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.
ReactionMechanismGenerator · Nov 14, 2012 · 3f34b23 · 3f34b23
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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"