expose and parse the mechanics grid size in XML

modules/PhysiCell_settings.cpp

@@ -154,6 +154,9 @@ PhysiCell_Settings::PhysiCell_Settings()
 
 	intracellular_save_interval = 60;  
 	enable_intracellular_saves = false; 
+
+	// <options>
+    mechanics_voxel_size = 30.0;
 
 	// parallel options 
 
@@ -299,6 +302,27 @@ void PhysiCell_Settings::read_from_pugixml( void )
 			SeedRandom(seed);
 		}
 
+		double mechanics_voxel_size_val;
+        pugi::xml_node mechanics_voxel_size_node = xml_find_node(node_options, "mechanics_voxel_size");
+		if (mechanics_voxel_size_node)
+		{ 
+            mechanics_voxel_size_val = xml_get_my_double_value(mechanics_voxel_size_node ); 
+            if (mechanics_voxel_size_val > 0.0)
+            {
+                PhysiCell_settings.mechanics_voxel_size = mechanics_voxel_size_val;  // Update global value
+                std::cout << "Setting PhysiCell_settings.mechanics_voxel_size = " << PhysiCell_settings.mechanics_voxel_size << std::endl;
+            }
+            else
+            {
+                std::cout << "XML Error: mechanics_voxel_size must be > 0. Leaving at default value= " << mechanics_voxel_size << std::endl;
+            }
+        }
+		else
+		{
+			std::cout << "mechanics_voxel_size not found in XML <options>, leaving at default value= " << mechanics_voxel_size << std::endl;
+		}
+
+
 		// other options can go here, eventually
 	}
 

modules/PhysiCell_settings.h

@@ -128,6 +128,9 @@ class PhysiCell_Settings
 	double intracellular_save_interval = 60; 
 	bool enable_intracellular_saves = false; 
 
+    // <options>
+	double mechanics_voxel_size = 30.0; 
+
 	// cell rules option
 	bool rules_enabled = false; 
 	std::string rules_protocol = "Cell Behavior Hypothesis Grammar (CBHG)"; 

sample_projects/asymmetric_division/config/PhysiCell_settings.xml

@@ -52,6 +52,7 @@
         <virtual_wall_at_domain_edge>true</virtual_wall_at_domain_edge>
         <disable_automated_spring_adhesions>false</disable_automated_spring_adhesions>
         <random_seed>0</random_seed>
+        <mechanics_voxel_size>30</mechanics_voxel_size>
     </options>
 
     <microenvironment_setup>

sample_projects/asymmetric_division/main.cpp

@@ -118,8 +118,7 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
 
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
-	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
+	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, PhysiCell_settings.mechanics_voxel_size );
 
 	/* Users typically start modifying here. START USERMODS */ 
 

sample_projects/biorobots/config/PhysiCell_settings.xml

@@ -61,6 +61,7 @@
         <virtual_wall_at_domain_edge>true</virtual_wall_at_domain_edge>
         <disable_automated_spring_adhesions>true</disable_automated_spring_adhesions>
         <random_seed>0</random_seed>
+        <mechanics_voxel_size>30</mechanics_voxel_size>
     </options>
 
     <microenvironment_setup>

sample_projects/biorobots/main.cpp

@@ -118,8 +118,7 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
 
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
-	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
+	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, PhysiCell_settings.mechanics_voxel_size );
 
 	/* Users typically start modifying here. START USERMODS */ 
 

sample_projects/cancer_biorobots/config/PhysiCell_settings.xml

@@ -61,6 +61,7 @@
         <virtual_wall_at_domain_edge>true</virtual_wall_at_domain_edge>
         <disable_automated_spring_adhesions>true</disable_automated_spring_adhesions>
         <random_seed>0</random_seed>
+        <mechanics_voxel_size>30</mechanics_voxel_size>
     </options>
 
     <microenvironment_setup>

sample_projects/cancer_biorobots/main.cpp

@@ -118,8 +118,7 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
 
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
-	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
+	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, PhysiCell_settings.mechanics_voxel_size );
 
 	/* Users typically start modifying here. START USERMODS */ 
 

sample_projects/cancer_immune/config/PhysiCell_settings.xml

@@ -124,6 +124,7 @@
 		<legacy_random_points_on_sphere_in_divide>false</legacy_random_points_on_sphere_in_divide>
 		<virtual_wall_at_domain_edge>true</virtual_wall_at_domain_edge>
         <disable_automated_spring_adhesions>true</disable_automated_spring_adhesions>
+        <mechanics_voxel_size>30</mechanics_voxel_size>
 	</options>	
 
 	<microenvironment_setup>

sample_projects/cancer_immune/main-cancer_immune_3D.cpp

@@ -121,8 +121,7 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
 
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
-	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
+	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, PhysiCell_settings.mechanics_voxel_size );
 
 	create_cell_types();
 	setup_tissue();

sample_projects/celltypes3/config/PhysiCell_settings.xml

@@ -121,6 +121,7 @@
 	<options>
 		<legacy_random_points_on_sphere_in_divide>false</legacy_random_points_on_sphere_in_divide>
         <disable_automated_spring_adhesions>false</disable_automated_spring_adhesions>
+        <mechanics_voxel_size>30</mechanics_voxel_size>
 	</options>	
 
