Richard West

icon indicating a website link http://www.northeastern.edu/comocheng/ icon indicating an email [email protected]

icon company Northeastern University icon location Boston, MA icon location Associate Professor of Chemical Engineering at Northeastern University, head of @CoMoChEng research group, and a developer of @ReactionMechanismGenerator.

Results 233 comments of Richard West

dasslAUTO runs differently on monch versus Windows.

Jeff, did you get bored of this? I have just found that the RMG jobs when fortran codes are compiled on gfortran vs g95 diverge (see https://gist.github.com/786699 ) and I...

Apparent InChIKey collision.

You're right that wiping the c-InChI-1 and the SYMMETRY programs does kill the job in a related way (I did this myself) but I think you then end up with...

Apparent InChIKey collision.

I think he was using my script which copies everything to a temporary folder ($TMPDIR - set by the grid engine) on the scratch drive of the compute node and...

Apparent InChIKey collision.

$TMPDIR is unique to the job. For my job number 79895 currently running in the long queue, it is `/tmp/79895.1.long1`

RMG does not handle multiple kinetics from different rxn families properly

Each reaction that is an instance of TemplateReaction should have a reactionTemplate attribute that specifies which ReactionTemplate it came from. The equality check .equals() could insist that these, as well...

Reversibility of reactions

There was talk in the meeting today about trying to make this more robust, either automatic or user-configurable, rather than having exceptional reaction families hard-coded.

number of plog rates written to pdepnetworks set to fame default

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

number of plog rates written to pdepnetworks set to fame default

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....

Populate Reactions finds different rate from RMG job when there are multiple rate rules

It would be good if they both used the same bit of code to do this, so they always did the same thing. IIRC the RMG-Java project has a lot...

ERROR: java.lang.NullPointerException (path reaction has no structure)

It looks to me that there must have been no `structure` in the reaction that was being checked by `reactionPrunableQ`. This occured when iterating over `PathReactions` from a `PDepNetwork`, when...