EI/VirtualLeaf Changeset - bb80657b6912 · Centrum Wiskunde & Informatica (CWI)

Changeset - bb80657b6912

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Michael Guravage - 15 years ago 2010-10-08 16:58:27
michael.guravage@cwi.nl

Export Cell Data at interval specified in the leafML file or explicitly via the file menu.
Added new parameters to VirtualLeafpar.tmpl
Added GPL boilerplate to make_{parameter,pardialog}_source.pl files.
Added new parameters to auxin_growth.xml. See respective ChangeLog files for details.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed data/leaves/ChangeLog
changed data/leaves/auxin_growth.xml
changed src/ChangeLog
changed src/VirtualLeafpar.tmpl
changed src/canvas.cpp
changed src/canvas.h
changed src/parameter.cpp
changed src/parameter.h
changed src/pardialog.cpp
changed src/pardialog.h
changed src/perl/ChangeLog
changed src/perl/make_parameter_source.pl
changed src/perl/make_pardialog_source.pl

8 files changed:

data/leaves/ChangeLog

data/leaves/auxin_growth.xml

src/ChangeLog

src/VirtualLeafpar.tmpl

src/canvas.cpp

src/canvas.h

src/parameter.cpp

1336

1299

src/parameter.h

Changeset was too big and was cut off... Show full diff anyway

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data/leaves/ChangeLog

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 -10-08    <guravage@caterpie.sen.cwi.nl>
 	* auxin_growth.xml: Added export_interval and export_fn_prefix parameters.
 -06-23    <guravage@caterpie.sen.cwi.nl>
 	* Added: tutorial3_init.xml
 	tutorial4_init.xml
 	tutorial5_init.xml
 	* Removed: bend.xml
 	circ.xml
 	explant.xml
 	init.xml
 	one_acc_point_van3.xml
 	one_acc_point_van3_growth.xml
 	one_acc_point_van3_growth2.xml
 	tissue.xml

