Combining intracellular models with a single model

Makefile

@@ -299,6 +299,17 @@ template_BM:
 	mkdir ./scripts/
 	cp ./sample_projects_intracellular/boolean/template_BM/scripts/* ./scripts/
 
+spheroid_tnf:
+	cp ./sample_projects_intracellular/spheroid_tnf/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects_intracellular/spheroid_tnf/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects_intracellular/spheroid_tnf/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp -r ./sample_projects_intracellular/spheroid_tnf/config/* ./config/
+	mkdir ./scripts/
+	cp ./sample_projects_intracellular/spheroid_tnf/scripts/* ./scripts/
+
 # early examples for convergence testing 
 
 physicell_test_mech1: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_mechanics_1.cpp 

addons/PhysiBoSS/src/maboss_intracellular.cpp

@@ -23,6 +23,8 @@ MaBoSSIntracellular::MaBoSSIntracellular(pugi::xml_node& node)
 
 MaBoSSIntracellular::MaBoSSIntracellular(MaBoSSIntracellular* copy) 
 {
+	pre_update_intracellular = copy->pre_update_intracellular;
+	post_update_intracellular = copy->post_update_intracellular;
 	intracellular_type = copy->intracellular_type;
 	bnd_filename = copy->bnd_filename;
 	cfg_filename = copy->cfg_filename;
@@ -424,7 +426,14 @@ void MaBoSSIntracellular::initialize_intracellular_from_pugixml(pugi::xml_node&
 }
 
 MaBoSSIntracellular* getMaBoSSModel(PhysiCell::Phenotype& phenotype) {
-	return static_cast<MaBoSSIntracellular*>(phenotype.intracellular);
+	for (auto* intracellular : phenotype.intracellulars)
+    {
+        if (intracellular->intracellular_type == "maboss")
+        {
+            return static_cast<MaBoSSIntracellular*>(intracellular);
+        }
+    }
+	return nullptr;
 }
 
 void MaBoSSIntracellular::display(std::ostream& os)
@@ -480,8 +489,16 @@ void MaBoSSIntracellular::save(std::string filename)
 	state_file << "ID,state" << std::endl;
 
 	for( auto cell : *PhysiCell::all_cells )
-		if (cell->phenotype.intracellular != NULL && cell->phenotype.intracellular->intracellular_type == "maboss")
-			state_file << cell->ID << "," << static_cast<MaBoSSIntracellular*>(cell->phenotype.intracellular)->get_state() << std::endl;
-
+	{
+		if (cell->phenotype.intracellulars.size() > 0)
+		{
+			// This only works if there is one maboss intracellular model per cell, which is the ok
+			for (auto& intracellular : cell->phenotype.intracellulars) {
+				if (intracellular->intracellular_type == "maboss") {
+					state_file << cell->ID << "," << static_cast<MaBoSSIntracellular*>(intracellular)->get_state() << std::endl;
+				}
+			}
+		} 
+	}	
 	state_file.close();
 }

addons/PhysiBoSS/src/maboss_intracellular.h

@@ -51,10 +51,10 @@ class MaBoSSIntracellular : public PhysiCell::Intracellular {
 	MaBoSSIntracellular(MaBoSSIntracellular* copy);
 
 	Intracellular* clone() {
-		return static_cast<Intracellular*>(new MaBoSSIntracellular(this));
+		return static_cast<PhysiCell::Intracellular*>(new MaBoSSIntracellular(this));
 	}
 	Intracellular* getIntracellularModel() {
-		return static_cast<Intracellular*>(this);
+		return static_cast<PhysiCell::Intracellular*>(this);
 	}
 
 	void initialize_intracellular_from_pugixml(pugi::xml_node& node);
@@ -80,9 +80,9 @@ class MaBoSSIntracellular : public PhysiCell::Intracellular {
 		return PhysiCell::PhysiCell_globals.current_time >= this->next_physiboss_run;
 	}
 
-	void inherit(PhysiCell::Cell * cell) {
+	void inherit(PhysiCell::Intracellular* intracellular) {
 		maboss.inherit_state(
-			static_cast<MaBoSSIntracellular*>(cell->phenotype.intracellular)->maboss.get_maboss_state(), 
+			static_cast<MaBoSSIntracellular*>(intracellular)->maboss.get_maboss_state(), 
 			inherit_state, inherit_nodes
 		);
 	}

addons/libRoadrunner/CMakeLists.txt

@@ -36,7 +36,7 @@ FetchContent_Declare(
 FetchContent_MakeAvailable(roadrunner)
 
 target_include_directories(libRoadrunner
-                           PUBLIC ${roadrunner_SOURCE_DIR}/include/rr/C)
+                           PUBLIC ${roadrunner_SOURCE_DIR}/include/rr)
 target_link_directories(libRoadrunner PUBLIC ${roadrunner_SOURCE_DIR}/lib)
 target_link_libraries(libRoadrunner PUBLIC roadrunner_c_api)
 target_compile_definitions(libRoadrunner PUBLIC ADDON_ROADRUNNER)