EI/VirtualLeaf Changeset - 3f0977faba37 · Centrum Wiskunde & Informatica (CWI)

Changeset - 3f0977faba37

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Michael Guravage - 15 years ago 2010-06-03 15:54:37
michael.guravage@cwi.nl

Tweaked project files to delete/regenerate parameter and pardialog files only if perl is installed. Added new top-level Makefiles. See ChangeLogs for more details.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
added src/Makefile
added src/build_models/Makefile
added src/parameter.cpp
added src/parameter.h
added src/pardialog.cpp
added src/pardialog.h
changed .hgignore
changed src/ChangeLog
changed src/VirtualLeaf.pro
changed src/build_models/ChangeLog
changed src/libplugin.pro

11 files changed with 3082 insertions and 15 deletions:

.hgignore

src/ChangeLog

src/Makefile

src/VirtualLeaf.pro

src/build_models/ChangeLog

src/build_models/Makefile

src/libplugin.pro

src/parameter.cpp

1886

src/parameter.h

149

src/pardialog.cpp

806

src/pardialog.h

145

0 comments (0 inline, 0 general)

.hgignore

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@@ @@ -12,14 +12,10 @@ syntax: glob @@
 *.Release
 *.so
 *.vars
 *Makefile
+*Makefile.*
 *make.out
 *moc_*.cpp
 src/parameter.h
 src/parameter.cpp
 src/default.par
 src/pardialog.h
 src/pardialog.cpp
 bin*
 # switch to regexp syntax.

src/ChangeLog

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 -06-03    <guravage@caterpie.sen.cwi.nl>
 	* pardialog.h: Added default versions of this automatically generated file.
 	* pardialog.cpp: ditto.
 	* parameter.h: ditto.
 	* parameter.cpp: ditto.
 	* VirtualLeaf.pro: delete/generate  parameter.{h,cpp}and pardialog.{h,cpp} only if perl is installed.
  	* libplugin.pro: dito.
 	* Makefile: Added top-level Makefile
 -05-10    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Added -fPIC option to QMAKE_CXXFLAGS.

src/Makefile

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@@ new file 100644 @@
 # $Id$
 all: VirtualLeaf libplugin plugins
 VirtualLeaf: Makefile.VirtualLeaf
 	make -f Makefile.VirtualLeaf
 Makefile.VirtualLeaf: VirtualLeaf.pro
 	qmake -makefile -o $@ $<
 libplugin: Makefile.libplugin
 	make -f Makefile.libplugin
 Makefile.libplugin: libplugin.pro
 	qmake -makefile -o $@ $<
 plugins:
 	make -C build_models
 clean:
 	make -f Makefile.libplugin clean
 	make -f Makefile.VirtualLeaf clean
 	make -C build_models clean
 #finis

src/VirtualLeaf.pro

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@@ @@ -50,6 +50,11 @@ QT += qt3support @@
+}
 win32 {
  system(WHERE /Q perl && IF errorlevel 0 (DEL parameter.cpp parameter.h pardialog.cpp pardialog.h)
  system(WHERE /Q perl && IF errorlevel 0 (perl $$PERLDIR\make_parameter_source.pl $$PARTMPL)
  system(WHERE /Q perl && IF errorlevel 0 (perl $$PERLDIR\make_pardialog_source.pl $$PARTMPL)
 #system(WHERE /Q perl && IF errorlevel 0 (perl $$PERLDIR\make_xmlwritecode.pl -h $$REACTIONS)
  CONFIG += console
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
@@ @@ -93,7 +98,10 @@ macx:release { @@
+}
 unix {
  system(rm -f parameter.cpp parameter.h)
  system(if `which perl > /dev/null 2>&1` ; then rm -f parameter.cpp parameter.h pardialog.cpp pardialog.h; fi)
  system(if `which perl > /dev/null 2>&1` ; then perl $$PERLDIR/make_parameter_source.pl $$PARTMPL; fi)
  system(if `which perl > /dev/null 2>&1` ; then perl $$PERLDIR/make_pardialog_source.pl $$PARTMPL; fi)
 #system(if `which perl > /dev/null 2>&1` ; then perl $$PERLDIR/make_xmlwritecode.pl -h $$REACTIONS; fi)
  CC = /usr/bin/gcc
  QWTDIR = /ufs/guravage/opt/qwt-5.2.1-svn
  QMAKE_LIBDIR += $$QWTDIR/lib
@@ @@ -102,10 +110,6 @@ unix { @@
  LIBS += -lxml2 -lz -lm
+}
 system(perl $$PERLDIR/make_parameter_source.pl $$PARTMPL)
 system(perl $$PERLDIR/make_pardialog_source.pl $$PARTMPL)
 #system(perl $$PERLDIR/make_xmlwritecode.pl -h $$REACTIONS)
 # Input
 HEADERS += \
  apoplastitem.h \

src/build_models/ChangeLog

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 -06-03    <guravage@caterpie.sen.cwi.nl>
 	* Makefile: Added top-level Makefile.
 -05-10    <guravage@caterpie.sen.cwi.nl>
 	* plugin_test.pro: Added -fPIC option to QMAKE_CXXFLAGS.

src/build_models/Makefile

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@@ new file 100644 @@
 # $Id$
 all: plugin_auxingrowth plugin_leaf plugin_meinhardt plugin_test
 plugin_auxingrowth: Makefile.plugin_auxingrowth
 	make -f Makefile.plugin_auxingrowth
 Makefile.plugin_auxingrowth: plugin_auxingrowth.pro
 	qmake -makefile -o $@ $<
 plugin_leaf: Makefile.plugin_leaf
 	make -f Makefile.plugin_leaf
 Makefile.plugin_leaf: plugin_leaf.pro
 	qmake -makefile -o $@ $<
 plugin_meinhardt: Makefile.plugin_meinhardt
 	make -f Makefile.plugin_meinhardt
 Makefile.plugin_meinhardt: plugin_meinhardt.pro
 	qmake -makefile -o $@ $<
 plugin_test: Makefile.plugin_test
 	make -f Makefile.plugin_test
 Makefile.plugin_test: plugin_test.pro
 	qmake -makefile -o $@ $<
 clean:
 	make -f Makefile.plugin_auxingrowth clean
 	make -f Makefile.plugin_leaf clean
 	make -f Makefile.plugin_meinhardt clean
 	make -f Makefile.plugin_test clean
 #finis

src/libplugin.pro

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@@ @@ -63,14 +63,22 @@ SOURCES = \ @@
  warning.cpp
 unix {
  system(rm -f parameter.cpp parameter.h) # this is performed here when qmake is envoked and not in the resulting makefile.
  system(if `which perl > /dev/null 2>&1` ; then rm -f parameter.cpp parameter.h pardialog.cpp pardialog.h; fi)
  system(if `which perl > /dev/null 2>&1` ; then perl $$PERLDIR/make_parameter_source.pl $$PARTMPL; fi)
  system(if `which perl > /dev/null 2>&1` ; then perl $$PERLDIR/make_pardialog_source.pl $$PARTMPL; fi)
 #system(if `which perl > /dev/null 2>&1` ; then perl $$PERLDIR/make_xmlwritecode.pl -h $$REACTIONS; fi)
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
  LIBS += -lxml2 -lz -lm
+}
 win32 {
  system(DEL parameter.cpp parameter.h)
  system(WHERE /Q perl && IF errorlevel 0 (DEL parameter.cpp parameter.h pardialog.cpp pardialog.h)
  system(WHERE /Q perl && IF errorlevel 0 (perl $$PERLDIR\make_parameter_source.pl $$PARTMPL)
  system(WHERE /Q perl && IF errorlevel 0 (perl $$PERLDIR\make_pardialog_source.pl $$PARTMPL)
 #system(WHERE /Q perl && IF errorlevel 0 (perl $$PERLDIR\make_xmlwritecode.pl -h $$REACTIONS)
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
@@ @@ -78,7 +86,4 @@ win32 { @@
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 system(perl $$PERLDIR/make_parameter_source.pl $$PARTMPL)
 system(perl $$PERLDIR/make_pardialog_source.pl $$PARTMPL)
 #system(perl $$PERLDIR/make_xmlwritecode.pl -h $$REACTIONS)
+#

