Crash Analysis report could be better for heterogeous catalysis and electrochemistry

[rwest]

At very least the units are hard-coded for gas phase.

ReactionMechanismSimulator.jl/src/Debugging.jl

Line 180 in 74e04f2

kunitsf = "m^3/(mol*s)"

but also for electrochemistry we're getting a lot of NaN for the G values.

@Torrie01 can add details if/when helpful

[Torrie01]

In the report below we can see some reactions it reports HX G(T): -2.027404831368713 kcal/mol but for others it reports HX G(T): NaN kcal/mol. Why would it be different?

Crash Analysis Report
rt/rmedian > 10.0, rt=-2.9403578523282965e11, rt/rmedian=7.620225888455094e13 
Reaction:
Index: 2
CHO2X<=>CO2HX
kf: 36.97869548664073 s^-1
krev: 2.775283962290439e12 s^-1
Reactants: 
	CHO2X G(T): NaN kcal/mol
Products: 
	CO2HX G(T): NaN kcal/mol
rt/rmedian > 10.0, rt=-4.684741367966359, rt/rmedian=1214.096693183995 
Reaction:
Index: 3
vacantX+CHO2X<=>OX+CHOX
kf: 1.961996133737021e-23 m^3/(mol*s)
krev: 3.756147198450599e7 m^3/(mol*s)
Reactants: 
	vacantX G(T): NaN kcal/mol
	CHO2X G(T): NaN kcal/mol
Products: 
	OX G(T): NaN kcal/mol
	CHOX G(T): NaN kcal/mol
rt/rmedian > 10.0, rt=0.04305228217805624, rt/rmedian=11.157421364563506 
Reaction:
Index: 7
CO2HX+CO2HX<=>CO2X+CH2O2X
kf: 138074.3963351819 m^3/(mol*s)
krev: 8.929923470627135e-7 m^3/(mol*s)
Reactants: 
	CO2HX G(T): NaN kcal/mol
	CO2HX G(T): NaN kcal/mol
Products: 
	CO2X G(T): NaN kcal/mol
	CH2O2X G(T): NaN kcal/mol
rt/rmedian > 10.0, rt=0.8085920248435966, rt/rmedian=209.55455731459517 
Reaction:
Index: 9
CHOX+CO2HX<=>CO2X+CH2OX
kf: 6.48315548340354e6 m^3/(mol*s)
krev: 1.6644484231326716e-7 m^3/(mol*s)
Reactants: 
	CHOX G(T): NaN kcal/mol
	CO2HX G(T): NaN kcal/mol
Products: 
	CO2X G(T): NaN kcal/mol
	CH2OX G(T): NaN kcal/mol
rt/rmedian > 10.0, rt=77.52395367907877, rt/rmedian=20091.093277402593 
Reaction:
Index: 13
CHOX+CHO2X<=>OCX+CH2O2X
kf: 6.215740818063366e8 m^3/(mol*s)
krev: 0.00836656169311941 m^3/(mol*s)
Reactants: 
	CHOX G(T): NaN kcal/mol
	CHO2X G(T): NaN kcal/mol
Products: 
	OCX G(T): NaN kcal/mol
	CH2O2X G(T): NaN kcal/mol
rt/rmedian > 10.0, rt=2.4727371219966723, rt/rmedian=640.8340881863229 
Reaction:
Index: 14
CHOX+CH2O2X<=>CHO2X+CH2OX
kf: 3.965198453345883e7 m^3/(mol*s)
krev: 2.0972896292871977e-6 m^3/(mol*s)
Reactants: 
	CHOX G(T): NaN kcal/mol
	CH2O2X G(T): NaN kcal/mol
Products: 
	CHO2X G(T): NaN kcal/mol
	CH2OX G(T): NaN kcal/mol
rt/rmedian > 10.0, rt=-0.7776300048122708, rt/rmedian=201.5304460175723 
Reaction:
Index: 20
OCX+CH2OX<=>CHOX+CHOX
kf: 1.1097307079099376e-17 m^3/(mol*s)
krev: 1.558726797587704e7 m^3/(mol*s)
Reactants: 
	OCX G(T): NaN kcal/mol
	CH2OX G(T): NaN kcal/mol
Products: 
	CHOX G(T): NaN kcal/mol
	CHOX G(T): NaN kcal/mol
rt/rmedian > 10.0, rt=-1.008242207606359, rt/rmedian=261.2958611874861 
Reaction:
Index: 21
HOX+OCX<=>vacantX+CO2HX
kf: 3.9978442246680557e12 m^3/(mol*s)
krev: 3.2335668896097466e6 m^3/(mol*s)
Reactants: 
