# HG changeset patch
# User Michael Guravage <michael.guravage@cwi.nl>
# Date 2010-06-17 12:25:40
# Node ID a58b80c85b6f11fefdf9bdfd30a37644d4aa838f
# Parent  121f7720db6288cfbec7dbe0e9da43e7a9f01aa9

Cleanup: e.g. removed commented out and otherwise disabled code.
--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'

changed src/OptionFileDialog.cpp
changed src/OptionFileDialog.h
changed src/UniqueMessage.cpp
changed src/VirtualLeaf.cpp
changed src/apoplastitem.cpp
changed src/apoplastitem.h
changed src/build_models/auxingrowthplugin.cpp
changed src/build_models/meinhardtplugin.cpp
changed src/build_models/testplugin.h
changed src/canvas.cpp
changed src/canvas.h
changed src/cell.cpp
changed src/cell.h
changed src/cellbase.cpp
changed src/cellbase.h
changed src/data_plot.cpp
changed src/data_plot.h
changed src/flux_function.h
changed src/forwardeuler.cpp
changed src/infobar.h
changed src/mainbase.cpp
changed src/mainbase.h
changed src/matrix.cpp
changed src/mesh.h
changed src/modelcatalogue.cpp
changed src/node.cpp
changed src/node.h
changed src/nodeitem.cpp
changed src/nodeset.h
changed src/output.cpp
changed src/output.h
changed src/parse.cpp
changed src/parse.h
changed src/random.cpp
changed src/random.h
changed src/sqr.h
changed src/vector.h
changed src/vleafmodel.h
changed src/wall.cpp
changed src/wallbase.cpp
changed src/wallbase.h
changed src/wallitem.cpp
changed src/wallitem.h
changed src/warning.cpp
changed src/warning.h
changed src/xmlwrite.cpp

diff --git a/src/OptionFileDialog.cpp b/src/OptionFileDialog.cpp
--- a/src/OptionFileDialog.cpp
+++ b/src/OptionFileDialog.cpp
@@ -36,11 +36,7 @@ OptionFileDialog::OptionFileDialog(QWidg
 	parcheck = new QCheckBox("parameters", this);
 	parcheck -> setCheckState(Qt::Checked);
 	
-	//timecheck = new QCheckBox("time",this);
-	//timecheck -> setCheckState(Qt::Checked);
-	
 	addToolButton(geometrycheck);
-	//addToolButton(timecheck);
 	addToolButton(parcheck);
 
 };
diff --git a/src/OptionFileDialog.h b/src/OptionFileDialog.h
--- a/src/OptionFileDialog.h
+++ b/src/OptionFileDialog.h
@@ -20,6 +20,9 @@
  *
  */
 
+#ifndef _OPTIONFILEDIALOG_H_
+#define _OPTIONFILEDIALOG_H_
+
 #include <Q3FileDialog>
 #include <QCheckBox>
 
@@ -35,7 +38,6 @@ public:
 private:
 	QCheckBox *geometrycheck;	
 	QCheckBox *parcheck;
-	//QCheckBox *timecheck;
-	
+};
 
-};
+#endif
diff --git a/src/UniqueMessage.cpp b/src/UniqueMessage.cpp
--- a/src/UniqueMessage.cpp
+++ b/src/UniqueMessage.cpp
@@ -42,8 +42,6 @@ QDialog(parent, f) {
 	boxtext = text;
 	
 	show_again = new QCheckBox(tr("Do not show this message again"));
-	//addButton(show_again, QMessageBox::ActionRole);
-	//addButton(QMessageBox::Ok);
 	okButton = new QPushButton(tr("Ok"));
 		
 	if (issued_messages.contains(boxtext) ) {
@@ -51,8 +49,6 @@ QDialog(parent, f) {
 		cerr << "Saw message before\n";
 		display = false;
 	} else {
-		//cerr << "First time message\n";
-		//issued_messages << text;
 		display=true;
 	}
 	
diff --git a/src/VirtualLeaf.cpp b/src/VirtualLeaf.cpp
--- a/src/VirtualLeaf.cpp
+++ b/src/VirtualLeaf.cpp
@@ -57,18 +57,11 @@
 #include <QDir>
 #include "modelcatalogue.h"
 
-/* #define _xstr_(s) _str_(s)
-   #define _str_(s) #s
-   #include _xstr_(REACTIONS_HEADER)
-*/
-
 static const std::string _module_id("$Id$");
 
 extern Parameter par;
 
 MainBase *main_window = 0;
-//double auxin_account = 0.;
-
 
 #ifdef XFIGGRAPHICS
 #define TIMESTEP double Graphics::TimeStep(void)
@@ -192,16 +185,6 @@ void MainBase::Plot(int resize_stride) {
       fname.fill('0');
       fname.width(6);
 	
-      /* 
-	 fname << frame << ".pdf";
-	 if (par.storage_stride <= par.xml_storage_stride) {
-	 frame++;
-	 }
-			
-	 // Write high-res JPG snapshot every plot step
-	 Save(fname.str().c_str(), "PDF");
-      */
-			
       fname << frame << ".jpg";
       if (par.storage_stride <= par.xml_storage_stride) {
 	frame++;
@@ -277,36 +260,16 @@ TIMESTEP {
       //mesh.LoopCurrentCells(mem_fun(&plugin->CellHouseKeeping)); // this includes cell division
 				
       // Reaction diffusion	
-      /*CelltoCellTransport *transport_f = &TestPlugin::CelltoCellTransport;
-	CellReaction *cellreaction_f = new plugin->CellDynamics();
-	WallReaction *wall_f = new WallDynamics();*/
-				
       mesh.ReactDiffuse(par.rd_dt);
 				
       t++;
 				
       Plot(par.resize_stride);
 		
-      /*QVector< QPair<double, int> > angles=mesh.VertexAnglesValues();
-	QString afname=QString("Angles/anglesvalues%1.dat").arg(t,6,10,QChar('0'));
-	ofstream af(afname.toStdString().c_str());
-      */
-		
-      /*for (QVector< QPair<qreal, int> >::const_iterator v=angles.begin();
-	v!=angles.end();
-	v++) {
-	af << v->first << " " << v->second << endl;
-	}
-      */
     }
 		
   } else {
 			
-    /*  TransportFunction *transport_f = new CelltoCellTransport();
-	CellReaction *cellreaction_f = new CellDynamics();
-	WallReaction *wall_f = new WallDynamics();
-			
-	mesh.ReactDiffuse_New(transport_f, cellreaction_f, wall_f, par.rd_dt);*/
     mesh.ReactDiffuse(par.rd_dt);
 		
     Plot(par.resize_stride);
@@ -322,21 +285,7 @@ TIMESTEP {
 				
 /* Called if a cell is clicked */
 void Cell::OnClick(QMouseEvent *e) {
-
   e = NULL; // use assignment merely to obviate compilation warning
-
-  /* #ifdef HAVE_QWT
-  // Launch DataPlot window
-  QStringList curvenames;
-  for (int i=0;i<NChem();i++) {
-  curvenames += QString("Chem #%1").arg(i);
-  }
-  PlotDialog *plot = new PlotDialog((Main *)main_window, QString("Monitor for Cell %1").arg(Index()), curvenames);
-  QObject::connect(this, SIGNAL(ChemMonValue(double, double *)),
-  plot, SLOT(AddValue(double,double *)));
-  #endif
-  */
-  //getMesh().plugin->OnClick(*this);
 }
 				
 
@@ -478,17 +427,6 @@ int main(int argc,char **argv) {
       QObject::connect( qApp, SIGNAL(lastWindowClosed()), qApp, SLOT(quit()) );
     }
 
-    // Load plugins
-    /*QVector<SimPluginInterface *> plugins = LoadPlugins();
-      InstallPlugin(plugins[0], main_window);
-	  
-      cerr << "List of models:" << endl;
-      foreach (SimPluginInterface *p, plugins) {
-      cerr << p->ModelID().toStdString() << endl;
-      }
-    */
-
-	 	  
     // Install model or read catalogue of models
     ModelCatalogue model_catalogue(&mesh, useGUI?(Main *)main_window:0,modelfile);
     if (useGUI)
diff --git a/src/apoplastitem.cpp b/src/apoplastitem.cpp
--- a/src/apoplastitem.cpp
+++ b/src/apoplastitem.cpp
@@ -43,8 +43,8 @@ ApoplastItem::ApoplastItem( Wall *w, QGr
 	Vector offs = Cell::Offset();
 	double factor = Cell::Factor();
 	
-	Vector from = ( offs + *(w->N1()) ) * factor;// + (wn==1?-1:1) * par.outlinewidth;// * 0.2 * factor * perp;
-	Vector to = ( offs + *(w->N2()) ) *factor;// + (wn==1?-1:1) * par.outlinewidth;// * 0.2 * factor * perp;
+	Vector from = ( offs + *(w->N1()) ) * factor;
+	Vector to = ( offs + *(w->N2()) ) *factor;
 	
 	
 	setLine(( from.x ),
@@ -70,6 +70,6 @@ void ApoplastItem::setColor(void) {
 }
 
 void ApoplastItem::OnClick(QMouseEvent *e) {
-  e = NULL; // merely to obviate compile time warning
+  e = NULL; // merely to obviate compilation warnings
 }
 
diff --git a/src/apoplastitem.h b/src/apoplastitem.h
--- a/src/apoplastitem.h
+++ b/src/apoplastitem.h
@@ -40,8 +40,6 @@ public:
 	virtual ~ApoplastItem() {}
 	Wall &getWall(void) const { return *class_cast<Wall*>(obj); }
 	void OnClick(QMouseEvent *e);  
-	//virtual void userMove(double dx, double dy);  
-	//virtual void paint( QPainter * painter, const QStyleOptionGraphicsItem * option, QWidget * widget = 0);
 	void setColor(void);
 private:
 	int wn;
diff --git a/src/build_models/auxingrowthplugin.cpp b/src/build_models/auxingrowthplugin.cpp
--- a/src/build_models/auxingrowthplugin.cpp
+++ b/src/build_models/auxingrowthplugin.cpp
@@ -58,16 +58,6 @@ void AuxinGrowthPlugin::OnDivide(ParentI
 		w->setTransporter(daughter1, 1, 0.);
 	}
 	
-	//daughter1.LoopWalls(Wall::setTransporter(&daughter1, 1, 0.));
-	
-	
-	/* for (list<Wall *>::const_iterator w=daughter2.walls.begin();
-		 w!=daughter2.walls.end();
-		 w++) {
-		// reset transporter value
-		(*w)->setTransporter(&daughter2, 1, 0.);
-	}
-	*/
 }
 
 void AuxinGrowthPlugin::SetCellColor(CellBase *c, QColor *color) { 
@@ -106,7 +96,6 @@ void AuxinGrowthPlugin::CelltoCellTransp
 		if (w->AuxinSource()) {
 			double aux_flux = par->leaf_tip_source * w->Length();
 			dchem_c1[0]+= aux_flux;
-			// dchem_c2 is undefined..!
 			return;
 		} else {
 			return;
@@ -119,7 +108,6 @@ void AuxinGrowthPlugin::CelltoCellTransp
 		if (w->AuxinSource()) {
 			double aux_flux = par->leaf_tip_source * w->Length();
 			dchem_c2[0] += aux_flux;
-			// dchem_c1 is undefined...!
 			return;
 		} else {
 			
@@ -167,7 +155,6 @@ void AuxinGrowthPlugin::WallDynamics(Wal
 		if (w->AuxinSink()) {
 			
 			dw1[0] = 0.; dw2[0] = 0.;
-			//dw1[2] = 0.; dw2[2] = 0.;
             
 			// assume high auxin concentration in SAM, to convince PIN1 to polarize to it
 			// exocytosis regulated0
@@ -180,7 +167,7 @@ void AuxinGrowthPlugin::WallDynamics(Wal
 			return;
 			
 		} else {
-			dw1[0]=dw2[0]=dw1[1]=dw2[1];//=dw1[2]=dw2[2];
+			dw1[0]=dw2[0]=dw1[1]=dw2[1];
 			return;
 		}
     }
@@ -189,7 +176,6 @@ void AuxinGrowthPlugin::WallDynamics(Wal
 		if (w->AuxinSink())  {
 			
 			dw1[0] = 0.; dw2[0] = 0.;
-			//dw1[2] = 0.; dw2[2] = 0.;
 			
 			// assume high auxin concentration in SAM, to convince PIN1 to polarize to it
 			// exocytosis regulated
@@ -201,7 +187,7 @@ void AuxinGrowthPlugin::WallDynamics(Wal
 			return;
 			
 		}  else {
-			dw1[0]=dw2[0]=dw1[1]=dw2[1];//=dw1[2]=dw2[2];
+			dw1[0]=dw2[0]=dw1[1]=dw2[1];
 			return;
 		}
     }
@@ -237,8 +223,6 @@ void AuxinGrowthPlugin::WallDynamics(Wal
     /* PIN1 of neighboring vascular cell inhibits PIN1 endocytosis */
     
     dw1[0] = 0.; dw2[0] = 0.;
-    //dw1[2] = 0.; dw2[2] = 0.;
-    
     dw1[1] = dPijdt1;
     dw2[1] = dPijdt2;
 }
@@ -264,14 +248,6 @@ void AuxinGrowthPlugin::CellDynamics(Cel
 		// exocytosis regulated:
 	
 	dPidt = -par->k1 * c->ReduceCellAndWalls<double>( far_3_arg_mem_fun( *this, &AuxinGrowthPlugin::complex_PijAj ) ) + par->k2 * sum_Pij;
-	/*for ( list<Wall *>::const_iterator w = c->walls.begin();
-		 w!=walls.end();
-		 w++) {
-		if ((*w)->C1() == c)
-			dPidt +=  complex_PijAj( (*w)->C1(), (*w)->C2(), *w );
-		else
-			dPidt +=  complex_PijAj( (*w)->C2(), (*w)->C1(), *w );
-	}*/
 	