src/parameter.cpp

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@@ new file 100644 @@
 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  The Virtual Leaf is free software: you can redistribute it and/or modify
  *  it under the terms of the GNU General Public License as published by
  *  the Free Software Foundation, either version 3 of the License, or
  *  (at your option) any later version.
+ *
  *  The Virtual Leaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include "parameter.h"
 #include <cstdio>
 #include <cstring>
 #include <cstdlib>
 #include <cerrno>
 #include <iostream>
 #include <sstream>
 #include "output.h"
 #include "parse.h"
 #include "xmlwrite.h"
 #include "warning.h"
 #include <QLocale>
 using namespace std;
 static const std::string _module_id("$Id$");
 Parameter::Parameter() {
   arrowcolor = strdup("white");
   arrowsize = 100;
   textcolor = strdup("red");
   cellnumsize = 1;
   nodenumsize = 1;
   node_mag = 1.0;
   outlinewidth = 1.0;
   cell_outline_color = strdup("forestgreen");
   resize_stride = 10;
   T = 1.0;
   lambda_length = 100.;
   lambda_celllength = 0.;
   target_length = 60.;
   cell_expansion_rate = 1.;
   cell_div_expansion_rate = 0.;
   auxin_dependent_growth = true;
   ode_accuracy = 1e-4;
   mc_stepsize = 0.4;
   mc_cell_stepsize = 0.2;
   energy_threshold = 1000.;
   bend_lambda = 0.;
   alignment_lambda = 0.;
   rel_cell_div_threshold = 2.;
   rel_perimeter_stiffness = 2;
   collapse_node_threshold = 0.05;
   morphogen_div_threshold = 0.2;
   morphogen_expansion_threshold = 0.01;
   copy_wall = true;
   source = 0.;
   D = new double[15];
   D[0] = 0.;
   D[1] = 0.0;
   D[2] = 0.0;
   D[3] = 0.;
   D[4] = 0.;
   D[5] = 0.;
   D[6] = 0.;
   D[7] = 0.;
   D[8] = 0.;
   D[9] = 0.;
   D[10] = 0.;
   D[11] = 0.;
   D[12] = 0.;
   D[13] = 0.;
   D[14] = 0.;
   initval = new double[15];
   initval[0] = 0.;
   initval[1] = 0.;
   initval[2] = 0.;
   initval[3] = 0.;
   initval[4] = 0.;
   initval[5] = 0.;
   initval[6] = 0.;
   initval[7] = 0.;
   initval[8] = 0.;
   initval[9] = 0.;
   initval[10] = 0.;
   initval[11] = 0.;
   initval[12] = 0.;
   initval[13] = 0.;
   initval[14] = 0.;
   k1 = 1.;
   k2 = 0.3;
   r = 1.;
   kr = 1.;
   km = 1.;
   Pi_tot = 1.;
   transport = 0.036;
   ka = 1;
   pin_prod = 0.001;
   pin_prod_in_epidermis = 0.1;
   pin_breakdown = 0.001;
   pin_breakdown_internal = 0.001;
   aux1prod = 0.001;
   aux1prodmeso = 0.;
   aux1decay = 0.001;
   aux1decaymeso = 0.1;
   aux1transport = 0.036;
   aux_cons = 0.;
   aux_breakdown = 0.;
   kaux1 = 1;
   kap = 1;
   leaf_tip_source = 0.001;
   sam_efflux = 0.0001;
   sam_auxin = 10.;
   sam_auxin_breakdown = 0;
   van3prod = 0.002;
   van3autokat = 0.1;
   van3sat = 10;
   k2van3 = 0.3;
   dt = 0.1;
   rd_dt = 1.0;
   datadir = strdup(".");
   movie = false;
   nit = 100000;
   maxt = 1000.;
   storage_stride = 10;
   xml_storage_stride = 500;
   rseed = -1;
   constituous_expansion_limit = 16;
   vessel_inh_level = 1;
   vessel_expansion_rate = 0.25;
   d = 0.;
   e = 0.;
   f = 0.;
   c = 0.;
   mu = 0.;
   nu = 0.;
   rho0 = 0.;
   rho1 = 0.;
   c0 = 0.;
   gamma = 0.;
   eps = 0.;
   k = new double[15];
   k[0] = 0.;
   k[1] = 0.0;
   k[2] = 0.0;
   k[3] = 0.;
   k[4] = 0.;
   k[5] = 0.;
   k[6] = 0.;
   k[7] = 0.;
   k[8] = 0.;
   k[9] = 0.;
   k[10] = 0.;
   k[11] = 0.;
   k[12] = 0.;
   k[13] = 0.;
   k[14] = 0.;
   i1 = 0;
   i2 = 0;
   i3 = 0;
   i4 = 0;
   i5 = 0;
   s1 = strdup("");
   s2 = strdup("");
   s3 = strdup("");
   b1 = false;
   b2 = false;
   b3 = false;
   b4 = false;
   dir1 = strdup(".");
   dir2 = strdup(".");
+}
 Parameter::~Parameter() {
   // destruct parameter object
   // free string parameter
   CleanUp();
+}
 void Parameter::CleanUp(void) {
   if (arrowcolor)
      free(arrowcolor);
   if (textcolor)
      free(textcolor);
   if (cell_outline_color)
      free(cell_outline_color);
   if (D)
      free(D);
   if (initval)
      free(initval);
   if (datadir)
      free(datadir);
   if (k)
      free(k);
   if (s1)
      free(s1);
   if (s2)
      free(s2);
   if (s3)
      free(s3);
   if (dir1)
      free(dir1);
   if (dir2)
      free(dir2);
+}
 void Parameter::Read(const char *filename) {
   static bool ReadP=false;
   if (ReadP) {
     //throw "Run Time Error in parameter.cpp: Please Read parameter file only once!!";
     CleanUp();
   } else
     ReadP=true;
   FILE *fp=OpenReadFile(filename);
   arrowcolor = sgetpar(fp, "arrowcolor", "white", true);
   arrowsize = fgetpar(fp, "arrowsize", 100, true);
   textcolor = sgetpar(fp, "textcolor", "red", true);
   cellnumsize = igetpar(fp, "cellnumsize", 1, true);
   nodenumsize = igetpar(fp, "nodenumsize", 1, true);
   node_mag = fgetpar(fp, "node_mag", 1.0, true);
   outlinewidth = fgetpar(fp, "outlinewidth", 1.0, true);
   cell_outline_color = sgetpar(fp, "cell_outline_color", "forestgreen", true);
   resize_stride = igetpar(fp, "resize_stride", 10, true);
   T = fgetpar(fp, "T", 1.0, true);
   lambda_length = fgetpar(fp, "lambda_length", 100., true);
   lambda_celllength = fgetpar(fp, "lambda_celllength", 0., true);
   target_length = fgetpar(fp, "target_length", 60., true);
   cell_expansion_rate = fgetpar(fp, "cell_expansion_rate", 1., true);
   cell_div_expansion_rate = fgetpar(fp, "cell_div_expansion_rate", 0., true);
   auxin_dependent_growth = bgetpar(fp, "auxin_dependent_growth", true, true);
   ode_accuracy = fgetpar(fp, "ode_accuracy", 1e-4, true);
   mc_stepsize = fgetpar(fp, "mc_stepsize", 0.4, true);
   mc_cell_stepsize = fgetpar(fp, "mc_cell_stepsize", 0.2, true);
   energy_threshold = fgetpar(fp, "energy_threshold", 1000., true);
   bend_lambda = fgetpar(fp, "bend_lambda", 0., true);
   alignment_lambda = fgetpar(fp, "alignment_lambda", 0., true);
   rel_cell_div_threshold = fgetpar(fp, "rel_cell_div_threshold", 2., true);
   rel_perimeter_stiffness = fgetpar(fp, "rel_perimeter_stiffness", 2, true);
   collapse_node_threshold = fgetpar(fp, "collapse_node_threshold", 0.05, true);
   morphogen_div_threshold = fgetpar(fp, "morphogen_div_threshold", 0.2, true);
   morphogen_expansion_threshold = fgetpar(fp, "morphogen_expansion_threshold", 0.01, true);
   copy_wall = bgetpar(fp, "copy_wall", true, true);
   source = fgetpar(fp, "source", 0., true);
   D = dgetparlist(fp, "D", 15, true);
   initval = dgetparlist(fp, "initval", 15, true);
   k1 = fgetpar(fp, "k1", 1., true);
   k2 = fgetpar(fp, "k2", 0.3, true);
   r = fgetpar(fp, "r", 1., true);
   kr = fgetpar(fp, "kr", 1., true);
   km = fgetpar(fp, "km", 1., true);
   Pi_tot = fgetpar(fp, "Pi_tot", 1., true);
   transport = fgetpar(fp, "transport", 0.036, true);
   ka = fgetpar(fp, "ka", 1, true);
   pin_prod = fgetpar(fp, "pin_prod", 0.001, true);
   pin_prod_in_epidermis = fgetpar(fp, "pin_prod_in_epidermis", 0.1, true);
   pin_breakdown = fgetpar(fp, "pin_breakdown", 0.001, true);
   pin_breakdown_internal = fgetpar(fp, "pin_breakdown_internal", 0.001, true);
   aux1prod = fgetpar(fp, "aux1prod", 0.001, true);
   aux1prodmeso = fgetpar(fp, "aux1prodmeso", 0., true);
   aux1decay = fgetpar(fp, "aux1decay", 0.001, true);
   aux1decaymeso = fgetpar(fp, "aux1decaymeso", 0.1, true);
   aux1transport = fgetpar(fp, "aux1transport", 0.036, true);
   aux_cons = fgetpar(fp, "aux_cons", 0., true);
   aux_breakdown = fgetpar(fp, "aux_breakdown", 0., true);
   kaux1 = fgetpar(fp, "kaux1", 1, true);
   kap = fgetpar(fp, "kap", 1, true);
   leaf_tip_source = fgetpar(fp, "leaf_tip_source", 0.001, true);
   sam_efflux = fgetpar(fp, "sam_efflux", 0.0001, true);
   sam_auxin = fgetpar(fp, "sam_auxin", 10., true);
   sam_auxin_breakdown = fgetpar(fp, "sam_auxin_breakdown", 0, true);
   van3prod = fgetpar(fp, "van3prod", 0.002, true);
   van3autokat = fgetpar(fp, "van3autokat", 0.1, true);
   van3sat = fgetpar(fp, "van3sat", 10, true);
   k2van3 = fgetpar(fp, "k2van3", 0.3, true);
   dt = fgetpar(fp, "dt", 0.1, true);
   rd_dt = fgetpar(fp, "rd_dt", 1.0, true);
   datadir = sgetpar(fp, "datadir", ".", true);
   if (strcmp(datadir, "."))
     MakeDir(datadir);
   movie = bgetpar(fp, "movie", false, true);
   nit = igetpar(fp, "nit", 100000, true);
   maxt = fgetpar(fp, "maxt", 1000., true);
   storage_stride = igetpar(fp, "storage_stride", 10, true);
   xml_storage_stride = igetpar(fp, "xml_storage_stride", 500, true);
   rseed = igetpar(fp, "rseed", -1, true);
   constituous_expansion_limit = igetpar(fp, "constituous_expansion_limit", 16, true);
   vessel_inh_level = fgetpar(fp, "vessel_inh_level", 1, true);
   vessel_expansion_rate = fgetpar(fp, "vessel_expansion_rate", 0.25, true);
   d = fgetpar(fp, "d", 0., true);
   e = fgetpar(fp, "e", 0., true);
   f = fgetpar(fp, "f", 0., true);
   c = fgetpar(fp, "c", 0., true);
   mu = fgetpar(fp, "mu", 0., true);
   nu = fgetpar(fp, "nu", 0., true);
   rho0 = fgetpar(fp, "rho0", 0., true);
   rho1 = fgetpar(fp, "rho1", 0., true);
   c0 = fgetpar(fp, "c0", 0., true);
   gamma = fgetpar(fp, "gamma", 0., true);
   eps = fgetpar(fp, "eps", 0., true);
   k = dgetparlist(fp, "k", 15, true);
   i1 = igetpar(fp, "i1", 0, true);
   i2 = igetpar(fp, "i2", 0, true);
   i3 = igetpar(fp, "i3", 0, true);
   i4 = igetpar(fp, "i4", 0, true);
   i5 = igetpar(fp, "i5", 0, true);
   s1 = sgetpar(fp, "s1", "", true);
   s2 = sgetpar(fp, "s2", "", true);
   s3 = sgetpar(fp, "s3", "", true);
   b1 = bgetpar(fp, "b1", false, true);
   b2 = bgetpar(fp, "b2", false, true);
   b3 = bgetpar(fp, "b3", false, true);
   b4 = bgetpar(fp, "b4", false, true);
   dir1 = sgetpar(fp, "dir1", ".", true);
   if (strcmp(dir1, "."))
     MakeDir(dir1);
   dir2 = sgetpar(fp, "dir2", ".", true);
   if (strcmp(dir2, "."))
     MakeDir(dir2);
+}
 const char *sbool(const bool &p) {
   const char *true_str="true";
   const char *false_str="false";
   if (p)
     return true_str;
   else
     return false_str;
+}
 void Parameter::Write(ostream &os) const {
   if (arrowcolor)
     os << " arrowcolor = " << arrowcolor << endl;
   os << " arrowsize = " << arrowsize << endl;
   if (textcolor)
     os << " textcolor = " << textcolor << endl;
   os << " cellnumsize = " << cellnumsize << endl;
   os << " nodenumsize = " << nodenumsize << endl;
   os << " node_mag = " << node_mag << endl;
   os << " outlinewidth = " << outlinewidth << endl;
   if (cell_outline_color)
     os << " cell_outline_color = " << cell_outline_color << endl;
   os << " resize_stride = " << resize_stride << endl;
   os << " T = " << T << endl;
   os << " lambda_length = " << lambda_length << endl;
   os << " lambda_celllength = " << lambda_celllength << endl;
   os << " target_length = " << target_length << endl;
   os << " cell_expansion_rate = " << cell_expansion_rate << endl;
   os << " cell_div_expansion_rate = " << cell_div_expansion_rate << endl;
   os << " auxin_dependent_growth = " << sbool(auxin_dependent_growth) << endl;
   os << " ode_accuracy = " << ode_accuracy << endl;
   os << " mc_stepsize = " << mc_stepsize << endl;
   os << " mc_cell_stepsize = " << mc_cell_stepsize << endl;
   os << " energy_threshold = " << energy_threshold << endl;
   os << " bend_lambda = " << bend_lambda << endl;
   os << " alignment_lambda = " << alignment_lambda << endl;
   os << " rel_cell_div_threshold = " << rel_cell_div_threshold << endl;
   os << " rel_perimeter_stiffness = " << rel_perimeter_stiffness << endl;
   os << " collapse_node_threshold = " << collapse_node_threshold << endl;
   os << " morphogen_div_threshold = " << morphogen_div_threshold << endl;
   os << " morphogen_expansion_threshold = " << morphogen_expansion_threshold << endl;
   os << " copy_wall = " << sbool(copy_wall) << endl;
   os << " source = " << source << endl;
   os << " D = "<< D[0] << ", " << D[1] << ", " << D[2] << ", " << D[3] << ", " << D[4] << ", " << D[5] << ", " << D[6] << ", " << D[7] << ", " << D[8] << ", " << D[9] << ", " << D[10] << ", " << D[11] << ", " << D[12] << ", " << D[13] << ", " << D[14] << endl;
   os << " initval = "<< initval[0] << ", " << initval[1] << ", " << initval[2] << ", " << initval[3] << ", " << initval[4] << ", " << initval[5] << ", " << initval[6] << ", " << initval[7] << ", " << initval[8] << ", " << initval[9] << ", " << initval[10] << ", " << initval[11] << ", " << initval[12] << ", " << initval[13] << ", " << initval[14] << endl;
   os << " k1 = " << k1 << endl;
   os << " k2 = " << k2 << endl;
   os << " r = " << r << endl;
   os << " kr = " << kr << endl;
   os << " km = " << km << endl;
   os << " Pi_tot = " << Pi_tot << endl;
   os << " transport = " << transport << endl;
   os << " ka = " << ka << endl;
   os << " pin_prod = " << pin_prod << endl;
   os << " pin_prod_in_epidermis = " << pin_prod_in_epidermis << endl;
   os << " pin_breakdown = " << pin_breakdown << endl;
   os << " pin_breakdown_internal = " << pin_breakdown_internal << endl;
   os << " aux1prod = " << aux1prod << endl;
   os << " aux1prodmeso = " << aux1prodmeso << endl;
   os << " aux1decay = " << aux1decay << endl;
   os << " aux1decaymeso = " << aux1decaymeso << endl;
   os << " aux1transport = " << aux1transport << endl;
   os << " aux_cons = " << aux_cons << endl;
   os << " aux_breakdown = " << aux_breakdown << endl;
   os << " kaux1 = " << kaux1 << endl;
   os << " kap = " << kap << endl;
   os << " leaf_tip_source = " << leaf_tip_source << endl;
   os << " sam_efflux = " << sam_efflux << endl;
   os << " sam_auxin = " << sam_auxin << endl;
   os << " sam_auxin_breakdown = " << sam_auxin_breakdown << endl;
   os << " van3prod = " << van3prod << endl;
   os << " van3autokat = " << van3autokat << endl;
   os << " van3sat = " << van3sat << endl;
   os << " k2van3 = " << k2van3 << endl;
   os << " dt = " << dt << endl;
   os << " rd_dt = " << rd_dt << endl;
   if (datadir)
     os << " datadir = " << datadir << endl;
   os << " movie = " << sbool(movie) << endl;
   os << " nit = " << nit << endl;
   os << " maxt = " << maxt << endl;
   os << " storage_stride = " << storage_stride << endl;
   os << " xml_storage_stride = " << xml_storage_stride << endl;
   os << " rseed = " << rseed << endl;
   os << " constituous_expansion_limit = " << constituous_expansion_limit << endl;
   os << " vessel_inh_level = " << vessel_inh_level << endl;
   os << " vessel_expansion_rate = " << vessel_expansion_rate << endl;
   os << " d = " << d << endl;
   os << " e = " << e << endl;
   os << " f = " << f << endl;
   os << " c = " << c << endl;
   os << " mu = " << mu << endl;
   os << " nu = " << nu << endl;
   os << " rho0 = " << rho0 << endl;
   os << " rho1 = " << rho1 << endl;
   os << " c0 = " << c0 << endl;
   os << " gamma = " << gamma << endl;
   os << " eps = " << eps << endl;
   os << " k = "<< k[0] << ", " << k[1] << ", " << k[2] << ", " << k[3] << ", " << k[4] << ", " << k[5] << ", " << k[6] << ", " << k[7] << ", " << k[8] << ", " << k[9] << ", " << k[10] << ", " << k[11] << ", " << k[12] << ", " << k[13] << ", " << k[14] << endl;
   os << " i1 = " << i1 << endl;
   os << " i2 = " << i2 << endl;
   os << " i3 = " << i3 << endl;
   os << " i4 = " << i4 << endl;
   os << " i5 = " << i5 << endl;
   if (s1)
     os << " s1 = " << s1 << endl;
   if (s2)
     os << " s2 = " << s2 << endl;
   if (s3)
     os << " s3 = " << s3 << endl;
   os << " b1 = " << sbool(b1) << endl;
   os << " b2 = " << sbool(b2) << endl;
   os << " b3 = " << sbool(b3) << endl;
   os << " b4 = " << sbool(b4) << endl;
   if (dir1)
     os << " dir1 = " << dir1 << endl;
   if (dir2)
     os << " dir2 = " << dir2 << endl;
+}
 void Parameter::XMLAdd(xmlNode *root) const {
   xmlNode *xmlparameter = xmlNewChild(root, NULL, BAD_CAST "parameter", NULL);
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "arrowcolor" );
   ostringstream text;
   if (arrowcolor)
     text << arrowcolor;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "arrowsize" );
   ostringstream text;
   text << arrowsize;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "textcolor" );
   ostringstream text;
   if (textcolor)
     text << textcolor;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "cellnumsize" );
   ostringstream text;
   text << cellnumsize;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "nodenumsize" );
   ostringstream text;
   text << nodenumsize;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "node_mag" );
   ostringstream text;
   text << node_mag;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "outlinewidth" );
   ostringstream text;
   text << outlinewidth;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "cell_outline_color" );
   ostringstream text;
   if (cell_outline_color)
     text << cell_outline_color;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "resize_stride" );
   ostringstream text;
   text << resize_stride;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "T" );
   ostringstream text;
   text << T;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "lambda_length" );
   ostringstream text;
   text << lambda_length;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "lambda_celllength" );
   ostringstream text;
   text << lambda_celllength;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "target_length" );
   ostringstream text;
   text << target_length;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "cell_expansion_rate" );
   ostringstream text;
   text << cell_expansion_rate;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "cell_div_expansion_rate" );
   ostringstream text;
   text << cell_div_expansion_rate;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "auxin_dependent_growth" );
   ostringstream text;
 text << sbool(auxin_dependent_growth);
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "ode_accuracy" );
   ostringstream text;
   text << ode_accuracy;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "mc_stepsize" );
   ostringstream text;
   text << mc_stepsize;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "mc_cell_stepsize" );
   ostringstream text;
   text << mc_cell_stepsize;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "energy_threshold" );
   ostringstream text;
   text << energy_threshold;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "bend_lambda" );
   ostringstream text;
   text << bend_lambda;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "alignment_lambda" );
   ostringstream text;
   text << alignment_lambda;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "rel_cell_div_threshold" );
   ostringstream text;
   text << rel_cell_div_threshold;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "rel_perimeter_stiffness" );
   ostringstream text;
   text << rel_perimeter_stiffness;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "collapse_node_threshold" );
   ostringstream text;
   text << collapse_node_threshold;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "morphogen_div_threshold" );
   ostringstream text;
   text << morphogen_div_threshold;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "morphogen_expansion_threshold" );
   ostringstream text;
   text << morphogen_expansion_threshold;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "copy_wall" );
   ostringstream text;
 text << sbool(copy_wall);
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "source" );
   ostringstream text;
   text << source;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "D" );
   xmlNode *xmlvalarray = xmlNewChild(xmlpar, NULL, BAD_CAST "valarray", NULL);
+  {
     ostringstream text;
     text << D[0];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << D[1];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << D[2];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << D[3];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << D[4];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << D[5];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << D[6];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << D[7];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << D[8];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << D[9];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << D[10];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << D[11];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << D[12];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << D[13];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << D[14];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "initval" );
   xmlNode *xmlvalarray = xmlNewChild(xmlpar, NULL, BAD_CAST "valarray", NULL);
+  {
     ostringstream text;
     text << initval[0];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << initval[1];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << initval[2];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << initval[3];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << initval[4];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << initval[5];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << initval[6];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << initval[7];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << initval[8];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << initval[9];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << initval[10];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << initval[11];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << initval[12];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << initval[13];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << initval[14];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "k1" );
   ostringstream text;
   text << k1;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "k2" );
   ostringstream text;
   text << k2;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "r" );
   ostringstream text;
   text << r;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "kr" );
   ostringstream text;
   text << kr;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "km" );
   ostringstream text;
   text << km;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "Pi_tot" );
   ostringstream text;
   text << Pi_tot;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "transport" );
   ostringstream text;
   text << transport;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "ka" );
   ostringstream text;
