Commit 0e543ced authored by Arnau Montagud's avatar Arnau Montagud
Browse files

fixing heterogeneity cell definitions, removing hidden files from MacOS

parent 7d507970
VERSION := $(shell grep . VERSION.txt | cut -f1 -d:)
PROGRAM_NAME := heterogeneity.exe
CC := mpic++
# CC := g++-mp-7 # typical macports compiler name
# CC := g++-7 # typical homebrew compiler name
# Check for environment definitions of compiler
# e.g., on CC = g++-7 on OSX
ifdef PHYSICELL_CPP
CC := $(PHYSICELL_CPP)
endif
ARCH := native # best auto-tuning
# ARCH := core2 # a reasonably safe default for most CPUs since 2007
# ARCH := corei7
# ARCH := corei7-avx # earlier i7
# ARCH := core-avx-i # i7 ivy bridge or newer
# ARCH := core-avx2 # i7 with Haswell or newer
# ARCH := nehalem
# ARCH := westmere
# ARCH := sandybridge # circa 2011
# ARCH := ivybridge # circa 2012
# ARCH := haswell # circa 2013
# ARCH := broadwell # circa 2014
# ARCH := skylake # circa 2015
# ARCH := bonnell
# ARCH := silvermont
# ARCH := skylake-avx512
# ARCH := nocona #64-bit pentium 4 or later
# CFLAGS := -march=$(ARCH) -Ofast -s -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11
CFLAGS := -march=$(ARCH) -O3 -fomit-frame-pointer -mfpmath=both -m64 -std=c++11 -g -fopenmp
COMPILE_COMMAND := $(CC) $(CFLAGS)
DistPhy_OBJECTS:= DistPhy_Environment.o DistPhy_Cartesian.o DistPhy_Utils.o DistPhy_Collective.o
BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o \
BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o
PhysiCell_core_OBJECTS := PhysiCell_phenotype.o PhysiCell_cell_container.o PhysiCell_standard_models.o PhysiCell_cell.o PhysiCell_custom.o PhysiCell_utilities.o PhysiCell_constants.o
PhysiCell_module_OBJECTS := PhysiCell_SVG.o PhysiCell_pathology.o PhysiCell_MultiCellDS.o PhysiCell_various_outputs.o \
PhysiCell_pugixml.o PhysiCell_settings.o
# put your custom objects here (they should be in the custom_modules directory)
PhysiCell_custom_module_OBJECTS := heterogeneity.o
pugixml_OBJECTS := pugixml.o
PhysiCell_OBJECTS := $(BioFVM_OBJECTS) $(pugixml_OBJECTS) $(PhysiCell_core_OBJECTS) $(PhysiCell_module_OBJECTS) $(DistPhy_OBJECTS)
ALL_OBJECTS := $(PhysiCell_OBJECTS) $(PhysiCell_custom_module_OBJECTS)
# compile the project
all: main.cpp $(ALL_OBJECTS)
$(COMPILE_COMMAND) -o $(PROGRAM_NAME) $(ALL_OBJECTS) main.cpp
# PhysiCell core components
DistPhy_Environment.o: ./DistPhy/DistPhy_Environment.cpp
$(COMPILE_COMMAND) -c ./DistPhy/DistPhy_Environment.cpp
DistPhy_Cartesian.o: ./DistPhy/DistPhy_Cartesian.cpp
$(COMPILE_COMMAND) -c ./DistPhy/DistPhy_Cartesian.cpp
DistPhy_Utils.o: ./DistPhy/DistPhy_Utils.cpp
$(COMPILE_COMMAND) -c ./DistPhy/DistPhy_Utils.cpp
DistPhy_Collective.o: ./DistPhy/DistPhy_Collective.cpp
$(COMPILE_COMMAND) -c ./DistPhy/DistPhy_Collective.cpp
PhysiCell_phenotype.o: ./core/PhysiCell_phenotype.cpp
$(COMPILE_COMMAND) -c ./core/PhysiCell_phenotype.cpp
PhysiCell_digital_cell_line.o: ./core/PhysiCell_digital_cell_line.cpp
$(COMPILE_COMMAND) -c ./core/PhysiCell_digital_cell_line.cpp
PhysiCell_cell.o: ./core/PhysiCell_cell.cpp
$(COMPILE_COMMAND) -c ./core/PhysiCell_cell.cpp
PhysiCell_cell_container.o: ./core/PhysiCell_cell_container.cpp
$(COMPILE_COMMAND) -c ./core/PhysiCell_cell_container.cpp
PhysiCell_standard_models.o: ./core/PhysiCell_standard_models.cpp