 	// production of PIN depends on auxin concentration
 	dPidt +=  (c->AtBoundaryP()?par->pin_prod_in_epidermis:par->pin_prod) * c->Chemical(0) - c->Chemical(1) * par->pin_breakdown;
diff --git a/src/build_models/meinhardtplugin.cpp b/src/build_models/meinhardtplugin.cpp
--- a/src/build_models/meinhardtplugin.cpp
+++ b/src/build_models/meinhardtplugin.cpp
@@ -117,19 +117,13 @@ void MeinhardtPlugin::CellDynamics(CellB
 	double A = c->Chemical(1);
 	double H = c->Chemical(2);
 	double S = c->Chemical(3);
-	//double expansin = c->Chemical(4);
+
 	
 	
     dchem[0] = ( par->d * A - par->e * Y + Y*Y/(1 + par->f * Y*Y ) );
 	dchem[1] = ( par->c * A*A*S/H - par->mu * A + par->rho0*Y );
 	dchem[2] = ( par->c * A*A*S - par->nu*H + par->rho1*Y );
 	dchem[3] = ( par->c0 - par->gamma*S - par->eps * Y * S );
-	//dchem[4] = ( -par->expansindecay * expansin );
-	//for (int i=0;i<4;i++) { cerr << "[ " << dchem[i] << " ]"; } cerr << endl;
-	 
-//	cerr << "Chemicals: "; for (int i=0;i<NChem();i++) { cerr << c->Chemical(i) << " "; } cerr << endl; 
-	
-// test:	dchem[0] = 0.01 * c->Chemical(0) * ( 1. - c->Chemical(0));
 }
 
 
diff --git a/src/build_models/testplugin.h b/src/build_models/testplugin.h
--- a/src/build_models/testplugin.h
+++ b/src/build_models/testplugin.h
@@ -20,6 +20,8 @@
  *
  */
 
+#ifndef _TESTPLUGIN_H_
+#define _TESTPLUGIN_H_
 
 #include <QObject>
 #include <QtGui>
@@ -55,6 +57,4 @@ public:
 	virtual int NChem(void) { return 0; }
 };
 
-
-
-
+#endif
diff --git a/src/canvas.cpp b/src/canvas.cpp
--- a/src/canvas.cpp
+++ b/src/canvas.cpp
@@ -163,11 +163,6 @@ void FigureEditor::mousePressEvent(QMous
 #endif
   
 
-  /*  if (dynamic_cast<Main *>(parent())->RotationModeP()) {
-  // if in rotation mode, exit it upon a mouse click
-  dynamic_cast<Main *>(parent())->ExitRotationMode();
-  }*/
-  
   QList<QGraphicsItem *> l=scene()->items(p);
 
 #ifdef QDEBUG  
@@ -175,45 +170,6 @@ void FigureEditor::mousePressEvent(QMous
   qDebug() << "Mouse button modifier: " << e->modifiers() << endl;
 #endif
 
-
-    /*  if (rotation_mid_point) {
-    
-    // calculate rotation angle alpha
-    QPointF q_v1 = intersection_line->line().p2();
-    - intersection_line->line().p1();
-    QPointF q_v2 = angle_line->line().p2();
-    - angle_line->line().p1();
-    
-    Vector v1(q_v1.x(),q_v1.y());
-    Vector v2(q_v2.x(),q_v2.y());
-    
-    cerr << "v1 = " << v1 << endl;
-    cerr << "v2 = " << v2 << endl;
-    
-    
-    rot_angle = v1.SignedAngle(v2);
-    cerr << "Angle is " << rot_angle << endl;
-    
-    const QPointF &q_c(angle_line->line().p1());
-    Vector center = Vector(q_c.x(), q_c.y()) / Cell::Factor() - Cell::Offset();
-    
-    cerr << "Center is " << center << endl;
-    
-    mesh.Rotate(rot_angle, center);
-    delete angle_line;
-    angle_line=0;
-    delete intersection_line;
-    intersection_line=0;
-    
-    viewport()->setMouseTracking( FALSE );
-    dynamic_cast<Main *>(parent())->Plot();
-    
-    
-    return;
-    
-    }*/
-  
-   
     if (e->button()==Qt::RightButton || l.size()==0) {
     
       //cerr << "Drawing an intersection line from " << p.x() << ", " << p.y() << endl;
@@ -225,19 +181,11 @@ void FigureEditor::mousePressEvent(QMous
     }
   
     for (QList<QGraphicsItem *>::Iterator it=l.begin(); it!=l.end(); ++it) {
-      /*if ( (*it)->rtti() == imageRTTI ) {
-	ImageItem *item= (ImageItem*)(*it);
-	if ( !item->hit( p ) )
-	continue;
-	}*/
       #ifdef QDEBUG
       qDebug() << typeid(**it).name() << endl;
       #endif
 
       if ( !strcmp(typeid(**it).name(),"8NodeItem")) {
-	//moving = dynamic_cast<NodeItem*>(*it);
-	//moving = *it;
-	//moving_start = p;
       
 	stringstream data_strstream;
 	data_strstream << (dynamic_cast<NodeItem*>(*it))->getNode();
@@ -249,19 +197,6 @@ void FigureEditor::mousePressEvent(QMous
 	if ( !strcmp(typeid(**it).name(),"8CellItem") ) {
       
 	  Cell &c=((dynamic_cast<CellItem *>(*it))->getCell());      
-	  //static int old_stride=100;
-	  //if (!c.Source()) {
-	  /* if (!c.Source()) {
-	     c.SetChemical(0,par.cellsource);
-	     //flag=true;
-	     //c.SetSource(0,par.cellsource);
-	     //c.Fix();
-	     //cerr << "Setting source\n";
-			
-	     } else { 
-	     //c.UnsetSource();
-	     cerr << "Unsetting source\n";
-	     } */
 	  // OnClick to be defined in end-user code
 	  c.OnClick(e);
 	} else {
@@ -300,15 +235,13 @@ void FigureEditor::mouseMoveEvent(QMouse
     
     mesh.Rotate(d_alpha, ( Vector(rotation_midpoint) + Cell::Offset() ) / Cell::Factor() );
     
-    //viewport()->setMouseTracking( FALSE );
     dynamic_cast<Main *>(parent())->Plot(0);
 	  FullRedraw();
     return;
   }
   if ( moving ) {
-    //QPoint p = matrix().inverted().map(e->pos());
+
     QPointF p = mapToScene(e->pos());
-    
     moving->userMove(p.x() - moving_start.x(),
 		     p.y() - moving_start.y());
     moving_start = p;
@@ -319,28 +252,16 @@ void FigureEditor::mouseMoveEvent(QMouse
   //cerr << "event";
   
   // keep track of intersection line to interactively cut a growing leaf
-  /* if (angle_line) {
-
-    QPointF sp = angle_line -> line().p1(); // startpoint
-    //QPointF ep = matrix().inverted().map(e->pos()); // endpoint
-    QPointF ep = mapToScene(e->pos()); // endpoint
-    angle_line -> setLine( QLineF(sp, ep) ); 
-    scene()->update();
-  
-    } else { */
     
   if ( intersection_line ) {
     
     QPointF sp = intersection_line -> line().p1(); // startpoint
-    //QPointF ep = matrix().inverted().map(e->pos()); // endpoint
     QPointF ep = mapToScene(e->pos()); // endpoint
     intersection_line -> setLine( QLineF(sp, ep) ); 
     scene()->update();
     // Need this for Mac
     FullRedraw();
     }
-  /* } */
-  
 }
 
 //void FigureEditor::contentsMouseReleaseEvent(QMouseEvent* e)
@@ -356,7 +277,6 @@ void FigureEditor::mouseReleaseEvent(QMo
       qDebug() << "Trying to cut leaf" << endl;
       #endif
       QPointF sp = intersection_line -> line().p1(); // startpoint
-      //QPointF ep = matrix().inverted().map(e->pos()); // endpoint
       QPointF ep = mapToScene(e->pos());
 
       intersection_line -> setLine( QLineF(sp, ep) ); 
@@ -376,14 +296,12 @@ void FigureEditor::mouseReleaseEvent(QMo
       Vector startpoint = Vector(sp.x(), sp.y()) / Cell::Factor() - Cell::Offset();
       Vector endpoint = Vector(ep.x(), ep.y()) / Cell::Factor() - Cell::Offset();
     
-      // Mesh &m(intersected_cells.front()->getCell().getMesh());
       NodeSet *node_set = new NodeSet;
       
       for (vector<CellItem *>::iterator it = intersected_cells.begin();
 	   it != intersected_cells.end();
 	   it++) {
       
-	//(*it)->Mark();
 	(*it)->setBrush(QBrush("purple"));
        
 	Cell &c=(*it)->getCell();
@@ -412,7 +330,6 @@ void FigureEditor::mouseReleaseEvent(QMo
       mesh.TestIllegalWalls();
       // Do the actual cutting and removing
       if (intersected_cells.size()) {
-	//      Mesh &m(intersected_cells.front()->getCell().getMesh());
 	mesh.CutAwayBelowLine( startpoint, endpoint ); 
 	
 	// Correct flags of nodeset
@@ -465,19 +382,11 @@ void FigureEditor::mouseReleaseEvent(QMo
       
       if (intersection_line /* && !angle_line*/) {
 	
-	//QPointF p = matrix().inverted().map(e->pos());
 	QPointF p = mapToScene(e->pos());
 	QPointF sp = intersection_line->line().p1();
 	
 	viewport()->setMouseTracking( TRUE );
-	/* angle_line = new QGraphicsLineItem( 0, scene() );
-	angle_line->setPen( QPen( QColor("Blue"), 3, Qt::DashLine ) );
-	angle_line->setLine( QLineF(sp, p) );
-	angle_line->setZValue( 100 );
-	angle_line->show();
-	*/
       } 
-            
     }
 }
 
@@ -500,9 +409,7 @@ vector <CellItem *> FigureEditor::getInt
     #endif
     
     if ( !strcmp(typeid(**it).name(),"8CellItem") ) {
-      
       colliding_cells.push_back(dynamic_cast<CellItem *>(*it));
-      
     }
   }
   
@@ -555,8 +462,6 @@ Main::Main(QGraphicsScene& c, Mesh &m, Q
   Q3MainWindow(parent,name,f),
   MainBase(c,m),
   mesh(m)
-	   
-	  //canvas(c)
 {
   editor = new FigureEditor(canvas,mesh, this);
 
@@ -570,18 +475,16 @@ Main::Main(QGraphicsScene& c, Mesh &m, Q
   QMenuBar* menu = menuBar();
   
   Q3PopupMenu* file = new Q3PopupMenu( menu );
- // file->insertItem("&Fill canvas", this, SLOT(init()), Qt::CTRL+Qt::Key_F);
+
 	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->insertItem("&New view", this, SLOT(newView()), Qt::CTRL+Qt::Key_N);
+
    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("Read &parameters", this, SLOT(readPars()));
-  //file->insertItem("&Write parameters", this, SLOT(savePars()));
 	
 	file->insertSeparator();
 	file->insertItem("&Print...", this, SLOT(print()), Qt::CTRL+Qt::Key_P);
@@ -598,25 +501,19 @@ Main::Main(QGraphicsScene& c, Mesh &m, Q
   menu->insertItem("&Edit", edit);
 
   run = new Q3PopupMenu( menu );
-  //  edit->insertItem("Add &Polygon", this, SLOT(addPolygon()), ALT+Key_P);
-  //edit->insertItem("Add &Line", this, SLOT(addLine()), ALT+Key_L);
   running = false;
 	paused_id = run->insertItem("&Simulation paused", this, SLOT(togglePaused()), Qt::Key_S);
   run->setItemChecked(paused_id, FALSE);
 
-  //run->insertItem("&Divide Cell", this, SLOT(Divide()), Qt::CTRL+Qt::Key_D);
- // run->insertItem("&Restart Simulation", this, SLOT(RestartSim())); 
   menu->insertItem("&Run", run);
   
   view = new Q3PopupMenu( menu );
-  //view->insertItem("&Enlarge", this, SLOT(enlarge()), SHIFT+CTRL+Key_Plus);
-  //view->insertItem("Shr&ink", this, SLOT(shrink()), SHIFT+CTRL+Key_Minus);
 	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);
-  //view->insertItem("Cell monitor", this, SLOT(cellmonitor()));
+
   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);
@@ -638,7 +535,6 @@ Main::Main(QGraphicsScene& c, Mesh &m, Q
   view->setItemChecked(apoplasts_id, FALSE);
  	view->insertSeparator();
 	  only_boundary_id = view->insertItem("Show only leaf &boundary", this, SLOT(toggleLeafBoundary()));
-  //only_boundary_id = view->insertItem("Show only leaf &boundary", 0,0);
 	view->insertSeparator();
 	movie_frames_id = view->insertItem("Start saving movie &frames", this, SLOT(toggleMovieFrames()));
   view->setItemChecked(movie_frames_id, par.movie);
@@ -648,8 +544,6 @@ Main::Main(QGraphicsScene& c, Mesh &m, Q
   
   
   options = new Q3PopupMenu( menu );
-  /* dbf_id = options->insertItem("Double buffer", this, SLOT(toggleDoubleBuffer()));
-     options->setItemChecked(dbf_id, TRUE);*/
   dyn_cells_id = options->insertItem("Cell growth", this, SLOT(toggleDynCells()));
   options->setItemChecked(dyn_cells_id, true);
 