   text << ka;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "pin_prod" );
   ostringstream text;
   text << pin_prod;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "pin_prod_in_epidermis" );
   ostringstream text;
   text << pin_prod_in_epidermis;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "pin_breakdown" );
   ostringstream text;
   text << pin_breakdown;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "pin_breakdown_internal" );
   ostringstream text;
   text << pin_breakdown_internal;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "aux1prod" );
   ostringstream text;
   text << aux1prod;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "aux1prodmeso" );
   ostringstream text;
   text << aux1prodmeso;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "aux1decay" );
   ostringstream text;
   text << aux1decay;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "aux1decaymeso" );
   ostringstream text;
   text << aux1decaymeso;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "aux1transport" );
   ostringstream text;
   text << aux1transport;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "aux_cons" );
   ostringstream text;
   text << aux_cons;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "aux_breakdown" );
   ostringstream text;
   text << aux_breakdown;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "kaux1" );
   ostringstream text;
   text << kaux1;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "kap" );
   ostringstream text;
   text << kap;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "leaf_tip_source" );
   ostringstream text;
   text << leaf_tip_source;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "sam_efflux" );
   ostringstream text;
   text << sam_efflux;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "sam_auxin" );
   ostringstream text;
   text << sam_auxin;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "sam_auxin_breakdown" );
   ostringstream text;
   text << sam_auxin_breakdown;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "van3prod" );
   ostringstream text;
   text << van3prod;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "van3autokat" );
   ostringstream text;
   text << van3autokat;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "van3sat" );
   ostringstream text;
   text << van3sat;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "k2van3" );
   ostringstream text;
   text << k2van3;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "dt" );
   ostringstream text;
   text << dt;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "rd_dt" );
   ostringstream text;
   text << rd_dt;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "datadir" );
   ostringstream text;
   if (datadir)
     text << datadir;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "movie" );
   ostringstream text;
 text << sbool(movie);
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "nit" );
   ostringstream text;
   text << nit;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "maxt" );
   ostringstream text;
   text << maxt;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "storage_stride" );
   ostringstream text;
   text << storage_stride;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "xml_storage_stride" );
   ostringstream text;
   text << xml_storage_stride;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "rseed" );
   ostringstream text;
   text << rseed;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "constituous_expansion_limit" );
   ostringstream text;
   text << constituous_expansion_limit;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "vessel_inh_level" );
   ostringstream text;
   text << vessel_inh_level;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "vessel_expansion_rate" );
   ostringstream text;
   text << vessel_expansion_rate;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "d" );
   ostringstream text;
   text << d;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "e" );
   ostringstream text;
   text << e;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "f" );
   ostringstream text;
   text << f;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "c" );
   ostringstream text;
   text << c;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "mu" );
   ostringstream text;
   text << mu;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "nu" );
   ostringstream text;
   text << nu;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "rho0" );
   ostringstream text;
   text << rho0;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "rho1" );
   ostringstream text;
   text << rho1;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "c0" );
   ostringstream text;
   text << c0;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "gamma" );
   ostringstream text;
   text << gamma;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "eps" );
   ostringstream text;
   text << eps;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "k" );
   xmlNode *xmlvalarray = xmlNewChild(xmlpar, NULL, BAD_CAST "valarray", NULL);
+  {
     ostringstream text;
     text << k[0];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << k[1];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << k[2];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << k[3];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << k[4];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << k[5];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << k[6];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << k[7];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << k[8];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << k[9];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << k[10];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << k[11];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << k[12];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << k[13];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << k[14];
     xmlNode *xmlval = xmlNewChild(xmlvalarray, NULL, BAD_CAST "val", NULL);
     xmlNewProp(xmlval, BAD_CAST "v", BAD_CAST text.str().c_str());
+  }
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "i1" );
   ostringstream text;
   text << i1;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "i2" );
   ostringstream text;
   text << i2;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "i3" );
   ostringstream text;
   text << i3;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "i4" );
   ostringstream text;
   text << i4;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "i5" );
   ostringstream text;
   text << i5;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "s1" );
   ostringstream text;
   if (s1)
     text << s1;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "s2" );
   ostringstream text;
   if (s2)
     text << s2;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "s3" );
   ostringstream text;
   if (s3)
     text << s3;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "b1" );
   ostringstream text;
 text << sbool(b1);
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "b2" );
   ostringstream text;
 text << sbool(b2);
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "b3" );
   ostringstream text;
 text << sbool(b3);
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "b4" );
   ostringstream text;
 text << sbool(b4);
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "dir1" );
   ostringstream text;
   if (dir1)
     text << dir1;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "dir2" );
   ostringstream text;
   if (dir2)
     text << dir2;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+}
 void Parameter::AssignValToPar(const char *namec, const char *valc) {
   QLocale standardlocale(QLocale::C);
   bool ok;
 if (!strcmp(namec, "arrowcolor")) {
   if (arrowcolor) { free(arrowcolor); }
   arrowcolor=strdup(valc);
+}
 if (!strcmp(namec, "arrowsize")) {
   arrowsize = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'arrowsize' from XML file.",valc); }
+}
 if (!strcmp(namec, "textcolor")) {
   if (textcolor) { free(textcolor); }
   textcolor=strdup(valc);
+}
 if (!strcmp(namec, "cellnumsize")) {
   cellnumsize = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'cellnumsize' from XML file.",valc); }
+}
 if (!strcmp(namec, "nodenumsize")) {
   nodenumsize = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'nodenumsize' from XML file.",valc); }
+}
 if (!strcmp(namec, "node_mag")) {
   node_mag = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'node_mag' from XML file.",valc); }
+}
 if (!strcmp(namec, "outlinewidth")) {
   outlinewidth = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'outlinewidth' from XML file.",valc); }
+}
 if (!strcmp(namec, "cell_outline_color")) {
   if (cell_outline_color) { free(cell_outline_color); }
   cell_outline_color=strdup(valc);
+}
 if (!strcmp(namec, "resize_stride")) {
   resize_stride = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'resize_stride' from XML file.",valc); }
+}
 if (!strcmp(namec, "T")) {
   T = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'T' from XML file.",valc); }
+}
 if (!strcmp(namec, "lambda_length")) {
   lambda_length = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'lambda_length' from XML file.",valc); }
+}
 if (!strcmp(namec, "lambda_celllength")) {
   lambda_celllength = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'lambda_celllength' from XML file.",valc); }
+}
 if (!strcmp(namec, "target_length")) {
   target_length = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'target_length' from XML file.",valc); }
+}
 if (!strcmp(namec, "cell_expansion_rate")) {
   cell_expansion_rate = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'cell_expansion_rate' from XML file.",valc); }
+}
 if (!strcmp(namec, "cell_div_expansion_rate")) {
   cell_div_expansion_rate = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'cell_div_expansion_rate' from XML file.",valc); }
+}
 if (!strcmp(namec, "auxin_dependent_growth")) {
 auxin_dependent_growth = strtobool(valc);
+}
 if (!strcmp(namec, "ode_accuracy")) {
   ode_accuracy = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'ode_accuracy' from XML file.",valc); }
+}
 if (!strcmp(namec, "mc_stepsize")) {
   mc_stepsize = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'mc_stepsize' from XML file.",valc); }
+}
 if (!strcmp(namec, "mc_cell_stepsize")) {
   mc_cell_stepsize = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'mc_cell_stepsize' from XML file.",valc); }
+}
 if (!strcmp(namec, "energy_threshold")) {
   energy_threshold = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'energy_threshold' from XML file.",valc); }
+}
 if (!strcmp(namec, "bend_lambda")) {
   bend_lambda = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'bend_lambda' from XML file.",valc); }
+}
 if (!strcmp(namec, "alignment_lambda")) {
   alignment_lambda = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'alignment_lambda' from XML file.",valc); }
+}
 if (!strcmp(namec, "rel_cell_div_threshold")) {
   rel_cell_div_threshold = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'rel_cell_div_threshold' from XML file.",valc); }
+}
 if (!strcmp(namec, "rel_perimeter_stiffness")) {
   rel_perimeter_stiffness = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'rel_perimeter_stiffness' from XML file.",valc); }
+}
 if (!strcmp(namec, "collapse_node_threshold")) {
   collapse_node_threshold = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'collapse_node_threshold' from XML file.",valc); }
+}
 if (!strcmp(namec, "morphogen_div_threshold")) {
   morphogen_div_threshold = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'morphogen_div_threshold' from XML file.",valc); }
+}
 if (!strcmp(namec, "morphogen_expansion_threshold")) {
   morphogen_expansion_threshold = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'morphogen_expansion_threshold' from XML file.",valc); }
+}
 if (!strcmp(namec, "copy_wall")) {
 copy_wall = strtobool(valc);
+}
 if (!strcmp(namec, "source")) {
   source = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'source' from XML file.",valc); }
+}
 if (!strcmp(namec, "k1")) {
   k1 = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'k1' from XML file.",valc); }
+}
 if (!strcmp(namec, "k2")) {
   k2 = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'k2' from XML file.",valc); }
+}
 if (!strcmp(namec, "r")) {
   r = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'r' from XML file.",valc); }
+}
 if (!strcmp(namec, "kr")) {
   kr = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'kr' from XML file.",valc); }
+}
 if (!strcmp(namec, "km")) {
   km = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'km' from XML file.",valc); }
+}
 if (!strcmp(namec, "Pi_tot")) {
   Pi_tot = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'Pi_tot' from XML file.",valc); }
+}
 if (!strcmp(namec, "transport")) {
   transport = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'transport' from XML file.",valc); }
+}
 if (!strcmp(namec, "ka")) {
   ka = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'ka' from XML file.",valc); }
+}
 if (!strcmp(namec, "pin_prod")) {
   pin_prod = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'pin_prod' from XML file.",valc); }
+}
 if (!strcmp(namec, "pin_prod_in_epidermis")) {
   pin_prod_in_epidermis = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'pin_prod_in_epidermis' from XML file.",valc); }
+}
 if (!strcmp(namec, "pin_breakdown")) {
   pin_breakdown = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'pin_breakdown' from XML file.",valc); }
+}
 if (!strcmp(namec, "pin_breakdown_internal")) {
   pin_breakdown_internal = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'pin_breakdown_internal' from XML file.",valc); }
+}
 if (!strcmp(namec, "aux1prod")) {
   aux1prod = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'aux1prod' from XML file.",valc); }
+}
 if (!strcmp(namec, "aux1prodmeso")) {
   aux1prodmeso = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'aux1prodmeso' from XML file.",valc); }
+}
 if (!strcmp(namec, "aux1decay")) {
   aux1decay = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'aux1decay' from XML file.",valc); }
+}
 if (!strcmp(namec, "aux1decaymeso")) {
   aux1decaymeso = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'aux1decaymeso' from XML file.",valc); }
+}
 if (!strcmp(namec, "aux1transport")) {
   aux1transport = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'aux1transport' from XML file.",valc); }
+}
 if (!strcmp(namec, "aux_cons")) {
   aux_cons = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'aux_cons' from XML file.",valc); }
+}
 if (!strcmp(namec, "aux_breakdown")) {
   aux_breakdown = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'aux_breakdown' from XML file.",valc); }
+}
 if (!strcmp(namec, "kaux1")) {
   kaux1 = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'kaux1' from XML file.",valc); }
+}
 if (!strcmp(namec, "kap")) {
   kap = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'kap' from XML file.",valc); }
+}
 if (!strcmp(namec, "leaf_tip_source")) {
   leaf_tip_source = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'leaf_tip_source' from XML file.",valc); }
+}
 if (!strcmp(namec, "sam_efflux")) {
   sam_efflux = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'sam_efflux' from XML file.",valc); }
+}
 if (!strcmp(namec, "sam_auxin")) {
   sam_auxin = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'sam_auxin' from XML file.",valc); }
+}
 if (!strcmp(namec, "sam_auxin_breakdown")) {
   sam_auxin_breakdown = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'sam_auxin_breakdown' from XML file.",valc); }
+}
 if (!strcmp(namec, "van3prod")) {
   van3prod = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'van3prod' from XML file.",valc); }
+}
 if (!strcmp(namec, "van3autokat")) {
   van3autokat = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'van3autokat' from XML file.",valc); }
+}
 if (!strcmp(namec, "van3sat")) {
   van3sat = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'van3sat' from XML file.",valc); }
+}
 if (!strcmp(namec, "k2van3")) {
   k2van3 = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'k2van3' from XML file.",valc); }
+}
 if (!strcmp(namec, "dt")) {
   dt = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'dt' from XML file.",valc); }
+}
 if (!strcmp(namec, "rd_dt")) {
   rd_dt = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'rd_dt' from XML file.",valc); }
+}
 if (!strcmp(namec, "datadir")) {
   if (datadir) { free(datadir); }
   datadir=strdup(valc);
+}
 if (!strcmp(namec, "movie")) {
 movie = strtobool(valc);
+}
 if (!strcmp(namec, "nit")) {
   nit = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'nit' from XML file.",valc); }
+}
 if (!strcmp(namec, "maxt")) {
   maxt = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'maxt' from XML file.",valc); }
+}
 if (!strcmp(namec, "storage_stride")) {
   storage_stride = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'storage_stride' from XML file.",valc); }
+}
 if (!strcmp(namec, "xml_storage_stride")) {
   xml_storage_stride = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'xml_storage_stride' from XML file.",valc); }
+}
 if (!strcmp(namec, "rseed")) {
   rseed = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'rseed' from XML file.",valc); }
+}
 if (!strcmp(namec, "constituous_expansion_limit")) {
   constituous_expansion_limit = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'constituous_expansion_limit' from XML file.",valc); }
+}
 if (!strcmp(namec, "vessel_inh_level")) {
   vessel_inh_level = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'vessel_inh_level' from XML file.",valc); }
+}
 if (!strcmp(namec, "vessel_expansion_rate")) {
   vessel_expansion_rate = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'vessel_expansion_rate' from XML file.",valc); }
+}
 if (!strcmp(namec, "d")) {
   d = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'd' from XML file.",valc); }
+}
 if (!strcmp(namec, "e")) {
   e = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'e' from XML file.",valc); }
+}
 if (!strcmp(namec, "f")) {
   f = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'f' from XML file.",valc); }
+}
 if (!strcmp(namec, "c")) {
   c = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'c' from XML file.",valc); }
+}
 if (!strcmp(namec, "mu")) {
   mu = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'mu' from XML file.",valc); }
+}
 if (!strcmp(namec, "nu")) {
   nu = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'nu' from XML file.",valc); }
+}
 if (!strcmp(namec, "rho0")) {
   rho0 = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'rho0' from XML file.",valc); }
+}
 if (!strcmp(namec, "rho1")) {
   rho1 = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'rho1' from XML file.",valc); }
+}
 if (!strcmp(namec, "c0")) {
   c0 = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'c0' from XML file.",valc); }
+}
 if (!strcmp(namec, "gamma")) {
   gamma = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'gamma' from XML file.",valc); }
+}
 if (!strcmp(namec, "eps")) {
   eps = standardlocale.toDouble(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to double while reading parameter 'eps' from XML file.",valc); }
+}
 if (!strcmp(namec, "i1")) {
   i1 = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'i1' from XML file.",valc); }
+}
 if (!strcmp(namec, "i2")) {
   i2 = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'i2' from XML file.",valc); }
+}
 if (!strcmp(namec, "i3")) {
   i3 = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'i3' from XML file.",valc); }
+}
 if (!strcmp(namec, "i4")) {
   i4 = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'i4' from XML file.",valc); }
+}
 if (!strcmp(namec, "i5")) {
   i5 = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'i5' from XML file.",valc); }
+}
 if (!strcmp(namec, "s1")) {
   if (s1) { free(s1); }
   s1=strdup(valc);
+}
 if (!strcmp(namec, "s2")) {
   if (s2) { free(s2); }
   s2=strdup(valc);
+}
 if (!strcmp(namec, "s3")) {
   if (s3) { free(s3); }
   s3=strdup(valc);
+}
 if (!strcmp(namec, "b1")) {
 b1 = strtobool(valc);
+}
 if (!strcmp(namec, "b2")) {
 b2 = strtobool(valc);
+}
 if (!strcmp(namec, "b3")) {
 b3 = strtobool(valc);
+}
 if (!strcmp(namec, "b4")) {
 b4 = strtobool(valc);
+}
 if (!strcmp(namec, "dir1")) {
   if (dir1) { free(dir1); }
   dir1=strdup(valc);
+}
 if (!strcmp(namec, "dir2")) {
   if (dir2) { free(dir2); }
   dir2=strdup(valc);
+}
+}
 void Parameter::AssignValArrayToPar(const char *namec, vector<double> valarray) {
 if (!strcmp(namec, "D")) {
   int i=0;
   vector<double>::const_iterator v=valarray.begin();
   while (v!=valarray.end() && i <= 14 ) {
      D[i++]=*(v++);
+  }
+}
 if (!strcmp(namec, "initval")) {
   int i=0;
   vector<double>::const_iterator v=valarray.begin();
   while (v!=valarray.end() && i <= 14 ) {
      initval[i++]=*(v++);
+  }
+}
 if (!strcmp(namec, "k")) {
   int i=0;
   vector<double>::const_iterator v=valarray.begin();
   while (v!=valarray.end() && i <= 14 ) {
      k[i++]=*(v++);
+  }
+}
+}
 /* void Parameter::XMLRead(xmlNode *root) {
   xmlNode *cur = root->xmlChildrenNode;
   while (cur!=NULL) {
     if ((!xmlStrcmp(cur->name, (const xmlChar *)"parameter"))){
       xmlNode *par_node = cur->xmlChildrenNode;
       while (par_node!=NULL) {
+	{
 	  if (!xmlStrcmp(par_node->name, (const xmlChar *)"par")) {
 	    xmlChar *namec = xmlGetProp(par_node, BAD_CAST "name");
 	    xmlChar *valc = xmlGetProp(par_node, BAD_CAST "val");
 	    if (valc) {
 	      AssignValToPar((const char*)namec,(const char*)valc);
 	    } else {
 	      // Probably a valarray
 	      xmlNode *sub_par_node = par_node->xmlChildrenNode;
 	      vector<double> valarray;
 	      while (sub_par_node != NULL) {
 		if (!xmlStrcmp(sub_par_node->name, (const xmlChar *)"valarray")) {
 		  valarray = XMLIO::XMLReadValArray(sub_par_node);
+		}
 		sub_par_node = sub_par_node->next;
+	      }
 	      AssignValArrayToPar((const char*)namec, valarray);
+	    }
+	  }
+	}
 	par_node = par_node->next;
+      }
+    }
     cur=cur->next;
+  }
 }*/
 ostream &operator<<(ostream &os, Parameter &p) {
   p.Write(os);
   return os;
+}

