Commit 4ce02d06 authored by gsaxena's avatar gsaxena
Browse files

Changed the project name of template to pred-prey-mpi, changed its directory...

Changed the project name of template to pred-prey-mpi, changed its directory name to pred_prey_mpi in sample_projects, made changes to sample_projects Makefile-default and in top-level directory Makefiles to reflect this. Did same for heterogeneity-sample --> heterogeneity-sample-mpi, heterogeneity_mpi directory, made changes to Makefile.
parent e059aedb
......@@ -62,8 +62,8 @@ all:
# sample projects
list-projects:
@echo "Sample projects: template2D template3D biorobots-sample cancer-biorobots-sample heterogeneity-sample"
@echo " cancer-immune-sample virus-macrophage-sample template pred-prey-farmer"
@echo "Sample projects: template2D template3D biorobots-sample cancer-biorobots-sample heterogeneity-sample-mpi"
@echo " cancer-immune-sample virus-macrophage-sample pred-prey-mpi pred-prey-farmer"
@echo ""
@echo "Sample intracellular projects: ode-energy-sample physiboss-cell-lines-sample cancer-metabolism-sample"
@echo "physiboss-cell-lines-mpi physiboss-tnf-model physiboss-tnf-model-mpi"
......@@ -88,14 +88,14 @@ template3D:
cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
cp ./sample_projects/template3D/config/* ./config/
template:
cp ./sample_projects/template/custom_modules/* ./custom_modules/
pred-prey-mpi:
cp ./sample_projects/pred_prey_mpi/custom_modules/* ./custom_modules/
touch main.cpp && cp main.cpp main-backup.cpp
cp ./sample_projects/template/main.cpp ./main.cpp
cp ./sample_projects/pred_prey_mpi/main.cpp ./main.cpp
cp Makefile Makefile-backup
cp ./sample_projects/template/Makefile .
cp ./sample_projects/pred_prey_mpi/Makefile .
cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
cp ./sample_projects/template/config/* ./config/
cp ./sample_projects/pred_prey_mpi/config/* ./config/
# sample projects
......@@ -117,14 +117,14 @@ cancer-biorobots-sample:
cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
cp ./sample_projects/cancer_biorobots/config/* ./config/
heterogeneity-sample:
cp ./sample_projects/heterogeneity/custom_modules/* ./custom_modules/
heterogeneity-sample-mpi:
cp ./sample_projects/heterogeneity_mpi/custom_modules/* ./custom_modules/
touch main.cpp && cp main.cpp main-backup.cpp
cp ./sample_projects/heterogeneity/main-heterogeneity.cpp ./main.cpp
cp ./sample_projects/heterogeneity_mpi/main-heterogeneity.cpp ./main.cpp
cp Makefile Makefile-backup
cp ./sample_projects/heterogeneity/Makefile .
cp ./sample_projects/heterogeneity_mpi/Makefile .
cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
cp ./sample_projects/heterogeneity/config/* ./config/
cp ./sample_projects/heterogeneity_mpi/config/* ./config/
cancer-immune-sample:
cp ./sample_projects/cancer_immune/custom_modules/* ./custom_modules/
......
......@@ -62,8 +62,8 @@ all:
# sample projects
list-projects:
@echo "Sample projects: template2D template3D biorobots-sample cancer-biorobots-sample heterogeneity-sample"
@echo " cancer-immune-sample virus-macrophage-sample template pred-prey-farmer"
@echo "Sample projects: template2D template3D biorobots-sample cancer-biorobots-sample heterogeneity-sample-mpi"
@echo " cancer-immune-sample virus-macrophage-sample pred-prey-mpi pred-prey-farmer"
@echo ""
@echo "Sample intracellular projects: ode-energy-sample physiboss-cell-lines-sample cancer-metabolism-sample"
@echo "physiboss-cell-lines-mpi physiboss-tnf-model physiboss-tnf-model-mpi"
......@@ -88,14 +88,14 @@ template3D:
cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
cp ./sample_projects/template3D/config/* ./config/
template:
cp ./sample_projects/template/custom_modules/* ./custom_modules/
pred-prey-mpi:
cp ./sample_projects/pred_prey_mpi/custom_modules/* ./custom_modules/
touch main.cpp && cp main.cpp main-backup.cpp
cp ./sample_projects/template/main.cpp ./main.cpp
cp ./sample_projects/pred_prey_mpi/main.cpp ./main.cpp
cp Makefile Makefile-backup
cp ./sample_projects/template/Makefile .