@@ -673,30 +567,10 @@ Main::Main(QGraphicsScene& c, Mesh &m, Q
   helpmenu->insertSeparator();
 
   helpmenu->insertItem("&About", this, SLOT(help()) ); //, Key_F1);
-  //help->insertItem( "What's &This", this , SLOT(whatsThis()), SHIFT+Key_F1);
   menu->insertItem("&Help",helpmenu);
-  //QSlider *flux_arrow_slider = new QSlider( 0, 10000, 1, 100, Qt::Horizontal, this, "flux arrow size");
-  //QSpinBox *stride  = new QSpinBox( 1, 1000, 1, this, "stride");
-  
-	    
-  //QGridLayout *controlgrid = new QGridLayout( this, 1, 2, 10);
-  // 2x1, 10 pixel border
-  
-  //controlgrid->addWidget( stride, 0, 0);
-  //controlgrid->addWidget( flux_arrow_slider, 0, 1);
-  //controlgrid->setColStretch( 1, 10 );
-  
-  
-  //flux_arrow_size = 1.;
-  //flux_arrow_slider -> setMinimumSize( 200,50);
-  //connect( flux_arrow_slider, SIGNAL( valueChanged( int ) ), this, SLOT( setFluxArrowSize(int) ) );
-  
   statusBar();
-  
   setCentralWidget(editor);
-
   printer = 0;
-
   init();
     
   // Start timer which repetitively invokes
@@ -709,20 +583,6 @@ Main::Main(QGraphicsScene& c, Mesh &m, Q
   setCaption(caption);
   gifanim = 0;
 	
-	// A little bit of PSB/CWI decoration ;-)
-	/*dockwindow = new Q3DockWindow();
-	addDockWindow(dockwindow);
-	QLabel *viblab = new QLabel; viblab->setPixmap(QPixmap(cwi_xpm));
-	QString virtleafstring("<h1>The Virtual Leaf</h1>\n<center><b>Model:</b> <i>%1</i></center>");
-	QLabel *virtleaf = new QLabel(virtleafstring.arg(mesh.ModelID()));
-	QLabel *psblab = new QLabel; psblab->setPixmap(QPixmap(PSB_xpm));
-	dockwindow->setHorizontalStretchable(true);
-	dockwindow->boxLayout()->addWidget(viblab);//,Qt::AlignLeft);
-	dockwindow->boxLayout()->addStretch();
-	dockwindow->boxLayout()->addWidget(virtleaf);//, Qt::AlignHCenter);
-	dockwindow->boxLayout()->addStretch();
-	dockwindow->boxLayout()->addWidget(psblab);//, Qt::AlignRight);*/
-	//QString virtleafstring("<h1>The Virtual Leaf</h1>\n<center><b>Model:</b> <i>%1</i></center>");
 	infobar = new InfoBar();
 	addDockWindow(infobar);
 
@@ -783,9 +643,6 @@ void Main::EditParameters() {
 
 void Main::savePars() {
   
-  // bool timer_active;
-  /* if (timer_active=timer->isActive())
-     imer->stop();*/
   stopSimulation();
   
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
@@ -826,10 +683,6 @@ void Main::readPars() {
 
 void Main::saveStateXML() {
   
-   
-  //   bool timer_active;
-  //   if (timer_active=timer->isActive())
-  //     timer->stop();
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
   fd->setMode( Q3FileDialog::AnyFile );
@@ -863,9 +716,6 @@ void Main::saveStateXML() {
 void Main::snapshot() {
   
    
-  //   bool timer_active;
-  //   if (timer_active=timer->isActive())
-  //     timer->stop();
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "Save snapshot", TRUE );
   fd->setMode( Q3FileDialog::AnyFile );
@@ -931,8 +781,6 @@ void Main::readPrevStateXML() {
     readStateXML((const char *)next_file);
     
   }
-  
-  
 }
 
 int Main::readStateXML(const char *filename, bool geometry, bool pars, bool simtime) {
@@ -953,7 +801,7 @@ int Main::readStateXML(const char *filen
     currentFile =  QString(filename);
 	
     Plot();
-    QString status_message = QString("Succesfully read leaf from file %1. Time is %2 h.\n").arg(currentFile).arg(mesh.getTimeHours().c_str());
+    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);
@@ -1081,26 +929,6 @@ void Main::readStateXML() {
 	
     if (readStateXML((const char *)fileName,fd->readGeometryP(), fd->readParametersP()) )
       return readStateXML(); // user can try again
-    
-//     try {
-//       mesh.XMLRead((const char *)fileName);
-//       currentFile =  fileName;
-//     } catch (const char *error_message) {
-//       QMessageBox mb( "Read leaf from XML file",
-// 		      QString(error_message),
-// 		      QMessageBox::Critical,
-// 		      QMessageBox::Ok | QMessageBox::Default,
-// 		      QMessageBox::NoButton,
-// 		      QMessageBox::NoButton);
-//       mb.exec();
-//       return readStateXML(); // user can try again
-//     }
-    
-//     Vector bbll,bbur;
-//     mesh.BoundingBox(bbll,bbur);
-    
-//     //FitLeafToCanvas();
-//     Plot();
   }
 }
 
@@ -1133,24 +961,13 @@ void Main::help()
     QMessageBox::aboutQt( this, "Virtual Leaf" );
   }
 
-/* void Main::toggleDoubleBuffer()
-{
-  bool s = !options->isItemChecked(dbf_id);
-  options->setItemChecked(dbf_id,s);
-  canvas.setDoubleBuffering(s);
-}
-*/
   void Main::toggleShowCellCenters()
   {
-    //bool s = !view->isItemChecked(com_id);
-    //view->setItemChecked(com_id,s);
     Plot();
   }
 
   void Main::toggleShowWalls()
   {
-    //bool s = !view->isItemChecked(cell_walls_id);
-    //view->setItemChecked(cell_walls_id,s);
     Plot();
   }
 void Main::toggleShowApoplasts()
@@ -1159,50 +976,30 @@ void Main::toggleShowApoplasts()
 }
   void Main::toggleShowNodes()
   {
-    //bool s = !view->isItemChecked(mesh_id);
-    //view->setItemChecked(mesh_id,s);
     Plot();
   }
 
   void Main::toggleNodeNumbers(void) {
-  
-    //bool s = !view->isItemChecked(node_number_id);
-    //view->setItemChecked(node_number_id,s);
     Plot();
   }
 
   void Main::toggleCellNumbers(void) {
-  
-    //bool s = !view->isItemChecked(cell_number_id);
-    //view->setItemChecked(cell_number_id,s);
     Plot();
   }
 
   void Main::toggleCellAxes(void) {
-  
-    //bool s = !view->isItemChecked(cell_axes_id);
-    //view->setItemChecked(cell_axes_id,s);
     Plot();
   }
 
   void Main::toggleCellStrain(void) {
-  
-    //bool s = !view->isItemChecked(cell_strain_id);
-    //view->setItemChecked(cell_strain_id,s);
     Plot();
   }
 
   void Main::toggleShowFluxes(void) {
-  
-    //bool s = !view->isItemChecked(fluxes_id);
-    //view->setItemChecked(fluxes_id,s);
     Plot();
   }
 
-  void Main::toggleShowBorderCells()
-  {
-    //bool s = !view->isItemChecked(border_id);
-    //view->setItemChecked(border_id,s);
+  void Main::toggleShowBorderCells(){
     Plot();
   }
 
@@ -1210,34 +1007,19 @@ void Main::toggleHideCells(void) {
 	Plot();
 	editor->FullRedraw();
 }
-  void Main::toggleMovieFrames()
-  {
-    //bool s = !view->isItemChecked(movie_frames_id);
-    //view->setItemChecked(movie_frames_id,s);
-  }
+  void Main::toggleMovieFrames(){}
+
+  void Main::toggleLeafBoundary(){}
 
-  void Main::toggleLeafBoundary()
-  {
-    //bool s = !view->isItemChecked(only_boundary_id);
-    //view->setItemChecked(only_boundary_id,s);
-  }
-
-  void Main::toggleDynCells()
-  {
-    //bool s = !options->isItemChecked(dyn_cells_id);
-    //options->setItemChecked(dyn_cells_id,s);
-  }
-
-
+  void Main::toggleDynCells() {}
+  
   void Main::startSimulation(void) {
-    //run->setItemChecked(paused_id, false);
     timer->start( 0 );
     statusBar()->message("Simulation started");
     running = true;
   }
 
   void Main::stopSimulation(void) {
-    //run->setItemChecked(paused_id, true);
     timer->stop();
     cerr << "Stopping simulation" << endl;
     statusBar()->message("Simulation paused");
@@ -1264,19 +1046,14 @@ void Main::toggleHideCells(void) {
 
   void Main::enlarge()
   {
-    //canvas.resize(canvas.width()*4/3, canvas.height()*4/3);
     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::scrollBy(int dx, int dy) {
-    editor->scrollBy(dx,dy);
-    }*/
 
   void Main::scale(double factor) {
     QMatrix m = editor->matrix();
@@ -1365,70 +1142,6 @@ void Main::toggleHideCells(void) {
     //startSimulation();
   }
 
-  /*
-    void Main::SaveToGifAnim(void) {
-  
-    if (gifanim) {
-    
-    QPixmap image(canvas.width(), canvas.height());
-    QPainter im(&image);
-    
-    
-    canvas.drawArea(QRect(0,0,canvas.width(),canvas.height()),&im,FALSE);
-    QFile conversionpipe;
-    conversionpipe.open ( IO_WriteOnly, popen("pngtopnm | ppmtogif > tmp.gif", "w") );
-    image.save( &conversionpipe, "PNG");
-    conversionpipe.close();
-    
-    QFile readconvertedimage("tmp.gif");
-    readconvertedimage.open(IO_ReadOnly);
-    int c;
-    while ( (c=readconvertedimage.getch())!=-1) {
-    gifanim->putch(c);
-    }
-    }
-    }*/
-
-  /* void Main::StartGifAnim(QString fname) {
-  
-  if (gifanim) {
-  QMessageBox::information( this, "Animation",
-  "Already making another animation."
-  "Please end it and try again.",
-  QMessageBox::Ok );
-  } else {
-    
-  QString cmdline("gifsicle --multifile - > ");
-  cmdline += fname;
-    
-  gifanim = new QFile;
-  gifanim->open( IO_WriteOnly, 
-  popen((const char *)cmdline, "w") );
-    
-  */   /* QStringList cmdline;
-	  cmdline << "gifsicle" << "--multifile" << "-";
-	  gifanim = new QProcess( cmdline );
-       
-	  cmdline.clear();
-	  cmdline << "pngtopnm";
-	  pngtopnm = new QProcess( cmdline );
-	  pngtopnm->start();
-       
-	  cmdline.clear();
-	  cmdline << "ppmtogif";
-	  ppmtogif = new QProcess( cmdline );
-	  ppmtogif->start();*/
-       /*  }
-
-       }*/
-
-       /*void Main::EndGifAnim(void) {
-  
-       if (gifanim)
-       gifanim->close();
-
-       }*/
-
 
 void Main::FitCanvasToWindow(void) {
   
@@ -1495,8 +1208,6 @@ void Main::CleanMesh(void) {
 	Plot();
 	
 	editor->FullRedraw();
-	
-  //  repaint();
 }
 
 void Main::CleanMeshChemicals(void) {
@@ -1512,8 +1223,6 @@ void Main::CleanMeshChemicals(void) {
 	Plot();
 	
 	editor->FullRedraw();
-	
-	//  repaint();
 }
 
 void Main::CleanMeshTransporters(void) {
@@ -1528,8 +1237,6 @@ void Main::CleanMeshTransporters(void) {
 	Plot();
 	
 	editor->FullRedraw();
-	
-	//  repaint();
 }
 
 void Main::RandomizeMesh(void) {
diff --git a/src/canvas.h b/src/canvas.h
--- a/src/canvas.h
+++ b/src/canvas.h
@@ -75,9 +75,6 @@ class FigureEditor : public QGraphicsVie
   void FullRedraw(void);
 
 protected:
-  /* void contentsMousePressEvent(QMouseEvent*);
-  void contentsMouseMoveEvent(QMouseEvent*);
-  void contentsMouseReleaseEvent(QMouseEvent*);*/
   void mousePressEvent(QMouseEvent*);
   void mouseMoveEvent(QMouseEvent*);
   void mouseReleaseEvent(QMouseEvent*);
@@ -134,10 +131,6 @@ class Main : public Q3MainWindow, public
   virtual double getFluxArrowsize(void) {
     return flux_arrow_size;
   }
-  //void Save(const char *fname, const char *format);
-  /*void StartGifAnim(QString fname);
-    void SaveToGifAnim(void);
-    void EndGifAnim(void);*/
     
   void FitCanvasToWindow();
   void FitLeafToCanvas(void);
@@ -147,12 +140,9 @@ class Main : public Q3MainWindow, public
 
   void help();
   void TimeStepWrap();
-  //void scrollBy(int dx, int dy);
   void togglePaused();
   void setFluxArrowSize(int size);
-  //void Divide(void);
   void RestartSim(void);
-  //void toggleDoubleBuffer(void);
   void toggleShowCellCenters(void);
   void toggleShowNodes(void);
   void toggleShowBorderCells(void);
@@ -162,7 +152,7 @@ class Main : public Q3MainWindow, public
   void toggleCellAxes(void);
   void toggleCellStrain(void);
   void toggleShowWalls(void);
-	void toggleShowApoplasts(void);
+  void toggleShowApoplasts(void);
   void toggleDynCells(void);
   void toggleMovieFrames(void);
   void toggleLeafBoundary(void);
@@ -214,13 +204,6 @@ class Main : public Q3MainWindow, public
   void clear();
   void init();
   virtual void CutSAM() { MainBase::CutSAM(); Refresh();}
-/*   void cellmonitor() { */
-/*     PlotDialog *plot = new PlotDialog(this); */
-/*     cerr << "Attempting to launch a cell monitor\n"; */
-/*   } */
-  
-  //void addPolygon();
-  //void addLine();
 
   void enlarge();
   void shrink();
@@ -243,7 +226,6 @@ class Main : public Q3MainWindow, public
  private:
   NodeSet *node_set;
   FigureEditor *editor;
-  //QCanvas& canvas;
   Q3PopupMenu* options;
   Q3PopupMenu *view;
   Q3PopupMenu *run;
diff --git a/src/cell.cpp b/src/cell.cpp
--- a/src/cell.cpp
+++ b/src/cell.cpp
@@ -94,10 +94,7 @@ void Cell::DivideOverAxis(Vector axis) {
 			
 			new_node_locations.push_back(i);
 			
