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@ physicelldataloader : next release v4.0.1.
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6 files changed

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6 files changed

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‎test/pcmodel/Makefile‎

Lines changed: 108 additions & 108 deletions
Original file line numberDiff line numberDiff line change
@@ -3,11 +3,11 @@ PROGRAM_NAME := project
33

44
CC := g++
55
# CC := g++-mp-7 # typical macports compiler name
6-
# CC := g++-7 # typical homebrew compiler name
6+
# CC := g++-7 # typical homebrew compiler name
77

8-
# Check for environment definitions of compiler
8+
# Check for environment definitions of compiler
99
# e.g., on CC = g++-7 on OSX
10-
ifdef PHYSICELL_CPP
10+
ifdef PHYSICELL_CPP
1111
CC := $(PHYSICELL_CPP)
1212
endif
1313

@@ -18,8 +18,8 @@ endif
1818
ARCH := native # best auto-tuning
1919
# ARCH := core2 # a reasonably safe default for most CPUs since 2007
2020
# ARCH := corei7
21-
# ARCH := corei7-avx # earlier i7
22-
# ARCH := core-avx-i # i7 ivy bridge or newer
21+
# ARCH := corei7-avx # earlier i7
22+
# ARCH := core-avx-i # i7 ivy bridge or newer
2323
# ARCH := core-avx2 # i7 with Haswell or newer
2424
# ARCH := nehalem
2525
# ARCH := westmere
@@ -31,7 +31,7 @@ ARCH := native # best auto-tuning
3131
# ARCH := bonnell
3232
# ARCH := silvermont
3333
# ARCH := skylake-avx512
34-
# ARCH := nocona #64-bit pentium 4 or later
34+
# ARCH := nocona #64-bit pentium 4 or later
3535

3636
# CFLAGS := -march=$(ARCH) -Ofast -s -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11
3737
CFLAGS := -march=$(ARCH) -O3 -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11
@@ -53,7 +53,7 @@ COMPILE_COMMAND := $(CC) $(CFLAGS) $(EXTRA_FLAGS)
5353
LINK_COMMAND := $(CC) $(CFLAGS_LINK) $(EXTRA_FLAGS)
5454

5555
BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o \
56-
BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o
56+
BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o
5757

5858
PhysiCell_core_OBJECTS := PhysiCell_phenotype.o PhysiCell_cell_container.o PhysiCell_standard_models.o \
5959
PhysiCell_cell.o PhysiCell_custom.o PhysiCell_utilities.o PhysiCell_constants.o PhysiCell_basic_signaling.o \
@@ -71,10 +71,10 @@ pugixml_OBJECTS := pugixml.o
7171
PhysiCell_OBJECTS := $(BioFVM_OBJECTS) $(pugixml_OBJECTS) $(PhysiCell_core_OBJECTS) $(PhysiCell_module_OBJECTS)
7272
ALL_OBJECTS := $(PhysiCell_OBJECTS) $(PhysiCell_custom_module_OBJECTS)
7373

74-
# compile the project
74+
# compile the project
7575

7676
all: main.cpp $(ALL_OBJECTS)
77-
$(COMPILE_COMMAND) -o $(PROGRAM_NAME) $(ALL_OBJECTS) main.cpp
77+
$(COMPILE_COMMAND) -o $(PROGRAM_NAME) $(ALL_OBJECTS) main.cpp
7878
make name
7979

8080
static: main.cpp $(ALL_OBJECTS) $(MaBoSS)
@@ -85,70 +85,70 @@ name:
8585
@echo "Executable name is" $(PROGRAM_NAME)
8686
@echo ""
8787

88-
# PhysiCell core components
88+
# PhysiCell core components
8989

9090
PhysiCell_phenotype.o: ./core/PhysiCell_phenotype.cpp
9191
$(COMPILE_COMMAND) -c ./core/PhysiCell_phenotype.cpp
92-
92+
9393
PhysiCell_digital_cell_line.o: ./core/PhysiCell_digital_cell_line.cpp
9494
$(COMPILE_COMMAND) -c ./core/PhysiCell_digital_cell_line.cpp
9595

9696
PhysiCell_cell.o: ./core/PhysiCell_cell.cpp
97-
$(COMPILE_COMMAND) -c ./core/PhysiCell_cell.cpp
97+
$(COMPILE_COMMAND) -c ./core/PhysiCell_cell.cpp
9898

