fixup! Adjust Test to new reaction interface and anable to fixed reaction tests for CI

AntoniaBerger · AntoniaBerger · commit 5a845a1696a0 · 2025-12-02T16:22:21.000+01:00
diff --git a/src/libcadet/model/reaction/ReactionSystem.hpp b/src/libcadet/model/reaction/ReactionSystem.hpp
@@ -219,10 +219,10 @@ struct ReactionSystem
 					}
 
                     // Pop scope if reaction model used parameter provider
-					if (dynReaction[i]->usesParamProviderInDiscretizationConfig())
+					//if (dynReaction[i]->usesParamProviderInDiscretizationConfig())
 						paramProvider.popScope();
 				}
-
+            
             return reactionConfSuccess;
 	    }
 
diff --git a/test/Crystallization.cpp b/test/Crystallization.cpp
@@ -106,7 +106,7 @@ TEST_CASE("Crystallization Jacobian verification for a CSTR with initial distrib
 	pp_setup.pushScope("unit_001");
 
 	// set the discretization scheme
-	pp_setup.pushScope("reaction_bulk");
+	pp_setup.pushScope("liquid_reaction_000");
 	pp_setup.set("CRY_GROWTH_SCHEME_ORDER", 4);
 	pp_setup.popScope();
 
@@ -124,7 +124,7 @@ TEST_CASE("Crystallization Jacobian verification for a CSTR with initial distrib
 	pp_setup.pushScope("unit_001");
 
 	// set the discretization scheme
-	pp_setup.pushScope("reaction_bulk");
+	pp_setup.pushScope("liquid_reaction_000");
 	pp_setup.set("CRY_GROWTH_SCHEME_ORDER", 3);
 	pp_setup.popScope();
 
@@ -142,7 +142,7 @@ TEST_CASE("Crystallization Jacobian verification for a CSTR with primary nucleat
 	pp_setup.pushScope("unit_001");
 
 	// set the discretization scheme
-	pp_setup.pushScope("reaction_bulk");
+	pp_setup.pushScope("liquid_reaction_000");
 	pp_setup.set("CRY_GROWTH_SCHEME_ORDER", 1);
 	pp_setup.popScope();
 
@@ -160,7 +160,7 @@ TEST_CASE("Crystallization Jacobian verification for a CSTR with primary nucleat
 	pp_setup.pushScope("unit_001");
 
 	// set the discretization scheme
-	pp_setup.pushScope("reaction_bulk");
+	pp_setup.pushScope("liquid_reaction_000");
 	pp_setup.set("CRY_GROWTH_SCHEME_ORDER", 1);
 	pp_setup.popScope();
 
@@ -178,7 +178,7 @@ TEST_CASE("Crystallization Jacobian verification for a CSTR with primary and sec
 	pp_setup.pushScope("unit_001");
 
 	// set the discretization scheme
-	pp_setup.pushScope("reaction_bulk");
+	pp_setup.pushScope("liquid_reaction_000");
 	pp_setup.set("CRY_GROWTH_SCHEME_ORDER", 3);
 	pp_setup.popScope();
 