-		} // else {
-		//       //cerr << "cross.z * prev_cross_z = " << cross.z * prev_cross_z << endl;
-		//     }
-		
+		}		
 		prev_cross_z=cross.z;
 	}
 	
@@ -220,52 +217,6 @@ void Cell::Apoptose(void) {
 	
 	
 	
-	/*
-	 // correct boundary polygon if this cell touches the boundary
-	 
-	 // find the first living boundary node after a dead node
-	 bool node_found = false;
-	 for (list<Node *>::iterator n=nodes.begin();
-	 n!=nodes.end();
-	 n++) {
-	 
-	 Node &no(*(*n));
-	 
-	 if (no.DeadP()) {
-	 
-	 list<Node *>::iterator first_node = n; 
-	 if (++next_node == nodes.end()) first_node=nodes.begin();
-	 
-	 if (!(*(*first_node)).DeadP() && ((*first_node)->boundary)) {
-	 node_found=true;
-	 break;
-	 }
-	 
-	 }
-	 }
-	 
-	 // locate it in the boundary_polygon
-	 if (node_found) {
-	 list<Node *>::iterator insert_it = find(mesh->boundary_polygon->nodes.begin(),
-	 mesh->boundary_polygon->nodes.end(),
-	 ++first_node);
-	 if (insert_it!=owners.end()) {
-	 
-	 if (insert_it==owners.end()) insert_it=owners.begin();
-	 
-	 for (list<Node *>::iterator n=insert_it;
-	 n!=nodes.end();
-	 n++) {
-	 
-	 Node &no(*(*n));
-	 
-	 mesh->boundary_polygon->nodes.insert(
-	 
-	 }
-	 
-	 
-	 }
-	 } */
 	// mark cell as dead
 	MarkDead();
 }
@@ -364,8 +315,6 @@ bool Cell::DivideOverGivenLine(const Vec
 		double ub = 
 		((v2.x - v1.x)*(v1.y-v3.y) - (v2.y- v1.y)*(v1.x - v3.x))/denominator;
 		
-		/* double intersec_x = v1.x + ua*(v2.x-v1.x);
-		 double intersec_y = v1.y + ua*(v2.y-v1.y);*/
 		
 		//cerr << "Edge " << *i << " to " << *nb << ": ua = " << ua << ", ub = " << ub << ":  ";
 		// this construction with "TINY" should simulate open/closed interval <0,1]
@@ -433,8 +382,6 @@ void Cell::DivideWalls(ItList new_node_l
 	}
 	
 	daughter->cell_type = cell_type;
-	//extern double auxin_account;
-	//auxin_account += daughter->chem[0];
 	
 	for (int i=0;i<NChem();i++) {
 		daughter->new_chem[i]=new_chem[i];
@@ -448,7 +395,6 @@ void Cell::DivideWalls(ItList new_node_l
 	
 	target_area/=2;
 	daughter->cellvec=cellvec;
-//	daughter->BaseArea()  = base_area;
 	
 	
 	// Division currently only works for convex cells: i.e. if the division line
@@ -617,11 +563,6 @@ void Cell::DivideWalls(ItList new_node_l
 				(new_node_ind[i])->fixed = true;
 				
 				// All this we'll do later for the node set only
-				/* (new_node_ind[i])->boundary = true;
-				 (new_node_ind[i])->sam = true;
-				 boundary_touched_flag = true;
-				 boundary = SAM;
-				 daughter->boundary = SAM;*/
 			}
 			
 			// if new node is inserted into the boundary
@@ -806,7 +747,7 @@ void Cell::DivideWalls(ItList new_node_l
 			
 			if (w == walls.end()) {
 			        #ifdef QDEBUG
-			  qDebug() << "Whoops, wall element not found...!" << endl;
+			        qDebug() << "Whoops, wall element not found...!" << endl;
 			        qDebug() << "Cell ID: " << neighbor_cell->Index() << endl;
 				qDebug() << "My cell ID: " << Index() << endl;
                                 #endif
@@ -839,18 +780,6 @@ void Cell::DivideWalls(ItList new_node_l
 					}
 					
 					
-					//new_wall->ResetTransporterConcentrations(orig_length);
-					//(*w)->ResetTransporterConcentrations(orig_length);
-					
-					// reset the transporter concentrations
-					
-					
-					/*	  new_wall->SetLength();
-					 new_wall->CorrectLength(orig_length);
-					 
-					 (*w)->SetLength();
-					 (*w)->CorrectLength(orig_length);*/
-					
 					// 3. Give wall elements to appropriate cells
 					if (new_wall->n1 != new_wall->n2) {
 						
@@ -1001,11 +930,8 @@ void Cell::DivideWalls(ItList new_node_l
 		
 		if (!fix_cellwall)
 			node->boundary = false;
-		else { // if fix_cellwall is true, that is if we are cutting off
-			// part of a leaf to make a nice initial condition, we also want to make it part of the boundary
-			//node->boundary = true;
+		else {
 			node->fixed = true;
-			//node->sam = true;
 		}
 		
 		ins_pos=daughter->nodes.insert(ins_pos, node );
@@ -1100,10 +1026,6 @@ void Cell::DivideWalls(ItList new_node_l
 		}
 	}
 	
-	//neighbors.push_back( daughter );
-	//daughter->neighbors.push_back( this );
-	
-	
 	//cerr << "Cell " << index << " has been dividing, and gave birth to Cell " << daughter->index << endl;
 	
 	// now reconstruct neighbor list for all "broken" neighbors
@@ -1118,8 +1040,6 @@ void Cell::DivideWalls(ItList new_node_l
 	daughter->ConstructNeighborList();
 	
 	m->plugin->OnDivide(&parent_info, daughter, this);
-	// wall->OnWallInsert();
-	//daughter->OnDivide();
 	
 	daughter->div_counter=(++div_counter);
 	
@@ -1166,19 +1086,17 @@ double Cell::Displace(double dx, double 
 		 i!=nodes.end();
 		 i++) {
 		
-		//if ((*i)->Fixed()) return; // commented out 01/12/05
+
 		for (list<Neighbor>::const_iterator n=(*i)->owners.begin();
 			 n!=(*i)->owners.end();
 			 n++) {
 			
 			if (n->getCell()!=this) {
-				//if (!(m->getNode(n->nb1).Fixed() && m->getNode(n->nb2).Fixed())) {
 				length_edges.push_back( pair <Node *,Node *> (*i, n->nb1) );
 				length_edges.push_back( pair <Node *,Node *> (*i, n->nb2) );
 				old_length += 
 				DSQR(Node::target_length-(*(*i)-*(n->nb1)).Norm())+
 				DSQR(Node::target_length-(*(*i)-*(n->nb2)).Norm());
-				//}
 			}
 		}
 	}
@@ -1230,22 +1148,6 @@ double Cell::Displace(double dx, double 
 		
 		//cerr << endl;
 		
-		/*vector<double> area1;
-		 vector<double> area2;
-		 m->ExtractFromCells( mem_fun_ref(&Cell::Area), back_inserter(area1) );
-		 m->ExtractFromCells( mem_fun_ref(&Cell::CalcArea), back_inserter(area2));
-		 vector<double>::iterator i=area1.begin();
-		 vector<double>::iterator j=area2.begin();
-		 int c=0;
-		 for (;
-		 i!=area1.end();
-		 (i++, j++)) {
-		 if ( (*i-*j) > 1e-10) {
-		 cerr << c++ << " " << *i << " " << *j << endl;
-		 abort();
-		 }
-		 }*/
-		
 	} else {
 		
 		Move ( -1*movement);
@@ -1351,8 +1253,6 @@ bool Cell::SelfIntersect(void) {
 			double ub = 
 			((v2.x - v1.x)*(v1.y-v3.y) - (v2.y- v1.y)*(v1.x - v3.x))/denominator;
 			
-			/* double intersec_x = v1.x + ua*(v2.x-v1.x);
-			 double intersec_y = v1.y + ua*(v2.y-v1.y);*/
 			
 			if ( ( TINY < ua && ua < 1.-TINY ) && ( TINY < ub && ub < 1.-TINY ) ) {
 				//cerr << "ua = " << ua << ", ub = " << ub << endl;
@@ -1426,9 +1326,6 @@ bool Cell::MoveSelfIntersectsP(Node *mov
 			double ub = 
 			((neighbor_of_moving_node[j].x - new_pos.x)*(new_pos.y-v3.y) - (neighbor_of_moving_node[j].y- new_pos.y)*(new_pos.x - v3.x))/denominator;
 			
-			/* double intersec_x = new_pos.x + ua*(neighbor_of_moving_node[j].x-new_pos.x);
-			 double intersec_y = new_pos.y + ua*(neighbor_of_moving_node[j].y-new_pos.y);*/
-			
 			if ( ( TINY < ua && ua < 1.-TINY ) && ( TINY < ub && ub < 1.-TINY ) ) {
 				//cerr << "ua = " << ua << ", ub = " << ub << endl;
 				return true;
@@ -1472,9 +1369,6 @@ bool Cell::IntersectsWithLineP(const Vec
 		double ub = 
 		((v2.x - v1.x)*(v1.y-v3.y) - (v2.y- v1.y)*(v1.x - v3.x))/denominator;
 		
-		/* double intersec_x = v1.x + ua*(v2.x-v1.x);
-		 double intersec_y = v1.y + ua*(v2.y-v1.y);*/
-		
 		if ( ( TINY < ua && ua < 1.-TINY ) && ( TINY < ub && ub < 1.-TINY ) ) {
 			return true;
 		}
@@ -1571,14 +1465,12 @@ void Cell::ConstructWalls(void) {
 		
 		// One Wall for each neighbor, so we should be able to correctly construct neighbor lists here.
 		if (duplicates[0]==this) {
-			//walls. new Wall(*nb,*i,duplicates[0],duplicates[1]) );
 			AddWall(  new Wall(*nb,*i,duplicates[0],duplicates[1]) );
 			if (!duplicates[1]->BoundaryPolP()) {
 				
 				neighbors.push_back(duplicates[1]);
 			}
 		} else {
-			//walls.push_back( new Wall(*nb,*i,duplicates[1],duplicates[0]) ); 
 			AddWall ( new Wall(*nb,*i,duplicates[1],duplicates[0]) );
 			if (!duplicates[0]->BoundaryPolP()) {
 				neighbors.push_back(duplicates[0]);
@@ -1724,26 +1616,9 @@ void Cell::DrawNodes(QGraphicsScene *c) 
 		 n++) {
 		Node *i=*n;
 		
-		//QCanvasEllipse *item = new QCanvasEllipse( 10, 10, c);
+
 		NodeItem *item = new NodeItem ( &(*i), c );
-		//QGraphicsRectItem *item = new QGraphicsRectItem(-50, -50, 50, 50, 0, c);
-		//disk->setBrush( QColor("IndianRed") );
-		
-		/*if (i->sam) {
-		 item->setBrush( purple );
-		 } else {
-		 if (i->boundary) {
-		 item->setBrush( deep_sky_blue );
-		 } 
-		 else {
-		 item->setBrush( indian_red );
-		 }
-		 }*/
 		item->setColor();
-		
-		/*(if (item->getNode().DeadP()) {
-		 item->setBrush( QBrush (Qt::Dense6Pattern) );
-		 }*/
 		item->setZValue(5);
 		item->show();
 		item ->setPos(((offset[0]+i->x)*factor),
@@ -1754,16 +1629,6 @@ void Cell::DrawNodes(QGraphicsScene *c) 
 
 void Cell::DrawIndex(QGraphicsScene *c) const {
 	
-	//  stringstream text;
-	//     text << index;
-	//     Vector centroid = Centroid();
-	//     QCanvasText *number = new QCanvasText ( QString (text.str()), c );
-	//     number->setColor( QColor(par.textcolor) );
-	//     number->setZ(20);
-	//     number->setFont( QFont( "Helvetica", par.cellnumsize, QFont::Bold) );
-	//     number->show();
-	//     number -> move((int)((offset[0]+centroid.x)*factor),
-	// 		   (int)((offset[1]+centroid.y)*factor) );
 	DrawText( c, QString("%1").arg(index));
 }
 
@@ -1775,7 +1640,6 @@ void Cell::DrawText(QGraphicsScene *c, c
 	ctext->setPen( QPen(QColor(par.textcolor)) );
 	ctext->setZValue(20);
 	ctext->setFont( QFont( "Helvetica", par.cellnumsize, QFont::Bold) );
-	//ctext->setTextFlags(Qt::AlignCenter);
 	ctext->show();
 	ctext ->setPos(((offset[0]+centroid.x)*factor),
 				   ((offset[1]+centroid.y)*factor) );
@@ -1815,61 +1679,12 @@ void Cell::DrawAxis(QGraphicsScene *c) c
 void Cell::DrawStrain(QGraphicsScene *c) const {
   c = NULL; // assignment merely to obviate compilation warning
 	MyWarning::warning("Sorry, Cell::DrawStrain temporarily not implemented.");
-	/* Vector long_axis;
-	double width;
-	Length(&long_axis, &width);
-	
-	//cerr << "Length is "  << length << endl;
-	long_axis.Normalise();
-	Vector short_axis=long_axis.Perp2D();
-    
-	//  To test method "Strain" temporarily substitute "short_axis" for "strain" 
-	Vector strain = Strain();
-	//strain.Normalise();
-	//static ofstream strainf("strain.dat");
-	//strainf << strain.Norm() << endl;
-	Vector centroid = Centroid();
-	// Vector from = centroid - 0.5 * width * short_axis;
-    // Vector to = centroid + 0.5 * width *short_axis;
-	Vector from = centroid - 0.5 * strain;
-	Vector to = centroid + 0.5 * strain;
-	
-	QGraphicsArrowItem *arrow = new QGraphicsArrowItem(0, c);
-	arrow->setPen( QPen(QColor(par.arrowcolor),100) );
-    
-	arrow->setLine( ( (offset[0]+from.x)*factor ),
-				   ( (offset[1]+from.y)*factor ), 
-				   ( (offset[0]+to.x)*factor ),
-				   ( (offset[1]+to.y)*factor ) );
-	arrow->setZValue(10.);
-	arrow->show();
-	*/
 }
 
