Merge pull request MathCancer#25 from MathCancer/development

Development

Author: MathCancer

.gitignore

@@ -0,0 +1,5 @@
+
+*.o
+unit-test-conservation.exe
+Makefile-backup
+*.exe

BioFVM/BioFVM_microenvironment.cpp

@@ -267,6 +267,11 @@ void Microenvironment::set_substrate_dirichlet_activation( int substrate_index ,
 	return; 
 }
 
+double Microenvironment::get_substrate_dirichlet_activation( int substrate_index )
+{
+	return dirichlet_activation_vector[substrate_index]; 
+}
+
 void Microenvironment::apply_dirichlet_conditions( void )
 {
 	/*
@@ -716,13 +721,23 @@ void Microenvironment::display_information( std::ostream& os )
 		os << "   " << density_names[i] << ":" << std::endl
 		<< "     units: " << density_units[i] << std::endl 
 		<< "     diffusion coefficient: " << diffusion_coefficients[i]  
-		<< " " << spatial_units << "^2 / " << time_units << std::endl
+			<< " " << spatial_units << "^2 / " << time_units << std::endl
 		<< "     decay rate: " << decay_rates[i] 
-		<< " " << time_units << "^-1" << std::endl 
-		<< "     diffusion length scale: " << sqrt( diffusion_coefficients[i] / ( 1e-12 + decay_rates[i] ) ) << " " 
-		<< spatial_units << std::endl << std::endl; 
+			<< " " << time_units << "^-1" << std::endl 
+		<< "     diffusion length scale: " << sqrt( diffusion_coefficients[i] / ( 1e-12 + decay_rates[i] ) ) 
+			<< " " << spatial_units << std::endl 
+		<< "     initial condition: " << default_microenvironment_options.initial_condition_vector[i] 
+			<< " " << density_units[i] << std::endl 
+		<< "     boundary condition: " << default_microenvironment_options.Dirichlet_condition_vector[i] 
+			<< " " << density_units[i] << " (enabled: "; 
+		if( dirichlet_activation_vector[i] == true )
+		{ os << "true"; }
+		else
+		{ os << "false"; }
+		os << ")" << std::endl; 
 	}
 	os << std::endl; 
+	
 	return; 
 }
 
@@ -862,6 +877,7 @@ std::vector<gradient>& Microenvironment::gradient_vector(int n )
 		compute_gradient_vector( n );
 	}
 
+	
 	return gradient_vectors[n];
 }
 
@@ -878,7 +894,6 @@ std::vector<gradient>& Microenvironment::nearest_gradient_vector( std::vector<do
 
 void Microenvironment::compute_all_gradient_vectors( void )
 {
-	// 
 	static double two_dx = mesh.dx; 
 	static double two_dy = mesh.dy; 
 	static double two_dz = mesh.dz; 
@@ -1172,6 +1187,12 @@ 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] ); 
+	}
+	
 	microenvironment.display_information( std::cout );
 	return;
 }

BioFVM/BioFVM_microenvironment.h

@@ -127,9 +127,8 @@ class Microenvironment
 	*/
 	std::vector< std::vector<double> > dirichlet_value_vectors; 
 	std::vector<bool> dirichlet_activation_vector; 	
-		
  public:
- 
+	
 	/*! The mesh for the diffusing quantities */ 
 	Cartesian_Mesh mesh;
 	Agent_Container * agent_container;	
@@ -239,6 +238,7 @@ class Microenvironment
 	void apply_dirichlet_conditions( void ); 
 
 	void set_substrate_dirichlet_activation( int substrate_index , bool new_value ); 
+	double get_substrate_dirichlet_activation( int substrate_index ); 
 
 	bool& is_dirichlet_node( int voxel_index ); 
 

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 1.5.2) [1].    
+We implemented and solved the model using PhysiCell (Version 1.6.0) [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 1.5.2) [1].
 Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM  
     as below:                                                               
 
-We implemented and solved the model using PhysiCell (Version 1.5.2) [1],    
+We implemented and solved the model using PhysiCell (Version 1.6.0) [1],    
 with BioFVM [2] to solve the transport equations.                           
 
 [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, 

Makefile

@@ -250,8 +250,7 @@ reset:
 	touch ./custom_modules/empty.txt 
 	touch ALL_CITATIONS.txt 
 	rm ALL_CITATIONS.txt 
-	cp ./config/PhysiCell_settings_default.xml ./config/PhysiCell_settings.xml 
-	touch ./output/empty.txt
+	cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml 
 
 clean:
 	rm -f *.o