9999
PhysiCell_cell_container.o: ./core/PhysiCell_cell_container.cpp
100-
$(COMPILE_COMMAND) -c ./core/PhysiCell_cell_container.cpp
101-
100+
$(COMPILE_COMMAND) -c ./core/PhysiCell_cell_container.cpp
101+
102102
PhysiCell_standard_models.o: ./core/PhysiCell_standard_models.cpp
103-
$(COMPILE_COMMAND) -c ./core/PhysiCell_standard_models.cpp
104-
103+
$(COMPILE_COMMAND) -c ./core/PhysiCell_standard_models.cpp
104+
105105
PhysiCell_utilities.o: ./core/PhysiCell_utilities.cpp
106-
$(COMPILE_COMMAND) -c ./core/PhysiCell_utilities.cpp
107-
106+
$(COMPILE_COMMAND) -c ./core/PhysiCell_utilities.cpp
107+
108108
PhysiCell_custom.o: ./core/PhysiCell_custom.cpp
109-
$(COMPILE_COMMAND) -c ./core/PhysiCell_custom.cpp
110-
109+
$(COMPILE_COMMAND) -c ./core/PhysiCell_custom.cpp
110+
111111
PhysiCell_constants.o: ./core/PhysiCell_constants.cpp
112-
$(COMPILE_COMMAND) -c ./core/PhysiCell_constants.cpp
113-
112+
$(COMPILE_COMMAND) -c ./core/PhysiCell_constants.cpp
113+
114114
PhysiCell_signal_behavior.o: ./core/PhysiCell_signal_behavior.cpp
115-
$(COMPILE_COMMAND) -c ./core/PhysiCell_signal_behavior.cpp
116-
115+
$(COMPILE_COMMAND) -c ./core/PhysiCell_signal_behavior.cpp
116+
117117
PhysiCell_rules.o: ./core/PhysiCell_rules.cpp
118-
$(COMPILE_COMMAND) -c ./core/PhysiCell_rules.cpp
118+
$(COMPILE_COMMAND) -c ./core/PhysiCell_rules.cpp
119119

120120
# BioFVM core components (needed by PhysiCell)
121-
121+
122122
BioFVM_vector.o: ./BioFVM/BioFVM_vector.cpp
123-
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_vector.cpp
123+
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_vector.cpp
124124

125125
BioFVM_agent_container.o: ./BioFVM/BioFVM_agent_container.cpp
126-
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_agent_container.cpp
127-
126+
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_agent_container.cpp
127+
128128
BioFVM_mesh.o: ./BioFVM/BioFVM_mesh.cpp
129-
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_mesh.cpp
129+
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_mesh.cpp
130130

131131
BioFVM_microenvironment.o: ./BioFVM/BioFVM_microenvironment.cpp
132-
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_microenvironment.cpp
132+
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_microenvironment.cpp
133133

134134
BioFVM_solvers.o: ./BioFVM/BioFVM_solvers.cpp
135-
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_solvers.cpp
135+
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_solvers.cpp
136136

137137
BioFVM_utilities.o: ./BioFVM/BioFVM_utilities.cpp
138-
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_utilities.cpp
139-
138+
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_utilities.cpp
139+
140140
BioFVM_basic_agent.o: ./BioFVM/BioFVM_basic_agent.cpp
141-
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_basic_agent.cpp
142-
141+
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_basic_agent.cpp
142+
143143
BioFVM_matlab.o: ./BioFVM/BioFVM_matlab.cpp
144144
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_matlab.cpp
145145

146146
BioFVM_MultiCellDS.o: ./BioFVM/BioFVM_MultiCellDS.cpp
147147
$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_MultiCellDS.cpp
148-
148+
149149
pugixml.o: ./BioFVM/pugixml.cpp
150150
$(COMPILE_COMMAND) -c ./BioFVM/pugixml.cpp
151-
151+
152152
# standard PhysiCell modules
153153

154154
PhysiCell_SVG.o: ./modules/PhysiCell_SVG.cpp
@@ -165,158 +165,158 @@ PhysiCell_various_outputs.o: ./modules/PhysiCell_various_outputs.cpp
165165

166166
PhysiCell_pugixml.o: ./modules/PhysiCell_pugixml.cpp
167167
$(COMPILE_COMMAND) -c ./modules/PhysiCell_pugixml.cpp
168-
168+
169169
PhysiCell_settings.o: ./modules/PhysiCell_settings.cpp
170170
$(COMPILE_COMMAND) -c ./modules/PhysiCell_settings.cpp
171-
171+
172172
PhysiCell_basic_signaling.o: ./core/PhysiCell_basic_signaling.cpp
173-
$(COMPILE_COMMAND) -c ./core/PhysiCell_basic_signaling.cpp
174-
173+
$(COMPILE_COMMAND) -c ./core/PhysiCell_basic_signaling.cpp
174+
175175
PhysiCell_geometry.o: ./modules/PhysiCell_geometry.cpp
176-
$(COMPILE_COMMAND) -c ./modules/PhysiCell_geometry.cpp
177-
176+
$(COMPILE_COMMAND) -c ./modules/PhysiCell_geometry.cpp
177+
178178
# user-defined PhysiCell modules
179179

