diff --git a/src/Makefile b/src/Makefile
--- a/src/Makefile
+++ b/src/Makefile
@@ -1,27 +1,854 @@
-# $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) $(INCPATH) -o moc_UniqueMessage.o moc_UniqueMessage.cpp
+
+####### Install
+
+install: FORCE
+
+uninstall: FORCE
+
+FORCE:
+
diff --git a/src/TutorialCode/Tutorial1A/mymodel.cpp b/src/TutorialCode/Tutorial1A/mymodel.cpp
new file mode 100644
--- /dev/null
+++ b/src/TutorialCode/Tutorial1A/mymodel.cpp
@@ -0,0 +1,70 @@
+/*
+ *
+ * This file is part of the Virtual Leaf.
+ *
+ * The Virtual Leaf is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * The Virtual Leaf is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with the Virtual Leaf. If not, see .
+ *
+ * Copyright 2010 Roeland Merks.
+ *
+ */
+
+#include
+#include
+
+#include "simplugin.h"
+
+#include "parameter.h"
+
+#include "wallbase.h"
+#include "cellbase.h"
+#include "mymodel.h"
+
+static const std::string _module_id("$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)
diff --git a/src/TutorialCode/Tutorial1A/mymodel.h b/src/TutorialCode/Tutorial1A/mymodel.h
new file mode 100644
--- /dev/null
+++ b/src/TutorialCode/Tutorial1A/mymodel.h
@@ -0,0 +1,60 @@
+/*
+ * $Id$
+ *
+ * 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 .
+ *
+ * Copyright 2010 Roeland Merks.
+ *
+ */
+
+
+#include
+#include
+#include
+#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);
+};
+
+
+
+
diff --git a/src/TutorialCode/Tutorial1A/mymodel.pro b/src/TutorialCode/Tutorial1A/mymodel.pro
new file mode 100644
--- /dev/null
+++ b/src/TutorialCode/Tutorial1A/mymodel.pro
@@ -0,0 +1,61 @@
+#
+# $Id$
+#
+# 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 .
+#
+# 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
diff --git a/src/TutorialCode/Tutorial1B/mymodel.cpp b/src/TutorialCode/Tutorial1B/mymodel.cpp
new file mode 100644
--- /dev/null
+++ b/src/TutorialCode/Tutorial1B/mymodel.cpp
@@ -0,0 +1,73 @@
+/*
+ *
+ * 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 .
+ *
+ * Copyright 2010 Roeland Merks.
+ *
+ */
+
+#include
+#include
+
+#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)
diff --git a/src/TutorialCode/Tutorial1B/mymodel.h b/src/TutorialCode/Tutorial1B/mymodel.h
new file mode 100644
--- /dev/null
+++ b/src/TutorialCode/Tutorial1B/mymodel.h
@@ -0,0 +1,60 @@
+/*
+ * $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 .
+ *
+ * Copyright 2010 Roeland Merks.
+ *
+ */
+
+
+#include
+#include
+#include
+#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);
+};
+
+
+
+
diff --git a/src/TutorialCode/Tutorial1B/mymodel.pro b/src/TutorialCode/Tutorial1B/mymodel.pro
new file mode 100644
--- /dev/null
+++ b/src/TutorialCode/Tutorial1B/mymodel.pro
@@ -0,0 +1,61 @@
+#
+# $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 .
+#
+# 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
diff --git a/src/TutorialCode/Tutorial1C/mymodel.cpp b/src/TutorialCode/Tutorial1C/mymodel.cpp
new file mode 100644
--- /dev/null
+++ b/src/TutorialCode/Tutorial1C/mymodel.cpp
@@ -0,0 +1,72 @@
+/*
+ *
+ * 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 .
+ *
+ * Copyright 2010 Roeland Merks.
+ *
+ */
+
+#include
+#include
+
+#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)
diff --git a/src/TutorialCode/Tutorial1C/mymodel.h b/src/TutorialCode/Tutorial1C/mymodel.h
new file mode 100644
--- /dev/null
+++ b/src/TutorialCode/Tutorial1C/mymodel.h
@@ -0,0 +1,60 @@
+/*
+ * $Id$
+ *
+ * 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 .