data/leaves/auxin_growth.xml

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 <?xml version="1.0" encoding="UTF-8"?>
 <!--
   $Rev$:  Revision of last commit
   $Author$:  Author of last commit
   $Source$:  Source file
   $Date$:  Date of last commit
   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.
 -->
 <leaf name="/Users/roel/VLeafClean_plugin/Snapshot/VLeafMacOSX/auxin_growth.xml" date="Sat Aug 29 18:28:19 2009" simtime="11660">
   <parameter>
     <par name="export_interval" val="1000"/>
     <par name="export_fn_prefix" val="CELLDATA_"/>
     <par name="arrowcolor" val="white"/>
     <par name="arrowsize" val="10"/>
     <par name="textcolor" val="red"/>
     <par name="cellnumsize" val="1"/>
     <par name="nodenumsize" val="1"/>
     <par name="node_mag" val="1"/>
     <par name="outlinewidth" val="1"/>
     <par name="cell_outline_color" val="forestgreen"/>
     <par name="resize_stride" val="10"/>
     <par name="T" val="1"/>
     <par name="lambda_length" val="100"/>
     <par name="lambda_celllength" val="0"/>
     <par name="target_length" val="60"/>
     <par name="cell_expansion_rate" val="10"/>
     <par name="cell_div_expansion_rate" val="10"/>
     <par name="auxin_dependent_growth" val="true"/>
     <par name="ode_accuracy" val="0.0001"/>
     <par name="mc_stepsize" val="0.4"/>
     <par name="mc_cell_stepsize" val="0.2"/>
     <par name="energy_threshold" val="1000"/>
     <par name="bend_lambda" val="0"/>
     <par name="alignment_lambda" val="0"/>
     <par name="rel_cell_div_threshold" val="2"/>
     <par name="rel_perimeter_stiffness" val="2"/>
     <par name="collapse_node_threshold" val="0.05"/>
     <par name="morphogen_div_threshold" val="0.2"/>
     <par name="morphogen_expansion_threshold" val="0.01"/>
     <par name="copy_wall" val="true"/>
     <par name="source" val="0"/>
     <par name="D">
       <valarray>
         <val v="1e-06"/>
         <val v="0"/>
         <val v="0"/>
         <val v="0"/>
       </valarray>
     </par>
     <par name="initval">
       <valarray>
         <val v="0"/>
         <val v="1"/>
         <val v="0"/>
         <val v="0"/>
       </valarray>
     </par>
     <par name="k1" val="1"/>
     <par name="k2" val="0.3"/>
     <par name="r" val="1"/>
     <par name="kr" val="1"/>
     <par name="km" val="1"/>
     <par name="Pi_tot" val="1"/>
     <par name="transport" val="0.36"/>
     <par name="ka" val="1"/>
     <par name="pin_prod" val="0"/>
     <par name="pin_prod_in_epidermis" val="0"/>
     <par name="pin_breakdown" val="0"/>
     <par name="pin_breakdown_internal" val="0.001"/>
     <par name="aux1prod" val="0.001"/>
     <par name="aux1prodmeso" val="0"/>
     <par name="aux1decay" val="0.001"/>
     <par name="aux1decaymeso" val="0.1"/>
     <par name="aux1transport" val="0.036"/>
     <par name="aux_cons" val="0"/>
     <par name="aux_breakdown" val="0.0001"/>
     <par name="kaux1" val="1"/>
     <par name="kap" val="1"/>
     <par name="leaf_tip_source" val="0.0001"/>
     <par name="sam_efflux" val="0.0001"/>
     <par name="sam_auxin" val="10"/>
     <par name="sam_auxin_breakdown" val="0"/>
     <par name="dt" val="0.1"/>
     <par name="rd_dt" val="10"/>
     <par name="datadir" val="auxin_growth"/>
     <par name="movie" val="true"/>
     <par name="nit" val="100000"/>
     <par name="maxt" val="1e+06"/>
     <par name="storage_stride" val="10"/>
     <par name="xml_storage_stride" val="500"/>
     <par name="rseed" val="-1"/>
     <par name="constituous_expansion_limit" val="16"/>
     <par name="vessel_inh_level" val="1"/>
     <par name="vessel_expansion_rate" val="0.25"/>
     <par name="d" val="0"/>
     <par name="e" val="0"/>
     <par name="f" val="0"/>
     <par name="c" val="0"/>
     <par name="mu" val="0"/>
     <par name="nu" val="0"/>
     <par name="rho0" val="0"/>
     <par name="rho1" val="0"/>
     <par name="c0" val="0"/>
     <par name="gamma" val="0"/>
     <par name="eps" val="0"/>
   </parameter>
   <code name="VirtualLeaf.cpp">#include &lt;fstream&gt;
 #include &lt;sstream&gt;
 #include &lt;cstring&gt;
 #include &lt;functional&gt;
 #include &lt;getopt.h&gt;
 #include &lt;cerrno&gt;
 #include "mesh.h"
 #include "parameter.h"
 #include "random.h"
 #include "pi.h"
 #include "cellitem.h"
 #include "canvas.h"
 #include "cell.h"
 #include "output.h"
 #include &lt;qwidget.h&gt;
 #include &lt;q3process.h&gt;
 #include &lt;qapplication.h&gt;
 #include &lt;QDesktopWidget&gt;
 #include &lt;QGraphicsScene&gt;
 #include &lt;QMessageBox&gt;
 //Added by qt3to4:
 #include &lt;QMouseEvent&gt;
 #include &lt;unistd.h&gt;
 #include &lt;q3textstream.h&gt;
 #ifdef HAVE_QWT
 #include "data_plot.h"
 #endif
 #include &lt;QPalette&gt;
 #include &lt;QBrush&gt;
 #include &lt;QToolTip&gt;
 #include "simplugin.h"
 #include "testplugin.h"
 /* #define _xstr_(s) _str_(s)
 #define _str_(s) #s
 #include _xstr_(REACTIONS_HEADER)
 */
 extern Parameter par;
 MainBase *main_window = 0;
 double auxin_account = 0.;
 TestPlugin *plugin = new TestPlugin();
 #ifdef XFIGGRAPHICS
 #define TIMESTEP double Graphics::TimeStep(void)
 #endif
 class PrintNode {
 public:
   void operator() (const Node &amp;n) const
+  {
     cerr &lt;&lt; n.Index() &lt;&lt; ": " &lt;&lt; n &lt;&lt;  endl;
+  }
 };
 class EdgeSource {
 public:
   void operator() (Cell &amp;c) {
     if (c.AtBoundaryP()) {
       cerr &lt;&lt; "Cell " &lt;&lt; c.Index() &lt;&lt; " is a source cell.\n";
       c.SetSource(0,par.source);
     } else {
       cerr &lt;&lt; "Cell " &lt;&lt; c.Index() &lt;&lt; " is _not_ a source cell.\n";
+    }
+  }
 };
 class CellInfo {
 public:
   void operator() (Cell &amp;c,std::ostream &amp;os) const {
     os &lt;&lt; "Cell " &lt;&lt; c.index &lt;&lt; " says: " &lt;&lt; endl;
     os &lt;&lt; "c.nodes.size() = " &lt;&lt; c.nodes.size() &lt;&lt; endl;
     for (list&lt;Node *&gt;::iterator i=c.nodes.begin();
 	 i!=c.nodes.end();
 	 i++) {
       cerr &lt;&lt; (*i)-&gt;Index() &lt;&lt; " ";
+    }
     cerr &lt;&lt; endl;
+  }
 };
 double PINSum(Cell &amp;c) {
 	return c.Chemical(1) + c.SumTransporters(1);// + c.ReduceCellAndWalls&lt;double&gt;( complex_PijAj );
+}
 class DrawCell {
 public:
   void operator() (Cell &amp;c,QGraphicsScene &amp;canvas, MainBase &amp;m) const {
     if (m.ShowBorderCellsP() || c.Boundary()==Cell::None) {
       if (!m.ShowBoundaryOnlyP() &amp;&amp; !m.HideCellsP())
 	if (m.ShowToolTipsP()) {
 	  QString info_string=QString("Cell %1, chemicals: ( %2, %3, %4, %5, %6)\n %7 of PIN1 at walls.\n Area is %8\n PIN sum is %9\n Circumference is %10\n Boundary type is %11").arg(c.Index()).arg(c.Chemical(0)).arg(c.Chemical(1)).arg(c.Chemical(2)).arg(c.Chemical(3)).arg(c.Chemical(4)).arg(c.SumTransporters(1)).arg(c.Area()).arg(PINSum(c)).arg(c.Circumference()).arg(c.BoundaryStr());
 	  info_string += "\n" + c.printednodelist();
 	  c.Draw(&amp;canvas, info_string);
 	} else {
 	  c.Draw(&amp;canvas);
+	}
       if (m.ShowCentersP())
 	c.DrawCenter(&amp;canvas);
     if (m.ShowFluxesP())
 	c.DrawFluxes(&amp;canvas, par.arrowsize);
+       }
+  }
 };
 Mesh mesh;
 bool batch=false;
 void MainBase::Plot(int resize_stride) {
   clear();
   static int count=0;
   if (resize_stride) {
     if ( !((++count)%resize_stride) ) {
       FitLeafToCanvas();
+    }
+  }
   mesh.LoopCells(DrawCell(),canvas,*this);
   if (ShowNodeNumbersP())
     mesh.LoopNodes( bind2nd (mem_fun_ref ( &amp;Node::DrawIndex), &amp;canvas ) ) ;
   if (ShowCellNumbersP())
     mesh.LoopCells( bind2nd (mem_fun_ref ( &amp;Cell::DrawIndex), &amp;canvas ) ) ;
   if (ShowCellAxesP())
     mesh.LoopCells( bind2nd (mem_fun_ref ( &amp;Cell::DrawAxis), &amp;canvas ) );
   if (ShowCellStrainP())
     mesh.LoopCells( bind2nd (mem_fun_ref ( &amp;Cell::DrawStrain), &amp;canvas ) );
   if (ShowWallsP())
     mesh.LoopWalls( bind2nd( mem_fun_ref( &amp;Wall::Draw ), &amp;canvas ) );
 	if (ShowApoplastsP())
 		mesh.LoopWalls( bind2nd( mem_fun_ref( &amp;Wall::DrawApoplast ), &amp;canvas ) );
 	if (ShowMeshP())
     mesh.DrawNodes(&amp;canvas);
   if (ShowBoundaryOnlyP())
     mesh.DrawBoundary(&amp;canvas);
 	if ( ( batch || MovieFramesP() )) {
 		static int frame = 0;
 		// frame numbers are sequential for the most frequently written file type.
 		// for the less frequently written file type they match the other type
 		if (!(count%par.storage_stride) )  {
 			stringstream fname;
 			fname &lt;&lt; par.datadir &lt;&lt; "/leaf.";
 			fname.fill('0');
 			fname.width(6);
 			/*
 			 fname &lt;&lt; frame &lt;&lt; ".pdf";
 			if (par.storage_stride &lt;= par.xml_storage_stride) {
 				frame++;
+			}
 			// Write high-res JPG snapshot every plot step
 			Save(fname.str().c_str(), "PDF");
 			*/
 			fname &lt;&lt; frame &lt;&lt; ".jpg";
 			if (par.storage_stride &lt;= par.xml_storage_stride) {
 				frame++;
+			}
 			// Write high-res JPG snapshot every plot step
 			Save(fname.str().c_str(), "JPEG",1024,768);
+		}
 		if (!(count%par.xml_storage_stride)) {
 			stringstream fname;
 			fname &lt;&lt; par.datadir &lt;&lt; "/leaf.";
 			fname.fill('0');
 			fname.width(6);
 			fname &lt;&lt; frame &lt;&lt; ".xml";
 			if (par.xml_storage_stride &lt; par.storage_stride) {
 				frame++;
+			}
 			// Write XML file every ten plot steps
 			mesh.XMLSave(fname.str().c_str(), XMLSettingsTree());
+		}
+	}
+}
 void Cell::Flux(double *flux, double *D)  {
   // loop over cell edges
   for (int c=0;c&lt;Cell::nchem;c++) flux[c]=0.;
   for (list&lt;Wall *&gt;::iterator i=walls.begin();
        i!=walls.end();
        i++) {
     // leaf cannot take up chemicals from environment ("no flux boundary")
     if ((*i)-&gt;c2-&gt;BoundaryPolP()) continue;
     // flux depends on edge length and concentration difference
     for (int c=0;c&lt;Cell::nchem;c++) {
       double phi = (*i)-&gt;length * ( D[c] ) * ( (*i)-&gt;c2-&gt;chem[c] - chem[c] );
       if ((*i)-&gt;c1!=this) {
 	cerr &lt;&lt; "Warning, bad cells boundary: " &lt;&lt; (*i)-&gt;c1-&gt;index &lt;&lt; ", " &lt;&lt; index &lt;&lt; endl;
+      }
       flux[c] += phi;
+    }
+  }
+}
 INIT {
 	if (leaffile) {
     xmlNode *settings;
     mesh.XMLRead(leaffile, &amp;settings);
     main_window-&gt;XMLReadSettings(settings);
     xmlFree(settings);
     main_window-&gt;UserMessage(QString("Ready. Time is %1").arg(mesh.getTimeHours().c_str()));
   } else {
 	  Cell &amp;circle=mesh.CircularCell(0,0,10,10);
     circle.SetTargetArea(circle.CalcArea());
 	  mesh.SetBaseArea();
 	// clean up chemicals
 	  for (int c=0; c&lt;Cell::NChem(); c++) {
 		  circle.SetChemical(c, 0.);
+      }
+  }
+}
 TIMESTEP {
   static int i=0;
   static int t=0;
   static int ncells;
   if (!batch) {
     UserMessage(QString("Time: %1").arg(mesh.getTimeHours().c_str()),0);
+  }
   ncells=mesh.NCells();
   double dh;
   if(DynamicCellsP()) {
     dh = mesh.DisplaceNodes();
     // Only allow for node insertion, cell division and cell growth
     // if the system has equillibrized
     // i.e. cell wall tension equillibrization is much faster
     // than biological processes, including division, cell wall yielding
     // and cell expansion
     mesh.InsertNodes(); // (this amounts to cell wall yielding)
     if ( (-dh) &lt; par.energy_threshold) {
       mesh.IncreaseCellCapacityIfNecessary();
 		mesh.LoopCurrentCells(&amp;TestPlugin::CellHouseKeeping); // this includes cell division
       // Reaction diffusion
 		/*CelltoCellTransport *transport_f = &amp;TestPlugin::CelltoCellTransport;
       CellReaction *cellreaction_f = new plugin-&gt;CellDynamics();
       WallReaction *wall_f = new WallDynamics();*/
       mesh.ReactDiffuse(plugin, par.rd_dt);
       t++;
       Plot(par.resize_stride);
 		/*QVector&lt; QPair&lt;double, int&gt; &gt; angles=mesh.VertexAnglesValues();
 		QString afname=QString("Angles/anglesvalues%1.dat").arg(t,6,10,QChar('0'));
 		ofstream af(afname.toStdString().c_str());
 		*/
 		/*for (QVector&lt; QPair&lt;qreal, int&gt; &gt;::const_iterator v=angles.begin();
 			 v!=angles.end();
 			 v++) {
 			af &lt;&lt; v-&gt;first &lt;&lt; " " &lt;&lt; v-&gt;second &lt;&lt; endl;
+			}
 			*/
+			}
 			} else {
   /*  TransportFunction *transport_f = new CelltoCellTransport();
     CellReaction *cellreaction_f = new CellDynamics();
     WallReaction *wall_f = new WallDynamics();
     mesh.ReactDiffuse_New(transport_f, cellreaction_f, wall_f, par.rd_dt);*/
 				mesh.ReactDiffuse(plugin, par.rd_dt);
     Plot(par.resize_stride);
+  }
   i++;
   return mesh.getTime();
+}
 /* Called if a cell is clicked */
 void Cell::OnClick(QMouseEvent *e) {
+}
 void Wall::OnWallInsert(void) {
+}
 int main(int argc,char **argv) {
   try {
     int c;
     char *leaffile=0;
     while (1) {
       //int this_option_optind = optind ? optind : 1;
       int option_index = 0;
       static struct option long_options[] = {
 	{"batch", 0, 0, 0},
 	{"leaffile", 2, 0, 0}
       };
       // short option 'p' creates trouble for non-commandline usage on MacOSX. Option -p changed to -P (capital)
       static char *short_options = "bl";
       c = getopt_long (argc, argv, "bl:",
 		       long_options, &amp;option_index);
       if (c == -1)
 	break;
       if (c==0) {
 	printf ("option %s", long_options[option_index].name);
 	if (optarg)
 	  printf (" with arg %s", optarg);
 	printf ("\n");
 	c = short_options[option_index];
+      }
       switch (c) {
       case 'b':
 	cerr &lt;&lt; "Running in batch mode\n";
 	batch=true;
 	break;
       case 'l':
 	leaffile=strdup(optarg);
 	if (!leaffile) {
 	  throw("Out of memory");
+	}
 	printf("Reading leaf state file '%s'\n", leaffile);
 	break;
       case '?':
 	break;
       default:
 	printf ("?? getopt returned character code 0%o ??\n", c);
+      }
+    }
     if (optind &lt; argc) {
       printf ("non-option ARGV-elements: ");
       while (optind &lt; argc)
 	printf ("%s ", argv[optind++]);
       printf ("\n");
+    }
 	  MakeDir("Angles");
     bool useGUI = !batch;
     QApplication app(argc,argv,useGUI);
     QPalette tooltippalette = QToolTip::palette();
     QColor transparentcolor = QColor(tooltippalette.brush(QPalette::Window).color());
     tooltippalette.setBrush (QPalette::Window, QBrush (transparentcolor) );
     QToolTip::setPalette( tooltippalette );
     QGraphicsScene canvas(0,0,8000,6000);
     if (useGUI) {
          main_window=new Main(canvas, mesh);
       if ( QApplication::desktop()-&gt;width() &gt; ((Main *)main_window)-&gt;width() + 10
 	   &amp;&amp; QApplication::desktop()-&gt;height() &gt; ((Main *)main_window)-&gt;height() +30 ) {
 	((Main *)main_window)-&gt;show();
 	((Main *)main_window)-&gt;resize( ((Main *)main_window)-&gt;sizeHint());
     } else {
         ((Main *)main_window)-&gt;showMaximized();
+    }
   } else {
         main_window=new MainBase(canvas, mesh);
+ }
     canvas.setSceneRect(QRectF());
     if (!batch) {
       QObject::connect( qApp, SIGNAL(lastWindowClosed()), qApp, SLOT(quit()) );
+    }
     main_window-&gt;Init(leaffile);
     Cell::SetMagnification(10);
     Cell::setOffset(0,0);
     main_window-&gt;FitLeafToCanvas();
     main_window-&gt;Plot();
     if (batch) {
       double t=0.;
       do {
 	t = main_window-&gt;TimeStep();
       } while (t &lt; par.maxt);
     } else
       return app.exec();
   } catch (const char *message) {
     if (batch) {
       cerr &lt;&lt; "Exception caught:" &lt;&lt; endl;
       cerr &lt;&lt; message &lt;&lt; endl;
       abort();
     } else {
       QString qmess=QString("Exception caught: %1").arg(message);
       QMessageBox::critical(0, "Critical Error", qmess);
       abort();
+    }
   } catch (ios_base::failure) {
     stringstream error_message;
     error_message &lt;&lt; "I/O failure: " &lt;&lt; strerror(errno);
     if (batch) {
       cerr &lt;&lt; error_message.str() &lt;&lt;endl;
       abort();
     } else {
       QString qmess(error_message.str().c_str());
       QMessageBox::critical(0, "I/O Error", qmess );
       abort();
+    }
+  }
+}
 </code>
   <code name="reactions_pce_growth.h">
 // Executed after the cellular mechanics steps have equillibrized
 class CellHouseKeeping {
 public:
 	void operator() (Cell &amp;c) const {
 		c.EnlargeTargetArea(par.cell_expansion_rate);
 		if (c.Area() &gt; par.rel_cell_div_threshold * c.BaseArea() ) {
 			c.Divide();
+		}
+	}
 };
 // The number of chemical species in the cels
 const int Cell::nchem = 0;
 // Differential equations describing transport of chemicals from cell to cell
 class CelltoCellTransport : public TransportFunction {
  public:
 	virtual void operator()(Wall *w, double *dchem_c1, double *dchem_c2) {}
  };
 // Differential equations describing chemical reactions taking place at or near the cell walls
 // (e.g. PIN accumulation)
 class WallDynamics : public WallReaction {
  public:
 	virtual void operator()(Wall *w, double *dw1, double *dw2) {};
 };
 // Differential equations describing chemical reactions inside the cells
 class CellDynamics : public CellReaction {
  public:
 	virtual void operator()(Cell *c, double *dchem) {
 	};
 };
 // Rules for cell coloring
 void Cell::SetColor(QColor &amp;color) { }
 // To be executed after cell division
 void Cell::OnDivide(ParentInfo &amp;parent_info, Cell &amp;daughter) {}
 </code>
   <nodes n="22" target_length="3.09017">
     <node x="22.9634" y="-2.37264" fixed="false" boundary="true" sam="false"/>
     <node x="14.6882" y="17.9118" fixed="false" boundary="true" sam="false"/>
     <node x="1.57936" y="25.1246" fixed="false" boundary="true" sam="false"/>
     <node x="-9.0893" y="22.8165" fixed="false" boundary="true" sam="false"/>
     <node x="-19.7055" y="16.962" fixed="false" boundary="true" sam="false"/>
     <node x="-22.6839" y="5.00143" fixed="false" boundary="true" sam="false"/>
     <node x="-14.7271" y="-15.2131" fixed="false" boundary="true" sam="false"/>
     <node x="-6.78413" y="-23.4002" fixed="false" boundary="true" sam="false"/>
     <node x="3.60766" y="-25.1355" fixed="false" boundary="true" sam="false"/>
     <node x="21.3032" y="-13.6899" fixed="false" boundary="true" sam="false"/>
     <node x="17.4704" y="7.41573" fixed="false" boundary="true" sam="false"/>
     <node x="-17.5799" y="-5.20265" fixed="false" boundary="true" sam="false"/>
     <node x="9.86837" y="4.69636" fixed="false" boundary="false" sam="false"/>
     <node x="-9.28449" y="-3.92969" fixed="false" boundary="false" sam="false"/>
     <node x="12.5597" y="-20.5161" fixed="false" boundary="true" sam="false"/>
     <node x="-1.62187" y="-3.10623" fixed="false" boundary="false" sam="false"/>
     <node x="7.55765" y="-14.4922" fixed="false" boundary="false" sam="false"/>
     <node x="2.97596" y="-8.80653" fixed="false" boundary="false" sam="false"/>
     <node x="1.95125" y="3.2756" fixed="false" boundary="false" sam="false"/>
     <node x="-6.54614" y="15.4702" fixed="false" boundary="false" sam="false"/>
     <node x="-2.72983" y="8.96705" fixed="false" boundary="false" sam="false"/>
     <node x="9.33552" y="23.0046" fixed="false" boundary="true" sam="false"/>
   </nodes>
   <cells n="4" offsetx="0" offsety="0" magnification="10" base_area="293.893" nchem="2">
     <cell index="0" area="405.845" target_area="548.609" target_length="60" lambda_celllength="0" stiffness="0" fixed="false" pin_fixed="false" at_boundary="true" dead="false" source="false" boundary="None" div_counter="2" cell_type="0">
       <node n="13"/>
       <node n="11"/>
       <node n="6"/>
       <node n="7"/>
       <node n="8"/>
       <node n="14"/>
       <node n="16"/>
       <node n="17"/>
       <node n="15"/>
       <wall w="6"/>
       <wall w="0"/>
       <wall w="1"/>
       <chem n="2">
         <val v="0.251808"/>
         <val v="0.481961"/>
       </chem>
     </cell>
     <cell index="1" area="385.557" target_area="547.081" target_length="60" lambda_celllength="0" stiffness="0" fixed="false" pin_fixed="false" at_boundary="true" dead="false" source="false" boundary="None" div_counter="2" cell_type="0">
       <node n="12"/>
       <node n="10"/>
       <node n="1"/>
       <node n="21"/>
       <node n="2"/>
       <node n="3"/>
       <node n="19"/>
       <node n="20"/>
       <node n="18"/>
       <wall w="3"/>
       <wall w="4"/>
       <wall w="5"/>
       <chem n="2">
         <val v="0.250735"/>
         <val v="0.481961"/>
       </chem>
     </cell>
     <cell index="2" area="422.94" target_area="565.987" target_length="60" lambda_celllength="0" stiffness="0" fixed="false" pin_fixed="false" at_boundary="true" dead="false" source="false" boundary="None" div_counter="2" cell_type="0">
       <node n="9"/>
       <node n="0"/>
       <node n="10"/>
       <node n="12"/>
       <node n="18"/>
       <node n="15"/>
       <node n="17"/>
       <node n="16"/>
       <node n="14"/>
       <wall w="1"/>
       <wall w="2"/>
       <wall w="8"/>
       <wall w="4"/>
       <chem n="2">
         <val v="0.307348"/>
         <val v="0.481245"/>
       </chem>
     </cell>
     <cell index="3" area="432.871" target_area="573.317" target_length="60" lambda_celllength="0" stiffness="0" fixed="false" pin_fixed="false" at_boundary="true" dead="false" source="false" boundary="None" div_counter="2" cell_type="0">
       <node n="4"/>
       <node n="5"/>
       <node n="11"/>
       <node n="13"/>
       <node n="15"/>
       <node n="18"/>
       <node n="20"/>
       <node n="19"/>
       <node n="3"/>
       <wall w="5"/>
       <wall w="6"/>
       <wall w="7"/>
       <wall w="8"/>
       <chem n="2">
         <val v="0.321108"/>
         <val v="0.481222"/>
       </chem>
     </cell>
     <boundary_polygon index="-1" area="1647.21" target_area="1" target_length="60" lambda_celllength="0" stiffness="0" fixed="false" pin_fixed="false" at_boundary="false" dead="false" source="false" boundary="None" div_counter="0" cell_type="0">
       <node n="0"/>
       <node n="10"/>
       <node n="1"/>
       <node n="21"/>
       <node n="2"/>
       <node n="3"/>
       <node n="4"/>