diff --git a/test/data/configuration_CSTR_MichaelisMenten_twoSubs_benchmark1.json b/test/data/configuration_CSTR_MichaelisMenten_twoSubs_benchmark1.json
@@ -22,6 +22,7 @@
       ],
       "INIT_LIQUID_VOLUME": 10,
       "NCOMP": 3,
+      "NREAC_LIQUID": 1,
       "UNIT_TYPE": "CSTR",
       "liquid_reaction_000": {
         "TYPE": "MICHAELIS_MENTEN",
diff --git a/test/data/configuration_CSTR_MichaelisMenten_twoSubs_twoInhib_benchmark1.json b/test/data/configuration_CSTR_MichaelisMenten_twoSubs_twoInhib_benchmark1.json
@@ -23,6 +23,7 @@
             "INIT_LIQUID_VOLUME": 1000,
             "NCOMP": 3,
             "UNIT_TYPE": "CSTR",
+            "NREAC_LIQUID": 1,
           "liquid_reaction_000": {
             "TYPE": "MICHAELIS_MENTEN",
             "MM_KI_C": [
diff --git a/test/data/configuration_CSTR_MicroKineticsSMA_twoSubs_benchmark1.json b/test/data/configuration_CSTR_MicroKineticsSMA_twoSubs_benchmark1.json
@@ -26,24 +26,25 @@
       ],
       "INIT_LIQUID_VOLUME": 10,
       "NCOMP": 7,
-      "REACTION_MODEL": "MASS_ACTION_LAW",
+      "NREAC_LIQUID": 1,
       "UNIT_TYPE": "CSTR",
-      "reaction_bulk": {
-        "MAL_KBWD_BULK": [
+      "liquid_reaction_000": {
+        "TYPE": "MASS_ACTION_LAW",
+        "MAL_KBWD": [
           700000000.0,
           800000000.0,
           800000000.0,
           700000000.0,
           0
         ],
-        "MAL_KFWD_BULK": [
+        "MAL_KFWD": [
           1000000000.0,
           1000000000.0,
           1000000000.0,
           1000000000.0,
           120000.0
         ],
-        "MAL_STOICHIOMETRY_BULK": [
+        "MAL_STOICHIOMETRY": [
           -1,
           0,
           0,
diff --git a/test/data/configuration_CSTR_MicroKineticsSMA_twoSubs_twoInhib_benchmark1.json b/test/data/configuration_CSTR_MicroKineticsSMA_twoSubs_twoInhib_benchmark1.json
@@ -32,10 +32,11 @@
         ],
         "INIT_LIQUID_VOLUME": 1,
         "NCOMP": 12,
-        "REACTION_MODEL": "MASS_ACTION_LAW",
+        "NREAC_LIQUID": 1,
         "UNIT_TYPE": "CSTR",
-        "reaction_bulk": {
-          "MAL_KBWD_BULK": [
+        "liquid_reaction_000": {
+          "TYPE": "MASS_ACTION_LAW",
+          "MAL_KBWD": [
             7000.0,
             8000.0,
             0.0,
@@ -44,7 +45,7 @@
             3000.0,
             4000.0
           ],
-          "MAL_KFWD_BULK": [
+          "MAL_KFWD": [
             10000.0,
             10000.0,
             120.0,
@@ -53,7 +54,7 @@
             10000.0,
             10000.0
           ],
-          "MAL_STOICHIOMETRY_BULK": [
+          "MAL_STOICHIOMETRY": [
             -1,
             0,
             0,
@@ -150,7 +151,6 @@
             0,
             1
           ]
-          ]
         }
       }
     },
diff --git a/test/data/model_MCT1ch_noEx_noReac_benchmark1.json b/test/data/model_MCT1ch_noEx_noReac_benchmark1.json
@@ -652,23 +652,24 @@