src/parameter.h

➞

Show inline comments

@@ new file 100644 @@
 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  The Virtual Leaf is free software: you can redistribute it and/or modify
  *  it under the terms of the GNU General Public License as published by
  *  the Free Software Foundation, either version 3 of the License, or
  *  (at your option) any later version.
+ *
  *  The Virtual Leaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #ifndef _PARAMETER_H_
 #define _PARAMETER_H_
 #include "vector.h"
 #include <vector>
 #include <libxml/parser.h>
 #include <libxml/tree.h>
 class Parameter {
  public:
   Parameter();
   ~Parameter();
   void CleanUp(void);
   void Read(const char *filename);
   void Write(ostream &os) const;
   void XMLAdd(xmlNode *root) const;
   void XMLRead(xmlNode *root);
   void AssignValToPar(const char *namec, const char *valc);
   void AssignValArrayToPar(const char *namec, vector<double> valarray);
   char * arrowcolor;
   double arrowsize;
   char * textcolor;
   int cellnumsize;
   int nodenumsize;
   double node_mag;
   double outlinewidth;
   char * cell_outline_color;
   int resize_stride;
   double T;
   double lambda_length;
   double lambda_celllength;
   double target_length;
   double cell_expansion_rate;
   double cell_div_expansion_rate;
   bool auxin_dependent_growth;
   double ode_accuracy;
   double mc_stepsize;
   double mc_cell_stepsize;
   double energy_threshold;
   double bend_lambda;
   double alignment_lambda;
   double rel_cell_div_threshold;
   double rel_perimeter_stiffness;
   double collapse_node_threshold;
   double morphogen_div_threshold;
   double morphogen_expansion_threshold;
   bool copy_wall;
   double source;
   double * D;
   double * initval;
   double k1;
   double k2;
   double r;
   double kr;
   double km;
   double Pi_tot;
   double transport;
   double ka;
   double pin_prod;
   double pin_prod_in_epidermis;
   double pin_breakdown;
   double pin_breakdown_internal;
   double aux1prod;
   double aux1prodmeso;
   double aux1decay;
   double aux1decaymeso;
   double aux1transport;
   double aux_cons;
   double aux_breakdown;
   double kaux1;
   double kap;
   double leaf_tip_source;
   double sam_efflux;
   double sam_auxin;
   double sam_auxin_breakdown;
   double van3prod;
   double van3autokat;
   double van3sat;
   double k2van3;
   double dt;
   double rd_dt;
   char * datadir;
   bool movie;
   int nit;
   double maxt;
   int storage_stride;
   int xml_storage_stride;
   int rseed;
   int constituous_expansion_limit;
   double vessel_inh_level;
   double vessel_expansion_rate;
   double d;
   double e;
   double f;
   double c;
   double mu;
   double nu;
   double rho0;
   double rho1;
   double c0;
   double gamma;
   double eps;
   double * k;
   int i1;
   int i2;
   int i3;
   int i4;
   int i5;
   char * s1;
   char * s2;
   char * s3;
   bool b1;
   bool b2;
   bool b3;
   bool b4;
   char * dir1;
   char * dir2;
  private:
 };
 ostream &operator<<(ostream &os, Parameter &p);
 const char *sbool(const bool &p);
 #endif

