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Makefile save function sets the PROJ variable in the Makefile to the actual name the project was saved with. #260

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Makefile save function sets the PROJ variable in the Makefile to the actual name the project was saved with. #260

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5c1693b
changes to the cp command from make save and make load to allow user …
elmbeech Jun 5, 2024
1bcc768
the Makefile-default reset function is now compatible with the config…
elmbeech Jun 7, 2024
ec3ed6e
updated Makefile reset function, so that the function is compatible w…
elmbeech Jun 9, 2024
085838e
Merge branch 'development' of github.com:MathCancer/PhysiCell into pa…
elmbeech Jun 9, 2024
364101e
updated Makefile checkpoint function, so that the function is compati…
elmbeech Jun 9, 2024
74d3b12
the Makefile reset function now uses sample_projects/PhysiCell_settin…
elmbeech Jun 9, 2024
ef5e722
the Makefile save function sets the PROJ variable in the Makefile to …
elmbeech Jun 9, 2024
e334eb6
Makefile save function sets the PROJ variable is now solved with awk …
elmbeech Jun 11, 2024
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32 changes: 16 additions & 16 deletions Makefile
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -387,17 +387,16 @@ PhysiCell_geometry.o: ./modules/PhysiCell_geometry.cpp
# cleanup

reset:
rm -f *.cpp PhysiCell_cell.o
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 ./config/*.csv

make clean
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
rm -fr ./config/*
cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml

clean:
rm -f *.o
rm -f $(PROGRAM_NAME)*
Expand All @@ -410,7 +409,7 @@ data-cleanup:
# archival

checkpoint:
zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/*
zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/*

zip:
zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/*
Expand Down Expand Up @@ -491,17 +490,18 @@ save:
mkdir -p ./user_projects/$(PROJ)/custom_modules
mkdir -p ./user_projects/$(PROJ)/config
cp main.cpp ./user_projects/$(PROJ)
awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile
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
cp -r ./config/* ./user_projects/$(PROJ)/config
cp -r ./custom_modules/* ./user_projects/$(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/$(PROJ)/custom_modules/* ./custom_modules/
cp -r ./user_projects/$(PROJ)/config/* ./config/
cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/

pack:
@echo " "
Expand Down
32 changes: 16 additions & 16 deletions sample_projects/Makefile-default
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -387,17 +387,16 @@ PhysiCell_geometry.o: ./modules/PhysiCell_geometry.cpp
# cleanup

reset:
rm -f *.cpp PhysiCell_cell.o
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 ./config/*.csv

make clean
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
rm -fr ./config/*
cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml

clean:
rm -f *.o
rm -f $(PROGRAM_NAME)*
Expand All @@ -410,7 +409,7 @@ data-cleanup:
# archival

checkpoint:
zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/*
zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/*

zip:
zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/*
Expand Down Expand Up @@ -491,17 +490,18 @@ save:
mkdir -p ./user_projects/$(PROJ)/custom_modules
mkdir -p ./user_projects/$(PROJ)/config
cp main.cpp ./user_projects/$(PROJ)
awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile
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
cp -r ./config/* ./user_projects/$(PROJ)/config
cp -r ./custom_modules/* ./user_projects/$(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/$(PROJ)/custom_modules/* ./custom_modules/
cp -r ./user_projects/$(PROJ)/config/* ./config/
cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/

pack:
@echo " "
Expand Down
271 changes: 271 additions & 0 deletions sample_projects/PhysiCell_settings.xml-default
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,271 @@
<PhysiCell_settings version="devel-version">

<domain>
<x_min>-500</x_min>
<x_max>500</x_max>
<y_min>-500</y_min>
<y_max>500</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">14400</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>6</omp_num_threads>
</parallel>