       "INIT_C": [
         0
       ],
-      "MAL_EXPONENTS_BULK_FWD": [
+      "MAL_EXPONENTS_FWD": [
         0,
         1,
         1,
         0
       ],
       "NCOMP": 1,
-      "REACTION_MODEL": "MASS_ACTION_LAW",
+      "NREAC_LIQUID": 1,
       "UNIT_TYPE": "MULTI_CHANNEL_TRANSPORT",
-      "reaction_bulk": {
-        "MAL_KBWD_BULK": [
+      "liquid_reaction_000": {
+        "TYPE": "MASS_ACTION_LAW",
+        "MAL_KBWD": [
           0
         ],
-        "MAL_KFWD_BULK": [
+        "MAL_KFWD": [
           0
         ],
-        "MAL_STOICHIOMETRY_BULK": [
+        "MAL_STOICHIOMETRY": [
           -1
         ]
       }
diff --git a/test/data/model_MCT1ch_noEx_reac_benchmark1.json b/test/data/model_MCT1ch_noEx_reac_benchmark1.json
@@ -652,23 +652,24 @@
       "INIT_C": [
         0
       ],
-      "MAL_EXPONENTS_BULK_FWD": [
+      "MAL_EXPONENTS_FWD": [
         0,
         1,
         1,
         0
       ],
       "NCOMP": 1,
-      "REACTION_MODEL": "MASS_ACTION_LAW",
       "UNIT_TYPE": "MULTI_CHANNEL_TRANSPORT",
-      "reaction_bulk": {
-        "MAL_KBWD_BULK": [
+      "NREAC_LIQUID": 1,
+      "liquid_reaction_000": {
+        "TYPE": "MASS_ACTION_LAW",
+        "MAL_KBWD": [
           0
         ],
-        "MAL_KFWD_BULK": [
+        "MAL_KFWD": [
           0.000567
         ],
-        "MAL_STOICHIOMETRY_BULK": [
+        "MAL_STOICHIOMETRY": [
           -1
         ]
       }
diff --git a/test/data/model_MCT2ch_oneWayEx_reac_benchmark1.json b/test/data/model_MCT2ch_oneWayEx_reac_benchmark1.json
@@ -663,23 +663,24 @@
       "INIT_C": [
         0
       ],
-      "MAL_EXPONENTS_BULK_FWD": [
+      "MAL_EXPONENTS_FWD": [
         0,
         1,
         1,
         0
       ],
       "NCOMP": 1,
-      "REACTION_MODEL": "MASS_ACTION_LAW",
+      "NREAC_LIQUID": 1,
       "UNIT_TYPE": "MULTI_CHANNEL_TRANSPORT",
-      "reaction_bulk": {
-        "MAL_KBWD_BULK": [
+      "liquid_reaction_000": {
+        "TYPE": "MASS_ACTION_LAW",
+        "MAL_KBWD": [
           0
         ],
-        "MAL_KFWD_BULK": [
+        "MAL_KFWD": [
           0.000567
         ],
-        "MAL_STOICHIOMETRY_BULK": [
+        "MAL_STOICHIOMETRY": [
           -1
         ]
       }
diff --git a/test/data/model_MCT3ch_twoWayExc_reac_benchmark1.json b/test/data/model_MCT3ch_twoWayExc_reac_benchmark1.json
@@ -664,23 +664,24 @@
       "INIT_C": [
         0
       ],
-      "MAL_EXPONENTS_BULK_FWD": [
+      "MAL_EXPONENTS_FWD": [
         0,
         1,
         1,
         0
       ],
       "NCOMP": 1,
-      "REACTION_MODEL": "MASS_ACTION_LAW",
       "UNIT_TYPE": "MULTI_CHANNEL_TRANSPORT",
-      "reaction_bulk": {
-        "MAL_KBWD_BULK": [
+      "NREAC_LIQUID": 1,
+      "liquid_reaction_000": {
+        "TYPE": "MASS_ACTION_LAW",
+        "MAL_KBWD": [
           0
         ],
-        "MAL_KFWD_BULK": [
