EI/VirtualLeaf Changeset - e7eab96321ce · Centrum Wiskunde & Informatica (CWI)

Changeset - e7eab96321ce

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Roeland Merks - 15 years ago 2010-06-09 16:14:29
roeland.merks@cwi.nl

Added finalized tutorial code. Added new header files that provide simplified constructs for summing up concentrations in walls. Also added a new function for resetting all walls of a cell.
New menu items in canvas for resetting chemical values only in cells or only in walls.

--
user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
added src/TutorialCode/Tutorial1A/mymodel.cpp
added src/TutorialCode/Tutorial1A/mymodel.h
added src/TutorialCode/Tutorial1A/mymodel.pro
added src/TutorialCode/Tutorial1B/mymodel.cpp
added src/TutorialCode/Tutorial1B/mymodel.h
added src/TutorialCode/Tutorial1B/mymodel.pro
added src/TutorialCode/Tutorial1C/mymodel.cpp
added src/TutorialCode/Tutorial1C/mymodel.h
added src/TutorialCode/Tutorial1C/mymodel.pro
added src/TutorialCode/Tutorial1D/mymodel.cpp
added src/TutorialCode/Tutorial1D/mymodel.h
added src/TutorialCode/Tutorial1D/mymodel.pro
added src/TutorialCode/Tutorial3/tutorial3_init.xml
added src/TutorialCode/Tutorial4/auxin_growth_init.xml
added src/TutorialCode/Tutorial4/mymodel
added src/TutorialCode/Tutorial4/tutorial4_init.xml
added src/TutorialCode/Tutorial5/mymodel
added src/TutorialCode/Tutorial5/tutorial5_init.xml
added src/flux_function.h
added src/vleafmodel.h
changed src/Makefile
changed src/TutorialCode/Tutorial2/mymodel.cpp
changed src/TutorialCode/Tutorial3/mymodel.cpp
changed src/TutorialCode/Tutorial4/mymodel.cpp
changed src/TutorialCode/Tutorial4/mymodel.h
changed src/TutorialCode/Tutorial5/mymodel.cpp
changed src/TutorialCode/Tutorial5/mymodel.h
changed src/VirtualLeaf.pro
changed src/cellbase.cpp
changed src/cellbase.h

15 files changed:

src/Makefile

845

src/TutorialCode/Tutorial1A/mymodel.cpp

src/TutorialCode/Tutorial1A/mymodel.h

src/TutorialCode/Tutorial1A/mymodel.pro

src/TutorialCode/Tutorial1B/mymodel.cpp

src/TutorialCode/Tutorial1B/mymodel.h

src/TutorialCode/Tutorial1B/mymodel.pro

src/TutorialCode/Tutorial1C/mymodel.cpp

src/TutorialCode/Tutorial1C/mymodel.h

src/TutorialCode/Tutorial1C/mymodel.pro

src/TutorialCode/Tutorial1D/mymodel.cpp

src/TutorialCode/Tutorial1D/mymodel.h

src/TutorialCode/Tutorial1D/mymodel.pro

src/TutorialCode/Tutorial2/mymodel.cpp

src/TutorialCode/Tutorial3/mymodel.cpp

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src/Makefile

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 # $Id: Makefile,v 3f0977faba37 2010/06/03 15:54:37 michael $
 #############################################################################
 # Makefile for building: ../bin/VirtualLeaf
 # Generated by qmake (2.01a) (Qt 4.4.1) on: Wed Jun 9 16:00:42 2010
 # Project:  VirtualLeaf.pro
 # Template: app
 # Command: /ufs/merks/Trolltech/Qt-4.4.1/bin/qmake -unix -o Makefile VirtualLeaf.pro
 #############################################################################
 ####### Compiler, tools and options
 CC            = gcc
 CXX           = g++
 DEFINES       = -DQTGRAPHICS -DREACTIONS_HEADER= -DREACTIONS_HEADER_STRING="" -DFLEMING -DQT_NO_DEBUG -DQT_QT3SUPPORT_LIB -DQT3_SUPPORT -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED
 CFLAGS        = -m64 -pipe -O2 -D_REENTRANT -Wall -W $(DEFINES)
 CXXFLAGS      = -m64 -pipe -fexceptions -fPIC -I/usr/include/libxml2 -DQTGRAPHICS -O2 -D_REENTRANT -Wall -W $(DEFINES)
 INCPATH       = -I../../../Trolltech/Qt-4.4.1/mkspecs/linux-g++-64 -I. -I../../../Trolltech/Qt-4.4.1/include/QtCore -I../../../Trolltech/Qt-4.4.1/include/QtCore -I../../../Trolltech/Qt-4.4.1/include/QtGui -I../../../Trolltech/Qt-4.4.1/include/QtGui -I../../../Trolltech/Qt-4.4.1/include/Qt3Support -I../../../Trolltech/Qt-4.4.1/include/Qt3Support -I../../../Trolltech/Qt-4.4.1/include -I. -I.
 LINK          = g++
 LFLAGS        = -m64 -fPIC -Wl,-rpath,/ufs/merks/Trolltech/Qt-4.4.1/lib
 LIBS          = $(SUBLIBS)  -L/ufs/guravage/opt/qwt-5.2.1-svn/lib -L/ufs/merks/Trolltech/Qt-4.4.1/lib -lxml2 -lQt3Support -L/ufs/merks/Trolltech/Qt-4.4.1/lib -lQtSql -pthread -pthread -pthread -pthread -lQtXml -pthread -pthread -pthread -pthread -L/usr/X11R6/lib64 -pthread -pthread -pthread -pthread -pthread -pthread -lQtNetwork -pthread -pthread -pthread -pthread -pthread -pthread -lQtGui -pthread -lpng -lSM -lICE -pthread -pthread -lXi -lXrender -lXrandr -lfreetype -lfontconfig -lXext -lX11 -lQtCore -lz -lm -pthread -lgthread-2.0 -lrt -lglib-2.0 -ldl -lpthread
 AR            = ar cqs
 RANLIB        =
 QMAKE         = /ufs/merks/Trolltech/Qt-4.4.1/bin/qmake
 TAR           = tar -cf
 COMPRESS      = gzip -9f
 COPY          = cp -f
 SED           = sed
 COPY_FILE     = $(COPY)
 COPY_DIR      = $(COPY) -r
 INSTALL_FILE  = install -m 644 -p
 INSTALL_DIR   = $(COPY_DIR)
 INSTALL_PROGRAM = install -m 755 -p
 DEL_FILE      = rm -f
 SYMLINK       = ln -sf
 DEL_DIR       = rmdir
 MOVE          = mv -f
 CHK_DIR_EXISTS= test -d
 MKDIR         = mkdir -p
 ####### Output directory
 OBJECTS_DIR   = ./
 ####### Files
 QMAKE = qmake
 SOURCES       = apoplastitem.cpp \
 		canvas.cpp \
 		cellbase.cpp \
 		cell.cpp \
 		cellitem.cpp \
 		mainbase.cpp \
 		matrix.cpp \
 		mesh.cpp \
 		miscq.cpp \
 		modelcatalogue.cpp \
 		Neighbor.cpp \
 		node.cpp \
 		nodeitem.cpp \
 		nodeset.cpp \
 		OptionFileDialog.cpp \
 		output.cpp \
 		parameter.cpp \
 		pardialog.cpp \
 		parse.cpp \
 		random.cpp \
 		rungekutta.cpp \
 		simitembase.cpp \
 		transporterdialog.cpp \
 		UniqueMessage.cpp \
 		vector.cpp \
 		wallbase.cpp \
 		wall.cpp \
 		wallitem.cpp \
 		warning.cpp \
 		xmlwritecode.cpp \
 		xmlwrite.cpp \
 		VirtualLeaf.cpp moc_canvas.cpp \
 		moc_cellbase.cpp \
 		moc_cell.cpp \
 		moc_infobar.cpp \
 		moc_modelcatalogue.cpp \
 		moc_OptionFileDialog.cpp \
 		moc_pardialog.cpp \
 		moc_transporterdialog.cpp \
 		moc_UniqueMessage.cpp
 OBJECTS       = apoplastitem.o \
 		canvas.o \
 		cellbase.o \
 		cell.o \
 		cellitem.o \
 		mainbase.o \
 		matrix.o \
 		mesh.o \
 		miscq.o \
 		modelcatalogue.o \
 		Neighbor.o \
 		node.o \
 		nodeitem.o \
 		nodeset.o \
 		OptionFileDialog.o \
 		output.o \
 		parameter.o \
 		pardialog.o \
 		parse.o \
 		random.o \
 		rungekutta.o \
 		simitembase.o \
 		transporterdialog.o \
 		UniqueMessage.o \
 		vector.o \
 		wallbase.o \
 		wall.o \
 		wallitem.o \
 		warning.o \
 		xmlwritecode.o \
 		xmlwrite.o \
 		VirtualLeaf.o \
 		moc_canvas.o \
 		moc_cellbase.o \
 		moc_cell.o \
 		moc_infobar.o \
 		moc_modelcatalogue.o \
 		moc_OptionFileDialog.o \
 		moc_pardialog.o \
 		moc_transporterdialog.o \
 		moc_UniqueMessage.o
 DIST          = ../../../Trolltech/Qt-4.4.1/mkspecs/common/g++.conf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/common/unix.conf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/common/linux.conf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/qconfig.pri \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/qt_functions.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/qt_config.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/exclusive_builds.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/default_pre.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/release.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/default_post.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/qt.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/unix/thread.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/moc.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/warn_on.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/resources.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/uic.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/yacc.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/lex.prf \
 		VirtualLeaf.pro
 QMAKE_TARGET  = VirtualLeaf
 DESTDIR       = ../bin/
 TARGET        = ../bin/VirtualLeaf
 all: VirtualLeaf libplugin plugins
 first: all
 ####### Implicit rules
 .SUFFIXES: .o .c .cpp .cc .cxx .C
 .cpp.o:
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
 .cc.o:
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
 .cxx.o:
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
 .C.o:
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
 .c.o:
 	$(CC) -c $(CFLAGS) $(INCPATH) -o "$@" "$<"
 ####### Build rules
 all: Makefile $(TARGET)
 $(TARGET):  $(OBJECTS)
 	@$(CHK_DIR_EXISTS) ../bin/ || $(MKDIR) ../bin/
 	$(LINK) $(LFLAGS) -o $(TARGET) $(OBJECTS) $(OBJCOMP) $(LIBS)
 VirtualLeaf: Makefile.VirtualLeaf
 	make -f Makefile.VirtualLeaf
 Makefile: VirtualLeaf.pro  ../../../Trolltech/Qt-4.4.1/mkspecs/linux-g++-64/qmake.conf ../../../Trolltech/Qt-4.4.1/mkspecs/common/g++.conf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/common/unix.conf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/common/linux.conf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/qconfig.pri \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/qt_functions.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/qt_config.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/exclusive_builds.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/default_pre.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/release.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/default_post.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/qt.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/unix/thread.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/moc.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/warn_on.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/resources.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/uic.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/yacc.prf \
 		../../../Trolltech/Qt-4.4.1/mkspecs/features/lex.prf \
 		/ufs/merks/Trolltech/Qt-4.4.1/lib/libQt3Support.prl \
 		/ufs/merks/Trolltech/Qt-4.4.1/lib/libQtSql.prl \
 		/ufs/merks/Trolltech/Qt-4.4.1/lib/libQtCore.prl \
 		/ufs/merks/Trolltech/Qt-4.4.1/lib/libQtXml.prl \
 		/ufs/merks/Trolltech/Qt-4.4.1/lib/libQtGui.prl \
 		/ufs/merks/Trolltech/Qt-4.4.1/lib/libQtNetwork.prl
 	$(QMAKE) -unix -o Makefile VirtualLeaf.pro
 ../../../Trolltech/Qt-4.4.1/mkspecs/common/g++.conf:
