From 3f34b2361937ecdb6329ebfcfd64a39c598d6a8a Mon Sep 17 00:00:00 2001 From: Josh Allen Date: Wed, 14 Nov 2012 17:06:07 -0500 Subject: [PATCH] Some bugfixes to database syntax. Fixed several incorrect adjacency lists with bonds listed in only one direction or between wrong atom indices. Commented out a few items in libraries that don't have corresponding entries in the dictionary. Fixed a rate rule to use an integer index (not "100_R2"). These changes help make the database importable into RMG-Py, which has more tight error-checking. --- .../kinetics_groups/H_Abstraction/rateLibrary.txt | 2 +- .../intra_substitutionCS_cyclization/forbiddenGroups.txt | 2 +- .../kinetics_libraries/Sulfur/TP_Song/species.txt | 4 ++-- databases/RMG_database/thermo_groups/Radical_Dictionary.txt | 4 ++-- .../thermo_libraries/SulfurLibrary/Dictionary.txt | 6 +++--- .../RMG_database/thermo_libraries/SulfurLibrary/Library.txt | 2 +- .../thermo_libraries/primaryThermoLibrary/Library.txt | 2 +- 7 files changed, 11 insertions(+), 11 deletions(-) diff --git a/databases/RMG_database/kinetics_groups/H_Abstraction/rateLibrary.txt b/databases/RMG_database/kinetics_groups/H_Abstraction/rateLibrary.txt index 2c31d0be..4698ee4c 100755 --- a/databases/RMG_database/kinetics_groups/H_Abstraction/rateLibrary.txt +++ b/databases/RMG_database/kinetics_groups/H_Abstraction/rateLibrary.txt @@ -200,7 +200,7 @@ Arrhenius_EP 185. C/H3/CO O_pri_rad 295-600 5.17E+05 2.20 0 1.00 0 0 0 0 3 Taylor et al. [127] Transition state theory. 186. C/H3/O C_methyl 300-2000 2.05E-04 4.90 0 6.72 0 0 0 0 2 Jodkowski et al. [100] ab initio calculations. 187. C/H3/O O_pri_rad 300-2000 8.14E+03 2.80 0 -0.42 0 0 0 0 2 Jodkowski et al. [100] ab initio calculations. -100_R2 C/H3/O H_rad 300-2000 4.51E+02 3.20 0 3.49 0 0 0 0 2 Jodkowski et al. [100] ab initio calculations. added by Greg Magoon 08/25/09 +1001. C/H3/O H_rad 300-2000 4.51E+02 3.20 0 3.49 0 0 0 0 2 Jodkowski et al. [100] ab initio calculations. added by Greg Magoon 08/25/09 188. C/H2/NonDeC O2b 300-2500 1.985E+13 0 0 47.69 *10.0 0 0 0 4 Tsang [91] literature review. 189. C/H2/NonDeC CH2_triplet 300-2500 7.55E-01 3.46 0 7.47 *10.0 0 0 0 4 Tsang [91] literature review. 190. C/H2/NonDeC O_atom_triplet 300-2500 2.39E+04 2.71 0 2.11 *2.0 0 0 0 4 Tsang [91] literature review. diff --git a/databases/RMG_database/kinetics_groups/intra_substitutionCS_cyclization/forbiddenGroups.txt b/databases/RMG_database/kinetics_groups/intra_substitutionCS_cyclization/forbiddenGroups.txt index 0d49008c..058b8ca8 100644 --- a/databases/RMG_database/kinetics_groups/intra_substitutionCS_cyclization/forbiddenGroups.txt +++ b/databases/RMG_database/kinetics_groups/intra_substitutionCS_cyclization/forbiddenGroups.txt @@ -1,3 +1,3 @@ 1and3_bound -1 *3 (R!H) 1 {2,{S,D}} +1 *3 R!H 1 {2,{S,D}} 2 *1 Cs 0 {1,{S,D}} diff --git a/databases/RMG_database/kinetics_libraries/Sulfur/TP_Song/species.txt b/databases/RMG_database/kinetics_libraries/Sulfur/TP_Song/species.txt index 8caaf208..ebaf38e4 100644 --- a/databases/RMG_database/kinetics_libraries/Sulfur/TP_Song/species.txt +++ b/databases/RMG_database/kinetics_libraries/Sulfur/TP_Song/species.txt @@ -27,8 +27,8 @@ IM2 //2 C 0 {1,D} {3,S} //3 C 0 {2,S} {4,D} //4 C 0 {3,D} {5,S} -5 C 2 {4,S} {1,S} -6 H 0 {1,S} +//5 C 2 {4,S} {1,S} +//6 H 0 {1,S} IM4 1 S 0 {2,D} diff --git a/databases/RMG_database/thermo_groups/Radical_Dictionary.txt b/databases/RMG_database/thermo_groups/Radical_Dictionary.txt index 357849a5..bc562a01 100644 --- a/databases/RMG_database/thermo_groups/Radical_Dictionary.txt +++ b/databases/RMG_database/thermo_groups/Radical_Dictionary.txt @@ -85,7 +85,7 @@ bridgehead_norbornyl 5 Cs 0 {2,S} {4,S} 6 Cs 0 {2,S} {7,S} 7 Cs 0 {1,S} {6,S} -8 H 0 {4,S} +8 H 0 {1,S} cyclopropane 1 * Cs 1 {2,S} {3,S} {4,S} @@ -222,7 +222,7 @@ bicyclo[3.1.0]hexane-C5-3 4 Cs 0 {2,S} {6,S} 5 Cs 0 {1,S} {6,S} 6 * Cs 1 {4,S} {5,S} -7 H 0 {6,S} +7 H 0 {1,S} bicyclo[3.1.0]hexane-C3 1 Cs 0 {2,S} {3,S} {5,S} diff --git a/databases/RMG_database/thermo_libraries/SulfurLibrary/Dictionary.txt b/databases/RMG_database/thermo_libraries/SulfurLibrary/Dictionary.txt index 566a2b48..4e855613 100644 --- a/databases/RMG_database/thermo_libraries/SulfurLibrary/Dictionary.txt +++ b/databases/RMG_database/thermo_libraries/SulfurLibrary/Dictionary.txt @@ -224,21 +224,21 @@ propane2thione but3ene2thione 1 C 0 {2,S} -2 C 0 {3,D} {4,S} +2 C 0 {1,S} {3,D} {4,S} 3 S 0 {2,D} 4 C 0 {2,S} {5,D} 5 C 0 {4,D} but3yne2thione 1 C 0 {2,S} -2 C 0 {3,D} {4,S} +2 C 0 {1,S} {3,D} {4,S} 3 S 0 {2,D} 4 C 0 {2,S} {5,T} 5 C 0 {4,T} HCSCSCH3 1 C 0 {2,S} -2 C 0 {3,S} {4,D} +2 C 0 {1,S} {3,S} {4,D} 3 C 0 {2,S} {5,D} 4 S 0 {2,D} 5 S 0 {3,D} diff --git a/databases/RMG_database/thermo_libraries/SulfurLibrary/Library.txt b/databases/RMG_database/thermo_libraries/SulfurLibrary/Library.txt index 643bd299..27c85d30 100644 --- a/databases/RMG_database/thermo_libraries/SulfurLibrary/Library.txt +++ b/databases/RMG_database/thermo_libraries/SulfurLibrary/Library.txt @@ -126,7 +126,7 @@ ethanyl-11-dithiol 34.44 86.47 22.75 25.10 27.51 29.71 33.37 36.19 40.61 1.00 1. ethenyl-1-thiol 72.21 69.43 17.75 19.74 21.26 22.51 24.50 25.95 28.09 1.00 1.00 1.00 //thioformyl 68.00 56.38 8.77 9.46 10.04 10.52 11.21 11.76 12.62 1.00 1.00 1.00 "Expt available [7]" thioacetyl 56.91 66.09 12.69 14.77 16.75 18.50 21.25 23.30 26.46 1.00 1.00 1.00 -SCjj 76.02 76.71 18.23 20.95 23.22 25.10 27.99 30.10 33.33 1.00 1.00 1.00 +//SCjj 76.02 76.71 18.23 20.95 23.22 25.10 27.99 30.10 33.33 1.00 1.00 1.00 Sjj 66.20 40.11 4.97 4.97 4.97 4.97 4.97 5.13 5.06 1.00 1.00 1.00 "H298, S298, Cp1000, Cp1500 from [10], rest from AGV" ethylthio 23.44 68.11 15.99 19.18 22.02 24.45 28.36 31.33 36.04 1.00 1.00 1.00 propyl-2-thio 17.69 74.74 21.15 26.05 30.33 33.91 39.51 43.69 50.26 1.00 1.00 1.00 diff --git a/databases/RMG_database/thermo_libraries/primaryThermoLibrary/Library.txt b/databases/RMG_database/thermo_libraries/primaryThermoLibrary/Library.txt index e489802d..5f919808 100644 --- a/databases/RMG_database/thermo_libraries/primaryThermoLibrary/Library.txt +++ b/databases/RMG_database/thermo_libraries/primaryThermoLibrary/Library.txt @@ -12,7 +12,7 @@ OCCO(S) 18.31 90.63 13.66 14.78 15.66 16.41 17.57 18.39 19.53 0.0 0.0 0.0 "QCI// OCCO 5.60 61.18 14.21 15.20 15.98 16.65 17.72 18.49 19.58 0.0 0.0 0.0 "QCI//DFT calculation by CFGoldsmith; Copied from DFT_QCI_thermo library" C3H2 113.99 56.44 10.61 12.79 14.81 16.48 18.71 20.33 22.59 0.0 0.0 0.0 "Burcat's recommended value for 16165-40-5: C3H2 CYCLOPROPENYLIDENE BI-RADICAL SINGLET on 3/25/2011 (MRH converted from NASA-7 to RMG format)" H 52.103 27.419 4.968 4.968 4.968 4.968 4.968 4.968 4.968 0.001 0.0005 0 "library value for H radical" -C2O2 14.90 57.613 11.00 12.00 13.00 14.00 15.00 16.00 17.00 0 0 0 "G03 CBSQB3 calculation - Cp values estimated poorly" +//C2O2 14.90 57.613 11.00 12.00 13.00 14.00 15.00 16.00 17.00 0 0 0 "G03 CBSQB3 calculation - Cp values estimated poorly" O2 -0.0010244 49.0236 7.0233 7.1986 7.4285 7.6673 8.0656 8.3363 8.7407 0.0 0.0 0.0 "from GRI-Mech 3.0" S2 29.19 55.96 7.81 8.17 8.40 8.54 8.70 8.78 8.87 0 0 0 "CBS-QB3 value A.G. Vandeputte" HCS 71.7 56.37 8.77 9.46 10.04 10.51 11.22 11.76 12.62 0 0 0 "NIST value + B3LYP/cbsb7 entropy and heat cap A.G. Vandeputte"