add comment parsing tests for autogenerated tree

Author: sevyharris

test/rmgpy/data/kinetics/kineticsTest.py

@@ -800,6 +800,49 @@ def test_parse_kinetics(self):
         assert "PDep" in sources[6]
         assert sources[6]["PDep"] == 7
 
+        # ------------------------------------------------------------------- #
+        # Source 7 comes from a node on an autogenerated tree
+        assert "Rate Rules" in sources[7]
+        family_label = sources[7]["Rate Rules"][0]
+        training_rxn = sources[7]["Rate Rules"][1]
+
+        assert family_label == "Disproportionation"
+
+        template_str = sources[7]["Rate Rules"][1]["template"][0].label
+        assert template_str == "Root_Ext-2R!H-R_2R!H->C_4R->C"
+
+        reconstructed_kinetics = self.database.kinetics.reconstruct_kinetics_from_source(reactions[7], sources[7], fix_barrier_height=True)
+        A = reconstructed_kinetics.A.value_si
+        n = reconstructed_kinetics.n.value_si
+        assert round(abs(reactions[7].kinetics.A.value_si - A), 7) == 0
+        assert round(abs(reactions[7].kinetics.n.value_si - n), 7) == 0
+
+        # ------------------------------------------------------------------- #
+        # Source 8 comes from a node on an autogenerated tree, but it's been broken up by the chemkin writer
+        assert "Rate Rules" in sources[8]
+        assert sources[8]["Rate Rules"][0] == "Disproportionation"
+
+        template_str = sources[8]["Rate Rules"][1]["template"][0].label
+        assert template_str == "Root_Ext-1R!H-R_N-4R->O_N-Sp-5R!H=1R!H_Ext-4CHNS-R_N-6R!H->S_4CHNS->C_N-Sp-6BrBrBrCCCClClClFFFIIINNNOOOPPPSiSiSi#4C_6BrCClFINOPSi->C_N-1R!H-inRing_N-Sp-6C-4C"
+
+        reconstructed_kinetics = self.database.kinetics.reconstruct_kinetics_from_source(reactions[8], sources[8], fix_barrier_height=True)
+        A = reconstructed_kinetics.A.value_si
+        n = reconstructed_kinetics.n.value_si
+        assert round(abs(reactions[8].kinetics.A.value_si - A), 7) == 0
+        assert round(abs(reactions[8].kinetics.n.value_si - n), 7) == 0
+
+        # ------------------------------------------------------------------- #
+        # Source 9 comes from a training reaction in an autogenerated tree
+        assert "Training" in sources[9]
+        assert sources[9]["Training"][0] == "Disproportionation"
+        training_rxn = sources[9]["Training"][1]
+        assert training_rxn.label == "CH3_r1 + C2H5 <=> CH4 + C2H4"
+
+        reconstructed_kinetics = self.database.kinetics.reconstruct_kinetics_from_source(reactions[9], sources[9], fix_barrier_height=True)
+        A = reconstructed_kinetics.A.value_si
+        n = reconstructed_kinetics.n.value_si
+        assert round(abs(reactions[9].kinetics.A.value_si - A), 7) == 0
+        assert round(abs(reactions[9].kinetics.n.value_si - n), 7) == 0
 
 class TestKinetics:
     @classmethod

test/rmgpy/test_data/parsing_data/chem_annotated.inp

@@ -22,6 +22,10 @@ SPECIES
     C2H6                ! C2H6
     C3H8                ! C3H8
     C2H3                ! C2H3
+    CH3CHCH3            ! CH3CHCH3
+    C3H6(28)            ! C3H6(28)
+    C3H5(41)            ! C3H5(41)
+    C3H5(43)            ! C3H5(43)
 END
 
 
@@ -156,6 +160,30 @@ C2H3                    C   2H   5          G   100.000  5000.000  900.33      1
  1.20640172E+04-2.91189784E+00 3.82177470E+00-3.43283353E-03 5.09227965E-05    3
 -6.20169997E-08 2.37053876E-11 1.30660155E+04 7.61665027E+00                   4
 
+! Thermo group additivity estimation: group(Cs-CsCsHH) + group(Cs-CsHHH) + group(Cs-CsHHH) + radical(CCJC)
+CH3CHCH3                C   3H   7          G   100.000  5000.000 1100.30      1
+ 3.65557541E+00 2.30584417E-02-9.41371372E-06 1.73592452E-09-1.20102267E-13    2
+ 8.11022490E+03 6.48192595E+00 3.21174698E+00 1.31075154E-02 1.99173550E-05    3
+-2.55877559E-08 8.25847355E-12 8.90792321E+03 1.18466459E+01                   4
+
+! Thermo group additivity estimation: group(Cs-(Cds-Cds)HHH) + group(Cds-CdsCsH) + group(Cds-CdsHH)
+C3H6(28)                C   3H   6          G   100.000  5000.000  988.01      1
+ 5.41216484E+00 1.72863881E-02-6.51346939E-06 1.20319805E-09-8.55900632E-14    2
+-5.03227589E+02-4.80221171E+00 3.30974061E+00 8.27528424E-03 3.37704020E-05    3
+-4.39292610E-08 1.58765570E-11 7.67476915E+02 9.64360494E+00                   4
+
+! Thermo group additivity estimation: group(Cs-(Cds-Cds)HHH) + group(Cds-CdsCsH) + group(Cds-CdsHH) + radical(Allyl_P)
+C3H5(41)                C   3H   5          G   100.000  5000.000  952.00      1
+ 7.55723004E+00 1.14809767E-02-3.63944718E-06 6.63565726E-10-4.95302876E-14    2
+ 1.71132508E+04-1.66628029E+01 3.31927862E+00 5.66515255E-03 4.27438657E-05    3
+-5.78817310E-08 2.21692287E-11 1.89906181E+04 9.19654133E+00                   4
+
+! Thermo group additivity estimation: group(Cs-(Cds-Cds)HHH) + group(Cds-CdsCsH) + group(Cds-CdsHH) + radical(Cds_P)
+C3H5(43)                C   3H   5          G   100.000  5000.000  997.88      1
+ 5.66476488E+00 1.44325185E-02-5.46732691E-06 1.00156654E-09-7.04849453E-14    2
+ 2.93870628E+04-4.48542547E+00 3.23406836E+00 1.18209872E-02 1.70300218E-05    3
+-2.64359176E-08 9.91187847E-12 3.04873071E+04 1.03183254E+01                   4
+
 END
 
