update sample projects

rheiland · rheiland · commit 848e7e82f266 · 2026-02-10T14:25:17.000-05:00
diff --git a/sample_projects/asymmetric_division/config/PhysiCell_settings.xml b/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>
diff --git a/sample_projects/asymmetric_division/main.cpp b/sample_projects/asymmetric_division/main.cpp
@@ -118,7 +118,8 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
  	
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
+	double mechanics_voxel_size = PhysiCell_settings.mechanics_voxel_size; 
+	std::cout << "Setting mechanics voxel size= " << mechanics_voxel_size << std::endl;
 	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
 	
 	/* Users typically start modifying here. START USERMODS */ 
diff --git a/sample_projects/biorobots/config/PhysiCell_settings.xml b/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>
diff --git a/sample_projects/biorobots/main.cpp b/sample_projects/biorobots/main.cpp
@@ -118,7 +118,8 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
  	
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
+	double mechanics_voxel_size = PhysiCell_settings.mechanics_voxel_size;
+	std::cout << "Setting mechanics voxel size= " << mechanics_voxel_size << std::endl; 
 	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
 	
 	/* Users typically start modifying here. START USERMODS */ 
diff --git a/sample_projects/cancer_biorobots/config/PhysiCell_settings.xml b/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>
diff --git a/sample_projects/cancer_biorobots/main.cpp b/sample_projects/cancer_biorobots/main.cpp
@@ -118,7 +118,8 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
  	
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
+	double mechanics_voxel_size = PhysiCell_settings.mechanics_voxel_size;
+	std::cout << "Setting mechanics voxel size= " << mechanics_voxel_size << std::endl; 
 	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
 	
 	/* Users typically start modifying here. START USERMODS */ 
diff --git a/sample_projects/cancer_immune/config/PhysiCell_settings.xml b/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>
diff --git a/sample_projects/celltypes3/config/PhysiCell_settings.xml b/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>
diff --git a/sample_projects/celltypes3/main.cpp b/sample_projects/celltypes3/main.cpp
@@ -108,7 +108,8 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
  	
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
+	double mechanics_voxel_size = PhysiCell_settings.mechanics_voxel_size;
+	std::cout << "Setting mechanics voxel size= " << mechanics_voxel_size << std::endl; 
 	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
 	
 	/* Users typically start modifying here. START USERMODS */ 
diff --git a/sample_projects/custom_division/config/PhysiCell_settings.xml b/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>
diff --git a/sample_projects/custom_division/main.cpp b/sample_projects/custom_division/main.cpp
@@ -118,7 +118,8 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
  	
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
+	double mechanics_voxel_size = PhysiCell_settings.mechanics_voxel_size;
+	std::cout << "Setting mechanics voxel size= " << mechanics_voxel_size << std::endl; 
 	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
 	
 	/* Users typically start modifying here. START USERMODS */ 
diff --git a/sample_projects/episode/config/PhysiCell_settings.xml b/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>
diff --git a/sample_projects/episode/main.cpp b/sample_projects/episode/main.cpp
@@ -141,7 +141,8 @@ 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;
+            double mechanics_voxel_size = PhysiCell_settings.mechanics_voxel_size; 
+	        std::cout << "Setting mechanics voxel size= " << mechanics_voxel_size << std::endl;
 			Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
 
 			// load cell type definition and setup tisse
diff --git a/sample_projects/heterogeneity/config/PhysiCell_settings.xml b/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>
diff --git a/sample_projects/heterogeneity/main.cpp b/sample_projects/heterogeneity/main.cpp
@@ -118,7 +118,8 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
  	
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
+	double mechanics_voxel_size = PhysiCell_settings.mechanics_voxel_size;
+	std::cout << "Setting mechanics voxel size= " << mechanics_voxel_size << std::endl; 
 	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
 	
 	/* Users typically start modifying here. START USERMODS */ 
diff --git a/sample_projects/immune_function/config/PhysiCell_settings.xml b/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>
diff --git a/sample_projects/immune_function/main.cpp b/sample_projects/immune_function/main.cpp
@@ -118,7 +118,8 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
  	