src/ChangeLog

➞

Show inline comments

 -10-08    <guravage@caterpie.sen.cwi.nl>
 	* pardialog.h:
 	* pardialog.cpp:
 	* parameter.h:
 	* parameter.cpp: Regenerated to include export_interval and export_fn_prefix.
 	* VirtualLeafpar.tmpl: Appended export_interval and export_fn_prefix.
 	* canvas.h (MainBase): Declared polymorphic exportCellData() functions.
 	* canvas.cpp:
 	(TimeStamp): New private TimeStamp() function.
 	(TimeStepWrap): Added invocation of exportCellData().
 	(exportCellData): Created two polymorphic functions: one with a
 	single QString argument, the other with no argument. The former is
 	called from TimeStepWrap() while the latter is called from the
 	"Export cell areas" item in the file menu.
 -10-07    <guravage@caterpie.sen.cwi.nl>
 	* canvas.cpp (exportCellData): Added a Q3FileDialog to inquire
 	where to write the exportCellData.
 -06-28    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf-install.nsi: Grab gpl3.txt from doc directory.
 	* canvas.cpp (gpl): gpl3.txt can be either in an ancestor doc
 	directory (Linux) or a decedent doc directory (Windows, via the
 	binary installer).
 	* VirtualLeaf-install.nsi: Add VirtualLeaf doc directory.
 -06-25    <guravage@caterpie.sen.cwi.nl>
 	* gpl3.txt: Moved gpl3.txt from doc to src directory.
 	* VirtualLeaf.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.
 	* libplugin.pro: Ditto.
 	* parameter.cpp: Result of adding datadir changes to make_parameter_source.pl.
 	* parameter.h: Ditto.
 	* output.h: Declared new function (AppendHomeDirIfPathRelative).
 	* output.cpp (AppendHomeDirIfPathRelative): Added new function.
 	* canvas.cpp (gpl): Moving gpl3.txt from doc to src obviates the need to docDir.cd("../doc").
 	* VirtualLeaf-install.nsi: Grab gpl3.txt from src directory.
 	Add missing libiconv/bin, libxml2bin and libz/bin directories.
 	Copy libiconv-2.dll, libxml2.dll and zlib1.dll from relative paths.
 	* VirtualLeaf.pro: copy gpl3.txt as part of QMAKE_POST_LINK.
 -06-24    <guravage@caterpie.sen.cwi.nl>
 	* libplugin.pro: Use correct library path.
 	* VirtualLeaf.pro: Ditto.
 	* VirtualLeaf.cpp (DrawCell): Iterate over NChem to construct info_string.
 -06-23    <guravage@caterpie.sen.cwi.nl>
 	* simitembase.cpp: Removed NULL assignments to unused variables.
 	* VirtualLeaf.cpp: Ditto.
 	* apoplastitem.cpp: Ditto.
 	* canvas.cpp: Ditto.
 	* cell.cpp: Ditto.
 	* cellbase.h: Ditto.
 	* forwardeuler.cpp: Ditto.
 	* mainbase.h: Ditto.
 	* nodeitem.cpp: Ditto.
 	* qcanvasarrow.h: Ditto.
 	* simitembase.cpp: Ditto.
 	* Makefile (clean): Add -f Makefile argument to each make invocation.
 	* VirtualLeaf-install.nsi: New gpl license text.
 	* VirtualLeaf.pro: Disabled console mode.
 	* mesh.cpp (Clear): Added parentheses to qDebug statments.
 	(TestIllegalWalls): Replaced qDebug().
 	* canvas.cpp (mouseReleaseEvent): Replaced qDebug() with cerr since qDebug complains about *node_set.
 	* wall.cpp (CorrectWall): Rplaced gDebug() with cerr in transform call and when printing *this.
 -06-22    <guravage@caterpie.sen.cwi.nl>
 	* Makefile (tutorials): Add tutorials target.
 -06-21    <guravage@caterpie.sen.cwi.nl>
 	* parameter.cpp: Added particular reassignment of datadir.
 	* canvas.cpp (gpl): Added GPL3 License text. Display detail text only if the source text file exists.
 -06-18    <guravage@caterpie.sen.cwi.nl>
 	* canvas.cpp (gpl): Added gpl slot to display GPL license.
 	* VirtualLeaf.pro: Changed default LIBXML2DIR, LIBICONVDIR and LIBZDIR to corresponding distribution lib directories.
 	* libplugin.pro: Ditto.
 	* Makefile (clean): add if stmt not to `touch` on windows.
 -06-17    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Removed perl references.
 	* libplugin.pro: Ditto.
 -06-15    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Removed xmlwritecode.cpp from SOURCES list.
 	* xmlwrite.cpp (XMLSave): Removed references to XMLWriteLeafSourceCode and XMLWriteReactionsCode.
 	* xmlwrite.h (XMLIO): Ditto!
 	* mesh.cpp (findNextBoundaryNode): Initialize Node *next_boundary_node = NULL;
 	* xmlwrite.cpp (XMLReadSimtime): Removed unused variable cur
 	(XMLReadWalls): viz_flux need not be declared twice; default value of 0.0.
 	(XMLReadCells): Removed unused count variable.
 	(XMLReadSimtime): Removed unused cur variable.
 	(XMLRead): Removed unused v_str variable.
 	* simitembase.cpp (userMove): Use assignment merely to obviate compilation warning.
 	(SimItemBase) Ditto.
 	* qcanvasarrow.h (QGraphicsLineItem): Use assignment merely to obviate compilation warning.
 	* output.cpp (OpenWriteFile): Removed unused par variable.
 	* nodeitem.cpp (paint): Use assignment merely to obviate compilation warning.
 	* forwardeuler.cpp (odeint): Use assignment merely to obviate compilation warning.
 	* cell.cpp (DivideOverGivenLine): Use assignment merely to obviate compilation warning.
 	* canvas.cpp (FigureEditor): Use assignments merely to obviate compilation errors.
 	(mousePressEvent): Removed unused item variable.
 	* apoplastitem.cpp
 	(ApoplastItem): Removed unused par variable.
 	(OnClick): Use NULL assignment merely to obviate compilation warning.
 	* mainbase.h (MainBase): Use assignment merely to obviate compilation warning.
 	* cellbase.h (CellsStaticDatamembers): Use assignment merely to obviate compilation warning.
 	* cell.cpp: Wrapped diagnostic output in QDEBUG blocks.
 	* VirtualLeaf.cpp ditto.
 	* canvas.cpp ditto.
 	* cell.cpp ditto.
 	* data_plot.cpp ditto.
 	* forwardeuler.cpp ditto.
 	* mesh.cpp ditto.
 	* mesh.h
 	* random.cpp ditto.
 	* wall.cpp ditto.
 	* wallbase.cpp ditto.
 	* wallitem.cpp ditto.
 -06-07    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Removed explicit perl invocation to regerenerate parameter files.
 	* libplugin.pro: ditto.
 -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/VirtualLeafpar.tmpl