180-
custom.o: ./custom_modules/custom.cpp
180+
custom.o: ./custom_modules/custom.cpp
181181
$(COMPILE_COMMAND) -c ./custom_modules/custom.cpp
182182

183183
# cleanup
184184

185185
reset:
186-
rm -f *.cpp
187-
cp ./sample_projects/Makefile-default Makefile
186+
rm -f *.cpp
187+
cp ./sample_projects/Makefile-default Makefile
188188
rm -f ./custom_modules/*
189-
touch ./custom_modules/empty.txt
190-
touch ALL_CITATIONS.txt
189+
touch ./custom_modules/empty.txt
190+
touch ALL_CITATIONS.txt
191191
touch ./core/PhysiCell_cell.cpp
192-
rm ALL_CITATIONS.txt
193-
cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml
192+
rm ALL_CITATIONS.txt
193+
cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml
194194
touch ./config/empty.csv
195195
rm -f ./config/*.csv
196-
196+
197197
clean:
198198
rm -f *.o
199199
rm -f $(PROGRAM_NAME)*
200-
200+
201201
data-cleanup:
202202
rm -rf ./output
203203
mkdir ./output
204204
touch ./output/empty.txt
205-
206-
# archival
207-
208-
checkpoint:
209-
zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/*
210-
205+
206+
# archival
207+
208+
checkpoint:
209+
zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/*
210+
211211
zip:
212-
zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/*
212+
zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/*
213213
cp latest.zip $$(date +%b_%d_%Y_%H%M).zip
214-
cp latest.zip VERSION_$(VERSION).zip
214+
cp latest.zip VERSION_$(VERSION).zip
215215
mv *.zip archives/
216-
216+
217217
tar:
218-
tar --ignore-failed-read -czf latest.tar Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/*
218+
tar --ignore-failed-read -czf latest.tar Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/*
219219
cp latest.tar $$(date +%b_%d_%Y_%H%M).tar
220220
cp latest.tar VERSION_$(VERSION).tar
221221
mv *.tar archives/
222222

223-
unzip:
224-
cp ./archives/latest.zip .
225-
unzip latest.zip
226-
227-
untar:
223+
unzip:
224+
cp ./archives/latest.zip .
225+
unzip latest.zip
226+
227+
untar:
228228
cp ./archives/latest.tar .
229229
tar -xzf latest.tar
230230

231-
# easier animation
231+
# easier animation
232232

233233
FRAMERATE := 24
234234
OUTPUT := output
235235

236-
jpeg:
237-
@magick identify -format "%h" $(OUTPUT)/initial.svg > __H.txt
238-
@magick identify -format "%w" $(OUTPUT)/initial.svg > __W.txt
239-
@expr 2 \* \( $$(grep . __H.txt) / 2 \) > __H1.txt
240-
@expr 2 \* \( $$(grep . __W.txt) / 2 \) > __W1.txt
241-
@echo "$$(grep . __W1.txt)!x$$(grep . __H1.txt)!" > __resize.txt
236+
jpeg:
237+
@magick identify -format "%h" $(OUTPUT)/initial.svg > __H.txt
238+
@magick identify -format "%w" $(OUTPUT)/initial.svg > __W.txt
239+
@expr 2 \* \( $$(grep . __H.txt) / 2 \) > __H1.txt
240+
@expr 2 \* \( $$(grep . __W.txt) / 2 \) > __W1.txt
241+
@echo "$$(grep . __W1.txt)!x$$(grep . __H1.txt)!" > __resize.txt
242242
@magick mogrify -format jpg -resize $$(grep . __resize.txt) $(OUTPUT)/s*.svg
243-
rm -f __H*.txt __W*.txt __resize.txt
244-
245-
gif:
246-
magick convert $(OUTPUT)/s*.svg $(OUTPUT)/out.gif
247-
243+
rm -f __H*.txt __W*.txt __resize.txt
244+
245+
gif:
246+
magick convert $(OUTPUT)/s*.svg $(OUTPUT)/out.gif
247+
248248
movie:
249249
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
250-
251-
# upgrade rules
252250

