From 6438e919d077cbc879f095affd77c7df34b3e38e Mon Sep 17 00:00:00 2001
From: Randy Heiland <randy.heiland@gmail.com>
Date: Sat, 13 Jul 2024 16:54:16 -0400
Subject: [PATCH 01/12] custom division, lineage

---
 core/PhysiCell_cell.cpp                       |  22 ++
 core/PhysiCell_cell.h                         |   2 +
 modules/PhysiCell_MultiCellDS.cpp             |  15 +
 sample_projects/custom_division/Makefile      | 314 ++++++++++++++++
 .../config/PhysiCell_settings.xml             | 349 ++++++++++++++++++
 .../custom_division/config/cell_rules.csv     |   0
 .../custom_division/config/cells.csv          |   5 +
 .../custom_division/custom_modules/custom.cpp | 232 ++++++++++++
 .../custom_division/custom_modules/custom.h   |  93 +++++
 sample_projects/custom_division/main.cpp      | 254 +++++++++++++
 10 files changed, 1286 insertions(+)
 create mode 100644 sample_projects/custom_division/Makefile
 create mode 100644 sample_projects/custom_division/config/PhysiCell_settings.xml
 create mode 100644 sample_projects/custom_division/config/cell_rules.csv
 create mode 100644 sample_projects/custom_division/config/cells.csv
 create mode 100644 sample_projects/custom_division/custom_modules/custom.cpp
 create mode 100644 sample_projects/custom_division/custom_modules/custom.h
 create mode 100644 sample_projects/custom_division/main.cpp

diff --git a/core/PhysiCell_cell.cpp b/core/PhysiCell_cell.cpp
index 32270263c..2496ddf90 100644
--- a/core/PhysiCell_cell.cpp
+++ b/core/PhysiCell_cell.cpp
@@ -418,6 +418,7 @@ Cell::Cell()
 	
 	is_movable = true;
 	is_out_of_domain = false;
+    generation = 0;
 	displacement.resize(3,0.0); // state? 
 	
 	assign_orientation();
@@ -563,6 +564,9 @@ Cell* Cell::divide( )
 	
 	Cell* child = create_cell(functions.instantiate_cell);
 	child->copy_data( this );	
+    // lineage tracking
+    generation = generation + 1;     // this (parent) cell has its generation incremented
+    child->generation = generation;  // its daughter cell has the same generation
 	child->copy_function_pointers(this);
 	child->parameters = parameters;
 	
@@ -649,6 +653,11 @@ Cell* Cell::divide( )
 	child->state.damage = 0.0; 
 	child->state.total_attack_time = 0.0; 
 
+    //rwh
+    // if( this->functions.cell_division_function && pC->is_out_of_domain == false )
+    if( this->functions.cell_division_function )
+        { this->functions.cell_division_function( this, child); }
+
 	return child;
 }
 
@@ -1306,6 +1315,7 @@ void Cell::ingest_cell( Cell* pCell_to_eat )
 		pCell_to_eat->functions.custom_cell_rule = NULL; 
 		pCell_to_eat->functions.update_phenotype = NULL; 
 		pCell_to_eat->functions.contact_function = NULL; 
+		pCell_to_eat->functions.cell_division_function = NULL; 
 		
 		// should set volume fuction to NULL too! 
 		pCell_to_eat->functions.volume_update_function = NULL; 
@@ -1531,6 +1541,7 @@ void Cell::fuse_cell( Cell* pCell_to_fuse )
 		pCell_to_fuse->functions.custom_cell_rule = NULL; 
 		pCell_to_fuse->functions.update_phenotype = NULL; 
 		pCell_to_fuse->functions.contact_function = NULL; 
+		pCell_to_fuse->functions.cell_division_function = NULL; 
 		pCell_to_fuse->functions.volume_update_function = NULL; 
 
 		// remove all adhesions 
@@ -1570,6 +1581,7 @@ void Cell::lyse_cell( void )
 	functions.custom_cell_rule = NULL; 
 	functions.update_phenotype = NULL; 
 	functions.contact_function = NULL; 
+	functions.cell_division_function = NULL; 
 	
 	// remove all adhesions 
 	
@@ -1660,6 +1672,14 @@ void display_ptr_as_bool( void (*ptr)(Cell*,Phenotype&,Cell*,Phenotype&,double),
 	return;
 }
 
+void display_ptr_as_bool( void (*ptr)(Cell*,Cell*), std::ostream& os )  //rwh
+{
+	if( ptr )
+	{ os << "true"; return; }
+	os << "false"; 
+	return;
+}
+
 void display_cell_definitions( std::ostream& os )
 {
 	for( int n=0; n < cell_definitions_by_index.size() ; n++ )
@@ -1743,6 +1763,8 @@ void display_cell_definitions( std::ostream& os )
 		os << std::endl;
 		os << "\t\t contact function: "; display_ptr_as_bool( pCF->contact_function , std::cout ); 
 		os << std::endl; 
+		os << "\t\t cell division function: "; display_ptr_as_bool( pCF->cell_division_function , std::cout ); 
+		os << std::endl; 
 		
 		// summarize motility 
 		
diff --git a/core/PhysiCell_cell.h b/core/PhysiCell_cell.h
index 5919e3fac..27f4906eb 100644
--- a/core/PhysiCell_cell.h
+++ b/core/PhysiCell_cell.h
@@ -188,6 +188,8 @@ class Cell : public Basic_Agent
 	
 	bool is_out_of_domain;
 	bool is_movable;
+
+    int generation;   // for lineage tracking
 	
