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Location: EI/VirtualLeaf/src/VirtualLeaf.pro - annotation

Roeland Merks
In response to referee's comment:

"However, (although it is probably not important for model developers), I was
still unable to load the model ‘Meinhardt 1976 with growth’ example from the
‘Models’ drop down menu, I got the ‘Fatal error’ message ‘stepwise underflow in

rkqs, with h=0.000000 and htry = 0.100000’. The model did work when I selected
the Meinhardt model in both the Models and the File -> Read leaf menus together,
it would be preferable if the models loaded from the Models menu worked

automatically. I am not sure that the update referred to in the author’s
response permits the loading of ‘My First Model in Virtual Leaf’ from the
‘Models’ drop down menu; I only got a cell that wiggled."

I made the following changes:

- meinhardt_plugin now reads "meinhardt_init.xml" by default
- changed the name of 'My First Model in Virtual Leaf’ to '0: Empty model template (does nothing)' to make it clear that the wiggle cell is the intended behavior for this model example.
- Added default parameter files for Tutorial1A-D and Tutorial2 to prevent variable behavior depending on the last parameter settings used.


--
user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
added data/leaves/tutorial1_init.xml
added data/leaves/tutorial2_init.xml
changed data/leaves/auxin_growth.xml
changed data/leaves/meinhardt_init.xml
changed src/TutorialCode/Tutorial0/tutorial0.cpp
changed src/TutorialCode/Tutorial1A/tutorial1A.h
changed src/TutorialCode/Tutorial1B/tutorial1B.h
changed src/TutorialCode/Tutorial1C/tutorial1C.h
changed src/TutorialCode/Tutorial1D/tutorial1D.h
changed src/TutorialCode/Tutorial2/tutorial2.h
changed src/build_models/meinhardtplugin.h
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#
#  $Id$
#
#  This file is part of the Virtual Leaf.
#
#  The Virtual Leaf is free software: you can redistribute it and/or modify
#  it under the terms of the GNU General Public License as published by
#  the Free Software Foundation, either version 3 of the License, or
#  (at your option) any later version.
#
#  The Virtual Leaf is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#  GNU General Public License for more details.
#
#  You should have received a copy of the GNU General Public License
#  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
#
#  Copyright 2010 Roeland Merks.
#

CONFIG += release
CONFIG -= debug
CONFIG += qt

QMAKE_CXXFLAGS += -fexceptions
QMAKE_CXXFLAGS += -Wall
QMAKE_CXXFLAGS += -Wno-write-strings
QMAKE_CXXFLAGS += -Wno-unused-parameter
QMAKE_CXXFLAGS_DEBUG += -g3
QMAKE_CXXFLAGS_DEBUG += -DQDEBUG

#REACTIONS = reactions_auxin_growth.h 
#REACTIONS = reactions_meinhardt.h
#REACTIONS = reactions_pce_growth.h
DEFINES += QTGRAPHICS
DEFINES += REACTIONS_HEADER=$${REACTIONS}
DEFINES += REACTIONS_HEADER_STRING=\"$${REACTIONS}\"
DEFINES += FLEMING

BINDIR = ../bin
LIBDIR = ../lib
DESTDIR = $$BINDIR
TARGET = VirtualLeaf
TEMPLATE = app
PARTMPL = $${TARGET}par.tmpl
MAINSRC = $${TARGET}.cpp
QT -= network sql xml
QT += qt3support

!win32 {
 GRAPHICS = qt #qwt
}

win32 {
 CONFIG -= console
 LIBXML2DIR = $${LIBDIR}\libxml2
 LIBICONVDIR = $${LIBDIR}\libiconv
 LIBZDIR = $${LIBDIR}\libz
 GRAPHICS = qt 
 RC_FILE = VirtualLeaf.rc
 QMAKE_CXXFLAGS += -DLIBXML_STATIC
 QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
 LIBS += -L$${LIBXML2DIR}\lib -lxml2 -L$${LIBICONVDIR}\lib -L$${LIBZDIR}\lib  -lz -lm -lwsock32 -liconv
}


macx:release {
 LIBS+= -dead_strip
}

unix {
 CC = /usr/bin/gcc 
 QWTDIR = /ufs/guravage/opt/qwt-5.2.1-svn
 QMAKE_LIBDIR += $$QWTDIR/lib 
 QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
 QMAKE_LFLAGS += -fPIC
 LIBS += -lxml2 -lz -lm 
}

# Input
HEADERS += \
# apoplastitem.h \
 canvas.h \
 cellbase.h \
 cell.h \
 cellitem.h \
 forwardeuler.h \
       hull.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 \
 $${PARTMPL}