<save>
<folder>output</folder>
<full_data>
<interval units="min">60</interval>
<enable>true</enable>
</full_data>
<SVG>
<interval units="min">60</interval>
<enable>true</enable>
</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>
</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">0</Dirichlet_boundary_condition>
<Dirichlet_options>
<boundary_value ID="xmin" enabled="True">38</boundary_value>
<boundary_value ID="xmax" enabled="True">10</boundary_value>
<boundary_value ID="ymin" enabled="True">10</boundary_value>
<boundary_value ID="ymax" enabled="True">38</boundary_value>
<boundary_value ID="zmin" enabled="False">0</boundary_value>
<boundary_value ID="zmax" enabled="False">0</boundary_value>
</Dirichlet_options>
</variable>
<variable name="necrotic debris" units="dimensionless" ID="1">
<physical_parameter_set>
<diffusion_coefficient units="micron^2/min">10</diffusion_coefficient>
<decay_rate units="1/min">.1</decay_rate>
</physical_parameter_set>
<initial_condition units="mmHg">0</initial_condition>
<Dirichlet_boundary_condition units="mmHg" enabled="False">0</Dirichlet_boundary_condition>
<Dirichlet_options>
<boundary_value ID="xmin" enabled="False">0</boundary_value>
<boundary_value ID="xmax" enabled="False">0</boundary_value>
<boundary_value ID="ymin" enabled="False">0</boundary_value>
<boundary_value ID="ymax" enabled="False">0</boundary_value>
<boundary_value ID="zmin" enabled="False">0</boundary_value>
<boundary_value ID="zmax" enabled="False">0</boundary_value>
</Dirichlet_options>
</variable>
<variable name="apoptotic debris" units="dimensionless" ID="2">
<physical_parameter_set>
<diffusion_coefficient units="micron^2/min">10</diffusion_coefficient>
<decay_rate units="1/min">0.1</decay_rate>
</physical_parameter_set>
<initial_condition units="mmHg">0</initial_condition>
<Dirichlet_boundary_condition units="mmHg" enabled="False">0</Dirichlet_boundary_condition>
<Dirichlet_options>
<boundary_value ID="xmin" enabled="False">0</boundary_value>
<boundary_value ID="xmax" enabled="False">0</boundary_value>
<boundary_value ID="ymin" enabled="False">0</boundary_value>
<boundary_value ID="ymax" enabled="False">0</boundary_value>
<boundary_value ID="zmin" enabled="False">0</boundary_value>
<boundary_value ID="zmax" enabled="False">0</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="malignant epithelial" ID="0">
<phenotype>
<cycle code="5" name="live">
<phase_transition_rates units="1/min">
<rate start_index="0" end_index="0" fixed_duration="false">0.000</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">2.80E-03</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="malignant epithelial">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>
<cell_BM_adhesion_strength units="micron/min">4.0</cell_BM_adhesion_strength>
<cell_BM_repulsion_strength units="micron/min">10.0</cell_BM_repulsion_strength>
<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_sensitivity substrate="necrotic debris">0.0</chemotactic_sensitivity>
<chemotactic_sensitivity substrate="apoptotic debris">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>
<substrate name="necrotic debris">
<secretion_rate units="1/min">0.0</secretion_rate>
<secretion_target units="substrate density">1</secretion_target>
<uptake_rate units="1/min">0.0</uptake_rate>
<net_export_rate units="total substrate/min">0.0</net_export_rate>
</substrate>
<substrate name="apoptotic debris">
<secretion_rate units="1/min">0.0</secretion_rate>
<secretion_target units="substrate density">1</secretion_target>
<uptake_rate units="1/min">0.0</uptake_rate>
<net_export_rate units="total substrate/min">0.0</net_export_rate>
</substrate>
</secretion>
<cell_interactions>
<dead_phagocytosis_rate units="1/min">0</dead_phagocytosis_rate>
<live_phagocytosis_rates>
<phagocytosis_rate name="malignant epithelial" units="1/min">0</phagocytosis_rate>
<phagocytosis_rate name="default" units="1/min">0</phagocytosis_rate>
</live_phagocytosis_rates>
<attack_rates>
<attack_rate name="malignant epithelial" units="1/min">0</attack_rate>
<attack_rate name="default" units="1/min">0</attack_rate>
</attack_rates>
<damage_rate units="1/min">1</damage_rate>
<fusion_rates>
<fusion_rate name="malignant epithelial" units="1/min">0</fusion_rate>
<fusion_rate name="default" units="1/min">0</fusion_rate>
</fusion_rates>
</cell_interactions>
<cell_transformations>
<transformation_rates>
<transformation_rate name="malignant epithelial" units="1/min">0</transformation_rate>
<transformation_rate name="default" 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="true">
<folder>./config</folder>
<filename>cell_rules_v2.csv</filename>
</ruleset>
</rulesets>
<settings />
</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>
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