cp ./sample_projects/pred_prey_mpi/Makefile .
cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
cp ./sample_projects/template/config/* ./config/
cp ./sample_projects/pred_prey_mpi/config/* ./config/
# sample projects
......@@ -117,14 +117,14 @@ cancer-biorobots-sample:
cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
cp ./sample_projects/cancer_biorobots/config/* ./config/
heterogeneity-sample:
cp ./sample_projects/heterogeneity/custom_modules/* ./custom_modules/
heterogeneity-sample-mpi:
cp ./sample_projects/heterogeneity_mpi/custom_modules/* ./custom_modules/
touch main.cpp && cp main.cpp main-backup.cpp
cp ./sample_projects/heterogeneity/main-heterogeneity.cpp ./main.cpp
cp ./sample_projects/heterogeneity_mpi/main-heterogeneity.cpp ./main.cpp
cp Makefile Makefile-backup
cp ./sample_projects/heterogeneity/Makefile .
cp ./sample_projects/heterogeneity_mpi/Makefile .
cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
cp ./sample_projects/heterogeneity/config/* ./config/
cp ./sample_projects/heterogeneity_mpi/config/* ./config/
cancer-immune-sample:
cp ./sample_projects/cancer_immune/custom_modules/* ./custom_modules/
......
<?xml version="1.0" encoding="UTF-8"?>
<!--
/*
###############################################################################
# If you use PhysiCell in your project, please cite PhysiCell and the version #
# number, such as below: #
# #
# We implemented and solved the model using PhysiCell (Version x.y.z) [1]. #
# #
# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- #
# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 #
# DOI: 10.1371/journal.pcbi.1005991 #
# #
# See VERSION.txt or call get_PhysiCell_version() to get the current version #
# x.y.z. Call display_citations() to get detailed information on all cite-#
# able software used in your PhysiCell application. #
# #
# Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM #
# as below: #
# #
# We implemented and solved the model using PhysiCell (Version x.y.z) [1], #
# with BioFVM [2] to solve the transport equations. #
# #
# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- #
# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 #
# DOI: 10.1371/journal.pcbi.1005991 #
# #
# [2] A Ghaffarizadeh, SH Friedman, and P Macklin, BioFVM: an efficient para- #
# llelized diffusive transport solver for 3-D biological simulations, #
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
###############################################################################
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2018, Paul Macklin and the PhysiCell Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
# modification, are permitted provided that the following conditions are met: #
# #
# 1. Redistributions of source code must retain the above copyright notice, #
# this list of conditions and the following disclaimer. #
# #
# 2. Redistributions in binary form must reproduce the above copyright #
# notice, this list of conditions and the following disclaimer in the #
# documentation and/or other materials provided with the distribution. #
# #
# 3. Neither the name of the copyright holder nor the names of its #
# contributors may be used to endorse or promote products derived from this #
# software without specific prior written permission. #
# #
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" #
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE #
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE #
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE #
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR #
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF #
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS #
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN #
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) #
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE #
# POSSIBILITY OF SUCH DAMAGE. #
# #
###############################################################################
*/
-->
<!--
<user_details />
-->
<PhysiCell_settings version="devel-version">
<domain>
<x_min>-240</x_min>
<x_max>240</x_max>
<y_min>-240</y_min>
<y_max>240</y_max>
<z_min>-240</z_min>
<z_max>240</z_max>
<dx>20</dx>
<dy>20</dy>
<dz>20</dz>
<use_2D>false</use_2D>
</domain>