+        "MAL_KFWD": [
           0.000567
         ],
-        "MAL_STOICHIOMETRY_BULK": [
+        "MAL_STOICHIOMETRY": [
           -1
         ]
       }
diff --git a/test/data/model_cry_CSTR_PBM_Agg_Frag_benchmark1.json b/test/data/model_cry_CSTR_PBM_Agg_Frag_benchmark1.json
@@ -307,10 +307,11 @@
             ],
             "INIT_VOLUME": 0.0005,
             "NCOMP": 52,
-            "REACTION_MODEL": "CRYSTALLIZATION",
+            "NREAC_LIQUID": 1,
             "UNIT_TYPE": "CSTR",
             "USE_ANALYTIC_JACOBIAN": 1,
-            "reaction_bulk": {
+            "liquid_reaction_000": {
+                "TYPE": "CRYSTALLIZATION",
                 "CRY_A": 1.0,
                 "CRY_AGGREGATION_INDEX": 0,
                 "CRY_AGGREGATION_RATE_CONSTANT": 5e-13,
diff --git a/test/data/model_cry_CSTR_PBM_growthSizeDep_benchmark1.json b/test/data/model_cry_CSTR_PBM_growthSizeDep_benchmark1.json
@@ -557,11 +557,12 @@
         "INIT_LIQUID_VOLUME": 0.0005,
         "NCOMP": 102,
         "CONST_SOLID_VOLUME": 0.0,
-        "REACTION_MODEL": "CRYSTALLIZATION",
+        "NREAC_LIQUID": 1,
         "CRYSTALLIZATION_MODE": 0,
         "UNIT_TYPE": "CSTR",
         "USE_ANALYTIC_JACOBIAN": 1,
-        "reaction_bulk": {
+        "liquid_reaction_000": {
+          "TYPE": "CRYSTALLIZATION",
           "CRY_A": 1.0,
           "CRY_B": 2.0,
           "CRY_BINS": [
diff --git a/test/data/model_cry_CSTR_PBM_growth_benchmark1.json b/test/data/model_cry_CSTR_PBM_growth_benchmark1.json
@@ -557,11 +557,12 @@
         "INIT_LIQUID_VOLUME": 0.0005,
         "NCOMP": 102,
         "CONST_SOLID_VOLUME": 0.0,
-        "REACTION_MODEL": "CRYSTALLIZATION",
+        "NREAC_LIQUID": 1,
         "CRYSTALLIZATION_MODE": 0,
         "UNIT_TYPE": "CSTR",
         "USE_ANALYTIC_JACOBIAN": 1,
-        "reaction_bulk": {
+        "liquid_reaction_000": {
+        "TYPE": "CRYSTALLIZATION",
           "CRY_A": 1.0,
           "CRY_B": 2.0,
           "CRY_BINS": [
diff --git a/test/data/model_cry_CSTR_PBM_primaryNucleationAndGrowth_benchmark1.json b/test/data/model_cry_CSTR_PBM_primaryNucleationAndGrowth_benchmark1.json
@@ -557,11 +557,12 @@
         "INIT_LIQUID_VOLUME": 0.0005,
         "NCOMP": 102,
         "CONST_SOLID_VOLUME": 0.0,
-        "REACTION_MODEL": "CRYSTALLIZATION",
+        "NREAC_LIQUID": 1,
         "CRYSTALLIZATION_MODE": 0,
         "UNIT_TYPE": "CSTR",
         "USE_ANALYTIC_JACOBIAN": 1,
-        "reaction_bulk": {
+        "liquid_reaction_000": {
+        "TYPE": "CRYSTALLIZATION",
           "CRY_A": 1.0,
           "CRY_B": 2.0,
           "CRY_BINS": [
diff --git a/test/data/model_cry_CSTR_PBM_primaryNucleationGrowthGrowthRateDispersion_benchmark1.json b/test/data/model_cry_CSTR_PBM_primaryNucleationGrowthGrowthRateDispersion_benchmark1.json
@@ -557,11 +557,12 @@
         "INIT_LIQUID_VOLUME": 0.0005,
         "NCOMP": 102,