+ *
+ * Copyright 2010 Roeland Merks.
+ *
+ */
+
+
+#include
+#include
+#include
+#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);
+};
+
+
+
+
diff --git a/src/TutorialCode/Tutorial1C/mymodel.pro b/src/TutorialCode/Tutorial1C/mymodel.pro
new file mode 100644
--- /dev/null
+++ b/src/TutorialCode/Tutorial1C/mymodel.pro
@@ -0,0 +1,61 @@
+#
+# $Id$
+#
+# 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 .
+#
+# 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
diff --git a/src/TutorialCode/Tutorial1D/mymodel.cpp b/src/TutorialCode/Tutorial1D/mymodel.cpp
new file mode 100644
--- /dev/null
+++ b/src/TutorialCode/Tutorial1D/mymodel.cpp
@@ -0,0 +1,75 @@
+/*
+ *
+ * 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 .
+ *
+ * Copyright 2010 Roeland Merks.
+ *
+ */
+
+#include
+#include
+
+#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)
diff --git a/src/TutorialCode/Tutorial1D/mymodel.h b/src/TutorialCode/Tutorial1D/mymodel.h
new file mode 100644
--- /dev/null
+++ b/src/TutorialCode/Tutorial1D/mymodel.h
@@ -0,0 +1,60 @@
+/*
+ * $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 .
+ *
+ * Copyright 2010 Roeland Merks.
+ *
+ */
+
+
+#include
+#include
+#include
+#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);
+};
+
+
+
+
diff --git a/src/TutorialCode/Tutorial1D/mymodel.pro b/src/TutorialCode/Tutorial1D/mymodel.pro
new file mode 100644
--- /dev/null
+++ b/src/TutorialCode/Tutorial1D/mymodel.pro
@@ -0,0 +1,61 @@
+#
+# $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 .
+#
+# 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
diff --git a/src/TutorialCode/Tutorial2/mymodel.cpp b/src/TutorialCode/Tutorial2/mymodel.cpp
--- a/src/TutorialCode/Tutorial2/mymodel.cpp
+++ b/src/TutorialCode/Tutorial2/mymodel.cpp
@@ -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;
+ }
}
diff --git a/src/TutorialCode/Tutorial3/mymodel.cpp b/src/TutorialCode/Tutorial3/mymodel.cpp
--- a/src/TutorialCode/Tutorial3/mymodel.cpp
+++ b/src/TutorialCode/Tutorial3/mymodel.cpp
@@ -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;
+ }
}
diff --git a/src/TutorialCode/Tutorial3/tutorial3_init.xml b/src/TutorialCode/Tutorial3/tutorial3_init.xml
new file mode 100644
--- /dev/null
+++ b/src/TutorialCode/Tutorial3/tutorial3_init.xml
@@ -0,0 +1,20702 @@
+
+
+
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+
+
+
+
+
+
+ #include <fstream>
+#include <sstream>
+#include <cstring>
+#include <functional>
+#include <getopt.h>
+#include <cerrno>
+#include "mesh.h"
+#include "parameter.h"
+#include "random.h"
+#include "pi.h"
+#include "cellitem.h"
+#include "canvas.h"
+#include "cell.h"
+#include "output.h"
+#include <qwidget.h>
+#include <q3process.h>
+#include <qapplication.h>
+#include <QDesktopWidget>
+#include <QGraphicsScene>
+#include <QMessageBox>
+//Added by qt3to4:
+#include <QMouseEvent>
+
+#include <unistd.h>
+#include <q3textstream.h>
+
+
+#ifdef HAVE_QWT
+#include "data_plot.h"
+#endif
+#include <QPalette>
+#include <QBrush>
+#include <QToolTip>
+#include "simplugin.h"
+#include "testplugin.h"
+
+/* #define _xstr_(s) _str_(s)