 	void flag_for_division( void ); // done 
 	void flag_for_removal( void ); // done 
diff --git a/modules/PhysiCell_MultiCellDS.cpp b/modules/PhysiCell_MultiCellDS.cpp
index f65369e1e..6d9a6afba 100644
--- a/modules/PhysiCell_MultiCellDS.cpp
+++ b/modules/PhysiCell_MultiCellDS.cpp
@@ -890,6 +890,18 @@ void add_PhysiCell_cells_to_open_xml_pugi_v2( pugi::xml_document& xml_dom, std::
 		data_start_indices.push_back( index ); 
 		cell_data_size += size; 
 		index += size; 
+
+        // generation
+		name = "generation"; 
+		size = 1; 
+		units="none";
+		data_names.push_back( name ); 
+		data_units.push_back(units); 
+		data_sizes.push_back( size ); 
+		data_start_indices.push_back( index ); 
+		cell_data_size += size; 
+		index += size; 
+
 		//					<label index="1" size="3">position</label>
 		name = "position"; 
 		size = 3; 
@@ -1754,6 +1766,9 @@ void add_PhysiCell_cells_to_open_xml_pugi_v2( pugi::xml_document& xml_dom, std::
 		// name = "ID"; 
 		dTemp = (double) pCell->ID;
 		std::fwrite( &( dTemp ) , sizeof(double) , 1 , fp ); 
+        // name = "generation"; 
+		dTemp = (double) pCell->generation;
+		std::fwrite( &( dTemp ) , sizeof(double) , 1 , fp ); 
 		// name = "position";    NOTE very different syntax for writing vectors!
         std::fwrite( pCell->position.data() , sizeof(double) , 3 , fp );
 		// name = "total_volume"; 
diff --git a/sample_projects/custom_division/Makefile b/sample_projects/custom_division/Makefile
new file mode 100644
index 000000000..e90a9966f
--- /dev/null
+++ b/sample_projects/custom_division/Makefile
@@ -0,0 +1,314 @@
+VERSION := $(shell grep . VERSION.txt | cut -f1 -d:)
+PROGRAM_NAME := project
+
+CC := g++
+# 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=$(ARCH) -O3 -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11
+
+ifeq ($(OS),Windows_NT)
+else
+	UNAME_S := $(shell uname -s)
+	ifeq ($(UNAME_S),Darwin)
+		UNAME_P := $(shell uname -p)
+		var := $(shell which $(CC) | xargs file)
+		ifeq ($(lastword $(var)),arm64)
+		  CFLAGS := -march=$(ARCH) -O3 -fomit-frame-pointer -fopenmp -m64 -std=c++11
+		endif
+	endif
+endif
+
+COMPILE_COMMAND := $(CC) $(CFLAGS) 
+
+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_basic_signaling.o \
+PhysiCell_signal_behavior.o PhysiCell_rules.o
+
+PhysiCell_module_OBJECTS := PhysiCell_SVG.o PhysiCell_pathology.o PhysiCell_MultiCellDS.o PhysiCell_various_outputs.o \
+PhysiCell_pugixml.o PhysiCell_settings.o PhysiCell_geometry.o
+
+# put your custom objects here (they should be in the custom_modules directory)
+
+PhysiCell_custom_module_OBJECTS := custom.o
+
+pugixml_OBJECTS := pugixml.o
+
+PhysiCell_OBJECTS := $(BioFVM_OBJECTS)  $(pugixml_OBJECTS) $(PhysiCell_core_OBJECTS) $(PhysiCell_module_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 
+	make name
+
+name:
+	@echo ""
+	@echo "Executable name is" $(PROGRAM_NAME)
+	@echo ""
+
+# PhysiCell core components	
+
+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 
+	
+PhysiCell_signal_behavior.o: ./core/PhysiCell_signal_behavior.cpp
+	$(COMPILE_COMMAND) -c ./core/PhysiCell_signal_behavior.cpp 
+
+PhysiCell_rules.o: ./core/PhysiCell_rules.cpp
+	$(COMPILE_COMMAND) -c ./core/PhysiCell_rules.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
+	
+PhysiCell_basic_signaling.o: ./core/PhysiCell_basic_signaling.cpp
+	$(COMPILE_COMMAND) -c ./core/PhysiCell_basic_signaling.cpp 	
+	
+PhysiCell_geometry.o: ./modules/PhysiCell_geometry.cpp
+	$(COMPILE_COMMAND) -c ./modules/PhysiCell_geometry.cpp 
+	
+# user-defined PhysiCell modules
+
+custom.o: ./custom_modules/custom.cpp 
+	$(COMPILE_COMMAND) -c ./custom_modules/custom.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 
+	touch ./core/PhysiCell_cell.cpp
+	rm ALL_CITATIONS.txt 
+	cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml 
+	touch ./config/empty.csv
+	rm -f ./config/*.csv
+	
+clean:
+	rm -f *.o
+	rm -f $(PROGRAM_NAME)*
+	
+data-cleanup:
+	rm -rf ./output
+	mkdir ./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
+
+# easier animation 
+
+FRAMERATE := 24
+OUTPUT := output
+
+jpeg: 
+	@magick identify -format "%h" $(OUTPUT)/initial.svg > __H.txt 
+	@magick identify -format "%w" $(OUTPUT)/initial.svg > __W.txt 
+	@expr 2 \* \( $$(grep . __H.txt) / 2 \) > __H1.txt 
+	@expr 2 \* \( $$(grep . __W.txt) / 2 \) > __W1.txt 
+	@echo "$$(grep . __W1.txt)!x$$(grep . __H1.txt)!" > __resize.txt 
+	@magick mogrify -format jpg -resize $$(grep . __resize.txt) $(OUTPUT)/s*.svg
+	rm -f __H*.txt __W*.txt __resize.txt 
+	
+gif: 
+	magick convert $(OUTPUT)/s*.svg $(OUTPUT)/out.gif 
+	 
+movie:
+	ffmpeg -r $(FRAMERATE) -f image2 -i $(OUTPUT)/snapshot%08d.jpg -vcodec libx264 -pix_fmt yuv420p -strict -2 -tune animation -crf 15 -acodec none $(OUTPUT)/out.mp4
+	
+# upgrade rules 
+
+SOURCE := PhysiCell_upgrade.zip 
+get-upgrade: 
+	@echo $$(curl https://raw.githubusercontent.com/MathCancer/PhysiCell/master/VERSION.txt) > VER.txt 
+	@echo https://github.com/MathCancer/PhysiCell/releases/download/$$(grep . VER.txt)/PhysiCell_V.$$(grep . VER.txt).zip > DL_FILE.txt 
+	rm -f VER.txt
+	$$(curl -L $$(grep . DL_FILE.txt) --output PhysiCell_upgrade.zip)
+	rm -f DL_FILE.txt 
+
+PhysiCell_upgrade.zip: 
+	make get-upgrade 
+
+upgrade: $(SOURCE)
+	unzip $(SOURCE) PhysiCell/VERSION.txt
+	mv -f PhysiCell/VERSION.txt . 
+	unzip $(SOURCE) PhysiCell/core/* 
+	cp -r PhysiCell/core/* core 
+	unzip $(SOURCE) PhysiCell/modules/* 
+	cp -r PhysiCell/modules/* modules 
+	unzip $(SOURCE) PhysiCell/sample_projects/* 
+	cp -r PhysiCell/sample_projects/* sample_projects 
+	unzip $(SOURCE) PhysiCell/BioFVM/* 
+	cp -r PhysiCell/BioFVM/* BioFVM
+	unzip $(SOURCE) PhysiCell/documentation/User_Guide.pdf
+	mv -f PhysiCell/documentation/User_Guide.pdf documentation
+	rm -f -r PhysiCell
+	rm -f $(SOURCE) 
+
+# use: make save PROJ=your_project_name
+PROJ := my_project
+
+save: 
+	echo "Saving project as $(PROJ) ... "
+	mkdir -p ./user_projects
+	mkdir -p ./user_projects/$(PROJ)
+	mkdir -p ./user_projects/$(PROJ)/custom_modules
+	mkdir -p ./user_projects/$(PROJ)/config 
+	cp main.cpp ./user_projects/$(PROJ)
+	cp Makefile ./user_projects/$(PROJ)
+	cp VERSION.txt ./user_projects/$(PROJ)
+	cp ./config/* ./user_projects/$(PROJ)/config
+	cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules
+
+load: 
+	echo "Loading project from $(PROJ) ... "
+	cp ./user_projects/$(PROJ)/main.cpp .
+	cp ./user_projects/$(PROJ)/Makefile .
+	cp ./user_projects/$(PROJ)/config/* ./config/ 
+	cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ 
+
+pack:
+	@echo " "
+	@echo "Preparing project $(PROJ) for sharing ... "
+	@echo " " 
+	cd ./user_projects && zip -r $(PROJ).zip $(PROJ)
+	@echo " "
+	@echo "Share ./user_projects/$(PROJ).zip ... "
+	@echo "Other users can unzip $(PROJ).zip in their ./user_projects, compile, and run."
+	@echo " " 
+
+unpack:
+	@echo " "
+	@echo "Preparing shared project $(PROJ).zip for use ... "
+	@echo " " 
+	cd ./user_projects && unzip $(PROJ).zip 
+	@echo " "
+	@echo "Load this project via make load PROJ=$(PROJ) ... "
+	@echo " " 	
+
+list-user-projects:
+	@echo "user projects::"
+	@cd ./user_projects && ls -dt1 * | grep . | sed 's!empty.txt!!'
diff --git a/sample_projects/custom_division/config/PhysiCell_settings.xml b/sample_projects/custom_division/config/PhysiCell_settings.xml
new file mode 100644
index 000000000..8987e89b6
--- /dev/null
+++ b/sample_projects/custom_division/config/PhysiCell_settings.xml
@@ -0,0 +1,349 @@
+<PhysiCell_settings version="devel-version">
+
+    <domain>
+        <x_min>-200</x_min>
+        <x_max>200</x_max>
+        <y_min>-200</y_min>
+        <y_max>200</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">5760.0</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>1</omp_num_threads>
+    </parallel>
+
+    <save>
+        <folder>output</folder>
+        <full_data>
+            <interval units="min">30</interval>
+            <enable>true</enable>
+        </full_data>
+        <SVG>
+            <interval units="min">30</interval>
+            <enable>true</enable>
+            <plot_substrate enabled="false" limits="false">
+                <substrate>oxygen</substrate>
+                <min_conc />
+                <max_conc />
+            </plot_substrate>
+        </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="oxygen" units="dimensionless" ID="0">
+            <physical_parameter_set>
+                <diffusion_coefficient units="micron^2/min">100000.0</diffusion_coefficient>
+                <decay_rate units="1/min">0.1</decay_rate>
+            </physical_parameter_set>
+            <initial_condition units="mmHg">38</initial_condition>
+            <Dirichlet_boundary_condition units="mmHg" enabled="True">38</Dirichlet_boundary_condition>
+            <Dirichlet_options>
+                <boundary_value ID="xmin" enabled="True">38</boundary_value>
+                <boundary_value ID="xmax" enabled="True">38</boundary_value>
+                <boundary_value ID="ymin" enabled="True">38</boundary_value>
+                <boundary_value ID="ymax" enabled="True">38</boundary_value>
+                <boundary_value ID="zmin" enabled="False">38</boundary_value>
+                <boundary_value ID="zmax" enabled="False">38</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="5" name="live">
+                    <phase_transition_rates units="1/min">
+                        <rate start_index="0" end_index="0" fixed_duration="false">0.001</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>
+                        <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">1.11667e-2</unlysed_fluid_change_rate>
+                            <lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
+                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-5</cytoplasmic_biomass_change_rate>
+                            <nuclear_biomass_change_rate units="1/min">2.16667e-3</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</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="ctype1">1</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>
+                    <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>oxygen</substrate>
+                            <direction>1</direction>
+                        </chemotaxis>
+                        <advanced_chemotaxis>
+                            <enabled>false</enabled>
+                            <normalize_each_gradient>false</normalize_each_gradient>
+                            <chemotactic_sensitivities>
+                                <chemotactic_sensitivity substrate="oxygen">0.0</chemotactic_sensitivity>
+                            </chemotactic_sensitivities>
+                        </advanced_chemotaxis>
+                    </options>
+                </motility>
+                <secretion>
+                    <substrate name="oxygen">
+                        <secretion_rate units="1/min">0</secretion_rate>
+                        <secretion_target units="substrate density">1</secretion_target>
+                        <uptake_rate units="1/min">10</uptake_rate>
+                        <net_export_rate units="total substrate/min">0</net_export_rate>
+                    </substrate>
+                </secretion>
+                <cell_interactions>
+                    <dead_phagocytosis_rate units="1/min">0</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>
+                    </live_phagocytosis_rates>
+                    <attack_rates>
+                        <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>
+                    <fusion_rates>
+                        <fusion_rate name="default" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="ctype1" units="1/min">0</fusion_rate>
+                    </fusion_rates>
+                </cell_interactions>
+                <cell_transformations>
+                    <transformation_rates>
+                        <transformation_rate name="default" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="ctype1" units="1/min">0</transformation_rate>
+                    </transformation_rates>
+                </cell_transformations>
+            </phenotype>
+            <custom_data>
+                <oncoprotein conserved="false" units="dimensionless" description="">1.0</oncoprotein>
+            </custom_data>
+        </cell_definition>
+        <cell_definition name="ctype1" ID="1">
+            <phenotype>
+                <cycle code="5" name="live">
+                    <phase_transition_rates units="1/min">
+                        <rate start_index="0" end_index="0" fixed_duration="false">0.00072</rate>
+                    </phase_transition_rates>
+                </cycle>
+                <death>
+                    <model code="100" name="apoptosis">
+                        <death_rate units="1/min">0</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">1.11667e-2</unlysed_fluid_change_rate>
+                            <lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
+                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-5</cytoplasmic_biomass_change_rate>
+                            <nuclear_biomass_change_rate units="1/min">2.16667e-3</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</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="ctype1">1</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>
+                    <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">0.05</speed>
+                    <persistence_time units="min">0</persistence_time>
+                    <migration_bias units="dimensionless">.5</migration_bias>
+                    <options>
+                        <enabled>true</enabled>
+                        <use_2D>true</use_2D>
+                        <chemotaxis>
+                            <enabled>true</enabled>
+                            <substrate>oxygen</substrate>
+                            <direction>1</direction>
+                        </chemotaxis>
+                        <advanced_chemotaxis>
+                            <enabled>false</enabled>
+                            <normalize_each_gradient>false</normalize_each_gradient>
+                            <chemotactic_sensitivities>
+                                <chemotactic_sensitivity substrate="oxygen">0.0</chemotactic_sensitivity>
+                            </chemotactic_sensitivities>
+                        </advanced_chemotaxis>
+                    </options>
+                </motility>
+                <secretion>
+                    <substrate name="oxygen">
+                        <secretion_rate units="1/min">0</secretion_rate>
+                        <secretion_target units="substrate density">1</secretion_target>
+                        <uptake_rate units="1/min">10</uptake_rate>
+                        <net_export_rate units="total substrate/min">0</net_export_rate>
+                    </substrate>
+                </secretion>
+                <cell_interactions>
+                    <dead_phagocytosis_rate units="1/min">0</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>
+                    </live_phagocytosis_rates>
+                    <attack_rates>
+                        <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>
+                    <fusion_rates>
+                        <fusion_rate name="default" units="1/min">0</fusion_rate>
+                        <fusion_rate name="ctype1" units="1/min">0</fusion_rate>
+                    </fusion_rates>
+                </cell_interactions>
+                <cell_transformations>
+                    <transformation_rates>
+                        <transformation_rate name="default" units="1/min">0</transformation_rate>
+                        <transformation_rate name="ctype1" units="1/min">0</transformation_rate>
+                    </transformation_rates>
+                </cell_transformations>
+            </phenotype>
+            <custom_data>
+                <oncoprotein conserved="false" units="dimensionless" description="">1.0</oncoprotein>
+            </custom_data>
+        </cell_definition>
+    </cell_definitions>
+
+    <initial_conditions>
+        <cell_positions type="csv" enabled="true">
+            <folder>./config</folder>
+            <filename>cells.csv</filename>
+        </cell_positions>
+    </initial_conditions>
+
+    <cell_rules>
+        <rulesets>
+            <ruleset protocol="CBHG" version="2.0" format="csv" enabled="false">
+                <folder>config</folder>
+                <filename>rules.csv</filename>
+            </ruleset>
+        </rulesets>
+    </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>
diff --git a/sample_projects/custom_division/config/cell_rules.csv b/sample_projects/custom_division/config/cell_rules.csv
new file mode 100644
index 000000000..e69de29bb
diff --git a/sample_projects/custom_division/config/cells.csv b/sample_projects/custom_division/config/cells.csv
new file mode 100644
index 000000000..88d88f63f
--- /dev/null
+++ b/sample_projects/custom_division/config/cells.csv
@@ -0,0 +1,5 @@
+x,y,z,type,volume,cycle entry,custom:GFP,custom:sample
+-80.,80.,0.0,default
+80.,80.,0.0,default
+-80.,-80.,0.0,default
+80.,-80.,0.0,default
diff --git a/sample_projects/custom_division/custom_modules/custom.cpp b/sample_projects/custom_division/custom_modules/custom.cpp
new file mode 100644
index 000000000..fbeab09ca
--- /dev/null
+++ b/sample_projects/custom_division/custom_modules/custom.cpp
@@ -0,0 +1,232 @@
+/*
+###############################################################################
+# 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) 2015-2021, 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.                                                 #
+#                                                                             #
+###############################################################################
+*/
+
+#include "./custom.h"
+
+void create_cell_types( void )
+{
+	// set the random seed 
+	SeedRandom( parameters.ints("random_seed") );  
+	
+	/* 
+	   Put any modifications to default cell definition here if you 
+	   want to have "inherited" by other cell types. 
+	   
+	   This is a good place to set default functions. 
+	*/ 
+	
+	initialize_default_cell_definition(); 
+	cell_defaults.phenotype.secretion.sync_to_microenvironment( &microenvironment ); 
+	
+	cell_defaults.functions.volume_update_function = standard_volume_update_function;
+	cell_defaults.functions.update_velocity = standard_update_cell_velocity;
+
+	cell_defaults.functions.update_migration_bias = NULL; 
+	cell_defaults.functions.update_phenotype = NULL; // update_cell_and_death_parameters_O2_based; 
+	cell_defaults.functions.custom_cell_rule = NULL; 
+	cell_defaults.functions.contact_function = NULL; 
+    cell_defaults.functions.cell_division_function = NULL; 
+	
+	cell_defaults.functions.add_cell_basement_membrane_interactions = NULL; 
+	cell_defaults.functions.calculate_distance_to_membrane = NULL; 
+	
+	/*
+	   This parses the cell definitions in the XML config file. 
+	*/
+	
+	initialize_cell_definitions_from_pugixml(); 
+
+	/*
+	   This builds the map of cell definitions and summarizes the setup. 
+	*/
+		
+	build_cell_definitions_maps(); 
+
+	/*
+	   This intializes cell signal and response dictionaries 
+	*/
+
+	setup_signal_behavior_dictionaries(); 	
+
+	/*
+       Cell rule definitions 
+	*/
+
+	setup_cell_rules(); 
+
+	/* 
+	   Put any modifications to individual cell definitions here. 
+	   
+	   This is a good place to set custom functions. 
+	*/ 
+	
+	cell_defaults.functions.update_phenotype = phenotype_function; 
+	cell_defaults.functions.custom_cell_rule = custom_function; 
+	cell_defaults.functions.contact_function = contact_function; 
+    cell_defaults.functions.cell_division_function = custom_division_function; 
+	
+	/*
+	   This builds the map of cell definitions and summarizes the setup. 
+	*/
+		
+	display_cell_definitions( std::cout ); 
+	
+	return; 
+}
+
+void setup_microenvironment( void )
+{
+	// set domain parameters 
+	
+	// put any custom code to set non-homogeneous initial conditions or 
+	// extra Dirichlet nodes here. 
+	
+	// initialize BioFVM 
+	
+	initialize_microenvironment(); 	
+	
+	return; 
+}
+
+void setup_tissue( void )
+{
+	double Xmin = microenvironment.mesh.bounding_box[0]; 
+	double Ymin = microenvironment.mesh.bounding_box[1]; 
+	double Zmin = microenvironment.mesh.bounding_box[2]; 
+
+	double Xmax = microenvironment.mesh.bounding_box[3]; 
+	double Ymax = microenvironment.mesh.bounding_box[4]; 
+	double Zmax = microenvironment.mesh.bounding_box[5]; 
+	
+	if( default_microenvironment_options.simulate_2D == true )
+	{
+		Zmin = 0.0; 
+		Zmax = 0.0; 
+	}
+	
+	double Xrange = Xmax - Xmin; 
+	double Yrange = Ymax - Ymin; 
+	double Zrange = Zmax - Zmin; 
+	
+	// create some of each type of cell 
+	
+	Cell* pC;
+	
+	for( int k=0; k < cell_definitions_by_index.size() ; k++ )
+	{
+		Cell_Definition* pCD = cell_definitions_by_index[k]; 
+		std::cout << "Placing cells of type " << pCD->name << " ... " << std::endl; 
+		for( int n = 0 ; n < parameters.ints("number_of_cells") ; n++ )
+		{
+			std::vector<double> position = {0,0,0}; 
+			position[0] = Xmin + UniformRandom()*Xrange; 
+			position[1] = Ymin + UniformRandom()*Yrange; 
+			position[2] = Zmin + UniformRandom()*Zrange; 
+			
+			pC = create_cell( *pCD ); 
+			pC->assign_position( position );
+		}
+	}
+	std::cout << std::endl; 
+	
+	// load cells from your CSV file (if enabled)
+	load_cells_from_pugixml();
+	set_parameters_from_distributions();
+	
+	return; 
+}
+
+std::vector<std::string> my_coloring_function( Cell* pCell )
+{ return paint_by_number_cell_coloring(pCell); }
+
+void phenotype_function( Cell* pCell, Phenotype& phenotype, double dt )
+{ return; }
+
+void custom_function( Cell* pCell, Phenotype& phenotype , double dt )
+{ return; } 
+
+void contact_function( Cell* pMe, Phenotype& phenoMe , Cell* pOther, Phenotype& phenoOther , double dt )
+{ return; } 
+
+void custom_division_function( Cell* pCell1, Cell* pCell2 )
+{ 
+    static int idx_default = find_cell_definition_index("default");
+    static int idx_ctype1 = find_cell_definition_index("ctype1");
+    std::cout << __FUNCTION__ << ": " << PhysiCell_globals.current_time << ": cell IDs= " << pCell1->ID << ", " << pCell2->ID << std::endl;
+
+    // Asymmetric division
+    if (UniformRandom() < 0.5)
+    {
+        pCell2->convert_to_cell_definition( *cell_definitions_by_index[idx_default] ); 
+    }
+    else
+    {
+        pCell2->convert_to_cell_definition( *cell_definitions_by_index[idx_ctype1] ); 
+    }
+
+    return; 
+}
\ No newline at end of file
diff --git a/sample_projects/custom_division/custom_modules/custom.h b/sample_projects/custom_division/custom_modules/custom.h
new file mode 100644
index 000000000..7e6b0f044
--- /dev/null
+++ b/sample_projects/custom_division/custom_modules/custom.h
@@ -0,0 +1,93 @@
+/*
+###############################################################################
+# 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) 2015-2021, 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.                                                 #
+#                                                                             #
+###############################################################################
+*/
+
+#include "../core/PhysiCell.h"
+#include "../modules/PhysiCell_standard_modules.h" 
+
+using namespace BioFVM; 
+using namespace PhysiCell;
+
+// setup functions to help us along 
+
+void create_cell_types( void );
+void setup_tissue( void ); 
+
+// set up the BioFVM microenvironment 
+void setup_microenvironment( void ); 
+
+// custom pathology coloring function 
+
+std::vector<std::string> my_coloring_function( Cell* );
+
+// custom functions can go here 
+
+void phenotype_function( Cell* pCell, Phenotype& phenotype, double dt );
+void custom_function( Cell* pCell, Phenotype& phenotype , double dt );
+
+void contact_function( Cell* pMe, Phenotype& phenoMe , Cell* pOther, Phenotype& phenoOther , double dt ); 
+
+void custom_division_function( Cell* pCell1, Cell* pCell2 );
diff --git a/sample_projects/custom_division/main.cpp b/sample_projects/custom_division/main.cpp
new file mode 100644
index 000000000..2f7e98c75
--- /dev/null
+++ b/sample_projects/custom_division/main.cpp
@@ -0,0 +1,254 @@
+/*
+###############################################################################
+# 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) 2015-2022, 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.                                                 #
+#                                                                             #
+###############################################################################
+*/
+
+#include <cstdio>
+#include <cstdlib>
+#include <iostream>
+#include <ctime>
+#include <cmath>
+#include <omp.h>
+#include <fstream>
+
+#include "./core/PhysiCell.h"
+#include "./modules/PhysiCell_standard_modules.h" 
+
+// put custom code modules here! 
+
+#include "./custom_modules/custom.h" 
+	
+using namespace BioFVM;
+using namespace PhysiCell;
+
+int main( int argc, char* argv[] )
+{
+	// load and parse settings file(s)
+	
+	bool XML_status = false; 
+	char copy_command [1024]; 
+	if( argc > 1 )
+	{
+		XML_status = load_PhysiCell_config_file( argv[1] ); 
+		sprintf( copy_command , "cp %s %s" , argv[1] , PhysiCell_settings.folder.c_str() ); 
+	}
+	else
+	{
+		XML_status = load_PhysiCell_config_file( "./config/PhysiCell_settings.xml" );
+		sprintf( copy_command , "cp ./config/PhysiCell_settings.xml %s" , PhysiCell_settings.folder.c_str() ); 
+	}
+	if( !XML_status )
+	{ exit(-1); }
+	
+	// copy config file to output directry 
+	system( copy_command ); 
+	
+	// OpenMP setup
+	omp_set_num_threads(PhysiCell_settings.omp_num_threads);
+	
+	// time setup 
+	std::string time_units = "min"; 
+
+	/* Microenvironment setup */ 
+	
+	setup_microenvironment(); // modify this in the custom code 
+	
+	/* PhysiCell setup */ 
+ 	
+	// set mechanics voxel size, and match the data structure to BioFVM
+	double mechanics_voxel_size = 30; 
+	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
+	
+	/* Users typically start modifying here. START USERMODS */ 
+	
+	create_cell_types();
+	
+	setup_tissue();
+
+	/* Users typically stop modifying here. END USERMODS */ 
+	
+	// set MultiCellDS save options 
+
+	set_save_biofvm_mesh_as_matlab( true ); 
+	set_save_biofvm_data_as_matlab( true ); 
+	set_save_biofvm_cell_data( true ); 
+	set_save_biofvm_cell_data_as_custom_matlab( true );
+	
+	// save a simulation snapshot 
+	
+	char filename[1024];
+	sprintf( filename , "%s/initial" , PhysiCell_settings.folder.c_str() ); 
+	save_PhysiCell_to_MultiCellDS_v2( filename , microenvironment , PhysiCell_globals.current_time ); 
+	
+	// save a quick SVG cross section through z = 0, after setting its 
+	// length bar to 200 microns 
+
+	PhysiCell_SVG_options.length_bar = 200; 
+
+	// for simplicity, set a pathology coloring function 
+	
+	std::vector<std::string> (*cell_coloring_function)(Cell*) = my_coloring_function;
+	std::string (*substrate_coloring_function)(double, double, double) = paint_by_density_percentage;
+
+	sprintf( filename , "%s/initial.svg" , PhysiCell_settings.folder.c_str() ); 
+	SVG_plot( filename , microenvironment, 0.0 , PhysiCell_globals.current_time, cell_coloring_function, substrate_coloring_function );
+	
+	sprintf( filename , "%s/legend.svg" , PhysiCell_settings.folder.c_str() ); 
+	create_plot_legend( filename , cell_coloring_function ); 
+	
+	display_citations(); 
+	
+	// set the performance timers 
+
+	BioFVM::RUNTIME_TIC();
+	BioFVM::TIC();
+	
+	std::ofstream report_file;
+	if( PhysiCell_settings.enable_legacy_saves == true )
+	{	
+		sprintf( filename , "%s/simulation_report.txt" , PhysiCell_settings.folder.c_str() ); 
+		
+		report_file.open(filename); 	// create the data log file 
+		report_file<<"simulated time\tnum cells\tnum division\tnum death\twall time"<<std::endl;
+	}
+	
+	// main loop 
+	
+	try 
+	{		
+		while( PhysiCell_globals.current_time < PhysiCell_settings.max_time + 0.1*diffusion_dt )
+		{
+			// save data if it's time. 
+			if( fabs( PhysiCell_globals.current_time - PhysiCell_globals.next_full_save_time ) < 0.01 * diffusion_dt )
+			{
+				display_simulation_status( std::cout ); 
+				if( PhysiCell_settings.enable_legacy_saves == true )
+				{	
+					log_output( PhysiCell_globals.current_time , PhysiCell_globals.full_output_index, microenvironment, report_file);
+				}
+				
+				if( PhysiCell_settings.enable_full_saves == true )
+				{	
+					sprintf( filename , "%s/output%08u" , PhysiCell_settings.folder.c_str(),  PhysiCell_globals.full_output_index ); 
+					
+					save_PhysiCell_to_MultiCellDS_v2( filename , microenvironment , PhysiCell_globals.current_time ); 
+				}
+				
+				PhysiCell_globals.full_output_index++; 
+				PhysiCell_globals.next_full_save_time += PhysiCell_settings.full_save_interval;
+			}
+			
+			// save SVG plot if it's time
+			if( fabs( PhysiCell_globals.current_time - PhysiCell_globals.next_SVG_save_time  ) < 0.01 * diffusion_dt )
+			{
+				if( PhysiCell_settings.enable_SVG_saves == true )
+				{	
+					sprintf( filename , "%s/snapshot%08u.svg" , PhysiCell_settings.folder.c_str() , PhysiCell_globals.SVG_output_index );
+					SVG_plot( filename , microenvironment, 0.0 , PhysiCell_globals.current_time, cell_coloring_function, substrate_coloring_function);
+
+					PhysiCell_globals.SVG_output_index++; 
+					PhysiCell_globals.next_SVG_save_time  += PhysiCell_settings.SVG_save_interval;
+				}
+			}
+
+			// update the microenvironment
+			microenvironment.simulate_diffusion_decay( diffusion_dt );
+			
+			// run PhysiCell 
+			((Cell_Container *)microenvironment.agent_container)->update_all_cells( PhysiCell_globals.current_time );
+			
+			/*
+			  Custom add-ons could potentially go here. 
+			*/
+			
+			PhysiCell_globals.current_time += diffusion_dt;
+		}
+		
+		if( PhysiCell_settings.enable_legacy_saves == true )
+		{			
+			log_output(PhysiCell_globals.current_time, PhysiCell_globals.full_output_index, microenvironment, report_file);
+			report_file.close();
+		}
+	}
+	catch( const std::exception& e )
+	{ // reference to the base of a polymorphic object
+		std::cout << e.what(); // information from length_error printed
+	}
+	
+	// save a final simulation snapshot 
+	
+	sprintf( filename , "%s/final" , PhysiCell_settings.folder.c_str() ); 
+	save_PhysiCell_to_MultiCellDS_v2( filename , microenvironment , PhysiCell_globals.current_time ); 
+	
+	sprintf( filename , "%s/final.svg" , PhysiCell_settings.folder.c_str() );
+	SVG_plot(filename, microenvironment, 0.0, PhysiCell_globals.current_time, cell_coloring_function, substrate_coloring_function);
+
+	// timer 
+	
+	std::cout << std::endl << "Total simulation runtime: " << std::endl; 
+	BioFVM::display_stopwatch_value( std::cout , BioFVM::runtime_stopwatch_value() ); 
+
+	return 0; 
+}