 	<microenvironment_setup>

sample_projects/celltypes3/main.cpp

@@ -108,8 +108,7 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
 
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
-	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
+	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, PhysiCell_settings.mechanics_voxel_size );
 
 	/* Users typically start modifying here. START USERMODS */ 
 

sample_projects/custom_division/config/PhysiCell_settings.xml

@@ -51,6 +51,7 @@
         <virtual_wall_at_domain_edge>true</virtual_wall_at_domain_edge>
         <disable_automated_spring_adhesions>false</disable_automated_spring_adhesions>
         <random_seed>0</random_seed>
+        <mechanics_voxel_size>30</mechanics_voxel_size>
     </options>
 
     <microenvironment_setup>

sample_projects/custom_division/main.cpp

@@ -118,8 +118,7 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
 
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
-	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
+	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, PhysiCell_settings.mechanics_voxel_size );
 
 	/* Users typically start modifying here. START USERMODS */ 
 

sample_projects/episode/config/PhysiCell_settings.xml

@@ -52,6 +52,7 @@
         <virtual_wall_at_domain_edge>true</virtual_wall_at_domain_edge>
         <disable_automated_spring_adhesions>false</disable_automated_spring_adhesions>
         <random_seed>74</random_seed>
+        <mechanics_voxel_size>30</mechanics_voxel_size>
     </options>
 
     <microenvironment_setup>

sample_projects/episode/main.cpp

@@ -141,8 +141,7 @@ int main( int argc, char* argv[] )
 			// setup microenviroment and mechanics voxel size and match the data structure to BioFVM
 			std::cout << "set densities ..." << std::endl;
 			setup_microenvironment();  // modify this in the custom code
-			double mechanics_voxel_size = 30;
-			Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
+	        Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, PhysiCell_settings.mechanics_voxel_size );
 
 			// load cell type definition and setup tisse
 			std::cout << "load cell type definition and setup tissue ..." << std::endl;
@@ -186,8 +185,7 @@ int main( int argc, char* argv[] )
 			std::cout << "reset densities ..." << std::endl;
 			set_microenvironment_initial_condition();
 			microenvironment.display_information( std::cout );
-			double mechanics_voxel_size = 30;
-			Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
+	        Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, PhysiCell_settings.mechanics_voxel_size );
 
 			// reset tissue
 			std::cout << "reset tissue ..." << std::endl;

sample_projects/heterogeneity/config/PhysiCell_settings.xml

@@ -61,6 +61,7 @@
         <virtual_wall_at_domain_edge>true</virtual_wall_at_domain_edge>
         <disable_automated_spring_adhesions>false</disable_automated_spring_adhesions>
         <random_seed>0</random_seed>
+        <mechanics_voxel_size>30</mechanics_voxel_size>
     </options>
 
     <microenvironment_setup>

sample_projects/heterogeneity/main.cpp

@@ -118,8 +118,7 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
 
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
-	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
+	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, PhysiCell_settings.mechanics_voxel_size );
 
 	/* Users typically start modifying here. START USERMODS */ 
 

sample_projects/immune_function/config/PhysiCell_settings.xml

@@ -45,6 +45,7 @@
         <legacy_random_points_on_sphere_in_divide>false</legacy_random_points_on_sphere_in_divide>
         <virtual_wall_at_domain_edge>true</virtual_wall_at_domain_edge>
         <disable_automated_spring_adhesions>false</disable_automated_spring_adhesions>
+        <mechanics_voxel_size>30</mechanics_voxel_size>
     </options>
 
     <microenvironment_setup>

sample_projects/immune_function/main.cpp

@@ -118,8 +118,7 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
 
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
-	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
+	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, PhysiCell_settings.mechanics_voxel_size );
 
 	/* Users typically start modifying here. START USERMODS */ 
 

sample_projects/interactions/config/PhysiCell_settings.xml

@@ -62,6 +62,7 @@
         <legacy_cell_defaults_copy>false</legacy_cell_defaults_copy>
         <disable_automated_spring_adhesions>false</disable_automated_spring_adhesions>
         <random_seed>0</random_seed>
+        <mechanics_voxel_size>30</mechanics_voxel_size>
     </options>
 
     <microenvironment_setup>

sample_projects/interactions/main.cpp

@@ -118,8 +118,7 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
 
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
-	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
+	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, PhysiCell_settings.mechanics_voxel_size );
 
 	/* Users typically start modifying here. START USERMODS */ 
 

sample_projects/mechano/config/PhysiCell_settings.xml

@@ -61,6 +61,7 @@
         <virtual_wall_at_domain_edge>true</virtual_wall_at_domain_edge>
         <disable_automated_spring_adhesions>false</disable_automated_spring_adhesions>
         <random_seed>0</random_seed>
+        <mechanics_voxel_size>30</mechanics_voxel_size>
     </options>
 