<overall>
<max_time units="min">720</max_time> <!-- 5 days * 24 h * 60 min -->
<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>2</omp_num_threads>
</parallel>
<save>
<folder>output</folder> <!-- use . for root -->
<full_data>
<interval units="min">120</interval>
<enable>true</enable>
</full_data>
<SVG>
<interval units="min">120</interval>
<enable>true</enable>
</SVG>
<legacy_data>
<enable>false</enable>
</legacy_data>
</save>
<microenvironment_setup>
<variable name="oxygen" units="mmHg" ID="0">
<physical_parameter_set>
<diffusion_coefficient units="micron^2/min">100000.00</diffusion_coefficient>
<decay_rate units="1/min">.1</decay_rate>
</physical_parameter_set>
<initial_condition units="mmHg">38.0</initial_condition>
<Dirichlet_boundary_condition units="mmHg" enabled="true">38.0</Dirichlet_boundary_condition>
</variable>
<options>
<calculate_gradients>false</calculate_gradients>
<track_internalized_substrates_in_each_agent>false</track_internalized_substrates_in_each_agent>
<!-- not yet supported -->
<initial_condition type="matlab" enabled="false">
<filename>./config/initial.mat</filename>
</initial_condition>
<!-- not yet supported -->
<dirichlet_nodes type="matlab" enabled="false">
<filename>./config/dirichlet.mat</filename>
</dirichlet_nodes>
</options>
</microenvironment_setup>
<user_parameters>
<tumor_radius type="double" units="micron">150.0</tumor_radius>
<oncoprotein_mean type="double" units="dimensionless">1.0</oncoprotein_mean>
<oncoprotein_sd type="double" units="dimensionless">0.25</oncoprotein_sd>
<oncoprotein_min type="double" units="dimensionless">0.0</oncoprotein_min>
<oncoprotein_max type="double" units="dimensionless">2</oncoprotein_max>
<random_seed type="int" units="dimensionless">0</random_seed>
</user_parameters>
</PhysiCell_settings>
<?xml version="1.0" encoding="UTF-8"?>
<!--
/*
###############################################################################
# If you use PhysiCell in your project, please cite PhysiCell and the version #
# number, such as below: #
# #
# We implemented and solved the model using PhysiCell (Version x.y.z) [1]. #
# #
# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- #
# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 #
# DOI: 10.1371/journal.pcbi.1005991 #
# #
# See VERSION.txt or call get_PhysiCell_version() to get the current version #
# x.y.z. Call display_citations() to get detailed information on all cite-#
# able software used in your PhysiCell application. #
# #
# Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM #
# as below: #
# #
# We implemented and solved the model using PhysiCell (Version x.y.z) [1], #
# with BioFVM [2] to solve the transport equations. #
# #
# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- #
# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 #
# DOI: 10.1371/journal.pcbi.1005991 #
# #
# [2] A Ghaffarizadeh, SH Friedman, and P Macklin, BioFVM: an efficient para- #
# llelized diffusive transport solver for 3-D biological simulations, #
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
###############################################################################
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2018, Paul Macklin and the PhysiCell Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
# modification, are permitted provided that the following conditions are met: #
# #
# 1. Redistributions of source code must retain the above copyright notice, #
# this list of conditions and the following disclaimer. #
# #
# 2. Redistributions in binary form must reproduce the above copyright #
# notice, this list of conditions and the following disclaimer in the #
# documentation and/or other materials provided with the distribution. #
# #
# 3. Neither the name of the copyright holder nor the names of its #
# contributors may be used to endorse or promote products derived from this #
# software without specific prior written permission. #
# #
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" #
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE #
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE #
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE #
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR #
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF #
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS #
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN #
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) #
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE #
# POSSIBILITY OF SUCH DAMAGE. #
# #
###############################################################################
*/
-->
<!--
<user_details />
-->
<PhysiCell_settings version="devel-version">
<domain>
<x_min>-240</x_min>
<x_max>240</x_max>
<y_min>-240</y_min>
<y_max>240</y_max>
<z_min>-240</z_min>
<z_max>240</z_max>
<dx>20</dx>
<dy>20</dy>
<dz>20</dz>
<use_2D>false</use_2D>
</domain>
<overall>
<max_time units="min">720</max_time> <!-- 5 days * 24 h * 60 min -->
<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>2</omp_num_threads>
</parallel>
<save>
<folder>output</folder> <!-- use . for root -->
<full_data>
<interval units="min">120</interval>
<enable>true</enable>
</full_data>
<SVG>
<interval units="min">120</interval>
<enable>true</enable>
</SVG>
<legacy_data>
<enable>false</enable>
</legacy_data>
</save>
<microenvironment_setup>
<variable name="oxygen" units="mmHg" ID="0">
<physical_parameter_set>
<diffusion_coefficient units="micron^2/min">100000.00</diffusion_coefficient>
<decay_rate units="1/min">.1</decay_rate>
</physical_parameter_set>
<initial_condition units="mmHg">38.0</initial_condition>
<Dirichlet_boundary_condition units="mmHg" enabled="true">38.0</Dirichlet_boundary_condition>
</variable>
<options>
<calculate_gradients>false</calculate_gradients>
<track_internalized_substrates_in_each_agent>false</track_internalized_substrates_in_each_agent>
<!-- not yet supported -->
<initial_condition type="matlab" enabled="false">
<filename>./config/initial.mat</filename>
</initial_condition>
<!-- not yet supported -->
<dirichlet_nodes type="matlab" enabled="false">
<filename>./config/dirichlet.mat</filename>
</dirichlet_nodes>
</options>
</microenvironment_setup>
<user_parameters>
<tumor_radius type="double" units="micron">150.0</tumor_radius>
<oncoprotein_mean type="double" units="dimensionless">1.0</oncoprotein_mean>
<oncoprotein_sd type="double" units="dimensionless">0.25</oncoprotein_sd>
<oncoprotein_min type="double" units="dimensionless">0.0</oncoprotein_min>
<oncoprotein_max type="double" units="dimensionless">2</oncoprotein_max>
<random_seed type="int" units="dimensionless">0</random_seed>
</user_parameters>
</PhysiCell_settings>
<?xml version="1.0" encoding="UTF-8"?>
<!--
/*
###############################################################################
# If you use PhysiCell in your project, please cite PhysiCell and the version #
# number, such as below: #
# #
# We implemented and solved the model using PhysiCell (Version x.y.z) [1]. #
# #
# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- #
# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 #
# DOI: 10.1371/journal.pcbi.1005991 #
# #
# See VERSION.txt or call get_PhysiCell_version() to get the current version #
# x.y.z. Call display_citations() to get detailed information on all cite-#
# able software used in your PhysiCell application. #
# #
# Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM #
# as below: #
# #
# We implemented and solved the model using PhysiCell (Version x.y.z) [1], #
# with BioFVM [2] to solve the transport equations. #
# #
# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- #
# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 #
# DOI: 10.1371/journal.pcbi.1005991 #
# #
# [2] A Ghaffarizadeh, SH Friedman, and P Macklin, BioFVM: an efficient para- #
# llelized diffusive transport solver for 3-D biological simulations, #
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
###############################################################################
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2018, Paul Macklin and the PhysiCell Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