$(COMPILE_COMMAND) -c ./core/PhysiCell_standard_models.cpp
PhysiCell_utilities.o: ./core/PhysiCell_utilities.cpp
$(COMPILE_COMMAND) -c ./core/PhysiCell_utilities.cpp
PhysiCell_custom.o: ./core/PhysiCell_custom.cpp
$(COMPILE_COMMAND) -c ./core/PhysiCell_custom.cpp
PhysiCell_constants.o: ./core/PhysiCell_constants.cpp
$(COMPILE_COMMAND) -c ./core/PhysiCell_constants.cpp
# BioFVM core components (needed by PhysiCell)
BioFVM_vector.o: ./BioFVM/BioFVM_vector.cpp
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_vector.cpp
BioFVM_agent_container.o: ./BioFVM/BioFVM_agent_container.cpp
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_agent_container.cpp
BioFVM_mesh.o: ./BioFVM/BioFVM_mesh.cpp
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_mesh.cpp
BioFVM_microenvironment.o: ./BioFVM/BioFVM_microenvironment.cpp
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_microenvironment.cpp
BioFVM_solvers.o: ./BioFVM/BioFVM_solvers.cpp
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_solvers.cpp
BioFVM_utilities.o: ./BioFVM/BioFVM_utilities.cpp
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_utilities.cpp
BioFVM_basic_agent.o: ./BioFVM/BioFVM_basic_agent.cpp
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_basic_agent.cpp
BioFVM_matlab.o: ./BioFVM/BioFVM_matlab.cpp
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_matlab.cpp
BioFVM_MultiCellDS.o: ./BioFVM/BioFVM_MultiCellDS.cpp
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_MultiCellDS.cpp
pugixml.o: ./BioFVM/pugixml.cpp
$(COMPILE_COMMAND) -c ./BioFVM/pugixml.cpp
# standard PhysiCell modules
PhysiCell_SVG.o: ./modules/PhysiCell_SVG.cpp
$(COMPILE_COMMAND) -c ./modules/PhysiCell_SVG.cpp
PhysiCell_pathology.o: ./modules/PhysiCell_pathology.cpp
$(COMPILE_COMMAND) -c ./modules/PhysiCell_pathology.cpp
PhysiCell_MultiCellDS.o: ./modules/PhysiCell_MultiCellDS.cpp
$(COMPILE_COMMAND) -c ./modules/PhysiCell_MultiCellDS.cpp
PhysiCell_various_outputs.o: ./modules/PhysiCell_various_outputs.cpp
$(COMPILE_COMMAND) -c ./modules/PhysiCell_various_outputs.cpp
PhysiCell_pugixml.o: ./modules/PhysiCell_pugixml.cpp
$(COMPILE_COMMAND) -c ./modules/PhysiCell_pugixml.cpp
PhysiCell_settings.o: ./modules/PhysiCell_settings.cpp
$(COMPILE_COMMAND) -c ./modules/PhysiCell_settings.cpp
# user-defined PhysiCell modules
heterogeneity.o: ./custom_modules/heterogeneity.cpp
$(COMPILE_COMMAND) -c ./custom_modules/heterogeneity.cpp
# cleanup
reset:
rm -f *.cpp
cp ./sample_projects/Makefile-default Makefile
rm -f ./custom_modules/*
touch ./custom_modules/empty.txt
touch ALL_CITATIONS.txt
rm ALL_CITATIONS.txt
cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml
clean:
rm -f *.o
rm -f $(PROGRAM_NAME)*
data-cleanup:
rm -f *.mat
rm -f *.xml
rm -f *.svg
rm -f ./output/*
touch ./output/empty.txt
# archival
checkpoint:
zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/*
zip:
zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/*
cp latest.zip $$(date +%b_%d_%Y_%H%M).zip
cp latest.zip VERSION_$(VERSION).zip
mv *.zip archives/
tar:
tar --ignore-failed-read -czf latest.tar Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/*
cp latest.tar $$(date +%b_%d_%Y_%H%M).tar
cp latest.tar VERSION_$(VERSION).tar
mv *.tar archives/
unzip:
cp ./archives/latest.zip .