src/pardialog.cpp

➞

Show inline comments

@@ new file 100644 @@
 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  The Virtual Leaf is free software: you can redistribute it and/or modify
  *  it under the terms of the GNU General Public License as published by
  *  the Free Software Foundation, either version 3 of the License, or
  *  (at your option) any later version.
+ *
  *  The Virtual Leaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include "pardialog.h"
 #include "parameter.h"
 #include <cstring>
 #include <qdialog.h>
 #include <qlabel.h>
 #include <qlineedit.h>
 #include <qmessagebox.h>
 static const std::string _module_id("$Id$");
 ParameterDialog::ParameterDialog(QWidget *parent, const char *name, Qt::WindowFlags f) : QDialog(parent,name,false,f) {
   extern Parameter par;
   arrowcolor_edit = new QLineEdit( QString("%1").arg(par.arrowcolor), this, "arrowcolor_edit" );
   arrowsize_edit = new QLineEdit( QString("%1").arg(par.arrowsize), this, "arrowsize_edit" );
   textcolor_edit = new QLineEdit( QString("%1").arg(par.textcolor), this, "textcolor_edit" );
   cellnumsize_edit = new QLineEdit( QString("%1").arg(par.cellnumsize), this, "cellnumsize_edit" );
   nodenumsize_edit = new QLineEdit( QString("%1").arg(par.nodenumsize), this, "nodenumsize_edit" );
   node_mag_edit = new QLineEdit( QString("%1").arg(par.node_mag), this, "node_mag_edit" );
   outlinewidth_edit = new QLineEdit( QString("%1").arg(par.outlinewidth), this, "outlinewidth_edit" );
   cell_outline_color_edit = new QLineEdit( QString("%1").arg(par.cell_outline_color), this, "cell_outline_color_edit" );
   resize_stride_edit = new QLineEdit( QString("%1").arg(par.resize_stride), this, "resize_stride_edit" );
   T_edit = new QLineEdit( QString("%1").arg(par.T), this, "T_edit" );
   lambda_length_edit = new QLineEdit( QString("%1").arg(par.lambda_length), this, "lambda_length_edit" );
   lambda_celllength_edit = new QLineEdit( QString("%1").arg(par.lambda_celllength), this, "lambda_celllength_edit" );
   target_length_edit = new QLineEdit( QString("%1").arg(par.target_length), this, "target_length_edit" );
   cell_expansion_rate_edit = new QLineEdit( QString("%1").arg(par.cell_expansion_rate), this, "cell_expansion_rate_edit" );
   cell_div_expansion_rate_edit = new QLineEdit( QString("%1").arg(par.cell_div_expansion_rate), this, "cell_div_expansion_rate_edit" );
   auxin_dependent_growth_edit = new QLineEdit( QString("%1").arg(sbool(par.auxin_dependent_growth)), this, "auxin_dependent_growth_edit" );
   ode_accuracy_edit = new QLineEdit( QString("%1").arg(par.ode_accuracy), this, "ode_accuracy_edit" );
   mc_stepsize_edit = new QLineEdit( QString("%1").arg(par.mc_stepsize), this, "mc_stepsize_edit" );
   mc_cell_stepsize_edit = new QLineEdit( QString("%1").arg(par.mc_cell_stepsize), this, "mc_cell_stepsize_edit" );
   energy_threshold_edit = new QLineEdit( QString("%1").arg(par.energy_threshold), this, "energy_threshold_edit" );
   bend_lambda_edit = new QLineEdit( QString("%1").arg(par.bend_lambda), this, "bend_lambda_edit" );
   alignment_lambda_edit = new QLineEdit( QString("%1").arg(par.alignment_lambda), this, "alignment_lambda_edit" );
   rel_cell_div_threshold_edit = new QLineEdit( QString("%1").arg(par.rel_cell_div_threshold), this, "rel_cell_div_threshold_edit" );
   rel_perimeter_stiffness_edit = new QLineEdit( QString("%1").arg(par.rel_perimeter_stiffness), this, "rel_perimeter_stiffness_edit" );
   collapse_node_threshold_edit = new QLineEdit( QString("%1").arg(par.collapse_node_threshold), this, "collapse_node_threshold_edit" );
   morphogen_div_threshold_edit = new QLineEdit( QString("%1").arg(par.morphogen_div_threshold), this, "morphogen_div_threshold_edit" );
   morphogen_expansion_threshold_edit = new QLineEdit( QString("%1").arg(par.morphogen_expansion_threshold), this, "morphogen_expansion_threshold_edit" );
   copy_wall_edit = new QLineEdit( QString("%1").arg(sbool(par.copy_wall)), this, "copy_wall_edit" );
   source_edit = new QLineEdit( QString("%1").arg(par.source), this, "source_edit" );
   QString D_string("%1,%2,%3,%4,%5,%6,%7,%8,%9,%10,%11,%12,%13,%14,%15");
   D_string = D_string.arg(par.D[0]).arg(par.D[1]).arg(par.D[2]).arg(par.D[3]).arg(par.D[4]).arg(par.D[5]).arg(par.D[6]).arg(par.D[7]).arg(par.D[8]).arg(par.D[9]).arg(par.D[10]).arg(par.D[11]).arg(par.D[12]).arg(par.D[13]).arg(par.D[14]);
   D_edit = new QLineEdit( D_string, this, "D_edit" );
   QString initval_string("%1,%2,%3,%4,%5,%6,%7,%8,%9,%10,%11,%12,%13,%14,%15");
   initval_string = initval_string.arg(par.initval[0]).arg(par.initval[1]).arg(par.initval[2]).arg(par.initval[3]).arg(par.initval[4]).arg(par.initval[5]).arg(par.initval[6]).arg(par.initval[7]).arg(par.initval[8]).arg(par.initval[9]).arg(par.initval[10]).arg(par.initval[11]).arg(par.initval[12]).arg(par.initval[13]).arg(par.initval[14]);
   initval_edit = new QLineEdit( initval_string, this, "initval_edit" );
   k1_edit = new QLineEdit( QString("%1").arg(par.k1), this, "k1_edit" );
   k2_edit = new QLineEdit( QString("%1").arg(par.k2), this, "k2_edit" );
   r_edit = new QLineEdit( QString("%1").arg(par.r), this, "r_edit" );
   kr_edit = new QLineEdit( QString("%1").arg(par.kr), this, "kr_edit" );
   km_edit = new QLineEdit( QString("%1").arg(par.km), this, "km_edit" );
   Pi_tot_edit = new QLineEdit( QString("%1").arg(par.Pi_tot), this, "Pi_tot_edit" );
   transport_edit = new QLineEdit( QString("%1").arg(par.transport), this, "transport_edit" );
   ka_edit = new QLineEdit( QString("%1").arg(par.ka), this, "ka_edit" );
   pin_prod_edit = new QLineEdit( QString("%1").arg(par.pin_prod), this, "pin_prod_edit" );
   pin_prod_in_epidermis_edit = new QLineEdit( QString("%1").arg(par.pin_prod_in_epidermis), this, "pin_prod_in_epidermis_edit" );
   pin_breakdown_edit = new QLineEdit( QString("%1").arg(par.pin_breakdown), this, "pin_breakdown_edit" );
   pin_breakdown_internal_edit = new QLineEdit( QString("%1").arg(par.pin_breakdown_internal), this, "pin_breakdown_internal_edit" );
   aux1prod_edit = new QLineEdit( QString("%1").arg(par.aux1prod), this, "aux1prod_edit" );
   aux1prodmeso_edit = new QLineEdit( QString("%1").arg(par.aux1prodmeso), this, "aux1prodmeso_edit" );
   aux1decay_edit = new QLineEdit( QString("%1").arg(par.aux1decay), this, "aux1decay_edit" );
   aux1decaymeso_edit = new QLineEdit( QString("%1").arg(par.aux1decaymeso), this, "aux1decaymeso_edit" );
   aux1transport_edit = new QLineEdit( QString("%1").arg(par.aux1transport), this, "aux1transport_edit" );
   aux_cons_edit = new QLineEdit( QString("%1").arg(par.aux_cons), this, "aux_cons_edit" );
   aux_breakdown_edit = new QLineEdit( QString("%1").arg(par.aux_breakdown), this, "aux_breakdown_edit" );
   kaux1_edit = new QLineEdit( QString("%1").arg(par.kaux1), this, "kaux1_edit" );
   kap_edit = new QLineEdit( QString("%1").arg(par.kap), this, "kap_edit" );
   leaf_tip_source_edit = new QLineEdit( QString("%1").arg(par.leaf_tip_source), this, "leaf_tip_source_edit" );
   sam_efflux_edit = new QLineEdit( QString("%1").arg(par.sam_efflux), this, "sam_efflux_edit" );
   sam_auxin_edit = new QLineEdit( QString("%1").arg(par.sam_auxin), this, "sam_auxin_edit" );
   sam_auxin_breakdown_edit = new QLineEdit( QString("%1").arg(par.sam_auxin_breakdown), this, "sam_auxin_breakdown_edit" );
   van3prod_edit = new QLineEdit( QString("%1").arg(par.van3prod), this, "van3prod_edit" );
   van3autokat_edit = new QLineEdit( QString("%1").arg(par.van3autokat), this, "van3autokat_edit" );
   van3sat_edit = new QLineEdit( QString("%1").arg(par.van3sat), this, "van3sat_edit" );
   k2van3_edit = new QLineEdit( QString("%1").arg(par.k2van3), this, "k2van3_edit" );
   dt_edit = new QLineEdit( QString("%1").arg(par.dt), this, "dt_edit" );
   rd_dt_edit = new QLineEdit( QString("%1").arg(par.rd_dt), this, "rd_dt_edit" );
   datadir_edit = new QLineEdit( QString("%1").arg(par.datadir), this, "datadir_edit" );
   movie_edit = new QLineEdit( QString("%1").arg(sbool(par.movie)), this, "movie_edit" );
   nit_edit = new QLineEdit( QString("%1").arg(par.nit), this, "nit_edit" );
   maxt_edit = new QLineEdit( QString("%1").arg(par.maxt), this, "maxt_edit" );
   storage_stride_edit = new QLineEdit( QString("%1").arg(par.storage_stride), this, "storage_stride_edit" );
   xml_storage_stride_edit = new QLineEdit( QString("%1").arg(par.xml_storage_stride), this, "xml_storage_stride_edit" );
   rseed_edit = new QLineEdit( QString("%1").arg(par.rseed), this, "rseed_edit" );
   constituous_expansion_limit_edit = new QLineEdit( QString("%1").arg(par.constituous_expansion_limit), this, "constituous_expansion_limit_edit" );
   vessel_inh_level_edit = new QLineEdit( QString("%1").arg(par.vessel_inh_level), this, "vessel_inh_level_edit" );
   vessel_expansion_rate_edit = new QLineEdit( QString("%1").arg(par.vessel_expansion_rate), this, "vessel_expansion_rate_edit" );
   d_edit = new QLineEdit( QString("%1").arg(par.d), this, "d_edit" );
   e_edit = new QLineEdit( QString("%1").arg(par.e), this, "e_edit" );
   f_edit = new QLineEdit( QString("%1").arg(par.f), this, "f_edit" );
   c_edit = new QLineEdit( QString("%1").arg(par.c), this, "c_edit" );
   mu_edit = new QLineEdit( QString("%1").arg(par.mu), this, "mu_edit" );
   nu_edit = new QLineEdit( QString("%1").arg(par.nu), this, "nu_edit" );
   rho0_edit = new QLineEdit( QString("%1").arg(par.rho0), this, "rho0_edit" );
   rho1_edit = new QLineEdit( QString("%1").arg(par.rho1), this, "rho1_edit" );
   c0_edit = new QLineEdit( QString("%1").arg(par.c0), this, "c0_edit" );
   gamma_edit = new QLineEdit( QString("%1").arg(par.gamma), this, "gamma_edit" );
   eps_edit = new QLineEdit( QString("%1").arg(par.eps), this, "eps_edit" );
   QString k_string("%1,%2,%3,%4,%5,%6,%7,%8,%9,%10,%11,%12,%13,%14,%15");
   k_string = k_string.arg(par.k[0]).arg(par.k[1]).arg(par.k[2]).arg(par.k[3]).arg(par.k[4]).arg(par.k[5]).arg(par.k[6]).arg(par.k[7]).arg(par.k[8]).arg(par.k[9]).arg(par.k[10]).arg(par.k[11]).arg(par.k[12]).arg(par.k[13]).arg(par.k[14]);
   k_edit = new QLineEdit( k_string, this, "k_edit" );
   i1_edit = new QLineEdit( QString("%1").arg(par.i1), this, "i1_edit" );
   i2_edit = new QLineEdit( QString("%1").arg(par.i2), this, "i2_edit" );
   i3_edit = new QLineEdit( QString("%1").arg(par.i3), this, "i3_edit" );
   i4_edit = new QLineEdit( QString("%1").arg(par.i4), this, "i4_edit" );
   i5_edit = new QLineEdit( QString("%1").arg(par.i5), this, "i5_edit" );
   s1_edit = new QLineEdit( QString("%1").arg(par.s1), this, "s1_edit" );
   s2_edit = new QLineEdit( QString("%1").arg(par.s2), this, "s2_edit" );
   s3_edit = new QLineEdit( QString("%1").arg(par.s3), this, "s3_edit" );
   b1_edit = new QLineEdit( QString("%1").arg(sbool(par.b1)), this, "b1_edit" );
   b2_edit = new QLineEdit( QString("%1").arg(sbool(par.b2)), this, "b2_edit" );
   b3_edit = new QLineEdit( QString("%1").arg(sbool(par.b3)), this, "b3_edit" );
   b4_edit = new QLineEdit( QString("%1").arg(sbool(par.b4)), this, "b4_edit" );
   dir1_edit = new QLineEdit( QString("%1").arg(par.dir1), this, "dir1_edit" );
   dir2_edit = new QLineEdit( QString("%1").arg(par.dir2), this, "dir2_edit" );
   // make a 1x1 grid; it will auto-expand
   QGridLayout *grid = new QGridLayout( this, 1, 1 );
   // add the first four widgets with (row, column) addressing
   setWindowTitle( QString( " Parameter values for The Virtual Leaf") );
   grid->addWidget( new QLabel( "<h3> Parameter values for The Virtual Leaf</h3>",this), 0, 0, 1, -1, Qt::AlignCenter);
   grid->addWidget( new QLabel( "", this), 0+1, 0, 1, -1);
   grid->addWidget( new QLabel( " <b>Visualization</b>", this), 3, 0, 1, 2 );
   grid->addWidget( new QLabel( "arrowcolor", this ),4, 0 );
   grid->addWidget( arrowcolor_edit, 4, 0+1  );
   grid->addWidget( new QLabel( "arrowsize", this ),5, 0 );
   grid->addWidget( arrowsize_edit, 5, 0+1  );
   grid->addWidget( new QLabel( "textcolor", this ),6, 0 );
   grid->addWidget( textcolor_edit, 6, 0+1  );
   grid->addWidget( new QLabel( "cellnumsize", this ),7, 0 );
   grid->addWidget( cellnumsize_edit, 7, 0+1  );
   grid->addWidget( new QLabel( "nodenumsize", this ),8, 0 );
   grid->addWidget( nodenumsize_edit, 8, 0+1  );
   grid->addWidget( new QLabel( "node_mag", this ),9, 0 );
   grid->addWidget( node_mag_edit, 9, 0+1  );
   grid->addWidget( new QLabel( "outlinewidth", this ),10, 0 );
   grid->addWidget( outlinewidth_edit, 10, 0+1  );
   grid->addWidget( new QLabel( "cell_outline_color", this ),11, 0 );
   grid->addWidget( cell_outline_color_edit, 11, 0+1  );
   grid->addWidget( new QLabel( "resize_stride", this ),12, 0 );
   grid->addWidget( resize_stride_edit, 12, 0+1  );
   grid->addWidget( new QLabel( "", this), 13, 0, 1, 2 );
   grid->addWidget( new QLabel( " <b>Cell mechanics</b>", this), 14, 0, 1, 2 );
   grid->addWidget( new QLabel( "T", this ),15, 0 );
   grid->addWidget( T_edit, 15, 0+1  );
   grid->addWidget( new QLabel( "lambda_length", this ),16, 0 );
   grid->addWidget( lambda_length_edit, 16, 0+1  );
   grid->addWidget( new QLabel( "lambda_celllength", this ),17, 0 );
   grid->addWidget( lambda_celllength_edit, 17, 0+1  );
   grid->addWidget( new QLabel( "target_length", this ),18, 0 );
   grid->addWidget( target_length_edit, 18, 0+1  );
   grid->addWidget( new QLabel( "cell_expansion_rate", this ),19, 0 );
   grid->addWidget( cell_expansion_rate_edit, 19, 0+1  );
   grid->addWidget( new QLabel( "cell_div_expansion_rate", this ),20, 0 );
   grid->addWidget( cell_div_expansion_rate_edit, 20, 0+1  );
   grid->addWidget( new QLabel( "auxin_dependent_growth", this ),21, 0 );
   grid->addWidget( auxin_dependent_growth_edit, 21, 0+1  );
   grid->addWidget( new QLabel( "ode_accuracy", this ),22, 0 );
   grid->addWidget( ode_accuracy_edit, 22, 0+1  );
   grid->addWidget( new QLabel( "mc_stepsize", this ),23, 0 );
   grid->addWidget( mc_stepsize_edit, 23, 0+1  );
   grid->addWidget( new QLabel( "mc_cell_stepsize", this ),24, 0 );
   grid->addWidget( mc_cell_stepsize_edit, 24, 0+1  );
   grid->addWidget( new QLabel( "energy_threshold", this ),25, 0 );
   grid->addWidget( energy_threshold_edit, 25, 0+1  );
   grid->addWidget( new QLabel( "bend_lambda", this ),26, 0 );
   grid->addWidget( bend_lambda_edit, 26, 0+1  );
   grid->addWidget( new QLabel( "alignment_lambda", this ),27, 0 );
   grid->addWidget( alignment_lambda_edit, 27, 0+1  );
   grid->addWidget( new QLabel( "rel_cell_div_threshold", this ),28, 0 );
   grid->addWidget( rel_cell_div_threshold_edit, 28, 0+1  );
   grid->addWidget( new QLabel( "rel_perimeter_stiffness", this ),29, 0 );
   grid->addWidget( rel_perimeter_stiffness_edit, 29, 0+1  );
   grid->addWidget( new QLabel( "collapse_node_threshold", this ),3, 2 );
   grid->addWidget( collapse_node_threshold_edit, 3, 2+1  );
   grid->addWidget( new QLabel( "morphogen_div_threshold", this ),4, 2 );
   grid->addWidget( morphogen_div_threshold_edit, 4, 2+1  );
   grid->addWidget( new QLabel( "morphogen_expansion_threshold", this ),5, 2 );
   grid->addWidget( morphogen_expansion_threshold_edit, 5, 2+1  );
   grid->addWidget( new QLabel( "copy_wall", this ),6, 2 );