➞

Show inline comments

 title = Parameter values for The Virtual Leaf / title
 label = <b>Visualization</b> / label
 arrowcolor = white / string
 arrowsize = 100 / double
 textcolor = red / string
 cellnumsize = 1 / int
 nodenumsize = 1 / int
 node_mag = 1.0 / double
 outlinewidth = 1.0 / double
 cell_outline_color = forestgreen / string
 resize_stride = 0 / int
 label = / label
 label = <b>Cell mechanics</b> / label
 T = 1.0 / double
 lambda_length = 100. / double
 lambda_celllength = 0. / double
 target_length = 60. / double
 cell_expansion_rate = 1. / double
 cell_div_expansion_rate = 0. / double
 auxin_dependent_growth = true / bool
 ode_accuracy = 1e-4 / double
 mc_stepsize = 0.4 / double
 mc_cell_stepsize = 0.2 / double
 energy_threshold = 1000. / double
 bend_lambda = 0. / double
 alignment_lambda = 0. / double
 rel_cell_div_threshold = 2. / double
 rel_perimeter_stiffness = 2 / double
 collapse_node_threshold = 0.05 / double
 morphogen_div_threshold = 0.2 / double
 morphogen_expansion_threshold = 0.01 / double
 copy_wall = true / bool
 label = / label
 label = <b>Auxin transport and PIN1 dynamics</b> / label
 source = 0. / double
 D = 0., 0.0, 0.0, 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0. / doublelist
 initval = 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0. / doublelist
 k1 = 1. / double
 k2 = 0.3 / double
 r = 1. / double
 kr = 1. / double
 #k3 = 1 / double
 #k4 = 0.3 / double
 km = 1. / double
 Pi_tot = 1. / double
 transport = 0.036 / double
 ka = 1 / double
 # d = 1e-06 / double
 # e = 0.01 / double
 # f = 10 / double
 pin_prod = 0.001 / double
 pin_prod_in_epidermis = 0.1 / double
 pin_breakdown = 0.001 / double
 pin_breakdown_internal = 0.001 / double
 aux1prod = 0.001 / double
 aux1prodmeso = 0. / double
 aux1decay = 0.001 / double
 aux1decaymeso = 0.1 / double
 aux1transport = 0.036 / double
 aux_cons = 0. / double
 aux_breakdown = 0. / double
 kaux1 = 1 / double
 kap = 1 / double
 leaf_tip_source = 0.001 / double
 sam_efflux = 0.0001 / double
 sam_auxin = 10. / double
 # gf_prod = 1e-3 / double
 # gf_decay = 1e-3 / double
 sam_auxin_breakdown = 0 / double
 #label = / label
 #label = <b>miscellaneous</b> / label
 van3prod = 0.002 / double
 van3autokat = 0.1 / double
 van3sat = 10 / double
 k2van3 = 0.3 / double
 #glvprod = 0.0 / double
 #glvbreakdown = 0. / double
 label = / label
 label = <b>Integration parameters</b> / label
 dt = 0.1 / double
 rd_dt = 1.0 / double
 datadir = . / directory
 movie = false / bool
 nit = 100000 / int
 maxt = 1000. / double
 storage_stride = 10 / int
 xml_storage_stride = 500 / int
 rseed = -1 / int
 #label = / label
 #label = <b>Parameters for new chemical</b> / label
 #glvproduction = 0. / double
 #glvdecay = 0. / double
 #glvdiffthreshold = 0. / double
 label = / label
 label = <b>Meinhardt leaf venation model</b> / label
 constituous_expansion_limit = 16 / int
 vessel_inh_level = 1 / double
 vessel_expansion_rate = 0.25 / double
 d = 0. / double
 e = 0. / double
 f = 0. / double
 c = 0. / double
 mu = 0. / double
 nu = 0. / double
 rho0 = 0. / double
 rho1 = 0. / double
 c0 = 0. / double
 gamma = 0. / double
 eps = 0. / double
 label = / label
 label = <b>User-defined parameters</b> / label
 k = 0., 0.0, 0.0, 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0. / doublelist
 i1 = 0 / int
 i2 = 0 / int
 i3 = 0 / int
 i4 = 0 / int
 i5 = 0 / int
 s1 =  / string
 s2 =  / string
 s3 =  / string
 b1 = false / bool
 b2 = false / bool
 b3 = false / bool
 b4 = false / bool
 dir1 = . / directory
 dir2 = . / directory
 export_interval = 0 / int
 export_fn_prefix = CellData_ / string

