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PhysiCell_settings.xml
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PhysiCell_settings.xml
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<PhysiCell_settings version="devel-version">
<domain>
<x_min>-1000</x_min>
<x_max>1000</x_max>
<y_min>-1000</y_min>
<y_max>1000</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">1220</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>output</folder>
<full_data>
<interval units="min">2</interval>
<enable>true</enable>
</full_data>
<SVG>
<interval units="min">2</interval>
<enable>true</enable>
</SVG>
<legacy_data>
<enable>false</enable>
</legacy_data>
</save>
<microenvironment_setup>
<variable name="director signal" units="dimensionless" ID="0">
<physical_parameter_set>
<diffusion_coefficient units="micron^2/min">1000</diffusion_coefficient>
<decay_rate units="1/min">.1</decay_rate>
</physical_parameter_set>
<initial_condition units="dimensionless">0</initial_condition>
<Dirichlet_boundary_condition units="dimensionless" enabled="false">1</Dirichlet_boundary_condition>
</variable>
<variable name="cargo signal" units="dimensionless" ID="1">
<physical_parameter_set>
<diffusion_coefficient units="micron^2/min">1000</diffusion_coefficient>
<decay_rate units="1/min">.4</decay_rate>
</physical_parameter_set>
<initial_condition units="dimensionless">0</initial_condition>
<Dirichlet_boundary_condition units="dimensionless" enabled="false">1</Dirichlet_boundary_condition>
</variable>
<options>
<calculate_gradients>true</calculate_gradients>
<track_internalized_substrates_in_each_agent>false</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>
<user_parameters>
<random_seed type="int" units="dimensionless">0</random_seed>
<cargo_signal_D type="double" units="micron/min^2">1e3</cargo_signal_D>
<cargo_signal_decay type="double" units="1/min">.4</cargo_signal_decay>
<director_signal_D type="double" units="micron/min^2">1e3</director_signal_D>
<director_signal_decay type="double" units="1/min">.1</director_signal_decay>
<elastic_coefficient type="double" units="1/min">0.05</elastic_coefficient>
<worker_motility_persistence_time type="double" units="min">5.0</worker_motility_persistence_time>
<worker_migration_speed type="double" units="micron/min">5.0</worker_migration_speed>
<attached_worker_migration_bias type="double" units="dimensionless">1.0</attached_worker_migration_bias>
<unattached_worker_migration_bias type="double" units="dimensionless">0.5</unattached_worker_migration_bias>
<number_of_directors type="int" units="none">15</number_of_directors>
<number_of_cargo_clusters type="int" units="none">100</number_of_cargo_clusters>
<number_of_workers type="int" units="none">50</number_of_workers>
<drop_threshold type="double" units="dimensionless">0.4</drop_threshold>
<worker_color type="string" units="none">red</worker_color>
<cargo_color type="string" units="none">blue</cargo_color>
<director_color type="string" units="none">limegreen</director_color>
</user_parameters>
</PhysiCell_settings>