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expose and parse the mechanics grid size in XML #413

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848e7e8
update sample projects
rheiland Feb 10, 2026
1cb79ae
add unique named main
rheiland Feb 10, 2026
20bc231
mech grid size in xml
rheiland Feb 10, 2026
95fea5f
add mechanics_voxel_size
rheiland Feb 10, 2026
79702d5
cleanup
rheiland Feb 17, 2026
1ed6aff
cleanup
rheiland Feb 19, 2026
8ffa631
cleanup
rheiland Feb 19, 2026
cdccd72
add unit test
rheiland Feb 21, 2026
954504e
add Makefile
rheiland Feb 21, 2026
b8ee96b
test case with missing param
rheiland Feb 22, 2026
828b6be
remove mechanics_voxel_size
rheiland Feb 22, 2026
cbdbb41
remove cout of mechanics_voxel_size
rheiland Feb 22, 2026
9b373b8
move Makefile
rheiland Feb 23, 2026
bf8e1fc
explain why different results
rheiland Mar 16, 2026
68bbf9b
init
rheiland Mar 20, 2026
4d174a8
Update README with new scenario details
rheiland Mar 20, 2026
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24 changes: 24 additions & 0 deletions modules/PhysiCell_settings.cpp
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Expand Up @@ -154,6 +154,9 @@ PhysiCell_Settings::PhysiCell_Settings()

intracellular_save_interval = 60;
enable_intracellular_saves = false;

// <options>
mechanics_voxel_size = 30.0;

// parallel options

Expand Down Expand Up @@ -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
}

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3 changes: 3 additions & 0 deletions modules/PhysiCell_settings.h
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Expand Up @@ -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)";
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1 change: 1 addition & 0 deletions sample_projects/asymmetric_division/config/PhysiCell_settings.xml
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Expand Up @@ -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>
Expand Down
3 changes: 1 addition & 2 deletions sample_projects/asymmetric_division/main.cpp
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Expand Up @@ -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 */

Expand Down
1 change: 1 addition & 0 deletions sample_projects/biorobots/config/PhysiCell_settings.xml
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Expand Up @@ -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>
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3 changes: 1 addition & 2 deletions sample_projects/biorobots/main.cpp
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Expand Up @@ -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 );

@drbergman drbergman Aug 21, 2026

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Is there a reason we need to reference the mechanics voxel size in main.cpp? Can't we have create_cell_container_for_microenvironment just read the voxel size in the PhysiCell_settings object?


/* Users typically start modifying here. START USERMODS */

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1 change: 1 addition & 0 deletions sample_projects/cancer_biorobots/config/PhysiCell_settings.xml
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Expand Up @@ -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>
Expand Down
3 changes: 1 addition & 2 deletions sample_projects/cancer_biorobots/main.cpp
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Expand Up @@ -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 */

Expand Down
1 change: 1 addition & 0 deletions sample_projects/cancer_immune/config/PhysiCell_settings.xml
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Expand Up @@ -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>
Expand Down
3 changes: 1 addition & 2 deletions sample_projects/cancer_immune/main-cancer_immune_3D.cpp
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Expand Up @@ -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();
Expand Down
1 change: 1 addition & 0 deletions sample_projects/celltypes3/config/PhysiCell_settings.xml
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Expand Up @@ -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>
Expand Down
3 changes: 1 addition & 2 deletions sample_projects/celltypes3/main.cpp
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Expand Up @@ -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 */

Expand Down
1 change: 1 addition & 0 deletions sample_projects/custom_division/config/PhysiCell_settings.xml
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Expand Up @@ -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>
Expand Down
3 changes: 1 addition & 2 deletions sample_projects/custom_division/main.cpp
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Expand Up @@ -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 */

Expand Down
1 change: 1 addition & 0 deletions sample_projects/episode/config/PhysiCell_settings.xml
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Expand Up @@ -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>
Expand Down
6 changes: 2 additions & 4 deletions sample_projects/episode/main.cpp
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Expand Up @@ -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;
Expand Down Expand Up @@ -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;
Expand Down
1 change: 1 addition & 0 deletions sample_projects/heterogeneity/config/PhysiCell_settings.xml
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Expand Up @@ -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>
Expand Down
3 changes: 1 addition & 2 deletions sample_projects/heterogeneity/main.cpp
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Expand Up @@ -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 */

Expand Down
1 change: 1 addition & 0 deletions sample_projects/immune_function/config/PhysiCell_settings.xml
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Expand Up @@ -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>
Expand Down
3 changes: 1 addition & 2 deletions sample_projects/immune_function/main.cpp
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Expand Up @@ -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 */

Expand Down
1 change: 1 addition & 0 deletions sample_projects/interactions/config/PhysiCell_settings.xml
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Expand Up @@ -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>
Expand Down
3 changes: 1 addition & 2 deletions sample_projects/interactions/main.cpp
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Expand Up @@ -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 */

Expand Down
1 change: 1 addition & 0 deletions sample_projects/mechano/config/PhysiCell_settings.xml
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Expand Up @@ -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>
Expand Down
3 changes: 1 addition & 2 deletions sample_projects/mechano/main.cpp
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Expand Up @@ -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 */

Expand Down
1 change: 1 addition & 0 deletions sample_projects/physimess/config/PhysiCell_settings.xml
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Expand Up @@ -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>
Expand Down
3 changes: 1 addition & 2 deletions sample_projects/physimess/main.cpp
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Expand Up @@ -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 */

Expand Down
1 change: 1 addition & 0 deletions sample_projects/pred_prey_farmer/config/PhysiCell_settings.xml
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Expand Up @@ -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>
Expand Down
3 changes: 1 addition & 2 deletions sample_projects/pred_prey_farmer/main.cpp
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Expand Up @@ -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 */

Expand Down
1 change: 1 addition & 0 deletions sample_projects/rules_sample/config/PhysiCell_settings.xml
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Expand Up @@ -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>
Expand Down
3 changes: 1 addition & 2 deletions sample_projects/rules_sample/main.cpp
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Expand Up @@ -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 */

Expand Down
1 change: 1 addition & 0 deletions sample_projects/template/config/PhysiCell_settings.xml
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Expand Up @@ -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>
Expand Down
3 changes: 1 addition & 2 deletions sample_projects/template/main.cpp
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Expand Up @@ -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 */

Expand Down
1 change: 1 addition & 0 deletions sample_projects/virus_macrophage/config/PhysiCell_settings.xml
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Expand Up @@ -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>
Expand Down
3 changes: 1 addition & 2 deletions sample_projects/virus_macrophage/main.cpp
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Expand Up @@ -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 */

Expand Down
1 change: 1 addition & 0 deletions sample_projects/worm/config/PhysiCell_settings.xml
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Expand Up @@ -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>
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3 changes: 1 addition & 2 deletions sample_projects/worm/main.cpp
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Expand Up @@ -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 */

Expand Down
1 change: 1 addition & 0 deletions sample_projects_intracellular/ode/ode_energy/config/PhysiCell_settings.xml
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Expand Up @@ -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>
Expand Down
3 changes: 1 addition & 2 deletions sample_projects_intracellular/ode/ode_energy/main.cpp
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Expand Up @@ -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 */

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