 ../../../Trolltech/Qt-4.4.1/mkspecs/common/unix.conf:
 ../../../Trolltech/Qt-4.4.1/mkspecs/common/linux.conf:
 ../../../Trolltech/Qt-4.4.1/mkspecs/qconfig.pri:
 ../../../Trolltech/Qt-4.4.1/mkspecs/features/qt_functions.prf:
 ../../../Trolltech/Qt-4.4.1/mkspecs/features/qt_config.prf:
 ../../../Trolltech/Qt-4.4.1/mkspecs/features/exclusive_builds.prf:
 ../../../Trolltech/Qt-4.4.1/mkspecs/features/default_pre.prf:
 ../../../Trolltech/Qt-4.4.1/mkspecs/features/release.prf:
 ../../../Trolltech/Qt-4.4.1/mkspecs/features/default_post.prf:
 ../../../Trolltech/Qt-4.4.1/mkspecs/features/qt.prf:
 ../../../Trolltech/Qt-4.4.1/mkspecs/features/unix/thread.prf:
 ../../../Trolltech/Qt-4.4.1/mkspecs/features/moc.prf:
 ../../../Trolltech/Qt-4.4.1/mkspecs/features/warn_on.prf:
 ../../../Trolltech/Qt-4.4.1/mkspecs/features/resources.prf:
 ../../../Trolltech/Qt-4.4.1/mkspecs/features/uic.prf:
 ../../../Trolltech/Qt-4.4.1/mkspecs/features/yacc.prf:
 ../../../Trolltech/Qt-4.4.1/mkspecs/features/lex.prf:
 /ufs/merks/Trolltech/Qt-4.4.1/lib/libQt3Support.prl:
 /ufs/merks/Trolltech/Qt-4.4.1/lib/libQtSql.prl:
 /ufs/merks/Trolltech/Qt-4.4.1/lib/libQtCore.prl:
 /ufs/merks/Trolltech/Qt-4.4.1/lib/libQtXml.prl:
 /ufs/merks/Trolltech/Qt-4.4.1/lib/libQtGui.prl:
 /ufs/merks/Trolltech/Qt-4.4.1/lib/libQtNetwork.prl:
 qmake:  FORCE
 	@$(QMAKE) -unix -o Makefile VirtualLeaf.pro
 dist:
 	@$(CHK_DIR_EXISTS) .tmp/VirtualLeaf1.0.0 || $(MKDIR) .tmp/VirtualLeaf1.0.0
 	$(COPY_FILE) --parents $(SOURCES) $(DIST) .tmp/VirtualLeaf1.0.0/ && $(COPY_FILE) --parents apoplastitem.h canvas.h cellbase.h cell.h cellitem.h infobar.h mainbase.h mainbase.h matrix.h mesh.h miscq.h modelcatalogue.h Neighbor.h node.h nodeitem.h nodeset.h OptionFileDialog.h output.h parameter.h pardialog.h parse.h pi.h qcanvasarrow.h random.h rungekutta.h simitembase.h simplugin.h sqr.h tiny.h transporterdialog.h UniqueMessage.h vector.h wallbase.h wall.h wallitem.h warning.h xmlwrite.h flux_function.h vleafmodel.h VirtualLeafpar.tmpl .tmp/VirtualLeaf1.0.0/ && $(COPY_FILE) --parents apoplastitem.cpp canvas.cpp cellbase.cpp cell.cpp cellitem.cpp mainbase.cpp matrix.cpp mesh.cpp miscq.cpp modelcatalogue.cpp Neighbor.cpp node.cpp nodeitem.cpp nodeset.cpp OptionFileDialog.cpp output.cpp parameter.cpp pardialog.cpp parse.cpp random.cpp rungekutta.cpp simitembase.cpp transporterdialog.cpp UniqueMessage.cpp vector.cpp wallbase.cpp wall.cpp wallitem.cpp warning.cpp xmlwritecode.cpp xmlwrite.cpp VirtualLeaf.cpp .tmp/VirtualLeaf1.0.0/ && (cd `dirname .tmp/VirtualLeaf1.0.0` && $(TAR) VirtualLeaf1.0.0.tar VirtualLeaf1.0.0 && $(COMPRESS) VirtualLeaf1.0.0.tar) && $(MOVE) `dirname .tmp/VirtualLeaf1.0.0`/VirtualLeaf1.0.0.tar.gz . && $(DEL_FILE) -r .tmp/VirtualLeaf1.0.0
 clean:compiler_clean
 	-$(DEL_FILE) $(OBJECTS)
 	-$(DEL_FILE) *~ core *.core
 ####### Sub-libraries
 distclean: clean
 	-$(DEL_FILE) $(TARGET)
 	-$(DEL_FILE) Makefile
 mocclean: compiler_moc_header_clean compiler_moc_source_clean
 mocables: compiler_moc_header_make_all compiler_moc_source_make_all
 compiler_moc_header_make_all: moc_canvas.cpp moc_cellbase.cpp moc_cell.cpp moc_infobar.cpp moc_modelcatalogue.cpp moc_OptionFileDialog.cpp moc_pardialog.cpp moc_transporterdialog.cpp moc_UniqueMessage.cpp
 compiler_moc_header_clean:
 	-$(DEL_FILE) moc_canvas.cpp moc_cellbase.cpp moc_cell.cpp moc_infobar.cpp moc_modelcatalogue.cpp moc_OptionFileDialog.cpp moc_pardialog.cpp moc_transporterdialog.cpp moc_UniqueMessage.cpp
 moc_canvas.cpp: simitembase.h \
 		mainbase.h \
 		mesh.h \
 		cell.h \
 		vector.h \
 		sqr.h \
 		parameter.h \
 		wall.h \
 		wallbase.h \
 		warning.h \
 		cellbase.h \
 		node.h \
 		random.h \
 		modelelement.h \
 		Neighbor.h \
 		simplugin.h \
 		cellitem.h \
 		infobar.h \
 		nodeitem.h \
 		data_plot.h \
 		curvecolors.h \
 		canvas.h
 	/ufs/merks/Trolltech/Qt-4.4.1/bin/moc $(DEFINES) $(INCPATH) canvas.h -o moc_canvas.cpp
 moc_cellbase.cpp: vector.h \
 		sqr.h \
 		parameter.h \
 		wall.h \
 		wallbase.h \
 		warning.h \
 		cellbase.h
 	/ufs/merks/Trolltech/Qt-4.4.1/bin/moc $(DEFINES) $(INCPATH) cellbase.h -o moc_cellbase.cpp
 Makefile.VirtualLeaf: VirtualLeaf.pro
 	$(QMAKE) -makefile -o $@ $<
 moc_cell.cpp: vector.h \
 		sqr.h \
 		parameter.h \
 		wall.h \
 		wallbase.h \
 		warning.h \
 		cellbase.h \
 		cell.h
 	/ufs/merks/Trolltech/Qt-4.4.1/bin/moc $(DEFINES) $(INCPATH) cell.h -o moc_cell.cpp
 moc_infobar.cpp: infobar.h
 	/ufs/merks/Trolltech/Qt-4.4.1/bin/moc $(DEFINES) $(INCPATH) infobar.h -o moc_infobar.cpp
 moc_modelcatalogue.cpp: warning.h \
 		cell.h \
 		vector.h \
 		sqr.h \
 		parameter.h \
 		wall.h \
 		wallbase.h \
 		cellbase.h \
 		mesh.h \
 		node.h \
 		random.h \
 		modelelement.h \
 		Neighbor.h \
 		simplugin.h \
 		canvas.h \
 		simitembase.h \
 		mainbase.h \
 		cellitem.h \
 		infobar.h \
 		nodeitem.h \
 		data_plot.h \
 		curvecolors.h \
 		modelcatalogue.h
 	/ufs/merks/Trolltech/Qt-4.4.1/bin/moc $(DEFINES) $(INCPATH) modelcatalogue.h -o moc_modelcatalogue.cpp
 moc_OptionFileDialog.cpp: OptionFileDialog.h
 	/ufs/merks/Trolltech/Qt-4.4.1/bin/moc $(DEFINES) $(INCPATH) OptionFileDialog.h -o moc_OptionFileDialog.cpp
 moc_pardialog.cpp: pardialog.h
 	/ufs/merks/Trolltech/Qt-4.4.1/bin/moc $(DEFINES) $(INCPATH) pardialog.h -o moc_pardialog.cpp
 moc_transporterdialog.cpp: transporterdialog.h
 	/ufs/merks/Trolltech/Qt-4.4.1/bin/moc $(DEFINES) $(INCPATH) transporterdialog.h -o moc_transporterdialog.cpp
 moc_UniqueMessage.cpp: UniqueMessage.h
 	/ufs/merks/Trolltech/Qt-4.4.1/bin/moc $(DEFINES) $(INCPATH) UniqueMessage.h -o moc_UniqueMessage.cpp
 compiler_rcc_make_all:
 compiler_rcc_clean:
 compiler_image_collection_make_all: qmake_image_collection.cpp
 compiler_image_collection_clean:
 	-$(DEL_FILE) qmake_image_collection.cpp
 compiler_moc_source_make_all:
 compiler_moc_source_clean:
 compiler_uic_make_all:
 compiler_uic_clean:
 compiler_yacc_decl_make_all:
 compiler_yacc_decl_clean:
 compiler_yacc_impl_make_all:
 compiler_yacc_impl_clean:
 compiler_lex_make_all:
 compiler_lex_clean:
 compiler_clean: compiler_moc_header_clean
 ####### Compile
 apoplastitem.o: apoplastitem.cpp canvas.h \
 		simitembase.h \
 		mainbase.h \
 		mesh.h \
 		cell.h \
 		vector.h \
 		sqr.h \
 		parameter.h \
 		wall.h \
 		wallbase.h \
 		warning.h \
 		cellbase.h \
 		node.h \
 		random.h \
 		modelelement.h \
 		Neighbor.h \
 		simplugin.h \
 		cellitem.h \
 		infobar.h \
 		nodeitem.h \
 		data_plot.h \
 		curvecolors.h \
 		apoplastitem.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o apoplastitem.o apoplastitem.cpp
 canvas.o: canvas.cpp pardialog.h \
 		parameter.h \
 		vector.h \
 		sqr.h \
 		canvas.h \
 		simitembase.h \
 		mainbase.h \
 		mesh.h \
 		cell.h \
 		wall.h \
 		wallbase.h \
 		warning.h \
 		cellbase.h \
 		node.h \
 		random.h \
 		modelelement.h \
 		Neighbor.h \
 		simplugin.h \
 		cellitem.h \
 		infobar.h \
 		nodeitem.h \
 		data_plot.h \
 		curvecolors.h \
 		nodeset.h \
 		wallitem.h \
 		xmlwrite.h \
 		miscq.h \
 		OptionFileDialog.h \
 		modelcatalogue.h \
 		psb.xpm \
 		cwi.xpm
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o canvas.o canvas.cpp
 libplugin: Makefile.libplugin
 	make -f Makefile.libplugin
 cellbase.o: cellbase.cpp nodeitem.h \
 		simitembase.h \
 		node.h \
 		vector.h \
 		sqr.h \
 		random.h \
 		parameter.h \
 		cell.h \
 		wall.h \
 		wallbase.h \
 		warning.h \
 		cellbase.h \
 		modelelement.h \
 		Neighbor.h \
 		cellitem.h \
 		qcanvasarrow.h \
 		nodeset.h \
 		mesh.h \
 		simplugin.h \
 		tiny.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o cellbase.o cellbase.cpp
 cell.o: cell.cpp cell.h \
 		vector.h \
 		sqr.h \
 		parameter.h \
 		wall.h \
 		wallbase.h \
 		warning.h \
 		cellbase.h \
 		node.h \
 		random.h \
 		modelelement.h \
 		Neighbor.h \
 		mesh.h \
 		simplugin.h \
 		tiny.h \
 		nodeset.h \
 		cellitem.h \
 		simitembase.h \
 		nodeitem.h \
 		qcanvasarrow.h \
 		canvas.h \
 		mainbase.h \
 		infobar.h \
 		data_plot.h \
 		curvecolors.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o cell.o cell.cpp
 cellitem.o: cellitem.cpp cellitem.h \
 		simitembase.h \
 		cell.h \
 		vector.h \
 		sqr.h \
 		parameter.h \
 		wall.h \
 		wallbase.h \
 		warning.h \
 		cellbase.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o cellitem.o cellitem.cpp
 mainbase.o: mainbase.cpp mainbase.h \
 		mesh.h \
 		cell.h \
 		vector.h \
 		sqr.h \
 		parameter.h \
 		wall.h \
 		wallbase.h \
 		warning.h \