From 6caac3ce4c00c8214ffdaf57ecd2da7febf74da8 Mon Sep 17 00:00:00 2001
From: Randy Heiland <randy.heiland@gmail.com>
Date: Sun, 14 Jul 2024 09:23:12 -0400
Subject: [PATCH 02/12] add cell_division_function

---
 core/PhysiCell_phenotype.h | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/core/PhysiCell_phenotype.h b/core/PhysiCell_phenotype.h
index 106b567a6..1b4ea59c2 100644
--- a/core/PhysiCell_phenotype.h
+++ b/core/PhysiCell_phenotype.h
@@ -496,6 +496,8 @@ class Cell_Functions
 	
 	void (*contact_function)(Cell* pMyself, Phenotype& my_phenotype, 
 		Cell* pOther, Phenotype& other_phenotype, double dt ); 
+
+    void (*cell_division_function)(Cell* pCell1, Cell* pCell2 );
 		
 	/* prototyping / beta in 1.5.0 */ 
 /*	

From 5077aad6a66a4ab7d20e287180ddfa405b797fa9 Mon Sep 17 00:00:00 2001
From: Randy Heiland <randy.heiland@gmail.com>
Date: Sun, 14 Jul 2024 17:15:21 -0400
Subject: [PATCH 03/12] update

---
 .../sample_division_lineage/Makefile          | 314 ++++++++++++++++
 .../config/PhysiCell_settings.xml             | 349 ++++++++++++++++++
 .../config/cell_rules.csv                     |   0
 .../sample_division_lineage/config/cells.csv  |   3 +
 .../custom_modules/custom.cpp                 | 236 ++++++++++++
 .../custom_modules/custom.h                   |  93 +++++
 .../sample_division_lineage/main.cpp          | 254 +++++++++++++
 7 files changed, 1249 insertions(+)
 create mode 100644 user_projects/sample_division_lineage/Makefile
 create mode 100644 user_projects/sample_division_lineage/config/PhysiCell_settings.xml
 create mode 100644 user_projects/sample_division_lineage/config/cell_rules.csv
 create mode 100644 user_projects/sample_division_lineage/config/cells.csv
 create mode 100644 user_projects/sample_division_lineage/custom_modules/custom.cpp
 create mode 100644 user_projects/sample_division_lineage/custom_modules/custom.h
 create mode 100644 user_projects/sample_division_lineage/main.cpp

