Makefile-default

VERSION := $(shell grep . VERSION.txt | cut -f1 -d:)
PROGRAM_NAME := project

CC := g++

# Check for environment definitions of compiler 
# e.g., on CC = g++-10 on OSX
ifdef PHYSICELL_CPP 
	CC := $(PHYSICELL_CPP)
endif

ARCH := native # best auto-tuning

# 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

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_module_OBJECTS := PhysiCell_SVG.o PhysiCell_pathology.o PhysiCell_MultiCellDS.o PhysiCell_various_outputs.o \
PhysiCell_pugixml.o PhysiCell_settings.o

# put your custom objects here (they should be in the custom_modules directory)

PhysiCell_custom_module_OBJECTS := .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)

EXAMPLES := ./examples/PhysiCell_test_mechanics_1.cpp ./examples/PhysiCell_test_mechanics_2.cpp \
 ./examples/PhysiCell_test_DCIS.cpp ./examples/PhysiCell_test_HDS.cpp \
 ./examples/PhysiCell_test_cell_cycle.cpp ./examples/PhysiCell_test_volume.cpp 

all: 
	make heterogeneity-sample
	make 

# sample projects 	
list-projects:
	@echo "Sample projects: template2D template3D biorobots-sample cancer-biorobots-sample heterogeneity-sample"
	@echo "                 cancer-immune-sample virus-macrophage-sample template spheroid-TNF drug-AGS ecm-try"
	@echo "                 arnau-model sorting physiboss-cell-lines"
	
template2D: 
	cp ./sample_projects/template2D/custom_modules/* ./custom_modules/
	touch main.cpp && cp main.cpp main-backup.cpp
	cp ./sample_projects/template2D/main-2D.cpp ./main.cpp 
	cp Makefile Makefile-backup
	cp ./sample_projects/template2D/Makefile .
	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
	cp ./sample_projects/template2D/config/* ./config/
	
template3D: 	
	cp ./sample_projects/template3D/custom_modules/* ./custom_modules/
	touch main.cpp && cp main.cpp main-backup.cpp
	cp ./sample_projects/template3D/main-3D.cpp ./main.cpp 
	cp Makefile Makefile-backup
	cp ./sample_projects/template3D/Makefile .
	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
	cp ./sample_projects/template3D/config/* ./config/
	
template:
	cp ./sample_projects/template/custom_modules/* ./custom_modules/
	touch main.cpp && cp main.cpp main-backup.cpp
	cp ./sample_projects/template/main.cpp ./main.cpp 
	cp Makefile Makefile-backup
	cp ./sample_projects/template/Makefile .
	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
	cp ./sample_projects/template/config/* ./config/
	
# sample projects 

biorobots-sample:
	cp ./sample_projects/biorobots/custom_modules/* ./custom_modules/
	touch main.cpp && cp main.cpp main-backup.cpp
	cp ./sample_projects/biorobots/main-biorobots.cpp ./main.cpp 
	cp Makefile Makefile-backup
	cp ./sample_projects/biorobots/Makefile .
	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
	cp ./sample_projects/biorobots/config/* ./config/
	
cancer-biorobots-sample:
	cp ./sample_projects/cancer_biorobots/custom_modules/* ./custom_modules/
	touch main.cpp && cp main.cpp main-backup.cpp
	cp ./sample_projects/cancer_biorobots/main-cancer_biorobots.cpp ./main.cpp 
	cp Makefile Makefile-backup
	cp ./sample_projects/cancer_biorobots/Makefile .
	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
	cp ./sample_projects/cancer_biorobots/config/* ./config/
	
heterogeneity-sample:
	cp ./sample_projects/heterogeneity/custom_modules/* ./custom_modules/
	touch main.cpp && cp main.cpp main-backup.cpp
	cp ./sample_projects/heterogeneity/main-heterogeneity.cpp ./main.cpp 
	cp Makefile Makefile-backup
	cp ./sample_projects/heterogeneity/Makefile .
	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
	cp ./sample_projects/heterogeneity/config/* ./config/
	