         "CONST_SOLID_VOLUME": 0.0,
-        "REACTION_MODEL": "CRYSTALLIZATION",
+        "NREAC_LIQUID": 1,
         "CRYSTALLIZATION_MODE": 0,
         "UNIT_TYPE": "CSTR",
         "USE_ANALYTIC_JACOBIAN": 1,
-        "reaction_bulk": {
+        "liquid_reaction_000": {
+            "TYPE": "CRYSTALLIZATION",
           "CRY_A": 1.0,
           "CRY_B": 2.0,
           "CRY_BINS": [
diff --git a/test/data/model_cry_CSTR_PBM_primarySecondaryNucleationAndGrowth_benchmark1.json b/test/data/model_cry_CSTR_PBM_primarySecondaryNucleationAndGrowth_benchmark1.json
@@ -557,11 +557,12 @@
         "INIT_LIQUID_VOLUME": 0.0005,
         "NCOMP": 102,
         "CONST_SOLID_VOLUME": 0.0,
-        "REACTION_MODEL": "CRYSTALLIZATION",
+        "NREAC_LIQUID": 1,
         "CRYSTALLIZATION_MODE": 0,
         "UNIT_TYPE": "CSTR",
         "USE_ANALYTIC_JACOBIAN": 1,
-        "reaction_bulk": {
+        "liquid_reaction_000": {
+            "TYPE": "CRYSTALLIZATION",
           "CRY_A": 1.0,
           "CRY_B": 2.0,
           "CRY_BINS": [
diff --git a/test/data/model_cry_CSTR_PBM_primarySecondaryNucleationGrowth_benchmark1.json b/test/data/model_cry_CSTR_PBM_primarySecondaryNucleationGrowth_benchmark1.json
@@ -362,7 +362,7 @@
           0.0
         ],
         "NCOMP": 52,
-        "REACTION_MODEL": "CRYSTALLIZATION",
+        "NREAC_LIQUID": 1,
         "CRYSTALLIZATION_MODE": 0,
         "TOTAL_POROSITY": 0.21,
         "UNIT_TYPE": "LUMPED_RATE_MODEL_WITHOUT_PORES",
@@ -434,7 +434,8 @@
             "WENO_ORDER": 2
           }
         },
-        "reaction": {
+        "liquid_reaction_000": {
+        "TYPE": "CRYSTALLIZATION",
           "CRY_A": 1.0,
           "CRY_B": 2.0,
           "CRY_BINS": [
diff --git a/test/data/model_cry_CSTR_aggFrag_benchmark1.json b/test/data/model_cry_CSTR_aggFrag_benchmark1.json
@@ -527,10 +527,11 @@
             ],
             "INIT_VOLUME": 0.0005,
             "NCOMP": 96,
-            "REACTION_MODEL": "CRYSTALLIZATION",
+            "NREAC_LIQUID": 1,
             "UNIT_TYPE": "CSTR",
             "USE_ANALYTIC_JACOBIAN": 1,
-            "reaction_bulk": {
+            "liquid_reaction_000": {
+                "TYPE": "CRYSTALLIZATION",
                 "CRY_AGGREGATION_INDEX": 0,
                 "CRY_AGGREGATION_RATE_CONSTANT": 0.2,
                 "CRY_BINS": [
diff --git a/test/data/model_cry_CSTR_aggregation_benchmark1.json b/test/data/model_cry_CSTR_aggregation_benchmark1.json
diff --git a/test/data/model_cry_CSTR_fragmentation_benchmark1.json b/test/data/model_cry_CSTR_fragmentation_benchmark1.json
diff --git a/test/data/model_cry_DPFR_PBM_aggregation_benchmark1.json b/test/data/model_cry_DPFR_PBM_aggregation_benchmark1.json
diff --git a/test/data/model_cry_DPFR_PBM_primarySecondaryNucleationGrowth_benchmark1.json b/test/data/model_cry_DPFR_PBM_primarySecondaryNucleationGrowth_benchmark1.json

