Merge pull request MathCancer#32 from MathCancer/development

Development

Author: MathCancer

.travis.yml

@@ -0,0 +1,27 @@
+# Enable C++ support
+language: cpp
+
+os: linux
+
+# Compiler selection
+compiler:
+  - g++
+
+# Build steps
+script:
+  - make
+  - make reset
+  - make biorobots-sample
+  - make reset
+  - make cancer-biorobots-sample
+  - make reset
+  - make cancer-immune-sample
+  - make reset
+  - make virus-macrophage-sample
+
+notifications:
+  email:
+    recipients:
+      - [email protected]
+    on_success: always # default: change  (always, never)
+    on_failure: always # default: always

BioFVM/BioFVM_microenvironment.cpp

@@ -911,6 +911,29 @@ void Microenvironment::compute_all_gradient_vectors( void )
 	{
 		for( unsigned int j=0; j < mesh.y_coordinates.size() ; j++ )
 		{
+			// endcaps 
+			for( unsigned int q=0; q < number_of_densities() ; q++ )
+			{
+				int i = 0; 
+				int n = voxel_index(i,j,k);
+				// x-derivative of qth substrate at voxel n
+				gradient_vectors[n][q][0] = (*p_density_vectors)[n+thomas_i_jump][q]; 
+				gradient_vectors[n][q][0] -= (*p_density_vectors)[n][q]; 
+				gradient_vectors[n][q][0] /= mesh.dx; 
+				
+				gradient_vector_computed[n] = true; 
+			}
+			for( unsigned int q=0; q < number_of_densities() ; q++ )
+			{
+				int i = mesh.x_coordinates.size()-1; 
+				int n = voxel_index(i,j,k);
+				// x-derivative of qth substrate at voxel n
+				gradient_vectors[n][q][0] = (*p_density_vectors)[n][q]; 
+				gradient_vectors[n][q][0] -= (*p_density_vectors)[n-thomas_i_jump][q]; 
+				gradient_vectors[n][q][0] /= mesh.dx; 
+				
+				gradient_vector_computed[n] = true; 
+			}
 
 			for( unsigned int i=1; i < mesh.x_coordinates.size()-1 ; i++ )
 			{
@@ -934,6 +957,29 @@ void Microenvironment::compute_all_gradient_vectors( void )
 	{
 		for( unsigned int i=0; i < mesh.x_coordinates.size() ; i++ )
 		{
+			// endcaps 
+			for( unsigned int q=0; q < number_of_densities() ; q++ )
+			{
+				int j = 0; 
+				int n = voxel_index(i,j,k);
+				// x-derivative of qth substrate at voxel n
+				gradient_vectors[n][q][1] = (*p_density_vectors)[n+thomas_j_jump][q]; 
+				gradient_vectors[n][q][1] -= (*p_density_vectors)[n][q]; 
+				gradient_vectors[n][q][1] /= mesh.dy; 
+				
+				gradient_vector_computed[n] = true; 
+			}
+			for( unsigned int q=0; q < number_of_densities() ; q++ )
+			{
+				int j = mesh.y_coordinates.size()-1; 
+				int n = voxel_index(i,j,k);
+				// x-derivative of qth substrate at voxel n
+				gradient_vectors[n][q][1] = (*p_density_vectors)[n][q]; 
+				gradient_vectors[n][q][1] -= (*p_density_vectors)[n-thomas_j_jump][q]; 
+				gradient_vectors[n][q][1] /= mesh.dy; 
+				
+				gradient_vector_computed[n] = true; 
+			}		
 
 			for( unsigned int j=1; j < mesh.y_coordinates.size()-1 ; j++ )
 			{
@@ -950,12 +996,39 @@ void Microenvironment::compute_all_gradient_vectors( void )
 
 		}
 	}
+	
+	// don't bother computing z component if there is no z-directoin 
+	if( mesh.z_coordinates.size() == 1 )
+	{ return; }
 