+#define _str_(s) #s
+#include _xstr_(REACTIONS_HEADER)
+*/
+extern Parameter par;
+
+MainBase *main_window = 0;
+double auxin_account = 0.;
+
+
+
+TestPlugin *plugin = new TestPlugin();
+
+#ifdef XFIGGRAPHICS
+#define TIMESTEP double Graphics::TimeStep(void)
+#endif
+
+class PrintNode {
+public:
+ void operator() (const Node &n) const
+ {
+ cerr << n.Index() << ": " << n << endl;
+ }
+};
+
+
+class EdgeSource {
+
+public:
+ void operator() (Cell &c) {
+
+ if (c.AtBoundaryP()) {
+ cerr << "Cell " << c.Index() << " is a source cell.\n";
+ c.SetSource(0,par.source);
+ } else {
+ cerr << "Cell " << c.Index() << " is _not_ a source cell.\n";
+ }
+ }
+
+};
+
+
+
+class CellInfo {
+public:
+ void operator() (Cell &c,std::ostream &os) const {
+ os << "Cell " << c.index << " says: " << endl;
+ os << "c.nodes.size() = " << c.nodes.size() << endl;
+ for (list<Node *>::iterator i=c.nodes.begin();
+ i!=c.nodes.end();
+ i++) {
+ cerr << (*i)->Index() << " ";
+ }
+ cerr << endl;
+ }
+};
+
+double PINSum(Cell &c) {
+
+ return c.Chemical(1) + c.SumTransporters(1);// + c.ReduceCellAndWalls<double>( complex_PijAj );
+
+}
+
+
+class DrawCell {
+public:
+ void operator() (Cell &c,QGraphicsScene &canvas, MainBase &m) const {
+ if (m.ShowBorderCellsP() || c.Boundary()==Cell::None) {
+ if (!m.ShowBoundaryOnlyP() && !m.HideCellsP())
+ if (m.ShowToolTipsP()) {
+ QString info_string=QString("Cell %1, chemicals: ( %2, %3, %4, %5, %6)\n %7 of PIN1 at walls.\n Area is %8\n PIN sum is %9\n Circumference is %10\n Boundary type is %11").arg(c.Index()).arg(c.Chemical(0)).arg(c.Chemical(1)).arg(c.Chemical(2)).arg(c.Chemical(3)).arg(c.Chemical(4)).arg(c.SumTransporters(1)).arg(c.Area()).arg(PINSum(c)).arg(c.Circumference()).arg(c.BoundaryStr());
+
+ info_string += "\n" + c.printednodelist();
+
+ c.Draw(&canvas, info_string);
+ } else {
+ c.Draw(&canvas);
+ }
+ if (m.ShowCentersP())
+ c.DrawCenter(&canvas);
+ if (m.ShowFluxesP())
+ c.DrawFluxes(&canvas, par.arrowsize);
+
+ }
+
+ }
+
+};
+
+Mesh mesh;
+bool batch=false;
+
+
+void MainBase::Plot(int resize_stride) {
+
+ clear();
+
+
+ static int count=0;
+ if (resize_stride) {
+ if ( !((++count)%resize_stride) ) {
+ FitLeafToCanvas();
+ }
+ }
+ mesh.LoopCells(DrawCell(),canvas,*this);
+
+ if (ShowNodeNumbersP())
+ mesh.LoopNodes( bind2nd (mem_fun_ref ( &Node::DrawIndex), &canvas ) ) ;
+ if (ShowCellNumbersP())
+ mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawIndex), &canvas ) ) ;
+
+ if (ShowCellAxesP())
+ mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawAxis), &canvas ) );
+
+ if (ShowCellStrainP())
+ mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawStrain), &canvas ) );
+
+ if (ShowWallsP())
+
+ mesh.LoopWalls( bind2nd( mem_fun_ref( &Wall::Draw ), &canvas ) );
+
+ if (ShowApoplastsP())
+ mesh.LoopWalls( bind2nd( mem_fun_ref( &Wall::DrawApoplast ), &canvas ) );
+
+ if (ShowMeshP())
+ mesh.DrawNodes(&canvas);
+
+ if (ShowBoundaryOnlyP())
+ mesh.DrawBoundary(&canvas);
+
+
+ if ( ( batch || MovieFramesP() )) {
+
+ static int frame = 0;
+ // frame numbers are sequential for the most frequently written file type.
