Merge pull request #191 from MathCancer/development

Development

.github/workflows/test-macosx.yml

@@ -43,4 +43,27 @@ jobs:
         
     - name: Run PhysiBoSS cell lines project
       run: |
-        ./PhysiBoSS_Cell_Lines
+        ./PhysiBoSS_Cell_Lines
+  
+  build_physimess:
+
+    runs-on: macos-11
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Install dependencies
+      run : brew install gcc@11
+
+    - name: Build PhysiMeSS project
+      run: |
+        make physimess-sample
+        make clean
+        make PHYSICELL_CPP=g++-11
+        
+    - name: Run PhysiMeSS project
+      run: |
+        ./project config/mymodel.xml
+        ./project config/Fibre_Initialisation/mymodel_initialisation.xml
+        ./project config/Cell_Fibre_Mechanics/mymodel_rotating.xml
+        

.github/workflows/test-ubuntu.yml

@@ -33,4 +33,18 @@ jobs:
         
     - name: Run PhysiBoSS cell lines project
       run: |
-        ./PhysiBoSS_Cell_Lines
+        ./PhysiBoSS_Cell_Lines
+        
+    - name: Build PhysiMeSS project
+      run: |
+        make reset
+        make physimess-sample
+        make clean
+        make
+        
+    - name: Run PhysiMeSS project
+      run: |
+        ./project config/mymodel.xml
+        ./project config/Fibre_Initialisation/mymodel_initialisation.xml
+        ./project config/Cell_Fibre_Mechanics/mymodel_rotating.xml
+        

.github/workflows/test-windows.yml

@@ -39,4 +39,18 @@ jobs:
       
     - name: Run PhysiBoSS cell lines project
       run: |
-        .\\PhysiBoSS_Cell_Lines.exe
+        .\\PhysiBoSS_Cell_Lines.exe
+        
+    - name: Build PhysiMeSS project
+      run: |
+        make reset
+        make physimess-sample
+        make clean
+        make
+        
+    - name: Run PhysiMeSS project
+      run: |
+        .\\project config\\mymodel.xml
+        .\\project config\\Fibre_Initialisation\\mymodel_initialisation.xml
+        .\\project config\\Cell_Fibre_Mechanics\\mymodel_rotating.xml
+        

.gitignore

@@ -22,3 +22,9 @@ project
 initial.svg
 initial.svg
 interaction_demo
+addons/libRoadrunner/roadrunner/
+addons/libRoadrunner/roadrunner-win64-vs14-cp35m.zip
+addons/PhysiBoSS/MaBoSS-env-2.0/
+addons/PhysiBoSS/libMaBoSS-*.tar.gz
+user_projects/*
+!user_projects/empty.txt

BioFVM/BioFVM_basic_agent.cpp

@@ -300,6 +300,10 @@ double Basic_Agent::get_total_volume()
 	return volume;
 }
 
+const std::vector<double>& Basic_Agent::get_previous_velocity( void ) {
+	return previous_velocity;
+}
+
 void Basic_Agent::simulate_secretion_and_uptake( Microenvironment* pS, double dt )
 {
 	if(!is_active)

BioFVM/BioFVM_basic_agent.h

@@ -111,7 +111,7 @@ class Basic_Agent
 	void update_position( double dt );
 
 	Basic_Agent(); 
-
+	virtual ~Basic_Agent(){};
 	// simulate secretion and uptake at the nearest voxel at the indicated microenvironment.
 	// if no microenvironment indicated, use the currently selected microenvironment. 
 	void simulate_secretion_and_uptake( Microenvironment* M, double dt ); 
@@ -125,6 +125,8 @@ class Basic_Agent
 	std::vector<double>& nearest_gradient( int substrate_index );
 	// directly access a vector of gradients, one gradient per substrate 
 	std::vector<gradient>& nearest_gradient_vector( void ); 
+
+	const std::vector<double>& get_previous_velocity( void );
 };
 
 extern std::vector<Basic_Agent*> all_basic_agents; 