253-
SOURCE := PhysiCell_upgrade.zip
254-
get-upgrade:
255-
@echo $$(curl https://raw.githubusercontent.com/MathCancer/PhysiCell/master/VERSION.txt) > VER.txt
256-
@echo https://github.com/MathCancer/PhysiCell/releases/download/$$(grep . VER.txt)/PhysiCell_V.$$(grep . VER.txt).zip > DL_FILE.txt
251+
# upgrade rules
252+
253+
SOURCE := PhysiCell_upgrade.zip
254+
get-upgrade:
255+
@echo $$(curl https://raw.githubusercontent.com/MathCancer/PhysiCell/master/VERSION.txt) > VER.txt
256+
@echo https://github.com/MathCancer/PhysiCell/releases/download/$$(grep . VER.txt)/PhysiCell_V.$$(grep . VER.txt).zip > DL_FILE.txt
257257
rm -f VER.txt
258258
$$(curl -L $$(grep . DL_FILE.txt) --output PhysiCell_upgrade.zip)
259-
rm -f DL_FILE.txt
259+
rm -f DL_FILE.txt
260260

261-
PhysiCell_upgrade.zip:
262-
make get-upgrade
261+
PhysiCell_upgrade.zip:
262+
make get-upgrade
263263

264264
upgrade: $(SOURCE)
265265
unzip $(SOURCE) PhysiCell/VERSION.txt
266-
mv -f PhysiCell/VERSION.txt .
267-
unzip $(SOURCE) PhysiCell/core/*
268-
cp -r PhysiCell/core/* core
269-
unzip $(SOURCE) PhysiCell/modules/*
270-
cp -r PhysiCell/modules/* modules
271-
unzip $(SOURCE) PhysiCell/sample_projects/*
272-
cp -r PhysiCell/sample_projects/* sample_projects
273-
unzip $(SOURCE) PhysiCell/BioFVM/*
266+
mv -f PhysiCell/VERSION.txt .
267+
unzip $(SOURCE) PhysiCell/core/*
268+
cp -r PhysiCell/core/* core
269+
unzip $(SOURCE) PhysiCell/modules/*
270+
cp -r PhysiCell/modules/* modules
271+
unzip $(SOURCE) PhysiCell/sample_projects/*
272+
cp -r PhysiCell/sample_projects/* sample_projects
273+
unzip $(SOURCE) PhysiCell/BioFVM/*
274274
cp -r PhysiCell/BioFVM/* BioFVM
275275
unzip $(SOURCE) PhysiCell/documentation/User_Guide.pdf
276276
mv -f PhysiCell/documentation/User_Guide.pdf documentation
277277
rm -f -r PhysiCell
278-
rm -f $(SOURCE)
278+
rm -f $(SOURCE)
279279

280280
# use: make save PROJ=your_project_name
281281
PROJ := my_project
282282

283-
save:
283+
save:
284284
echo "Saving project as $(PROJ) ... "
285285
mkdir -p ./user_projects
286286
mkdir -p ./user_projects/$(PROJ)
287287
mkdir -p ./user_projects/$(PROJ)/custom_modules
288-
mkdir -p ./user_projects/$(PROJ)/config
288+
mkdir -p ./user_projects/$(PROJ)/config
289289
cp main.cpp ./user_projects/$(PROJ)
290290
cp Makefile ./user_projects/$(PROJ)
291291
cp VERSION.txt ./user_projects/$(PROJ)
292292
cp ./config/* ./user_projects/$(PROJ)/config
293293
cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules
294294

295-
load:
295+
load:
296296
echo "Loading project from $(PROJ) ... "
297297
cp ./user_projects/$(PROJ)/main.cpp .
298298
cp ./user_projects/$(PROJ)/Makefile .
299-
cp ./user_projects/$(PROJ)/config/* ./config/
300-
cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/
299+
cp ./user_projects/$(PROJ)/config/* ./config/
300+
cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/
301301

302302
pack:
303303
@echo " "
304304
@echo "Preparing project $(PROJ) for sharing ... "
305-
@echo " "
305+
@echo " "
306306
cd ./user_projects && zip -r $(PROJ).zip $(PROJ)
307307
@echo " "
308308
@echo "Share ./user_projects/$(PROJ).zip ... "
309309
@echo "Other users can unzip $(PROJ).zip in their ./user_projects, compile, and run."
310-
@echo " "
310+
@echo " "
311311

312312
unpack:
313313
@echo " "
314314
@echo "Preparing shared project $(PROJ).zip for use ... "
315-
@echo " "
316-
cd ./user_projects && unzip $(PROJ).zip
315+
@echo " "
316+
cd ./user_projects && unzip $(PROJ).zip
317317
@echo " "
318318
@echo "Load this project via make load PROJ=$(PROJ) ... "
319-
@echo " "
319+
@echo " "
320320

321321
list-user-projects:
322322
@echo "user projects::"

‎test/pcmodel/config/PhysiCell_settings-backup.xml‎

Whitespace-only changes.

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