src/canvas.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  VirtualLeaf 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.
+ *
  *  VirtualLeaf 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 <time.h>
 #include <string>
 #include <fstream>
 #include <streambuf>
 #include <QGraphicsScene>
 #include <QGraphicsView>
 #include <qdatetime.h>
 #include <q3mainwindow.h>
 #include <qstatusbar.h>
 #include <qmessagebox.h>
 #include <qmenubar.h>
 #include <qapplication.h>
 #include <qpainter.h>
 #include <qprinter.h>
 #include <qlabel.h>
 #include <qimage.h>
 #include <q3progressdialog.h>
 #include <qtimer.h>
 #include <qslider.h>
 #include <qpixmap.h>
 #include <qfile.h>
 #include <qdir.h>
 #include <q3filedialog.h>
 #include <QGraphicsItem>
 #include <QList>
 #include <QDir>
 #include <QDebug>
 #include <set>
 //Added by qt3to4:
 #include <Q3ValueList>
 #include <Q3PopupMenu>
 #include <QMouseEvent>
 #include <typeinfo>
 #include <cstring>
 #include <q3process.h>
 #include <qlayout.h>
 #include <qspinbox.h>
 #include <fstream>
 #include <sstream>
 #include "pardialog.h"
 #include "parameter.h"
 #include "canvas.h"
 #include "node.h"
 #include "nodeset.h"
 #include "nodeitem.h"
 #include "cellitem.h"
 #include "wallitem.h"
 #include "mesh.h"
 #include "xmlwrite.h"
 #include "miscq.h"
 #include "OptionFileDialog.h"
 #include <cstdlib>
 #include <cstdio>
 #include "modelcatalogue.h"
 #include <algorithm>
 // Include VIB and PSB logos
 #include "psb.xpm"
 #include "cwi.xpm"
 static const std::string _module_id("$Id$");
 using namespace std;
 // We use a global variable to save memory - all the brushes and pens in
 // the mesh are shared.
 #define QUOTE_ME(s) QUOTE_ME_2NDLEV(s)
 #define QUOTE_ME_2NDLEV(s) #s
 static QColor dark_red("darkRed");
 static const int imageRTTI = 984376;
 extern Parameter par;
 const QString Main::caption("Virtual leaf");
 const QString Main::caption_with_file("Virtual leaf: %1");
 FigureEditor::FigureEditor(
 			   QGraphicsScene& c, Mesh &m, QWidget* parent,
 			   const char* name, Qt::WindowFlags f) :
   QGraphicsView(&c,parent), mesh(m)
+{
   intersection_line = 0;
   //angle_line = 0;
   setInteractive(true);
   moving = 0;
   rotation_mode = false;
+}
 void FigureEditor::clear()
+{
   QList<QGraphicsItem *> list = scene()->items();
   QList<QGraphicsItem *>::Iterator it = list.begin();
   for (; it != list.end(); ++it) {
     delete *it;
+  }
+}
 void FigureEditor::wheelEvent(QWheelEvent *event)
+{
   scaleView(pow((double)2, -event->delta() / 240.0));
+}
 void FigureEditor::scaleView (qreal scaleFactor)
+{
   qreal factor = matrix().scale(scaleFactor, scaleFactor).mapRect(QRectF(0, 0, 1, 1)). width();
   if (factor < 0.07 || factor > 100) return;
   scale (scaleFactor, scaleFactor);
+}
 void FigureEditor::Save(const char *fname, const char *format, int sizex, int sizey)
+{
   QImage *image = new QImage(sizex, sizey, QImage::Format_RGB32);
   image->fill(QColor(Qt::white).rgb());
   QPainter *painter=new QPainter(image);
   render(painter);
   image->save(QString(fname),format);
   delete painter;
   delete image;
+}
 void FigureEditor::mousePressEvent(QMouseEvent* e)
+{
   static QList<Node*> selected;
   emit MousePressed();
   //QPointF p = matrix().inverted().map(e->pos());
   QPointF p = mapToScene(e->pos());
 #ifdef QDEBUG
   qDebug() << endl << "MousePressEvent location: (" << p.x() << "," << p.y() << ")." << endl;
   qDebug() << "Magnification:  " << Cell::Magnification() << endl;
   qDebug() << "Offsets:  " << Cell::Offset() << endl;
 #endif
   QList<QGraphicsItem *> l=scene()->items(p);
 #ifdef QDEBUG
   qDebug() << "MousePressEvents, items: " << l.size() << endl;
   qDebug() << "Mouse button modifier: " << e->modifiers() << endl;
 #endif
   if (e->button()==Qt::RightButton || l.size()==0) {
     //cerr << "Drawing an intersection line from " << p.x() << ", " << p.y() << endl;
     intersection_line = new QGraphicsLineItem( 0, scene() );
     intersection_line->setPen( QPen( QColor("red"), 3, Qt::DashLine ) );
     intersection_line->setLine( QLineF(p,p) );
     intersection_line->setZValue( 100 );
     intersection_line->show();
+  }
   for (QList<QGraphicsItem *>::Iterator it=l.begin(); it!=l.end(); ++it) {
 #ifdef QDEBUG
     qDebug() << typeid(**it).name() << endl;
 #endif
     if ( !strcmp(typeid(**it).name(),"8NodeItem")) {
       stringstream data_strstream;
       data_strstream << (dynamic_cast<NodeItem*>(*it))->getNode();
       dynamic_cast<Main *>(parent())->UserMessage(QString(data_strstream.str().c_str()));
       (dynamic_cast<NodeItem*>(*it))->OnClick(e->button());
+    }
     else
       if ( !strcmp(typeid(**it).name(),"8CellItem") ) {
 	Cell &c=((dynamic_cast<CellItem *>(*it))->getCell());
 	// OnClick to be defined in end-user code
 	c.OnClick(e);
       } else {
 	if ( !strcmp(typeid(**it).name(),"8WallItem") ) {
 	  (dynamic_cast<WallItem *>(*it))->OnClick(e);
+	}
+      }
+  }
   FullRedraw();
   moving = 0;
+}
 void FigureEditor::mouseMoveEvent(QMouseEvent* e)
+{
   // User chooses "rotation mode" and we can rotate the object around its center of mass
   if (dynamic_cast<Main *>(parent())->RotationModeP()) {
     QPointF p = mapToScene(e->pos());
     p.setX(p.x() / Cell::Magnification());
     p.setY(p.y() / Cell::Magnification());
     // get object's center of mass
     QPointF rotation_midpoint = mesh.Centroid()*Cell::Factor() - Cell::Offset();
     // calculate rotation angle
     double dy = (rotation_midpoint.y() - p.y());
     double dx = (rotation_midpoint.x() - p.x());
     double new_rot_angle = atan2(dx, dy);
     double d_alpha = new_rot_angle - rot_angle;
     rot_angle = new_rot_angle;
     mesh.Rotate(d_alpha, ( Vector(rotation_midpoint) + Cell::Offset() ) / Cell::Factor() );
     dynamic_cast<Main *>(parent())->Plot(0);
     FullRedraw();
     return;
+  }
   if ( moving ) {
     QPointF p = mapToScene(e->pos());
     moving->userMove(p.x() - moving_start.x(),
 		     p.y() - moving_start.y());
     moving_start = p;
     scene()->update();
+  }
   //cerr << "event";
   // keep track of intersection line to interactively cut a growing leaf
   if ( intersection_line ) {
     QPointF sp = intersection_line -> line().p1(); // startpoint
     QPointF ep = mapToScene(e->pos()); // endpoint
     intersection_line -> setLine( QLineF(sp, ep) );
     scene()->update();
     // Need this for Mac
     FullRedraw();
+  }
+}
 //void FigureEditor::contentsMouseReleaseEvent(QMouseEvent* e)
 void FigureEditor::mouseReleaseEvent(QMouseEvent* e)
+{
   emit MouseReleased();
   // intersection line for leaf was finished now.
   if (e->button()==Qt::LeftButton) {
     if (intersection_line ) {
 #ifdef QDEBUG
       qDebug() << "Trying to cut leaf" << endl;
 #endif
       QPointF sp = intersection_line -> line().p1(); // startpoint
       QPointF ep = mapToScene(e->pos());
       intersection_line -> setLine( QLineF(sp, ep) );
       intersection_line -> show();
       vector <CellItem *> intersected_cells = getIntersectedCells();
       // no cells selected, do nothing
       if (intersected_cells.size()==0) {
 #ifdef QDEBUG
 	qDebug() << "No cells detected :-(" << endl;
 #endif
 	return;
+      }
       Vector startpoint = Vector(sp.x(), sp.y()) / Cell::Factor() - Cell::Offset();
       Vector endpoint = Vector(ep.x(), ep.y()) / Cell::Factor() - Cell::Offset();
       NodeSet *node_set = new NodeSet;
       for (vector<CellItem *>::iterator it = intersected_cells.begin(); it != intersected_cells.end(); it++) {
 	(*it)->setBrush(QBrush("purple"));
 	Cell &c=(*it)->getCell();
 	// sometimes the cell hasn't properly divided yet before the
 	// next division is called?  so check for it?  let's find a way
 	// to do this later. Note that this functionality currently
 	// might result in a segmentation fault for users who are
 	// quickly dragging and releasing division lines...
 	scene()->update();
 #ifdef QDEBUG
 	qDebug() << "Dividing Cell " << c.Index() << endl;
 #endif
 	c.DivideOverGivenLine( startpoint, endpoint, true, node_set);
+      }
       node_set->CleanUp();
       mesh.AddNodeSet(node_set);
 #ifdef QDEBUG
       qDebug() << "Done DivideOverGivenLine" << endl;
 #endif
       mesh.TestIllegalWalls();
       // Do the actual cutting and removing
       if (intersected_cells.size()) {
 	mesh.CutAwayBelowLine( startpoint, endpoint );
 	// Correct flags of nodeset
 	for (NodeSet::iterator i = node_set->begin(); i != node_set->end(); i++) {
 	  (*i)->SetSAM();
 	  (*i)->SetBoundary();
+	}
 	// Make cells attached to nodeset part of the boundary
 	// This is a temporary solution for the following:
 	//   If a cell attached to a NodeSet divides (with a division plane intersecting the node set),
 	//   we must insert a new node into the node set.
 	// For now, we add a layer of "virtual cells" inbetween.
 	list<Cell *> cells_attached_to_nodeset = node_set->getCells();
 	for ( list<Cell *>::iterator c = cells_attached_to_nodeset.begin(); c != cells_attached_to_nodeset.end(); c++) {
 	  (*c)->SetBoundary(Cell::SAM);
+	}
 #ifdef QDEBUG
 	qDebug() << "Done CutAwayBelowLine" << endl;
 #endif
 	mesh.TestIllegalWalls();
 	mesh.RepairBoundaryPolygon();
 #ifdef QDEBUG
 	qDebug() << "Done RepairBoundaryPolygon" << endl;
 #endif
 	mesh.TestIllegalWalls();
 	mesh.CleanUpWalls();
 #ifdef QDEBUG
 	qDebug() << "Done CleanUpWalls" << endl;
 #endif
 	mesh.TestIllegalWalls();
+      }
       dynamic_cast<Main *>(parent())->Plot();
 #ifdef QDEBUG
       cerr << "NodeSet of cutting line: " << *node_set << endl;
 #endif
+    }
   } else
     if (e->button()==Qt::RightButton) {
       if (intersection_line /* && !angle_line*/) {
 	QPointF p = mapToScene(e->pos());
 	QPointF sp = intersection_line->line().p1();
 	viewport()->setMouseTracking( TRUE );
+      }
+    }
+}
 // returns a vector of pointer to cells colliding with intersection line
 vector <CellItem *> FigureEditor::getIntersectedCells(void)
+{
   vector <CellItem *> colliding_cells;
   QList<QGraphicsItem *> l = intersection_line->collidingItems( );
 #ifdef QDEBUG
   qDebug() <<  "l.size() = " << l.size() << endl;
 #endif
   for (QList<QGraphicsItem *>::Iterator it=l.begin(); it!=l.end(); ++it) {
 #ifdef QDEBUG
     qDebug() << typeid(**it).name() << endl;
 #endif
     if ( !strcmp(typeid(**it).name(),"8CellItem") ) {
       colliding_cells.push_back(dynamic_cast<CellItem *>(*it));
+    }
+  }
   delete intersection_line;
   intersection_line = 0;
   return colliding_cells;
+}
 void FigureEditor::FullRedraw(void)
+{
   QList<QRectF> rl;
   rl << sceneRect();
   updateScene(rl);
+}
 NodeItem *FigureEditor::selectedNodeItem(QList<QGraphicsItem *> graphicItems) const
+{
   NodeItem *nodeItem = 0;
   // graphicItems is a list of the QgraphicItems under the mouse click event
   QList<QGraphicsItem *>::Iterator it = graphicItems.begin();
   for (; it != graphicItems.end(); ++it) {
     if ( !strcmp(typeid(**it).name(),"8NodeItem")) {
       // the object under the mouse click is a Nodeitem
       nodeItem = dynamic_cast<NodeItem *>(*it);
       // indicate we've selected it
       nodeItem->setBrush(dark_red);
       break;
+    }
+  }
   return nodeItem;
+}
 void FigureEditor::insertNode(QPointF p)
+{
   Node *node = new Node(p.x(), p.y(), 0);
   mesh.AddNode(node);
   scene()->clearSelection();
   dynamic_cast<Main *>(parent())->Plot();
   FullRedraw();
 #ifdef QDEBUG
   qDebug() << "Node: " << p << endl;
 #endif
+}
 static uint mainCount = 0;
 Main::Main(QGraphicsScene& c, Mesh &m, QWidget* parent, const char* name, Qt::WindowFlags f) :
   Q3MainWindow(parent,name,f),
   MainBase(c,m),
   mesh(m)
+{
   editor = new FigureEditor(canvas,mesh, this);
 #ifdef QDEBUG
   qDebug() << "Interactive = " << editor->isEnabled();
 #endif
   working_dir = 0;
   QObject::connect( editor, SIGNAL(MousePressed()), this, SLOT(PauseIfRunning()));
   QObject::connect( editor, SIGNAL(MouseReleased()), this, SLOT(ContIfRunning()));
   QMenuBar* menu = menuBar();
   Q3PopupMenu* file = new Q3PopupMenu( menu );
   file->insertItem("&Read leaf", this, SLOT(readStateXML()));
   file->insertItem("&Save leaf", this, SLOT(saveStateXML()));
   file->insertItem("Snapshot", this, SLOT(snapshot()), Qt::CTRL+Qt::SHIFT+Qt::Key_S);
   file->insertSeparator();
   file->insertItem("Read next leaf", this, SLOT(readNextStateXML()), Qt::Key_PageDown);
   file->insertItem("Read previous leaf", this, SLOT(readPrevStateXML()), Qt::Key_PageUp);
   file->insertItem("Read last leaf", this, SLOT(readLastStateXML()), Qt::Key_End);
   file->insertItem("Read first leaf", this, SLOT(readFirstStateXML()), Qt::Key_Home);
   file->insertItem("Export cell areas", this, SLOT(exportCellData()));
   file->insertSeparator();
   file->insertItem("&Print...", this, SLOT(print()), Qt::CTRL+Qt::Key_P);
   file->insertSeparator();
   file->insertItem("E&xit", qApp, SLOT(quit()), Qt::CTRL+Qt::Key_Q);
   menu->insertItem("&File", file);
   Q3PopupMenu* edit = new Q3PopupMenu( menu );
   edit->insertItem("Reset Chemicals and Transporters", this, SLOT( CleanMesh()), Qt::CTRL+Qt::Key_R );
   edit->insertItem("Reset Chemicals", this, SLOT( CleanMeshChemicals()) );
   edit->insertItem("Reset Transporters", this, SLOT( CleanMeshTransporters()) );
   edit->insertItem("Randomize PIN1 Transporters", this, SLOT( RandomizeMesh()) );
   edit->insertItem("Cut away SAM", this, SLOT( CutSAM() ));
   menu->insertItem("&Edit", edit);
   run = new Q3PopupMenu( menu );
   running = false;
   paused_id = run->insertItem("&Simulation paused", this, SLOT(togglePaused()), Qt::Key_S);
   run->setItemChecked(paused_id, FALSE);
   menu->insertItem("&Run", run);
   view = new Q3PopupMenu( menu );
   view->insertItem("&Zoom in", this, SLOT(zoomIn()), Qt::CTRL+Qt::Key_Equal);
   view->insertItem("Zoom &out", this, SLOT(zoomOut()), Qt::CTRL+Qt::Key_Minus);
   view->insertSeparator();
   com_id = view->insertItem("Show cell &centers", this, SLOT(toggleShowCellCenters()));
   view->setItemChecked(com_id, FALSE);
   mesh_id = view->insertItem("Show &nodes", this, SLOT(toggleShowNodes()), Qt::CTRL+Qt::SHIFT+Qt::Key_N);
   view->setItemChecked(mesh_id, TRUE);
   node_number_id = view->insertItem("Show node numbers", this, SLOT(toggleNodeNumbers()), Qt::CTRL+Qt::SHIFT+Qt::Key_M);
   view->setItemChecked(node_number_id, FALSE);
   cell_number_id = view->insertItem("Show cell numbers", this, SLOT(toggleCellNumbers()));
   view->setItemChecked(cell_number_id, FALSE);
   hide_cells_id = view->insertItem("Hide cells", this, SLOT(toggleHideCells()));
   view->setItemChecked(hide_cells_id, FALSE);
   border_id = view->insertItem("Show &border cells", this, SLOT(toggleShowBorderCells()));
   view->setItemChecked(border_id, FALSE);
   cell_axes_id = view->insertItem("Show cell &axes", this, SLOT(toggleCellAxes()));
   cell_strain_id = view->insertItem("Show cell &strain", this, SLOT(toggleCellStrain()));
   view->setItemChecked(cell_axes_id, FALSE);
   fluxes_id = view->insertItem("Show &fluxes", this, SLOT(toggleShowFluxes()));
   view->setItemChecked(fluxes_id, FALSE);
   cell_walls_id = view->insertItem("Show transporters", this, SLOT(toggleShowWalls()));
   view->setItemChecked(cell_walls_id, FALSE);
  // apoplasts_id = view->insertItem("Show apoplasts", this, SLOT(toggleShowApoplasts()));
  // view->setItemChecked(apoplasts_id, FALSE);
   view->insertSeparator();
   only_boundary_id = view->insertItem("Show only leaf &boundary", this, SLOT(toggleLeafBoundary()));
   view->insertSeparator();
   movie_frames_id = view->insertItem("Start saving movie &frames", this, SLOT(toggleMovieFrames()));
   view->setItemChecked(movie_frames_id, par.movie);
   view->setItemChecked(only_boundary_id, FALSE);
   menu->insertItem("&View", view);
   options = new Q3PopupMenu( menu );
   dyn_cells_id = options->insertItem("Cell growth", this, SLOT(toggleDynCells()));
   options->setItemChecked(dyn_cells_id, true);
   options->insertItem("Edit &parameters", this, SLOT(EditParameters()), Qt::CTRL+Qt::Key_E);
   rotation_mode_id = options->insertItem("Rotate leaf", this, SLOT(EnterRotationMode()), Qt::CTRL + Qt::SHIFT + Qt::Key_R);
   options->setItemChecked(rotation_mode_id, false);
   menu->insertItem("&Options",options);
   // Menu of models
   modelmenu = new QMenu( menu );
   menu->insertItem("&Models", modelmenu);
   menu->insertSeparator();
   helpmenu = new Q3PopupMenu( menu );
   tooltips_id = helpmenu->insertItem("Show Cell&Info", this, SLOT(Refresh()));
   helpmenu->setItemChecked(tooltips_id, true);
   helpmenu->insertSeparator();
     //helpmenu->insertSeparator();
   helpmenu->insertItem("&LICENSE", this, SLOT(gpl()) );
   helpmenu->insertItem("About", this, SLOT(about()) ); //, Key_F1);
 	menu->insertItem("&Help",helpmenu);
   statusBar();
   setCentralWidget(editor);
   printer = 0;
   init();
   // Start timer which repetitively invokes
   // a simulation time step
   timer = new QTimer( this );
   connect( timer, SIGNAL(timeout()), SLOT(TimeStepWrap()) );
   stopSimulation();
   statusBar()->addWidget(new QLabel("Ready."));
   setCaption(caption);
   gifanim = 0;
   infobar = new InfoBar();
   addDockWindow(infobar);
+}
 void Main::RefreshInfoBar(void)
+{
   infobar->SetText(mesh.ModelID());
+}
 void Main::UserMessage(QString message, int timeout)
+{
   statusBar()->showMessage(message, timeout);
+}
 void Main::init()
+{
   clear();
   static int r=24;
   srand(++r);
   mainCount++;
+}
 Main::~Main()
+{
   delete printer;
   if ( !--mainCount ) {
+  }
   //EndGifAnim();
+}
 void Main::newView()
+{
   // Open a new view... have it delete when closed.
   Main *m = new Main(canvas, mesh, 0, 0, Qt::WDestructiveClose);
   qApp->setMainWidget(m);
   m->show();
   qApp->setMainWidget(0);
+}
 void Main::EditParameters()
+{
   ParameterDialog *pardial = new ParameterDialog(this, "stridediag");
   // Make sure the values in the parameter dialog are updated after a file is read
   // each method changing the parameters (reading XML or PAR files) should
   // emit this signal
   QObject::connect(   this, SIGNAL( ParsChanged() ), pardial, SLOT( Reset() ) );
+}
 void Main::savePars()
+{
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
   fd->setMode( Q3FileDialog::AnyFile );
   fd->setFilter( "Parameter files (*.par)");
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     ofstream parfile((const char *)fileName);
     par.Write(parfile);
+  }
   startSimulation();
+}
 void Main::readPars()
+{
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
   fd->setMode( Q3FileDialog::ExistingFile );
   fd->setFilter( "Parameter files (*.par)");
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     par.Read((const char *)fileName);
+  }
   emit ParsChanged();
+}
 void Main::saveStateXML()
+{