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
+	double mechanics_voxel_size = PhysiCell_settings.mechanics_voxel_size;
+	std::cout << "Setting mechanics voxel size= " << mechanics_voxel_size << std::endl; 
 	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
 	
 	/* Users typically start modifying here. START USERMODS */ 
diff --git a/sample_projects/interactions/config/PhysiCell_settings.xml b/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>
diff --git a/sample_projects/interactions/main.cpp b/sample_projects/interactions/main.cpp
@@ -118,7 +118,8 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
  	
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
+	double mechanics_voxel_size = PhysiCell_settings.mechanics_voxel_size;
+	std::cout << "Setting mechanics voxel size= " << mechanics_voxel_size << std::endl; 
 	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
 	
 	/* Users typically start modifying here. START USERMODS */ 
diff --git a/sample_projects/mechano/config/PhysiCell_settings.xml b/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>
diff --git a/sample_projects/mechano/main.cpp b/sample_projects/mechano/main.cpp
@@ -118,7 +118,8 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
  	
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
+	double mechanics_voxel_size = PhysiCell_settings.mechanics_voxel_size;
+	std::cout << "Setting mechanics voxel size= " << mechanics_voxel_size << std::endl; 
 	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
 	
 	/* Users typically start modifying here. START USERMODS */ 
diff --git a/sample_projects/physimess/config/PhysiCell_settings.xml b/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>
diff --git a/sample_projects/physimess/main.cpp b/sample_projects/physimess/main.cpp
@@ -118,7 +118,8 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
  	
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
+	double mechanics_voxel_size = PhysiCell_settings.mechanics_voxel_size;
+	std::cout << "Setting mechanics voxel size= " << mechanics_voxel_size << std::endl; 
 	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
 	
 	/* Users typically start modifying here. START USERMODS */ 
diff --git a/sample_projects/pred_prey_farmer/config/PhysiCell_settings.xml b/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>
diff --git a/sample_projects/pred_prey_farmer/main.cpp b/sample_projects/pred_prey_farmer/main.cpp
@@ -118,7 +118,8 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
  	
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
+	double mechanics_voxel_size = PhysiCell_settings.mechanics_voxel_size;
+	std::cout << "Setting mechanics voxel size= " << mechanics_voxel_size << std::endl; 
 	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
 	
 	/* Users typically start modifying here. START USERMODS */ 
diff --git a/sample_projects/rules_sample/config/PhysiCell_settings.xml b/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>
diff --git a/sample_projects/rules_sample/main.cpp b/sample_projects/rules_sample/main.cpp
@@ -118,7 +118,8 @@ int main( int argc, char* argv[] )
 	/* PhysiCell setup */ 
  	
 	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
+	double mechanics_voxel_size = PhysiCell_settings.mechanics_voxel_size;
+	std::cout << "Setting mechanics voxel size= " << mechanics_voxel_size << std::endl; 
 	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
 	
 	/* Users typically start modifying here. START USERMODS */ 
diff --git a/sample_projects/template/config/PhysiCell_settings-0.xml b/sample_projects/template/config/PhysiCell_settings-0.xml
diff --git a/sample_projects/template/config/PhysiCell_settings.xml b/sample_projects/template/config/PhysiCell_settings.xml
diff --git a/sample_projects/template/main.cpp b/sample_projects/template/main.cpp
diff --git a/sample_projects/virus_macrophage/config/PhysiCell_settings.xml b/sample_projects/virus_macrophage/config/PhysiCell_settings.xml
diff --git a/sample_projects/virus_macrophage/main.cpp b/sample_projects/virus_macrophage/main.cpp
diff --git a/sample_projects/worm/config/PhysiCell_settings.xml b/sample_projects/worm/config/PhysiCell_settings.xml
diff --git a/sample_projects/worm/main.cpp b/sample_projects/worm/main.cpp
diff --git a/sample_projects_intracellular/ode/ode_energy/config/PhysiCell_settings.xml b/sample_projects_intracellular/ode/ode_energy/config/PhysiCell_settings.xml
diff --git a/sample_projects_intracellular/ode/ode_energy/main.cpp b/sample_projects_intracellular/ode/ode_energy/main.cpp