   grid->addWidget( copy_wall_edit, 6, 2+1  );
   grid->addWidget( new QLabel( "", this), 7, 2, 1, 2 );
   grid->addWidget( new QLabel( " <b>Auxin transport and PIN1 dynamics</b>", this), 8, 2, 1, 2 );
   grid->addWidget( new QLabel( "source", this ),9, 2 );
   grid->addWidget( source_edit, 9, 2+1  );
   grid->addWidget( new QLabel( "D", this ),10, 2 );
   grid->addWidget( D_edit, 10, 2+1  );
   grid->addWidget( new QLabel( "initval", this ),11, 2 );
   grid->addWidget( initval_edit, 11, 2+1  );
   grid->addWidget( new QLabel( "k1", this ),12, 2 );
   grid->addWidget( k1_edit, 12, 2+1  );
   grid->addWidget( new QLabel( "k2", this ),13, 2 );
   grid->addWidget( k2_edit, 13, 2+1  );
   grid->addWidget( new QLabel( "r", this ),14, 2 );
   grid->addWidget( r_edit, 14, 2+1  );
   grid->addWidget( new QLabel( "kr", this ),15, 2 );
   grid->addWidget( kr_edit, 15, 2+1  );
   grid->addWidget( new QLabel( "km", this ),16, 2 );
   grid->addWidget( km_edit, 16, 2+1  );
   grid->addWidget( new QLabel( "Pi_tot", this ),17, 2 );
   grid->addWidget( Pi_tot_edit, 17, 2+1  );
   grid->addWidget( new QLabel( "transport", this ),18, 2 );
   grid->addWidget( transport_edit, 18, 2+1  );
   grid->addWidget( new QLabel( "ka", this ),19, 2 );
   grid->addWidget( ka_edit, 19, 2+1  );
   grid->addWidget( new QLabel( "pin_prod", this ),20, 2 );
   grid->addWidget( pin_prod_edit, 20, 2+1  );
   grid->addWidget( new QLabel( "pin_prod_in_epidermis", this ),21, 2 );
   grid->addWidget( pin_prod_in_epidermis_edit, 21, 2+1  );
   grid->addWidget( new QLabel( "pin_breakdown", this ),22, 2 );
   grid->addWidget( pin_breakdown_edit, 22, 2+1  );
   grid->addWidget( new QLabel( "pin_breakdown_internal", this ),23, 2 );
   grid->addWidget( pin_breakdown_internal_edit, 23, 2+1  );
   grid->addWidget( new QLabel( "aux1prod", this ),24, 2 );
   grid->addWidget( aux1prod_edit, 24, 2+1  );
   grid->addWidget( new QLabel( "aux1prodmeso", this ),25, 2 );
   grid->addWidget( aux1prodmeso_edit, 25, 2+1  );
   grid->addWidget( new QLabel( "aux1decay", this ),26, 2 );
   grid->addWidget( aux1decay_edit, 26, 2+1  );
   grid->addWidget( new QLabel( "aux1decaymeso", this ),27, 2 );
   grid->addWidget( aux1decaymeso_edit, 27, 2+1  );
   grid->addWidget( new QLabel( "aux1transport", this ),28, 2 );
   grid->addWidget( aux1transport_edit, 28, 2+1  );
   grid->addWidget( new QLabel( "aux_cons", this ),29, 2 );
   grid->addWidget( aux_cons_edit, 29, 2+1  );
   grid->addWidget( new QLabel( "aux_breakdown", this ),3, 4 );
   grid->addWidget( aux_breakdown_edit, 3, 4+1  );
   grid->addWidget( new QLabel( "kaux1", this ),4, 4 );
   grid->addWidget( kaux1_edit, 4, 4+1  );
   grid->addWidget( new QLabel( "kap", this ),5, 4 );
   grid->addWidget( kap_edit, 5, 4+1  );
   grid->addWidget( new QLabel( "leaf_tip_source", this ),6, 4 );
   grid->addWidget( leaf_tip_source_edit, 6, 4+1  );
   grid->addWidget( new QLabel( "sam_efflux", this ),7, 4 );
   grid->addWidget( sam_efflux_edit, 7, 4+1  );
   grid->addWidget( new QLabel( "sam_auxin", this ),8, 4 );
   grid->addWidget( sam_auxin_edit, 8, 4+1  );
   grid->addWidget( new QLabel( "sam_auxin_breakdown", this ),9, 4 );
   grid->addWidget( sam_auxin_breakdown_edit, 9, 4+1  );
   grid->addWidget( new QLabel( "van3prod", this ),10, 4 );
   grid->addWidget( van3prod_edit, 10, 4+1  );
   grid->addWidget( new QLabel( "van3autokat", this ),11, 4 );
   grid->addWidget( van3autokat_edit, 11, 4+1  );
   grid->addWidget( new QLabel( "van3sat", this ),12, 4 );
   grid->addWidget( van3sat_edit, 12, 4+1  );
   grid->addWidget( new QLabel( "k2van3", this ),13, 4 );
   grid->addWidget( k2van3_edit, 13, 4+1  );
   grid->addWidget( new QLabel( "", this), 14, 4, 1, 2 );
   grid->addWidget( new QLabel( " <b>Integration parameters</b>", this), 15, 4, 1, 2 );
   grid->addWidget( new QLabel( "dt", this ),16, 4 );
   grid->addWidget( dt_edit, 16, 4+1  );
   grid->addWidget( new QLabel( "rd_dt", this ),17, 4 );
   grid->addWidget( rd_dt_edit, 17, 4+1  );
   grid->addWidget( new QLabel( "datadir", this ),18, 4 );
   grid->addWidget( datadir_edit, 18, 4+1  );
   grid->addWidget( new QLabel( "movie", this ),19, 4 );
   grid->addWidget( movie_edit, 19, 4+1  );
   grid->addWidget( new QLabel( "nit", this ),20, 4 );
   grid->addWidget( nit_edit, 20, 4+1  );
   grid->addWidget( new QLabel( "maxt", this ),21, 4 );
   grid->addWidget( maxt_edit, 21, 4+1  );
   grid->addWidget( new QLabel( "storage_stride", this ),22, 4 );
   grid->addWidget( storage_stride_edit, 22, 4+1  );
   grid->addWidget( new QLabel( "xml_storage_stride", this ),23, 4 );
   grid->addWidget( xml_storage_stride_edit, 23, 4+1  );
   grid->addWidget( new QLabel( "rseed", this ),24, 4 );
   grid->addWidget( rseed_edit, 24, 4+1  );
   grid->addWidget( new QLabel( "", this), 25, 4, 1, 2 );
   grid->addWidget( new QLabel( " <b>Meinhardt leaf venation model</b>", this), 26, 4, 1, 2 );
   grid->addWidget( new QLabel( "constituous_expansion_limit", this ),27, 4 );
   grid->addWidget( constituous_expansion_limit_edit, 27, 4+1  );
   grid->addWidget( new QLabel( "vessel_inh_level", this ),28, 4 );
   grid->addWidget( vessel_inh_level_edit, 28, 4+1  );
   grid->addWidget( new QLabel( "vessel_expansion_rate", this ),29, 4 );
   grid->addWidget( vessel_expansion_rate_edit, 29, 4+1  );
   grid->addWidget( new QLabel( "d", this ),3, 6 );
   grid->addWidget( d_edit, 3, 6+1  );
   grid->addWidget( new QLabel( "e", this ),4, 6 );
   grid->addWidget( e_edit, 4, 6+1  );
   grid->addWidget( new QLabel( "f", this ),5, 6 );
   grid->addWidget( f_edit, 5, 6+1  );
   grid->addWidget( new QLabel( "c", this ),6, 6 );
   grid->addWidget( c_edit, 6, 6+1  );
   grid->addWidget( new QLabel( "mu", this ),7, 6 );
   grid->addWidget( mu_edit, 7, 6+1  );
   grid->addWidget( new QLabel( "nu", this ),8, 6 );
   grid->addWidget( nu_edit, 8, 6+1  );
   grid->addWidget( new QLabel( "rho0", this ),9, 6 );
   grid->addWidget( rho0_edit, 9, 6+1  );
   grid->addWidget( new QLabel( "rho1", this ),10, 6 );
   grid->addWidget( rho1_edit, 10, 6+1  );
   grid->addWidget( new QLabel( "c0", this ),11, 6 );
   grid->addWidget( c0_edit, 11, 6+1  );
   grid->addWidget( new QLabel( "gamma", this ),12, 6 );
   grid->addWidget( gamma_edit, 12, 6+1  );
   grid->addWidget( new QLabel( "eps", this ),13, 6 );
   grid->addWidget( eps_edit, 13, 6+1  );
   grid->addWidget( new QLabel( "", this), 14, 6, 1, 2 );
   grid->addWidget( new QLabel( " <b>User-defined parameters</b>", this), 15, 6, 1, 2 );
   grid->addWidget( new QLabel( "k", this ),16, 6 );
   grid->addWidget( k_edit, 16, 6+1  );
   grid->addWidget( new QLabel( "i1", this ),17, 6 );
   grid->addWidget( i1_edit, 17, 6+1  );
   grid->addWidget( new QLabel( "i2", this ),18, 6 );
   grid->addWidget( i2_edit, 18, 6+1  );
   grid->addWidget( new QLabel( "i3", this ),19, 6 );
   grid->addWidget( i3_edit, 19, 6+1  );
   grid->addWidget( new QLabel( "i4", this ),20, 6 );
   grid->addWidget( i4_edit, 20, 6+1  );
   grid->addWidget( new QLabel( "i5", this ),21, 6 );
   grid->addWidget( i5_edit, 21, 6+1  );
   grid->addWidget( new QLabel( "s1", this ),22, 6 );
   grid->addWidget( s1_edit, 22, 6+1  );
   grid->addWidget( new QLabel( "s2", this ),23, 6 );
   grid->addWidget( s2_edit, 23, 6+1  );
   grid->addWidget( new QLabel( "s3", this ),24, 6 );
   grid->addWidget( s3_edit, 24, 6+1  );
   grid->addWidget( new QLabel( "b1", this ),25, 6 );
   grid->addWidget( b1_edit, 25, 6+1  );
   grid->addWidget( new QLabel( "b2", this ),26, 6 );
   grid->addWidget( b2_edit, 26, 6+1  );
   grid->addWidget( new QLabel( "b3", this ),27, 6 );
   grid->addWidget( b3_edit, 27, 6+1  );
   grid->addWidget( new QLabel( "b4", this ),28, 6 );
   grid->addWidget( b4_edit, 28, 6+1  );
   grid->addWidget( new QLabel( "dir1", this ),29, 6 );
   grid->addWidget( dir1_edit, 29, 6+1  );
   grid->addWidget( new QLabel( "dir2", this ),3, 8 );
   grid->addWidget( dir2_edit, 3, 8+1  );
   QPushButton *pb = new QPushButton( "&Write", this );
   grid->addWidget(pb, 31, 6 );
   connect( pb, SIGNAL( clicked() ), this, SLOT( write() ) );
   QPushButton *pb2 = new QPushButton( "&Close", this );
   grid->addWidget(pb2,31, 6+1 );
   connect( pb2, SIGNAL( clicked() ), this, SLOT( close() ) );
   QPushButton *pb3 = new QPushButton( "&Reset", this );
   grid->addWidget(pb3, 31, 6+2 );
   connect( pb3, SIGNAL( clicked() ), this, SLOT( Reset() ) );
   show();
 };
 ParameterDialog::~ParameterDialog(void) {
 delete arrowcolor_edit;
 delete arrowsize_edit;
 delete textcolor_edit;
 delete cellnumsize_edit;
 delete nodenumsize_edit;
 delete node_mag_edit;
 delete outlinewidth_edit;
 delete cell_outline_color_edit;
 delete resize_stride_edit;
 delete T_edit;
 delete lambda_length_edit;
 delete lambda_celllength_edit;
 delete target_length_edit;
 delete cell_expansion_rate_edit;
 delete cell_div_expansion_rate_edit;
 delete auxin_dependent_growth_edit;
 delete ode_accuracy_edit;
 delete mc_stepsize_edit;
 delete mc_cell_stepsize_edit;
 delete energy_threshold_edit;
 delete bend_lambda_edit;
 delete alignment_lambda_edit;
 delete rel_cell_div_threshold_edit;
 delete rel_perimeter_stiffness_edit;
 delete collapse_node_threshold_edit;
 delete morphogen_div_threshold_edit;
 delete morphogen_expansion_threshold_edit;
 delete copy_wall_edit;
 delete source_edit;
 delete D_edit;
 delete initval_edit;
 delete k1_edit;
 delete k2_edit;
 delete r_edit;
 delete kr_edit;
 delete km_edit;
 delete Pi_tot_edit;
 delete transport_edit;
 delete ka_edit;
 delete pin_prod_edit;
 delete pin_prod_in_epidermis_edit;
 delete pin_breakdown_edit;
 delete pin_breakdown_internal_edit;
 delete aux1prod_edit;
 delete aux1prodmeso_edit;
 delete aux1decay_edit;
 delete aux1decaymeso_edit;
 delete aux1transport_edit;
 delete aux_cons_edit;
 delete aux_breakdown_edit;
 delete kaux1_edit;
 delete kap_edit;
 delete leaf_tip_source_edit;
 delete sam_efflux_edit;
 delete sam_auxin_edit;
 delete sam_auxin_breakdown_edit;
 delete van3prod_edit;
 delete van3autokat_edit;
 delete van3sat_edit;
 delete k2van3_edit;
 delete dt_edit;
 delete rd_dt_edit;
 delete datadir_edit;
 delete movie_edit;
 delete nit_edit;
 delete maxt_edit;
 delete storage_stride_edit;
 delete xml_storage_stride_edit;
 delete rseed_edit;
 delete constituous_expansion_limit_edit;
 delete vessel_inh_level_edit;
 delete vessel_expansion_rate_edit;
 delete d_edit;
 delete e_edit;
 delete f_edit;
 delete c_edit;
 delete mu_edit;
 delete nu_edit;
 delete rho0_edit;
 delete rho1_edit;
 delete c0_edit;
 delete gamma_edit;
 delete eps_edit;
 delete k_edit;
 delete i1_edit;
 delete i2_edit;
 delete i3_edit;
 delete i4_edit;
 delete i5_edit;
 delete s1_edit;
 delete s2_edit;
 delete s3_edit;
 delete b1_edit;
 delete b2_edit;
 delete b3_edit;
 delete b4_edit;
 delete dir1_edit;
 delete dir2_edit;
+}
 void ParameterDialog::write(void) {
   extern Parameter par;
   QString tmpval;
   par.arrowcolor = strdup((const char *)arrowcolor_edit->text());
   par.arrowsize = arrowsize_edit->text().toDouble();
   par.textcolor = strdup((const char *)textcolor_edit->text());
   par.cellnumsize = cellnumsize_edit->text().toInt();
   par.nodenumsize = nodenumsize_edit->text().toInt();
   par.node_mag = node_mag_edit->text().toDouble();
   par.outlinewidth = outlinewidth_edit->text().toDouble();
   par.cell_outline_color = strdup((const char *)cell_outline_color_edit->text());
   par.resize_stride = resize_stride_edit->text().toInt();
   par.T = T_edit->text().toDouble();
   par.lambda_length = lambda_length_edit->text().toDouble();
   par.lambda_celllength = lambda_celllength_edit->text().toDouble();
   par.target_length = target_length_edit->text().toDouble();
   par.cell_expansion_rate = cell_expansion_rate_edit->text().toDouble();
   par.cell_div_expansion_rate = cell_div_expansion_rate_edit->text().toDouble();
   tmpval = auxin_dependent_growth_edit->text().stripWhiteSpace();
   if (tmpval == "true" || tmpval == "yes" ) par.auxin_dependent_growth = true;
   else if (tmpval == "false" || tmpval == "no") par.auxin_dependent_growth = false;
   else {
     if (QMessageBox::question(this, "Syntax error", tr("Value %1 of parameter %2 is not recognized as Boolean.\nDo you mean TRUE or FALSE?").arg(tmpval).arg("auxin_dependent_growth"),"True","False", QString::null, 0, 1)==0) par.auxin_dependent_growth=true;
       else par.auxin_dependent_growth=false;
+  }
   par.ode_accuracy = ode_accuracy_edit->text().toDouble();
   par.mc_stepsize = mc_stepsize_edit->text().toDouble();
   par.mc_cell_stepsize = mc_cell_stepsize_edit->text().toDouble();
   par.energy_threshold = energy_threshold_edit->text().toDouble();
   par.bend_lambda = bend_lambda_edit->text().toDouble();
   par.alignment_lambda = alignment_lambda_edit->text().toDouble();
   par.rel_cell_div_threshold = rel_cell_div_threshold_edit->text().toDouble();
   par.rel_perimeter_stiffness = rel_perimeter_stiffness_edit->text().toDouble();
   par.collapse_node_threshold = collapse_node_threshold_edit->text().toDouble();
   par.morphogen_div_threshold = morphogen_div_threshold_edit->text().toDouble();
   par.morphogen_expansion_threshold = morphogen_expansion_threshold_edit->text().toDouble();
   tmpval = copy_wall_edit->text().stripWhiteSpace();
   if (tmpval == "true" || tmpval == "yes" ) par.copy_wall = true;
   else if (tmpval == "false" || tmpval == "no") par.copy_wall = false;
   else {
     if (QMessageBox::question(this, "Syntax error", tr("Value %1 of parameter %2 is not recognized as Boolean.\nDo you mean TRUE or FALSE?").arg(tmpval).arg("copy_wall"),"True","False", QString::null, 0, 1)==0) par.copy_wall=true;
       else par.copy_wall=false;
+  }
   par.source = source_edit->text().toDouble();
   tmpval = D_edit->text().section(',', 0, 0);
   par.D[0] = tmpval.toDouble();
   tmpval = D_edit->text().section(',', 1, 1);
   par.D[1] = tmpval.toDouble();
   tmpval = D_edit->text().section(',', 2, 2);
   par.D[2] = tmpval.toDouble();
   tmpval = D_edit->text().section(',', 3, 3);
   par.D[3] = tmpval.toDouble();
   tmpval = D_edit->text().section(',', 4, 4);
   par.D[4] = tmpval.toDouble();
   tmpval = D_edit->text().section(',', 5, 5);
   par.D[5] = tmpval.toDouble();
   tmpval = D_edit->text().section(',', 6, 6);
   par.D[6] = tmpval.toDouble();
   tmpval = D_edit->text().section(',', 7, 7);
   par.D[7] = tmpval.toDouble();
   tmpval = D_edit->text().section(',', 8, 8);
   par.D[8] = tmpval.toDouble();
   tmpval = D_edit->text().section(',', 9, 9);
   par.D[9] = tmpval.toDouble();
   tmpval = D_edit->text().section(',', 10, 10);
   par.D[10] = tmpval.toDouble();
   tmpval = D_edit->text().section(',', 11, 11);
   par.D[11] = tmpval.toDouble();
   tmpval = D_edit->text().section(',', 12, 12);
   par.D[12] = tmpval.toDouble();
   tmpval = D_edit->text().section(',', 13, 13);
   par.D[13] = tmpval.toDouble();
   tmpval = D_edit->text().section(',', 14, 14);
   par.D[14] = tmpval.toDouble();
   tmpval = initval_edit->text().section(',', 0, 0);
   par.initval[0] = tmpval.toDouble();
   tmpval = initval_edit->text().section(',', 1, 1);
   par.initval[1] = tmpval.toDouble();
