ReactionMechanismGenerator / RMG-Py

Python version of the amazing Reaction Mechanism Generator (RMG).
http://reactionmechanismgenerator.github.io/RMG-Py/
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Model Resurrection has failed #2697

Open NellyMitnik opened 3 months ago

NellyMitnik commented 3 months ago

Bug Description

Hi, I'm trying to run a sensitivity analysis (SA) in RMG for 9 different conditions (range of T and P). I've noticed that when reaching 1 bar specifically (independently of the temperature value) I get an error. Meaning, that the SA rus well for pressures under 1 bar. Once it reaches 1 bar, it fails. I get the following traceback:

input.py:1353 options WARNING Generate Output HTML option was turned on. Note that this will slow down model generation.
input.py:1360 options WARNING Edge species saving was turned on. This will slow down model generation for large simulations.
input.py:1582 read_input_file INFO 
loader.py:86 load_rmg_py_job INFO Thermo file has default temperature range 300.0 to 1000.0 and 1000.0 to 5000.0
rmg_constantTP.py:218 simulate INFO At time 3.0806e+05 s, reached target termination RateRatio: 0.009860084728969775
rmg_constantTP.py:218 simulate INFO At time 6.3024e+04 s, reached target termination RateRatio: 0.009690732673983354
rmg_constantTP.py:218 simulate ERROR Trying to step from time 0.0 to 1e-12 resulted in a solver (DASPK) error: nans in moles
rmg_constantTP.py:218 simulate INFO Resurrecting Model...
rmg_constantTP.py:218 simulate ERROR Model Resurrection has failed
rmg_constantTP.py:218 simulate ERROR Core species names: ['Ar', 'Ne', 'furfuryl(1)', 'acetylene(2)', 'ethylene(3)', 'propyne(4)', '1,3-butadiene(5)', 'furan(6)', 'C5H6(7)', 'C4H2(8)', 'ketene(9)', 'C5H4O-CPDone(10)', 'benzene(11)', '2MF(12)', 'methanol(13)', 'C3H4-A(14)', 'methane(15)', 'FORMALDEHYDE(16)', 'C4H4(17)', 'CO(18)', 'furfural(19)', 'H2(20)', 'H2O(21)', 'CO2(22)', 'C3H4O(23)', 'C5H6O2(24)', 'C5H6O2(25)', 'OH(26)', 'C5H5O(27)', 'C5H5O(28)', 'C5H5O(29)', 'C5H6O2(30)', 'C5H5O(31)', 'C#C[CH]C(32)', 'C5H5O(33)', 'n-C4H5(34)', 'C4H5(35)', 'H(36)', 'vinyl(37)', '[CH2]C#CC(38)', 'C5H5O(39)', 'INT3(40)', 'P29(41)', 'C5H6O2(42)', 'C5H6O2(43)', 'P2(44)', 'P10(45)', 'C5H5O2(46)', 'INT13(47)', 'C4H5O(48)', 'C5H5O2(49)', 'C4H5O(50)', 'C4H5O(51)', 'P14(52)', '[CH]1CC1(53)', 'C5H6O2(54)', 'C4H7O2(55)', 'P47(56)', 'CH2OH(57)', 'P11(58)', 'C4H5(59)', 'C5H6O2(60)', 'C#C[C]C(61)', 'C5H7O3(62)', 'C#CC[CH2](63)', 'C4H5(64)', 'cch2(65)', 'C4H4(66)', 'hcccch2(67)', 'C3H6O(68)', 'P19(69)', 'C5H6O(70)', 'C5H6O(71)', 'HCCOH(72)', 'C5H6O(73)', 'C5H5O2(74)', 'C5H5O2(75)', 'C4H5O(76)', 'C4H6(77)', 'C4H5O(78)', 'C2H2O(79)', 'R1_44(80)', 'C3H2O(81)', 'CH3O(82)', 'C8H11O2(83)', 'C8H11O2(84)', 'C5H6O2(85)', 'C6H10(86)', 'CH2CHO(87)', 'C8H11O2(88)', 'C8H11O2(89)', 'C8H11O2(90)', 'P1(91)', 'C5H5O2(92)', 'C5H5O2(93)', 'C3H6(94)', 'C4H6O(95)', 'HCCO(96)', 'C2H2O2(97)', 'C2H2O2(98)', 'CH3CO(99)', 'C4H2(100)', 'CHCHO(101)', 'C2H2O(102)', 'CH2(172)', 'CH2(S)(176)', 'C5H6O2(540)', 'C5H6O2(784)', 'C5H6O2(791)', 'C4H6(984)', 'C5H6O2(2029)', 'C4H6(3560)', 'C5H6O2(3760)', 'C5H6O2(3763)', 'C4H3(3848)', '[C]1CCC1(8907)', 'C5H6O2(11630)', 'C5H6O2(11633)', 'C5H6O2(15542)', 'C5H6O2(15545)', 'C5H6O2(15675)', 'C5H6O2(15680)', 'C5H6O2(17435)', 'C5H6O2(17606)', 'C5H6O2(17869)', 'C5H6O2(17993)', 'C4H3(20046)']
rmg_constantTP.py:218 simulate ERROR Core species moles: array([nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
       nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
       nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
       nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
       nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
       nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
       nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
       nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
       nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
       nan, nan, nan, nan, nan, nan, nan, nan, nan, nan])
rmg_constantTP.py:218 simulate ERROR Volume: nan
rmg_constantTP.py:218 simulate ERROR Core species net rates: array([nan,  0., nan, nan, nan, nan, nan, nan,  0., nan, nan,  0., nan,
       nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
       nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
       nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
       nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
       nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
       nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
       nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
       nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
       nan, nan, nan, nan, nan, nan, nan, nan, nan, nan])
rmg_constantTP.py:218 simulate ERROR Edge species net rates: array([], dtype=float64)
rmg_constantTP.py:218 simulate ERROR Network leak rates: array([], dtype=float64)
Traceback (most recent call last):
  File "rmgpy/solver/base.pyx", line 735, in rmgpy.solver.base.ReactionSystem.simulate
pydas.daspk.DASPKError: nans in moles

Also another error:

File "rmgpy/solver/base.pyx", line 572, in rmgpy.solver.base.ReactionSystem.simulate
  File "rmgpy/solver/base.pyx", line 782, in rmgpy.solver.base.ReactionSystem.simulate
ValueError: invalid_objects could not be filled during resurrection process

Expected Behavior

SA should not crash when reaching the condition of (T, P=1 bar)

How To Reproduce

RMG and RMG-db are up to date. I use self-imported libraries from the RMG-db branch furan_derivatives.

Installation Information

OS (include version if known): (Linux) Installation method: (e.g. installation from source, with anaconda)

Appreciate your help in solving this bug!

input.txt chem_annotated.txt species_dictionary.txt tran.txt