BioFVM/BioFVM_microenvironment.cpp

@@ -152,7 +152,7 @@ Microenvironment::Microenvironment()
 	one_third /= 3.0;
 
 	dirichlet_value_vectors.assign( mesh.voxels.size(), one ); 
-	dirichlet_activation_vector.assign( 1 , true ); 
+	dirichlet_activation_vector.assign( 1 , false );
 
 	dirichlet_activation_vectors.assign( 1 , dirichlet_activation_vector ); 
 
@@ -212,7 +212,7 @@ void Microenvironment::update_dirichlet_node( int voxel_index , int substrate_in
 	dirichlet_value_vectors[voxel_index][substrate_index] = new_value; 
 
 	dirichlet_activation_vectors[voxel_index][substrate_index] = true; 
-	
+
 	return; 
 }
 
@@ -250,6 +250,12 @@ bool Microenvironment::get_substrate_dirichlet_activation( int substrate_index )
 	return dirichlet_activation_vector[substrate_index]; 
 }
 
+// TODO? fix confusing swapped usage of args
+double Microenvironment::get_substrate_dirichlet_value( int substrate_index, int index )
+{ 
+    return dirichlet_value_vectors[index][substrate_index]; 
+}  
+
 // new functions for finer-grained control of Dirichlet conditions -- 1.7.0
 
 void Microenvironment::set_substrate_dirichlet_activation( int substrate_index , int index, bool new_value )
@@ -261,6 +267,7 @@ void Microenvironment::set_substrate_dirichlet_activation( int substrate_index ,
 bool Microenvironment::get_substrate_dirichlet_activation( int substrate_index, int index )
 { return dirichlet_activation_vectors[index][substrate_index]; }
 
+
 void Microenvironment::apply_dirichlet_conditions( void )
 {
 	/*
@@ -436,12 +443,12 @@ void Microenvironment::resize_densities( int new_size )
 	one_third /= 3.0; 
 
 	dirichlet_value_vectors.assign( mesh.voxels.size(), one ); 
-	dirichlet_activation_vector.assign( new_size, true ); 
+	dirichlet_activation_vector.assign( new_size, false );
 
 	dirichlet_activation_vectors.assign( mesh.voxels.size(), dirichlet_activation_vector ); 
 
 	default_microenvironment_options.Dirichlet_condition_vector.assign( new_size , 1.0 );  
-	default_microenvironment_options.Dirichlet_activation_vector.assign( new_size, true ); 
+	default_microenvironment_options.Dirichlet_activation_vector.assign( new_size, false );
 
 	default_microenvironment_options.initial_condition_vector.assign( new_size , 1.0 ); 
 
@@ -512,7 +519,7 @@ void Microenvironment::add_density( void )
 
 	// Fixes in PhysiCell preview November 2017
 	default_microenvironment_options.Dirichlet_condition_vector.push_back( 1.0 ); //  = one; 
-	default_microenvironment_options.Dirichlet_activation_vector.push_back( true ); // assign( number_of_densities(), true ); 
+	default_microenvironment_options.Dirichlet_activation_vector.push_back( false );
 
 	default_microenvironment_options.initial_condition_vector.push_back( 1.0 ); 
 
@@ -577,15 +584,14 @@ void Microenvironment::add_density( std::string name , std::string units )
 	one_third /= 3.0; 
 
 	dirichlet_value_vectors.assign( mesh.voxels.size(), one ); 
-	dirichlet_activation_vector.push_back( true ); 
+	dirichlet_activation_vector.push_back( false );
 	dirichlet_activation_vectors.assign( mesh.voxels.size(), dirichlet_activation_vector ); 
 
 	// fix in PhysiCell preview November 2017 
 	default_microenvironment_options.Dirichlet_condition_vector.push_back( 1.0 ); //  = one; 
-	default_microenvironment_options.Dirichlet_activation_vector.push_back( true ); // assign( number_of_densities(), true ); 
+	default_microenvironment_options.Dirichlet_activation_vector.push_back( false ); // assign( number_of_densities(), false ); 
 