 	#pragma omp parallel for 
 	for( unsigned int j=0; j < mesh.y_coordinates.size() ; j++ )
 	{
 		for( unsigned int i=0; i < mesh.x_coordinates.size() ; i++ )
 		{
+			// endcaps 
+			for( unsigned int q=0; q < number_of_densities() ; q++ )
+			{
+				int k = 0; 
+				int n = voxel_index(i,j,k);
+				// x-derivative of qth substrate at voxel n
+				gradient_vectors[n][q][2] = (*p_density_vectors)[n+thomas_k_jump][q]; 
+				gradient_vectors[n][q][2] -= (*p_density_vectors)[n][q]; 
+				gradient_vectors[n][q][2] /= mesh.dz; 
+				
+				gradient_vector_computed[n] = true; 
+			}
+			for( unsigned int q=0; q < number_of_densities() ; q++ )
+			{
+				int k = mesh.z_coordinates.size()-1; 
+				int n = voxel_index(i,j,k);
+				// x-derivative of qth substrate at voxel n
+				gradient_vectors[n][q][2] = (*p_density_vectors)[n][q]; 
+				gradient_vectors[n][q][2] -= (*p_density_vectors)[n-thomas_k_jump][q]; 
+				gradient_vectors[n][q][2] /= mesh.dz; 
+				
+				gradient_vector_computed[n] = true; 
+			}			
 
 			for( unsigned int k=1; k < mesh.z_coordinates.size()-1 ; k++ )
 			{
@@ -1006,6 +1079,10 @@ void Microenvironment::compute_gradient_vector( int n )
 		}
 	}
 
+	// don't bother computing y and z component if there is no y-direction. (1D)
+	if( mesh.y_coordinates.size() == 1 )
+	{ return; }	
+	
 	// d/dy 
 	if( indices[1] > 0 && indices[1] < mesh.y_coordinates.size()-1 )
 	{
@@ -1018,6 +1095,10 @@ void Microenvironment::compute_gradient_vector( int n )
 		}
 	}
 
+	// don't bother computing z component if there is no z-direction (2D) 
+	if( mesh.z_coordinates.size() == 1 )
+	{ return; }
+	
 	// d/dz 
 	if( indices[2] > 0 && indices[2] < mesh.z_coordinates.size()-1 )
 	{

BioFVM/BioFVM_solvers.cpp

@@ -84,8 +84,8 @@ void diffusion_decay_solver__constant_coefficients_explicit_uniform_mesh( Microe
 		std::cout	<< std::endl << "Using solver: " << __FUNCTION__ << std::endl 
 					<< "     (constant diffusion coefficient with explicit stepping, implicit decay, uniform mesh) ... " << std::endl << std::endl;  
 
-		if( M.mesh.uniform_mesh == false )
-		{ std::cout << "Error. This code is only supported for uniform meshes." << std::endl; }
+		if( M.mesh.regular_mesh == false )
+		{ std::cout << "Error. This code is only supported for regular meshes." << std::endl; }
 
 		precomputations_and_constants_done = true; 
 	}
@@ -95,9 +95,9 @@ void diffusion_decay_solver__constant_coefficients_explicit_uniform_mesh( Microe
 
 void diffusion_decay_solver__constant_coefficients_LOD_3D( Microenvironment& M, double dt )
 {
-	if( M.mesh.uniform_mesh == false || M.mesh.Cartesian_mesh == false )
+	if( M.mesh.regular_mesh == false || M.mesh.Cartesian_mesh == false )
 	{
-		std::cout << "Error: This algorithm is written for uniform Cartesian meshes. Try: other solvers!" << std::endl << std::endl; 
+		std::cout << "Error: This algorithm is written for regular Cartesian meshes. Try: other solvers!" << std::endl << std::endl; 
 	return; 
 	}
 
@@ -301,9 +301,9 @@ void diffusion_decay_solver__constant_coefficients_LOD_3D( Microenvironment& M,
 
 void diffusion_decay_solver__constant_coefficients_LOD_2D( Microenvironment& M, double dt )
 {
-	if( M.mesh.uniform_mesh == false )
+	if( M.mesh.regular_mesh == false )
 	{
-		std::cout << "Error: This algorithm is written for uniform Cartesian meshes. Try: something else." << std::endl << std::endl; 
+		std::cout << "Error: This algorithm is written for regular Cartesian meshes. Try: something else." << std::endl << std::endl; 
 		return; 
 	}
 