+ // for the less frequently written file type they match the other type
+ if (!(count%par.storage_stride) ) {
+
+ stringstream fname;
+ fname << par.datadir << "/leaf.";
+ fname.fill('0');
+ fname.width(6);
+
+ /*
+ fname << frame << ".pdf";
+ if (par.storage_stride <= par.xml_storage_stride) {
+ frame++;
+ }
+
+ // Write high-res JPG snapshot every plot step
+ Save(fname.str().c_str(), "PDF");
+ */
+
+ fname << frame << ".jpg";
+ if (par.storage_stride <= par.xml_storage_stride) {
+ frame++;
+ }
+
+ // Write high-res JPG snapshot every plot step
+ Save(fname.str().c_str(), "JPEG",1024,768);
+
+ }
+
+ if (!(count%par.xml_storage_stride)) {
+ stringstream fname;
+ fname << par.datadir << "/leaf.";
+ fname.fill('0');
+ fname.width(6);
+ fname << frame << ".xml";
+
+ if (par.xml_storage_stride < par.storage_stride) {
+ frame++;
+ }
+ // Write XML file every ten plot steps
+ mesh.XMLSave(fname.str().c_str(), XMLSettingsTree());
+ }
+
+ }
+}
+
+
+void Cell::Flux(double *flux, double *D) {
+
+
+ // loop over cell edges
+
+ for (int c=0;c<Cell::nchem;c++) flux[c]=0.;
+
+ for (list<Wall *>::iterator i=walls.begin();
+ i!=walls.end();
+ i++) {
+
+
+ // leaf cannot take up chemicals from environment ("no flux boundary")
+ if ((*i)->c2->BoundaryPolP()) continue;
+
+
+ // flux depends on edge length and concentration difference
+ for (int c=0;c<Cell::nchem;c++) {
+ double phi = (*i)->length * ( D[c] ) * ( (*i)->c2->chem[c] - chem[c] );
+
+ if ((*i)->c1!=this) {
+ cerr << "Warning, bad cells boundary: " << (*i)->c1->index << ", " << index << endl;
+ }
+
+ flux[c] += phi;
+ }
+ }
+
+}
+
+INIT {
+
+ if (leaffile) {
+ xmlNode *settings;
+ mesh.XMLRead(leaffile, &settings);
+ main_window->XMLReadSettings(settings);
+ xmlFree(settings);
+ main_window->UserMessage(QString("Ready. Time is %1").arg(mesh.getTimeHours().c_str()));
+
+ } else {
+
+ Cell &circle=mesh.CircularCell(0,0,10,10);
+
+ circle.SetTargetArea(circle.CalcArea());
+ mesh.SetBaseArea();
+ // clean up chemicals
+ for (int c=0; c<Cell::NChem(); c++) {
+ circle.SetChemical(c, 0.);
+ }
+ }
+}
+
+TIMESTEP {
+
+ static int i=0;
+ static int t=0;
+ static int ncells;
+
+ if (!batch) {
+ UserMessage(QString("Time: %1").arg(mesh.getTimeHours().c_str()),0);
+ }
+
+ ncells=mesh.NCells();
+
+
+ double dh;
+
+ if(DynamicCellsP()) {
+ dh = mesh.DisplaceNodes();
+
+ // Only allow for node insertion, cell division and cell growth
+ // if the system has equillibrized
+ // i.e. cell wall tension equillibrization is much faster
+ // than biological processes, including division, cell wall yielding
+ // and cell expansion
+ mesh.InsertNodes(); // (this amounts to cell wall yielding)
+
+ if ( (-dh) < par.energy_threshold) {
+
+ mesh.IncreaseCellCapacityIfNecessary();
+ mesh.LoopCurrentCells(&TestPlugin::CellHouseKeeping); // this includes cell division
+
+ // Reaction diffusion
+ /*CelltoCellTransport *transport_f = &TestPlugin::CelltoCellTransport;
+ CellReaction *cellreaction_f = new plugin->CellDynamics();
+ WallReaction *wall_f = new WallDynamics();*/