# modification, are permitted provided that the following conditions are met: #
# #
# 1. Redistributions of source code must retain the above copyright notice, #
# this list of conditions and the following disclaimer. #
# #
# 2. Redistributions in binary form must reproduce the above copyright #
# notice, this list of conditions and the following disclaimer in the #
# documentation and/or other materials provided with the distribution. #
# #
# 3. Neither the name of the copyright holder nor the names of its #
# contributors may be used to endorse or promote products derived from this #
# software without specific prior written permission. #
# #
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" #
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE #
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE #
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE #
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR #
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF #
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS #
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN #
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) #
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE #
# POSSIBILITY OF SUCH DAMAGE. #
# #
###############################################################################
*/
-->
<!--
<user_details />
-->
<PhysiCell_settings version="devel-version">
<domain>
<!-- <x_min>-2700</x_min> -->
<!-- <x_max>2700</x_max> -->
<!-- <y_min>-600</y_min> -->
<!-- <y_max>600</y_max> -->
<!-- <z_min>-600</z_min> -->
<!-- <z_max>600</z_max> -->
<x_min>-3000</x_min>
<x_max>3000</x_max>
<y_min>-1000</y_min>
<y_max>1000</y_max>
<z_min>-1000</z_min>
<z_max>1000</z_max>
<dx>20</dx>
<dy>20</dy>
<dz>20</dz>
<use_2D>false</use_2D>
</domain>
<overall>
<max_time units="min">8000</max_time> <!-- 1400 -->
<time_units>min</time_units>
<space_units>micron</space_units>
<dt_diffusion units="min">0.02</dt_diffusion>
<dt_mechanics units="min">0.1</dt_mechanics>
<dt_phenotype units="min">2</dt_phenotype>
</overall>
<parallel>
<omp_num_threads>1</omp_num_threads>
</parallel>
<save>
<folder>output</folder> <!-- use . for root -->
<full_data>
<interval units="min">100</interval>
<enable>false</enable>
</full_data>
<SVG>
<interval units="min">100</interval>
<enable>true</enable>
</SVG>
<legacy_data>
<enable>false</enable>
</legacy_data>
</save>
<microenvironment_setup>
<variable name="oxygen" units="mmHg" ID="0">
<physical_parameter_set>
<diffusion_coefficient units="micron^2/min">100000.0</diffusion_coefficient>
<decay_rate units="1/min">.1</decay_rate>
</physical_parameter_set>
<initial_condition units="mmHg">38.0</initial_condition>
<Dirichlet_boundary_condition units="mmHg" enabled="true">38.0</Dirichlet_boundary_condition>
</variable>
<variable name="tnf" units="TNF/um^3" ID="1">
<physical_parameter_set>
<diffusion_coefficient units="micron^2/min">1200.0</diffusion_coefficient>
<decay_rate units="1/min">.0275</decay_rate>
</physical_parameter_set>
<initial_condition units="molecules/voxel">0.0</initial_condition>
<Dirichlet_boundary_condition units="molecules/voxel" enabled="false">0.0</Dirichlet_boundary_condition>
</variable>
<options>
<calculate_gradients>true</calculate_gradients>
<track_internalized_substrates_in_each_agent>true</track_internalized_substrates_in_each_agent>
<!-- not yet supported -->
<initial_condition type="matlab" enabled="false">
<filename>./config/initial.mat</filename>
</initial_condition>
<!-- not yet supported -->
<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="5" name="live_cells_cycle_model">
<!-- using higher than normal significant digits to match divisions in default code -->
<phase_transition_rates units="1/min">
<!-- Cycle duration -->
<rate start_index="0" end_index="0" fixed_duration="false">0.00075</rate>
</phase_transition_rates>
</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>
<!--
<phase_transition_rates units="1/min">
<rate start_index="0" end_index="1" fixed_duration="false">0.00193798</rate>
</phase_transition_rates> -->
<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">
<rate units="1/min">0.0</rate>
<phase_durations units="min">
<duration index="0" fixed_duration="true">0</duration>
<duration index="1" fixed_duration="true">86400</duration>
</phase_durations>
<!--
<transition_rates units="1/min">
<rate start_index="0" end_index="1" fixed_duration="false">9e9</rate>
<rate start_index="1" end_index="2" fixed_duration="true">1.15741e-5</rate>
</transition_rates>
-->
<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>