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Seed Mechanisms revisited #153

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Seed Mechanisms revisited #153

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8c7ba80
Don't merge restart with seed mechanisms.
rwest Mar 2, 2011
e1a76e3
Remove 'IF (should generate reactions from seed mechanism)' block.
rwest Mar 2, 2011
043f87a
Don't recalculate all initial library reactions redundantly.
rwest Mar 2, 2011
0c2ff34
Fix indenting.
rwest Mar 2, 2011
b6ab684
Add the seed mechanisms to the edge not the core.
rwest Mar 2, 2011
6700e0d
GenerateReactions field removed from Seed Mechanisms.
rwest Mar 2, 2011
1882a5e
Tidying indents, whitespace, comments.
rwest Mar 2, 2011
23e23ed
Remove redundant code in addUnreactedSpeciesSet()
rwest Mar 2, 2011
acabd18
Prevent seed mechanism species from being pruned.
rwest Mar 2, 2011
eba55cf
Store seed mechanism in CoreEdgeReactionModel instance.
rwest Mar 2, 2011
28e1d9c
Chemkin species lists now use CoreAndSeedSpecies not CoreSpecies.
rwest Mar 2, 2011
e4bcf13
Chemkin mechanism first reports seed, then pdep, then nonpdep.
rwest Mar 2, 2011
5fa0ffa
Added/tweaked Logger output.
rwest Mar 2, 2011
a963df3
Revert "BUG FIX: P-dep rxns in Seed Mechanisms listed in reactions.tx…
rwest Mar 2, 2011
5f5ada9
If pdep network reaction is in a seed mechanism, exclude it from the …
rwest Mar 2, 2011
bfc03a1
No longer store the PDep paths in the Species object.
rwest Mar 3, 2011
2e45880
Whitespace, indenting, comments
rwest Mar 3, 2011
0f824ba
Bugfix: Don't accidentally add Seed species to Core Species set.
rwest Mar 3, 2011
46f0d22
Debug assistance in JDAS when excluding reactions from the ODE set.
rwest Mar 3, 2011
2781618
Report size of chemkin file when writing it.
rwest Mar 3, 2011
4b4384a
Write the chemkin files less often.
rwest Mar 3, 2011
773b29b
Seed Mechanisms reactions now added to core or edge properly.
rwest Mar 3, 2011
a58e000
Merge branch 'master' into seedmech
rwest Mar 10, 2011
226aeaf
Check is a Seed Mechanism exists before grabbing species/reactions
mrharper Mar 12, 2011
92cef7e
Checking against "pdep" reactions in ReactionLibrary reactions.txt file
mrharper Mar 12, 2011
85e6ecc
Fixing indentations in GUI.java
mrharper Mar 12, 2011
1ddea81
Fixing indentations in GUI.java
mrharper Mar 12, 2011
c57622a
Updating RMG GUI re: GenerateReactions field for SeedMechanism
mrharper Mar 12, 2011
e806852
Merge branch 'seedmech' of github.com:GreenGroup/RMG-Java into seedmech
rwest Mar 12, 2011
4805f6d
Some tidying up in ReactionLibrary.java
rwest Mar 15, 2011
d8685d4
Automatically change indentation in SeedMechanism.java
rwest Mar 15, 2011
cc61d0a
Fix PDepReaction.setHighPKinetics(Kinetics kin)
rwest Mar 16, 2011
4d9329c
Reduce code duplication in SeedMechanism creation of third body react…
rwest Mar 16, 2011
c1af224
Add some comments to SeedMechanism reading
rwest Mar 16, 2011
49a1a51
Read in Chebyshev and PLog reactions from Seed Mechanisms and Reactio…
rwest Mar 16, 2011
36833f6
Added a Logger.logStackTrace(e) call in some exception handling.
rwest Mar 16, 2011
480a50a
Move one of Glarborg/C1's sets of reactions into PLOG format in pdepr…
rwest Mar 16, 2011
e422ef4
Shuffling reactions in Glarborg C3 in order to get ready for PLOGing …
rwest Mar 16, 2011
bb1a9c5
Glarborg PLOG work: Adding 0 rates for missing duplicates.
rwest Mar 16, 2011
2c2db2f
Glarborg PLOG: adding the pressures.
rwest Mar 16, 2011
bdc4b0f
Glarborg PLOG: reformat the reactions into PLOG format
rwest Mar 16, 2011
09473a9
Glarborg PLOG: put the highest available P value as high-P limit.
rwest Mar 16, 2011
e0a0b1b
Give well-skipping reaction a zero high-p limit.
rwest Mar 16, 2011
18707e2
Converted some more duplicates to PLOGs
rwest Mar 16, 2011
bb0b4d4
Fix typo in one of the reactions.
rwest Mar 16, 2011
128946e
Converting more duplicates to PLOGs
rwest Mar 16, 2011
005ae97
Another conversion - with some guesswork.
rwest Mar 16, 2011
a91ec31
One more conversion to PLOG, and some annotations.
rwest Mar 16, 2011
a872f35
Three more conversions to PLOG
rwest Mar 16, 2011
b2346e8
Convert several more Glarborg expressions into PLOG
rwest Mar 16, 2011
ce81259
Last (?) conversion to PLOG in Glarborg/C3/reactions.full
rwest Mar 16, 2011
bfcd800
Moving comments to make more RMG-friendly
rwest Mar 16, 2011
675d779
Two more conversions to PLOG
rwest Mar 16, 2011
cbecd8a
A couple of corrections to the new PLOG rates
rwest Mar 16, 2011
2a6a1a0
Moved 3 reactions into pdepreactions in Glarborg/C1
connie Mar 18, 2011
917a595
Plog reactions removed from reactions.txt file to pdepreactions.txt f…
connie Mar 24, 2011
467b285
Correcting CH3+HO2=CH3O+OH kinetics in Glarborg libraries
mrharper Mar 14, 2011
615c465
Remove duplicated commented reactions from reactions.txt files.
rwest Mar 25, 2011
3d17192
Move comments from plog lines.
rwest Mar 25, 2011
1df0ee8
Uncommenting reactions that shouldn't have been commented.
rwest Mar 25, 2011
6e9d4ea
Remove _light mechanisms from Glarborg folder.
rwest Mar 25, 2011
f777cb4
Merge branch 'glarborgplog' into seedmech
rwest Mar 28, 2011
a87e417
Merge remote branch 'official/master' into seedmech.
rwest Mar 28, 2011
ff08383
Merge branch 'master' into seedmech, again.
rwest Mar 28, 2011
3b51f30
Set mode of PDepArrhenius type PDepRateConstants
rwest Mar 28, 2011
5082479
Break Restart! Number of PLOG rates could be different for each react…
rwest Mar 28, 2011
75d9dcd
PLOG pressures could be different for each instance of PDepArrheniusK…
rwest Mar 28, 2011
dd7c3f3
Remove redundant 'pkl' parameter from SeedMechanism.readReactions and…
rwest Mar 28, 2011
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159 changes: 158 additions & 1 deletion databases/RMG_database/kinetics_libraries/Glarborg/C1/pdepreactions.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -118,4 +118,161 @@ H + H + M = H2 + M 7.0E17 -1.000 0 0.0 0.0 0.0