+
+ mesh.ReactDiffuse(plugin, par.rd_dt);
+
+
+ t++;
+
+ Plot(par.resize_stride);
+
+ /*QVector< QPair<double, int> > angles=mesh.VertexAnglesValues();
+ QString afname=QString("Angles/anglesvalues%1.dat").arg(t,6,10,QChar('0'));
+ ofstream af(afname.toStdString().c_str());
+ */
+
+ /*for (QVector< QPair<qreal, int> >::const_iterator v=angles.begin();
+ v!=angles.end();
+ v++) {
+ af << v->first << " " << v->second << endl;
+ }
+ */
+ }
+
+ } else {
+
+ /* TransportFunction *transport_f = new CelltoCellTransport();
+ CellReaction *cellreaction_f = new CellDynamics();
+ WallReaction *wall_f = new WallDynamics();
+
+ mesh.ReactDiffuse_New(transport_f, cellreaction_f, wall_f, par.rd_dt);*/
+ mesh.ReactDiffuse(plugin, par.rd_dt);
+
+ Plot(par.resize_stride);
+
+ }
+
+
+
+
+
+ i++;
+ return mesh.getTime();
+
+}
+
+
+
+/* Called if a cell is clicked */
+void Cell::OnClick(QMouseEvent *e) {
+
+}
+
+
+
+void Wall::OnWallInsert(void) {
+
+
+}
+
+
+
+
+int main(int argc,char **argv) {
+
+ try {
+
+
+ int c;
+
+
+ char *leaffile=0;
+
+
+ while (1) {
+
+ //int this_option_optind = optind ? optind : 1;
+ int option_index = 0;
+ static struct option long_options[] = {
+ {"batch", 0, 0, 0},
+ {"leaffile", 2, 0, 0}
+ };
+
+ // short option 'p' creates trouble for non-commandline usage on MacOSX. Option -p changed to -P (capital)
+ static char *short_options = "bl";
+ c = getopt_long (argc, argv, "bl:",
+ long_options, &option_index);
+ if (c == -1)
+ break;
+
+
+ if (c==0) {
+ printf ("option %s", long_options[option_index].name);
+ if (optarg)
+ printf (" with arg %s", optarg);
+ printf ("\n");
+
+ c = short_options[option_index];
+ }
+
+ switch (c) {
+ case 'b':
+ cerr << "Running in batch mode\n";
+ batch=true;
+ break;
+
+ case 'l':
+ leaffile=strdup(optarg);
+ if (!leaffile) {
+ throw("Out of memory");
+ }
+ printf("Reading leaf state file '%s'\n", leaffile);
+ break;
+
+ case '?':
+ break;
+
+ default:
+ printf ("?? getopt returned character code 0%o ??\n", c);
+ }
+ }
+
+
+ if (optind < argc) {
+ printf ("non-option ARGV-elements: ");
+ while (optind < argc)
+ printf ("%s ", argv[optind++]);
+ printf ("\n");
+ }
+
+ MakeDir("Angles");
+ bool useGUI = !batch;
+ QApplication app(argc,argv,useGUI);
+
+
+
+ QPalette tooltippalette = QToolTip::palette();
+ QColor transparentcolor = QColor(tooltippalette.brush(QPalette::Window).color());
+
+ tooltippalette.setBrush (QPalette::Window, QBrush (transparentcolor) );
+ QToolTip::setPalette( tooltippalette );
+
+ QGraphicsScene canvas(0,0,8000,6000);
+
+ if (useGUI) {
+ main_window=new Main(canvas, mesh);
+ if ( QApplication::desktop()->width() > ((Main *)main_window)->width() + 10
+ && QApplication::desktop()->height() > ((Main *)main_window)->height() +30 ) {
+
+ ((Main *)main_window)->show();
+ ((Main *)main_window)->resize( ((Main *)main_window)->sizeHint());
+ } else {
+ ((Main *)main_window)->showMaximized();
+ }
+ } else {
+ main_window=new MainBase(canvas, mesh);
+
+ }
+
+
+
+ canvas.setSceneRect(QRectF());
+ if (!batch) {