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
   fd->setMode( Q3FileDialog::AnyFile );
   fd->setFilter( "XML (*.xml)");
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     if ( QFile::exists( fileName ) &&
 	 QMessageBox::question(
 			       this,
 			       tr("Overwrite File? -- Leaf Growth"),
 			       tr("A file called %1 already exists."
 				  "Do you want to overwrite it?")
 			       .arg( fileName ),
 			       tr("&Yes"), tr("&No"),
 			       QString::null, 1, 1 ) ) {
       return saveStateXML();
     } else {
       mesh.XMLSave((const char *)fileName, XMLSettingsTree());
+    }
+  }
+}
 void Main::snapshot()
+{
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "Save snapshot", TRUE );
   fd->setMode( Q3FileDialog::AnyFile );
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     if ( QFile::exists( fileName ) &&
 	 QMessageBox::question(
 			       this,
 			       tr("Overwrite File? -- Leaf Growth"),
 			       tr("A file called %1 already exists."
 				  "Do you want to overwrite it?")
 			       .arg( fileName ),
 			       tr("&Yes"), tr("&No"),
 			       QString::null, 1, 1 ) ) {
       return snapshot();
     } else {
       // extract extension from filename
       QString extension = getExtension(fileName);
       // Save bitmaps at 1024x768
       Save((const char *)fileName, extension, 1024, 768);
+    }
+  }
+}
 void Main::readPrevStateXML()
+{
   // if we have already read a file, read the next file
   if (!currentFile.isEmpty() && working_dir) {
     QString next_file;
     QStringList xml_files = working_dir->entryList("*.xml");
     QString currentFile_nopath = currentFile.section( '/', -1 );
     QString currentFile_path = currentFile.section( '/', 0, -2 );
     QList<QString>::iterator f = xml_files.find( currentFile_nopath );
     if (f == xml_files.end()) {
       return;
+    }
     if (f==xml_files.begin()) {
       QMessageBox mb( "Read previous leaf",
 		      "No more files",
 		      QMessageBox::Information,
 		      QMessageBox::Ok | QMessageBox::Default,
 		      QMessageBox::NoButton,
 		      QMessageBox::NoButton);
       mb.exec();
       return;
+    }
     next_file = *(--f);
     next_file = currentFile_path+"/"+next_file;
     readStateXML((const char *)next_file);
+  }
+}
 int Main::readStateXML(const char *filename, bool geometry, bool pars, bool simtime)
+{
   try {
     xmlNode *settings;
     mesh.XMLRead((const char *)filename, &settings, geometry, pars, simtime);
 #ifdef QDEBUG
     qDebug() << "Reading done."<< endl;
 #endif
     XMLReadSettings(settings);
     xmlFree(settings);
     Cell::SetMagnification(1);
     Cell::setOffset(0,0);
     FitLeafToCanvas();
     currentFile =  QString(filename);
     Plot();
     QString status_message = QString("Successfully read leaf from file %1. Time is %2 h.").arg(currentFile).arg(mesh.getTimeHours().c_str());
     cerr << status_message.toStdString() << endl;
     setCaption(caption_with_file.arg(filename));
     statusBar()->message(status_message);
     emit ParsChanged();
 #ifdef QDEBUG
     qDebug() << "Done. Returning 0." << endl;
 #endif
     return 0;
   } catch (const char *error_message) {
     QMessageBox mb( "Read leaf from XML file",
 		    QString(error_message),
 		    QMessageBox::Critical,
 		    QMessageBox::Ok | QMessageBox::Default,
 		    Qt::NoButton,
 		    Qt::NoButton);
     mb.exec();
     return 1;
+  }
+}
 void Main::readNextStateXML()
+{
   // if we have already read a file, read the next file
   if (!currentFile.isEmpty() && working_dir) {
     QString next_file;
     QStringList xml_files = working_dir->entryList("*.xml");
     QString currentFile_nopath = currentFile.section( '/', -1 );
     QString currentFile_path = currentFile.section( '/', 0, -2 );
     QList<QString>::iterator f = xml_files.find( currentFile_nopath );
     if (f == xml_files.end()) {
       return;
+    }
     ++f;
     if (f==xml_files.end()) {
       QMessageBox mb( "Read next leaf",
 		      "No more files",
 		      QMessageBox::Information,
 		      QMessageBox::Ok | QMessageBox::Default,
 		      QMessageBox::NoButton,
 		      QMessageBox::NoButton);
       mb.exec();
       return;
+    }
     next_file = *f;
     next_file = currentFile_path+"/"+next_file;
     readStateXML((const char*)next_file);
+  }
+}
 void Main::readLastStateXML()
+{
   // if we have already read a file, read the next file
   if (!currentFile.isEmpty() && working_dir) {
     QString next_file;
     QStringList xml_files = working_dir->entryList("*.xml");
     QString currentFile_nopath = currentFile.section( '/', -1 );
     QString currentFile_path = currentFile.section( '/', 0, -2 );
     next_file = xml_files.back();
     next_file = currentFile_path+"/"+next_file;
     readStateXML((const char*)next_file);
+  }
+}
 void Main::readFirstStateXML()
+{
   // if we have already read a file, read the next file
   if (!currentFile.isEmpty() && working_dir) {
     QString next_file;
     QStringList xml_files = working_dir->entryList("*.xml");
     QString currentFile_nopath = currentFile.section( '/', -1 );
     QString currentFile_path = currentFile.section( '/', 0, -2 );
     next_file = xml_files.front();
     next_file = currentFile_path+"/"+next_file;
     readStateXML((const char*)next_file);
+  }
+}
 void Main::readStateXML()
+{
   //  extern Mesh mesh;
   stopSimulation();
 #ifdef QDEBUG
   qDebug() << "Trying to open an OptionFileDialog" << endl;
 #endif
   OptionFileDialog *fd = new OptionFileDialog( this, "read dialog", TRUE );
   fd->setMode( OptionFileDialog::ExistingFile );
   fd->setFilter( "XML files (*.xml)");
   if (working_dir) {
     fd->setDir(*working_dir);
+  }
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     if (working_dir) {
       delete working_dir;
+    }
     working_dir = fd->dir();
     if (readStateXML((const char *)fileName,fd->readGeometryP(), fd->readParametersP()) )
       return readStateXML(); // user can try again
+  }
+}
 void Main::clear()
+{
   editor->clear();
+}
 void Main::about()
+{
   static QMessageBox* about = new QMessageBox
     ( "VirtualLeaf V1.0",
       "<h3>VirtualLeaf V1.0</h3>"
       "<p>"
       "An Open Source framework for cell-based modeling of plant tissue growth and development <br>"
       "(c) 2005-2008, Roeland Merks <i>et al.</i><br>"
       "    <a href=\"http://www.psb.vib-ugent.be\">VIB Department Plant Systems Biology</a>, "
       "Ghent, Belgium <br>"
       "(c) 2008-2010, <a href=\"http://www.cwi.nl/~merks\">Roeland Merks <i>et al.</i></a> <br>"
       "    <a href=\"http://www.cwi.nl\">Centrum Wiskunde & Informatica</a> and <a href=\"http://www.ncsb.nl\">Netherlands Consortium for Systems Biology</a>, Amsterdam, Netherlands <br>"
 "<br>VirtualLeaf 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.<br>"
       "<br>If you use this code for your projects, please cite our paper:"
 "<br>Merks, Guravage, Inze, and Beemster. An Open Source framework for cell-based modeling of plant tissue growth and development. <i>Plant Physiology,</i> submitted.<br> . <br>"
       "<br>Please share your model plugins and extensions at <a href=\"http://virtualleaf.googlecode.com\">http://virtualleaf.googlecode.com</a>.",
       QMessageBox::Information, 1, 0, 0, this, 0, FALSE );
   about->setButtonText( 1, "Dismiss" );
   about->show();
+}
 void Main::gpl()
+{
   static QMessageBox* gpl = new QMessageBox ( "GPL License", "",
       QMessageBox::Information, 1, 0, 0, this, 0, FALSE );
   QDir docDir(QApplication::applicationDirPath());
   docDir.cd("../doc"); // Where Linux expects gpl3.txt
   QString path = docDir.filePath("gpl3.txt");
   if (!docDir.exists("gpl3.txt")){
     docDir = QApplication::applicationDirPath();
     docDir.cd("doc"); // Where Windows expects gpl3.txt
     path = docDir.filePath("gpl3.txt");
+  }
   // At this point path points either to the linux variant, which
   // exists, or the windows variant, which may exist. Testing the
   // ifstream object will determine whether we've found gpl3.txt.
   std::ifstream file(path.toStdString().c_str());
   std::string str;
   if (file) {
     file.seekg(0, std::ios::end);
     str.reserve(file.tellg());
     file.seekg(0, std::ios::beg);
     str.assign((std::istreambuf_iterator<char>(file)),
 	       std::istreambuf_iterator<char>());
     gpl->setDetailedText(QString(str.c_str()));
+  }
   gpl->setText(QString( "<h3>GNU GENERAL PUBLIC LICENSE</h3>"
 			"<p>Version 3, 29 June 2007</p>"
 			"<p>Copyright &copy; 2007 Free Software Foundation, Inc. "
 			"&lt;<a href=\"http://fsf.org/\">http://fsf.org/</a>&gt;</p><p>"
 			"Everyone is permitted to copy and distribute verbatim copies "
 			"of this license document, but changing it is not allowed.</p>"
 			"<h2>GNU GENERAL PUBLIC LICENSE</h2>"));
   gpl->setButtonText( 1, "Dismiss" );
   gpl->show();
+}
 void Main::aboutQt(){
   QMessageBox::aboutQt( this, "Virtual Leaf" );
+}
 void Main::toggleShowCellCenters()
+{
   Plot();
+}
 void Main::toggleShowWalls()
+{
   Plot();
+}
 void Main::toggleShowApoplasts()
+{
   Plot();
+}
 void Main::toggleShowNodes()
+{
   Plot();
+}
 void Main::toggleNodeNumbers(void)
+{
   Plot();
+}
 void Main::toggleCellNumbers(void)
+{
   Plot();
+}
 void Main::toggleCellAxes(void)
+{
   Plot();
+}
 void Main::toggleCellStrain(void)
+{
   Plot();
+}
 void Main::toggleShowFluxes(void)
+{
   Plot();
+}
 void Main::toggleShowBorderCells()
+{
   Plot();
+}
 void Main::toggleHideCells(void)
+{
   Plot();
   editor->FullRedraw();
+}
 void Main::toggleMovieFrames(){}
 void Main::toggleLeafBoundary(){}
 void Main::toggleDynCells() {}
 void Main::startSimulation(void)
+{
   timer->start( 0 );
   statusBar()->message("Simulation started");
   running = true;
+}
 void Main::stopSimulation(void)
+{
   timer->stop();
   cerr << "Stopping simulation" << endl;
   statusBar()->message("Simulation paused");
   running = false;
+}
 void Main::togglePaused()
+{
   bool s = run->isItemChecked(paused_id);
   if (s) {
     cerr << "Calling start simulation" << endl;
     startSimulation();
   } else {
     cerr << "Calling stop simulation" << endl;
     stopSimulation();
+  }
+}
 void Main::setFluxArrowSize(int size)
+{
   flux_arrow_size = size/100.;
+}
 void Main::enlarge()
+{
   canvas.setSceneRect( QRectF( 0,0, canvas.width()*4./3., canvas.height()*4./3.) );
+}
 void Main::shrink()
+{
   canvas.setSceneRect( QRectF( 0,0, canvas.width()*3/4, canvas.height()*3/4) );
+}
 void Main::scale(double factor)
+{
   QMatrix m = editor->matrix();
   m.scale(factor, factor);
   editor->setMatrix( m );
+}
 void Main::zoomIn()
+{
   QMatrix m = editor->matrix();
   m.scale( 1.1, 1.1 );
   editor->setMatrix( m );
+}
 void Main::zoomOut()
+{
   QMatrix m = editor->matrix();
   m.scale( 0.9, 0.9 );
   editor->setMatrix( m );
+}
 void Main::print()
+{
   if ( !printer ) printer = new QPrinter;
   if ( printer->setup(this) ) {
     //    extern Mesh mesh;
     Vector bbll,bbur;
     mesh.BoundingBox(bbll,bbur);
 #ifdef QDEBUG
     qDebug() << "bbll = " << bbll << endl;
     qDebug() << "bbur = " << bbur << endl;
 #endif
     double cw = (bbur.x - bbll.x);
     double ch = (bbur.y - bbll.y);
     QPainter pp(printer);
     QRect vp=pp.viewport();
 #ifdef QDEBUG
     qDebug() << "Paper width = " << vp.width() << " x " << vp.height() << endl;
 #endif
     // Note that Cell is also translated...
     pp.translate(-bbur.x,-bbur.y);
     if (cw>ch) {
       pp.scale(vp.width()/(2*cw*Cell::Magnification()), vp.width()/(2*cw*Cell::Magnification()));
     } else {
       pp.scale(vp.height()/(2*ch*Cell::Magnification()), vp.height()/(2*ch*Cell::Magnification()));
+    }
     canvas.render(&pp, QRectF(), QRectF(0.,0.,canvas.width(),canvas.height()));
+  }
+}
 void Main::TimeStepWrap(void)
+{
   static int t=0;
   TimeStep();
   t++;
   if ((par.export_interval > 0) && ((t % par.export_interval) == 0)){
     this->exportCellData(QString(par.datadir) + QString('/') + QString(par.export_fn_prefix) + this->TimeStamp());
+  }
   // check number of timesteps
   if (t==par.nit) {
     emit SimulationDone();
+  }
+}
 QString Main::TimeStamp(){
   time_t rawtime;
   struct tm * timeinfo;
   char buffer [15];
   time ( &rawtime );
   timeinfo = localtime ( &rawtime );
   strftime (buffer,15,"%Y%m%d%H%M%S",timeinfo);
   return QString(buffer);
+}
 void Main::RestartSim(void)
+{
   stopSimulation();
   if ( QMessageBox::question(
 			     this,
 			     tr("Restart simulation?"),
 			     tr("Restart simulation.\n"
 				"Are you sure?"),
 			     QMessageBox::Yes | QMessageBox::No, QMessageBox::NoButton ) == QMessageBox::Yes ) {
     cerr << "Restarting simulation" << endl;
     //    extern Mesh mesh;
     mesh.Clear();
     Init();
     Plot();
     editor->FullRedraw();
+  }
   //startSimulation();
+}
 void Main::FitCanvasToWindow(void)
+{
   double scale_factor_x = (double)editor->width()/(double)canvas.width();
   double scale_factor_y = (double)editor->height()/(double)canvas.height();
   double scale_factor = scale_factor_x > scale_factor_y ? scale_factor_x : scale_factor_y;
   QMatrix m = editor->matrix();
 #ifdef QDEBUG
   qDebug() << "editor->width() = " << editor->width() << endl;
   qDebug() << "editor->height() = " << editor->height() << endl;
   qDebug() << "scale_factor = " << scale_factor << endl;
   qDebug() << "scale_factor_x = " << scale_factor_x << endl;
   qDebug() << "scale_factor_y = " << scale_factor_y << endl;
 #endif
   m.scale( scale_factor, scale_factor );
   editor->setMatrix( m );
   editor->show();
+}
 void Main::PauseIfRunning(void)
+{
   if (running) {
     timer->stop();
+  }
+}
 void Main::ContIfRunning(void)
+{
   if (running) {
     timer->start( 0 );
+  }
+}
 void Main::FitLeafToCanvas(void)
+{
   Vector ll,ur;
   mesh.BoundingBox(ll, ur);
   ll*=Cell::Magnification(); ur*=Cell::Magnification();
   // give the leaf some space
   Vector border = ((ur-ll)/5.);
   QRectF bb( ll.x - border.x, ll.y - border.y, ur.x-ll.x + 2*border.x, ur.y-ll.y + 2*border.y );
   // cerr << ur << ", " << ll << endl;
   // editor->fitInView(bb, Qt::KeepAspectRatio);
   editor->ensureVisible(bb);
   //editor->setTransform(viewport);
+}
 void Main::CleanMesh(void)
+{
   vector<double> clean_chem(Cell::NChem());
   vector<double> clean_transporters(Cell::NChem());
   for (int i=0;i<Cell::NChem();i++) {
     clean_chem[i]=par.initval[i];
     clean_transporters[i]=0.;
+  }
   mesh.CleanChemicals(clean_chem);
   mesh.CleanTransporters(clean_transporters);
   mesh.setTime(0);
   Plot();
   editor->FullRedraw();
+}
 void Main::CleanMeshChemicals(void)
+{
   vector<double> clean_chem(Cell::NChem());
   for (int i=0;i<Cell::NChem();i++) {
     clean_chem[i]=par.initval[i];
+  }
   mesh.CleanChemicals(clean_chem);
   mesh.setTime(0);
   Plot();
   editor->FullRedraw();
+}
 void Main::CleanMeshTransporters(void)
+{
   vector<double> clean_transporters(Cell::NChem());
   for (int i=0;i<Cell::NChem();i++) {
     clean_transporters[i]=0.;
+  }
   mesh.CleanTransporters(clean_transporters);
   mesh.setTime(0);
   Plot();
   editor->FullRedraw();
+}
 void Main::RandomizeMesh(void)
+{
   vector<double> max_chem(Cell::NChem());
   vector<double> max_transporters(Cell::NChem());
   for (int i=0;i<Cell::NChem();i++) {
     max_transporters[i]=0.;
     max_chem[i]=par.initval[i];
+  }
   // Amount of PIN1 at walls
   max_transporters[1] = 0.01;
   mesh.RandomizeChemicals(max_chem, max_transporters);
   Plot();
+}
 void Main::XMLReadSettings(xmlNode *settings)
+{
   MainBase::XMLReadSettings(settings);
   view->setItemChecked(com_id, showcentersp);
   view->setItemChecked(mesh_id, showmeshp);
   view->setItemChecked(border_id, showbordercellp);
   view->setItemChecked(node_number_id, shownodenumbersp);
   view->setItemChecked(cell_number_id, showcellnumbersp);
   view->setItemChecked(cell_axes_id, showcellsaxesp);
   view->setItemChecked(cell_strain_id, showcellstrainp);
   view->setItemChecked(movie_frames_id, movieframesp);
   view->setItemChecked(only_boundary_id, showboundaryonlyp);
   view->setItemChecked(fluxes_id, showfluxesp);
   view->setItemChecked(hide_cells_id, hidecellsp);
   options->setItemChecked(dyn_cells_id, dynamicscellsp);
   view->setItemChecked( cell_walls_id, showwallsp);
  // view->setItemChecked( apoplasts_id, showapoplastsp);
   editor->setTransform(viewport);
+}
 xmlNode *Main::XMLSettingsTree(void)
+{
   showcentersp = view->isItemChecked(com_id);
   showmeshp = view->isItemChecked(mesh_id);
   showbordercellp =  view->isItemChecked(border_id);
   shownodenumbersp =  view->isItemChecked(node_number_id);
   showcellnumbersp =  view->isItemChecked(cell_number_id);
   showcellsaxesp = view->isItemChecked( cell_axes_id );
   showcellstrainp = view->isItemChecked( cell_strain_id );
   movieframesp = view->isItemChecked(movie_frames_id);;
   showboundaryonlyp =  view->isItemChecked(only_boundary_id);
   showfluxesp = view->isItemChecked(fluxes_id);
   dynamicscellsp = options->isItemChecked(dyn_cells_id);
   showwallsp = view->isItemChecked( cell_walls_id);
   //showapoplastsp = view->isItemChecked( apoplasts_id);
   hidecellsp = view->isItemChecked( hide_cells_id);
   xmlNode *settings = MainBase::XMLSettingsTree();
   QTransform viewport(editor->transform());
   xmlAddChild(settings, XMLViewportTree(viewport));
   return settings;
+}
 void Main::exportCellData(void) {
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
   QString fileName;
 void Main::exportCellData(QString fileName) {
   stopSimulation();
   fd->setMode( Q3FileDialog::AnyFile );
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
 #ifdef QDEBUG
-    qDebug() << "exportCellData filename: " << fileName << endl;
+  qDebug() << "exportCellData fileName: " << fileName << endl;
 #endif
   // perhaps make this more general: a popup window were user selects data he wants to export
   // can go to "settings" section of XML file as well so this can also be measured off-line
   // mesh.CSVExport would take an QMap or so to record all options
   // first line gives legenda
     QFile file(fileName);
     if ( file.open( IO_WriteOnly ) ) {
       QTextStream stream( &file );
       mesh.CSVExportCellData(stream);
       mesh.CSVExportMeshData(stream);
       file.close();
+    }
   QFile file(fileName);
   if ( file.open( IO_WriteOnly ) ) {
     QTextStream stream( &file );
     mesh.CSVExportCellData(stream);
     mesh.CSVExportMeshData(stream);
     file.close();
+  }
+}
 void Main::exportCellData() {
   QString fileName;
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
   stopSimulation();
   fd->setMode( Q3FileDialog::AnyFile );
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
+  }
   this->exportCellData(fileName);
+}
 /* finis */