cancer-immune-sample:
	cp ./sample_projects/cancer_immune/custom_modules/* ./custom_modules/
	touch main.cpp && cp main.cpp main-backup.cpp
	cp ./sample_projects/cancer_immune/main-cancer_immune_3D.cpp ./main.cpp 
	cp Makefile Makefile-backup
	cp ./sample_projects/cancer_immune/Makefile .
	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
	cp ./sample_projects/cancer_immune/config/* ./config/
	
virus-macrophage-sample:
	cp ./sample_projects/virus_macrophage/custom_modules/* ./custom_modules/
	touch main.cpp && cp main.cpp main-backup.cpp
	cp ./sample_projects/virus_macrophage/main-virus_macrophage.cpp ./main.cpp 
	cp Makefile Makefile-backup
	cp ./sample_projects/virus_macrophage/Makefile .
	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
	cp ./sample_projects/virus_macrophage/config/* ./config/
	
beta-testing:
	cp ./sample_projects/beta_testing/custom_modules/* ./custom_modules/
	touch main.cpp && cp main.cpp main-backup.cpp
	cp ./sample_projects/beta_testing/main-beta.cpp ./main.cpp 
	cp Makefile Makefile-backup
	cp ./sample_projects/beta_testing/Makefile .
	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
	cp ./sample_projects/beta_testing/config/* ./config/

spheroid-TNF: 	
	cp ./sample_projects/spheroid_TNF/custom_modules/* ./custom_modules/
	touch main.cpp && cp main.cpp main-backup.cpp
	cp ./sample_projects/spheroid_TNF/main-spheroid_TNF.cpp ./main.cpp 
	cp Makefile Makefile-backup
	cp ./sample_projects/spheroid_TNF/Makefile .
	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
	cp -r ./sample_projects/spheroid_TNF/config/* ./config/
	mkdir ./scripts/
	cp ./sample_projects/spheroid_TNF/scripts/* ./scripts/

spheroid-TNF-v2: 	
	cp ./sample_projects/spheroid_TNF_v2/custom_modules/* ./custom_modules/
	touch main.cpp && cp main.cpp main-backup.cpp
	cp ./sample_projects/spheroid_TNF_v2/main-spheroid_TNF.cpp ./main.cpp 
	cp Makefile Makefile-backup
	cp ./sample_projects/spheroid_TNF_v2/Makefile .
	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
	cp -r ./sample_projects/spheroid_TNF_v2/config/* ./config/
	mkdir ./scripts/
	cp ./sample_projects/spheroid_TNF_v2/scripts/* ./scripts/
	
ecm-try: 	
	cp -r ./sample_projects/ECM_try/custom_modules/* ./custom_modules/
	touch main.cpp && cp main.cpp main-backup.cpp
	cp ./sample_projects/ECM_try/main_ECM_try.cpp ./main.cpp 
	cp Makefile Makefile-backup
	cp ./sample_projects/ECM_try/Makefile .
	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
	cp -r ./sample_projects/ECM_try/config/* ./config/
	mkdir ./scripts/
	cp ./sample_projects/ECM_try/scripts/* ./scripts/

arnau-model: 	
	cp -r ./sample_projects/Arnau_model/custom_modules/* ./custom_modules/
	touch main.cpp && cp main.cpp main-backup.cpp
	cp ./sample_projects/Arnau_model/main_arnau_model.cpp ./main.cpp 
	cp Makefile Makefile-backup
	cp ./sample_projects/Arnau_model/Makefile .
	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
	cp -r ./sample_projects/Arnau_model/config/* ./config/
	mkdir ./scripts/
	cp ./sample_projects/Arnau_model/scripts/* ./scripts/

sorting: 	
	cp -r ./sample_projects/sorting/custom_modules/* ./custom_modules/
	touch main.cpp && cp main.cpp main-backup.cpp
	cp ./sample_projects/sorting/main_sorting.cpp ./main.cpp 
	cp Makefile Makefile-backup
	cp ./sample_projects/sorting/Makefile .
	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
	cp -r ./sample_projects/sorting/config/* ./config/
	mkdir ./scripts/
	cp ./sample_projects/sorting/scripts/* ./scripts/