SOURCES += \
# apoplastitem.cpp \
 canvas.cpp \
 cellbase.cpp \
 cell.cpp \
 cellitem.cpp \
 forwardeuler.cpp \
 hull.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 \
 xmlwrite.cpp \
 $$MAINSRC

contains( TARGET, leaf_fleming ) {
 DEFINES += FLEMING	
}

contains(GRAPHICS, qwt) {
 #macx:LIBS += -L$$QWTDIR/lib -lqwt
 #win32:LIBS += -L$$QWTDIR/lib -lqwt5
 #LIBS += -L$$QWTDIR/lib -lqwt
 INCLUDEPATH += $$QWTDIR/include
 DEFINES += HAVE_QWT
 HEADERS += data_plot.h
 SOURCES += data_plot.cpp
}

contains( GRAPHICS, qt ) {
 message( "Building Qt executable" )
 QMAKE_CXXFLAGS += -DQTGRAPHICS # -fpermissive
}

contains( GRAPHICS, xfig ) {
 message("Building Xfig executable (background runnable).")
 QMAKE_CXXFLAGS += -DXFIGGRAPHICS
}

contains( GRAPHICS, x11 ) {
 !unix {
  error("X11 graphics only available on Unix systems.")
 }
 message("Building X11 executable")
 SOURCES += x11graph.cpp
 HEADERS += x11graph.h
 QMAKE_CXXFLAGS += -DX11GRAPHICS
 CONFIG -= qt
 CONFIG += x11
 unix:LIBS += -lpng
}

#contains( GRAPHICS, qwt ) {
# 	QMAKE_POST_LINK = "install_name_tool -change libqwt.5.dylib $$QWTDIR/lib/libqwt.dylib $${TARGET}.app/Contents/MacOS/$${TARGET}; \
#}

# MACOSX packaging
macx {
ICON = leaficon.icns
QMAKE_POST_LINK = "\
	#install_name_tool -change libqwt.5.dylib $$QWTDIR/lib/libqwt.dylib $${TARGET}.app/Contents/MacOS/$${TARGET}; \
	cp leaficon.icns $${DESTDIR}/$${TARGET}.app; \
	cp ../doc/gpl3.txt $${DESTDIR}/$${TARGET}.app/Contents/MacOS/.                                    ; \
	mkdir $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \
	cp -R /Library/Frameworks/QtCore.framework $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \
	cp -R /Library/Frameworks/QtGui.framework $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \
	cp -R /Library/Frameworks/Qt3Support.framework $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \
	#cp /usr/local/qwt/lib/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \
	#install_name_tool -id @executable_path/../Frameworks/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/libqwt.dylib; \
	install_name_tool -change /usr/local/qwt/lib/libqwt.dylib @executable_path/../Frameworks/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET};\
	install_name_tool -id @executable_path/../Frameworks/QtCore.framework/Versions/Current/QtCore $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/QtCore.framework/Versions/4.0/QtCore; \
	install_name_tool -id @executable_path/../Frameworks/QtGui.framework/Versions/Current/QtGui $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/QtGui.framework/Versions/4.0/QtGui; \
	install_name_tool -id @executable_path/../Frameworks/Qt3Support.framework/Versions/Current/Qt3Support $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/Qt3Support.framework/Versions/4.0/Qt3Support; \
	install_name_tool -change Frameworks/QtCore.framework/Versions/Current/QtCore @executable_path/../Frameworks/QtCore.framework/Versions/4.0/QtCore $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET}; \
	install_name_tool -change Frameworks/QtGui.framework/Versions/Current/QtGui @executable_path/../Frameworks/QtGui.framework/Versions/4.0/QtGui $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET}; \
	install_name_tool -change Frameworks/Qt3Support.framework/Versions/Current/Qt3Support @executable_path/../Frameworks/Qt3Support.framework/Versions/4.0/Qt3Support $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET}; \
	install_name_tool -change Frameworks/QtCore.framework/Versions/Current/QtCore @executable_path/../Frameworks/QtCore.framework/Versions/4.0/QtCore $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/Qt3Support.framework/Versions/4.0/Qt3Support; \
	install_name_tool -change Frameworks/QtGui.framework/Versions/Current/QtGui @executable_path/../Frameworks/QtGui.framework/Versions/4.0/QtGui $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/Qt3Support.framework/Versions/4.0/Qt3Support; \
	install_name_tool -change Frameworks/QtCore.framework/Versions/Current/QtCore @executable_path/../Frameworks/QtCore.framework/Versions/4.0/QtCore $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/Qt3Support.framework/Versions/4.0/Qt3Support; "
}

# finis