488359E-04 0.00000000E+00 0.00000000E+00 0.00000000E+00
2.47535795E-04 1.12068517E-10 0.00000000E+00 -1.13682030E-10 0.00000000E+00
-9.98422293E-04 0.00000000E+00 2.55814908E-04 -2.22523522E-10 0.00000000E+00
-1.20803522E-05 -2.17874126E-05 -3.21255272E-05 7.25459893E-04 -1.46383949E-04
1.62365589E-10 2.20782971E-04 -1.05228297E-09 0.00000000E+00 -2.25305690E-04
4.41087839E-10 2.44753689E-04 3.78449779E-06 -2.48538187E-04 -1.28271967E-10
0.00000000E+00 -1.42309569E-10 7.32239965E-05 1.32062493E-04 1.94726069E-04
-1.01350462E-03 -3.38190530E-04 -6.24648739E-10 -1.63752251E-05 2.15397884E-04
0.00000000E+00 -4.01522796E-04 5.67759887E-04 1.24411416E-04 -8.89662675E-05
-3.54451482E-05 2.51817461E-04 -2.51973979E-10 0.00000000E+00 7.32245918E-05
1.32063567E-04 1.94727652E-04 -1.01350656E-03 -3.38190784E-04 -3.61087529E-09
-1.63702518E-05 -2.15396605E-04 6.42734247E-10 -4.01524134E-04 -5.67761002E-04
1.24411699E-04 -8.89665088E-05 -3.54451901E-05 -2.51817937E-04 0.00000000E+00
1.44584800E-10
MO 2 OCC NO = 2.00000000 ORB. ENERGY = -0.70531573
-3.93475122E-03 -7.33215126E-03 -1.23567028E-02 -1.84360992E-02 -2.23312624E-02
-1.85812741E-02 -6.90118182E-03 3.66369232E-05 -3.95682309E-02 -7.39089345E-02
-1.25793379E-01 -1.92387092E-01 -2.50210826E-01 -2.53270075E-01 -1.66765501E-01
1.13993422E-01 3.47893612E-02 1.51846254E-02 -9.24947668E-09 2.42163926E-05
-3.37247356E-08 -8.33614050E-09 2.18251538E-05 -3.03945990E-08 -6.05257858E-09
1.58464770E-05 -2.20684499E-08 -1.35705740E-08 4.95639156E-04 -1.60986184E-07
-1.73810523E-09 3.88557464E-05 -7.76712445E-09 8.67489066E-03 8.38833722E-03
-1.70632279E-02 5.72686272E-08 -3.07203023E-09 -4.68523437E-10 1.16283229E-03
9.85816445E-04 -2.14864874E-03 1.35077922E-08 1.03115817E-08 1.23030984E-08
3.30933872E-03 -9.64276996E-10 -2.08183290E-09 1.93793031E-08 7.76708401E-10
-9.78781477E-03 5.46879030E-09 -1.40201396E-04 -1.64864721E-08 1.42648977E-09
2.43539246E-02 4.39233060E-02 6.47648890E-02 3.79025492E-02 5.85888716E-03
1.81389699E-08 -1.52827934E-02 -1.46059042E-07 -8.35285773E-09 -3.32420645E-04
5.47396526E-08 1.90030678E-03 -7.04881261E-04 -1.19542552E-03 6.16459719E-08
-5.47321827E-10 -1.02876284E-08 2.43167291E-02 4.38562224E-02 6.46659744E-02
3.88007578E-02 6.01554753E-03 -7.91090978E-08 7.61311582E-03 -1.32365965E-02
1.21934793E-08 4.33432997E-04 -6.97340658E-04 -7.31074827E-05 1.37411113E-03
-1.30100365E-03 -2.46278491E-03 -2.79534233E-08 -7.35226250E-09 2.43168241E-02
4.38563937E-02 6.46662269E-02 3.88003984E-02 6.01549406E-03 -4.81097887E-07
7.61377259E-03 1.32367270E-02 1.01381608E-07 4.33160503E-04 6.97171652E-04
-7.31033558E-05 1.37409384E-03 -1.30099048E-03 2.46265791E-03 6.51631445E-09
1.43483007E-08
MO 3 OCC NO = 2.00000000 ORB. ENERGY = -0.49902967
-1.59432070E-08 -2.97091222E-08 -5.00680880E-08 -7.47011763E-08 -9.04839766E-08
-7.52894102E-08 -2.79628784E-08 1.48449042E-10 1.99140480E-08 3.71971664E-08
6.33097645E-08 9.68252986E-08 1.25927045E-07 1.27466715E-07 8.39303683E-08
-5.73710378E-08 1.58011537E-07 6.51835189E-08 -4.66400547E-09 5.02474795E-04
2.85621660E-01 -4.20345996E-09 4.52858106E-04 2.57418054E-01 -3.05198451E-09
3.28804352E-04 1.86902200E-01 -1.54278574E-08 1.21759950E-04 6.94055784E-02
-1.98294847E-09 7.63999982E-06 4.37168539E-03 3.72246894E-05 -3.72654300E-05
4.07406210E-08 -4.24922273E-02 1.44652998E-09 -6.01075996E-09 5.39157309E-06
-5.40369882E-06 1.21257381E-08 -6.24002436E-03 1.04144375E-08 2.31852125E-08
8.05046429E-07 5.12867244E-04 -3.60959125E-10 4.94216813E-04 3.46719410E-09
1.11723816E-06 -2.38431672E-09 -3.53237744E-06 -2.03281855E-03 4.14137957E-09
7.42985746E-05 1.34000539E-04 1.97583717E-04 1.30458842E-04 3.50417768E-05
2.18918912E-08 -3.41511399E-05 7.63405955E-03 -9.61156640E-09 -5.23062472E-06
4.16640659E-03 1.96182718E-06 -2.74262559E-06 7.80798408E-07 -8.26011788E-03
3.01683990E-09 -1.80423663E-08 3.65077485E-02 6.58432278E-02 9.70858010E-02
6.39276393E-02 1.71810596E-02 1.28150088E-07 1.16422544E-02 -1.25171412E-02
-3.05383711E-08 3.04667523E-03 -1.10928545E-03 1.06207452E-03 -1.43727975E-03
3.75205226E-04 -3.91611949E-03 1.93585667E-08 -7.04830909E-09 -3.65818384E-02
-6.59768521E-02 -9.72828299E-02 -6.40582435E-02 -1.72162056E-02 -6.74676149E-07
-1.16380223E-02 -1.25578499E-02 1.49399303E-07 -3.03870890E-03 -1.12021100E-03
