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config.xml
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config.xml
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<PhysiCell_settings version="devel-version">
<domain>
<x_min>-500</x_min>
<x_max>500</x_max>
<y_min>-500</y_min>
<y_max>500</y_max>
<z_min>-10</z_min>
<z_max>10</z_max>
<dx>20</dx>
<dy>20</dy>
<dz>20</dz>
<use_2D>true</use_2D>
</domain>
<overall>
<max_time units="min">7200</max_time>
<time_units>min</time_units>
<space_units>micron</space_units>
<dt_diffusion units="min">0.01</dt_diffusion>
<dt_mechanics units="min">0.1</dt_mechanics>
<dt_phenotype units="min">6</dt_phenotype>
</overall>
<parallel>
<omp_num_threads>4</omp_num_threads>
</parallel>
<save>
<folder>tmpdir</folder>
<full_data>
<interval units="min">60</interval>
<enable>true</enable>
</full_data>
<SVG>
<interval units="min">60</interval>
<enable>true</enable>
</SVG>
<legacy_data>
<enable>false</enable>
</legacy_data>
</save>
<options>
<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>
</options>
<microenvironment_setup>
<variable name="substrate" units="dimensionless" ID="0">
<physical_parameter_set>
<diffusion_coefficient units="micron^2/min">100000.0</diffusion_coefficient>
<decay_rate units="1/min">10</decay_rate>
</physical_parameter_set>
<initial_condition units="mmHg">0</initial_condition>
<Dirichlet_boundary_condition units="mmHg" enabled="True">0</Dirichlet_boundary_condition>
<Dirichlet_options>
<boundary_value ID="xmin" enabled="True">0</boundary_value>
<boundary_value ID="xmax" enabled="True">0</boundary_value>
<boundary_value ID="ymin" enabled="True">0</boundary_value>
<boundary_value ID="ymax" enabled="True">0</boundary_value>
<boundary_value ID="zmin" enabled="True">0</boundary_value>
<boundary_value ID="zmax" enabled="True">0</boundary_value>
</Dirichlet_options>
</variable>
<options>
<calculate_gradients>true</calculate_gradients>
<track_internalized_substrates_in_each_agent>true</track_internalized_substrates_in_each_agent>
<initial_condition type="matlab" enabled="false">
<filename>./config/initial.mat</filename>
</initial_condition>
<dirichlet_nodes type="matlab" enabled="false">
<filename>./config/dirichlet.mat</filename>
</dirichlet_nodes>
</options>
</microenvironment_setup>
<cell_definitions>
<cell_definition name="default" ID="0">
<phenotype>
<cycle code="6" name="Flow cytometry model (separated)">
<phase_durations units="min">
<duration index="0" fixed_duration="false">300.0</duration>
<duration index="1" fixed_duration="true">480</duration>
<duration index="2" fixed_duration="true">240</duration>
<duration index="3" fixed_duration="true">60</duration>
</phase_durations>
</cycle>
<death>
<model code="100" name="apoptosis">
<death_rate units="1/min">5.31667e-05</death_rate>
<phase_durations units="min">
<duration index="0" fixed_duration="true">516</duration>
</phase_durations>
<parameters>
<unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
<lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
<cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
<nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
<calcification_rate units="1/min">0</calcification_rate>
<relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
</parameters>
</model>
<model code="101" name="necrosis">
<death_rate units="1/min">0.0</death_rate>
<phase_durations units="min">
<duration index="0" fixed_duration="true">0</duration>
<duration index="1" fixed_duration="true">86400</duration>
</phase_durations>
<parameters>
<unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
<lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
<cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
<nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
<calcification_rate units="1/min">0</calcification_rate>
<relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