diff --git a/user_projects/sample_division_lineage/Makefile b/user_projects/sample_division_lineage/Makefile
new file mode 100644
index 000000000..e90a9966f
--- /dev/null
+++ b/user_projects/sample_division_lineage/Makefile
@@ -0,0 +1,314 @@
+VERSION := $(shell grep . VERSION.txt | cut -f1 -d:)
+PROGRAM_NAME := project
+
+CC := g++
+# 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=$(ARCH) -O3 -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11
+
+ifeq ($(OS),Windows_NT)
+else
+	UNAME_S := $(shell uname -s)
+	ifeq ($(UNAME_S),Darwin)
+		UNAME_P := $(shell uname -p)
+		var := $(shell which $(CC) | xargs file)
+		ifeq ($(lastword $(var)),arm64)
+		  CFLAGS := -march=$(ARCH) -O3 -fomit-frame-pointer -fopenmp -m64 -std=c++11
+		endif
+	endif
+endif
+
+COMPILE_COMMAND := $(CC) $(CFLAGS) 
+
+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_basic_signaling.o \
+PhysiCell_signal_behavior.o PhysiCell_rules.o
+
+PhysiCell_module_OBJECTS := PhysiCell_SVG.o PhysiCell_pathology.o PhysiCell_MultiCellDS.o PhysiCell_various_outputs.o \
+PhysiCell_pugixml.o PhysiCell_settings.o PhysiCell_geometry.o
+
+# put your custom objects here (they should be in the custom_modules directory)
+
+PhysiCell_custom_module_OBJECTS := custom.o
+
+pugixml_OBJECTS := pugixml.o
+
+PhysiCell_OBJECTS := $(BioFVM_OBJECTS)  $(pugixml_OBJECTS) $(PhysiCell_core_OBJECTS) $(PhysiCell_module_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 
+	make name
+
+name:
+	@echo ""
+	@echo "Executable name is" $(PROGRAM_NAME)
+	@echo ""
+
+# PhysiCell core components	
+
+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 
+	
+PhysiCell_signal_behavior.o: ./core/PhysiCell_signal_behavior.cpp
+	$(COMPILE_COMMAND) -c ./core/PhysiCell_signal_behavior.cpp 
+
+PhysiCell_rules.o: ./core/PhysiCell_rules.cpp
+	$(COMPILE_COMMAND) -c ./core/PhysiCell_rules.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
+	
+PhysiCell_basic_signaling.o: ./core/PhysiCell_basic_signaling.cpp
+	$(COMPILE_COMMAND) -c ./core/PhysiCell_basic_signaling.cpp 	
+	
+PhysiCell_geometry.o: ./modules/PhysiCell_geometry.cpp
+	$(COMPILE_COMMAND) -c ./modules/PhysiCell_geometry.cpp 
+	
+# user-defined PhysiCell modules
+
+custom.o: ./custom_modules/custom.cpp 
+	$(COMPILE_COMMAND) -c ./custom_modules/custom.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 
+	touch ./core/PhysiCell_cell.cpp
+	rm ALL_CITATIONS.txt 
+	cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml 
+	touch ./config/empty.csv
+	rm -f ./config/*.csv
+	
+clean:
+	rm -f *.o
+	rm -f $(PROGRAM_NAME)*
+	
+data-cleanup:
+	rm -rf ./output
+	mkdir ./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
+
+# easier animation 
+
+FRAMERATE := 24
+OUTPUT := output
+
+jpeg: 
+	@magick identify -format "%h" $(OUTPUT)/initial.svg > __H.txt 
+	@magick identify -format "%w" $(OUTPUT)/initial.svg > __W.txt 
+	@expr 2 \* \( $$(grep . __H.txt) / 2 \) > __H1.txt 
+	@expr 2 \* \( $$(grep . __W.txt) / 2 \) > __W1.txt 
+	@echo "$$(grep . __W1.txt)!x$$(grep . __H1.txt)!" > __resize.txt 
+	@magick mogrify -format jpg -resize $$(grep . __resize.txt) $(OUTPUT)/s*.svg
+	rm -f __H*.txt __W*.txt __resize.txt 
+	
+gif: 
+	magick convert $(OUTPUT)/s*.svg $(OUTPUT)/out.gif 
+	 
+movie:
+	ffmpeg -r $(FRAMERATE) -f image2 -i $(OUTPUT)/snapshot%08d.jpg -vcodec libx264 -pix_fmt yuv420p -strict -2 -tune animation -crf 15 -acodec none $(OUTPUT)/out.mp4
+	
+# upgrade rules 
+
+SOURCE := PhysiCell_upgrade.zip 
+get-upgrade: 
+	@echo $$(curl https://raw.githubusercontent.com/MathCancer/PhysiCell/master/VERSION.txt) > VER.txt 
+	@echo https://github.com/MathCancer/PhysiCell/releases/download/$$(grep . VER.txt)/PhysiCell_V.$$(grep . VER.txt).zip > DL_FILE.txt 
+	rm -f VER.txt
+	$$(curl -L $$(grep . DL_FILE.txt) --output PhysiCell_upgrade.zip)
+	rm -f DL_FILE.txt 
+
+PhysiCell_upgrade.zip: 
+	make get-upgrade 
+
+upgrade: $(SOURCE)
+	unzip $(SOURCE) PhysiCell/VERSION.txt
+	mv -f PhysiCell/VERSION.txt . 
+	unzip $(SOURCE) PhysiCell/core/* 
+	cp -r PhysiCell/core/* core 
+	unzip $(SOURCE) PhysiCell/modules/* 
+	cp -r PhysiCell/modules/* modules 
+	unzip $(SOURCE) PhysiCell/sample_projects/* 
+	cp -r PhysiCell/sample_projects/* sample_projects 
+	unzip $(SOURCE) PhysiCell/BioFVM/* 
+	cp -r PhysiCell/BioFVM/* BioFVM
+	unzip $(SOURCE) PhysiCell/documentation/User_Guide.pdf
+	mv -f PhysiCell/documentation/User_Guide.pdf documentation
+	rm -f -r PhysiCell
+	rm -f $(SOURCE) 
+
+# use: make save PROJ=your_project_name
+PROJ := my_project
+
+save: 
+	echo "Saving project as $(PROJ) ... "
+	mkdir -p ./user_projects
+	mkdir -p ./user_projects/$(PROJ)
+	mkdir -p ./user_projects/$(PROJ)/custom_modules
+	mkdir -p ./user_projects/$(PROJ)/config 
+	cp main.cpp ./user_projects/$(PROJ)
+	cp Makefile ./user_projects/$(PROJ)
+	cp VERSION.txt ./user_projects/$(PROJ)
+	cp ./config/* ./user_projects/$(PROJ)/config
+	cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules
+
+load: 
+	echo "Loading project from $(PROJ) ... "
+	cp ./user_projects/$(PROJ)/main.cpp .
+	cp ./user_projects/$(PROJ)/Makefile .
+	cp ./user_projects/$(PROJ)/config/* ./config/ 
+	cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ 
+
+pack:
+	@echo " "
+	@echo "Preparing project $(PROJ) for sharing ... "
+	@echo " " 
+	cd ./user_projects && zip -r $(PROJ).zip $(PROJ)
+	@echo " "
+	@echo "Share ./user_projects/$(PROJ).zip ... "
+	@echo "Other users can unzip $(PROJ).zip in their ./user_projects, compile, and run."
+	@echo " " 
+
+unpack:
+	@echo " "
+	@echo "Preparing shared project $(PROJ).zip for use ... "
+	@echo " " 
+	cd ./user_projects && unzip $(PROJ).zip 
+	@echo " "
+	@echo "Load this project via make load PROJ=$(PROJ) ... "
+	@echo " " 	
+
+list-user-projects:
+	@echo "user projects::"
+	@cd ./user_projects && ls -dt1 * | grep . | sed 's!empty.txt!!'
diff --git a/user_projects/sample_division_lineage/config/PhysiCell_settings.xml b/user_projects/sample_division_lineage/config/PhysiCell_settings.xml
new file mode 100644
index 000000000..43b85b8d3
--- /dev/null
+++ b/user_projects/sample_division_lineage/config/PhysiCell_settings.xml
@@ -0,0 +1,349 @@
+<PhysiCell_settings version="devel-version">
+
+    <domain>
+        <x_min>-200</x_min>
+        <x_max>200</x_max>
+        <y_min>-200</y_min>
+        <y_max>200</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">5760.0</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>1</omp_num_threads>
+    </parallel>
+
+    <save>
+        <folder>output</folder>
+        <full_data>
+            <interval units="min">30</interval>
+            <enable>true</enable>
+        </full_data>
+        <SVG>
+            <interval units="min">30</interval>
+            <enable>true</enable>
+            <plot_substrate enabled="false" limits="false">
+                <substrate>oxygen</substrate>
+                <min_conc />
+                <max_conc />
+            </plot_substrate>
+        </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="oxygen" units="dimensionless" ID="0">
+            <physical_parameter_set>
+                <diffusion_coefficient units="micron^2/min">1000.0</diffusion_coefficient>
+                <decay_rate units="1/min">0.1</decay_rate>
+            </physical_parameter_set>
+            <initial_condition units="mmHg">38</initial_condition>
+            <Dirichlet_boundary_condition units="mmHg" enabled="True">38</Dirichlet_boundary_condition>
+            <Dirichlet_options>
+                <boundary_value ID="xmin" enabled="True">38</boundary_value>
+                <boundary_value ID="xmax" enabled="True">38</boundary_value>
+                <boundary_value ID="ymin" enabled="True">38</boundary_value>
+                <boundary_value ID="ymax" enabled="True">38</boundary_value>
+                <boundary_value ID="zmin" enabled="False">38</boundary_value>
+                <boundary_value ID="zmax" enabled="False">38</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="5" name="live">
+                    <phase_durations units="min">
+                        <duration index="0" fixed_duration="true">660</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">1.11667e-2</unlysed_fluid_change_rate>
+                            <lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
+                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-5</cytoplasmic_biomass_change_rate>
+                            <nuclear_biomass_change_rate units="1/min">2.16667e-3</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</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="ctype1">1</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>
+                    <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>oxygen</substrate>
+                            <direction>1</direction>
+                        </chemotaxis>
+                        <advanced_chemotaxis>
+                            <enabled>false</enabled>
+                            <normalize_each_gradient>false</normalize_each_gradient>
+                            <chemotactic_sensitivities>
+                                <chemotactic_sensitivity substrate="oxygen">0.0</chemotactic_sensitivity>
+                            </chemotactic_sensitivities>
+                        </advanced_chemotaxis>
+                    </options>
+                </motility>
+                <secretion>
+                    <substrate name="oxygen">
+                        <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</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>
+                    </live_phagocytosis_rates>
+                    <attack_rates>
+                        <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>
+                    <fusion_rates>
+                        <fusion_rate name="default" units="1/min">0.0</fusion_rate>
+                        <fusion_rate name="ctype1" units="1/min">0</fusion_rate>
+                    </fusion_rates>
+                </cell_interactions>
+                <cell_transformations>
+                    <transformation_rates>
+                        <transformation_rate name="default" units="1/min">0.0</transformation_rate>
+                        <transformation_rate name="ctype1" units="1/min">0</transformation_rate>
+                    </transformation_rates>
+                </cell_transformations>
+            </phenotype>
+            <custom_data>
+                <sample conserved="false" units="dimensionless" description="">1.0</sample>
+            </custom_data>
+        </cell_definition>
+        <cell_definition name="ctype1" ID="1">
+            <phenotype>
+                <cycle code="5" name="live">
+                    <phase_durations units="min">
+                        <duration index="0" fixed_duration="true">660</duration>
+                    </phase_durations>
+                </cycle>
+                <death>
+                    <model code="100" name="apoptosis">
+                        <death_rate units="1/min">0</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">1.11667e-2</unlysed_fluid_change_rate>
+                            <lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
+                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-5</cytoplasmic_biomass_change_rate>
+                            <nuclear_biomass_change_rate units="1/min">2.16667e-3</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</cell_adhesion_affinity>
+                        <cell_adhesion_affinity name="ctype1">1</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>
+                    <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">0.05</speed>
+                    <persistence_time units="min">0</persistence_time>
+                    <migration_bias units="dimensionless">.5</migration_bias>
+                    <options>
+                        <enabled>true</enabled>
+                        <use_2D>true</use_2D>
+                        <chemotaxis>
+                            <enabled>true</enabled>
+                            <substrate>oxygen</substrate>
+                            <direction>1</direction>
+                        </chemotaxis>
+                        <advanced_chemotaxis>
+                            <enabled>false</enabled>
+                            <normalize_each_gradient>false</normalize_each_gradient>
+                            <chemotactic_sensitivities>
+                                <chemotactic_sensitivity substrate="oxygen">0.0</chemotactic_sensitivity>
+                            </chemotactic_sensitivities>
+                        </advanced_chemotaxis>
+                    </options>
+                </motility>
+                <secretion>
+                    <substrate name="oxygen">
+                        <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</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>
+                    </live_phagocytosis_rates>
+                    <attack_rates>
+                        <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>
+                    <fusion_rates>
+                        <fusion_rate name="default" units="1/min">0</fusion_rate>
+                        <fusion_rate name="ctype1" units="1/min">0</fusion_rate>
+                    </fusion_rates>
+                </cell_interactions>
+                <cell_transformations>
+                    <transformation_rates>
+                        <transformation_rate name="default" units="1/min">0</transformation_rate>
+                        <transformation_rate name="ctype1" units="1/min">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="true">
+            <folder>./config</folder>
+            <filename>cells.csv</filename>
+        </cell_positions>
+    </initial_conditions>
+
+    <cell_rules>
+        <rulesets>
+            <ruleset protocol="CBHG" version="2.0" format="csv" enabled="false">
+                <folder>config</folder>
+                <filename>rules.csv</filename>
+            </ruleset>
+        </rulesets>
+    </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>
\ No newline at end of file
diff --git a/user_projects/sample_division_lineage/config/cell_rules.csv b/user_projects/sample_division_lineage/config/cell_rules.csv
new file mode 100644
index 000000000..e69de29bb
diff --git a/user_projects/sample_division_lineage/config/cells.csv b/user_projects/sample_division_lineage/config/cells.csv
new file mode 100644
index 000000000..f19c4d4f4
--- /dev/null
+++ b/user_projects/sample_division_lineage/config/cells.csv
@@ -0,0 +1,3 @@
+x,y,z,type,volume,cycle entry,custom:GFP,custom:sample
+-80.,80.,0.0,default
+80.,-80.,0.0,default
diff --git a/user_projects/sample_division_lineage/custom_modules/custom.cpp b/user_projects/sample_division_lineage/custom_modules/custom.cpp
new file mode 100644
index 000000000..acbb1a395
--- /dev/null
+++ b/user_projects/sample_division_lineage/custom_modules/custom.cpp
@@ -0,0 +1,236 @@
+/*
+###############################################################################
+# 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) 2015-2021, 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.                                                 #
+#                                                                             #
+###############################################################################
+*/
+
+#include "./custom.h"
+
+void create_cell_types( void )
+{
+	// set the random seed 
+	SeedRandom( parameters.ints("random_seed") );  
+	
+	/* 
+	   Put any modifications to default cell definition here if you 
+	   want to have "inherited" by other cell types. 
+	   
+	   This is a good place to set default functions. 
+	*/ 
+	
+	initialize_default_cell_definition(); 
+	cell_defaults.phenotype.secretion.sync_to_microenvironment( &microenvironment ); 
+	
+	cell_defaults.functions.volume_update_function = standard_volume_update_function;
+	cell_defaults.functions.update_velocity = standard_update_cell_velocity;
+
+	cell_defaults.functions.update_migration_bias = NULL; 
+	cell_defaults.functions.update_phenotype = NULL; // update_cell_and_death_parameters_O2_based; 
+	cell_defaults.functions.custom_cell_rule = NULL; 
+	cell_defaults.functions.contact_function = NULL; 
+    cell_defaults.functions.cell_division_function = NULL; 
+	
+	cell_defaults.functions.add_cell_basement_membrane_interactions = NULL; 
+	cell_defaults.functions.calculate_distance_to_membrane = NULL; 
+	
+	/*
+	   This parses the cell definitions in the XML config file. 
+	*/
+	
+	initialize_cell_definitions_from_pugixml(); 
+
+	/*
+	   This builds the map of cell definitions and summarizes the setup. 
+	*/
+		
+	build_cell_definitions_maps(); 
+
+	/*
+	   This intializes cell signal and response dictionaries 
+	*/
+
+	setup_signal_behavior_dictionaries(); 	
+
+	/*
+       Cell rule definitions 
+	*/
+
+	setup_cell_rules(); 
+
+	/* 
+	   Put any modifications to individual cell definitions here. 
+	   
+	   This is a good place to set custom functions. 
+	*/ 
+	
+	cell_defaults.functions.update_phenotype = phenotype_function; 
+	cell_defaults.functions.custom_cell_rule = custom_function; 
+	cell_defaults.functions.contact_function = contact_function; 
+    cell_defaults.functions.cell_division_function = custom_division_function; 
+
+    int idx_ctype1 = find_cell_definition_index("ctype1");
+    Cell_Definition* pCD = cell_definitions_by_index[idx_ctype1]; 
+    pCD->functions.cell_division_function = custom_division_function; 
+	
+	/*
+	   This builds the map of cell definitions and summarizes the setup. 
+	*/
+		
+	display_cell_definitions( std::cout ); 
+	
+	return; 
+}
+
+void setup_microenvironment( void )
+{
+	// set domain parameters 
+	
+	// put any custom code to set non-homogeneous initial conditions or 
+	// extra Dirichlet nodes here. 
+	
+	// initialize BioFVM 
+	
+	initialize_microenvironment(); 	
+	
+	return; 
+}
+
+void setup_tissue( void )
+{
+	double Xmin = microenvironment.mesh.bounding_box[0]; 
+	double Ymin = microenvironment.mesh.bounding_box[1]; 
+	double Zmin = microenvironment.mesh.bounding_box[2]; 
+
+	double Xmax = microenvironment.mesh.bounding_box[3]; 
+	double Ymax = microenvironment.mesh.bounding_box[4]; 
+	double Zmax = microenvironment.mesh.bounding_box[5]; 
+	
+	if( default_microenvironment_options.simulate_2D == true )
+	{
+		Zmin = 0.0; 
+		Zmax = 0.0; 
+	}
+	
+	double Xrange = Xmax - Xmin; 
+	double Yrange = Ymax - Ymin; 
+	double Zrange = Zmax - Zmin; 
+	
+	// create some of each type of cell 
+	
+	Cell* pC;
+	
+	for( int k=0; k < cell_definitions_by_index.size() ; k++ )
+	{
+		Cell_Definition* pCD = cell_definitions_by_index[k]; 
+		std::cout << "Placing cells of type " << pCD->name << " ... " << std::endl; 
+		for( int n = 0 ; n < parameters.ints("number_of_cells") ; n++ )
+		{
+			std::vector<double> position = {0,0,0}; 
+			position[0] = Xmin + UniformRandom()*Xrange; 
+			position[1] = Ymin + UniformRandom()*Yrange; 
+			position[2] = Zmin + UniformRandom()*Zrange; 
+			
+			pC = create_cell( *pCD ); 
+			pC->assign_position( position );
+		}
+	}
+	std::cout << std::endl; 
+	
+	// load cells from your CSV file (if enabled)
+	load_cells_from_pugixml();
+	set_parameters_from_distributions();
+	
+	return; 
+}
+
+std::vector<std::string> my_coloring_function( Cell* pCell )
+{ return paint_by_number_cell_coloring(pCell); }
+
+void phenotype_function( Cell* pCell, Phenotype& phenotype, double dt )
+{ return; }
+
+void custom_function( Cell* pCell, Phenotype& phenotype , double dt )
+{ return; } 
+
+void contact_function( Cell* pMe, Phenotype& phenoMe , Cell* pOther, Phenotype& phenoOther , double dt )
+{ return; } 
+
+void custom_division_function( Cell* pCell1, Cell* pCell2 )
+{ 
+    static int idx_default = find_cell_definition_index("default");
+    static int idx_ctype1 = find_cell_definition_index("ctype1");
+    std::cout << __FUNCTION__ << ": t=" << PhysiCell_globals.current_time << ": cell IDs= " << pCell1->ID << ", " << pCell2->ID << ", pCell1->type_name= " << pCell1->type_name << std::endl;
+
+    // Asymmetric division
+    if (UniformRandom() < 0.5)
+    {
+        pCell2->convert_to_cell_definition( *cell_definitions_by_index[idx_default] ); 
+    }
+    else
+    {
+        pCell2->convert_to_cell_definition( *cell_definitions_by_index[idx_ctype1] ); 
+    }
+
+    return; 
+}
\ No newline at end of file
diff --git a/user_projects/sample_division_lineage/custom_modules/custom.h b/user_projects/sample_division_lineage/custom_modules/custom.h
new file mode 100644
index 000000000..7e6b0f044
--- /dev/null
+++ b/user_projects/sample_division_lineage/custom_modules/custom.h
@@ -0,0 +1,93 @@
+/*
+###############################################################################
+# 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) 2015-2021, 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.                                                 #
+#                                                                             #
+###############################################################################
+*/
+
+#include "../core/PhysiCell.h"
+#include "../modules/PhysiCell_standard_modules.h" 
+
+using namespace BioFVM; 
+using namespace PhysiCell;
+
+// setup functions to help us along 
+
+void create_cell_types( void );
+void setup_tissue( void ); 
+
+// set up the BioFVM microenvironment 
+void setup_microenvironment( void ); 
+
+// custom pathology coloring function 
+
+std::vector<std::string> my_coloring_function( Cell* );
+
+// custom functions can go here 
+
+void phenotype_function( Cell* pCell, Phenotype& phenotype, double dt );
+void custom_function( Cell* pCell, Phenotype& phenotype , double dt );
+
+void contact_function( Cell* pMe, Phenotype& phenoMe , Cell* pOther, Phenotype& phenoOther , double dt ); 
+
+void custom_division_function( Cell* pCell1, Cell* pCell2 );
diff --git a/user_projects/sample_division_lineage/main.cpp b/user_projects/sample_division_lineage/main.cpp
new file mode 100644
index 000000000..2f7e98c75
--- /dev/null
+++ b/user_projects/sample_division_lineage/main.cpp
@@ -0,0 +1,254 @@
+/*
+###############################################################################
+# 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) 2015-2022, 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.                                                 #
+#                                                                             #
+###############################################################################
+*/
+
+#include <cstdio>
+#include <cstdlib>
+#include <iostream>
+#include <ctime>
+#include <cmath>
+#include <omp.h>
+#include <fstream>
+
+#include "./core/PhysiCell.h"
+#include "./modules/PhysiCell_standard_modules.h" 
+
+// put custom code modules here! 
+
+#include "./custom_modules/custom.h" 
+	
+using namespace BioFVM;
+using namespace PhysiCell;
+
+int main( int argc, char* argv[] )
+{
+	// load and parse settings file(s)
+	
+	bool XML_status = false; 
+	char copy_command [1024]; 
+	if( argc > 1 )
+	{
+		XML_status = load_PhysiCell_config_file( argv[1] ); 
+		sprintf( copy_command , "cp %s %s" , argv[1] , PhysiCell_settings.folder.c_str() ); 
+	}
+	else
+	{
+		XML_status = load_PhysiCell_config_file( "./config/PhysiCell_settings.xml" );
+		sprintf( copy_command , "cp ./config/PhysiCell_settings.xml %s" , PhysiCell_settings.folder.c_str() ); 
+	}
+	if( !XML_status )
+	{ exit(-1); }
+	
+	// copy config file to output directry 
+	system( copy_command ); 
+	
+	// OpenMP setup
+	omp_set_num_threads(PhysiCell_settings.omp_num_threads);
+	
+	// time setup 
+	std::string time_units = "min"; 
+
+	/* Microenvironment setup */ 
+	
+	setup_microenvironment(); // modify this in the custom code 
+	
+	/* PhysiCell setup */ 
+ 	
+	// set mechanics voxel size, and match the data structure to BioFVM
+	double mechanics_voxel_size = 30; 
+	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
+	
+	/* Users typically start modifying here. START USERMODS */ 
+	
+	create_cell_types();
+	
+	setup_tissue();
+
+	/* Users typically stop modifying here. END USERMODS */ 
+	
+	// set MultiCellDS save options 
+
+	set_save_biofvm_mesh_as_matlab( true ); 
+	set_save_biofvm_data_as_matlab( true ); 
+	set_save_biofvm_cell_data( true ); 
+	set_save_biofvm_cell_data_as_custom_matlab( true );
+	
+	// save a simulation snapshot 
+	
+	char filename[1024];
+	sprintf( filename , "%s/initial" , PhysiCell_settings.folder.c_str() ); 
+	save_PhysiCell_to_MultiCellDS_v2( filename , microenvironment , PhysiCell_globals.current_time ); 
+	
+	// save a quick SVG cross section through z = 0, after setting its 
+	// length bar to 200 microns 
+
+	PhysiCell_SVG_options.length_bar = 200; 
+
+	// for simplicity, set a pathology coloring function 
+	
+	std::vector<std::string> (*cell_coloring_function)(Cell*) = my_coloring_function;
+	std::string (*substrate_coloring_function)(double, double, double) = paint_by_density_percentage;
+
+	sprintf( filename , "%s/initial.svg" , PhysiCell_settings.folder.c_str() ); 
+	SVG_plot( filename , microenvironment, 0.0 , PhysiCell_globals.current_time, cell_coloring_function, substrate_coloring_function );
+	
+	sprintf( filename , "%s/legend.svg" , PhysiCell_settings.folder.c_str() ); 
+	create_plot_legend( filename , cell_coloring_function ); 
+	
+	display_citations(); 
+	
+	// set the performance timers 
+
+	BioFVM::RUNTIME_TIC();
+	BioFVM::TIC();
+	
+	std::ofstream report_file;
+	if( PhysiCell_settings.enable_legacy_saves == true )
+	{	
+		sprintf( filename , "%s/simulation_report.txt" , PhysiCell_settings.folder.c_str() ); 
+		
+		report_file.open(filename); 	// create the data log file 
+		report_file<<"simulated time\tnum cells\tnum division\tnum death\twall time"<<std::endl;
+	}
+	
+	// main loop 
+	
+	try 
+	{		
+		while( PhysiCell_globals.current_time < PhysiCell_settings.max_time + 0.1*diffusion_dt )
+		{
+			// save data if it's time. 
+			if( fabs( PhysiCell_globals.current_time - PhysiCell_globals.next_full_save_time ) < 0.01 * diffusion_dt )
+			{
+				display_simulation_status( std::cout ); 
+				if( PhysiCell_settings.enable_legacy_saves == true )
+				{	
+					log_output( PhysiCell_globals.current_time , PhysiCell_globals.full_output_index, microenvironment, report_file);
+				}
+				
+				if( PhysiCell_settings.enable_full_saves == true )
+				{	
+					sprintf( filename , "%s/output%08u" , PhysiCell_settings.folder.c_str(),  PhysiCell_globals.full_output_index ); 
+					
+					save_PhysiCell_to_MultiCellDS_v2( filename , microenvironment , PhysiCell_globals.current_time ); 
+				}
+				
+				PhysiCell_globals.full_output_index++; 
+				PhysiCell_globals.next_full_save_time += PhysiCell_settings.full_save_interval;
+			}
+			
+			// save SVG plot if it's time
+			if( fabs( PhysiCell_globals.current_time - PhysiCell_globals.next_SVG_save_time  ) < 0.01 * diffusion_dt )
+			{
+				if( PhysiCell_settings.enable_SVG_saves == true )
+				{	
+					sprintf( filename , "%s/snapshot%08u.svg" , PhysiCell_settings.folder.c_str() , PhysiCell_globals.SVG_output_index );
+					SVG_plot( filename , microenvironment, 0.0 , PhysiCell_globals.current_time, cell_coloring_function, substrate_coloring_function);
+
+					PhysiCell_globals.SVG_output_index++; 
+					PhysiCell_globals.next_SVG_save_time  += PhysiCell_settings.SVG_save_interval;
+				}
+			}
+
+			// update the microenvironment
+			microenvironment.simulate_diffusion_decay( diffusion_dt );
+			
+			// run PhysiCell 
+			((Cell_Container *)microenvironment.agent_container)->update_all_cells( PhysiCell_globals.current_time );
+			
+			/*
+			  Custom add-ons could potentially go here. 
+			*/
+			
+			PhysiCell_globals.current_time += diffusion_dt;
+		}
+		
+		if( PhysiCell_settings.enable_legacy_saves == true )
+		{			
+			log_output(PhysiCell_globals.current_time, PhysiCell_globals.full_output_index, microenvironment, report_file);
+			report_file.close();
+		}
+	}
+	catch( const std::exception& e )
+	{ // reference to the base of a polymorphic object
+		std::cout << e.what(); // information from length_error printed
+	}
+	
+	// save a final simulation snapshot 
+	
+	sprintf( filename , "%s/final" , PhysiCell_settings.folder.c_str() ); 
+	save_PhysiCell_to_MultiCellDS_v2( filename , microenvironment , PhysiCell_globals.current_time ); 
+	
+	sprintf( filename , "%s/final.svg" , PhysiCell_settings.folder.c_str() );
+	SVG_plot(filename, microenvironment, 0.0, PhysiCell_globals.current_time, cell_coloring_function, substrate_coloring_function);
+
+	// timer 
+	
+	std::cout << std::endl << "Total simulation runtime: " << std::endl; 
+	BioFVM::display_stopwatch_value( std::cout , BioFVM::runtime_stopwatch_value() ); 
+
+	return 0; 
+}

