Animation error

General Discussion Support
1

Animation gives error.

I believe this to be a bug with Avogadro

Environment Information

Avogadro version: 1.2.0
Operating system and version: MacOSx Catalina 10.15.5

Expected Behavior

Run animation

Actual Behavior

Gives error on number of atoms

Steps to Reproduce

This reduced file works

4
Coordinates from ORCA-job neb_im0
O -0.71757527640845 3.27255670342635 -0.21341428601752
H 0.09748542544738 2.73904818516935 -0.28600586316577
H -0.71623825806287 3.53201899242492 0.71824209379912
C -0.86071513205204 0.04811159261163 -0.07123897741138
4
Coordinates from ORCA-job neb_im1
O -0.03706251988087 2.92416166292318 0.30394640595799
H -0.09230814665986 2.78828670737963 -0.65771646009116
H 0.12162341614408 2.04743088878286 0.71604459776907
C -1.16373733969043 0.13174126043788 -0.13212530887677

This original file gives the error
14
Coordinates from ORCA-job neb_im0
O -0.71757527640845 3.27255670342635 -0.21341428601752
H 0.09748542544738 2.73904818516935 -0.28600586316577
H -0.71623825806287 3.53201899242492 0.71824209379912
C -0.86071513205204 0.04811159261163 -0.07123897741138
C 0.64645812348370 0.16179126897473 -0.05132329191457
H -1.23046583749470 -0.49437144060594 0.81320973256122
H -1.19925205538525 -0.50827293596051 -0.96002881274633
H -1.27434576664529 1.06436846515291 -0.09367428115930
O 1.23775890800209 1.21656573678054 -0.09021466192236
O 1.37487982611498 -0.97060390422094 0.01279763618429
C 0.76521315455830 -2.25258012460761 0.04781520234372
H 1.58543494763672 -2.98089656828969 0.09035324817016
H 0.16309685890962 -2.44641922263442 -0.85504328636026
H 0.12826508189582 -2.38131674822135 0.93852554763897
14
Coordinates from ORCA-job neb_im1
O -0.03706251988087 2.92416166292318 0.30394640595799
H -0.09230814665986 2.78828670737963 -0.65771646009116
H 0.12162341614408 2.04743088878286 0.71604459776907
C -1.16373733969043 0.13174126043788 -0.13212530887677
C 0.36129069505892 0.25968069411509 -0.12402381003792
H -1.58985471052441 -0.56501575626225 0.60175210385469
H -1.36296368053532 -0.22729661813282 -1.15099464826518
H -1.65623640512614 1.11182380485718 -0.03564062841375
O 0.94759039210569 1.00628886539064 -0.84028271309391
O 1.06278711389633 -0.60211726038840 0.65478892394815
C 0.87681574469013 -1.95524544229854 0.25102542194909
H 1.86704392299568 -2.42556451940834 0.22097128610697
H 0.44334357587397 -2.00910896314276 -0.76322658686505
H 0.22166794165221 -2.48506532425334 0.95548141605779

The only difference is the number of atoms was reduced from 14 to 4.

Please upload files if appropriate here (or via file-sharing service like Dropbox or Pastebin)

2

Steps to reproduce.
Double click on the file to open in Avagadro.
Go to Extensions/Annimation
Select Load file, select the same file

Load error is:
Trajectory file xxx disagrees on the number of atom s in the present molecule.

3

Repeat. Changed file (below) to 9 molecules
Works fine !

9
Coordinates from ORCA-job neb_im0
O -0.71757527640845 3.27255670342635 -0.21341428601752
H 0.09748542544738 2.73904818516935 -0.28600586316577
H -0.71623825806287 3.53201899242492 0.71824209379912
C -0.86071513205204 0.04811159261163 -0.07123897741138
C 0.64645812348370 0.16179126897473 -0.05132329191457
H -1.23046583749470 -0.49437144060594 0.81320973256122
H -1.19925205538525 -0.50827293596051 -0.96002881274633
H -1.27434576664529 1.06436846515291 -0.09367428115930
O 1.23775890800209 1.21656573678054 -0.09021466192236
9
Coordinates from ORCA-job neb_im1
O -0.03706251988087 2.92416166292318 0.30394640595799
H -0.09230814665986 2.78828670737963 -0.65771646009116
H 0.12162341614408 2.04743088878286 0.71604459776907
C -1.16373733969043 0.13174126043788 -0.13212530887677
C 0.36129069505892 0.25968069411509 -0.12402381003792
H -1.58985471052441 -0.56501575626225 0.60175210385469
H -1.36296368053532 -0.22729661813282 -1.15099464826518
H -1.65623640512614 1.11182380485718 -0.03564062841375
O 0.94759039210569 1.00628886539064 -0.84028271309391

4

Tried 10, no error, but does not run!

10
Coordinates from ORCA-job neb_im0
O -0.71757527640845 3.27255670342635 -0.21341428601752
H 0.09748542544738 2.73904818516935 -0.28600586316577
H -0.71623825806287 3.53201899242492 0.71824209379912
C -0.86071513205204 0.04811159261163 -0.07123897741138
C 0.64645812348370 0.16179126897473 -0.05132329191457
H -1.23046583749470 -0.49437144060594 0.81320973256122
H -1.19925205538525 -0.50827293596051 -0.96002881274633
H -1.27434576664529 1.06436846515291 -0.09367428115930
O 1.23775890800209 1.21656573678054 -0.09021466192236
O 1.37487982611498 -0.97060390422094 0.01279763618429
10
Coordinates from ORCA-job neb_im1
O -0.03706251988087 2.92416166292318 0.30394640595799
H -0.09230814665986 2.78828670737963 -0.65771646009116
H 0.12162341614408 2.04743088878286 0.71604459776907
C -1.16373733969043 0.13174126043788 -0.13212530887677
C 0.36129069505892 0.25968069411509 -0.12402381003792
H -1.58985471052441 -0.56501575626225 0.60175210385469
H -1.36296368053532 -0.22729661813282 -1.15099464826518
H -1.65623640512614 1.11182380485718 -0.03564062841375
O 0.94759039210569 1.00628886539064 -0.84028271309391
O 1.06278711389633 -0.60211726038840 0.65478892394815

5

Repeated from scratch.

Started with the above 14 element file. Fail
Tried 13. Fail
Tried 12. Fail
Tried 11. Fail
Tried 10. Fail
Tried 9. File works

Suggested solution: Check the code that reads the size of the molecule !

6

Note: This is the example molecular reaction from the FAccTS tutorial website.

" Finding transition states with NEB-TS

Suppose you wanted to predict the transition state (TS) for the hydrolysis of methyl-acetate into acetic acid and methanol:"

https://www.orcasoftware.de/tutorials/react/nebts.html