-// Draw connecting lines to neighbors
-/*void Cell::DrawTriangles(QCanvas &c) {
- 
- for (list<Neighbor>::const_iterator nb=nb_list.begin();
- nb!=nb_list.end();
- nb++) {
- QCanvasLine *line = new QCanvasLine(&c);
- line->setPen( QPen(QColor("black"),2) );
- line->setZ(2);
- 
- line->setPoints((offset[0]+x)*factor,(offset[1]+y)*factor, 
- (offset[0]+nb->c->x)*factor,(offset[1]+nb->c->y)*factor);
- line->setZ(10);
- line->show();
- }
- 
- }*/
-
-
 
 void Cell::DrawFluxes(QGraphicsScene *c, double arrowsize)  {
 	
 	// get the mean flux through this cell
-	//Vector vec_flux = ReduceWalls( mem_fun_ref( &Wall::VizFlux ), Vector() );
 	Vector vec_flux = ReduceCellAndWalls<Vector>( PINdir );
 	
 	vec_flux.Normalise();
@@ -2012,7 +1827,6 @@ list<Wall *>::iterator Cell::RemoveWall(
 void Cell::EmitValues(double t) {
 	
 	//  cerr << "Attempting to emit " << t << ", " << chem[0] << ", " << chem[1] << endl;
-	//chem[3] = SumTransporters( 1 );
 	emit ChemMonValue(t, chem);
 	
 }
diff --git a/src/cell.h b/src/cell.h
--- a/src/cell.h
+++ b/src/cell.h
@@ -91,10 +91,6 @@ public:
 		return factor;
     }
     
-    // return node "i"
-    // wrapped around, i.e. node n==node 0
-    // will not work if i < -nodes.size()
-    //Node &getNode(int i) const;
     void DivideOverAxis(Vector axis); // divide cell over axis
     bool DivideOverGivenLine(const Vector v1, const Vector v2, bool wall_fixed = false, NodeSet *node_set = 0); // divide over the line (if line and cell intersect)
 	
diff --git a/src/cellbase.cpp b/src/cellbase.cpp
--- a/src/cellbase.cpp
+++ b/src/cellbase.cpp
@@ -40,9 +40,7 @@
 #endif
 #include "nodeset.h"
 
-//#include "cond_operator.h"
 #include "cellbase.h"
-//#include "node.h"
 #include "wall.h"
 #include "random.h"
 #include "parameter.h" 
@@ -56,12 +54,6 @@ extern Parameter par;
 
 const char* CellBase::boundary_type_names[4] = {"None", "NoFlux", "SourceSink", "SAM"};
 
-// These statics have moved to class "CellsStaticDatamembers"
-
-//double CellBase::static_base_area = 0.;
-//int CellBase::ncells=0;
-//int CellBase::NChem()=0;
-
 #ifndef VLEAFPLUGIN
 CellsStaticDatamembers *CellBase::static_data_members = new CellsStaticDatamembers();
 #else
@@ -188,7 +180,7 @@ CellBase::CellBase(const CellBase &src) 
 
 CellBase CellBase::operator=(const CellBase &src) {
 	Vector::operator=(src);
-	//  QObject::operator=(src);
+
 	for (int i=0;i<NChem();i++) {
 		chem[i]=src.chem[i];
 	}
@@ -351,13 +343,6 @@ Vector CellBase::Centroid(void) const {
 	return centroid;
 }
 
-/*Node &CellBase::getNode(list<Node *>::const_iterator i) const {
-
-if (i==
-	return m->getNode(i);
-  }*/
-
-
 
 
 void CellBase::SetIntegrals(void) const {
@@ -408,17 +393,9 @@ void CellBase::SetIntegrals(void) const 
 			 (*nb)->x*(*i)->y);
 	}
 	
-	//area/=2.0;
+
 	area = fabs(area)/2.0;
 	
-	/* intgrl_x/=6.;
-	intgrl_y/=6.;
-	
-	intgrl_xx/=12.;
-	intgrl_xy/=24.;
-	intgrl_yy/=12.;*/
-	
-	
 }
 
 double CellBase::Length(Vector *long_axis, double *width)  const {
@@ -447,9 +424,6 @@ double CellBase::Length(Vector *long_axi
 	// see: http://scienceworld.wolfram.com/physics/MomentofInertiaEllipse.html
 	//    cerr << "n = " << n << "\n";
 	
-	// Vector eigenvectors[2];
-	// eigenvectors[0] = Vector(-(-ixx + iyy ) + rhs2, ixy, 0);
-	// eigenvectors[1] = Vector(-(-ixx + iyy ) - rhs2, ixy, 0);
 	if (long_axis) {
 		*long_axis = Vector(-ixy, lambda_b - ixx, 0);
 		//   cerr << "ixx = " << ixx << ", ixy = " << ixy << ", iyy = " << iyy << ", area = " << area << endl;
@@ -531,9 +505,6 @@ double CellBase::CalcLength(Vector *long
 	// see: http://scienceworld.wolfram.com/physics/MomentofInertiaEllipse.html
 	//    cerr << "n = " << n << "\n";
 	
-	// Vector eigenvectors[2];
-	// eigenvectors[0] = Vector(-(-ixx + iyy ) + rhs2, ixy, 0);
-	// eigenvectors[1] = Vector(-(-ixx + iyy ) - rhs2, ixy, 0);
 	if (long_axis) {
 		*long_axis = Vector(-ixy, lambda_b - ixx, 0);
 		//   cerr << "ixx = " << ixx << ", ixy = " << ixy << ", iyy = " << iyy << ", my_area = " << my_area << endl;
@@ -550,15 +521,6 @@ double CellBase::CalcLength(Vector *long
 }
 
 
-// void CellBase::NodeRemoved(int n) {
-//   for (list<Node *>::iterator i=nodes.begin();
-//        i!=nodes.end();
-//        i++) {
-//     if ((*i)->Index()>n) {
-//       (*i)->index--;
-//     }
-//   }
-// }
 
 void CellBase::ConstructNeighborList(void) {
 	
@@ -567,7 +529,7 @@ void CellBase::ConstructNeighborList(voi
 		 list<Wall *>::const_iterator wit=walls.begin();
 		 // somehow the reverse_iterator returns by walls needs to be casted to const to let this work.
 		 // it seems to me it is a bug in the STL implementation...
-		 //wit!=(list<Wall *>::const_reverse_iterator)walls.rend();
+
 		 wit!=walls.end();
 		 wit++) {
 		
@@ -580,20 +542,7 @@ void CellBase::ConstructNeighborList(voi
 	}
 	
 	
-	/*
-	 for (list<CellBase *>::iterator e=neighbors.begin();
-		  e!=neighbors.end();
-		  e++) {
-		 cerr << (*e)->Index() << " ";
-		 if ((*e)->CellBase::BoundaryPolP()) {
-			 cerr << " b ";
-		 }
-	 }
-	 */
 	// remove all boundary_polygons from the list
-	
-	
-    
 	list <CellBase *>::iterator e=neighbors.begin();
 	at_boundary=false;
 	
@@ -614,334 +563,6 @@ void CellBase::ConstructNeighborList(voi
   } while(1);
 	
 }
-
-// CellBase constructs its neighbor list from its node lists
-// Assumes, obviously, that the node lists are up to date
-// (i.e. call ConstructConnections before calling this method)
-// We'll keep this one private, anyway.
-/* void CellBase::ConstructNeighborList(void) {
-
-//  extern ofstream debug_stream;
-
-neighbors.clear();
-
-//  debug_stream << "Nodes: ";
-//  copy(nodes.begin(),nodes.end(),ostream_iterator<Node>(debug_stream, " "));
-//debug_stream << endl;
-
-for (list<Node *>::const_iterator i=nodes.begin();
-	 i!=nodes.end();
-	 i++) {
-    
-    // collect all cells to which my nodes are connected on one list
-    //transform((*i)->cells.begin(),(*i)->cells.end(), back_inserter(neighbors), mem_fun_ref(&Neighbor::CellBase));
-	
-    // index of next node 
-    list<Node *>::const_iterator nn=i;
-    ++nn;
-    if (nn==nodes.end()) 
-		nn=nodes.begin();
-	
-    //    debug_stream << "Node " << *i << ", Neighbor " << *nn << endl;
-    // debug_stream << "Owners: ";
-    //    copy((*i)->cells.begin(),(*i)->cells.end(),ostream_iterator<Neighbor>(debug_stream, " "));
-    // debug_stream << endl;
-    
-    for (list<Neighbor>::const_iterator nb=(*i)->owners.begin();
-		 nb!=(*i)->owners.end();
-		 nb++) {
-		
-		// collect info about neighboring cells, not about myself
-		if (nb->CellBase!=this) {
-			
-			// make sure the whole edge touches this putative neighbor
-			// if (*nn == nb->nb1 || *nn == nb->nb2) {
-			//walls.push_back( new Wall(*i,*nn,this,nb->CellBase) );
-			//debug_stream << "Adding edge " << walls.back() << " to CellBase " << index << endl;
-			//}
-			
-			neighbors.push_back( nb->CellBase );
-		} 
-    }
-
-
-}
-
-neighbors.sort();
-
-list<CellBase *>::iterator e=unique(neighbors.begin(),neighbors.end());
-
-// iterator e point to the end of the subsequence of unique elements
-// remove every thing that comes after it
-
-neighbors.erase(e, neighbors.end());
-
-// okay, now neighbors contains all neighbors of this CellBase, including itself
-
-// A future optimization for the diffusion algorithm: now we list
-// each of the edges of a (curved) CellBase boundary separately.  We
-// could keep track just of the total length per CellBase boundary
-
-// the following is not necessary anymore. Is
-// checked at earlier stage
-// // remove myself from the list
-//   e = find(neighbors.begin(),neighbors.end(),index);
-//   if (e!=neighbors.end())
-//   neighbors.erase(e);
-//    
-
-// remove boundary_polygon from the list (CellBase identity <0 )
-e=neighbors.begin();
-at_boundary=false;
-do { 
-    e = find_if(neighbors.begin(),neighbors.end(),mem_fun(&CellBase::BoundaryPolP));
-    if (e!=neighbors.end()) {
-		e=neighbors.erase(e);
-		at_boundary=true;
-    } else {
-		break;
-    }
-} while(1);
-
-
-}*/
-
-
-/*void Cell::print_nblist(void) const {
-//  cerr << "{ ";
-
-for (list<Neighbor>::const_iterator i=nb_list.begin();
-	 i!=nb_list.end();
-	 i++) {
-	//    cerr << "(" << i->c->index << " " << i->Dij << ")";
-	
-}
-//  cerr << "}" << endl;
-}
-*/
-
-
-// Tests whether Cell p (given as Vector, remember that Cell is a
-// Vector) is within polygon formed by nearest neighbor cells
-// 
-// Based on algorithm and code by Paul Bourke, see
-// http://astronomy.swin.edu.au/~pbourke/geometry/insidepoly/
-//
-// Note: works for 2D only; projects everything on z=0;
-/*
-#define MIN(x,y) (x < y ? x : y)
-#define MAX(x,y) (x > y ? x : y)
- */
-/*bool Cell::CellInsidePolygonP(Vector &p)
-{
-    int counter = 0;
-    double xinters;
-    Vector p1,p2;
-	
-    //p1 = polygon[0];
-    p1 = *(nb_list.begin()->c);
-	
-    int N=nb_list.size();
-    list<Neighbor>::const_iterator nb=nb_list.begin();
-	
-    for (int i=1;i<=N;i++) {
-		
-		nb++;
-		
-		if (nb!=nb_list.end()) {
-			p2 = *(nb->c);
-		} else {
-			p2 = *(nb_list.begin()->c);
-		}
-		
-		if (p.y > MIN(p1.y,p2.y)) {
-			if (p.y <= MAX(p1.y,p2.y)) {
-				if (p.x <= MAX(p1.x,p2.x)) {
-					if (p1.y != p2.y) {
-						xinters = (p.y-p1.y)*(p2.x-p1.x)/(p2.y-p1.y)+p1.x;
-						if (p1.x == p2.x || p.x <= xinters)
-							counter++;
-					}
-				}
-			}
-		}
-		p1 = p2;
-    }
-	
-    if (counter % 2 == 0)
-		return false;
-    else
-		return true;
-	
-}*/
-
-
-/* // at new position cell should be able to "see" all polygon sides
-bool Cell::NewPointValidP(Vector &p) {
-	
-	//int ninvtri=0;
-	for (list<Neighbor>::const_iterator nb=nb_list.begin();
-		 nb!=nb_list.end();
-		 nb++) {
-		
-		Vector p1=*(nb->c); // first neighbor
-		list<Neighbor>::const_iterator nextv=nb; nextv++;
-		
-		
-		if (nextv==nb_list.end()) {
-			if (Boundary()==None) {
-				nextv=nb_list.begin();
-			} else continue;
-		}
-		
-		Vector p2=*(nextv->c);
-		
-		Vector v1=(p1-p);
-		Vector v2=(p2-p1);
-		
-		Vector cross=v1*v2;
-		//    //cerr << "[" << cross << "]" << endl;
-		
-		if (cross.z<0) {
-			// One of the triangles has "inverted".
-			//if (Boundary()==None || ninvtri) 
-			return false;
-			//else 
-			// accept one "inverted" triangle
-			//ninvtri++;
-		}
-	}
-	return true;
-    
-}*/
-
-
-
-
-// void Cell::CheckForDivision(void) {
-//  //  if (/* Chemical(0)<0.4 && */ /* differentiated cells do not divide */ area > 2*base_area /* || Length()>50 */) {
-
-//  if (area > par.rel_cell_div_threshold * base_area ) {
-//    /* remark no longer valid? //m->IncreaseCellCapacityIfNecessary();
-//      // Note that calling Divide as follows prevents trouble if cell
-//      // vector is relocated */
-//      Divide();
-//  }
-//}
-
-/* void Cell::CheckForGFDrivenDivision(void) {
-if (area > base_area && chem[0]>par.gf_div_threshold) {
-    //int ind=index;
-    if (index==1) return; // petiole does not divide
-	
-    // remark no longer valid?
-    //m->IncreaseCellCapacityIfNecessary();
-    // Note that calling Divide as follows prevents trouble if cell
-    // vector is relocated
-    Vector horizontal(1,0,0);
-    Vector vertical(0,1,0);
-    double r; 
-    if ((r=RANDOM())>par.vertdivprob) {
-		DivideOverAxis(horizontal);
-    } else {
-		cerr << "[" << r << "]";
-		DivideOverAxis(vertical);
-    }
-}
-}
-*/
-
-
-
-// return (a measure of) the strain of this cell
-/*Vector CellBase::Strain(void) const {
-	
-	cerr << "Sorry, CellBase::strain currently not implemented" << endl;
-	std::exit(1);
-	
-	// Reason: we do not want to include "Node" in the plugins (Node::target_length below), and we do need Strain anyway...
-	
-	
-	// go over all wall elements of the cell
-	 Vector Fvec;
-	
-	for (list<Node *>::const_iterator n=nodes.begin();
-		 n!=nodes.end();
-		 n++) {
-		
-		list<Node *>::const_iterator nn=n; nn++;
-		if (nn==nodes.end()) nn=nodes.begin();
-		
-		Vector wall_element = *(*n) - *(*nn);
-		
-		// assume k=1 (Hooke's constant), for now
-		double Fscal  = (Node::target_length - wall_element.Norm())/Node::target_length;
-		
-		
-		Fvec += Fscal * wall_element.Normalised();
-		
-	}
-	
-	return Fvec; 
-} */
-
-
-
-/* void Cell::Flux(double *flux, double D)  {
-
-// Algorithm according to Rudge & Haseloff 2005
-// (will we need to take cell area into account?)
-// For the time being, we don't: assume cell area is 
-// mainly determined by vacuole.
-
-// Currently implements Rolland-Lagan-Mitchison algorithm
-// Rolland-Lagan and Prusinkiewicz, The Plant Journal (2005), 44, 854-865
-
-// currently I only implemented passive, diffusive transport 
-// active transport will be added later
-
-// loop over cell edges
-
-for (int c=0;c<Cell::NChem();c++) flux[c]=0.;
-
-for (list<Wall>::iterator i=walls.begin();
-	 i!=walls.end();
-	 i++) {
-    
-    
-	// leaf cannot take up chemicals from environment ("no flux boundary")
-	if (i->c2 < 0) continue;
-    
-	// calculate edge length 
-	// (will later be updated during node displacement for efficiency)
-	double edge_length = (m->nodes[i->n1]-m->nodes[i->n2]).Norm();
-    
-	// D is "background diffusion coefficient" (Rolland-Lagan)
-	
-	
-	// flux depends on edge length and concentration difference */
-	// i->phi = edge_length * ( /* i->D +*/ D ) * ( m->cells[i->c2].chem[0] - chem[0] );
-	/*
-	 if (m->cells[i->c1].index!=index) {
-		 cerr << "Warning, bad cells boundary: " << m->cells[i->c1].index << ", " << index << endl;
-	 }
-	 
-	 flux[0] += i->phi;
-	 //double deltaD = par.alpha * (i->phi*i->phi) - par.gamma * i->D; // Note beta=0
-	 //i->D += par.dt*deltaD; 
-	 
-	 //cerr << "[ i->D = " << i->D << ", deltaD = " << deltaD << "]";
-	 //if (i->D > par.Dmax) i->D=par.Dmax;
-	 
-	 // first calculate all fluxes, we update diffusion coefficient afterwards.
-	 
-	 // cerr << "[ " << edge_length << ", " << m->cells[i->c2].chem[0] << " - " << chem[0] << "]";
-	 
-}
-
-
-}
-*/
 	