physiboss-cell-lines:
	cp -r ./sample_projects/physiboss_cell_lines/custom_modules/* ./custom_modules/
	touch main.cpp && cp main.cpp main-backup.cpp
	cp ./sample_projects/physiboss_cell_lines/main.cpp ./main.cpp 
	cp Makefile Makefile-backup
	cp ./sample_projects/physiboss_cell_lines/Makefile .
	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
	cp -r ./sample_projects/physiboss_cell_lines/config/* ./config/
	mkdir ./scripts/
	cp ./sample_projects/physiboss_cell_lines/scripts/* ./scripts/

covid19:
	cp -r ./sample_projects/covid19/custom_modules/* ./custom_modules/
	touch main.cpp && cp main.cpp main-backup.cpp
	cp ./sample_projects/covid19/main.cpp ./main.cpp 
	cp Makefile Makefile-backup
	cp ./sample_projects/covid19/Makefile .
	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
	cp -r ./sample_projects/covid19/config/* ./config/
	mkdir -p ./scripts/
	cp ./sample_projects/covid19/scripts/* ./scripts/

mycovid19:
	cp -r ./sample_projects/mycovid19/custom_modules/* ./custom_modules/
	touch main.cpp && cp main.cpp main-backup.cpp
	cp ./sample_projects/mycovid19/main.cpp ./main.cpp 
	cp Makefile Makefile-backup
	cp ./sample_projects/mycovid19/Makefile .
	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
	cp -r ./sample_projects/mycovid19/config/* ./config/
	mkdir -p ./scripts/
	cp ./sample_projects/mycovid19/scripts/* ./scripts/

drug-AGS: 	
	cp ./sample_projects/drug_AGS/custom_modules/* ./custom_modules/
	touch main.cpp && cp main.cpp main-backup.cpp
	cp ./sample_projects/drug_AGS/main-drug_AGS.cpp ./main.cpp 
	cp Makefile Makefile-backup
	cp ./sample_projects/drug_AGS/Makefile .
	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
	cp -r ./sample_projects/drug_AGS/config/* ./config/
	mkdir ./scripts/
	cp ./sample_projects/drug_AGS/scripts/* ./scripts/

test_sbml1:
	cp ./sample_projects/test_sbml1/custom_modules/* ./custom_modules/
	touch main.cpp && cp main.cpp main-backup.cpp
	cp ./sample_projects/test_sbml1/main-test_sbml1.cpp ./main.cpp 
	cp Makefile Makefile-backup
	cp ./sample_projects/test_sbml1/Makefile .
	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
	cp ./sample_projects/test_sbml1/config/* ./config/

roadrunner_simple1:
	cp ./sample_projects/roadrunner_simple1/custom_modules/* ./custom_modules/
	touch main.cpp && cp main.cpp main-backup.cpp
	cp ./sample_projects/roadrunner_simple1/main_roadrunner_simple1.cpp ./main.cpp 
	cp Makefile Makefile-backup
	cp ./sample_projects/roadrunner_simple1/Makefile .
	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
	cp ./sample_projects/roadrunner_simple1/config/* ./config/
	
# early examples for convergence testing 

physicell_test_mech1: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_mechanics_1.cpp 
	$(COMPILE_COMMAND) -o test_mech1 $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_mechanics_1.cpp

physicell_test_mech2: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_mechanics_2.cpp 
	$(COMPILE_COMMAND) -o test_mech2 $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_mechanics_2.cpp
	
physicell_test_DCIS: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_DCIS.cpp 
	$(COMPILE_COMMAND) -o test_DCIS $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_DCIS.cpp

physicell_test_HDS: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_HDS.cpp 
	$(COMPILE_COMMAND) -o test_HDS $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_HDS.cpp

physicell_test_cell_cycle: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_cell_cycle.cpp 
	$(COMPILE_COMMAND) -o test_cycle $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_cell_cycle.cpp