-1.04973989E-03 1.42561223E-03 -3.75872343E-04 -3.90748059E-03 2.03308348E-08
2.17365485E-08
MO 4 OCC NO = 2.00000000 ORB. ENERGY = -0.49901625
1.62107328E-05 3.02076392E-05 5.09082269E-05 7.59546567E-05 9.20022913E-05
7.65527612E-05 2.84320935E-05 -1.50940006E-07 -1.49081907E-05 -2.78467969E-05
-4.73953886E-05 -7.24860169E-05 -9.42723652E-05 -9.54250038E-05 -6.28325260E-05
4.29494985E-05 -3.23843084E-05 -6.54068586E-06 -5.23478644E-10 -2.85611529E-01
5.02493669E-04 -4.71787938E-10 -2.57408923E-01 4.52875116E-04 -3.42548637E-10
-1.86895571E-01 3.28816702E-04 -1.87760207E-09 -6.93109213E-02 1.22026738E-04
-3.44994056E-10 -4.35336737E-03 7.69025588E-06 -2.12079695E-02 2.12055288E-02
2.44067001E-06 -7.46569341E-05 9.59329559E-10 1.20973859E-09 -3.10525983E-03
3.11262624E-03 -7.36640741E-06 -1.09711332E-05 3.25519227E-09 2.66992026E-09
-4.99021842E-04 8.92034655E-07 -8.38824956E-10 9.05622861E-07 3.77680992E-10
-5.29046143E-04 2.13879388E-09 2.02611167E-03 -3.58172683E-06 0.00000000E+00
-4.21919849E-02 -7.60949822E-02 -1.12202007E-01 -7.40136781E-02 -1.98930286E-02
1.45102486E-08 1.92694041E-02 1.32952935E-05 -4.42336563E-09 2.93851158E-03
7.35327951E-06 -1.05220876E-03 1.47862590E-03 -4.26417141E-04 -1.43859422E-05
3.36490825E-10 -1.56210308E-09 2.11659341E-02 3.81736338E-02 5.62870007E-02
3.71047261E-02 9.98513878E-03 -2.75759641E-08 -8.80006896E-04 -1.16606657E-02
4.11431563E-09 -2.39646760E-03 -3.07347656E-03 -3.51050170E-03 3.30097184E-03
2.09529852E-04 2.47318669E-03 -1.73927783E-08 -1.38086847E-09 2.10373859E-02
3.79417918E-02 5.59451498E-02 3.68793468E-02 9.92460623E-03 -9.75970068E-08
-9.20767515E-04 1.16165623E-02 2.09353317E-08 -2.40732429E-03 3.06946848E-03
-3.51415750E-03 3.30593372E-03 2.08223782E-04 -2.48714299E-03 1.10193576E-09
2.28330126E-09
END DATA
THE SCF ENERGY = -26.513493167366 THE VIRIAL(-V/T)= 2.00023177
Okay, I can reproduce the crash. This weekend’s pretty busy but I’ll see if I can get to it.
Thanks!
Thank you for the reply!
Now waiting for a new AppImage, in the same time I will also try to make the program from Git sources together with the QTAIM plugin, if it is possible.
It won’t be any different building from source. The crash is reproducible on my Mac from source.
I’ll let you know when there’s a fix.
Okay, there are a clearly a bunch of bugs in the QTAIM extension.
Here’s a fix that at least prevents the crash - there should be a link to the AppImage posted as a comment in ~1-2 hours once it builds on GitHub:
OpenChemistry:master
← ghutchis:fix-qtaim-crash
opened 10:14PM - 17 Sep 22 UTC
Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
Developer Certific… ate of Origin
Version 1.1
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license document, but changing it is not allowed.
Developer's Certificate of Origin 1.1
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(a) The contribution was created in whole or in part by me and I
have the right to submit it under the open source license
indicated in the file; or
(b) The contribution is based upon previous work that, to the best
of my knowledge, is covered under an appropriate open source
license and I have the right under that license to submit that
work with modifications, whether created in whole or in part
by me, under the same open source license (unless I am
permitted to submit under a different license), as indicated
in the file; or
(c) The contribution was provided directly to me by some other
person who certified (a), (b) or (c) and I have not modified
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(d) I understand and agree that this project and the contribution
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There’s a bunch of other really weird bits - the “fix” just stops the commands from requesting the QTAIM rendering. (The request was causing the crash … the rendering is fine.)
But … if you click the QTAIM checkbox in the rendering list, it displays properly … it just doesn’t show the check. Gotta fix that one too.
In the meantime, at least QTAIM should work and not crash and I’ll work more when I have a bit more time in a few days.
Now that minimal QTAIM analysis in Avogadro2 is rendered successfully.
Thank you very much!
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Closed
September 23, 2022, 9:31pm
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