 	// Save the cell to a stream so we can reconstruct its state later
 	void CellBase::Dump(ostream &os) const {
diff --git a/src/cellbase.h b/src/cellbase.h
--- a/src/cellbase.h
+++ b/src/cellbase.h
@@ -108,8 +108,6 @@ class CellBase :  public QObject, public
 	virtual bool BoundaryPolP(void) const { return false; } 
 	
 	
-	//  CellBase(const Vector &src); // not allowed (we cannot know to which mesh 
-	/// the CellBase will belong...)
     CellBase operator=(const CellBase &src); // assignment operator
     CellBase operator=(const Vector &src);
   
@@ -158,8 +156,6 @@ class CellBase :  public QObject, public
 
     boundary_type SetBoundary(boundary_type bound) {
       if (bound!=None) {
-	//area=0.;
-	//length=0.;
       }
       return boundary=bound;
     }
@@ -229,7 +225,6 @@ class CellBase :  public QObject, public
 		flag_for_divide = true;
 	}
 	
-	//Vector Strain(void) const;
 
     inline double Circumference(void) const {
       double sum=0.;
@@ -251,13 +246,11 @@ class CellBase :  public QObject, public
 		}
 		return wall_list;
 	}
-  //  void XFigPrint(std::ostream &os) const;
     
     void Dump(ostream &os) const;
    	
 	QString printednodelist(void);
  
-   // void OnDivide(ParentInfo &parent_info, CellBase &daughter);
 
     
     inline bool DeadP(void) { return dead; }
@@ -343,13 +336,6 @@ class CellBase :  public QObject, public
       return sum;
     }
     
-	/* template<class Op> void LoopWalls(Op f) {
-		for (list<Wall *>::const_iterator w=walls.begin();
-			 w!=walls.end();
-			 w++) {
-			( **w)->f;
-		}
-	}*/
 	
     //! Sum transporters at this CellBase's side of the walls
     double SumTransporters(int ch) {
@@ -463,9 +449,6 @@ protected:
 	
 	int cell_type;
 	
-    //double length;
-    //Vector meanflux;
-    //int valence;
     
     // for length constraint
     mutable double intgrl_xx, intgrl_xy, intgrl_yy, intgrl_x, intgrl_y;
diff --git a/src/data_plot.cpp b/src/data_plot.cpp
--- a/src/data_plot.cpp
+++ b/src/data_plot.cpp
@@ -63,10 +63,6 @@ DataPlot::DataPlot(QWidget *parent, cons
   // Disable polygon clipping
   QwtPainter::setDeviceClipping(false);
 
-  // We don't need the cache here
-  //canvas()->setPaintAttribute(QwtPlotCanvas::PaintCached, false);
-  //canvas()->setPaintAttribute(QwtPlotCanvas::PaintPacked, false);
-
   alignScales();
     
   //  Initialize data
@@ -105,24 +101,8 @@ DataPlot::DataPlot(QWidget *parent, cons
 
   setAxisTitle(QwtPlot::yLeft, "Level");
   setAxisScale(QwtPlot::yLeft, 0, 10);
-    
-  //    setTimerInterval(0.0); 
 
   data_pos = 0;
-  
-
-  // open file for writing
-  /* QString fname(title);
-  fname.replace(QString(" "),QString());
-  fname.append(".dat");
-  std::cerr << "Writing to file " << fname.toStdString() << std::endl;
-  
-  datfile = new QFile(fname);
-  if (!datfile->open(QIODevice::WriteOnly | QIODevice::Text))
-    return;
-  
-  datstream.setDevice(datfile);
-  */
 
 }
 
@@ -156,19 +136,6 @@ void DataPlot::alignScales()
     }
 }
 
-/* void DataPlot::setTimerInterval(double ms)
-{
-    d_interval = qRound(ms);
-
-    if ( d_timerId >= 0 )
-    {
-        killTimer(d_timerId);
-        d_timerId = -1;
-    }
-    if (d_interval >= 0 )
-        d_timerId = startTimer(d_interval);
-}
-*/
 
 //  Generate new values 
 void DataPlot::AddValue(double t,double *x)
@@ -192,16 +159,11 @@ void DataPlot::AddValue(double t,double 
 
   d_t[data_pos] = t;
 
-  // datstream << t;
-
   for ( int i=0;i<ncurves;i++) {
     curves[i].setRawData(d_t, d_x[i], data_pos);
     d_x[i][data_pos] = x[i];
-    //datstream << " " << x[i];
   }
 					       
-  //datstream << "\n";
-  
   setAxisScale(QwtPlot::xBottom, d_t[0], t);
   
   data_pos++;
diff --git a/src/data_plot.h b/src/data_plot.h
--- a/src/data_plot.h
+++ b/src/data_plot.h
@@ -42,7 +42,6 @@ public:
   DataPlot(QWidget *parent, const QString title, const QStringList curvenames);
   virtual ~DataPlot(void);
 public slots:
-    //    void setTimerInterval(double interval);
     void AddValue(double t, double *x);
 
 private:
@@ -74,7 +73,6 @@ Q_OBJECT
   PlotDialog(QWidget *parent, const QString title, const QStringList curvenames);
   ~PlotDialog(void);
   public slots:
-    //    void setTimerInterval(double interval);
   void AddValue(double t, double *x) {
     //std::cerr << "AddValue receives: " << t << ", " << y << ", " << z << std::endl;
     plot->AddValue(t,x);
diff --git a/src/flux_function.h b/src/flux_function.h
--- a/src/flux_function.h
+++ b/src/flux_function.h
@@ -1,12 +1,30 @@
 /*
- *  flux_function.h
- *  VirtualLeaf
+ *
+ *  $Id$
+ *
+ *  This file is part of the Virtual Leaf.
+ *
+ *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
  *
- *  Created by Roeland Merks on 07-06-10.
- *  Copyright 2010 __MyCompanyName__. All rights reserved.
+ *  The Virtual Leaf is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ *  Copyright 2010 Roeland Merks.
  *
  */
 
+
+#ifndef _FLUX_FUNCTION_h_
+#define _FLUX_FUNCTION_h_
+
 // This header file defines a macro "SumFluxFromWalls" that attempts to hide this 
 // horrendously confusing member function wrapper construct from VirtualLeaf's end users
 
@@ -20,3 +38,4 @@
 #define SumFluxFromWalls( _vleafcellp_, _flux_function_ ) \
 (( _vleafcellp_->ReduceCellAndWalls<double>( far_3_arg_mem_fun( *this, &_flux_function_ ) ) ))
 
+#endif
diff --git a/src/forwardeuler.cpp b/src/forwardeuler.cpp
--- a/src/forwardeuler.cpp
+++ b/src/forwardeuler.cpp
@@ -32,16 +32,6 @@ static const string _module_id("$Id$");
 
 // The value Errcon equals (5/Safety) raised to the power (1/PGrow), see use below.
 
-/* static float maxarg1,maxarg2;
-   #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1) > (maxarg2) ?	\
-   (maxarg1) : (maxarg2))
-   static float minarg1,minarg2;
-   #define FMIN(a,b) (minarg1=(a),minarg2=(b),(minarg1) < (minarg2) ?	\
-   (minarg1) : (minarg2))
-   #define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a))
-*/
-
-
 const double ForwardEuler::Safety  = 0.9;
 const double ForwardEuler::PGrow = -0.2;
 const double ForwardEuler::Pshrnk = -0.25;
diff --git a/src/infobar.h b/src/infobar.h
--- a/src/infobar.h
+++ b/src/infobar.h
@@ -41,12 +41,9 @@ public:
 		SetText("undefined");
 		
 		setHorizontalStretchable(true);
-		//dockwindow->boxLayout()->addWidget(viblab);//,Qt::AlignLeft);
 		boxLayout()->addStretch();
 		boxLayout()->addWidget(virtleaf);//, Qt::AlignHCenter);
 		boxLayout()->addStretch();
-	
-		//dockwindow->boxLayout()->addWidget(psblab);//, Qt::AlignRight);
 	}
 	
 	void SetText(QString text) {
@@ -54,7 +51,6 @@ public:
 	}
 	
 private:
-	//Q3DockWindow *dockwindow;
 	QLabel *virtleaf;
 };
 
diff --git a/src/mainbase.cpp b/src/mainbase.cpp
--- a/src/mainbase.cpp
+++ b/src/mainbase.cpp
@@ -220,14 +220,11 @@ void MainBase::Save(const char *fname, c
 	// 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 );
-	
 	if (!QString(format).contains("pdf", Qt::CaseInsensitive)) {
 	