-	default_microenvironment_options.Dirichlet_all.push_back( true ); 
-//	default_microenvironment_options.Dirichlet_interior.push_back( true ); 
+	default_microenvironment_options.Dirichlet_all.push_back( false );
 	default_microenvironment_options.Dirichlet_xmin.push_back( false ); 
 	default_microenvironment_options.Dirichlet_xmax.push_back( false ); 
 	default_microenvironment_options.Dirichlet_ymin.push_back( false ); 
@@ -647,12 +653,12 @@ void Microenvironment::add_density( std::string name , std::string units, double
 	one_third /= 3.0; 
 
 	dirichlet_value_vectors.assign( mesh.voxels.size(), one ); 
-	dirichlet_activation_vector.push_back( true ); 
+	dirichlet_activation_vector.push_back( false ); 
 	dirichlet_activation_vectors.assign( mesh.voxels.size(), dirichlet_activation_vector ); 
 
 	// fix in PhysiCell preview November 2017 
 	default_microenvironment_options.Dirichlet_condition_vector.push_back( 1.0 ); // = one; 
-	default_microenvironment_options.Dirichlet_activation_vector.push_back( true ); // assign( number_of_densities(), true ); 
+	default_microenvironment_options.Dirichlet_activation_vector.push_back( false ); // assign( number_of_densities(), false ); 
 
 	default_microenvironment_options.initial_condition_vector.push_back( 1.0 ); 
 
@@ -1219,7 +1225,7 @@ Microenvironment_Options::Microenvironment_Options()
 
 	outer_Dirichlet_conditions = false; 
 	Dirichlet_condition_vector.assign( pMicroenvironment->number_of_densities() , 1.0 ); 
-	Dirichlet_activation_vector.assign( pMicroenvironment->number_of_densities() , true ); 
+	Dirichlet_activation_vector.assign( pMicroenvironment->number_of_densities() , false ); 
 
 	initial_condition_vector.resize(0); //  = Dirichlet_condition_vector; 
 
@@ -1523,11 +1529,13 @@ void initialize_microenvironment( void )
 	}
 */
 
-	// set the Dirichlet condition activation vector to match the microenvironment options 
-	for( int i=0 ; i < default_microenvironment_options.Dirichlet_activation_vector.size(); i++ )
-	{
-		microenvironment.set_substrate_dirichlet_activation( i , default_microenvironment_options.Dirichlet_activation_vector[i] ); 
-	}
+    // April 2023: no longer necessary after flipping our approach and doing an "additive" instead of "subtractive" DCs handling. I.e., we assume DC activation is false by default; make true on-demand.
+
+	// // set the Dirichlet condition activation vector to match the microenvironment options 
+	// for( int i=0 ; i < default_microenvironment_options.Dirichlet_activation_vector.size(); i++ )
+	// {
+	// 	microenvironment.set_substrate_dirichlet_activation( i , default_microenvironment_options.Dirichlet_activation_vector[i] ); 
+	// }
 
 	microenvironment.display_information( std::cout );
 	return;

BioFVM/BioFVM_microenvironment.h

@@ -252,6 +252,8 @@ class Microenvironment
 	void set_substrate_dirichlet_activation( int substrate_index , int index, bool new_value );  
 	void set_substrate_dirichlet_activation( int index, std::vector<bool>& new_value ); 
 	bool get_substrate_dirichlet_activation( int substrate_index, int index );  
+
+    double get_substrate_dirichlet_value( int substrate_index, int index );
 
 	bool& is_dirichlet_node( int voxel_index ); 
 

BioFVM/BioFVM_vector.cpp

@@ -319,7 +319,7 @@ void randomize( std::vector<double>* v )
 
 /* axpy and related BLAS-type operations */ 
 
-void axpy( std::vector<double>* y, double& a , std::vector<double>& x )
+void axpy( std::vector<double>* y, const double& a , const std::vector<double>& x )
 {
  for( unsigned int i=0; i < (*y).size() ; i++ )
  {
@@ -328,7 +328,7 @@ void axpy( std::vector<double>* y, double& a , std::vector<double>& x )
  return ; 
 }
 
