Missing guest molecules in sH structure

[eszter137]

Hi,

it seems the sH clathrate structure doesn't include the cages information in genice/lattices/sH.py so it won't have guest molecules in the generated structure.
(This was my command line:
genice --rep 2 2 2 --seed 0 --format=exyz --water tip3p -g 12=ch4 sH)

I was wondering if the information for the cages could be added.

Many thanks,
Eszter

[vitroid]

Thank you very much for your report.

sH.py has been updated to include cage information in the develop branch, but it was not reflected in the master. The new sH.py is now included in the latest GenIce. Update it with the pip command.

[eszter137]

Thank you very much!
Sorry, it is strange but it seems there might have been a problem with the commit: the page https://github.com/vitroid/GenIce/tree/master/genice/lattices shows that it is the DOH.py that changed 4 hours ago with the commit and the latest change for sH.py was 3 years ago.

[vitroid]

It is ok. sH.py is actually a link file (aka alias) to DOH.py. The name "DOH" comes from the Zeolite database. The structures of clathrate hydrate type H and zeolite DOH are topologically identical.

[vitroid]

Here are data for DOH: https://asia.iza-structure.org/IZA-SC/framework.php?STC=DOH

[eszter137]

Apologies, it was me messing up - it seems I had 2 versions of genice (because of having one pip in the conda environment and one outside) and it seems I updated the one that was not the default for the genice command. Now I uninstalled the other one and it works fine.
Thank you very much again!