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Segmentation fault with MOPAC2016


#1

Dear Avogadro team!
I’ve just install Avogadro 1.2 from Ubuntu 18 repository and onfortunately received “Segmentation Fault” while opening MOPAC2016 out-files (even test dataset shipped with MOPAC). Could You please kindly look for a solution (if it’s exists).

Environment Information

Avogadro version: 1.2.0
Operating system and version: Kubuntu 18.04 (bionic)

Expected Behavior

Out files from MOPAC2016 should be opened

Actual Behavior

Segmentation Fault

Steps to Reproduce

Every time while opening MOPAC 2016 out files


#2

For one, it would greatly help to have one of the files (there are many versions of MOPAC 2016).

But my guess is that it’s an issue with the version of Open Babel used by the package. There were some changes to the MOPAC output format that did crash older versions of OB.

What version of Open Babel was installed with the Avogadro package?


#3

Dear Geoff,
Thank You for Your care!
My MOPAC2016 version is the academic, single node, binary
My openbabel version is 2.3.2 (installed from repository)
I’ve just prepared very simple water geometry optimization file, unfortunately segmentation failed again. Input file is:

AUX LARGE CHARGE=0 SINGLET PM6
water

O 0.000000 1 0.000000 1 0.000000 1 0 0 0
H 0.970000 1 0.000000 1 0.000000 1 1 0 0
H 0.970000 1 109.471000 1 0.000000 1 1 2 0

Output file is here

https://www.dropbox.com/s/egmvzhq5zue884g/water.out?dl=0


#4

Open Babel 2.3.2 is ancient - from 2012. Version 2.4.1 is from 2016:


#5

Just installed openbabel 2.4.1 from sources:

Open Babel 2.4.1 – Jul 10 2018 – 17:22:47
Usage:

And re-installed avogadro. Not working again :frowning:


#6

I will investigate, but it does work for me with current Open Babel. That doesn’t work with Avogadro 1.2, so I’ll see if there’s an appropriate patch.