 		cellbase.h \
 		node.h \
 		random.h \
 		modelelement.h \
 		Neighbor.h \
 		simplugin.h \
 		xmlwrite.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o mainbase.o mainbase.cpp
 matrix.o: matrix.cpp vector.h \
 		sqr.h \
 		matrix.h \
 		tiny.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o matrix.o matrix.cpp
 mesh.o: mesh.cpp mesh.h \
 		cell.h \
 		vector.h \
 		sqr.h \
 		parameter.h \
 		wall.h \
 		wallbase.h \
 		warning.h \
 		cellbase.h \
 		node.h \
 		random.h \
 		modelelement.h \
 		Neighbor.h \
 		simplugin.h \
 		tiny.h \
 		pi.h \
 		parse.h \
 		matrix.h \
 		nodeset.h \
 		nodeitem.h \
 		simitembase.h \
 		rungekutta.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o mesh.o mesh.cpp
 Makefile.libplugin: libplugin.pro
 	$(QMAKE) -makefile -o $@ $<
 miscq.o: miscq.cpp
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o miscq.o miscq.cpp
 modelcatalogue.o: modelcatalogue.cpp modelcatalogue.h \
 		warning.h \
 		cell.h \
 		vector.h \
 		sqr.h \
 		parameter.h \
 		wall.h \
 		wallbase.h \
 		cellbase.h \
 		mesh.h \
 		node.h \
 		random.h \
 		modelelement.h \
 		Neighbor.h \
 		simplugin.h \
 		canvas.h \
 		simitembase.h \
 		mainbase.h \
 		cellitem.h \
 		infobar.h \
 		nodeitem.h \
 		data_plot.h \
 		curvecolors.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o modelcatalogue.o modelcatalogue.cpp
 Neighbor.o: Neighbor.cpp Neighbor.h \
 		cell.h \
 		vector.h \
 		sqr.h \
 		parameter.h \
 		wall.h \
 		wallbase.h \
 		warning.h \
 		cellbase.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o Neighbor.o Neighbor.cpp
 node.o: node.cpp node.h \
 		vector.h \
 		sqr.h \
 		random.h \
 		parameter.h \
 		cell.h \
 		wall.h \
 		wallbase.h \
 		warning.h \
 		cellbase.h \
 		modelelement.h \
 		Neighbor.h \
 		mesh.h \
 		simplugin.h \
 		pi.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o node.o node.cpp
 nodeitem.o: nodeitem.cpp nodeitem.h \
 		simitembase.h \
 		node.h \
 		vector.h \
 		sqr.h \
 		random.h \
 		parameter.h \
 		cell.h \
 		wall.h \
 		wallbase.h \
 		warning.h \
 		cellbase.h \
 		modelelement.h \
 		Neighbor.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o nodeitem.o nodeitem.cpp
 nodeset.o: nodeset.cpp nodeset.h \
 		node.h \
 		vector.h \
 		sqr.h \
 		random.h \
 		parameter.h \
 		cell.h \
 		wall.h \
 		wallbase.h \
 		warning.h \
 		cellbase.h \
 		modelelement.h \
 		Neighbor.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o nodeset.o nodeset.cpp
 OptionFileDialog.o: OptionFileDialog.cpp OptionFileDialog.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o OptionFileDialog.o OptionFileDialog.cpp
 output.o: output.cpp warning.h \
 		parameter.h \
 		vector.h \
 		sqr.h \
 		output.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o output.o output.cpp
 parameter.o: parameter.cpp parameter.h \
 		vector.h \
 		sqr.h \
 		output.h \
 		parse.h \
 		xmlwrite.h \
 		warning.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o parameter.o parameter.cpp
 pardialog.o: pardialog.cpp pardialog.h \
 		parameter.h \
 		vector.h \
 		sqr.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o pardialog.o pardialog.cpp
 plugins:
 	make -C build_models
 parse.o: parse.cpp warning.h \
 		parse.h \
 		output.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o parse.o parse.cpp
 random.o: random.cpp random.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o random.o random.cpp
 rungekutta.o: rungekutta.cpp rungekutta.h \
 		warning.h \
 		maxmin.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o rungekutta.o rungekutta.cpp
 simitembase.o: simitembase.cpp simitembase.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o simitembase.o simitembase.cpp
 transporterdialog.o: transporterdialog.cpp canvas.h \
 		simitembase.h \
 		mainbase.h \
 		mesh.h \
 		cell.h \
 		vector.h \
 		sqr.h \
 		parameter.h \
 		wall.h \
 		wallbase.h \
 		warning.h \
 		cellbase.h \
 		node.h \
 		random.h \
 		modelelement.h \
 		Neighbor.h \
 		simplugin.h \
 		cellitem.h \
 		infobar.h \
 		nodeitem.h \
 		data_plot.h \
 		curvecolors.h \
 		transporterdialog.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o transporterdialog.o transporterdialog.cpp
 UniqueMessage.o: UniqueMessage.cpp UniqueMessage.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o UniqueMessage.o UniqueMessage.cpp
 vector.o: vector.cpp sqr.h \
 		pi.h \
 		vector.h \
 		tiny.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o vector.o vector.cpp
 wallbase.o: wallbase.cpp wall.h \
 		wallbase.h \
 		vector.h \
 		sqr.h \
 		node.h \
 		random.h \
 		parameter.h \
 		cell.h \
 		warning.h \
 		cellbase.h \
 		modelelement.h \
 		Neighbor.h \
 		mesh.h \
 		simplugin.h \
 		wallitem.h \
 		simitembase.h \
 		apoplastitem.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o wallbase.o wallbase.cpp
 wall.o: wall.cpp wall.h \
 		wallbase.h \
 		vector.h \
 		sqr.h \
 		cell.h \
 		parameter.h \
 		warning.h \
 		cellbase.h \
 		wallitem.h \
 		simitembase.h \
 		node.h \
 		random.h \
 		modelelement.h \
 		Neighbor.h \
 		apoplastitem.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o wall.o wall.cpp
 clean:
 	make -f Makefile.libplugin clean
 	make -f Makefile.VirtualLeaf clean
 	make -C build_models clean
 wallitem.o: wallitem.cpp canvas.h \
 		simitembase.h \
 		mainbase.h \
 		mesh.h \
 		cell.h \
 		vector.h \
 		sqr.h \
 		parameter.h \
 		wall.h \
 		wallbase.h \
 		warning.h \
 		cellbase.h \
 		node.h \
 		random.h \
 		modelelement.h \
 		Neighbor.h \
 		simplugin.h \
 		cellitem.h \
 		infobar.h \
 		nodeitem.h \
 		data_plot.h \
 		curvecolors.h \
 		wallitem.h \
 		transporterdialog.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o wallitem.o wallitem.cpp
 warning.o: warning.cpp warning.h \
 		canvas.h \
 		simitembase.h \
 		mainbase.h \
 		mesh.h \
 		cell.h \
 		vector.h \
 		sqr.h \
 		parameter.h \
 		wall.h \
 		wallbase.h \
 		cellbase.h \
 		node.h \
 		random.h \
 		modelelement.h \
 		Neighbor.h \
 		simplugin.h \
 		cellitem.h \
 		infobar.h \
 		nodeitem.h \
 		data_plot.h \
 		curvecolors.h \
 		UniqueMessage.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o warning.o warning.cpp
 xmlwritecode.o: xmlwritecode.cpp xmlwrite.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o xmlwritecode.o xmlwritecode.cpp
 #finis
 xmlwrite.o: xmlwrite.cpp mesh.h \
 		cell.h \
 		vector.h \
 		sqr.h \
 		parameter.h \
 		wall.h \
 		wallbase.h \
 		warning.h \
 		cellbase.h \
 		node.h \
 		random.h \
 		modelelement.h \
 		Neighbor.h \
 		simplugin.h \
 		xmlwrite.h \
 		nodeset.h \
 		output.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o xmlwrite.o xmlwrite.cpp
 VirtualLeaf.o: VirtualLeaf.cpp mesh.h \
 		cell.h \
 		vector.h \
 		sqr.h \
 		parameter.h \
 		wall.h \
 		wallbase.h \
 		warning.h \
 		cellbase.h \
 		node.h \
 		random.h \
 		modelelement.h \
 		Neighbor.h \
 		simplugin.h \
 		pi.h \
 		cellitem.h \
 		simitembase.h \
 		canvas.h \
 		mainbase.h \
 		infobar.h \
 		nodeitem.h \
 		data_plot.h \
 		curvecolors.h \
 		output.h \
 		modelcatalogue.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o VirtualLeaf.o VirtualLeaf.cpp
 moc_canvas.o: moc_canvas.cpp
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o moc_canvas.o moc_canvas.cpp
 moc_cellbase.o: moc_cellbase.cpp
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o moc_cellbase.o moc_cellbase.cpp
 moc_cell.o: moc_cell.cpp
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o moc_cell.o moc_cell.cpp
 moc_infobar.o: moc_infobar.cpp
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o moc_infobar.o moc_infobar.cpp
 moc_modelcatalogue.o: moc_modelcatalogue.cpp
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o moc_modelcatalogue.o moc_modelcatalogue.cpp
 moc_OptionFileDialog.o: moc_OptionFileDialog.cpp
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o moc_OptionFileDialog.o moc_OptionFileDialog.cpp
 moc_pardialog.o: moc_pardialog.cpp
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o moc_pardialog.o moc_pardialog.cpp
 moc_transporterdialog.o: moc_transporterdialog.cpp
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o moc_transporterdialog.o moc_transporterdialog.cpp
 moc_UniqueMessage.o: moc_UniqueMessage.cpp
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o moc_UniqueMessage.o moc_UniqueMessage.cpp
 ####### Install
 install:   FORCE
 uninstall:   FORCE
 FORCE:

src/TutorialCode/Tutorial1A/mymodel.cpp

➞

Show inline comments

@@ new file 100644 @@
 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  The Virtual Leaf is free software: you can redistribute it and/or modify
  *  it under the terms of the GNU General Public License as published by
  *  the Free Software Foundation, either version 3 of the License, or
  *  (at your option) any later version.
+ *
  *  The Virtual Leaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include <QObject>
 #include <QtGui>
 #include "simplugin.h"
 #include "parameter.h"
 #include "wallbase.h"
 #include "cellbase.h"
 #include "mymodel.h"
 static const std::string _module_id("$Id$");
 QString MyModel::ModelID(void) {
   // specify the name of your model here
   return QString( "Cell growth" );
+}
 // return the number of chemicals your model uses
 int MyModel::NChem(void) { return 0; }
 // To be executed after cell division
 void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
   // rules to be executed after cell division go here
   // (e.g., cell differentiation rules)
+}
 void MyModel::SetCellColor(CellBase *c, QColor *color) {
   // add cell coloring rules here
+}
 void MyModel::CellHouseKeeping(CellBase *c) {
   // add cell behavioral rules here
 	c->EnlargeTargetArea(par->cell_expansion_rate);
+}
 void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
   // add biochemical transport rules here
+}
 void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) {
   // add biochemical networks for reactions occuring at walls here
+}
 void MyModel::CellDynamics(CellBase *c, double *dchem) {
   // add biochemical networks for intracellular reactions here
+}
 Q_EXPORT_PLUGIN2(mymodel, MyModel)