+ QObject::connect( qApp, SIGNAL(lastWindowClosed()), qApp, SLOT(quit()) );
+ }
+
+
+
+ main_window->Init(leaffile);
+
+ Cell::SetMagnification(1);
+ Cell::setOffset(0,0);
+
+ main_window->FitLeafToCanvas();
+
+
+
+ main_window->Plot();
+
+
+
+ if (batch) {
+ double t=0.;
+ do {
+ t = main_window->TimeStep();
+ } while (t < par.maxt);
+
+ } else
+ return app.exec();
+
+
+ } catch (const char *message) {
+ if (batch) {
+ cerr << "Exception caught:" << endl;
+ cerr << message << endl;
+ abort();
+ } else {
+ QString qmess=QString("Exception caught: %1").arg(message);
+ QMessageBox::critical(0, "Critical Error", qmess);
+ abort();
+ }
+ } catch (ios_base::failure) {
+ stringstream error_message;
+ error_message << "I/O failure: " << strerror(errno);
+ if (batch) {
+ cerr << error_message.str() <<endl;
+ abort();
+ } else {
+ QString qmess(error_message.str().c_str());
+ QMessageBox::critical(0, "I/O Error", qmess );
+ abort();
+ }
+ }
+
+}
+
+
+
+// Executed after the cellular mechanics steps have equillibrized
+class CellHouseKeeping {
+public:
+ void operator() (Cell &c) const {
+
+ c.EnlargeTargetArea(par.cell_expansion_rate);
+
+ if (c.Area() > par.rel_cell_div_threshold * c.BaseArea() ) {
+ c.Divide();
+ }
+ }
+};
+
+// The number of chemical species in the cels
+const int Cell::nchem = 0;
+
+// Differential equations describing transport of chemicals from cell to cell
+class CelltoCellTransport : public TransportFunction {
+
+ public:
+ virtual void operator()(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)
+class WallDynamics : public WallReaction {
+ public:
+ virtual void operator()(Wall *w, double *dw1, double *dw2) {};
+
+};
+
+
+// Differential equations describing chemical reactions inside the cells
+class CellDynamics : public CellReaction {
+ public:
+ virtual void operator()(Cell *c, double *dchem) {
+
+ };
+
+};
+
+// Rules for cell coloring
+void Cell::SetColor(QColor &color) { }
+
+// To be executed after cell division
+void Cell::OnDivide(ParentInfo &parent_info, Cell &daughter) {}
+
+
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diff --git a/src/TutorialCode/Tutorial4/mymodel b/src/TutorialCode/Tutorial4/mymodel
new file mode 100644
--- /dev/null
+++ b/src/TutorialCode/Tutorial4/mymodel
@@ -0,0 +1,147 @@
+/*
+ *
+ * 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 .
+ *
+ * Copyright 2010 Roeland Merks.
+ *
+ */
+
+#include
+#include
+#include
+#include "simplugin.h"
+
+#include "parameter.h"
+
+#include "wallbase.h"
+#include "cellbase.h"
+#include "mymodel.h"
+#include "flux_function.h"
+
+static const std::string _module_id("$Id$");
+
+QString MyModel::ModelID(void) {
+ // specify the name of your model here
+ return QString( "new auxin transport 2" );
+}
+
+// return the number of chemicals your model uses
+int MyModel::NChem(void) { return 2; }
+
+// To be executed after cell division
+void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
+
+ // After divisions, parent and daughter cells get a standard stock of PINs.