From 4b7ba7da8738eff16339d88dbc84aa70b3594fbe Mon Sep 17 00:00:00 2001
From: Randy Heiland <randy.heiland@gmail.com>
Date: Sun, 14 Jul 2024 17:18:49 -0400
Subject: [PATCH 04/12] update

---
 core/PhysiCell_cell.cpp           | 10 ++++++++--
 core/PhysiCell_cell.h             |  1 +
 modules/PhysiCell_MultiCellDS.cpp | 14 ++++++++++++++
 3 files changed, 23 insertions(+), 2 deletions(-)

diff --git a/core/PhysiCell_cell.cpp b/core/PhysiCell_cell.cpp
index 2496ddf90..5c53aa1be 100644
--- a/core/PhysiCell_cell.cpp
+++ b/core/PhysiCell_cell.cpp
@@ -419,6 +419,7 @@ Cell::Cell()
 	is_movable = true;
 	is_out_of_domain = false;
     generation = 0;
+    parentID = -1;   // overridden in create_cell() and divide()
 	displacement.resize(3,0.0); // state? 
 	
 	assign_orientation();
@@ -565,8 +566,12 @@ Cell* Cell::divide( )
 	Cell* child = create_cell(functions.instantiate_cell);
 	child->copy_data( this );	
     // lineage tracking
-    generation = generation + 1;     // this (parent) cell has its generation incremented
-    child->generation = generation;  // its daughter cell has the same generation
+    // generation = generation + 1;     // this (parent) cell has its generation incremented
+    // child->generation = generation;  // daughter cell has the same generation
+    child->generation = generation + 1;
+    // child->parentID = parentID;
+    parentID = ID;
+    child->parentID = ID;
 	child->copy_function_pointers(this);
 	child->parameters = parameters;
 	
@@ -1075,6 +1080,7 @@ Cell* create_cell( Cell* (*custom_instantiate)())
 	} else {
 		pNew = standard_instantiate_cell();
 	}
+    pNew->parentID = pNew->ID;
 	
 	(*all_cells).push_back( pNew ); 
 	pNew->index=(*all_cells).size()-1;
diff --git a/core/PhysiCell_cell.h b/core/PhysiCell_cell.h
index 27f4906eb..59566d24d 100644
--- a/core/PhysiCell_cell.h
+++ b/core/PhysiCell_cell.h
@@ -190,6 +190,7 @@ class Cell : public Basic_Agent
 	bool is_movable;
 
     int generation;   // for lineage tracking
+    int parentID;   // for lineage tracking
 	
 	void flag_for_division( void ); // done 
 	void flag_for_removal( void ); // done 
diff --git a/modules/PhysiCell_MultiCellDS.cpp b/modules/PhysiCell_MultiCellDS.cpp
index 6d9a6afba..860e278a9 100644
--- a/modules/PhysiCell_MultiCellDS.cpp
+++ b/modules/PhysiCell_MultiCellDS.cpp
@@ -902,6 +902,17 @@ void add_PhysiCell_cells_to_open_xml_pugi_v2( pugi::xml_document& xml_dom, std::
 		cell_data_size += size; 
 		index += size; 
 
+        // parentID
+		name = "parentID"; 
+		size = 1; 
+		units="none";
+		data_names.push_back( name ); 
+		data_units.push_back(units); 
+		data_sizes.push_back( size ); 
+		data_start_indices.push_back( index ); 
+		cell_data_size += size; 
+		index += size; 
+
 		//					<label index="1" size="3">position</label>
 		name = "position"; 
 		size = 3; 
@@ -1769,6 +1780,9 @@ void add_PhysiCell_cells_to_open_xml_pugi_v2( pugi::xml_document& xml_dom, std::
         // name = "generation"; 
 		dTemp = (double) pCell->generation;
 		std::fwrite( &( dTemp ) , sizeof(double) , 1 , fp ); 
+        // name = "parentID"; 
+		dTemp = (double) pCell->parentID;
+		std::fwrite( &( dTemp ) , sizeof(double) , 1 , fp ); 
 		// name = "position";    NOTE very different syntax for writing vectors!
         std::fwrite( pCell->position.data() , sizeof(double) , 3 , fp );
 		// name = "total_volume"; 

From c73c26e604d62c4274c099c88ce3e290468c6fa0 Mon Sep 17 00:00:00 2001
From: Randy Heiland <randy.heiland@gmail.com>
Date: Sun, 14 Jul 2024 17:37:05 -0400
Subject: [PATCH 05/12] update

---
 core/PhysiCell_constants.cpp | 63 +++++++++++++++++++++++++++---
 core/PhysiCell_constants.h   | 74 ++++++++++++++++++------------------
 2 files changed, 94 insertions(+), 43 deletions(-)

diff --git a/core/PhysiCell_constants.cpp b/core/PhysiCell_constants.cpp
index 7727c40f2..8ade36f6b 100644
--- a/core/PhysiCell_constants.cpp
+++ b/core/PhysiCell_constants.cpp
@@ -76,12 +76,63 @@ double mechanics_dt = 0.1;
 double phenotype_dt = 6.0;
 double intracellular_dt = 0.01;
 
-std::unordered_map<std::string,int> cycle_model_codes = 
-{
-	{ "Ki67 (advanced)", PhysiCell_constants::advanced_Ki67_cycle_model}, 
-	{ "Ki67 (basic)" ,PhysiCell_constants::basic_Ki67_cycle_model},
-	{ "Flow cytometry model (basic)",PhysiCell_constants::flow_cytometry_cycle_model},
-	// { ,PhysiCell_constants::live_apoptotic_cycle_model}, // not implemented 
+
+// currently recognized cell cycle models 
+const int PhysiCell_constants::advanced_Ki67_cycle_model= 0;
+const int PhysiCell_constants::basic_Ki67_cycle_model=1;
+const int PhysiCell_constants::flow_cytometry_cycle_model=2;
+const int PhysiCell_constants::live_apoptotic_cycle_model=3;
+const int PhysiCell_constants::total_cells_cycle_model=4;
+const int PhysiCell_constants::live_cells_cycle_model = 5; 
+const int PhysiCell_constants::flow_cytometry_separated_cycle_model = 6; 
+const int PhysiCell_constants::cycling_quiescent_model = 7; 
+
+// currently recognized death models 
+const int PhysiCell_constants::apoptosis_death_model = 100; 
+const int PhysiCell_constants::necrosis_death_model = 101; 
+const int PhysiCell_constants::autophagy_death_model = 102; 
+
+const int PhysiCell_constants::custom_cycle_model=9999; 
+
+// currently recognized cell cycle and death phases 
+// cycle phases
+const int PhysiCell_constants::Ki67_positive_premitotic=0; 
+const int PhysiCell_constants::Ki67_positive_postmitotic=1; 
+const int PhysiCell_constants::Ki67_positive=2; 
+const int PhysiCell_constants::Ki67_negative=3; 
+const int PhysiCell_constants::G0G1_phase=4;
+const int PhysiCell_constants::G0_phase=5;
+const int PhysiCell_constants::G1_phase=6; 
+const int PhysiCell_constants::G1a_phase=7; 
+const int PhysiCell_constants::G1b_phase=8;
+const int PhysiCell_constants::G1c_phase=9;
+const int PhysiCell_constants::S_phase=10;
+const int PhysiCell_constants::G2M_phase=11;
+const int PhysiCell_constants::G2_phase=12;
+const int PhysiCell_constants::M_phase=13;
+const int PhysiCell_constants::live=14;
+
+const int PhysiCell_constants::G1pm_phase = 15;
+const int PhysiCell_constants::G1ps_phase = 16; 
+
+const int PhysiCell_constants::cycling = 17; 
+const int PhysiCell_constants::quiescent = 18; 
+
+
+const int PhysiCell_constants::custom_phase = 9999;
+// death phases
+const int PhysiCell_constants::apoptotic=100;
+const int PhysiCell_constants::necrotic_swelling=101;
+const int PhysiCell_constants::necrotic_lysed=102;
+const int PhysiCell_constants::necrotic=103; 
+const int PhysiCell_constants::debris=104; 
+
+std::unordered_map<std::string,int> cycle_model_codes = {
+
+    { "Ki67 (advanced)", PhysiCell_constants::advanced_Ki67_cycle_model}, 
+    { "Ki67 (basic)" ,PhysiCell_constants::basic_Ki67_cycle_model},
+    { "Flow cytometry model (basic)",PhysiCell_constants::flow_cytometry_cycle_model},
+// { ,PhysiCell_constants::live_apoptotic_cycle_model}, // not implemented 
 	// { ,PhysiCell_constants::total_cells_cycle_model}, // not implemented 
 	{ "Live",PhysiCell_constants::live_cells_cycle_model}, 
 	{ "Flow cytometry model (separated)",PhysiCell_constants::flow_cytometry_separated_cycle_model}, 
diff --git a/core/PhysiCell_constants.h b/core/PhysiCell_constants.h
index 476953148..58aef3c84 100644
--- a/core/PhysiCell_constants.h
+++ b/core/PhysiCell_constants.h
@@ -102,54 +102,54 @@ class PhysiCell_constants
 	static const int mesh_uz_face_index=5;
 	
 	// currently recognized cell cycle models 
-	static const int advanced_Ki67_cycle_model= 0;
-	static const int basic_Ki67_cycle_model=1;
-	static const int flow_cytometry_cycle_model=2;
-	static const int live_apoptotic_cycle_model=3;
-	static const int total_cells_cycle_model=4;
-	static const int live_cells_cycle_model = 5; 
-	static const int flow_cytometry_separated_cycle_model = 6; 
-	static const int cycling_quiescent_model = 7; 
+	static const int advanced_Ki67_cycle_model;
+	static const int basic_Ki67_cycle_model;
+	static const int flow_cytometry_cycle_model;
+	static const int live_apoptotic_cycle_model;
+	static const int total_cells_cycle_model;
+	static const int live_cells_cycle_model ; 
+	static const int flow_cytometry_separated_cycle_model ; 
+	static const int cycling_quiescent_model ; 
 	
 	// currently recognized death models 
-	static const int apoptosis_death_model = 100; 
-	static const int necrosis_death_model = 101; 
-	static const int autophagy_death_model = 102; 
+	static const int apoptosis_death_model ; 
+	static const int necrosis_death_model ; 
+	static const int autophagy_death_model ; 
 	
-	static const int custom_cycle_model=9999; 
+	static const int custom_cycle_model; 
 	