unzip latest.zip
untar:
cp ./archives/latest.tar .
tar -xzf latest.tar
VERSION := $(shell grep . VERSION.txt | cut -f1 -d:)
PROGRAM_NAME := heterogeneity.exe
CC := mpic++
# CC := g++-mp-7 # typical macports compiler name
# CC := g++-7 # typical homebrew compiler name
# Check for environment definitions of compiler
# e.g., on CC = g++-7 on OSX
ifdef PHYSICELL_CPP
CC := $(PHYSICELL_CPP)
endif
ARCH := native # best auto-tuning
# ARCH := core2 # a reasonably safe default for most CPUs since 2007
# ARCH := corei7
# ARCH := corei7-avx # earlier i7
# ARCH := core-avx-i # i7 ivy bridge or newer
# ARCH := core-avx2 # i7 with Haswell or newer
# ARCH := nehalem
# ARCH := westmere
# ARCH := sandybridge # circa 2011
# ARCH := ivybridge # circa 2012
# ARCH := haswell # circa 2013
# ARCH := broadwell # circa 2014
# ARCH := skylake # circa 2015
# ARCH := bonnell
# ARCH := silvermont
# ARCH := skylake-avx512
# ARCH := nocona #64-bit pentium 4 or later
# CFLAGS := -march=$(ARCH) -Ofast -s -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11
CFLAGS := -march=$(ARCH) -O3 -fomit-frame-pointer -mfpmath=both -m64 -std=c++11 -g -fopenmp
COMPILE_COMMAND := $(CC) $(CFLAGS)
DistPhy_OBJECTS:= DistPhy_Environment.o DistPhy_Cartesian.o DistPhy_Utils.o DistPhy_Collective.o
BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o \
BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o
PhysiCell_core_OBJECTS := PhysiCell_phenotype.o PhysiCell_cell_container.o PhysiCell_standard_models.o PhysiCell_cell.o PhysiCell_custom.o PhysiCell_utilities.o PhysiCell_constants.o
PhysiCell_module_OBJECTS := PhysiCell_SVG.o PhysiCell_pathology.o PhysiCell_MultiCellDS.o PhysiCell_various_outputs.o \
PhysiCell_pugixml.o PhysiCell_settings.o
# put your custom objects here (they should be in the custom_modules directory)
PhysiCell_custom_module_OBJECTS := heterogeneity.o
pugixml_OBJECTS := pugixml.o
PhysiCell_OBJECTS := $(BioFVM_OBJECTS) $(pugixml_OBJECTS) $(PhysiCell_core_OBJECTS) $(PhysiCell_module_OBJECTS) $(DistPhy_OBJECTS)
ALL_OBJECTS := $(PhysiCell_OBJECTS) $(PhysiCell_custom_module_OBJECTS)
# compile the project
all: main.cpp $(ALL_OBJECTS)
$(COMPILE_COMMAND) -o $(PROGRAM_NAME) $(ALL_OBJECTS) main.cpp
# PhysiCell core components
DistPhy_Environment.o: ./DistPhy/DistPhy_Environment.cpp
$(COMPILE_COMMAND) -c ./DistPhy/DistPhy_Environment.cpp
DistPhy_Cartesian.o: ./DistPhy/DistPhy_Cartesian.cpp
$(COMPILE_COMMAND) -c ./DistPhy/DistPhy_Cartesian.cpp
DistPhy_Utils.o: ./DistPhy/DistPhy_Utils.cpp
$(COMPILE_COMMAND) -c ./DistPhy/DistPhy_Utils.cpp
DistPhy_Collective.o: ./DistPhy/DistPhy_Collective.cpp
$(COMPILE_COMMAND) -c ./DistPhy/DistPhy_Collective.cpp
PhysiCell_phenotype.o: ./core/PhysiCell_phenotype.cpp
$(COMPILE_COMMAND) -c ./core/PhysiCell_phenotype.cpp
PhysiCell_digital_cell_line.o: ./core/PhysiCell_digital_cell_line.cpp
$(COMPILE_COMMAND) -c ./core/PhysiCell_digital_cell_line.cpp
PhysiCell_cell.o: ./core/PhysiCell_cell.cpp
$(COMPILE_COMMAND) -c ./core/PhysiCell_cell.cpp
PhysiCell_cell_container.o: ./core/PhysiCell_cell_container.cpp
$(COMPILE_COMMAND) -c ./core/PhysiCell_cell_container.cpp
PhysiCell_standard_models.o: ./core/PhysiCell_standard_models.cpp
$(COMPILE_COMMAND) -c ./core/PhysiCell_standard_models.cpp
PhysiCell_utilities.o: ./core/PhysiCell_utilities.cpp
