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:
+