	HOX G(T): NaN kcal/mol
	OCX G(T): NaN kcal/mol
Products: 
	vacantX G(T): NaN kcal/mol
	CO2HX G(T): NaN kcal/mol
rt/rmedian > 10.0, rt=4.113331085088e10, rt/rmedian=1.0660101115772281e13 
Reaction:
Index: 26
OX+CHOX<=>HOX+OCX
kf: 3.298e17 m^3/(mol*s)
krev: 15984.75755456966 m^3/(mol*s)
Reactants: 
	OX G(T): NaN kcal/mol
	CHOX G(T): NaN kcal/mol
Products: 
	HOX G(T): NaN kcal/mol
	OCX G(T): NaN kcal/mol
rt/rmedian > 10.0, rt=-0.1479158611771051, rt/rmedian=38.33384680583625 
Reaction:
Index: 35
HX+CHO2X<=>vacantX+CH2O2X
kf: 2278.430033862942 m^3/(mol*s)
krev: 948771.6890684594 m^3/(mol*s)
Reactants: 
	HX G(T): NaN kcal/mol
	CHO2X G(T): NaN kcal/mol
Products: 
	vacantX G(T): NaN kcal/mol
	CH2O2X G(T): NaN kcal/mol
rt/rmedian > 10.0, rt=-2.825851717400307e7, rt/rmedian=7.323472004204486e9 
Reaction:
Index: 37
HX+OCX<=>vacantX+CHOX
kf: 7.323765889355536 m^3/(mol*s)
krev: 2.265720597540188e14 m^3/(mol*s)
Reactants: 
	HX G(T): NaN kcal/mol
	OCX G(T): NaN kcal/mol
Products: 
	vacantX G(T): NaN kcal/mol
	CHOX G(T): NaN kcal/mol
dydt/dydtmedian > 10.0, dydt=7.077638947643877e8, dydt/dydtmedian=987.2694911843953 
Species:
Index: 9
	O=CC=O G(T): -74.68778534007275 kcal/mol
dydt/dydtmedian > 10.0, dydt=1.3878553790076754e9, dydt/dydtmedian=1935.938360244506 
Species:
Index: 1
	vacantX G(T): -6.800155994219934e-9 kcal/mol
dydt/dydtmedian > 10.0, dydt=2.940355244309446e11, dydt/dydtmedian=410154.15556301136 
Species:
Index: 3
	CHO2X G(T): -123.18150530205108 kcal/mol
dydt/dydtmedian > 10.0, dydt=-2.940360501031901e11, dydt/dydtmedian=410154.8888303823 
Species:
Index: 4
	CO2HX G(T): -108.2536037038775 kcal/mol
dydt/dydtmedian > 10.0, dydt=4.116130418710072e10, dydt/dydtmedian=57416.46351543981 
Species:
Index: 5
	OCX G(T): -49.559056320441755 kcal/mol
dydt/dydtmedian > 10.0, dydt=-4.113384182035291e10, dydt/dydtmedian=57378.15588623409 
Species:
Index: 6
	OX G(T): -48.54633233340393 kcal/mol
dydt/dydtmedian > 10.0, dydt=-4.2577204027151436e10, dydt/dydtmedian=59391.52147614616 
Species:
Index: 8
	CHOX G(T): -33.06895790206161 kcal/mol
dydt/dydtmedian > 10.0, dydt=4.1133575721889595e10, dydt/dydtmedian=57377.78470186537 
Species:
Index: 10
	HOX G(T): -50.33225306409341 kcal/mol
dydt/dydtmedian > 10.0, dydt=2.8258594728508532e7, dydt/dydtmedian=39.41829845458292 
Species:
Index: 12
	HX G(T): -2.027404831368713 kcal/mol

[mjohnson541]

I believe the reason this is happening is that the thermochemical parameters (particularly T) are not being passed to the getdebugreaction calls in

ReactionMechanismSimulator.jl/src/Debugging.jl

Line 125 in 74e04f2

push!(rxns,getdebugreaction(sim.reactions[i];tol=tol,kf=kfs[i],krev=krevs[i],rt=rt,ratio=NaN,index=i))

, but are being passed to the getdebugspecies calls. It may also be useful to tweak to handle voltage as well.

The DebugSpecies objects in each DebugReaction and the DebugSpecies objects outside are apparently all distinct objects as constructed...