     <microenvironment_setup>

sample_projects/mechano/main.cpp

@@ -118,8 +118,7 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
 
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
-	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
+	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, PhysiCell_settings.mechanics_voxel_size );
 
 	/* Users typically start modifying here. START USERMODS */ 
 

sample_projects/physimess/config/PhysiCell_settings.xml

@@ -61,6 +61,7 @@
         <virtual_wall_at_domain_edge>true</virtual_wall_at_domain_edge>
         <disable_automated_spring_adhesions>true</disable_automated_spring_adhesions>
         <random_seed>0</random_seed>
+        <mechanics_voxel_size>30</mechanics_voxel_size>
     </options>
 
     <microenvironment_setup>

sample_projects/physimess/main.cpp

@@ -118,8 +118,7 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
 
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
-	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
+	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, PhysiCell_settings.mechanics_voxel_size );
 
 	/* Users typically start modifying here. START USERMODS */ 
 

sample_projects/pred_prey_farmer/config/PhysiCell_settings.xml

@@ -122,6 +122,7 @@
 		<legacy_random_points_on_sphere_in_divide>false</legacy_random_points_on_sphere_in_divide>
 		<virtual_wall_at_domain_edge>true</virtual_wall_at_domain_edge>
         <disable_automated_spring_adhesions>false</disable_automated_spring_adhesions>
+        <mechanics_voxel_size>30</mechanics_voxel_size>
 	</options>	
 
 	<microenvironment_setup>

sample_projects/pred_prey_farmer/main.cpp

@@ -118,8 +118,7 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
 
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
-	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
+	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, PhysiCell_settings.mechanics_voxel_size );
 
 	/* Users typically start modifying here. START USERMODS */ 
 

sample_projects/rules_sample/config/PhysiCell_settings.xml

@@ -52,6 +52,7 @@
         <virtual_wall_at_domain_edge>true</virtual_wall_at_domain_edge>
         <disable_automated_spring_adhesions>false</disable_automated_spring_adhesions>
         <random_seed>0</random_seed>
+        <mechanics_voxel_size>30</mechanics_voxel_size>
     </options>
 
     <microenvironment_setup>

sample_projects/rules_sample/main.cpp

@@ -118,8 +118,7 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
 
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
-	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
+	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, PhysiCell_settings.mechanics_voxel_size );
 
 	/* Users typically start modifying here. START USERMODS */ 
 

sample_projects/template/config/PhysiCell_settings.xml

@@ -52,6 +52,7 @@
         <virtual_wall_at_domain_edge>true</virtual_wall_at_domain_edge>
         <disable_automated_spring_adhesions>false</disable_automated_spring_adhesions>
         <random_seed>0</random_seed>
+        <mechanics_voxel_size>30</mechanics_voxel_size>
     </options>
 
     <microenvironment_setup>

sample_projects/template/main.cpp

@@ -118,8 +118,7 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
 
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
-	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
+	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, PhysiCell_settings.mechanics_voxel_size );
 
 	/* Users typically start modifying here. START USERMODS */ 
 

sample_projects/virus_macrophage/config/PhysiCell_settings.xml

@@ -61,6 +61,7 @@
         <virtual_wall_at_domain_edge>true</virtual_wall_at_domain_edge>
         <disable_automated_spring_adhesions>false</disable_automated_spring_adhesions>
         <random_seed>0</random_seed>
+        <mechanics_voxel_size>30</mechanics_voxel_size>
     </options>
 
     <microenvironment_setup>

sample_projects/virus_macrophage/main.cpp

@@ -118,8 +118,7 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
 
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
-	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
+	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, PhysiCell_settings.mechanics_voxel_size );
 
 	/* Users typically start modifying here. START USERMODS */ 
 

sample_projects/worm/config/PhysiCell_settings.xml

@@ -61,6 +61,7 @@
         <virtual_wall_at_domain_edge>true</virtual_wall_at_domain_edge>
         <disable_automated_spring_adhesions>true</disable_automated_spring_adhesions>
         <random_seed>0</random_seed>
+        <mechanics_voxel_size>30</mechanics_voxel_size>
     </options>
 
     <microenvironment_setup>

sample_projects/worm/main.cpp

@@ -118,8 +118,7 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
 
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
-	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
+	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, PhysiCell_settings.mechanics_voxel_size );
 
 	/* Users typically start modifying here. START USERMODS */ 
 

sample_projects_intracellular/ode/ode_energy/config/PhysiCell_settings.xml

@@ -122,6 +122,7 @@
 		<legacy_random_points_on_sphere_in_divide>false</legacy_random_points_on_sphere_in_divide>
 		<virtual_wall_at_domain_edge>true</virtual_wall_at_domain_edge>
         <disable_automated_spring_adhesions>false</disable_automated_spring_adhesions>
+        <mechanics_voxel_size>30</mechanics_voxel_size>
 	</options>	
 
 	<microenvironment_setup>

sample_projects_intracellular/ode/ode_energy/main.cpp

@@ -109,8 +109,7 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
 
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
-	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
+	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, PhysiCell_settings.mechanics_voxel_size );
 
 	/* Users typically start modifying here. START USERMODS */