+ daughter1->SetChemical(1, par->initval[1]);
+ daughter2->SetChemical(1, par->initval[1]);
+
+
+}
+
+void MyModel::SetCellColor(CellBase *c, QColor *color) {
+ // add cell coloring rules here
+ // Red: PIN1
+ // Green: Auxin
+ color->setRgb(c->Chemical(1)/(1+c->Chemical(1)) * 255.,(c->Chemical(0)/(1+c->Chemical(0)) * 255.), 0);
+
+}
+
+void MyModel::CellHouseKeeping(CellBase *c) {
+ // add cell behavioral rules here
+
+ c->EnlargeTargetArea(c->Chemical(0)/(1.+c->Chemical(0))*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
+ double phi = w->Length() * par->D[0] * ( w->C2()->Chemical(0) - w->C1()->Chemical(0) );
+ dchem_c1[0]+=phi;
+ dchem_c2[0]-=phi;
+
+ // Active fluxes (PIN1 mediated transport)
+
+ // (Transporters measured in moles, here)
+ // 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;
+
+ // Influx at leaf "AuxinSource" (as specified in initial condition)
+ if (w->AuxinSource()) {
+ double aux_flux = par->leaf_tip_source * w->Length();
+ dchem_c1[0] += aux_flux;
+ dchem_c2[0] += aux_flux;
+ }
+}
+
+double MyModel::PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w) {
+ // PIN1 localization at wall
+ // Note: chemical 0 is Auxin (intracellular storage only)
+ // PIN1 is Chemical 1 (both in walls and intracellular storage)
+ //! \f$ \frac{d Pij/dt}{dt} = k_1 A_j \frac{P_i}{L_ij} - k_2 P_{ij} \f$
+ // Note that Pij is measured in term of concentration (mol/L)
+ // Pi in terms of quantity (mol)
+
+ // Equations as in Merks et al., Trends in Plant Science 2007
+
+ // calculate PIN translocation rate from cell to membrane
+ double adj_auxin = adjacent_cell->Chemical(0);
+ double receptor_level = adj_auxin * par->r / (par->kr + adj_auxin);
+ double pin_atwall; // pick the correct side of the Wall
+
+ if (w->C1() == this_cell) pin_atwall = w->Transporters1(1);
+ else pin_atwall=w->Transporters2(1);
+
+ // note: pin_flux is net flux from endosome to wall
+ double pin_flux = par->k1 * this_cell->Chemical(1) * receptor_level / ( par->km + this_cell->Chemical(1) ) - par->k2 * pin_atwall;
+ return pin_flux;
+
+
+}
+
+
+void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) {
+ // add biochemical networks for reactions occuring at walls here
+ dw1[0] = 0.; dw2[0] = 0.; // chemical 0 unused in walls
+ dw1[1] = PINflux(w->C1(),w->C2(),w);
+ dw2[1] = PINflux(w->C2(),w->C1(),w);
+ //static ofstream pf("pin_flux.dat");
+ //pf << dw1[1] << " " << dw2[1] << " " << w->C1()->Chemical(1) << " " << w->C2()->Chemical(1) << endl;
+
+}
+
+void MyModel::CellDynamics(CellBase *c, double *dchem) {
+ // add biochemical networks for intracellular reactions here
+
+ // sum all incoming fluxes of PINs
+ dchem[1] = - SumFluxFromWalls( c, MyModel::PINflux );
+
+ // auxin degradation
+ dchem[0] = - par->aux_breakdown * c->Chemical(0);
+
+
+}
+
+
+Q_EXPORT_PLUGIN2(mymodel, MyModel)
diff --git a/src/TutorialCode/Tutorial4/mymodel.cpp b/src/TutorialCode/Tutorial4/mymodel.cpp
--- a/src/TutorialCode/Tutorial4/mymodel.cpp
+++ b/src/TutorialCode/Tutorial4/mymodel.cpp
@@ -21,7 +21,7 @@
#include
#include
-
+#include
#include "simplugin.h"
#include "parameter.h"
@@ -29,33 +29,41 @@
#include "wallbase.h"
#include "cellbase.h"
#include "mymodel.h"
+#include "flux_function.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 QString( "new auxin transport 2" );
}
// 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)
+
+ // After divisions, parent and daughter cells get a standard stock of PINs.
