Merge pull request #158 from MathCancer/development

Official 1.12.0 release

BioFVM/BioFVM_vector.cpp

@@ -498,4 +498,22 @@ void vector3_to_list( const std::vector<double>& vect , char*& buffer , char del
 	return; 
 }
 
+double dot_product( std::vector<double>& a , std::vector<double>& b )
+{
+	double out = 0.0; 
+	for( unsigned int i=0 ; i < a.size() ; i++ )
+	{ out += ( a[i] * b[i] ); }
+	return out; 
+}
+
+std::vector<double> cross_product( std::vector<double>& a , std::vector<double>& b )
+{
+	std::vector<double> out( 3, 0.0 ); 
+	out[0] = a[1]*b[2] - a[2]*b[1]; 
+	out[1] = a[2]*b[0] - a[0]*b[2];
+	out[2] = a[0]*b[1] - a[1]*b[0];
+
+	return out; 
+} 
+
 };

BioFVM/BioFVM_vector.h

@@ -141,6 +141,9 @@ void vector_to_list( const std::vector<double>& vect , char*& buffer , char deli
 
 void vector3_to_list( const std::vector<double>& vect , char*& buffer , char delim ); 
 
+double dot_product( std::vector<double>& a , std::vector<double>& b ); 
+std::vector<double> cross_product( std::vector<double>& a , std::vector<double>& b );
+
 };
 
 #endif

CITATION.txt

@@ -1,7 +1,7 @@
 If you use PhysiCell in your project, please cite PhysiCell and the version 
 number, such as below:                                                      
 
-We implemented and solved the model using PhysiCell (Version 1.11.0) [1].    
+We implemented and solved the model using PhysiCell (Version 1.12.0) [1].    
 
 [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, 
     PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu-  
@@ -11,7 +11,7 @@ We implemented and solved the model using PhysiCell (Version 1.11.0) [1].
 Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM  
     as below:                                                               
 
-We implemented and solved the model using PhysiCell (Version 1.11.0) [1],    
+We implemented and solved the model using PhysiCell (Version 1.12.0) [1],    
 with BioFVM [2] to solve the transport equations.                           
 
 [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, 

Makefile

@@ -42,7 +42,7 @@ BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_contai
 
 PhysiCell_core_OBJECTS := PhysiCell_phenotype.o PhysiCell_cell_container.o PhysiCell_standard_models.o \
 PhysiCell_cell.o PhysiCell_custom.o PhysiCell_utilities.o PhysiCell_constants.o PhysiCell_basic_signaling.o \
-PhysiCell_signal_behavior.o 
+PhysiCell_signal_behavior.o PhyisiCell_rules.o
 
 PhysiCell_module_OBJECTS := PhysiCell_SVG.o PhysiCell_pathology.o PhysiCell_MultiCellDS.o PhysiCell_various_outputs.o \
 PhysiCell_pugixml.o PhysiCell_settings.o PhysiCell_geometry.o
@@ -73,7 +73,7 @@ name:
 list-projects:
 	@echo "Sample projects: template biorobots-sample cancer-biorobots-sample cancer-immune-sample"
 	@echo "                 celltypes3-sample heterogeneity-sample pred-prey-farmer virus-macrophage-sample"
-	@echo "                 worm-sample interaction-sample mechano-sample"
+	@echo "                 worm-sample interaction-sample mechano-sample rules-sample"
 	@echo ""
 	@echo "Sample intracellular projects: ode-energy-sample physiboss-cell-lines-sample cancer-metabolism-sample"
 	@echo ""
@@ -171,6 +171,24 @@ interaction-sample:
 	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
 	cp ./sample_projects/interactions/config/* ./config/
 
+mechano-sample:
+	cp ./sample_projects/mechano/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/mechano/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/mechano/Makefile .
+	cp ./sample_projects/mechano/config/* ./config/
+
+rules-sample:
+	cp ./sample_projects/rules_sample/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/rules_sample/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/rules_sample/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp ./sample_projects/rules_sample/config/* ./config/
+
+
 # ---- intracellular projects 
 ode-energy-sample:
 	cp ./sample_projects_intracellular/ode/ode_energy/custom_modules/* ./custom_modules/
@@ -208,13 +226,6 @@ cancer-metabolism-sample:
 	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
 	cp ./sample_projects_intracellular/fba/cancer_metabolism/config/* ./config/
 
-mechano-sample:
-	cp ./sample_projects/mechano/custom_modules/* ./custom_modules/
-	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects/mechano/main.cpp ./main.cpp 
-	cp Makefile Makefile-backup
-	cp ./sample_projects/mechano/Makefile .
-	cp ./sample_projects/mechano/config/* ./config/
 
 # early examples for convergence testing 
 
@@ -273,6 +284,9 @@ PhysiCell_constants.o: ./core/PhysiCell_constants.cpp
 PhysiCell_signal_behavior.o: ./core/PhysiCell_signal_behavior.cpp
 	$(COMPILE_COMMAND) -c ./core/PhysiCell_signal_behavior.cpp 
 
+PhysiCell_rules.o: ./core/PhysiCell_rules.cpp
+	$(COMPILE_COMMAND) -c ./core/PhysiCell_rules.cpp 
+
 # BioFVM core components (needed by PhysiCell)
 
 BioFVM_vector.o: ./BioFVM/BioFVM_vector.cpp
@@ -451,3 +465,7 @@ load:
 	cp ./user_projects/$(PROJ)/Makefile .
 	cp ./user_projects/$(PROJ)/config/* ./config/ 
 	cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ 
+
+list-user-projects:
+	@echo "user projects::"
+	@cd ./user_projects && ls -dt1 * | grep . | sed 's!empty.txt!!'