 		QImage *image = new QImage(QSize(sizex, sizey), QImage::Format_RGB32);
 		image->fill(QColor(Qt::white).rgb());
 		QPainter *painter=new QPainter(image);
-		//canvas.render(painter,QRectF(),QRectF(-5000,-5000, 10000, 10000));
 		canvas.render(painter);
 		if (!image->save(QString(fname))) {
 			MyWarning::warning("Image not saved successfully. Is the disk full or the extension not recognized?");
@@ -238,15 +235,7 @@ void MainBase::Save(const char *fname, c
 		QPrinter pdf(QPrinter::HighResolution);
 		pdf.setOutputFileName(fname);
 		pdf.setOutputFormat(QPrinter::PdfFormat);
-		//pdf.setPageSize(QPrinter::Custom);
 		QPainter painter(&pdf);
-		//	cerr << "Cell::Magnification() = " << Cell::Magnification() << endl;
-		//if (sizex==0 || sizey==0) {
-			// always fit to page
-		//	canvas.render(&painter);
-		//} else {
-		//	canvas.render(&painter,QRectF(),QRectF(-5000,-5000, 10000, 10000));
-		//}
 		canvas.render(&painter, QRectF(), QRectF(-5000,-5000, 10000, 10000));
 		
 		cerr << "Rendering to printer\n";
diff --git a/src/mainbase.h b/src/mainbase.h
--- a/src/mainbase.h
+++ b/src/mainbase.h
@@ -58,7 +58,7 @@ class MainBase  {
     showfluxesp = false;
     dynamicscellsp = true;
     showtooltipsp = false;
-	hidecellsp = false;
+    hidecellsp = false;
   }
     virtual ~MainBase() {};
     
@@ -77,12 +77,12 @@ class MainBase  {
     virtual bool ShowBoundaryOnlyP(void) {return showboundaryonlyp;}
     virtual bool ShowToolTipsP(void) {return showtooltipsp;}
     virtual bool ShowWallsP(void) {return showwallsp;}
-	virtual bool ShowApoplastsP(void) { return showapoplastsp;}
+    virtual bool ShowApoplastsP(void) { return showapoplastsp;}
     virtual bool ShowFluxesP(void) { return showfluxesp; }
     virtual bool DynamicCellsP(void) { return dynamicscellsp; }
     virtual void FitCanvasToWindow() {};
     virtual void FitLeafToCanvas() {};
-	virtual bool HideCellsP(void) { return hidecellsp; }
+    virtual bool HideCellsP(void) { return hidecellsp; }
     virtual void clear(void) {
       QList<QGraphicsItem *> list = canvas.items();
       QList<QGraphicsItem *>::Iterator it = list.begin();
@@ -94,26 +94,6 @@ class MainBase  {
     virtual void XMLReadSettings(xmlNode *settings);
     virtual double getFluxArrowsize(void) { return 10.;}
     
-    /* void Save(const char *fname, const char *format, int width=640) {
-      
-    //cerr << "Initializing Pixmap\n";
-      
-    cerr << "Saving to file " << fname << endl;
-    QPixmap *image=new QPixmap(width, (int) (((double)canvas.height()/
-    (double)canvas.width())*((double)width)));
-
-    //QPicture *image = new QPicture();
-      
-    //cerr << "Done initializing QPixmap image(640, " << (((double)canvas.height()/(double)canvas.width())*640.) << ")\n";
-    QPainter im(image);
-    //cerr << "Done initializing image\n";
-    im.scale((double)width/canvas.width(),(double)width/canvas.width());
-    canvas.render(&im, QRectF(0,0,canvas.width(),canvas.height()) );
-    //im.end();      
-    image->save(QString(fname), format);
-    }*/
-    
-
     void Save(const char *fname, const char *format, int sizex=640, int sizey=480);
     void CutSAM(void);
 	
@@ -140,11 +120,11 @@ class MainBase  {
     bool movieframesp;
     bool showboundaryonlyp;
     bool showwallsp;
-	bool showapoplastsp;
+    bool showapoplastsp;
     bool showfluxesp;
     bool dynamicscellsp;
     bool showtooltipsp;
-	bool hidecellsp;
+    bool hidecellsp;
 };
 
 //#include <qapplication.h>
diff --git a/src/matrix.cpp b/src/matrix.cpp
--- a/src/matrix.cpp
+++ b/src/matrix.cpp
@@ -42,8 +42,6 @@ Matrix::Matrix(const Vector &c1, const V
 void Matrix::Alloc(void) {
 
   // constructor
-//  mat=(double **)malloc(3*sizeof(double *));
-//  mat[0]=(double *)malloc(9*sizeof(double));
   mat = new double*[3];
   mat[0] = new double[9];
   for (int i=1;i<3;i++)
@@ -54,8 +52,6 @@ void Matrix::Alloc(void) {
 Matrix::~Matrix() {
  
   // destructor
-  //free(mat[0]);
-  //free(mat);
   delete[] mat[0];
   delete[] mat;
 }
diff --git a/src/mesh.h b/src/mesh.h
--- a/src/mesh.h
+++ b/src/mesh.h
@@ -59,7 +59,6 @@ public:
 	}
 };
 
-//template<class P> P& deref_ptr<P>( P *obj) { return *obj; }
 template<class P> P& deref_ptr ( P *obj) { return *obj; }
 
 
@@ -80,19 +79,14 @@ public:
 		cells.reserve(2);
 		nodes.reserve(500);
 		
-		//boundary_polygon = new BoundaryPolygon();
-		
 		time = 0.;
 		plugin = 0;
 	};
 	~Mesh(void) {
 		delete boundary_polygon;
-		/* if (plugin)
-			delete plugin;*/
 	};
 	
 	void Clean(void);
-	//void Plane(int xwidth, int ywidth, int nx, int ny, bool randomP=false);
 	Cell &EllipticCell(double xc, double yc, double ra, double rb, int nnodes=10, double rotation=0);
 	Cell &CircularCell(double xc, double yc, double r, int nnodes=10) {
 		return EllipticCell(xc, yc, r, r, nnodes, 0);
@@ -102,11 +96,6 @@ public:
 	Cell *RectangularCell(const Vector ll, const Vector ur, double rotation = 0);
 	void CellFiles(const Vector ll, const Vector ur);
 	
-	/*  void GMVoutput(ostream &os, 
-	 const char *codename=0, const char *codever=0,
-	 const char *comments=0);*/
-	//void RandPoints(int npoints);
-	
 	inline Cell &getCell(int i) {
 		if ((unsigned)i<cells.size())
 			return *cells[i];
@@ -116,14 +105,10 @@ public:
                         qDebug() << "size is " << cells.size() << endl;
                         #endif
 			abort();
-			//	throw("Index out of range in Mesh::getCell");
 		}
 	}
 	
 	inline Node &getNode(int i) {
-		//if (i >= nodes.size() || i < 0) {
-		//  cerr << "Mesh::getNode: Warning. Index " << i << " out of range.\n";
-		// }
 		return *nodes[i];    
 	}
 	
@@ -134,35 +119,13 @@ public:
 	inline int nnodes(void) {
 		return nodes.size();
 	}
-	//void SortNBLists(void);
-	
-	/*template<class Op> void LoopCells(Op f) {
-	 for (vector<Cell>::iterator i=cells.begin();
-	 i!=cells.end();
-	 i++) {
-	 f(*i); 
-	 }
-	 }*/
-	
-	/*! \brief Calls function f for all Cells f.
-	 
-	 Using this template requires some fiddling with function adaptors bind2nd and mem_fun_ref.
-	 
-	 Example usage for calling a member function on each cell:
-	 
-	 mesh.LoopCells( bind2nd (mem_fun_ref( &Cell::DrawDiffEdges), &canvas ) );
-	 
-	 This calls Cell's member function DrawDiffEdges, taking one
-	 argument canvas, on all Cell objects in the current Mesh.
-	 
-	 */
+
 	template<class Op> void LoopCells(Op f) {
 		for (vector <Cell *>::iterator i=cells.begin();
 			 i!=cells.end();
 			 i++) {
 			f(**i);
 		}
-		//for_each(cells.begin(),cells.end(),f);
 	}
 	
 	template<class Op> void LoopWalls(Op f) {
@@ -182,7 +145,6 @@ public:
 			f(**i);
 			
 		}
-		//for_each(cells.begin(),cells.end(),f);
 	}
 	
 	template<class Op> void LoopNodes(Op f) {
@@ -256,13 +218,6 @@ public:
 			}
 		}
 	}
-/*	template<class Op1, class Cont> void ExtractFromCells(Op1 f, Cont res) {
-		for (vector<Cell>::iterator i=cells.begin();
-			 i!=cells.end();
-			 i++) {
-			*(res++) = ( f(*i) );
-		}
-	}*/
 	
 	// Apply "f" to cell i
 	// i.e. this is an adapter which allows you to call a function
@@ -335,7 +290,6 @@ public:
 			os << node_insertion_queue.front() << endl;
 			node_insertion_queue.pop();
 		}
-		//copy (node_insertion_queue.begin(),node_insertion_queue.end(),ostream_iterator<Edge>(cerr, " "));
 	}
 	
 	void InsertNodes(void) {
@@ -351,9 +305,7 @@ public:
 	
 	void Clear(); 
 	
-	//  template<class ReactFunction> ReactDiffuse(const double D, ReactFunction& react) {
 	void ReactDiffuse( double delta_t = 1 );
-	//void Diffuse(const double D);
 	double SumChemical(int ch);
 	void SetChemical(int ch, double value) {
 		for (vector<Cell *>::iterator c=cells.begin();
@@ -427,8 +379,6 @@ public:
 	QVector<qreal> VertexAngles(void);
 	QVector< QPair<qreal,int> > VertexAnglesValues(void);
 	void SetSimPlugin(SimPluginInterface *new_plugin) {
-		/* if (plugin) 
-			delete plugin;*/
 		plugin=new_plugin;
 	}
 	QString ModelID(void) { return plugin?plugin->ModelID():QString("undefined"); }
@@ -473,12 +423,7 @@ private:
 		return c;
 	}
 	
-	//int Delaunay(void);
 	void CircumCircle(double x1,double y1,double x2,double y2,double x3,double y3,
 					  double *xc,double *yc,double *r);
-	
-	
-	// void RenumberCells(void);
-	
 };
 #endif
diff --git a/src/modelcatalogue.cpp b/src/modelcatalogue.cpp
--- a/src/modelcatalogue.cpp
+++ b/src/modelcatalogue.cpp
@@ -104,9 +104,6 @@ void ModelCatalogue::LoadPlugin(const ch
     MyWarning::error("Directory 'models' not found!");
   }
 	
-	
-  //QVector<SimPluginInterface *> plugins;
-	
   QStringList modelnames=pluginDir.entryList(QDir::Files);
   if (modelnames.empty()) {
     MyWarning::error("Model %s not found - hint: do not include path in filename.",model);
@@ -160,6 +157,4 @@ void ModelCatalogue::InstallModel(SimPlu
     mainwin->RefreshInfoBar();
     mainwin->Init(0);
   }
-  //	mesh->StandardInit();
-	
 }
diff --git a/src/node.cpp b/src/node.cpp
--- a/src/node.cpp
+++ b/src/node.cpp
@@ -185,8 +185,6 @@ QVector<qreal> Node::NeighbourAngles(voi
 		Vector v1 = (*this - *i->nb1).Normalised();
 		Vector v2 = (*this - *i->nb2).Normalised();	
 	
-		//angles.push_back(atan2(v2.y,v2.x)-atan2(v1.y,v1.x));
-		//angles.push_back(atan2(v2.y,v2.x)-atan2(v1.y,v1.x));
 		double angle = v1.SignedAngle(v2);
 		if (angle<0) {
 			//cerr << "Changing sign of angle " << angle << endl;
diff --git a/src/node.h b/src/node.h
--- a/src/node.h
+++ b/src/node.h
@@ -125,11 +125,9 @@ public:
     boundary = !boundary;
   }
   
-  //void Displace(void);
 
   Cell &getCell(const Neighbor &i);
   
-  //Node &getNode(int i);
   ostream &print(ostream &os) const;
   void XMLAdd(xmlNodePtr nodes_node) const;
   
@@ -164,24 +162,6 @@ public:
     return dead;
   }
 
-  /*void UpdateAfterNodeRemoved(int n) {
-    for (list<Neighbor>::iterator i=owners.begin();
-    i!=owners.end();
-    i++) {
-    if (i->nb1>=n) i->nb1--;
-    if (i->nb2>=n) i->nb2--;
-    }
-    }
- 
-    void UpdateAfterCellRemoved(int n) {
-    for (list<Neighbor>::iterator i=owners.begin();
-    i!=owners.end();
-    i++) {
-    if (i->cell>=n) i->cell--;
-    }
-    }
-  */
-  
   inline void Mark(void) {
     marked=true;
   }
@@ -198,7 +178,6 @@ public:
     z = p.z;
   }
   inline bool SamP(void) const { return sam; }
-  //enum boundary_type {NoBoundary, Noflux, SourceSink, SAM};
 
   //!\brief Calculate angles with neighboring vertices
   //! Sum of angles should be 2*Pi
diff --git a/src/nodeitem.cpp b/src/nodeitem.cpp
--- a/src/nodeitem.cpp
+++ b/src/nodeitem.cpp
@@ -54,29 +54,10 @@ void NodeItem::userMove(double dx, doubl
 void NodeItem::paint(QPainter *painter, const QStyleOptionGraphicsItem *option, QWidget *)
 {
 
-  // from Qt4.2 example: "elastic nodes"
-  //painter->setPen(Qt::NoPen);
-  //painter->setBrush(Qt::darkGray);
-  //painter->drawEllipse(-70, -70, 200, 200);
-  
-  /* QRadialGradient gradient(-30, -30, 100);
-     
-  if (option->state & QStyle::State_Sunken) {
-  gradient.setCenter(30, 30);
-  gradient.setFocalPoint(30, 30);
-  gradient.setColorAt(1, QColor(Qt::yellow).light(120));
-  gradient.setColorAt(0, QColor(Qt::darkYellow).light(120));
-  } else {
-  gradient.setColorAt(0, Qt::yellow);
-  gradient.setColorAt(1, Qt::darkYellow);
-  }
-  
-  painter->setBrush(gradient); */
   option = NULL; // use assignment merely to obviate compilation warning
   
   painter->setBrush(brush);
   painter->setPen(Qt::NoPen);
-  // const static double mag=20.;
   painter->drawEllipse(ellipsesize);
 }
 
diff --git a/src/nodeset.h b/src/nodeset.h
--- a/src/nodeset.h
+++ b/src/nodeset.h
@@ -31,8 +31,6 @@
 #include <iterator>
 #include "node.h"
 
