"ValueError: No pressure specified" when checking collision limits with surfaceReactor

[rwest]

Bug Description

At the end of running a job with surface chemistry, RMG crashed when doing the collision limit checks:

Performing final model checks...
Traceback (most recent call last):
  File "rmgpy/kinetics/arrhenius.pyx", line 739, in rmgpy.kinetics.arrhenius.PDepArrhenius.getRateCoefficient
ValueError: No pressure specified to pressure-dependent PDepArrhenius.getRateCoefficient().
Exception ValueError: ValueError('No pressure specified to pressure-dependent PDepArrhenius.getRateCoefficient().',) in 'rmgpy.reaction.Reaction.getRateCoefficient' ignored
Traceback (most recent call last):
  File "rmgpy/kinetics/arrhenius.pyx", line 739, in rmgpy.kinetics.arrhenius.PDepArrhenius.getRateCoefficient
ValueError: No pressure specified to pressure-dependent PDepArrhenius.getRateCoefficient().
Exception ValueError: ValueError('No pressure specified to pressure-dependent PDepArrhenius.getRateCoefficient().',) in 'rmgpy.reaction.Reaction.getRateCoefficient' ignored
Traceback (most recent call last):
  File "rmgpy/kinetics/arrhenius.pyx", line 739, in rmgpy.kinetics.arrhenius.PDepArrhenius.getRateCoefficient
ValueError: No pressure specified to pressure-dependent PDepArrhenius.getRateCoefficient().
Exception ValueError: ValueError('No pressure specified to pressure-dependent PDepArrhenius.getRateCoefficient().',) in 'rmgpy.reaction.Reaction.getRateCoefficient' ignored
Traceback (most recent call last):
  File "/Users/rwest/Code/Cat/RMG-Py/rmg.py", line 181, in <module>
    main()
  File "/Users/rwest/Code/Cat/RMG-Py/rmg.py", line 166, in main
    cProfile.runctx(command, global_vars, local_vars, stats_file)
  File "/Users/rwest/anaconda/envs/rmg230/lib/python2.7/cProfile.py", line 49, in runctx
    prof = prof.runctx(statement, globals, locals)
  File "/Users/rwest/anaconda/envs/rmg230/lib/python2.7/cProfile.py", line 140, in runctx
    exec cmd in globals, locals
  File "<string>", line 1, in <module>
  File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/rmg/main.py", line 934, in execute
    self.check_model()
  File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/rmg/main.py", line 1148, in check_model
    p_min=self.Pmin, p_max=self.Pmax)
  File "rmgpy/reaction.py", line 1233, in rmgpy.reaction.Reaction.check_collision_limit_violation
  File "rmgpy/reaction.py", line 1266, in rmgpy.reaction.Reaction.check_collision_limit_violation
  File "rmgpy/kinetics/arrhenius.pyx", line 729, in rmgpy.kinetics.arrhenius.PDepArrhenius.getRateCoefficient
  File "rmgpy/kinetics/arrhenius.pyx", line 739, in rmgpy.kinetics.arrhenius.PDepArrhenius.getRateCoefficient
ValueError: No pressure specified to pressure-dependent PDepArrhenius.getRateCoefficient().

This is mentioned in #1590 and cfgoldsmith#61 but here are more details and hopefully some clues on how to fix it.

How To Reproduce

Features of the input file that I think are relevant:

• No pressure dependence block
• surfaceReactors (which have an initialPressure of 1.0 bar)
• reactionLibraries = [('Surface/CPOX_Pt/Deutschmann2006', False),('BurkeH2O2inN2',False),('FFCM1(-)',False),('NOx2018',False)],
• seedMechanisms = [],
• generatedSpeciesConstraints( allowed=['reaction libraries'],)

Expected Behavior

It wouldn't crash

What I think is the problem

My guess is that although RMG was told to generate new reactions without pressure dependence module, a pressure dependent PDepArrhenius reaction is coming in via one of the gas phase reaction libraries (as it should), but because the reactor model is a surfaceReactor not a simpleReactor, it doesn't have an attribute P but instead has initialP:

cdef class SimpleReactor(ReactionSystem):
    cdef public ScalarQuantity P

cdef class SurfaceReactor(ReactionSystem):
        cdef public ScalarQuantity initialP

So that one or both of these lines don't know what pressures to use:

• "rmgpy/rmg/main.py", line 1148, in check_model
• "rmgpy/reaction.py", line 1233, in rmgpy.reaction.Reaction.check_collision_limit_violation

Installation Information

Describe your installation method and system information.

• Mac OS X
• built from source, in an anaconda environment, using the 2.4.0 tagged commits from github

The current git HEAD for RMG-Py is:
	caebd4895dfaee296b6562b28f89e6c350422cca
	Fri Jun 14 18:30:27 2019 -0400
The current git HEAD for RMG-database is:
	08b8214e8b4c869411f498cb50acb76b012520b4
	Fri Jun 14 18:15:05 2019 -0400

[github-actions]

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