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ReactionMechanismGenerator / RMG-Java

The Java version of RMG: Reaction Mechanism Generator
http://rmg.sourceforge.net/
MIT License
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NullPointerException at jing.rxn.Reaction.getDirection(Reaction.java:924) #246

Open rajeshdparmar opened 12 years ago

rajeshdparmar commented 12 years ago

This is probably associated with some previous issues. Please find the error message as well as location of the folder as below.

Folder location:

rajesh@pharos:~/Rajesh/New_jobs_after_Jan-30-2012/Decane_chemistry/with-PM3-trial$

Error Message:

Writing Restart Core Species
Writing Restart Core Reactions
Writing Restart Edge Species
Writing Restart Edge Reactions
ERROR: java.lang.NullPointerException
    at jing.rxn.Reaction.getDirection(Reaction.java:924)
    at jing.rxnSys.ReactionModelGenerator.writePDepNetworks(ReactionModelGenerator.java:2838)
    at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1588)
    at RMG.main(RMG.java:96)
faribas commented 12 years ago

We just got this too:

Writing Restart Core Species
Writing Restart Core Reactions
Writing Restart Edge Species
Writing Restart Edge Reactions
ERROR: java.lang.NullPointerException
    at jing.rxn.Reaction.getDirection(Reaction.java:924)
    at jing.rxnSys.ReactionModelGenerator.writePDepNetworks(ReactionModelGenerator.java:2838)
    at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1588)
    at RMG.main(RMG.java:96)

...after running for about 20 hours.

rwest commented 12 years ago

See also issues #207 and #216 (although they're not much more informative than this one - they just reveal that it's been a problem for a while).

It's strange that it doesn't show up very quickly or frequently though.

rwest commented 12 years ago

getDirection is just:

  public int getDirection() {
      return getStructure().getDirection();  // <---- line 924
  }

so getStructure must be returning null. That prompted me to look at issue #185, which was about PDep Path reactions with no structure. In fact, it looks like while debugging that issue we turned it into this one (see my comment on that issue) so they are indeed the same.

@gmagoon any memory of that issue? Did we give up? It seems to still exist...

I suggest discussion continues on issue #185, as it has more context. The issue is to do with pruning...