+ daughter1->SetChemical(1, par->initval[1]);
+ daughter2->SetChemical(1, par->initval[1]);
+
+
}
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"); }
-
+ // Red: PIN1
+ // Green: Auxin
+ color->setRgb(c->Chemical(1)/(1+c->Chemical(1)) * 255.,(c->Chemical(0)/(1+c->Chemical(0)) * 255.), 0);
+
}
void MyModel::CellHouseKeeping(CellBase *c) {
// add cell behavioral rules here
- c->EnlargeTargetArea(par->cell_expansion_rate);
+
+ c->EnlargeTargetArea(c->Chemical(0)/(1.+c->Chemical(0))*par->cell_expansion_rate);
+
if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) {
c->Divide();
}
@@ -63,12 +71,74 @@ 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;
+
+ // Active fluxes (PIN1 mediated transport)
+
+ // (Transporters measured in moles, here)
+ // 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;
+
+ // Influx at leaf "AuxinSource" (as specified in initial condition)
+ if (w->AuxinSource()) {
+ double aux_flux = par->leaf_tip_source * w->Length();
+ dchem_c1[0] += aux_flux;
+ dchem_c2[0] += aux_flux;
+ }
}
+
+double MyModel::PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w) {
+ // PIN1 localization at wall
+ // Note: chemical 0 is Auxin (intracellular storage only)
+ // PIN1 is Chemical 1 (both in walls and intracellular storage)
+ //! \f$ \frac{d Pij/dt}{dt} = k_1 A_j \frac{P_i}{L_ij} - k_2 P_{ij} \f$
+ // Note that Pij is measured in term of concentration (mol/L)
+ // Pi in terms of quantity (mol)
+
+ // Equations as in Merks et al., Trends in Plant Science 2007
+
+ // calculate PIN translocation rate from cell to membrane
+ double adj_auxin = adjacent_cell->Chemical(0);
+ double receptor_level = adj_auxin * par->r / (par->kr + adj_auxin);
+ double pin_atwall; // pick the correct side of the Wall
+
+ if (w->C1() == this_cell) pin_atwall = w->Transporters1(1);
+ else pin_atwall=w->Transporters2(1);
+
+ // note: pin_flux is net flux from endosome to wall
+ double pin_flux = par->k1 * this_cell->Chemical(1) * receptor_level / ( par->km + this_cell->Chemical(1) ) - par->k2 * pin_atwall;
+ return pin_flux;
+
+
+}
+
+
void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) {
// add biochemical networks for reactions occuring at walls here
+ dw1[0] = 0.; dw2[0] = 0.; // chemical 0 unused in walls
+ dw1[1] = PINflux(w->C1(),w->C2(),w);
+ dw2[1] = PINflux(w->C2(),w->C1(),w);
+ //static ofstream pf("pin_flux.dat");
+ //pf << dw1[1] << " " << dw2[1] << " " << w->C1()->Chemical(1) << " " << w->C2()->Chemical(1) << endl;
+
}
+
void MyModel::CellDynamics(CellBase *c, double *dchem) {
- // add biochemical networks for intracellular reactions here
+ // add biochemical networks for intracellular reactions here
+
+ // sum all incoming fluxes of PINs
+ dchem[1] = - SumFluxFromWalls( c, MyModel::PINflux );
+
+
+
}
diff --git a/src/TutorialCode/Tutorial4/mymodel.h b/src/TutorialCode/Tutorial4/mymodel.h
--- a/src/TutorialCode/Tutorial4/mymodel.h
+++ b/src/TutorialCode/Tutorial4/mymodel.h
@@ -53,6 +53,8 @@ public:
virtual void SetCellColor(CellBase *c, QColor *color);
// return number of chemicals
virtual int NChem(void);
+
+ virtual double PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w);
};
diff --git a/src/TutorialCode/Tutorial4/tutorial4_init.xml b/src/TutorialCode/Tutorial4/tutorial4_init.xml
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