BioFVM/BioFVM_vector.cpp

@@ -199,6 +199,22 @@ std::vector<double> normalize( std::vector<double>& v )
 
  for( unsigned int i=0; i < v.size(); i++ )
  { output[i] /= norm ; }
+
+ // If the norm is small, normalizing doens't make sense. 
+ // Just set the entire vector to zero. 
+ static bool I_warned_you = false; 
+ if( norm <= 1e-16 )
+ { 
+  if( I_warned_you == false )
+  {
+   std::cout << "Warning and FYI: Very small vector are normalized to 0 vector" << std::endl << std::endl; 
+   I_warned_you = true; 
+  }
+
+  for( unsigned int i=0; i < v.size(); i++ )
+  { output[i] = 0.0; }
+ }
+
  return output; 
 }
 
@@ -213,6 +229,22 @@ void normalize( std::vector<double>* v )
 
  for( unsigned int i=0; i < v->size(); i++ )
  { (*v)[i] /=  norm ; }
+
+ // If the norm is small, normalizing doens't make sense. 
+ // Just set the entire vector to zero. 
+ static bool I_warned_you = false; 
+ if( norm <= 1e-16 )
+ { 
+  if( I_warned_you == false )
+  {
+   std::cout << "Warning and FYI: Very small vectors are normalized to 0 vector" << std::endl << std::endl; 
+   I_warned_you = true; 
+  }
+
+  for( unsigned int i=0; i < v->size(); i++ )
+  { (*v)[i] = 0.0; }
+ }
+
  return; 
 }
 

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 1.6.0) [1].    
+We implemented and solved the model using PhysiCell (Version 1.6.1) [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 1.6.0) [1].
 Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM  
     as below:                                                               
 
-We implemented and solved the model using PhysiCell (Version 1.6.0) [1],    
+We implemented and solved the model using PhysiCell (Version 1.6.1) [1],    
 with BioFVM [2] to solve the transport equations.                           
 
 [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, 

Makefile

@@ -38,7 +38,7 @@ BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM
 BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o 
 
 PhysiCell_core_OBJECTS := PhysiCell_phenotype.o PhysiCell_cell_container.o PhysiCell_standard_models.o \
-PhysiCell_cell.o PhysiCell_custom.o PhysiCell_utilities.o 
+PhysiCell_cell.o PhysiCell_custom.o PhysiCell_utilities.o PhysiCell_constants.o
 
 PhysiCell_module_OBJECTS := PhysiCell_SVG.o PhysiCell_pathology.o PhysiCell_MultiCellDS.o PhysiCell_various_outputs.o \
 PhysiCell_pugixml.o PhysiCell_settings.o
@@ -61,6 +61,9 @@ all:
 	make 
 
 # sample projects 	
+list-projects:
+	@echo "Sample projects: template2D template3D biorobots-sample cancer-biorobots-sample heterogeneity-sample"
+	@echo "                 cancer-immune-sample virus-macrophage-sample"
 
 template2D: 
 	cp ./sample_projects/template2D/custom_modules/* ./custom_modules/
@@ -187,6 +190,9 @@ PhysiCell_utilities.o: ./core/PhysiCell_utilities.cpp
 PhysiCell_custom.o: ./core/PhysiCell_custom.cpp
 	$(COMPILE_COMMAND) -c ./core/PhysiCell_custom.cpp 
 
+PhysiCell_constants.o: ./core/PhysiCell_constants.cpp
+	$(COMPILE_COMMAND) -c ./core/PhysiCell_constants.cpp 
+	
 # BioFVM core components (needed by PhysiCell)
 
 BioFVM_vector.o: ./BioFVM/BioFVM_vector.cpp
@@ -264,6 +270,9 @@ data-cleanup:
 	touch ./output/empty.txt
 
 # archival 
+
+checkpoint: 
+	zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* 
 
 zip:
 	zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/*