   tmpval = initval_edit->text().section(',', 2, 2);
   par.initval[2] = tmpval.toDouble();
   tmpval = initval_edit->text().section(',', 3, 3);
   par.initval[3] = tmpval.toDouble();
   tmpval = initval_edit->text().section(',', 4, 4);
   par.initval[4] = tmpval.toDouble();
   tmpval = initval_edit->text().section(',', 5, 5);
   par.initval[5] = tmpval.toDouble();
   tmpval = initval_edit->text().section(',', 6, 6);
   par.initval[6] = tmpval.toDouble();
   tmpval = initval_edit->text().section(',', 7, 7);
   par.initval[7] = tmpval.toDouble();
   tmpval = initval_edit->text().section(',', 8, 8);
   par.initval[8] = tmpval.toDouble();
   tmpval = initval_edit->text().section(',', 9, 9);
   par.initval[9] = tmpval.toDouble();
   tmpval = initval_edit->text().section(',', 10, 10);
   par.initval[10] = tmpval.toDouble();
   tmpval = initval_edit->text().section(',', 11, 11);
   par.initval[11] = tmpval.toDouble();
   tmpval = initval_edit->text().section(',', 12, 12);
   par.initval[12] = tmpval.toDouble();
   tmpval = initval_edit->text().section(',', 13, 13);
   par.initval[13] = tmpval.toDouble();
   tmpval = initval_edit->text().section(',', 14, 14);
   par.initval[14] = tmpval.toDouble();
   par.k1 = k1_edit->text().toDouble();
   par.k2 = k2_edit->text().toDouble();
   par.r = r_edit->text().toDouble();
   par.kr = kr_edit->text().toDouble();
   par.km = km_edit->text().toDouble();
   par.Pi_tot = Pi_tot_edit->text().toDouble();
   par.transport = transport_edit->text().toDouble();
   par.ka = ka_edit->text().toDouble();
   par.pin_prod = pin_prod_edit->text().toDouble();
   par.pin_prod_in_epidermis = pin_prod_in_epidermis_edit->text().toDouble();
   par.pin_breakdown = pin_breakdown_edit->text().toDouble();
   par.pin_breakdown_internal = pin_breakdown_internal_edit->text().toDouble();
   par.aux1prod = aux1prod_edit->text().toDouble();
   par.aux1prodmeso = aux1prodmeso_edit->text().toDouble();
   par.aux1decay = aux1decay_edit->text().toDouble();
   par.aux1decaymeso = aux1decaymeso_edit->text().toDouble();
   par.aux1transport = aux1transport_edit->text().toDouble();
   par.aux_cons = aux_cons_edit->text().toDouble();
   par.aux_breakdown = aux_breakdown_edit->text().toDouble();
   par.kaux1 = kaux1_edit->text().toDouble();
   par.kap = kap_edit->text().toDouble();
   par.leaf_tip_source = leaf_tip_source_edit->text().toDouble();
   par.sam_efflux = sam_efflux_edit->text().toDouble();
   par.sam_auxin = sam_auxin_edit->text().toDouble();
   par.sam_auxin_breakdown = sam_auxin_breakdown_edit->text().toDouble();
   par.van3prod = van3prod_edit->text().toDouble();
   par.van3autokat = van3autokat_edit->text().toDouble();
   par.van3sat = van3sat_edit->text().toDouble();
   par.k2van3 = k2van3_edit->text().toDouble();
   par.dt = dt_edit->text().toDouble();
   par.rd_dt = rd_dt_edit->text().toDouble();
   par.datadir = strdup((const char *)datadir_edit->text());
   tmpval = movie_edit->text().stripWhiteSpace();
   if (tmpval == "true" || tmpval == "yes" ) par.movie = true;
   else if (tmpval == "false" || tmpval == "no") par.movie = false;
   else {
     if (QMessageBox::question(this, "Syntax error", tr("Value %1 of parameter %2 is not recognized as Boolean.\nDo you mean TRUE or FALSE?").arg(tmpval).arg("movie"),"True","False", QString::null, 0, 1)==0) par.movie=true;
       else par.movie=false;
+  }
   par.nit = nit_edit->text().toInt();
   par.maxt = maxt_edit->text().toDouble();
   par.storage_stride = storage_stride_edit->text().toInt();
   par.xml_storage_stride = xml_storage_stride_edit->text().toInt();
   par.rseed = rseed_edit->text().toInt();
   par.constituous_expansion_limit = constituous_expansion_limit_edit->text().toInt();
   par.vessel_inh_level = vessel_inh_level_edit->text().toDouble();
   par.vessel_expansion_rate = vessel_expansion_rate_edit->text().toDouble();
   par.d = d_edit->text().toDouble();
   par.e = e_edit->text().toDouble();
   par.f = f_edit->text().toDouble();
   par.c = c_edit->text().toDouble();
   par.mu = mu_edit->text().toDouble();
   par.nu = nu_edit->text().toDouble();
   par.rho0 = rho0_edit->text().toDouble();
   par.rho1 = rho1_edit->text().toDouble();
   par.c0 = c0_edit->text().toDouble();
   par.gamma = gamma_edit->text().toDouble();
   par.eps = eps_edit->text().toDouble();
   tmpval = k_edit->text().section(',', 0, 0);
   par.k[0] = tmpval.toDouble();
   tmpval = k_edit->text().section(',', 1, 1);
   par.k[1] = tmpval.toDouble();
   tmpval = k_edit->text().section(',', 2, 2);
   par.k[2] = tmpval.toDouble();
   tmpval = k_edit->text().section(',', 3, 3);
   par.k[3] = tmpval.toDouble();
   tmpval = k_edit->text().section(',', 4, 4);
   par.k[4] = tmpval.toDouble();
   tmpval = k_edit->text().section(',', 5, 5);
   par.k[5] = tmpval.toDouble();
   tmpval = k_edit->text().section(',', 6, 6);
   par.k[6] = tmpval.toDouble();
   tmpval = k_edit->text().section(',', 7, 7);
   par.k[7] = tmpval.toDouble();
   tmpval = k_edit->text().section(',', 8, 8);
   par.k[8] = tmpval.toDouble();
   tmpval = k_edit->text().section(',', 9, 9);
   par.k[9] = tmpval.toDouble();
   tmpval = k_edit->text().section(',', 10, 10);
   par.k[10] = tmpval.toDouble();
   tmpval = k_edit->text().section(',', 11, 11);
   par.k[11] = tmpval.toDouble();
   tmpval = k_edit->text().section(',', 12, 12);
   par.k[12] = tmpval.toDouble();
   tmpval = k_edit->text().section(',', 13, 13);
   par.k[13] = tmpval.toDouble();
   tmpval = k_edit->text().section(',', 14, 14);
   par.k[14] = tmpval.toDouble();
   par.i1 = i1_edit->text().toInt();
   par.i2 = i2_edit->text().toInt();
   par.i3 = i3_edit->text().toInt();
   par.i4 = i4_edit->text().toInt();
   par.i5 = i5_edit->text().toInt();
   par.s1 = strdup((const char *)s1_edit->text());
   par.s2 = strdup((const char *)s2_edit->text());
   par.s3 = strdup((const char *)s3_edit->text());
   tmpval = b1_edit->text().stripWhiteSpace();
   if (tmpval == "true" || tmpval == "yes" ) par.b1 = true;
   else if (tmpval == "false" || tmpval == "no") par.b1 = false;
   else {
     if (QMessageBox::question(this, "Syntax error", tr("Value %1 of parameter %2 is not recognized as Boolean.\nDo you mean TRUE or FALSE?").arg(tmpval).arg("b1"),"True","False", QString::null, 0, 1)==0) par.b1=true;
       else par.b1=false;
+  }
   tmpval = b2_edit->text().stripWhiteSpace();
   if (tmpval == "true" || tmpval == "yes" ) par.b2 = true;
   else if (tmpval == "false" || tmpval == "no") par.b2 = false;
   else {
     if (QMessageBox::question(this, "Syntax error", tr("Value %1 of parameter %2 is not recognized as Boolean.\nDo you mean TRUE or FALSE?").arg(tmpval).arg("b2"),"True","False", QString::null, 0, 1)==0) par.b2=true;
       else par.b2=false;
+  }
   tmpval = b3_edit->text().stripWhiteSpace();
   if (tmpval == "true" || tmpval == "yes" ) par.b3 = true;
   else if (tmpval == "false" || tmpval == "no") par.b3 = false;
   else {
     if (QMessageBox::question(this, "Syntax error", tr("Value %1 of parameter %2 is not recognized as Boolean.\nDo you mean TRUE or FALSE?").arg(tmpval).arg("b3"),"True","False", QString::null, 0, 1)==0) par.b3=true;
       else par.b3=false;
+  }
   tmpval = b4_edit->text().stripWhiteSpace();
   if (tmpval == "true" || tmpval == "yes" ) par.b4 = true;
   else if (tmpval == "false" || tmpval == "no") par.b4 = false;
   else {
     if (QMessageBox::question(this, "Syntax error", tr("Value %1 of parameter %2 is not recognized as Boolean.\nDo you mean TRUE or FALSE?").arg(tmpval).arg("b4"),"True","False", QString::null, 0, 1)==0) par.b4=true;
       else par.b4=false;
+  }
   par.dir1 = strdup((const char *)dir1_edit->text());
   par.dir2 = strdup((const char *)dir2_edit->text());
   Reset();
+}
 void ParameterDialog::Reset(void) {
   extern Parameter par;
   arrowcolor_edit->setText( QString("%1").arg(par.arrowcolor) );
   arrowsize_edit->setText( QString("%1").arg(par.arrowsize) );
   textcolor_edit->setText( QString("%1").arg(par.textcolor) );
   cellnumsize_edit->setText( QString("%1").arg(par.cellnumsize) );
   nodenumsize_edit->setText( QString("%1").arg(par.nodenumsize) );
   node_mag_edit->setText( QString("%1").arg(par.node_mag) );
   outlinewidth_edit->setText( QString("%1").arg(par.outlinewidth) );
   cell_outline_color_edit->setText( QString("%1").arg(par.cell_outline_color) );
   resize_stride_edit->setText( QString("%1").arg(par.resize_stride) );
   T_edit->setText( QString("%1").arg(par.T) );
   lambda_length_edit->setText( QString("%1").arg(par.lambda_length) );
   lambda_celllength_edit->setText( QString("%1").arg(par.lambda_celllength) );
   target_length_edit->setText( QString("%1").arg(par.target_length) );
   cell_expansion_rate_edit->setText( QString("%1").arg(par.cell_expansion_rate) );
   cell_div_expansion_rate_edit->setText( QString("%1").arg(par.cell_div_expansion_rate) );
   auxin_dependent_growth_edit->setText( QString("%1").arg(sbool(par.auxin_dependent_growth)));
   ode_accuracy_edit->setText( QString("%1").arg(par.ode_accuracy) );
   mc_stepsize_edit->setText( QString("%1").arg(par.mc_stepsize) );
   mc_cell_stepsize_edit->setText( QString("%1").arg(par.mc_cell_stepsize) );
   energy_threshold_edit->setText( QString("%1").arg(par.energy_threshold) );
   bend_lambda_edit->setText( QString("%1").arg(par.bend_lambda) );
   alignment_lambda_edit->setText( QString("%1").arg(par.alignment_lambda) );
   rel_cell_div_threshold_edit->setText( QString("%1").arg(par.rel_cell_div_threshold) );
   rel_perimeter_stiffness_edit->setText( QString("%1").arg(par.rel_perimeter_stiffness) );
   collapse_node_threshold_edit->setText( QString("%1").arg(par.collapse_node_threshold) );
   morphogen_div_threshold_edit->setText( QString("%1").arg(par.morphogen_div_threshold) );
   morphogen_expansion_threshold_edit->setText( QString("%1").arg(par.morphogen_expansion_threshold) );
   copy_wall_edit->setText( QString("%1").arg(sbool(par.copy_wall)));
   source_edit->setText( QString("%1").arg(par.source) );
   QString D_string("%1,%2,%3,%4,%5,%6,%7,%8,%9,%10,%11,%12,%13,%14,%15");
   D_string = D_string.arg(par.D[0]).arg(par.D[1]).arg(par.D[2]).arg(par.D[3]).arg(par.D[4]).arg(par.D[5]).arg(par.D[6]).arg(par.D[7]).arg(par.D[8]).arg(par.D[9]).arg(par.D[10]).arg(par.D[11]).arg(par.D[12]).arg(par.D[13]).arg(par.D[14]);
   D_edit->setText( D_string );
   QString initval_string("%1,%2,%3,%4,%5,%6,%7,%8,%9,%10,%11,%12,%13,%14,%15");
   initval_string = initval_string.arg(par.initval[0]).arg(par.initval[1]).arg(par.initval[2]).arg(par.initval[3]).arg(par.initval[4]).arg(par.initval[5]).arg(par.initval[6]).arg(par.initval[7]).arg(par.initval[8]).arg(par.initval[9]).arg(par.initval[10]).arg(par.initval[11]).arg(par.initval[12]).arg(par.initval[13]).arg(par.initval[14]);
   initval_edit->setText( initval_string );
   k1_edit->setText( QString("%1").arg(par.k1) );
   k2_edit->setText( QString("%1").arg(par.k2) );
   r_edit->setText( QString("%1").arg(par.r) );
   kr_edit->setText( QString("%1").arg(par.kr) );
   km_edit->setText( QString("%1").arg(par.km) );
   Pi_tot_edit->setText( QString("%1").arg(par.Pi_tot) );
   transport_edit->setText( QString("%1").arg(par.transport) );
   ka_edit->setText( QString("%1").arg(par.ka) );
   pin_prod_edit->setText( QString("%1").arg(par.pin_prod) );
   pin_prod_in_epidermis_edit->setText( QString("%1").arg(par.pin_prod_in_epidermis) );
   pin_breakdown_edit->setText( QString("%1").arg(par.pin_breakdown) );
   pin_breakdown_internal_edit->setText( QString("%1").arg(par.pin_breakdown_internal) );
   aux1prod_edit->setText( QString("%1").arg(par.aux1prod) );
   aux1prodmeso_edit->setText( QString("%1").arg(par.aux1prodmeso) );
   aux1decay_edit->setText( QString("%1").arg(par.aux1decay) );
   aux1decaymeso_edit->setText( QString("%1").arg(par.aux1decaymeso) );
   aux1transport_edit->setText( QString("%1").arg(par.aux1transport) );
   aux_cons_edit->setText( QString("%1").arg(par.aux_cons) );
   aux_breakdown_edit->setText( QString("%1").arg(par.aux_breakdown) );
   kaux1_edit->setText( QString("%1").arg(par.kaux1) );
   kap_edit->setText( QString("%1").arg(par.kap) );
   leaf_tip_source_edit->setText( QString("%1").arg(par.leaf_tip_source) );
   sam_efflux_edit->setText( QString("%1").arg(par.sam_efflux) );
   sam_auxin_edit->setText( QString("%1").arg(par.sam_auxin) );
   sam_auxin_breakdown_edit->setText( QString("%1").arg(par.sam_auxin_breakdown) );
   van3prod_edit->setText( QString("%1").arg(par.van3prod) );
   van3autokat_edit->setText( QString("%1").arg(par.van3autokat) );
   van3sat_edit->setText( QString("%1").arg(par.van3sat) );
   k2van3_edit->setText( QString("%1").arg(par.k2van3) );
   dt_edit->setText( QString("%1").arg(par.dt) );
   rd_dt_edit->setText( QString("%1").arg(par.rd_dt) );
   datadir_edit->setText( QString("%1").arg(par.datadir) );
   movie_edit->setText( QString("%1").arg(sbool(par.movie)));
   nit_edit->setText( QString("%1").arg(par.nit) );
   maxt_edit->setText( QString("%1").arg(par.maxt) );
   storage_stride_edit->setText( QString("%1").arg(par.storage_stride) );
   xml_storage_stride_edit->setText( QString("%1").arg(par.xml_storage_stride) );
   rseed_edit->setText( QString("%1").arg(par.rseed) );
   constituous_expansion_limit_edit->setText( QString("%1").arg(par.constituous_expansion_limit) );
   vessel_inh_level_edit->setText( QString("%1").arg(par.vessel_inh_level) );
   vessel_expansion_rate_edit->setText( QString("%1").arg(par.vessel_expansion_rate) );
   d_edit->setText( QString("%1").arg(par.d) );
   e_edit->setText( QString("%1").arg(par.e) );
   f_edit->setText( QString("%1").arg(par.f) );
   c_edit->setText( QString("%1").arg(par.c) );
   mu_edit->setText( QString("%1").arg(par.mu) );
   nu_edit->setText( QString("%1").arg(par.nu) );
   rho0_edit->setText( QString("%1").arg(par.rho0) );
   rho1_edit->setText( QString("%1").arg(par.rho1) );
   c0_edit->setText( QString("%1").arg(par.c0) );
   gamma_edit->setText( QString("%1").arg(par.gamma) );
   eps_edit->setText( QString("%1").arg(par.eps) );
   QString k_string("%1,%2,%3,%4,%5,%6,%7,%8,%9,%10,%11,%12,%13,%14,%15");
   k_string = k_string.arg(par.k[0]).arg(par.k[1]).arg(par.k[2]).arg(par.k[3]).arg(par.k[4]).arg(par.k[5]).arg(par.k[6]).arg(par.k[7]).arg(par.k[8]).arg(par.k[9]).arg(par.k[10]).arg(par.k[11]).arg(par.k[12]).arg(par.k[13]).arg(par.k[14]);
   k_edit->setText( k_string );
   i1_edit->setText( QString("%1").arg(par.i1) );
   i2_edit->setText( QString("%1").arg(par.i2) );
   i3_edit->setText( QString("%1").arg(par.i3) );
   i4_edit->setText( QString("%1").arg(par.i4) );
   i5_edit->setText( QString("%1").arg(par.i5) );
   s1_edit->setText( QString("%1").arg(par.s1) );
   s2_edit->setText( QString("%1").arg(par.s2) );
   s3_edit->setText( QString("%1").arg(par.s3) );
   b1_edit->setText( QString("%1").arg(sbool(par.b1)));
   b2_edit->setText( QString("%1").arg(sbool(par.b2)));
   b3_edit->setText( QString("%1").arg(sbool(par.b3)));
   b4_edit->setText( QString("%1").arg(sbool(par.b4)));
   dir1_edit->setText( QString("%1").arg(par.dir1) );
   dir2_edit->setText( QString("%1").arg(par.dir2) );
+}