src/TutorialCode/Tutorial1A/mymodel.h

➞

Show inline comments

@@ new file 100644 @@
 /*
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  The Virtual Leaf is free software: you can redistribute it and/or modify
  *  it under the terms of the GNU General Public License as published by
  *  the Free Software Foundation, either version 3 of the License, or
  *  (at your option) any later version.
+ *
  *  The Virtual Leaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include <QObject>
 #include <QtGui>
 #include <QString>
 #include "simplugin.h"
 class MyModel : public QObject, SimPluginInterface {
 	Q_OBJECT
 	Q_INTERFACES(SimPluginInterface);
 public:
 	virtual QString ModelID(void);
 	// Executed after the cellular mechanics steps have equillibrized
 	virtual void CellHouseKeeping (CellBase *c);
 	// Differential equations describing transport of chemicals from cell to cell
 	virtual void CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2);
 	// Differential equations describing chemical reactions taking place at or near the cell walls
 	// (e.g. PIN accumulation)
 	virtual void WallDynamics(Wall *w, double *dw1, double *dw2);
 	// Differential equations describing chemical reactions inside the cells
 	virtual void CellDynamics(CellBase *c, double *dchem);
 	// to be executed after a cell division
 	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);
 	// to be executed for coloring a cell
 	virtual void SetCellColor(CellBase *c, QColor *color);
 	// return number of chemicals
 	virtual int NChem(void);
 };

src/TutorialCode/Tutorial1A/mymodel.pro

➞

Show inline comments

@@ new file 100644 @@
+#
 # $Id$
+#
 #  This file is part of the Virtual Leaf.
+#
 #  The Virtual Leaf is free software: you can redistribute it and/or modify
 #  it under the terms of the GNU General Public License as published by
 #  the Free Software Foundation, either version 3 of the License, or
 #  (at your option) any later version.
+#
 #  The Virtual Leaf is distributed in the hope that it will be useful,
 #  but WITHOUT ANY WARRANTY; without even the implied warranty of
 #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 #  GNU General Public License for more details.
+#
 #  You should have received a copy of the GNU General Public License
 #  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+#
 #  Copyright 2010 Roeland Merks.
+#
 TARGET = mymodel
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/TutorialCode/Tutorial1B/mymodel.cpp

➞

Show inline comments

@@ new file 100644 @@
 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  The Virtual Leaf is free software: you can redistribute it and/or modify
  *  it under the terms of the GNU General Public License as published by
  *  the Free Software Foundation, either version 3 of the License, or
  *  (at your option) any later version.
+ *
  *  The Virtual Leaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include <QObject>
 #include <QtGui>
 #include "simplugin.h"
 #include "parameter.h"
 #include "wallbase.h"
 #include "cellbase.h"
 #include "mymodel.h"
 static const std::string _module_id("$Id$");
 QString MyModel::ModelID(void) {
   // specify the name of your model here
   return QString( "Cell growth and cell division" );
+}
 // return the number of chemicals your model uses
 int MyModel::NChem(void) { return 0; }
 // To be executed after cell division
 void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
   // rules to be executed after cell division go here
   // (e.g., cell differentiation rules)
+}
 void MyModel::SetCellColor(CellBase *c, QColor *color) {
   // add cell coloring rules here
+}
 void MyModel::CellHouseKeeping(CellBase *c) {
   // add cell behavioral rules here
 	c->EnlargeTargetArea(par->cell_expansion_rate);
 	if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) {
 		c->Divide();
+	}
+}
 void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
   // add biochemical transport rules here
+}
 void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) {
   // add biochemical networks for reactions occuring at walls here
+}
 void MyModel::CellDynamics(CellBase *c, double *dchem) {
   // add biochemical networks for intracellular reactions here
+}
 Q_EXPORT_PLUGIN2(mymodel, MyModel)

src/TutorialCode/Tutorial1B/mymodel.h

➞

Show inline comments

@@ new file 100644 @@
 /*
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  The Virtual Leaf is free software: you can redistribute it and/or modify
  *  it under the terms of the GNU General Public License as published by
  *  the Free Software Foundation, either version 3 of the License, or
  *  (at your option) any later version.
+ *
  *  The Virtual Leaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include <QObject>
 #include <QtGui>
 #include <QString>
 #include "simplugin.h"
 class MyModel : public QObject, SimPluginInterface {
 	Q_OBJECT
 	Q_INTERFACES(SimPluginInterface);
 public:
 	virtual QString ModelID(void);
 	// Executed after the cellular mechanics steps have equillibrized
 	virtual void CellHouseKeeping (CellBase *c);
 	// Differential equations describing transport of chemicals from cell to cell
 	virtual void CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2);
 	// Differential equations describing chemical reactions taking place at or near the cell walls
 	// (e.g. PIN accumulation)
 	virtual void WallDynamics(Wall *w, double *dw1, double *dw2);
 	// Differential equations describing chemical reactions inside the cells
 	virtual void CellDynamics(CellBase *c, double *dchem);
 	// to be executed after a cell division
 	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);
 	// to be executed for coloring a cell
 	virtual void SetCellColor(CellBase *c, QColor *color);
 	// return number of chemicals
 	virtual int NChem(void);
 };

src/TutorialCode/Tutorial1B/mymodel.pro

➞

Show inline comments

@@ new file 100644 @@
+#
 # $Id$
+#
 #  This file is part of the Virtual Leaf.
+#
 #  The Virtual Leaf is free software: you can redistribute it and/or modify
 #  it under the terms of the GNU General Public License as published by
 #  the Free Software Foundation, either version 3 of the License, or
 #  (at your option) any later version.
+#
 #  The Virtual Leaf is distributed in the hope that it will be useful,
 #  but WITHOUT ANY WARRANTY; without even the implied warranty of
 #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 #  GNU General Public License for more details.
+#
 #  You should have received a copy of the GNU General Public License
 #  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+#
 #  Copyright 2010 Roeland Merks.
+#
 TARGET = mymodel
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/TutorialCode/Tutorial1C/mymodel.cpp

