pyjac2foam.sh issues

[pkpavalavanni]

Hi,
I am trying to convert a detailed CRECK mechanism (492 species and 17790 reaction mechanism - http://creckmodeling.chem.polimi.it/menu-kinetics/menu-kinetics-detailed-mechanisms/107-category-kinetic-mechanisms/403-mechanisms-1911-tot-ht-lt).
While running the pyjac2foam.sh, it reports a formatting error, however, while looking at the reaction mechanism, it is not the case.
I am attaching the error and outfile along with the jacobian file where it is being reported as an error.

DLBFoam.zip

[kahilah]

Hi,

It seems that pyJac has generated a faulty line of c-code. Opening jacob_18.c in any code editor shows that you're missing parenthesis on line 15033. Either this error is introduced by pyjac python module or the file is edited afterwards. If the former is true, please file an issue to https://github.com/SLACKHA/pyJac

As an immediate action, you can try to fix the parenthesis manually by placing closing "))" at the of the line accordingly: ...dBdT[61])))))) * rho_inv; Please, check that parenthesis make sense from kinetics perspective.

Furthermore, as you're working with rather large chemical mechanisms, I'd like to encourage you to get familiar with the original publications of pyjac https://niemeyer-research-group.github.io/pyJac-paper/ as it is reported that you may get some challenges with compilers when problem size grows considerably.

[mahgadalla]

I think this is a pyJac bug, recall to have came across similar problem myself with an exotic kinetic mechanism. Had to fix it manually by appending parenthesis as noted above!