 	// currently recognized cell cycle and death phases 
 	// cycle phases
-	static const int Ki67_positive_premitotic=0; 
-	static const int Ki67_positive_postmitotic=1; 
-	static const int Ki67_positive=2; 
-	static const int Ki67_negative=3; 
-	static const int G0G1_phase=4;
-	static const int G0_phase=5;
-	static const int G1_phase=6; 
-	static const int G1a_phase=7; 
-	static const int G1b_phase=8;
-	static const int G1c_phase=9;
-	static const int S_phase=10;
-	static const int G2M_phase=11;
-	static const int G2_phase=12;
-	static const int M_phase=13;
-	static const int live=14;
+	static const int Ki67_positive_premitotic; 
+	static const int Ki67_positive_postmitotic; 
+	static const int Ki67_positive; 
+	static const int Ki67_negative; 
+	static const int G0G1_phase;
+	static const int G0_phase;
+	static const int G1_phase; 
+	static const int G1a_phase; 
+	static const int G1b_phase;
+	static const int G1c_phase;
+	static const int S_phase;
+	static const int G2M_phase;
+	static const int G2_phase;
+	static const int M_phase;
+	static const int live;
 	
-	static const int G1pm_phase = 15;
-	static const int G1ps_phase = 16; 
+	static const int G1pm_phase ;
+	static const int G1ps_phase ; 
 	
-	static const int cycling = 17; 
-	static const int quiescent = 18; 
+	static const int cycling ; 
+	static const int quiescent ; 
 	
 	
-	static const int custom_phase = 9999;
+	static const int custom_phase ;
 	// death phases
-	static const int apoptotic=100;
-	static const int necrotic_swelling=101;
-	static const int necrotic_lysed=102;
-	static const int necrotic=103; 
-	static const int debris=104; 
+	static const int apoptotic;
+	static const int necrotic_swelling;
+	static const int necrotic_lysed;
+	static const int necrotic; 
+	static const int debris; 
 };
 extern std::string time_units;
 extern std::string space_units;

From 145d9d0603b5cf4af79b2dac381e8540ef15c055 Mon Sep 17 00:00:00 2001
From: Randy Heiland <randy.heiland@gmail.com>
Date: Sun, 14 Jul 2024 17:56:08 -0400
Subject: [PATCH 06/12] update

---
 .../sample_division_lineage/config/PhysiCell_settings.xml       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/user_projects/sample_division_lineage/config/PhysiCell_settings.xml b/user_projects/sample_division_lineage/config/PhysiCell_settings.xml
index 43b85b8d3..eb76470f2 100644
--- a/user_projects/sample_division_lineage/config/PhysiCell_settings.xml
+++ b/user_projects/sample_division_lineage/config/PhysiCell_settings.xml
@@ -14,7 +14,7 @@
     </domain>
 
     <overall>
-        <max_time units="min">5760.0</max_time>
+        <max_time units="min">4320.0</max_time>
         <time_units>min</time_units>
         <space_units>micron</space_units>
         <dt_diffusion units="min">0.01</dt_diffusion>

From a4eccbe6ac3b2c6c20f109eed853a774b35685d2 Mon Sep 17 00:00:00 2001
From: Randy Heiland <randy.heiland@gmail.com>
Date: Mon, 15 Jul 2024 09:26:34 -0400
Subject: [PATCH 07/12] incr generation for both; stochastic cell cycle

---
 core/PhysiCell_cell.cpp                                     | 6 +++---
 .../sample_division_lineage/config/PhysiCell_settings.xml   | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/core/PhysiCell_cell.cpp b/core/PhysiCell_cell.cpp
index 5c53aa1be..f5b559bd7 100644
--- a/core/PhysiCell_cell.cpp
+++ b/core/PhysiCell_cell.cpp
@@ -566,9 +566,9 @@ Cell* Cell::divide( )
 	Cell* child = create_cell(functions.instantiate_cell);
 	child->copy_data( this );	
     // lineage tracking
-    // generation = generation + 1;     // this (parent) cell has its generation incremented
-    // child->generation = generation;  // daughter cell has the same generation
-    child->generation = generation + 1;
+    generation = generation + 1;     // this (parent) cell has its generation incremented
+    child->generation = generation;  // daughter cell has the same generation
+    // child->generation = generation + 1;
     // child->parentID = parentID;
     parentID = ID;
     child->parentID = ID;
diff --git a/user_projects/sample_division_lineage/config/PhysiCell_settings.xml b/user_projects/sample_division_lineage/config/PhysiCell_settings.xml
index eb76470f2..abdea1ab9 100644
--- a/user_projects/sample_division_lineage/config/PhysiCell_settings.xml
+++ b/user_projects/sample_division_lineage/config/PhysiCell_settings.xml
@@ -86,7 +86,7 @@
             <phenotype>
                 <cycle code="5" name="live">
                     <phase_durations units="min">
-                        <duration index="0" fixed_duration="true">660</duration>
+                        <duration index="0" fixed_duration="false">660</duration>
                     </phase_durations>
                 </cycle>
                 <death>
@@ -207,7 +207,7 @@
             <phenotype>
                 <cycle code="5" name="live">
                     <phase_durations units="min">
-                        <duration index="0" fixed_duration="true">660</duration>
+                        <duration index="0" fixed_duration="false">660</duration>
                     </phase_durations>
                 </cycle>
                 <death>

From 672ddd2a441430e644f5a678a8ba7ee6fd66de86 Mon Sep 17 00:00:00 2001
From: Randy Heiland <randy.heiland@gmail.com>
Date: Thu, 15 Aug 2024 06:38:50 -0400
Subject: [PATCH 08/12] remove user proj

---
 .../sample_division_lineage/Makefile          | 314 ----------------
 .../config/PhysiCell_settings.xml             | 349 ------------------
 .../config/cell_rules.csv                     |   0
 .../sample_division_lineage/config/cells.csv  |   3 -
 .../custom_modules/custom.cpp                 | 236 ------------
 .../custom_modules/custom.h                   |  93 -----
 .../sample_division_lineage/main.cpp          | 254 -------------
 7 files changed, 1249 deletions(-)
 delete mode 100644 user_projects/sample_division_lineage/Makefile
 delete mode 100644 user_projects/sample_division_lineage/config/PhysiCell_settings.xml
 delete mode 100644 user_projects/sample_division_lineage/config/cell_rules.csv
 delete mode 100644 user_projects/sample_division_lineage/config/cells.csv
 delete mode 100644 user_projects/sample_division_lineage/custom_modules/custom.cpp
 delete mode 100644 user_projects/sample_division_lineage/custom_modules/custom.h
 delete mode 100644 user_projects/sample_division_lineage/main.cpp

