number of plog rates written to pdepnetworks set to fame default

[nickvandewiele]

For now, the phrase
"Could be different for seed and library reactions,
but default for FAME-generated rates is probably "

that was written to pdepnetworks.txt in the restart folder is replaced
by the FAME default number of PLOGS.

WARNING: this is a temporary solution that (almost) certainly
works in absence of seed mechanisms and PKLs, PRLs but certainly
fails in presence of the latter. Check Github issue threads for more
information.

Tested successfully on the 1,3-Hexadiene example.

[rwest]

Does this break the use of PLOG in Seed Mechanisms? eg. try Glarborg/C2 as a seed.
See issue #245

[nickvandewiele]

One of the species in Glarborg is forbidden, for a reason unknown to me. I will try another seed mech.

CRITICAL: Input file error: Error in reading Seed Mechanism: GB
RMG cannot read entire Seed Mechanism: /home/nickv/RMG-Java/databases/RMG_database/kinetics_libraries/Glarborg/C2/
RMG cannot read the "species.txt" file in the Seed Mechanism: GB
The molecular structure
1  C 2T {2,D}
2  C 0 {1,D} {3,D}
3  O 0 {2,D}
 is forbidden by Carbene_D, and not allowed.

[rwest]

The error message (and documentation) have just been improved (as of this morning, see issue #249): you need to add a primary thermo library that contains the relevant species, eg. DFT_QCI_thermo

[nickvandewiele]

running the 13HXD example with read restart (i.e. run the example without seed mech, then rerun it with seed mech and increase error tolerance), P-Dep activated, and Glarborg/C2 as a seed mech seems to run fine.

That is after 8bff713.