PhysiCell_test_volume: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_volume.cpp 
	$(COMPILE_COMMAND) -o test_volume $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_volume.cpp
	
examples: $(PhysiCell_OBJECTS) 
	$(COMPILE_COMMAND) -o ./examples/test_mech1 ./examples/PhysiCell_test_mechanics_1.cpp $(PhysiCell_OBJECTS)
	$(COMPILE_COMMAND) -o ./examples/test_mech2 ./examples/PhysiCell_test_mechanics_2.cpp $(PhysiCell_OBJECTS)
	$(COMPILE_COMMAND) -o ./examples/test_DCIS ./examples/PhysiCell_test_DCIS.cpp $(PhysiCell_OBJECTS)
	$(COMPILE_COMMAND) -o ./examples/test_HDS ./examples/PhysiCell_test_HDS.cpp $(PhysiCell_OBJECTS)
	$(COMPILE_COMMAND) -o ./examples/test_cycle ./examples/PhysiCell_test_cell_cycle.cpp $(PhysiCell_OBJECTS)
	$(COMPILE_COMMAND) -o ./examples/test_volume ./examples/PhysiCell_test_volume.cpp $(PhysiCell_OBJECTS)

# 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 
	
# BioFVM core components (needed by PhysiCell)
	
BioFVM_vector.o: ./BioFVM/BioFVM_vector.cpp
	$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_vector.cpp 

BioFVM_agent_container.o: ./BioFVM/BioFVM_agent_container.cpp
	$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_agent_container.cpp 
	
BioFVM_mesh.o: ./BioFVM/BioFVM_mesh.cpp
	$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_mesh.cpp 

BioFVM_microenvironment.o: ./BioFVM/BioFVM_microenvironment.cpp
	$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_microenvironment.cpp 

BioFVM_solvers.o: ./BioFVM/BioFVM_solvers.cpp
	$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_solvers.cpp 

BioFVM_utilities.o: ./BioFVM/BioFVM_utilities.cpp
	$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_utilities.cpp 
	
BioFVM_basic_agent.o: ./BioFVM/BioFVM_basic_agent.cpp
	$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_basic_agent.cpp 
	
BioFVM_matlab.o: ./BioFVM/BioFVM_matlab.cpp
	$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_matlab.cpp

BioFVM_MultiCellDS.o: ./BioFVM/BioFVM_MultiCellDS.cpp
	$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_MultiCellDS.cpp
	
pugixml.o: ./BioFVM/pugixml.cpp
	$(COMPILE_COMMAND) -c ./BioFVM/pugixml.cpp
	
# standard PhysiCell modules

PhysiCell_SVG.o: ./modules/PhysiCell_SVG.cpp
	$(COMPILE_COMMAND) -c ./modules/PhysiCell_SVG.cpp

PhysiCell_pathology.o: ./modules/PhysiCell_pathology.cpp
	$(COMPILE_COMMAND) -c ./modules/PhysiCell_pathology.cpp

PhysiCell_MultiCellDS.o: ./modules/PhysiCell_MultiCellDS.cpp
	$(COMPILE_COMMAND) -c ./modules/PhysiCell_MultiCellDS.cpp

PhysiCell_various_outputs.o: ./modules/PhysiCell_various_outputs.cpp
	$(COMPILE_COMMAND) -c ./modules/PhysiCell_various_outputs.cpp
	
PhysiCell_pugixml.o: ./modules/PhysiCell_pugixml.cpp
	$(COMPILE_COMMAND) -c ./modules/PhysiCell_pugixml.cpp
	
PhysiCell_settings.o: ./modules/PhysiCell_settings.cpp
	$(COMPILE_COMMAND) -c ./modules/PhysiCell_settings.cpp	
	
# user-defined PhysiCell modules

# cleanup

reset:
	rm -f *.cpp 
	cp ./sample_projects/Makefile-default Makefile 
	rm -fr ./custom_modules/*
	touch ./custom_modules/empty.txt 
	touch ALL_CITATIONS.txt 
	rm ALL_CITATIONS.txt 
	cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml 
	
clean:
	rm -f *.o
	rm -f $(PROGRAM_NAME)*
	
data-cleanup:
	rm -f *.mat
	rm -f *.xml
	rm -f *.svg
	rm -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