 
@@ -228,5 +256,28 @@ HCCO(23)(+M)=O(2)+C2H(21)(+M)                       1.000e+00 0.000     0.000
     CHEB/ 4.629e-10    1.022e-09    -4.203e-02   -9.845e-09   -7.374e-09  /
     CHEB/ -2.262e-09   -1.025e-09   -3.546e-17   1.025e-09    2.262e-09   /
 
+! Reaction index: Chemkin #25; RMG #97
+! Template reaction: Disproportionation
+! Flux pairs: CH3CHCH3, C3H6(28); C2H5(27), C2H6; 
+! Estimated from node Root_Ext-2R!H-R_2R!H->C_4R->C
+! Multiplied by reaction path degeneracy 6.0
+C2H5(27)+CH3CHCH3<=>C2H6+C3H6(28)                   3.000e+11 0.000     0.000    
+
+! Reaction index: Chemkin #72; RMG #276
+! Template reaction: Disproportionation
+! Flux pairs: CH2CH2CH2, C3H6(28); C3H5(43), C3H5(41); 
+! Estimated from node Root_Ext-1R!H-R_N-4R->O_N-Sp-5R!H=1R!H_Ext-4CHNS-R_N-6R!H->S_4CHNS->C_N-
+! Sp-6BrBrBrCCCClClClFFFIIINNNOOOPPPSiSiSi#4C_6BrCClFINOPSi->C_N-1R!H-inRing_N-Sp-6C-4C
+! Multiplied by reaction path degeneracy 2.0
+C3H5(43)+CH2CH2CH2<=>C3H5(41)+C3H6(28)              2.420e+12 0.000     0.000    
+
+! Reaction index: Chemkin #4; RMG #37
+! Template reaction: Disproportionation
+! Flux pairs: C2H5(27), C2H4(26); CH3, CH4; 
+! Matched reaction 5 CH3_r1 + C2H5 <=> CH4 + C2H4 in Disproportionation/training
+! This reaction matched rate rule [Root_N-4R->H_4CNOS-u1_N-1R!H->O_N-4CNOS->O_4CNS->C_1CNS->C_Sp-2R!H-1C_2R!H->C]
+! family: Disproportionation
+CH3+C2H5(27)<=>CH4+C2H4(26)                         6.570e+14 -0.680    0.000    
+
 END
 

test/rmgpy/test_data/parsing_data/species_dictionary.txt

@@ -155,3 +155,49 @@ multiplicity 2
 3 H u0 p0 c0 {1,S}
 4 H u0 p0 c0 {1,S}
 5 H u0 p0 c0 {2,S}
+
+CH3CHCH3
+multiplicity 2
+1  C u0 p0 c0 {3,S} {4,S} {5,S} {6,S}
+2  C u0 p0 c0 {3,S} {7,S} {8,S} {9,S}
+3  C u1 p0 c0 {1,S} {2,S} {10,S}
+4  H u0 p0 c0 {1,S}
+5  H u0 p0 c0 {1,S}
+6  H u0 p0 c0 {1,S}
+7  H u0 p0 c0 {2,S}
+8  H u0 p0 c0 {2,S}
+9  H u0 p0 c0 {2,S}
+10 H u0 p0 c0 {3,S}
+
+C3H6(28)
+1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S}
+2 C u0 p0 c0 {1,S} {3,D} {7,S}
+3 C u0 p0 c0 {2,D} {8,S} {9,S}
+4 H u0 p0 c0 {1,S}
+5 H u0 p0 c0 {1,S}
+6 H u0 p0 c0 {1,S}
+7 H u0 p0 c0 {2,S}
+8 H u0 p0 c0 {3,S}
+9 H u0 p0 c0 {3,S}
+
+C3H5(41)
+multiplicity 2
+1 C u0 p0 c0 {2,S} {3,D} {4,S}
+2 C u1 p0 c0 {1,S} {7,S} {8,S}
+3 C u0 p0 c0 {1,D} {5,S} {6,S}
+4 H u0 p0 c0 {1,S}
+5 H u0 p0 c0 {3,S}
+6 H u0 p0 c0 {3,S}
+7 H u0 p0 c0 {2,S}
+8 H u0 p0 c0 {2,S}
+
+C3H5(43)
+multiplicity 2
+1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S}
+2 C u0 p0 c0 {1,S} {3,D} {7,S}
+3 C u1 p0 c0 {2,D} {8,S}
+4 H u0 p0 c0 {1,S}
+5 H u0 p0 c0 {1,S}
+6 H u0 p0 c0 {1,S}
+7 H u0 p0 c0 {2,S}
+8 H u0 p0 c0 {3,S}