Merge pull request #41 from drbergman/my-physicell-dev

1.14.2-drbergman-2.3.1

Author: drbergman

VERSION.txt

@@ -1 +1 @@
-1.14.2-drbergman-2.3.0
+1.14.2-drbergman-2.3.1

core/PhysiCell_cell.cpp

@@ -623,19 +623,24 @@ Cell* Cell::divide( )
 	rand_vec *= radius; // multiply direction times the displacement 
 	*/
 
+	// direction to displace daughter cell
 	std::vector<double> rand_vec = cell_division_orientation(); 
+	// make it orthogonal to the cell's orientation
 	rand_vec = rand_vec- phenotype.geometry.polarity*(rand_vec[0]*state.orientation[0]+ 
 		rand_vec[1]*state.orientation[1]+rand_vec[2]*state.orientation[2])*state.orientation;	
-	rand_vec *= phenotype.geometry.radius;
+	// make sure it is a unit vector
+	normalize( &rand_vec );
+	// push the cells far enough apart to avoid strong overlap, but still maintain some overlap
+	rand_vec *= 0.5 * phenotype.geometry.radius;
 
 	child->assign_position(position[0] + rand_vec[0],
 						   position[1] + rand_vec[1],
 						   position[2] + rand_vec[2]);
 
 	//change my position to keep the center of mass intact 
 	// and then see if I need to update my voxel index
-	static double negative_one_half = -0.5; 
-	axpy( &position, negative_one_half , rand_vec ); // position = position - 0.5*rand_vec; 
+	static double negative_one = -1.0; 
+	axpy( &position, negative_one , rand_vec ); // position = position - rand_vec; 
 
 	//If this cell has been moved outside of the boundaries, mark it as such.
 	//(If the child cell is outside of the boundaries, that has been taken care of in the assign_position function.)

core/PhysiCell_standard_models.cpp

@@ -1098,64 +1098,8 @@ double distance_to_domain_edge(Cell* pCell, Phenotype& phenotype, double dummy)
 			min_distance = temp_distance; 
 			nearest_boundary = 5; 
 		}			
-		
-		// check for 3D exceptions 
-		
-		// lines 
-		if( fabs( (pCell->position[0]) - (pCell->position[1]) ) < tolerance && 
-			fabs( (pCell->position[1]) - (pCell->position[2]) ) < tolerance && 
-			fabs( (pCell->position[0]) - (pCell->position[2]) ) < tolerance )
-		{
-			if( pCell->position[0] > 0 )
-			{
-				if( pCell->position[0] > 0 && pCell->position[1] > 0 )
-				{ pCell->displacement = { -one_over_sqrt_3 , -one_over_sqrt_3 , -one_over_sqrt_3 }; }
-				if( pCell->position[0] < 0 && pCell->position[1] > 0 )
-				{ pCell->displacement = { one_over_sqrt_3 , -one_over_sqrt_3 , -one_over_sqrt_3 }; }
-				
-				if( pCell->position[0] > 0 && pCell->position[1] < 0 )
-				{ pCell->displacement = { -one_over_sqrt_3 , one_over_sqrt_3 , -one_over_sqrt_3 }; }
-				if( pCell->position[0] < 0 && pCell->position[1] < 0 )
-				{ pCell->displacement = { one_over_sqrt_3 , one_over_sqrt_3 , -one_over_sqrt_3 }; }
-			} 
-			else
-			{
-				if( pCell->position[0] > 0 && pCell->position[1] > 0 )
-				{ pCell->displacement = { -one_over_sqrt_3 , -one_over_sqrt_3 , one_over_sqrt_3 }; }
-				if( pCell->position[0] < 0 && pCell->position[1] > 0 )
-				{ pCell->displacement = { one_over_sqrt_3 , -one_over_sqrt_3 , one_over_sqrt_3 }; }
-				
-				if( pCell->position[0] > 0 && pCell->position[1] < 0 )
-				{ pCell->displacement = { -one_over_sqrt_3 , one_over_sqrt_3 , one_over_sqrt_3 }; }
-				if( pCell->position[0] < 0 && pCell->position[1] < 0 )
-				{ pCell->displacement = { one_over_sqrt_3 , one_over_sqrt_3 , one_over_sqrt_3 }; }				
-			}
-			return min_distance; 
-		}
-		
-		// planes - let's not worry for today 
-		
-	}
-	else
-	{
-		// check for 2D  exceptions 
-		
-		if( fabs( (pCell->position[0]) - (pCell->position[1]) ) < tolerance )
-		{
-			if( pCell->position[0] > 0 && pCell->position[1] > 0 )
-			{ pCell->displacement = { -one_over_sqrt_2 , -one_over_sqrt_2 , 0 }; }
-			if( pCell->position[0] < 0 && pCell->position[1] > 0 )
-			{ pCell->displacement = { one_over_sqrt_2 , -one_over_sqrt_2 , 0 }; }
-			
-			if( pCell->position[0] > 0 && pCell->position[1] < 0 )
-			{ pCell->displacement = { -one_over_sqrt_2 , one_over_sqrt_2 , 0 }; }
-			if( pCell->position[0] < 0 && pCell->position[1] < 0 )
-			{ pCell->displacement = { one_over_sqrt_2 , one_over_sqrt_2 , 0 }; }
-			return min_distance; 
-		}
 	}
 
-	// no exceptions 
 	switch(nearest_boundary)
 	{
 		case 0:

modules/PhysiCell_settings.cpp

@@ -1266,17 +1266,18 @@ void set_intracellular_files(pugi::xml_node &node_config_intracellular, const pu
 	{
 		std::string rr_filename = base_path_to_filename + "_" + intracellular_type + ".xml";
 		// determine if file exists already
-		if (std::ifstream(rr_filename))
-		{ return; }
-		pugi::xml_node node_rr_root = node_this_intracellular.child("sbml");
-		pugi::xml_document rr_doc;
-		rr_doc.append_copy(node_rr_root);
-		rr_doc.save_file(rr_filename.c_str());
+		if (!std::ifstream(rr_filename))
+		{
+			pugi::xml_node node_rr_root = node_this_intracellular.child("sbml");
+			pugi::xml_document rr_doc;
+			rr_doc.append_copy(node_rr_root);
+			rr_doc.save_file(rr_filename.c_str());
+		}
 		pugi::xml_node node_sbml_filename = node_config_intracellular.child("sbml_filename");
 		if (!node_sbml_filename)
 		{
 			node_sbml_filename = node_config_intracellular.append_child("sbml_filename");
-			node_sbml_filename.append_child( pugi::node_pcdata );
+			node_sbml_filename.append_child(pugi::node_pcdata);
 		}
 		if (!node_sbml_filename.first_child().set_value(rr_filename.c_str()))
 		{
@@ -1291,4 +1292,4 @@ void set_intracellular_files(pugi::xml_node &node_config_intracellular, const pu
 	}
 	return;
 }
-}; 
+};