CH2(S) + M = CH2 + M 1.0E13 0.000 0 0.0 0.0 0.0
N2/0/ H2O/0/ AR/0/ H/0/
N2/0/ H2O/0/ AR/0/ H/0/


// *****************************************************************************
// PLOG Reactions: CO/CO2 subset *
// *****************************************************************************

// (0.001-2000 bar, 300<T<2000K)
// Well-skipping reaction, so high-P limit is zero.
CO + OH = CO2 + H 0.0 0.0 0 0.0 0.0 0.0
PLOG / 0.001 9.3E10 0.000 0 /
PLOG / 1 8.0E10 0.000 0 /
PLOG / 3 7.0E10 0.000 0 /
PLOG / 10 3.7E12 0.000 12518 /
PLOG / 20 2.9E12 0.000 11922 /
PLOG / 50 1.5E12 0.000 13909 /
PLOG / 80 1.5E11 0.000 1987 /
PLOG / 100 1.5E11 0.000 1987 /
PLOG / 650 2.3E11 0.200 4968 /
PLOG / 2000 3.7E07 1.340 2186 /
// DUPLICATE

// (0.001-2000 bar, 300<T<2000K)
CO + OH = CO2 + H 0.0 0.0 0 0.0 0.0 0.0
PLOG / 0.001 7.1E05 1.800 1133 /
PLOG / 1 8.8E05 1.770 954 /
PLOG / 3 2.9E05 1.900 397 /
PLOG / 10 9.3E07 1.100 0 /
PLOG / 20 4.5E07 1.200 0 /
PLOG / 50 5.8E06 1.500 0 /
PLOG / 80 2.5E05 1.900 0 /
PLOG / 100 1.9E05 1.940 0 /
PLOG / 650 7.0E05 1.700 298 /
PLOG / 2000 0.0 0.0 0 /
// DUPLICATE


// (0.001-2000 bar, 300<T<2000K)
CO + OH = HOCO 5.5E44 -11.000 7948 0.0 0.0 0.0
PLOG / 0.001 1.0E25 -6.000 2981 /
PLOG / 1 6.0E26 -5.600 2881 /
PLOG / 3 2.2E27 -5.600 3239 /
PLOG / 10 1.5E25 -5.000 1987 /
PLOG / 20 4.2E26 -5.700 1927 /
PLOG / 50 4.9E25 -5.200 1987 /
PLOG / 80 5.2E25 -5.200 1987 /
PLOG / 100 1.1E28 -6.000 2384 /
PLOG / 650 3.2E41 -10.000 6955 /
PLOG / 2000 5.5E44 -11.000 7948 /
// DUPLICATE

// (0.001 bar, 300<T<2000K)
CO + OH = HOCO 2.7E67 -17.000 22851 0.0 0.0 0.0
PLOG / 0.001 0.0 0.0 0 /
PLOG / 1 0.0 0.0 0 /
PLOG / 3 0.0 0.0 0 /
PLOG / 10 1.3E37 -8.400 7948 /
PLOG / 20 7.5E28 -6.000 3775 /
PLOG / 50 4.0E38 -9.000 6955 /
PLOG / 80 7.7E35 -8.000 6557 /
PLOG / 100 1.8E36 -8.000 7153 /
PLOG / 650 2.9E66 -17.100 19870 /
PLOG / 2000 2.7E67 -17.000 22851 /
// DUPLICATE

// (0.001 bar, 300<T<2000K)
CO + OH = HOCO 1.0E74 -18.000 37157 0.0 0.0 0.0
PLOG / 0.001 0.0 0.0 0 /
PLOG / 1 0.0 0.0 0 /
PLOG / 3 0.0 0.0 0 /
PLOG / 10 0.0 0.0 0 /
PLOG / 20 4.0E39 -9.000 9935 /
PLOG / 50 5.0E43 -10.000 13015 /
PLOG / 80 9.0E47 -11.200 15499 /
PLOG / 100 2.0E54 -13.000 19671 /
PLOG / 650 2.0E63 -15.200 27421 /
PLOG / 2000 1.0E74 -18.000 37157 /
// DUPLICATE


// (1-100 bar, 300<T<2000K)
// HOCO = CO2 + H 3.5E56*P[bar]^0.95 -15.000 46500
HOCO = CO2 + H 2.8E58 -15.000 46500 0.0 0.0 0.0
PLOG / 1 3.5E56 -15.000 46500 /
PLOG / 10 3.2E57 -15.000 46500 /
PLOG / 20 6.0E57 -15.000 46500 /
PLOG / 50 1.4E58 -15.000 46500 /
PLOG / 100 2.8E58 -15.000 46500 /
// DUPLICATE


// (1-100 bar, 300<T<2000K)
//HOCO = CO2 + H 2.5E69*P[bar]^0.95 -18.000 60000
HOCO = CO2 + H 2.0E71 -18.000 60000 0.0 0.0 0.0
PLOG / 1 2.5E69 -18.000 60000 /
PLOG / 10 2.2E70 -18.000 60000 /
PLOG / 20 4.3E70 -18.000 60000 /
PLOG / 50 1.0E71 -18.000 60000 /
PLOG / 100 2.0E71 -18.000 60000 /
// DUPLICATE


// *****************************************************************************
// PLOG Reactions: CH2O subset *
// *****************************************************************************


// General pressure dependency
//HCO = H + CO 9.83E11*P[bar]^0.865 -0.865 16755 0.0 0.0 0.0
HCO = H + CO 5.3E13 -0.865 16755 0.0 0.0 0.0
PLOG / 1 9.9E11 -0.865 16755 /
PLOG / 10 7.2E12 -0.865 16755 /
PLOG / 20 1.3E13 -0.865 16755 /
PLOG / 50 2.9E13 -0.865 16755 /
PLOG / 100 5.3E13 -0.865 16755 /

// *****************************************************************************
// PLOG Reactions: CH4 subset *
// *****************************************************************************


// fit to FER/TRO06
CH3 + O2 = CH3OO 1.1E19 -2.300 1800 0.0 0.0 0.0
PLOG / 1 5.0E22 -3.850 2000 /
PLOG / 10 3.4E21 -3.200 2300 /
PLOG / 20 4.1E20 -2.940 1900 /
PLOG / 50 2.8E18 -2.200 1400 /
PLOG / 100 1.1E19 -2.300 1800 /
// DUPLICATE

CH3 + O2 = CH3OO 4.1E30 -5.700 8750 0.0 0.0 0.0
PLOG / 1 0.0 0.0 0 /
PLOG / 10 0.0 0.0 0 /
PLOG / 20 3.3E29 -5.600 6850 /
PLOG / 50 5.6E28 -5.250 6850 /
PLOG / 100 4.1E30 -5.700 8750 /
// DUPLICATE

// High-P limit rate is Garborg's high-PL rate
CH3OOH = CH3O + OH 2.2E17 -0.420 44622 0.0 0.0 0.0
PLOG / 1 2.0E35 -6.700 47450 /
PLOG / 10 1.1E28 -4.150 46190 /
PLOG / 50 2.8E26 -3.500 46340 /
PLOG / 1000 2.2E17 -0.420 44622 / ! this is Glarborg's high-PL rate

// Since CFG converted all CH2OOH into CH2O + OH, this reaction is redundant.
// 1 atm
// CH2OOH => CH2O + OH 2.4E12 -0.925 1567 0.0 0.0 0.0
// 10 atm
//CH2OOH => CH2O + OH 2.5E13 -0.927 1579 0.0 0.0 0.0
// 100 atm
//CH2OOH => CH2O + OH 7.0E14 -1.064 1744 0.0 0.0 0.0
// However, if it did exist, it would look something like this in PLOG form:
// // High-P limit rate is Garborg's 100 atm rate
// CH2OOH => CH2O + OH 7.0E14 -1.064 1744 0.0 0.0 0.0
// PLOG / 1 2.4E12 -0.925 1567 /
// PLOG / 10 2.5E13 -0.927 1579 /
// PLOG / 100 7.0E14 -1.064 1744 /
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