diff --git a/user_projects/sample_division_lineage/Makefile b/user_projects/sample_division_lineage/Makefile
deleted file mode 100644
index e90a9966f..000000000
--- a/user_projects/sample_division_lineage/Makefile
+++ /dev/null
@@ -1,314 +0,0 @@
-VERSION := $(shell grep . VERSION.txt | cut -f1 -d:)
-PROGRAM_NAME := project
-
-CC := g++
-# 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=$(ARCH) -O3 -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11
-
-ifeq ($(OS),Windows_NT)
-else
-	UNAME_S := $(shell uname -s)
-	ifeq ($(UNAME_S),Darwin)
-		UNAME_P := $(shell uname -p)
-		var := $(shell which $(CC) | xargs file)
-		ifeq ($(lastword $(var)),arm64)
-		  CFLAGS := -march=$(ARCH) -O3 -fomit-frame-pointer -fopenmp -m64 -std=c++11
-		endif
-	endif
-endif
-
-COMPILE_COMMAND := $(CC) $(CFLAGS) 
-
-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_basic_signaling.o \
-PhysiCell_signal_behavior.o PhysiCell_rules.o
-
-PhysiCell_module_OBJECTS := PhysiCell_SVG.o PhysiCell_pathology.o PhysiCell_MultiCellDS.o PhysiCell_various_outputs.o \
-PhysiCell_pugixml.o PhysiCell_settings.o PhysiCell_geometry.o
-
-# put your custom objects here (they should be in the custom_modules directory)
-
-PhysiCell_custom_module_OBJECTS := custom.o
-
-pugixml_OBJECTS := pugixml.o
-
-PhysiCell_OBJECTS := $(BioFVM_OBJECTS)  $(pugixml_OBJECTS) $(PhysiCell_core_OBJECTS) $(PhysiCell_module_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 
-	make name
-
-name:
-	@echo ""
-	@echo "Executable name is" $(PROGRAM_NAME)
-	@echo ""
-
-# PhysiCell core components	
-
-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 
-	
-PhysiCell_signal_behavior.o: ./core/PhysiCell_signal_behavior.cpp
-	$(COMPILE_COMMAND) -c ./core/PhysiCell_signal_behavior.cpp 
-
-PhysiCell_rules.o: ./core/PhysiCell_rules.cpp
-	$(COMPILE_COMMAND) -c ./core/PhysiCell_rules.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
-	
-PhysiCell_basic_signaling.o: ./core/PhysiCell_basic_signaling.cpp
-	$(COMPILE_COMMAND) -c ./core/PhysiCell_basic_signaling.cpp 	
-	
-PhysiCell_geometry.o: ./modules/PhysiCell_geometry.cpp
-	$(COMPILE_COMMAND) -c ./modules/PhysiCell_geometry.cpp 
-	
-# user-defined PhysiCell modules
-
-custom.o: ./custom_modules/custom.cpp 
-	$(COMPILE_COMMAND) -c ./custom_modules/custom.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 
-	touch ./core/PhysiCell_cell.cpp
-	rm ALL_CITATIONS.txt 
-	cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml 
-	touch ./config/empty.csv
-	rm -f ./config/*.csv
-	
-clean:
-	rm -f *.o
-	rm -f $(PROGRAM_NAME)*
-	
-data-cleanup:
-	rm -rf ./output
-	mkdir ./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
-
-# easier animation 
-
-FRAMERATE := 24
-OUTPUT := output
-
-jpeg: 
-	@magick identify -format "%h" $(OUTPUT)/initial.svg > __H.txt 
-	@magick identify -format "%w" $(OUTPUT)/initial.svg > __W.txt 
-	@expr 2 \* \( $$(grep . __H.txt) / 2 \) > __H1.txt 
-	@expr 2 \* \( $$(grep . __W.txt) / 2 \) > __W1.txt 
-	@echo "$$(grep . __W1.txt)!x$$(grep . __H1.txt)!" > __resize.txt 
-	@magick mogrify -format jpg -resize $$(grep . __resize.txt) $(OUTPUT)/s*.svg
-	rm -f __H*.txt __W*.txt __resize.txt 
-	
-gif: 
-	magick convert $(OUTPUT)/s*.svg $(OUTPUT)/out.gif 
-	 
-movie:
-	ffmpeg -r $(FRAMERATE) -f image2 -i $(OUTPUT)/snapshot%08d.jpg -vcodec libx264 -pix_fmt yuv420p -strict -2 -tune animation -crf 15 -acodec none $(OUTPUT)/out.mp4
-	
-# upgrade rules 
-
-SOURCE := PhysiCell_upgrade.zip 
-get-upgrade: 
-	@echo $$(curl https://raw.githubusercontent.com/MathCancer/PhysiCell/master/VERSION.txt) > VER.txt 
-	@echo https://github.com/MathCancer/PhysiCell/releases/download/$$(grep . VER.txt)/PhysiCell_V.$$(grep . VER.txt).zip > DL_FILE.txt 
-	rm -f VER.txt
-	$$(curl -L $$(grep . DL_FILE.txt) --output PhysiCell_upgrade.zip)
-	rm -f DL_FILE.txt 
-
-PhysiCell_upgrade.zip: 
-	make get-upgrade 
-
-upgrade: $(SOURCE)
-	unzip $(SOURCE) PhysiCell/VERSION.txt
-	mv -f PhysiCell/VERSION.txt . 
-	unzip $(SOURCE) PhysiCell/core/* 
-	cp -r PhysiCell/core/* core 
-	unzip $(SOURCE) PhysiCell/modules/* 
-	cp -r PhysiCell/modules/* modules 
-	unzip $(SOURCE) PhysiCell/sample_projects/* 
-	cp -r PhysiCell/sample_projects/* sample_projects 
-	unzip $(SOURCE) PhysiCell/BioFVM/* 
-	cp -r PhysiCell/BioFVM/* BioFVM
-	unzip $(SOURCE) PhysiCell/documentation/User_Guide.pdf
-	mv -f PhysiCell/documentation/User_Guide.pdf documentation
-	rm -f -r PhysiCell
-	rm -f $(SOURCE) 
-
-# use: make save PROJ=your_project_name
-PROJ := my_project
-
-save: 
-	echo "Saving project as $(PROJ) ... "
-	mkdir -p ./user_projects
-	mkdir -p ./user_projects/$(PROJ)
-	mkdir -p ./user_projects/$(PROJ)/custom_modules
-	mkdir -p ./user_projects/$(PROJ)/config 
-	cp main.cpp ./user_projects/$(PROJ)
-	cp Makefile ./user_projects/$(PROJ)
-	cp VERSION.txt ./user_projects/$(PROJ)
-	cp ./config/* ./user_projects/$(PROJ)/config
-	cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules
-
-load: 
-	echo "Loading project from $(PROJ) ... "
-	cp ./user_projects/$(PROJ)/main.cpp .
-	cp ./user_projects/$(PROJ)/Makefile .
-	cp ./user_projects/$(PROJ)/config/* ./config/ 
-	cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ 
-
-pack:
-	@echo " "
-	@echo "Preparing project $(PROJ) for sharing ... "
-	@echo " " 
-	cd ./user_projects && zip -r $(PROJ).zip $(PROJ)
-	@echo " "
-	@echo "Share ./user_projects/$(PROJ).zip ... "
-	@echo "Other users can unzip $(PROJ).zip in their ./user_projects, compile, and run."
-	@echo " " 
-
-unpack:
-	@echo " "
-	@echo "Preparing shared project $(PROJ).zip for use ... "
-	@echo " " 
-	cd ./user_projects && unzip $(PROJ).zip 
-	@echo " "
-	@echo "Load this project via make load PROJ=$(PROJ) ... "
-	@echo " " 	
-
-list-user-projects:
-	@echo "user projects::"
-	@cd ./user_projects && ls -dt1 * | grep . | sed 's!empty.txt!!'
diff --git a/user_projects/sample_division_lineage/config/PhysiCell_settings.xml b/user_projects/sample_division_lineage/config/PhysiCell_settings.xml
deleted file mode 100644
index abdea1ab9..000000000
--- a/user_projects/sample_division_lineage/config/PhysiCell_settings.xml
+++ /dev/null
@@ -1,349 +0,0 @@
-<PhysiCell_settings version="devel-version">
-
-    <domain>
-        <x_min>-200</x_min>
-        <x_max>200</x_max>
-        <y_min>-200</y_min>
-        <y_max>200</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">4320.0</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>1</omp_num_threads>
-    </parallel>
-
-    <save>
-        <folder>output</folder>
-        <full_data>
-            <interval units="min">30</interval>
-            <enable>true</enable>
-        </full_data>
-        <SVG>
-            <interval units="min">30</interval>
-            <enable>true</enable>
-            <plot_substrate enabled="false" limits="false">
-                <substrate>oxygen</substrate>
-                <min_conc />
-                <max_conc />
-            </plot_substrate>
-        </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="oxygen" units="dimensionless" ID="0">
-            <physical_parameter_set>
-                <diffusion_coefficient units="micron^2/min">1000.0</diffusion_coefficient>
-                <decay_rate units="1/min">0.1</decay_rate>
-            </physical_parameter_set>
-            <initial_condition units="mmHg">38</initial_condition>
-            <Dirichlet_boundary_condition units="mmHg" enabled="True">38</Dirichlet_boundary_condition>
-            <Dirichlet_options>
-                <boundary_value ID="xmin" enabled="True">38</boundary_value>
-                <boundary_value ID="xmax" enabled="True">38</boundary_value>
-                <boundary_value ID="ymin" enabled="True">38</boundary_value>
-                <boundary_value ID="ymax" enabled="True">38</boundary_value>
-                <boundary_value ID="zmin" enabled="False">38</boundary_value>
-                <boundary_value ID="zmax" enabled="False">38</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="5" name="live">
-                    <phase_durations units="min">
-                        <duration index="0" fixed_duration="false">660</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">1.11667e-2</unlysed_fluid_change_rate>
-                            <lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
-                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-5</cytoplasmic_biomass_change_rate>
-                            <nuclear_biomass_change_rate units="1/min">2.16667e-3</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</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="ctype1">1</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>
-                    <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>oxygen</substrate>
-                            <direction>1</direction>
-                        </chemotaxis>
-                        <advanced_chemotaxis>
-                            <enabled>false</enabled>
-                            <normalize_each_gradient>false</normalize_each_gradient>
-                            <chemotactic_sensitivities>
-                                <chemotactic_sensitivity substrate="oxygen">0.0</chemotactic_sensitivity>
-                            </chemotactic_sensitivities>
-                        </advanced_chemotaxis>
-                    </options>
-                </motility>
-                <secretion>
-                    <substrate name="oxygen">
-                        <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</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>
-                    </live_phagocytosis_rates>
-                    <attack_rates>
-                        <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>
-                    <fusion_rates>
-                        <fusion_rate name="default" units="1/min">0.0</fusion_rate>
-                        <fusion_rate name="ctype1" units="1/min">0</fusion_rate>
-                    </fusion_rates>
-                </cell_interactions>
-                <cell_transformations>
-                    <transformation_rates>
-                        <transformation_rate name="default" units="1/min">0.0</transformation_rate>
-                        <transformation_rate name="ctype1" units="1/min">0</transformation_rate>
-                    </transformation_rates>
-                </cell_transformations>
-            </phenotype>
-            <custom_data>
-                <sample conserved="false" units="dimensionless" description="">1.0</sample>
-            </custom_data>
-        </cell_definition>
-        <cell_definition name="ctype1" ID="1">
-            <phenotype>
-                <cycle code="5" name="live">
-                    <phase_durations units="min">
-                        <duration index="0" fixed_duration="false">660</duration>
-                    </phase_durations>
-                </cycle>
-                <death>
-                    <model code="100" name="apoptosis">
-                        <death_rate units="1/min">0</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">1.11667e-2</unlysed_fluid_change_rate>
-                            <lysed_fluid_change_rate units="1/min">8.33333e-4</lysed_fluid_change_rate>
-                            <cytoplasmic_biomass_change_rate units="1/min">5.33333e-5</cytoplasmic_biomass_change_rate>
-                            <nuclear_biomass_change_rate units="1/min">2.16667e-3</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</cell_adhesion_affinity>
-                        <cell_adhesion_affinity name="ctype1">1</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>
-                    <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">0.05</speed>
-                    <persistence_time units="min">0</persistence_time>
-                    <migration_bias units="dimensionless">.5</migration_bias>
-                    <options>
-                        <enabled>true</enabled>
-                        <use_2D>true</use_2D>
-                        <chemotaxis>
-                            <enabled>true</enabled>
-                            <substrate>oxygen</substrate>
-                            <direction>1</direction>
-                        </chemotaxis>
-                        <advanced_chemotaxis>
-                            <enabled>false</enabled>
-                            <normalize_each_gradient>false</normalize_each_gradient>
-                            <chemotactic_sensitivities>
-                                <chemotactic_sensitivity substrate="oxygen">0.0</chemotactic_sensitivity>
-                            </chemotactic_sensitivities>
-                        </advanced_chemotaxis>
-                    </options>
-                </motility>
-                <secretion>
-                    <substrate name="oxygen">
-                        <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</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>
-                    </live_phagocytosis_rates>
-                    <attack_rates>
-                        <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>
-                    <fusion_rates>
-                        <fusion_rate name="default" units="1/min">0</fusion_rate>
-                        <fusion_rate name="ctype1" units="1/min">0</fusion_rate>
-                    </fusion_rates>
-                </cell_interactions>
-                <cell_transformations>
-                    <transformation_rates>
-                        <transformation_rate name="default" units="1/min">0</transformation_rate>
-                        <transformation_rate name="ctype1" units="1/min">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="true">
-            <folder>./config</folder>
-            <filename>cells.csv</filename>
-        </cell_positions>
-    </initial_conditions>
-
-    <cell_rules>
-        <rulesets>
-            <ruleset protocol="CBHG" version="2.0" format="csv" enabled="false">
-                <folder>config</folder>
-                <filename>rules.csv</filename>
-            </ruleset>
-        </rulesets>
-    </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>
\ No newline at end of file
diff --git a/user_projects/sample_division_lineage/config/cell_rules.csv b/user_projects/sample_division_lineage/config/cell_rules.csv
deleted file mode 100644
index e69de29bb..000000000
diff --git a/user_projects/sample_division_lineage/config/cells.csv b/user_projects/sample_division_lineage/config/cells.csv
deleted file mode 100644
index f19c4d4f4..000000000
--- a/user_projects/sample_division_lineage/config/cells.csv
+++ /dev/null
@@ -1,3 +0,0 @@
-x,y,z,type,volume,cycle entry,custom:GFP,custom:sample
--80.,80.,0.0,default
-80.,-80.,0.0,default
diff --git a/user_projects/sample_division_lineage/custom_modules/custom.cpp b/user_projects/sample_division_lineage/custom_modules/custom.cpp
deleted file mode 100644
index acbb1a395..000000000
--- a/user_projects/sample_division_lineage/custom_modules/custom.cpp
+++ /dev/null
@@ -1,236 +0,0 @@
-/*
-###############################################################################
-# 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) 2015-2021, 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.                                                 #
-#                                                                             #
-###############################################################################
-*/
-
-#include "./custom.h"
-
-void create_cell_types( void )
-{
-	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
-	
-	/* 
-	   Put any modifications to default cell definition here if you 
-	   want to have "inherited" by other cell types. 
-	   
-	   This is a good place to set default functions. 
-	*/ 
-	
-	initialize_default_cell_definition(); 
-	cell_defaults.phenotype.secretion.sync_to_microenvironment( &microenvironment ); 
-	
-	cell_defaults.functions.volume_update_function = standard_volume_update_function;
-	cell_defaults.functions.update_velocity = standard_update_cell_velocity;
-
-	cell_defaults.functions.update_migration_bias = NULL; 
-	cell_defaults.functions.update_phenotype = NULL; // update_cell_and_death_parameters_O2_based; 
-	cell_defaults.functions.custom_cell_rule = NULL; 
-	cell_defaults.functions.contact_function = NULL; 
-    cell_defaults.functions.cell_division_function = NULL; 
-	
-	cell_defaults.functions.add_cell_basement_membrane_interactions = NULL; 
-	cell_defaults.functions.calculate_distance_to_membrane = NULL; 
-	
-	/*
-	   This parses the cell definitions in the XML config file. 
-	*/
-	
-	initialize_cell_definitions_from_pugixml(); 
-
-	/*
-	   This builds the map of cell definitions and summarizes the setup. 
-	*/
-		
-	build_cell_definitions_maps(); 
-
-	/*
-	   This intializes cell signal and response dictionaries 
-	*/
-
-	setup_signal_behavior_dictionaries(); 	
-
-	/*
-       Cell rule definitions 
-	*/
-
-	setup_cell_rules(); 
-
-	/* 
-	   Put any modifications to individual cell definitions here. 
-	   
-	   This is a good place to set custom functions. 
-	*/ 
-	
-	cell_defaults.functions.update_phenotype = phenotype_function; 
-	cell_defaults.functions.custom_cell_rule = custom_function; 
-	cell_defaults.functions.contact_function = contact_function; 
-    cell_defaults.functions.cell_division_function = custom_division_function; 
-
-    int idx_ctype1 = find_cell_definition_index("ctype1");
-    Cell_Definition* pCD = cell_definitions_by_index[idx_ctype1]; 
-    pCD->functions.cell_division_function = custom_division_function; 
-	
-	/*
-	   This builds the map of cell definitions and summarizes the setup. 
-	*/
-		
-	display_cell_definitions( std::cout ); 
-	
-	return; 
-}
-
-void setup_microenvironment( void )
-{
-	// set domain parameters 
-	
-	// put any custom code to set non-homogeneous initial conditions or 
-	// extra Dirichlet nodes here. 
-	
-	// initialize BioFVM 
-	
-	initialize_microenvironment(); 	
-	
-	return; 
-}
-
-void setup_tissue( void )
-{
-	double Xmin = microenvironment.mesh.bounding_box[0]; 
-	double Ymin = microenvironment.mesh.bounding_box[1]; 
-	double Zmin = microenvironment.mesh.bounding_box[2]; 
-
-	double Xmax = microenvironment.mesh.bounding_box[3]; 
-	double Ymax = microenvironment.mesh.bounding_box[4]; 
-	double Zmax = microenvironment.mesh.bounding_box[5]; 
-	
-	if( default_microenvironment_options.simulate_2D == true )
-	{
-		Zmin = 0.0; 
-		Zmax = 0.0; 
-	}
-	
-	double Xrange = Xmax - Xmin; 
-	double Yrange = Ymax - Ymin; 
-	double Zrange = Zmax - Zmin; 
-	
-	// create some of each type of cell 
-	
-	Cell* pC;
-	
-	for( int k=0; k < cell_definitions_by_index.size() ; k++ )
-	{
-		Cell_Definition* pCD = cell_definitions_by_index[k]; 
-		std::cout << "Placing cells of type " << pCD->name << " ... " << std::endl; 
-		for( int n = 0 ; n < parameters.ints("number_of_cells") ; n++ )
-		{
-			std::vector<double> position = {0,0,0}; 
-			position[0] = Xmin + UniformRandom()*Xrange; 
-			position[1] = Ymin + UniformRandom()*Yrange; 
-			position[2] = Zmin + UniformRandom()*Zrange; 
-			
-			pC = create_cell( *pCD ); 
-			pC->assign_position( position );
-		}
-	}
-	std::cout << std::endl; 
-	
-	// load cells from your CSV file (if enabled)
-	load_cells_from_pugixml();
-	set_parameters_from_distributions();
-	
-	return; 
-}
-
-std::vector<std::string> my_coloring_function( Cell* pCell )
-{ return paint_by_number_cell_coloring(pCell); }
-
-void phenotype_function( Cell* pCell, Phenotype& phenotype, double dt )
-{ return; }
-
-void custom_function( Cell* pCell, Phenotype& phenotype , double dt )
-{ return; } 
-
-void contact_function( Cell* pMe, Phenotype& phenoMe , Cell* pOther, Phenotype& phenoOther , double dt )
-{ return; } 
-
-void custom_division_function( Cell* pCell1, Cell* pCell2 )
-{ 
-    static int idx_default = find_cell_definition_index("default");
-    static int idx_ctype1 = find_cell_definition_index("ctype1");
-    std::cout << __FUNCTION__ << ": t=" << PhysiCell_globals.current_time << ": cell IDs= " << pCell1->ID << ", " << pCell2->ID << ", pCell1->type_name= " << pCell1->type_name << std::endl;
-
-    // Asymmetric division
-    if (UniformRandom() < 0.5)
-    {
-        pCell2->convert_to_cell_definition( *cell_definitions_by_index[idx_default] ); 
-    }
-    else
-    {
-        pCell2->convert_to_cell_definition( *cell_definitions_by_index[idx_ctype1] ); 
-    }
-
-    return; 
-}
\ No newline at end of file
diff --git a/user_projects/sample_division_lineage/custom_modules/custom.h b/user_projects/sample_division_lineage/custom_modules/custom.h
deleted file mode 100644
index 7e6b0f044..000000000
--- a/user_projects/sample_division_lineage/custom_modules/custom.h
+++ /dev/null
@@ -1,93 +0,0 @@
-/*
-###############################################################################
-# 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) 2015-2021, 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.                                                 #
-#                                                                             #
-###############################################################################
-*/
-
-#include "../core/PhysiCell.h"
-#include "../modules/PhysiCell_standard_modules.h" 
-
-using namespace BioFVM; 
-using namespace PhysiCell;
-
-// setup functions to help us along 
-
-void create_cell_types( void );
-void setup_tissue( void ); 
-
-// set up the BioFVM microenvironment 
-void setup_microenvironment( void ); 
-
-// custom pathology coloring function 
-
-std::vector<std::string> my_coloring_function( Cell* );
-
-// custom functions can go here 
-
-void phenotype_function( Cell* pCell, Phenotype& phenotype, double dt );
-void custom_function( Cell* pCell, Phenotype& phenotype , double dt );
-
-void contact_function( Cell* pMe, Phenotype& phenoMe , Cell* pOther, Phenotype& phenoOther , double dt ); 
-
-void custom_division_function( Cell* pCell1, Cell* pCell2 );
diff --git a/user_projects/sample_division_lineage/main.cpp b/user_projects/sample_division_lineage/main.cpp
deleted file mode 100644
index 2f7e98c75..000000000
--- a/user_projects/sample_division_lineage/main.cpp
+++ /dev/null
@@ -1,254 +0,0 @@
-/*
-###############################################################################
-# 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) 2015-2022, 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.                                                 #
-#                                                                             #
-###############################################################################
-*/
-
-#include <cstdio>
-#include <cstdlib>
-#include <iostream>
-#include <ctime>
-#include <cmath>
-#include <omp.h>
-#include <fstream>
-
-#include "./core/PhysiCell.h"
-#include "./modules/PhysiCell_standard_modules.h" 
-
-// put custom code modules here! 
-
-#include "./custom_modules/custom.h" 
-	
-using namespace BioFVM;
-using namespace PhysiCell;
-
-int main( int argc, char* argv[] )
-{
-	// load and parse settings file(s)
-	
-	bool XML_status = false; 
-	char copy_command [1024]; 
-	if( argc > 1 )
-	{
-		XML_status = load_PhysiCell_config_file( argv[1] ); 
-		sprintf( copy_command , "cp %s %s" , argv[1] , PhysiCell_settings.folder.c_str() ); 
-	}
-	else
-	{
-		XML_status = load_PhysiCell_config_file( "./config/PhysiCell_settings.xml" );
-		sprintf( copy_command , "cp ./config/PhysiCell_settings.xml %s" , PhysiCell_settings.folder.c_str() ); 
-	}
-	if( !XML_status )
-	{ exit(-1); }
-	
-	// copy config file to output directry 
-	system( copy_command ); 
-	
-	// OpenMP setup
-	omp_set_num_threads(PhysiCell_settings.omp_num_threads);
-	
-	// time setup 
-	std::string time_units = "min"; 
-
-	/* Microenvironment setup */ 
-	
-	setup_microenvironment(); // modify this in the custom code 
-	
-	/* PhysiCell setup */ 
- 	
-	// set mechanics voxel size, and match the data structure to BioFVM
-	double mechanics_voxel_size = 30; 
-	Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size );
-	
-	/* Users typically start modifying here. START USERMODS */ 
-	
-	create_cell_types();
-	
-	setup_tissue();
-
-	/* Users typically stop modifying here. END USERMODS */ 
-	
-	// set MultiCellDS save options 
-
-	set_save_biofvm_mesh_as_matlab( true ); 
-	set_save_biofvm_data_as_matlab( true ); 
-	set_save_biofvm_cell_data( true ); 
-	set_save_biofvm_cell_data_as_custom_matlab( true );
-	
-	// save a simulation snapshot 
-	
-	char filename[1024];
-	sprintf( filename , "%s/initial" , PhysiCell_settings.folder.c_str() ); 
-	save_PhysiCell_to_MultiCellDS_v2( filename , microenvironment , PhysiCell_globals.current_time ); 
-	
-	// save a quick SVG cross section through z = 0, after setting its 
-	// length bar to 200 microns 
-
-	PhysiCell_SVG_options.length_bar = 200; 
-
-	// for simplicity, set a pathology coloring function 
-	
-	std::vector<std::string> (*cell_coloring_function)(Cell*) = my_coloring_function;
-	std::string (*substrate_coloring_function)(double, double, double) = paint_by_density_percentage;
-
-	sprintf( filename , "%s/initial.svg" , PhysiCell_settings.folder.c_str() ); 
-	SVG_plot( filename , microenvironment, 0.0 , PhysiCell_globals.current_time, cell_coloring_function, substrate_coloring_function );
-	
-	sprintf( filename , "%s/legend.svg" , PhysiCell_settings.folder.c_str() ); 
-	create_plot_legend( filename , cell_coloring_function ); 
-	
-	display_citations(); 
-	
-	// set the performance timers 
-
-	BioFVM::RUNTIME_TIC();
-	BioFVM::TIC();
-	
-	std::ofstream report_file;
-	if( PhysiCell_settings.enable_legacy_saves == true )
-	{	
-		sprintf( filename , "%s/simulation_report.txt" , PhysiCell_settings.folder.c_str() ); 
-		
-		report_file.open(filename); 	// create the data log file 
-		report_file<<"simulated time\tnum cells\tnum division\tnum death\twall time"<<std::endl;
-	}
-	
-	// main loop 
-	
-	try 
-	{		
-		while( PhysiCell_globals.current_time < PhysiCell_settings.max_time + 0.1*diffusion_dt )
-		{
-			// save data if it's time. 
-			if( fabs( PhysiCell_globals.current_time - PhysiCell_globals.next_full_save_time ) < 0.01 * diffusion_dt )
-			{
-				display_simulation_status( std::cout ); 
-				if( PhysiCell_settings.enable_legacy_saves == true )
-				{	
-					log_output( PhysiCell_globals.current_time , PhysiCell_globals.full_output_index, microenvironment, report_file);
-				}
-				
-				if( PhysiCell_settings.enable_full_saves == true )
-				{	
-					sprintf( filename , "%s/output%08u" , PhysiCell_settings.folder.c_str(),  PhysiCell_globals.full_output_index ); 
-					
-					save_PhysiCell_to_MultiCellDS_v2( filename , microenvironment , PhysiCell_globals.current_time ); 
-				}
-				
-				PhysiCell_globals.full_output_index++; 
-				PhysiCell_globals.next_full_save_time += PhysiCell_settings.full_save_interval;
-			}
-			
-			// save SVG plot if it's time
-			if( fabs( PhysiCell_globals.current_time - PhysiCell_globals.next_SVG_save_time  ) < 0.01 * diffusion_dt )
-			{
-				if( PhysiCell_settings.enable_SVG_saves == true )
-				{	
-					sprintf( filename , "%s/snapshot%08u.svg" , PhysiCell_settings.folder.c_str() , PhysiCell_globals.SVG_output_index );
-					SVG_plot( filename , microenvironment, 0.0 , PhysiCell_globals.current_time, cell_coloring_function, substrate_coloring_function);
-
-					PhysiCell_globals.SVG_output_index++; 
-					PhysiCell_globals.next_SVG_save_time  += PhysiCell_settings.SVG_save_interval;
-				}
-			}
-
-			// update the microenvironment
-			microenvironment.simulate_diffusion_decay( diffusion_dt );
-			
-			// run PhysiCell 
-			((Cell_Container *)microenvironment.agent_container)->update_all_cells( PhysiCell_globals.current_time );
-			
-			/*
-			  Custom add-ons could potentially go here. 
-			*/
-			
-			PhysiCell_globals.current_time += diffusion_dt;
-		}
-		
-		if( PhysiCell_settings.enable_legacy_saves == true )
-		{			
-			log_output(PhysiCell_globals.current_time, PhysiCell_globals.full_output_index, microenvironment, report_file);
-			report_file.close();
-		}
-	}
-	catch( const std::exception& e )
-	{ // reference to the base of a polymorphic object
-		std::cout << e.what(); // information from length_error printed
-	}
-	
-	// save a final simulation snapshot 
-	
-	sprintf( filename , "%s/final" , PhysiCell_settings.folder.c_str() ); 
-	save_PhysiCell_to_MultiCellDS_v2( filename , microenvironment , PhysiCell_globals.current_time ); 
-	
-	sprintf( filename , "%s/final.svg" , PhysiCell_settings.folder.c_str() );
-	SVG_plot(filename, microenvironment, 0.0, PhysiCell_globals.current_time, cell_coloring_function, substrate_coloring_function);
-
-	// timer 
-	
-	std::cout << std::endl << "Total simulation runtime: " << std::endl; 
-	BioFVM::display_stopwatch_value( std::cout , BioFVM::runtime_stopwatch_value() ); 
-
-	return 0; 
-}