Original file line number	Diff line number	Diff line change
`@@ -219,10 +219,10 @@ struct ReactionSystem`
`219`	`219`	`}`
`220`	`220`
`221`	`221`	`// Pop scope if reaction model used parameter provider`
`222`		`- if (dynReaction[i]->usesParamProviderInDiscretizationConfig())`
	`222`	`+ //if (dynReaction[i]->usesParamProviderInDiscretizationConfig())`
`223`	`223`	`paramProvider.popScope();`
`224`	`224`	`}`
`225`		`-`
	`225`	`+`
`226`	`226`	`return reactionConfSuccess;`
`227`	`227`	`}`
`228`	`228`
Original file line number	Diff line number	Diff line change
`@@ -652,23 +652,24 @@`
`652`	`652`	`"INIT_C": [`
`653`	`653`	`0`
`654`	`654`	`],`
`655`		`- "MAL_EXPONENTS_BULK_FWD": [`
	`655`	`+ "MAL_EXPONENTS_FWD": [`
`656`	`656`	`0,`
`657`	`657`	`1,`
`658`	`658`	`1,`
`659`	`659`	`0`
`660`	`660`	`],`
`661`	`661`	`"NCOMP": 1,`
`662`		`- "REACTION_MODEL": "MASS_ACTION_LAW",`
	`662`	`+ "NREAC_LIQUID": 1,`
`663`	`663`	`"UNIT_TYPE": "MULTI_CHANNEL_TRANSPORT",`
`664`		`- "reaction_bulk": {`
`665`		`- "MAL_KBWD_BULK": [`
	`664`	`+ "liquid_reaction_000": {`
	`665`	`+ "TYPE": "MASS_ACTION_LAW",`
	`666`	`+ "MAL_KBWD": [`
`666`	`667`	`0`
`667`	`668`	`],`
`668`		`- "MAL_KFWD_BULK": [`
	`669`	`+ "MAL_KFWD": [`
`669`	`670`	`0`
`670`	`671`	`],`
`671`		`- "MAL_STOICHIOMETRY_BULK": [`
	`672`	`+ "MAL_STOICHIOMETRY": [`
`672`	`673`	`-1`
`673`	`674`	`]`
`674`	`675`	`}`
Original file line number	Diff line number	Diff line change
`@@ -663,23 +663,24 @@`
`663`	`663`	`"INIT_C": [`
`664`	`664`	`0`
`665`	`665`	`],`
`666`		`- "MAL_EXPONENTS_BULK_FWD": [`
	`666`	`+ "MAL_EXPONENTS_FWD": [`
`667`	`667`	`0,`
`668`	`668`	`1,`
`669`	`669`	`1,`
`670`	`670`	`0`
`671`	`671`	`],`
`672`	`672`	`"NCOMP": 1,`
`673`		`- "REACTION_MODEL": "MASS_ACTION_LAW",`
	`673`	`+ "NREAC_LIQUID": 1,`
`674`	`674`	`"UNIT_TYPE": "MULTI_CHANNEL_TRANSPORT",`
`675`		`- "reaction_bulk": {`
`676`		`- "MAL_KBWD_BULK": [`
	`675`	`+ "liquid_reaction_000": {`
	`676`	`+ "TYPE": "MASS_ACTION_LAW",`
	`677`	`+ "MAL_KBWD": [`
`677`	`678`	`0`
`678`	`679`	`],`
`679`		`- "MAL_KFWD_BULK": [`
	`680`	`+ "MAL_KFWD": [`
`680`	`681`	`0.000567`
`681`	`682`	`],`
`682`		`- "MAL_STOICHIOMETRY_BULK": [`
	`683`	`+ "MAL_STOICHIOMETRY": [`
`683`	`684`	`-1`
`684`	`685`	`]`
`685`	`686`	`}`
Original file line number	Diff line number	Diff line change
`@@ -664,23 +664,24 @@`
`664`	`664`	`"INIT_C": [`
`665`	`665`	`0`
`666`	`666`	`],`
`667`		`- "MAL_EXPONENTS_BULK_FWD": [`
	`667`	`+ "MAL_EXPONENTS_FWD": [`
`668`	`668`	`0,`
`669`	`669`	`1,`
`670`	`670`	`1,`
`671`	`671`	`0`
`672`	`672`	`],`
`673`	`673`	`"NCOMP": 1,`
`674`		`- "REACTION_MODEL": "MASS_ACTION_LAW",`
`675`	`674`	`"UNIT_TYPE": "MULTI_CHANNEL_TRANSPORT",`
`676`		`- "reaction_bulk": {`
`677`		`- "MAL_KBWD_BULK": [`
	`675`	`+ "NREAC_LIQUID": 1,`
	`676`	`+ "liquid_reaction_000": {`
	`677`	`+ "TYPE": "MASS_ACTION_LAW",`
	`678`	`+ "MAL_KBWD": [`
`678`	`679`	`0`
`679`	`680`	`],`
`680`		`- "MAL_KFWD_BULK": [`
	`681`	`+ "MAL_KFWD": [`
`681`	`682`	`0.000567`
`682`	`683`	`],`
`683`		`- "MAL_STOICHIOMETRY_BULK": [`
	`684`	`+ "MAL_STOICHIOMETRY": [`
`684`	`685`	`-1`
`685`	`686`	`]`
`686`	`687`	`}`