➞

Show inline comments

@@ new file 100644 @@
 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  The Virtual Leaf is free software: you can redistribute it and/or modify
  *  it under the terms of the GNU General Public License as published by
  *  the Free Software Foundation, either version 3 of the License, or
  *  (at your option) any later version.
+ *
  *  The Virtual Leaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include <QObject>
 #include <QtGui>
 #include "simplugin.h"
 #include "parameter.h"
 #include "wallbase.h"
 #include "cellbase.h"
 #include "mymodel.h"
 static const std::string _module_id("$Id$");
 QString MyModel::ModelID(void) {
   // specify the name of your model here
   return QString( "Cell growth and cell division" );
+}
 // return the number of chemicals your model uses
 int MyModel::NChem(void) { return 0; }
 // To be executed after cell division
 void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
   // rules to be executed after cell division go here
   // (e.g., cell differentiation rules)
+}
 void MyModel::SetCellColor(CellBase *c, QColor *color) {
   // add cell coloring rules here
+}
 void MyModel::CellHouseKeeping(CellBase *c) {
   // add cell behavioral rules here
 	c->EnlargeTargetArea(par->cell_expansion_rate);
 	if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) {
 		c->DivideOverAxis(Vector(1,0,0));
+	}
+}
 void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
   // add biochemical transport rules here
+}
 void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) {
   // add biochemical networks for reactions occuring at walls here
+}
 void MyModel::CellDynamics(CellBase *c, double *dchem) {
   // add biochemical networks for intracellular reactions here
+}
 Q_EXPORT_PLUGIN2(mymodel, MyModel)

src/TutorialCode/Tutorial1C/mymodel.h

➞

Show inline comments

@@ new file 100644 @@
 /*
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  The Virtual Leaf is free software: you can redistribute it and/or modify
  *  it under the terms of the GNU General Public License as published by
  *  the Free Software Foundation, either version 3 of the License, or
  *  (at your option) any later version.
+ *
  *  The Virtual Leaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include <QObject>
 #include <QtGui>
 #include <QString>
 #include "simplugin.h"
 class MyModel : public QObject, SimPluginInterface {
 	Q_OBJECT
 	Q_INTERFACES(SimPluginInterface);
 public:
 	virtual QString ModelID(void);
 	// Executed after the cellular mechanics steps have equillibrized
 	virtual void CellHouseKeeping (CellBase *c);
 	// Differential equations describing transport of chemicals from cell to cell
 	virtual void CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2);
 	// Differential equations describing chemical reactions taking place at or near the cell walls
 	// (e.g. PIN accumulation)
 	virtual void WallDynamics(Wall *w, double *dw1, double *dw2);
 	// Differential equations describing chemical reactions inside the cells
 	virtual void CellDynamics(CellBase *c, double *dchem);
 	// to be executed after a cell division
 	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);
 	// to be executed for coloring a cell
 	virtual void SetCellColor(CellBase *c, QColor *color);
 	// return number of chemicals
 	virtual int NChem(void);
 };

src/TutorialCode/Tutorial1C/mymodel.pro

➞

Show inline comments

@@ new file 100644 @@
+#
 # $Id$
+#
 #  This file is part of the Virtual Leaf.
+#
 #  The Virtual Leaf is free software: you can redistribute it and/or modify
 #  it under the terms of the GNU General Public License as published by
 #  the Free Software Foundation, either version 3 of the License, or
 #  (at your option) any later version.
+#
 #  The Virtual Leaf is distributed in the hope that it will be useful,
 #  but WITHOUT ANY WARRANTY; without even the implied warranty of
 #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 #  GNU General Public License for more details.
+#
 #  You should have received a copy of the GNU General Public License
 #  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+#
 #  Copyright 2010 Roeland Merks.
+#
 TARGET = mymodel
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/TutorialCode/Tutorial1D/mymodel.cpp

➞

Show inline comments

@@ new file 100644 @@
 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  The Virtual Leaf is free software: you can redistribute it and/or modify
  *  it under the terms of the GNU General Public License as published by
  *  the Free Software Foundation, either version 3 of the License, or
  *  (at your option) any later version.
+ *
  *  The Virtual Leaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include <QObject>
 #include <QtGui>
 #include "simplugin.h"
 #include "parameter.h"
 #include "wallbase.h"
 #include "cellbase.h"
 #include "mymodel.h"
 static const std::string _module_id("$Id$");
 QString MyModel::ModelID(void) {
   // specify the name of your model here
   return QString( "Growth, division, coloring" );
+}
 // return the number of chemicals your model uses
 int MyModel::NChem(void) { return 0; }
 // To be executed after cell division
 void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
   // rules to be executed after cell division go here
   // (e.g., cell differentiation rules)
+}
 void MyModel::SetCellColor(CellBase *c, QColor *color) {
   // add cell coloring rules here
 	if (c->Area()/c->BaseArea()>1.8) { color->setNamedColor("blue"); }
 	else { color->setNamedColor("green"); }
+}
 void MyModel::CellHouseKeeping(CellBase *c) {
   // add cell behavioral rules here
 	c->EnlargeTargetArea(par->cell_expansion_rate);
 	if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) {
 		c->Divide();
+	}
+}
 void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
   // add biochemical transport rules here
+}
 void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) {
   // add biochemical networks for reactions occuring at walls here
+}
 void MyModel::CellDynamics(CellBase *c, double *dchem) {
   // add biochemical networks for intracellular reactions here
+}
 Q_EXPORT_PLUGIN2(mymodel, MyModel)

src/TutorialCode/Tutorial1D/mymodel.h

➞

Show inline comments

@@ new file 100644 @@
 /*
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  The Virtual Leaf is free software: you can redistribute it and/or modify
  *  it under the terms of the GNU General Public License as published by
  *  the Free Software Foundation, either version 3 of the License, or
  *  (at your option) any later version.
+ *
  *  The Virtual Leaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include <QObject>
 #include <QtGui>
 #include <QString>
 #include "simplugin.h"
 class MyModel : public QObject, SimPluginInterface {
 	Q_OBJECT
 	Q_INTERFACES(SimPluginInterface);
 public:
 	virtual QString ModelID(void);
 	// Executed after the cellular mechanics steps have equillibrized
 	virtual void CellHouseKeeping (CellBase *c);
 	// Differential equations describing transport of chemicals from cell to cell
 	virtual void CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2);
 	// Differential equations describing chemical reactions taking place at or near the cell walls
 	// (e.g. PIN accumulation)
 	virtual void WallDynamics(Wall *w, double *dw1, double *dw2);
 	// Differential equations describing chemical reactions inside the cells
 	virtual void CellDynamics(CellBase *c, double *dchem);
 	// to be executed after a cell division
 	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);
 	// to be executed for coloring a cell
 	virtual void SetCellColor(CellBase *c, QColor *color);
 	// return number of chemicals
 	virtual int NChem(void);
 };

src/TutorialCode/Tutorial1D/mymodel.pro

➞

Show inline comments

@@ new file 100644 @@
+#
 # $Id$
+#
 #  This file is part of the Virtual Leaf.
+#
 #  The Virtual Leaf is free software: you can redistribute it and/or modify
 #  it under the terms of the GNU General Public License as published by
 #  the Free Software Foundation, either version 3 of the License, or
 #  (at your option) any later version.
+#
 #  The Virtual Leaf is distributed in the hope that it will be useful,
 #  but WITHOUT ANY WARRANTY; without even the implied warranty of
 #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 #  GNU General Public License for more details.
+#
 #  You should have received a copy of the GNU General Public License
 #  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+#
 #  Copyright 2010 Roeland Merks.
+#
 TARGET = mymodel
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/TutorialCode/Tutorial2/mymodel.cpp