-void axpy( std::vector<double>* y, std::vector<double>& a , std::vector<double>& x )
+void axpy( std::vector<double>* y, const std::vector<double>& a , const std::vector<double>& x )
 {
  for( unsigned int i=0; i < (*y).size() ; i++ )
  {
@@ -337,7 +337,7 @@ void axpy( std::vector<double>* y, std::vector<double>& a , std::vector<double>&
  return; 
 }
 
-void naxpy( std::vector<double>* y, double& a , std::vector<double>& x )
+void naxpy( std::vector<double>* y, const double& a , const std::vector<double>& x )
 {
  for( unsigned int i=0; i < (*y).size() ; i++ )
  {
@@ -346,7 +346,7 @@ void naxpy( std::vector<double>* y, double& a , std::vector<double>& x )
  return ; 
 }
 
-void naxpy( std::vector<double>* y, std::vector<double>& a , std::vector<double>& x )
+void naxpy( std::vector<double>* y, const std::vector<double>& a , const std::vector<double>& x )
 {
  for( unsigned int i=0; i < (*y).size() ; i++ )
  {
@@ -498,15 +498,15 @@ 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 dot_product( const std::vector<double>& a , const 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> cross_product( const std::vector<double>& a , const std::vector<double>& b )
 {
 	std::vector<double> out( 3, 0.0 ); 
 	out[0] = a[1]*b[2] - a[2]*b[1]; 

BioFVM/BioFVM_vector.h

@@ -103,14 +103,14 @@ void randomize( std::vector<double>* v );
 /* axpy and related BLAS-type operations */ 
 
 // y = y + a*x 
-void axpy( std::vector<double>* y, double& a , std::vector<double>& x );
+void axpy( std::vector<double>* y, const double& a , const std::vector<double>& x );
 // y = y + a.*x
-void axpy( std::vector<double>* y, std::vector<double>& a , std::vector<double>& x ); 
+void axpy( std::vector<double>* y, const std::vector<double>& a , const std::vector<double>& x ); 
 
 // y = y - a*x 
-void naxpy( std::vector<double>* y, double& a , std::vector<double>& x );
+void naxpy( std::vector<double>* y, const double& a , const std::vector<double>& x );
 // y = y - a.*x
-void naxpy( std::vector<double>* y, std::vector<double>& a , std::vector<double>& x ); 
+void naxpy( std::vector<double>* y, const std::vector<double>& a , const std::vector<double>& x ); 
 
 /* I may cut these from the final version */ 
 /* CLEANUP BEFORE RELEASE */ 
@@ -141,9 +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 );
-
+double dot_product( const std::vector<double>& a , const std::vector<double>& b );
+std::vector<double> cross_product( const std::vector<double>& a , const 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 1.12.0) [1].    
+We implemented and solved the model using PhysiCell (Version 1.13.0) [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 1.12.0) [1].
 Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM  
     as below:                                                               
 
-We implemented and solved the model using PhysiCell (Version 1.12.0) [1],    
+We implemented and solved the model using PhysiCell (Version 1.13.0) [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 PhyisiCell_rules.o
+PhysiCell_signal_behavior.o PhysiCell_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 rules-sample"
+	@echo "                 worm-sample interaction-sample mechano-sample rules-sample physimess-sample"
 	@echo ""
 	@echo "Sample intracellular projects: ode-energy-sample physiboss-cell-lines-sample cancer-metabolism-sample"
 	@echo ""
@@ -188,6 +188,14 @@ rules-sample:
 	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
 	cp ./sample_projects/rules_sample/config/* ./config/
 
+physimess-sample:
+	cp ./sample_projects/physimess/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/physimess/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/physimess/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp -r ./sample_projects/physimess/config/* ./config/
 
 # ---- intracellular projects 
 ode-energy-sample: