Logging the incorrect reactor conditions for range (surface) reactors.

[rwest]

Bug Description

Running a job with a temperature range on a surface reactor, i.e.

surfaceReactor(
    temperature=[(400,'K'),(2400,'K')],
    initialPressure=(1.0, 'bar'),
    nSims = 6,
    initialGasMoleFractions={
        'CH3OH': 0.16,
        (some rows deleted)
        'H2O': 0.04,
    },
    initialSurfaceCoverages={
        "X": 1.0,
    },
    surfaceVolumeRatio=(1.e5, 'm^-1'),
    terminationConversion = { "CH3OH": 0.95,},
    terminationTime=(10., 's'),
    terminationRateRatio=0.01,
)

near the beginning of the log file it reports

Warning: Initial gas mole fractions do not sum to one; renormalizing.


Surface reaction system 1
Gas phase mole fractions:
  H2O                  0.042553
  (some rows deleted)
  CH3OH                0.17021
Total gas phase:          1 moles
Pressure:                 1e+05 Pa
Temperature:              2.17222323179e-314 K
Reactor volume:           1.81e-318 m3
Surface/volume ratio:     1e+05 m2/m3
Surface site density:     2.9e-05 mol/m2
Surface sites in reactor: 5.24e-318 moles
Initial surface coverages (and amounts):
  X                  1 = 5.2376e-318 moles

The Temperature and Reactor volume lines are clearly incorrect and misleading.
It would be better to print something helpful here.

Hopefully, the reactors are in fact doing the correct thing, but this should probably also be checked.

How To Reproduce

Run a job with catalytic chemistry and a surface reactor using a range for Temperature (and perhaps the other range reactors too).
I've not checked behaviour for Simple reactors, but the bug may be there also.

Expected Behavior

The log file would tell you what it's doing and not mislead you with worrying numbers like T=2.17222323179e-314 K.

Installation Information

Describe your installation method and system information.

• OS: Mac OS Mojave 10.14.5
• Installation method: anaconda, from source
• RMG version information:
  • RMG-database: 2.4.0-14-ge461edb9 commit e461edb]
  • RMG-Py: commit cc2716c (HEAD -> catfix, official/catfix) which is pr Fix a few bugs and add tests: KineticsModel and uncertainty handling. #1705

Additional Context

It might be nice, when running range reactors, if each Simulation told you what conditions it was starting at before it starts running.

[rwest]

I was just about to open a new issue for this, and came across this one, so will paste here as a comment instead.

This is the section of my current input file:

surfaceReactor(
    temperature=[(400,'K'),(2000,'K')],
    initialPressure=(1.0, 'bar'),
    nSims = 6,
    initialGasMoleFractions={
        'gas1': 0.14,
        'gas2': 0.3,
        'gas3': 0.3,
        'gas4': 0.16,
        'gas5': 0.04,
    },
    initialSurfaceCoverages={
        "X": 1.0,
    },
    surfaceVolumeRatio=(1.e5, 'm^-1'),
    terminationConversion = { "gas1": 0.95,},
    terminationTime=(10., 's'),
    terminationRateRatio=0.01,
)

Near the start of the RMG log, is this:

Surface reaction system 1
Gas phase mole fractions:
  NH2NHOOH             0.14894
  NH2OH                0.31915
  HNO3                 0.31915
  CH3OH                0.17021
  H2O                  0.042553
Total gas phase:          1 moles
Pressure:                 1e+05 Pa
Temperature:              0.0 K
Reactor volume:           0 m3
Surface/volume ratio:     1e+05 m2/m3
Surface site density:     2.9e-05 mol/m2
Surface sites in reactor: 0 moles
Initial surface coverages (and amounts):
  X                  1 = 0 moles

It may just be a problem with the logging, and the simulations are all OK, but the calculation of surface site ratio seems to be starting with 1 mole of gas, then using a temperature of 0 K which leads to a volume of 0 m3 and hence a surface area of 0 m2 and a surface site balance of 0 moles.

Hopefully it's only the calculations that end up in the log file that needs fixing, but it's still a bug. We should also check the actual reactors are doing The Right Thing.

• RMG version information: 3.0 current master. 957ee80

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