src/canvas.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  VirtualLeaf 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.
+ *
  *  VirtualLeaf 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 _CANVAS_H_
 #define _CANVAS_H_
 #include <q3popupmenu.h>
 #include <q3mainwindow.h>
 #include <q3intdict.h>
 #include <QGraphicsScene>
 #include <QGraphicsView>
 #include <QList>
 #include <string>
 #include <sstream>
 //Added by qt3to4:
 #include <QMouseEvent>
 #include <vector>
 #include "simitembase.h"
 #include "mainbase.h"
 #include "cellitem.h"
 #include "infobar.h"
 #include "nodeitem.h"
 #include "cell.h"
 #ifdef HAVE_QWT
 #include "data_plot.h"
 #endif
 #include <libxml/xpath.h>
 #include <libxml/xmlreader.h>
 #if defined(Q_OS_MAC)
 #define PREFIX "cmd"
 #else
 #define PREFIX "crtl"
 #endif
 class QFile;
 class QDir;
 class ModelCatalogue;
 class InfoBar;
 class FigureEditor : public QGraphicsView {
   Q_OBJECT
     friend class Main;
  public:
   FigureEditor(QGraphicsScene&, Mesh&, QWidget* parent=0, const char* name=0, Qt::WFlags f=0);
   void clear();
   void Save(const char *fname, const char *format, int sizex=640, int sizey=480);
   void FullRedraw(void);
  protected:
   void mousePressEvent(QMouseEvent*);
   void mouseMoveEvent(QMouseEvent*);
   void mouseReleaseEvent(QMouseEvent*);
   void wheelEvent(QWheelEvent *event);
   void scaleView(qreal scaleFactor);
   vector <CellItem *> getIntersectedCells(void);
   void insertNode(QPointF p);
   NodeItem *selectedNodeItem(QList<QGraphicsItem *> l) const;
  signals:
   void status(const QString&);
   void MousePressed(void);
   void MouseReleased(void);
  protected:
   Mesh &mesh;
  private:
   //NodeItem* moving;
   SimItemBase *moving;
   QPointF moving_start;
   QGraphicsLineItem *intersection_line;
   bool rotation_mode;
   bool insert_mode;
   double rot_angle;
 };
 class Main : public Q3MainWindow, public MainBase {
   Q_OBJECT
     friend class ModelCatalogue; // needs to populate menu item models
  public:
   Main(QGraphicsScene&, Mesh&, QWidget* parent=0, const char* name=0, Qt::WFlags f=0);
   ~Main();
   virtual bool ShowCentersP(void) {return view->isItemChecked(com_id);}
   virtual bool ShowMeshP(void) {return view->isItemChecked(mesh_id);}
   virtual bool ShowBorderCellsP(void) {return view->isItemChecked(border_id);}
   virtual bool PausedP(void) {return run->isItemChecked(paused_id);}
   virtual bool ShowNodeNumbersP(void) {return view->isItemChecked(node_number_id);}
   virtual bool ShowCellNumbersP(void) {return view->isItemChecked(cell_number_id);}
   virtual bool ShowCellAxesP(void) {return view->isItemChecked(cell_axes_id);}
   virtual bool ShowCellStrainP(void) {return view->isItemChecked(cell_strain_id);}
   virtual bool MovieFramesP(void) {return view->isItemChecked(movie_frames_id);}
   virtual bool ShowBoundaryOnlyP(void) {return view->isItemChecked(only_boundary_id);}
   virtual bool ShowWallsP(void) {return view->isItemChecked(cell_walls_id);}
  // virtual bool ShowApoplastsP(void) { return view->isItemChecked(apoplasts_id);}
   virtual bool ShowFluxesP(void) { return view->isItemChecked(fluxes_id); }
   virtual bool DynamicCellsP(void) { return options->isItemChecked(dyn_cells_id); }
   virtual bool RotationModeP(void) { return options->isItemChecked(rotation_mode_id); }
   virtual bool InsertModeP(void) { return options->isItemChecked(insert_mode_id); }
   virtual bool ShowToolTipsP(void) { return helpmenu->isItemChecked(tooltips_id); }
   virtual bool HideCellsP(void) { return view->isItemChecked(hide_cells_id); }
   void scale(double factor);
   virtual double getFluxArrowsize(void)
+  {
     return flux_arrow_size;
+  }
   void FitCanvasToWindow();
   void FitLeafToCanvas(void);
   public slots:
   void about();
   void gpl();
   void TimeStepWrap();
   void togglePaused();
   void setFluxArrowSize(int size);
   void RestartSim(void);
   void toggleShowCellCenters(void);
   void toggleShowNodes(void);
   void toggleShowBorderCells(void);
   void toggleShowFluxes(void);
   void toggleNodeNumbers(void);
   void toggleCellNumbers(void);
   void toggleCellAxes(void);
   void toggleCellStrain(void);
   void toggleShowWalls(void);
   void toggleShowApoplasts(void);
   void toggleDynCells(void);
   void toggleMovieFrames(void);
   void toggleLeafBoundary(void);
   void toggleHideCells(void);
   void print();
   void startSimulation(void);
   void stopSimulation(void);
   void RefreshInfoBar(void);
   void EnterRotationMode(void)
+  {
     UserMessage("Rotation mode. Click mouse to exit.");
     if (editor) {
       editor->rot_angle = 0. ;
       // Exit rotation mode if mouse is clicked
       connect(editor, SIGNAL(MousePressed()), this, SLOT(ExitRotationMode()));
       editor->setMouseTracking(true);
+    }
+  }
   void ExitRotationMode(void)
+  {
     UserMessage("Exited rotation mode.",2000);
     options->setItemChecked(rotation_mode_id, false);
     if (editor)
       disconnect(editor, SIGNAL(MousePressed()), this, SLOT(ExitRotationMode()));
     editor->setMouseTracking(false);
+  }
   virtual void UserMessage(QString message, int timeout=0);
   void Refresh(void) { Plot(); }
   void PauseIfRunning(void);
   void ContIfRunning(void);
   virtual void XMLReadSettings(xmlNode *settings);
   private slots:
   void aboutQt();
   void newView();
   void EditParameters();
   void readStateXML();
   int readStateXML(const char *filename, bool geometry = true, bool pars=true, bool simtime = true);
   void readNextStateXML();
   void readPrevStateXML();
   void readFirstStateXML();
   void readLastStateXML();
   void exportCellData();
   void exportCellData(QString);
   void saveStateXML();
   void snapshot();
   void savePars();
   void readPars();
   void clear();
   void init();
   virtual void CutSAM() { MainBase::CutSAM(); Refresh();}
   void enlarge();
   void shrink();
   void zoomIn();
   void zoomOut();
   void CleanMesh();
   void CleanMeshChemicals(void);
   void CleanMeshTransporters(void);
   void RandomizeMesh();
   QString TimeStamp();
  signals:
   void SimulationDone(void);
   void ParsChanged(void);
  protected:
   Mesh &mesh;
  private:
   NodeSet *node_set;
   FigureEditor *editor;
   Q3PopupMenu* options;
   Q3PopupMenu *view;
   Q3PopupMenu *run;
   QMenu *modelmenu;
   Q3PopupMenu *helpmenu;
   QPrinter* printer;
   const QDir *working_dir;
   QString currentFile;
   //  toggle item states
   int dbf_id; // options->Double Buffer
   int com_id; // view->Show centers
   int mesh_id; // view->Show mesh
   int node_number_id; // view->Show Node numbers
   int cell_number_id; // view->Show Cell numbers
   int border_id; // view->Show border cells
   int paused_id; // run->Simulation paused
   int cell_axes_id; // view->Show cell axes
   int cell_strain_id; // view->Show cell strain
   int only_boundary_id; // view ->Show only leaf boundary
   int cell_walls_id; // view -> Show transporters
   //int apoplasts_id; // view -> Show apoplasts
   int tooltips_id; // help -> Show Cell Info
   int hide_cells_id; // view->Hide Cells
   double flux_arrow_size;
   int movie_frames_id;
   int fluxes_id;
   int dyn_cells_id;
   int rotation_mode_id;
   int insert_mode_id;
   QTimer *timer;
   QFile *gifanim;
   bool running;
   virtual xmlNode *XMLSettingsTree(void);
   static const QString caption;
   static const QString caption_with_file;
   InfoBar *infobar;
 };
 #endif
 /* finis*/