From efc9e63e5ffc81573222c3b45186790bac91b683 Mon Sep 17 00:00:00 2001
From: Randy Heiland <randy.heiland@gmail.com>
Date: Thu, 15 Aug 2024 07:58:03 -0400
Subject: [PATCH 09/12] cleanup

---
 core/PhysiCell_cell.cpp | 2 --
 1 file changed, 2 deletions(-)

diff --git a/core/PhysiCell_cell.cpp b/core/PhysiCell_cell.cpp
index f5b559bd7..6e1725a24 100644
--- a/core/PhysiCell_cell.cpp
+++ b/core/PhysiCell_cell.cpp
@@ -658,8 +658,6 @@ Cell* Cell::divide( )
 	child->state.damage = 0.0; 
 	child->state.total_attack_time = 0.0; 
 
-    //rwh
-    // if( this->functions.cell_division_function && pC->is_out_of_domain == false )
     if( this->functions.cell_division_function )
         { this->functions.cell_division_function( this, child); }
 

From 3b8c248c0b164d632c5201fab51d49b2f57af218 Mon Sep 17 00:00:00 2001
From: Randy Heiland <randy.heiland@gmail.com>
Date: Thu, 15 Aug 2024 07:59:51 -0400
Subject: [PATCH 10/12] cleanup

---
 core/PhysiCell_cell.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/core/PhysiCell_cell.cpp b/core/PhysiCell_cell.cpp
index 6e1725a24..74bed8840 100644
--- a/core/PhysiCell_cell.cpp
+++ b/core/PhysiCell_cell.cpp
@@ -1676,7 +1676,7 @@ void display_ptr_as_bool( void (*ptr)(Cell*,Phenotype&,Cell*,Phenotype&,double),
 	return;
 }
 
-void display_ptr_as_bool( void (*ptr)(Cell*,Cell*), std::ostream& os )  //rwh
+void display_ptr_as_bool( void (*ptr)(Cell*,Cell*), std::ostream& os )
 {
 	if( ptr )
 	{ os << "true"; return; }

From 6977a7aefd81d4d42100f722fbf9b92bb8ae94cd Mon Sep 17 00:00:00 2001
From: Randy Heiland <randy.heiland@gmail.com>
Date: Thu, 15 Aug 2024 08:26:43 -0400
Subject: [PATCH 11/12] add custom-division-sample

---
 sample_projects/Makefile-default | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/sample_projects/Makefile-default b/sample_projects/Makefile-default
index 02b313890..7ca39d93d 100644
--- a/sample_projects/Makefile-default
+++ b/sample_projects/Makefile-default
@@ -73,7 +73,7 @@ name:
 list-projects:
 	@echo "Sample projects: template biorobots-sample cancer-biorobots-sample cancer-immune-sample"
 	@echo "                 celltypes3-sample heterogeneity-sample pred-prey-farmer virus-macrophage-sample"
-	@echo "                 worm-sample interaction-sample mechano-sample rules-sample physimess-sample"
+	@echo "                 worm-sample interaction-sample mechano-sample rules-sample physimess-sample custom-division-sample"
 	@echo ""
 	@echo "Sample intracellular projects: template_BM ode-energy-sample physiboss-cell-lines-sample"
 	@echo "                 cancer-metabolism-sample physiboss-tutorial physiboss-tutorial-invasion"
@@ -198,6 +198,15 @@ physimess-sample:
 	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
 	cp -r ./sample_projects/physimess/config/* ./config/
 
+custom-division-sample:
+	cp ./sample_projects/custom_division/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/custom_division/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/custom_division/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp -r ./sample_projects/custom_division/config/* ./config/
+
 # ---- intracellular projects 
 ode-energy-sample:
 	cp ./sample_projects_intracellular/ode/ode_energy/custom_modules/* ./custom_modules/

From 1c47042e42209fe472cbcedc9bd944c504255fc5 Mon Sep 17 00:00:00 2001
From: Randy Heiland <randy.heiland@gmail.com>
Date: Thu, 15 Aug 2024 08:50:32 -0400
Subject: [PATCH 12/12] revert to original constants code

---
 core/PhysiCell_constants.cpp | 63 +++---------------------------
 core/PhysiCell_constants.h   | 74 ++++++++++++++++++------------------
 2 files changed, 43 insertions(+), 94 deletions(-)

diff --git a/core/PhysiCell_constants.cpp b/core/PhysiCell_constants.cpp
index 8ade36f6b..7727c40f2 100644
--- a/core/PhysiCell_constants.cpp
+++ b/core/PhysiCell_constants.cpp
@@ -76,63 +76,12 @@ double mechanics_dt = 0.1;
 double phenotype_dt = 6.0;
 double intracellular_dt = 0.01;
 
-
-// currently recognized cell cycle models 
-const int PhysiCell_constants::advanced_Ki67_cycle_model= 0;
-const int PhysiCell_constants::basic_Ki67_cycle_model=1;
-const int PhysiCell_constants::flow_cytometry_cycle_model=2;
-const int PhysiCell_constants::live_apoptotic_cycle_model=3;
-const int PhysiCell_constants::total_cells_cycle_model=4;
-const int PhysiCell_constants::live_cells_cycle_model = 5; 
-const int PhysiCell_constants::flow_cytometry_separated_cycle_model = 6; 
-const int PhysiCell_constants::cycling_quiescent_model = 7; 
-
-// currently recognized death models 
-const int PhysiCell_constants::apoptosis_death_model = 100; 
-const int PhysiCell_constants::necrosis_death_model = 101; 
-const int PhysiCell_constants::autophagy_death_model = 102; 
-
-const int PhysiCell_constants::custom_cycle_model=9999; 
-
-// currently recognized cell cycle and death phases 
-// cycle phases
-const int PhysiCell_constants::Ki67_positive_premitotic=0; 
-const int PhysiCell_constants::Ki67_positive_postmitotic=1; 
-const int PhysiCell_constants::Ki67_positive=2; 
-const int PhysiCell_constants::Ki67_negative=3; 
-const int PhysiCell_constants::G0G1_phase=4;
-const int PhysiCell_constants::G0_phase=5;
-const int PhysiCell_constants::G1_phase=6; 
-const int PhysiCell_constants::G1a_phase=7; 
-const int PhysiCell_constants::G1b_phase=8;
-const int PhysiCell_constants::G1c_phase=9;
-const int PhysiCell_constants::S_phase=10;
-const int PhysiCell_constants::G2M_phase=11;
-const int PhysiCell_constants::G2_phase=12;
-const int PhysiCell_constants::M_phase=13;
-const int PhysiCell_constants::live=14;
-
-const int PhysiCell_constants::G1pm_phase = 15;
-const int PhysiCell_constants::G1ps_phase = 16; 
-
-const int PhysiCell_constants::cycling = 17; 
-const int PhysiCell_constants::quiescent = 18; 
-
-
-const int PhysiCell_constants::custom_phase = 9999;
-// death phases
-const int PhysiCell_constants::apoptotic=100;
-const int PhysiCell_constants::necrotic_swelling=101;
-const int PhysiCell_constants::necrotic_lysed=102;
-const int PhysiCell_constants::necrotic=103; 
-const int PhysiCell_constants::debris=104; 
-
-std::unordered_map<std::string,int> cycle_model_codes = {
-
-    { "Ki67 (advanced)", PhysiCell_constants::advanced_Ki67_cycle_model}, 
-    { "Ki67 (basic)" ,PhysiCell_constants::basic_Ki67_cycle_model},
-    { "Flow cytometry model (basic)",PhysiCell_constants::flow_cytometry_cycle_model},
-// { ,PhysiCell_constants::live_apoptotic_cycle_model}, // not implemented 
+std::unordered_map<std::string,int> cycle_model_codes = 
+{
+	{ "Ki67 (advanced)", PhysiCell_constants::advanced_Ki67_cycle_model}, 
+	{ "Ki67 (basic)" ,PhysiCell_constants::basic_Ki67_cycle_model},
+	{ "Flow cytometry model (basic)",PhysiCell_constants::flow_cytometry_cycle_model},
+	// { ,PhysiCell_constants::live_apoptotic_cycle_model}, // not implemented 
 	// { ,PhysiCell_constants::total_cells_cycle_model}, // not implemented 
 	{ "Live",PhysiCell_constants::live_cells_cycle_model}, 
 	{ "Flow cytometry model (separated)",PhysiCell_constants::flow_cytometry_separated_cycle_model}, 
diff --git a/core/PhysiCell_constants.h b/core/PhysiCell_constants.h
index 58aef3c84..476953148 100644
--- a/core/PhysiCell_constants.h
+++ b/core/PhysiCell_constants.h
@@ -102,54 +102,54 @@ class PhysiCell_constants
 	static const int mesh_uz_face_index=5;
 	
 	// currently recognized cell cycle models 
-	static const int advanced_Ki67_cycle_model;
-	static const int basic_Ki67_cycle_model;
-	static const int flow_cytometry_cycle_model;
-	static const int live_apoptotic_cycle_model;
-	static const int total_cells_cycle_model;
-	static const int live_cells_cycle_model ; 
-	static const int flow_cytometry_separated_cycle_model ; 
-	static const int cycling_quiescent_model ; 
+	static const int advanced_Ki67_cycle_model= 0;
+	static const int basic_Ki67_cycle_model=1;
+	static const int flow_cytometry_cycle_model=2;
+	static const int live_apoptotic_cycle_model=3;
+	static const int total_cells_cycle_model=4;
+	static const int live_cells_cycle_model = 5; 
+	static const int flow_cytometry_separated_cycle_model = 6; 
+	static const int cycling_quiescent_model = 7; 
 	
 	// currently recognized death models 
-	static const int apoptosis_death_model ; 
-	static const int necrosis_death_model ; 
-	static const int autophagy_death_model ; 
+	static const int apoptosis_death_model = 100; 
+	static const int necrosis_death_model = 101; 
+	static const int autophagy_death_model = 102; 
 	
-	static const int custom_cycle_model; 
+	static const int custom_cycle_model=9999; 
 	
 	// currently recognized cell cycle and death phases 
 	// cycle phases
-	static const int Ki67_positive_premitotic; 
-	static const int Ki67_positive_postmitotic; 
-	static const int Ki67_positive; 
-	static const int Ki67_negative; 
-	static const int G0G1_phase;
-	static const int G0_phase;
-	static const int G1_phase; 
-	static const int G1a_phase; 
-	static const int G1b_phase;
-	static const int G1c_phase;
-	static const int S_phase;
-	static const int G2M_phase;
-	static const int G2_phase;
-	static const int M_phase;
-	static const int live;
+	static const int Ki67_positive_premitotic=0; 
+	static const int Ki67_positive_postmitotic=1; 
+	static const int Ki67_positive=2; 
+	static const int Ki67_negative=3; 
+	static const int G0G1_phase=4;
+	static const int G0_phase=5;
+	static const int G1_phase=6; 
+	static const int G1a_phase=7; 
+	static const int G1b_phase=8;
+	static const int G1c_phase=9;
+	static const int S_phase=10;
+	static const int G2M_phase=11;
+	static const int G2_phase=12;
+	static const int M_phase=13;
+	static const int live=14;
 	
-	static const int G1pm_phase ;
-	static const int G1ps_phase ; 
+	static const int G1pm_phase = 15;
+	static const int G1ps_phase = 16; 
 	
-	static const int cycling ; 
-	static const int quiescent ; 
+	static const int cycling = 17; 
+	static const int quiescent = 18; 
 	
 	
-	static const int custom_phase ;
+	static const int custom_phase = 9999;
 	// death phases
-	static const int apoptotic;
-	static const int necrotic_swelling;
-	static const int necrotic_lysed;
-	static const int necrotic; 
-	static const int debris; 
+	static const int apoptotic=100;
+	static const int necrotic_swelling=101;
+	static const int necrotic_lysed=102;
+	static const int necrotic=103; 
+	static const int debris=104; 
 };
 extern std::string time_units;
 extern std::string space_units;