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update sample projects to 1.14.0 #333

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update sample projects to 1.14.0 #333

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1,097 changes: 546 additions & 551 deletions sample_projects/biorobots/config/PhysiCell_settings.xml
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105 changes: 72 additions & 33 deletions sample_projects/cancer_biorobots/config/PhysiCell_settings.xml
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32 changes: 26 additions & 6 deletions sample_projects/custom_division/config/PhysiCell_settings.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,7 @@
<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>
<random_seed>0</random_seed>
</options>

<microenvironment_setup>
Expand Down Expand Up @@ -146,6 +147,7 @@
<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>
<maximum_number_of_attachments>12</maximum_number_of_attachments>
</mechanics>
<motility>
<speed units="micron/min">1</speed>
Expand Down Expand Up @@ -177,7 +179,9 @@
</substrate>
</secretion>
<cell_interactions>
<dead_phagocytosis_rate units="1/min">0</dead_phagocytosis_rate>
<apoptotic_phagocytosis_rate units="1/min">0</apoptotic_phagocytosis_rate>
<necrotic_phagocytosis_rate units="1/min">0</necrotic_phagocytosis_rate>
<other_dead_phagocytosis_rate units="1/min">0</other_dead_phagocytosis_rate>
<live_phagocytosis_rates>
<phagocytosis_rate name="default" units="1/min">0.0</phagocytosis_rate>
<phagocytosis_rate name="ctype1" units="1/min">0</phagocytosis_rate>
Expand All @@ -186,7 +190,8 @@
<attack_rate name="default" units="1/min">0.0</attack_rate>
<attack_rate name="ctype1" units="1/min">0</attack_rate>
</attack_rates>
<damage_rate units="1/min">1</damage_rate>
<attack_damage_rate units="1/min">1</attack_damage_rate>
<attack_duration units="min">0.1</attack_duration>
<fusion_rates>
<fusion_rate name="default" units="1/min">0.0</fusion_rate>
<fusion_rate name="ctype1" units="1/min">0</fusion_rate>
Expand All @@ -198,10 +203,16 @@
<transformation_rate name="ctype1" units="1/min">0</transformation_rate>
</transformation_rates>
</cell_transformations>
<cell_integrity>
<damage_rate units="1/min">0.0</damage_rate>
<damage_repair_rate units="1/min">0.0</damage_repair_rate>
</cell_integrity>
</phenotype>
<custom_data>
<oncoprotein conserved="false" units="dimensionless" description="">1.0</oncoprotein>
</custom_data>
<initial_parameter_distributions enabled="false">
</initial_parameter_distributions>
</cell_definition>
<cell_definition name="ctype1" ID="1">
<phenotype>
Expand Down Expand Up @@ -267,6 +278,7 @@
<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>
<maximum_number_of_attachments>12</maximum_number_of_attachments>
</mechanics>
<motility>
<speed units="micron/min">0.05</speed>
Expand Down Expand Up @@ -298,7 +310,9 @@
</substrate>
</secretion>
<cell_interactions>
<dead_phagocytosis_rate units="1/min">0</dead_phagocytosis_rate>
<apoptotic_phagocytosis_rate units="1/min">0</apoptotic_phagocytosis_rate>
<necrotic_phagocytosis_rate units="1/min">0</necrotic_phagocytosis_rate>
<other_dead_phagocytosis_rate units="1/min">0</other_dead_phagocytosis_rate>
<live_phagocytosis_rates>
<phagocytosis_rate name="default" units="1/min">0</phagocytosis_rate>
<phagocytosis_rate name="ctype1" units="1/min">0</phagocytosis_rate>
Expand All @@ -307,7 +321,8 @@
<attack_rate name="default" units="1/min">0</attack_rate>
<attack_rate name="ctype1" units="1/min">0</attack_rate>
</attack_rates>
<damage_rate units="1/min">1</damage_rate>
<attack_damage_rate units="1/min">1</attack_damage_rate>
<attack_duration units="min">0.1</attack_duration>
<fusion_rates>
<fusion_rate name="default" units="1/min">0</fusion_rate>
<fusion_rate name="ctype1" units="1/min">0</fusion_rate>
Expand All @@ -319,10 +334,16 @@
<transformation_rate name="ctype1" units="1/min">0</transformation_rate>
</transformation_rates>
</cell_transformations>
<cell_integrity>
<damage_rate units="1/min">0.0</damage_rate>
<damage_repair_rate units="1/min">0.0</damage_repair_rate>
</cell_integrity>
</phenotype>
<custom_data>
<oncoprotein conserved="false" units="dimensionless" description="">1.0</oncoprotein>
</custom_data>
<initial_parameter_distributions enabled="false">
</initial_parameter_distributions>
</cell_definition>
</cell_definitions>

Expand All @@ -343,7 +364,6 @@
</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)">0</number_of_cells>
</user_parameters>
</PhysiCell_settings>
</PhysiCell_settings>
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