</parameters>
</model>
</death>
<volume>
<total units="micron^3">2494</total>
<fluid_fraction units="dimensionless">0.75</fluid_fraction>
<nuclear units="micron^3">540</nuclear>
<fluid_change_rate units="1/min">0.05</fluid_change_rate>
<cytoplasmic_biomass_change_rate units="1/min">0.0045</cytoplasmic_biomass_change_rate>
<nuclear_biomass_change_rate units="1/min">0.0055</nuclear_biomass_change_rate>
<calcified_fraction units="dimensionless">0</calcified_fraction>
<calcification_rate units="1/min">0</calcification_rate>
<relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
</volume>
<mechanics>
<cell_cell_adhesion_strength units="micron/min">0.4</cell_cell_adhesion_strength>
<cell_cell_repulsion_strength units="micron/min">10.0</cell_cell_repulsion_strength>
<relative_maximum_adhesion_distance units="dimensionless">1.25</relative_maximum_adhesion_distance>
<cell_adhesion_affinities>
<cell_adhesion_affinity name="default">1.0</cell_adhesion_affinity>
</cell_adhesion_affinities>
<options>
<set_relative_equilibrium_distance enabled="false" units="dimensionless">1.8</set_relative_equilibrium_distance>
<set_absolute_equilibrium_distance enabled="false" units="micron">15.12</set_absolute_equilibrium_distance>
</options>
<cell_BM_adhesion_strength units="micron/min">4.0</cell_BM_adhesion_strength>
<cell_BM_repulsion_strength units="micron/min">10.0</cell_BM_repulsion_strength>
<attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
<attachment_rate units="1/min">0.0</attachment_rate>
<detachment_rate units="1/min">0.0</detachment_rate>
</mechanics>
<motility>
<speed units="micron/min">1</speed>
<persistence_time units="min">1</persistence_time>
<migration_bias units="dimensionless">.5</migration_bias>
<options>
<enabled>false</enabled>
<use_2D>true</use_2D>
<chemotaxis>
<enabled>false</enabled>
<substrate>substrate</substrate>
<direction>1</direction>
</chemotaxis>
<advanced_chemotaxis>
<enabled>false</enabled>
<normalize_each_gradient>false</normalize_each_gradient>
<chemotactic_sensitivities>
<chemotactic_sensitivity substrate="substrate">0.0</chemotactic_sensitivity>
</chemotactic_sensitivities>
</advanced_chemotaxis>
</options>
</motility>
<secretion>
<substrate name="substrate">
<secretion_rate units="1/min">0</secretion_rate>
<secretion_target units="substrate density">1</secretion_target>
<uptake_rate units="1/min">0</uptake_rate>
<net_export_rate units="total substrate/min">0</net_export_rate>
</substrate>
</secretion>
<cell_interactions>
<dead_phagocytosis_rate units="1/min">0.0</dead_phagocytosis_rate>
<live_phagocytosis_rates>
<phagocytosis_rate name="default" units="1/min">0.0</phagocytosis_rate>
</live_phagocytosis_rates>
<attack_rates>
<attack_rate name="default" units="1/min">0.0</attack_rate>
</attack_rates>
<damage_rate units="1/min">1.0</damage_rate>
<fusion_rates>
<fusion_rate name="default" units="1/min">0.0</fusion_rate>
</fusion_rates>
</cell_interactions>
<cell_transformations>
<transformation_rates>
<transformation_rate name="default" units="1/min">0.0</transformation_rate>
</transformation_rates>
</cell_transformations>
</phenotype>
<custom_data>
<sample conserved="false" units="dimensionless" description="">1.0</sample>
</custom_data>
</cell_definition>
</cell_definitions>
<initial_conditions>
<cell_positions type="csv" enabled="false">
<folder>.</folder>
<filename>mycells.csv</filename>
</cell_positions>
</initial_conditions>
<cell_rules>
<rulesets>
<ruleset protocol="CBHG" version="2.0" format="csv" enabled="true">
<folder>.</folder>
<filename>rules.csv</filename>
</ruleset>
</rulesets>
<settings />
</cell_rules>
<user_parameters>
<random_seed type="int" units="dimensionless" description="">0</random_seed>
<number_of_cells type="int" units="none" description="initial number of cells (for each cell type)">5</number_of_cells>
</user_parameters>
</PhysiCell_settings>