➞

Show inline comments

@@ @@ -34,26 +34,66 @@ static const std::string _module_id("$Id @@
 QString MyModel::ModelID(void) {
   // specify the name of your model here
-  return QString( "Cell growth and cell division" );
+  return QString( "Growth hormones" );
+}
 // return the number of chemicals your model uses
-int MyModel::NChem(void) { return 0; }
+int MyModel::NChem(void) { return 1; }
 // To be executed after cell division
 void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
   // rules to be executed after cell division go here
   // (e.g., cell differentiation rules)
 	// set one cell to source after first division
 	if (CellBase::NCells()==2) {
 		daughter1->SetCellType(1);
 		daughter2->SetCellType(0);
+	}
 	// if a source cells has divided, one of the daughters becomes the new source
 	if (daughter1->CellType()==1) {
 		// if both cells are at the tissue perimeter, choose at random
 		if (daughter1->AtBoundaryP() && daughter2->AtBoundaryP()) {
 			if (qrand()%2){
 				daughter1->SetCellType(1);
 				daughter2->SetCellType(0);
 			} else {
 				daughter1->SetCellType(0);
 				daughter2->SetCellType(1);
+			}
 		} else {
 			// otherwise choose the one that is still at the perimeter
 			if (daughter1->AtBoundaryP()) {
 				daughter1->SetCellType(1);
 				daughter2->SetCellType(0);
 			} else {
 				daughter1->SetCellType(0);
 				daughter2->SetCellType(1);
+			}
+		}
+	}
+}
 void MyModel::SetCellColor(CellBase *c, QColor *color) {
   // add cell coloring rules here
 	// white: high concentration of growth hormone, black low concentration
 	double val = 1.-c->Chemical(0)/(1.+c->Chemical(0));
 	color->setRgbF(val, val, val);
+}
 void MyModel::CellHouseKeeping(CellBase *c) {
   // add cell behavioral rules here
 	c->EnlargeTargetArea(par->cell_expansion_rate);
 	if (CellBase::NCells()==1)
 		// first cell expands unconditionally
 		c->EnlargeTargetArea(par->cell_expansion_rate);
 	else
 		c->EnlargeTargetArea(c->Chemical(0)*par->cell_expansion_rate);
 	if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) {
 		c->Divide();
+	}
@@ @@ -61,12 +101,19 @@ void MyModel::CellHouseKeeping(CellBase @@
 void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
   // add biochemical transport rules here
 	double phi = w->Length() * par->D[0] * ( w->C2()->Chemical(0) - w->C1()->Chemical(0) );
 	dchem_c1[0]+=phi;
 	dchem_c2[0]-=phi;
+}
 void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) {
   // add biochemical networks for reactions occuring at walls here
+}
 void MyModel::CellDynamics(CellBase *c, double *dchem) {
   // add biochemical networks for intracellular reactions here
 	if (c->CellType()==1) {
 		dchem[0] = par->leaf_tip_source;
+	}
+}

src/TutorialCode/Tutorial3/mymodel.cpp

➞

Show inline comments

@@ @@ -34,38 +34,99 @@ static const std::string _module_id("$Id @@
 QString MyModel::ModelID(void) {
   // specify the name of your model here
-  return QString( "Cell growth and cell division" );
+  return QString( "Growth hormones" );
+}
 // return the number of chemicals your model uses
-int MyModel::NChem(void) { return 0; }
+int MyModel::NChem(void) { return 2; }
 // To be executed after cell division
 void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
   // rules to be executed after cell division go here
   // (e.g., cell differentiation rules)
 	// set one cell to source after first division
 	if (CellBase::NCells()==2) {
 		daughter1->SetCellType(1);
 		daughter2->SetCellType(0);
+	}
 	// if a source cells has divided, one of the daughters becomes the new source
 	if (daughter1->CellType()==1) {
 		// if both cells are at the tissue perimeter, choose at random
 		if (daughter1->AtBoundaryP() && daughter2->AtBoundaryP()) {
 			if (qrand()%2){
 				daughter1->SetCellType(1);
 				daughter2->SetCellType(0);
 			} else {
 				daughter1->SetCellType(0);
 				daughter2->SetCellType(1);
+			}
 		} else {
 			// otherwise choose the one that is still at the perimeter
 			if (daughter1->AtBoundaryP()) {
 				daughter1->SetCellType(1);
 				daughter2->SetCellType(0);
 			} else {
 				daughter1->SetCellType(0);
 				daughter2->SetCellType(1);
+			}
+		}
+	}
+}
 void MyModel::SetCellColor(CellBase *c, QColor *color) {
   // add cell coloring rules here
 	// white: high concentration of growth hormone, black low concentration
 	double val = 1.-c->Chemical(0)/(1.+c->Chemical(0));
 	color->setRgbF(val, val, val);
+}
 void MyModel::CellHouseKeeping(CellBase *c) {
   // add cell behavioral rules here
 	c->EnlargeTargetArea(par->cell_expansion_rate);
 	if (CellBase::NCells()==1)
 		// first cell expands unconditionally
 		c->EnlargeTargetArea(par->cell_expansion_rate);
 	else
 		c->EnlargeTargetArea(c->Chemical(0)*par->cell_expansion_rate);
 	if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) {
-		c->DivideOverAxis(Vector(1,0,0));
+		c->Divide();
+	}
+}
 void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
   // add biochemical transport rules here
 	double phi = w->Length() * par->D[0] * ( w->C2()->Chemical(0) - w->C1()->Chemical(0) );
 	dchem_c1[0]+=phi;
 	dchem_c2[0]-=phi;
 	// directed transport
 	// efflux from cell 1 to cell 2
   	double trans12 = ( par->transport * w->Transporters1(1) *
 					  w->C1()->Chemical(0) / (par->ka + w->C1()->Chemical(0)) );
     // efflux from cell 2 to cell 1
     double trans21 = ( par->transport * w->Transporters2(1) *
 					  w->C2()->Chemical(0) / (par->ka + w->C2()->Chemical(0)) );
     dchem_c1[0] += trans21 - trans12;
     dchem_c2[0] += trans12 - trans21;
+}
 void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) {
   // add biochemical networks for reactions occuring at walls here
+}
 void MyModel::CellDynamics(CellBase *c, double *dchem) {
   // add biochemical networks for intracellular reactions here
 	if (c->CellType()==1) {
 		dchem[0] = par->leaf_tip_source;
+	}
+}

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