src/pardialog.h

➞

Show inline comments

@@ new file 100644 @@
 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  The Virtual Leaf is free software: you can redistribute it and/or modify
  *  it under the terms of the GNU General Public License as published by
  *  the Free Software Foundation, either version 3 of the License, or
  *  (at your option) any later version.
+ *
  *  The Virtual Leaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #ifndef PARAMETER_DIALOG_H
 #define PARAMETER_DIALOG_H
 #include <qdialog.h>
 #include <qspinbox.h>
 #include <qlineedit.h>
 #include <qlayout.h>
 #include <qpushbutton.h>
 #include <iostream>
 class ParameterDialog : public QDialog {
   Q_OBJECT
   public:
   ParameterDialog(QWidget *parent=0, const char *name = 0, Qt::WindowFlags f = 0);
   virtual ~ParameterDialog(void);
  public slots:
   void Reset(void);
 private slots:
   void write(void);
  private:
   QLineEdit *arrowcolor_edit;
   QLineEdit *arrowsize_edit;
   QLineEdit *textcolor_edit;
   QLineEdit *cellnumsize_edit;
   QLineEdit *nodenumsize_edit;
   QLineEdit *node_mag_edit;
   QLineEdit *outlinewidth_edit;
   QLineEdit *cell_outline_color_edit;
   QLineEdit *resize_stride_edit;
   QLineEdit *T_edit;
   QLineEdit *lambda_length_edit;
   QLineEdit *lambda_celllength_edit;
   QLineEdit *target_length_edit;
   QLineEdit *cell_expansion_rate_edit;
   QLineEdit *cell_div_expansion_rate_edit;
   QLineEdit *auxin_dependent_growth_edit;
   QLineEdit *ode_accuracy_edit;
   QLineEdit *mc_stepsize_edit;
   QLineEdit *mc_cell_stepsize_edit;
   QLineEdit *energy_threshold_edit;
   QLineEdit *bend_lambda_edit;
   QLineEdit *alignment_lambda_edit;
   QLineEdit *rel_cell_div_threshold_edit;
   QLineEdit *rel_perimeter_stiffness_edit;
   QLineEdit *collapse_node_threshold_edit;
   QLineEdit *morphogen_div_threshold_edit;
   QLineEdit *morphogen_expansion_threshold_edit;
   QLineEdit *copy_wall_edit;
   QLineEdit *source_edit;
   QLineEdit *D_edit;
   QLineEdit *initval_edit;
   QLineEdit *k1_edit;
   QLineEdit *k2_edit;
   QLineEdit *r_edit;
   QLineEdit *kr_edit;
   QLineEdit *km_edit;
   QLineEdit *Pi_tot_edit;
   QLineEdit *transport_edit;
   QLineEdit *ka_edit;
   QLineEdit *pin_prod_edit;
   QLineEdit *pin_prod_in_epidermis_edit;
   QLineEdit *pin_breakdown_edit;
   QLineEdit *pin_breakdown_internal_edit;
   QLineEdit *aux1prod_edit;
   QLineEdit *aux1prodmeso_edit;
   QLineEdit *aux1decay_edit;
   QLineEdit *aux1decaymeso_edit;
   QLineEdit *aux1transport_edit;
   QLineEdit *aux_cons_edit;
   QLineEdit *aux_breakdown_edit;
   QLineEdit *kaux1_edit;
   QLineEdit *kap_edit;
   QLineEdit *leaf_tip_source_edit;
   QLineEdit *sam_efflux_edit;
   QLineEdit *sam_auxin_edit;
   QLineEdit *sam_auxin_breakdown_edit;
   QLineEdit *van3prod_edit;
   QLineEdit *van3autokat_edit;
   QLineEdit *van3sat_edit;
   QLineEdit *k2van3_edit;
   QLineEdit *dt_edit;
   QLineEdit *rd_dt_edit;
   QLineEdit *datadir_edit;
   QLineEdit *movie_edit;
   QLineEdit *nit_edit;
   QLineEdit *maxt_edit;
   QLineEdit *storage_stride_edit;
   QLineEdit *xml_storage_stride_edit;
   QLineEdit *rseed_edit;
   QLineEdit *constituous_expansion_limit_edit;
   QLineEdit *vessel_inh_level_edit;
   QLineEdit *vessel_expansion_rate_edit;
   QLineEdit *d_edit;
   QLineEdit *e_edit;
   QLineEdit *f_edit;
   QLineEdit *c_edit;
   QLineEdit *mu_edit;
   QLineEdit *nu_edit;
   QLineEdit *rho0_edit;
   QLineEdit *rho1_edit;
   QLineEdit *c0_edit;
   QLineEdit *gamma_edit;
   QLineEdit *eps_edit;
   QLineEdit *k_edit;
   QLineEdit *i1_edit;
   QLineEdit *i2_edit;
   QLineEdit *i3_edit;
   QLineEdit *i4_edit;
   QLineEdit *i5_edit;
   QLineEdit *s1_edit;
   QLineEdit *s2_edit;
   QLineEdit *s3_edit;
   QLineEdit *b1_edit;
   QLineEdit *b2_edit;
   QLineEdit *b3_edit;
   QLineEdit *b4_edit;
   QLineEdit *dir1_edit;
   QLineEdit *dir2_edit;
 };
 #endif

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