src/parameter.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  VirtualLeaf 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.
+ *
  *  VirtualLeaf 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.
+ *
  */
 // Do not edit. All edits will be discarded.
 #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>
 #include <QDir>
 #include <QStringList>
 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 = 0;
   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(".");
   datadir = AppendHomeDirIfPathRelative(datadir);
   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(".");
   export_interval = 100;
   export_fn_prefix = strdup("CELLDATA");
+}
 Parameter::~Parameter() {
   // destruct parameter object
   // free string parameter
   CleanUp();
 // destruct parameter object
 // free string parameter
 CleanUp();
+}
 void Parameter::CleanUp(void) {
   if (arrowcolor)
     free(arrowcolor);
+     free(arrowcolor);
   if (textcolor)
     free(textcolor);
+     free(textcolor);
   if (cell_outline_color)
     free(cell_outline_color);
+     free(cell_outline_color);
   if (D)
     free(D);
+     free(D);
   if (initval)
     free(initval);
+     free(initval);
   if (datadir)
     free(datadir);
+     free(datadir);
   if (k)
     free(k);
+     free(k);
   if (s1)
     free(s1);
+     free(s1);
   if (s2)
     free(s2);
+     free(s2);
   if (s3)
     free(s3);
+     free(s3);
   if (dir1)
     free(dir1);
+     free(dir1);
   if (dir2)
     free(dir2);
      free(dir2);
   if (export_fn_prefix)
      free(export_fn_prefix);
+}
 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", 0, 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);
   datadir = AppendHomeDirIfPathRelative(datadir);
   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);
   export_interval = igetpar(fp, "export_interval", 100, true);
   export_fn_prefix = sgetpar(fp, "export_fn_prefix", "CELLDATA", true);
+}
 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 << " arrowcolor = " << arrowcolor << endl;
   os << " arrowsize = " << arrowsize << endl;
   if (textcolor)
-    os << " textcolor = " << textcolor << endl;
   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 << " 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) {
     QDir dataDir = QDir::home().relativeFilePath(datadir);
     os << " datadir = " << dataDir.dirName().toStdString() << endl;
+  }
   else {
     os << "datadir = ." << endl;
+  }
                                      QDir dataDir = QDir::home().relativeFilePath(datadir);
                                      os << " datadir = " << dataDir.dirName().toStdString() << endl;
+                                 }
                                  else {
                                      os << "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;
   os << " s1 = " << s1 << endl;
   if (s2)
-    os << " s2 = " << s2 << endl;
   os << " s2 = " << s2 << endl;
   if (s3)
-    os << " s3 = " << s3 << endl;
   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;
   os << " dir1 = " << dir1 << endl;
   if (dir2)
     os << " dir2 = " << dir2 << endl;
   os << " dir2 = " << dir2 << endl;
   os << " export_interval = " << export_interval << endl;
   if (export_fn_prefix)
   os << " export_fn_prefix = " << export_fn_prefix << 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;
     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;
   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;
 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;
   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;
 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;
 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;
 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;
 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;
   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;
 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;
 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;
 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;
 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;
 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;
 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;
 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;
 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;
 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;
 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;
 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());
+  }
 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);
+  {
     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());
     text << D[0];
     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 "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());
+    }
     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());
+  }
+  {
     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());
+    }
     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());
+  }
+  {
     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());
     text << initval[6];
     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 "r" );
     ostringstream text;
     text << r;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
     text << initval[7];
     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 "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());
     text << initval[8];
     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 "Pi_tot" );
     ostringstream text;
     text << Pi_tot;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
     text << initval[9];
     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 "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());
     text << initval[10];
     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 "pin_prod" );
     ostringstream text;
     text << pin_prod;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
     text << initval[11];
     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 "pin_prod_in_epidermis" );
     ostringstream text;
     text << pin_prod_in_epidermis;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
     text << initval[12];
     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 "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());
     text << initval[13];
     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 "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());
     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 "kap" );
     ostringstream text;
+}
+{
   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;
 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;
 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;
 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;
 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;
 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;
 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;
 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;
 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());
+  }
 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) {
                                      QDir dataDir = QDir::home().relativeFilePath(datadir);
                                      text << dataDir.dirName().toStdString();
+                                   }
 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);
+  {
     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) {
       QDir dataDir = QDir::home().relativeFilePath(datadir);
       text << dataDir.dirName().toStdString();
+    }
     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());
     text << k[0];
     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 "nu" );
     ostringstream text;
     text << nu;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
     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());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "rho0" );
     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 << rho0;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
     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());
+  }
+  {
     xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
     xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "rho1" );
     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 << rho1;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
     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());
+  }
+  {
     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());
     text << k[10];
     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 "gamma" );
     ostringstream text;
     text << gamma;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
     text << k[11];
     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 "eps" );
     ostringstream text;
     text << eps;
     xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
     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());
+  }
+  {
     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());
     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 "i2" );
     ostringstream text;
+}
+{
   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;
 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;
 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;
 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;
 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 (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 (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 (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 (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());
+  }
   if (dir2)
     text << dir2;
 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 "export_interval" );
   ostringstream text;
     text << export_interval;
 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 "export_fn_prefix" );
   ostringstream text;
   if (export_fn_prefix)
     text << export_fn_prefix;
 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);
     datadir = AppendHomeDirIfPathRelative(datadir);
+  }
   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);
 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);
   datadir = AppendHomeDirIfPathRelative(datadir);
+}
 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);
+}
 if (!strcmp(namec, "export_interval")) {
   export_interval = standardlocale.toInt(valc, &ok);
   if (!ok) { MyWarning::error("Read error: cannot convert string \"%s\" to integer while reading parameter 'export_interval' from XML file.",valc); }
+}
 if (!strcmp(namec, "export_fn_prefix")) {
   if (export_fn_prefix) { free(export_fn_prefix); }
   export_fn_prefix=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++);
+  }
+}
 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, "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++);
+  }
   if (!strcmp(namec, "k")) {
     int i=0;
     vector<double>::const_iterator v=valarray.begin();
     while (v!=valarray.end() && i <= 14 ) {
       k[i++]=*(v++);
+    }
+  }
+}
+}
 ostream &operator<<(ostream &os, Parameter &p) {
   p.Write(os);
   return os;
     p.Write(os);
     return os;
+}
 /* finis */

src/parameter.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
  *  VirtualLeaf 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.
+ *
  *  VirtualLeaf 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.
+ *
  */
 // WARNING: This file is automatically generated by make_parameter_source.pl. Do not edit.
 // All edits will be discarded.
 #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;
   int export_interval;
   char * export_fn_prefix;
  private:
  };
  ostream &operator<<(ostream &os, Parameter &p);
  const char *sbool(const bool &p);
 #endif
 /* finis */

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