$(COMPILE_COMMAND) -c ./core/PhysiCell_utilities.cpp
PhysiCell_custom.o: ./core/PhysiCell_custom.cpp
$(COMPILE_COMMAND) -c ./core/PhysiCell_custom.cpp
PhysiCell_constants.o: ./core/PhysiCell_constants.cpp
$(COMPILE_COMMAND) -c ./core/PhysiCell_constants.cpp
# BioFVM core components (needed by PhysiCell)
BioFVM_vector.o: ./BioFVM/BioFVM_vector.cpp
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_vector.cpp
BioFVM_agent_container.o: ./BioFVM/BioFVM_agent_container.cpp
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_agent_container.cpp
BioFVM_mesh.o: ./BioFVM/BioFVM_mesh.cpp
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_mesh.cpp
BioFVM_microenvironment.o: ./BioFVM/BioFVM_microenvironment.cpp
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_microenvironment.cpp
BioFVM_solvers.o: ./BioFVM/BioFVM_solvers.cpp
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_solvers.cpp
BioFVM_utilities.o: ./BioFVM/BioFVM_utilities.cpp
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_utilities.cpp
BioFVM_basic_agent.o: ./BioFVM/BioFVM_basic_agent.cpp
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_basic_agent.cpp
BioFVM_matlab.o: ./BioFVM/BioFVM_matlab.cpp
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_matlab.cpp
BioFVM_MultiCellDS.o: ./BioFVM/BioFVM_MultiCellDS.cpp
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_MultiCellDS.cpp
pugixml.o: ./BioFVM/pugixml.cpp
$(COMPILE_COMMAND) -c ./BioFVM/pugixml.cpp
# standard PhysiCell modules
PhysiCell_SVG.o: ./modules/PhysiCell_SVG.cpp
$(COMPILE_COMMAND) -c ./modules/PhysiCell_SVG.cpp
PhysiCell_pathology.o: ./modules/PhysiCell_pathology.cpp
$(COMPILE_COMMAND) -c ./modules/PhysiCell_pathology.cpp
PhysiCell_MultiCellDS.o: ./modules/PhysiCell_MultiCellDS.cpp
$(COMPILE_COMMAND) -c ./modules/PhysiCell_MultiCellDS.cpp
PhysiCell_various_outputs.o: ./modules/PhysiCell_various_outputs.cpp
$(COMPILE_COMMAND) -c ./modules/PhysiCell_various_outputs.cpp
PhysiCell_pugixml.o: ./modules/PhysiCell_pugixml.cpp
$(COMPILE_COMMAND) -c ./modules/PhysiCell_pugixml.cpp
PhysiCell_settings.o: ./modules/PhysiCell_settings.cpp
$(COMPILE_COMMAND) -c ./modules/PhysiCell_settings.cpp
# user-defined PhysiCell modules
heterogeneity.o: ./custom_modules/heterogeneity.cpp
$(COMPILE_COMMAND) -c ./custom_modules/heterogeneity.cpp
# cleanup
reset:
rm -f *.cpp
cp ./sample_projects/Makefile-default Makefile
rm -f ./custom_modules/*
touch ./custom_modules/empty.txt
touch ALL_CITATIONS.txt
rm ALL_CITATIONS.txt
cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml
clean:
rm -f *.o
rm -f $(PROGRAM_NAME)*
data-cleanup:
rm -f *.mat
rm -f *.xml
rm -f *.svg
rm -f ./output/*
touch ./output/empty.txt
# archival
checkpoint:
zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/*
zip:
zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/*
cp latest.zip $$(date +%b_%d_%Y_%H%M).zip
cp latest.zip VERSION_$(VERSION).zip
mv *.zip archives/
tar:
tar --ignore-failed-read -czf latest.tar Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/*
cp latest.tar $$(date +%b_%d_%Y_%H%M).tar
cp latest.tar VERSION_$(VERSION).tar
mv *.tar archives/
unzip:
cp ./archives/latest.zip .
unzip latest.zip
untar:
cp ./archives/latest.tar .
tar -xzf latest.tar
<?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 #