-//class xmlNode;
-
 class NodeSet : public list<Node *> {
   
  public:
@@ -48,10 +46,6 @@ class NodeSet : public list<Node *> {
     n->node_set = this;
   }
 
-  //  list <Node *? getNodes(void) {
-  //  return set;
-  //}
-
   list <Cell *> getCells(void) {
     
     list<Cell *> cellset;
@@ -156,7 +150,6 @@ class NodeSet : public list<Node *> {
 	
 	(*n)->x-=rx;
 	(*n)->y-=ry;
-	// (*n)->z -= rz;
 	  }
       
       
@@ -166,7 +159,6 @@ class NodeSet : public list<Node *> {
   void XMLAdd(xmlNode *root) const;
   void XMLRead(xmlNode *root, Mesh *m);
  private:
-  // list<Node *> set;
   bool done;
 };
 
diff --git a/src/output.cpp b/src/output.cpp
--- a/src/output.cpp
+++ b/src/output.cpp
@@ -24,7 +24,6 @@
 #include <string.h>
 #include <stdlib.h>
 #include <errno.h>
-//#include <unistd.h>
 #include <sys/types.h>
 #include <sys/stat.h>
 #include "warning.h"
@@ -85,31 +84,6 @@ int YesNoP(const char *message) {
     
 }
 
-/* //FILE *OpenWriteFile(char *filename) 
-// {
-//   FILE *fp;
-//   fprintf(stderr,"Opening %s for writing\n",filename);
-	
-//   if((OpenFileAndCheckExistance(&fp,filename,"r"))==TRUE) {
-// 	if (!YesNoP("File exists, overwrite?")) {
-// 	  fprintf(stderr," Could not open file %s for writing, exiting... \n"
-// 			  ,filename);
-// 	  exit(0);
-// 	}
-//   }
-  
-//   if (fp!=NULL) // file existed, but user wants to overwrite
-// 	fclose(fp);
-  
-//   if ((fp=fopen(filename,"w"))==NULL) {
-// 	fprintf(stderr," Could not open file %s for writing, exiting... \n"
-// 			,filename);
-// 	exit(0);
-//   }
-	
-//   return fp;
-// }
-*/
 
 FILE *OpenWriteFile(const char *filename) 
 {
@@ -151,55 +125,6 @@ FILE *OpenWriteFile(const char *filename
   return fp;
 }
 
-/*FILE *OpenGZippedWriteFile(const char *filename) 
-{
-
-  // Open file that is zipped while it is written
-  // uses a pipe
-    
-  char fname[FNAMESIZE];
-  char gzname[FNAMESIZE];
-
-  FILE *fp;
-  extern Parameter par;
-
-  // step 1, add ".gz" to the filename
-  sprintf(gzname, "%s.gz", filename);
-  
-  // and check whether it already exists
-  fprintf(stderr,"Opening %s for writing\n",gzname);
-	
-  if(FileExistsP(gzname)==TRUE) {
-  
-    if (par.interactive) {
-      if (!YesNoP("File exists, overwrite?")) {
-	fprintf(stderr," Could not open file %s for writing, exiting... \n"
-		,gzname);
-	exit(0);
-      }
-    } else {
-      // Rename old file 
-      snprintf(fname, FNAMESIZE-1, "%s~",gzname);
-      rename(gzname, fname);
-      
-    }
-  }
-  
-  //  strncpy(fname, gzname, FNAMESIZE-1);
-  char *command=new char[20+sizeof(gzname)];
-  sprintf(command, "gzip -c > %s", gzname);
-  
-  if ((fp=popen(command,"w"))==NULL) {
-    fprintf(stderr," Could not open file %s for writing: "
-	    ,fname);
-    perror("");
-    exit(-1);
-  }
-	
-  delete[] command;
-  return fp;
-}
-*/
 
 FILE *OpenReadFile(const char *filename) 
 {
@@ -331,8 +256,7 @@ char *Chext(char *filename) {
 }
 
 void MakeDir(const char *dirname) {
-  
-  cerr << "Entering MakeDir for name " << dirname << "\n";
+
 #ifdef QTGRAPHICS
   QFileInfo file_info(dirname);
   
@@ -341,7 +265,7 @@ void MakeDir(const char *dirname) {
     
     if (file_info.isDir()) {
       // OK 
-      cerr << "Using existing directory " << dirname << " for data storage.\n";
+      cerr << "Using existing directory " << dirname << " for data storage." << endl;
       return;
     } else {
       char *message = new char[MESS_BUF_SIZE+1];
@@ -415,49 +339,3 @@ void MakeDir(const char *dirname) {
 #endif
 }
 
-/*bool CanWeWriteP(char *filename) {
-
-  // check for the existance of file "filename"
-   // if it exists, ask the user whether we may overwrite it
-   //false: do not overwrite. true: do overwrite 
-   
-  
-  char message[MESS_BUF_SIZE];
-  char fname[FNAMESIZE];
-
-  extern const Parameter par;
-
-  int status;
-  status=access(filename, F_OK);
-  if (status < 0) {// file does not exist, or something else is wrong      
-    // check error code
-    if (errno!=ENOENT) {
-	
-      // another error occured 
-      snprintf(message, MESS_BUF_SIZE, "Error checking for existance of %s",filename);
-      perror(message);	      
-      exit(1);
-    }
-      
-  } else {
-      
-    // file exists, ask for permission to overwrite if interactive
-    if (par.interactive) {
-      snprintf(message, MESS_BUF_SIZE, "File %s exists. Overwrite? ",filename);
-      if (!YesNoP(message))
-	return false;
-      else 
-	return true;
-    } else {
-      // Rename old file 
-      snprintf(fname, FNAMESIZE-1, "%s~",filename);
-      rename(filename, fname);
-    }
-    
-    return true;
-  }
-    
-  // file does not exist, or user permits overwriting
-  return true;
-    
-}*/
diff --git a/src/output.h b/src/output.h
--- a/src/output.h
+++ b/src/output.h
@@ -1,55 +1,55 @@
-/*
- *
- *  $Id$
- *
- *  This file is part of the Virtual Leaf.
- *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
- *  it under the terms of the GNU General Public License as published by
- *  the Free Software Foundation, either version 3 of the License, or
- *  (at your option) any later version.
- *
- *  The Virtual Leaf is distributed in the hope that it will be useful,
- *  but WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *  GNU General Public License for more details.
- *
- *  You should have received a copy of the GNU General Public License
- *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
- *
- *  Copyright 2010 Roeland Merks.
- *
- */
-
-
-#ifndef _OUTPUT_H_
-#define _OUTPUT_H_
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-int OpenFileAndCheckExistance(FILE **fp,const char *fname,char *ftype);
-int YesNoP(const char *message);
-FILE *OpenWriteFile(const char *filename);
-FILE *OpenGZippedWriteFile(const char *filename);
-FILE *OpenReadFile(const char *filename);
-char *ReadLine(FILE *fp);
-void CheckFile(FILE *fp);
-int FileExistsP(const char *fname);
-char *Chext(char *filename);
-void MakeDir(const char *dirname);
-bool CanWeWriteP(char *filename);
-
-#ifdef __cplusplus
-}
-#endif
-
-
-#define MESS_BUF_SIZE 160
-#ifndef FALSE
-#define FALSE 0
-#define TRUE 1
-#endif
-
-#endif
+/*
+ *
+ *  $Id$
+ *
+ *  This file is part of the Virtual Leaf.
+ *
+ *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *
+ *  The Virtual Leaf is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ *  Copyright 2010 Roeland Merks.
+ *
+ */
+
+
+#ifndef _OUTPUT_H_
+#define _OUTPUT_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+int OpenFileAndCheckExistance(FILE **fp,const char *fname,char *ftype);
+int YesNoP(const char *message);
+FILE *OpenWriteFile(const char *filename);
+FILE *OpenGZippedWriteFile(const char *filename);
+FILE *OpenReadFile(const char *filename);
+char *ReadLine(FILE *fp);
+void CheckFile(FILE *fp);
+int FileExistsP(const char *fname);
+char *Chext(char *filename);
+void MakeDir(const char *dirname);
+bool CanWeWriteP(char *filename);
+
+#ifdef __cplusplus
+}
+#endif
+
+
+#define MESS_BUF_SIZE 160
+#ifndef FALSE
+#define FALSE 0
+#define TRUE 1
+#endif
+
+#endif
diff --git a/src/parse.cpp b/src/parse.cpp
--- a/src/parse.cpp
+++ b/src/parse.cpp
@@ -71,8 +71,7 @@ char *ParsePar(FILE *fp, char *parameter
 int igetpar(FILE *fp,char *parameter, bool wrapflag) {
   
   // overloaded compatibility function. Doesn't need default parameter
-  // default = 0
-  
+
   return igetpar(fp, parameter, 0, wrapflag);
 }
 
@@ -102,10 +101,7 @@ int igetpar(FILE *fp,char *parameter, in
 float fgetpar(FILE *fp,char *parameter, bool wrapflag) {
    
   // overloaded compatibility function. Doesn't need default parameter
-  // default = 0
-  
   return fgetpar(fp, parameter, 0., wrapflag);
-
 }
 
 float fgetpar(FILE *fp, char *parameter, double default_val, bool wrapflag) 
@@ -296,8 +292,6 @@ char *SearchToken(FILE *fp, char *token,
   int wrapped=false;
   long initial_position;
   
-  /*  rewind(fp); */
-
   char *tokenplusspace = (char *)malloc( (strlen(token)+3)*sizeof(char));
   strcpy(tokenplusspace, token);
   strcat(tokenplusspace," ");
diff --git a/src/parse.h b/src/parse.h
--- a/src/parse.h
+++ b/src/parse.h
@@ -1,46 +1,46 @@
-/*
- *
- *  $Id$
- *
- *  This file is part of the Virtual Leaf.
- *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
- *  it under the terms of the GNU General Public License as published by
- *  the Free Software Foundation, either version 3 of the License, or
- *  (at your option) any later version.
- *
- *  The Virtual Leaf is distributed in the hope that it will be useful,
- *  but WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *  GNU General Public License for more details.
- *
- *  You should have received a copy of the GNU General Public License
- *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
- *
- *  Copyright 2010 Roeland Merks.
- *
- */
-
-
-#ifndef _PARSE_H_
-#define _PARSE_H_
-
-char *ParsePar(FILE *fp, char *parameter, bool wrapflag);
-int igetpar(FILE *fp,char *parameter, bool wrapflag);
-int igetpar(FILE *fp,char *parameter, int default_val, bool wrapflag);
-float fgetpar(FILE *fp,char *parameter, bool wrapflag);
-float fgetpar(FILE *fp,char *parameter, double default_val, bool wrapflag);
-
-/* Get a list of n comma separated doubles */
-double *dgetparlist(FILE *fp,char *parameter, int n, bool wrapflag);
-char *sgetpar(FILE *fp,char *parameter, bool wrapflag);
-char *sgetpar(FILE *fp,char *parameter,const char *default_val, bool wrapflag);
-bool bgetpar(FILE *fp, char *parameter, bool wrapflag);
-bool bgetpar(FILE *fp, char *parameter, int default_val, bool wrapflag);
-char *SearchToken(FILE *fp, char *token, bool wrapflag);
-int TokenInLineP(char *line,char *token);
-void SkipToken(FILE *fp,char *token, bool wrapflag);
-void SkipLine(FILE *fp);
-char *bool_str(bool bool_var);
-
-#endif
+/*
+ *
+ *  $Id$
+ *
+ *  This file is part of the Virtual Leaf.
+ *
+ *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *
+ *  The Virtual Leaf is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ *  Copyright 2010 Roeland Merks.
+ *
+ */
+
+
+#ifndef _PARSE_H_
+#define _PARSE_H_
+
+char *ParsePar(FILE *fp, char *parameter, bool wrapflag);
+int igetpar(FILE *fp,char *parameter, bool wrapflag);
+int igetpar(FILE *fp,char *parameter, int default_val, bool wrapflag);
+float fgetpar(FILE *fp,char *parameter, bool wrapflag);
+float fgetpar(FILE *fp,char *parameter, double default_val, bool wrapflag);
+
+/* Get a list of n comma separated doubles */
+double *dgetparlist(FILE *fp,char *parameter, int n, bool wrapflag);
+char *sgetpar(FILE *fp,char *parameter, bool wrapflag);
+char *sgetpar(FILE *fp,char *parameter,const char *default_val, bool wrapflag);
+bool bgetpar(FILE *fp, char *parameter, bool wrapflag);
+bool bgetpar(FILE *fp, char *parameter, int default_val, bool wrapflag);
+char *SearchToken(FILE *fp, char *token, bool wrapflag);
+int TokenInLineP(char *line,char *token);
+void SkipToken(FILE *fp,char *token, bool wrapflag);
+void SkipLine(FILE *fp);
+char *bool_str(bool bool_var);
+
+#endif
diff --git a/src/random.cpp b/src/random.cpp
--- a/src/random.cpp
+++ b/src/random.cpp
@@ -141,24 +141,9 @@ int Randomize(void) {
   
   seed=abs((int)((t.time*t.millitm)%655337));
   Seed(seed);
-  fprintf(stderr,"Random seed is %d\n",seed);
+#ifdef QDEBUG
+  qdebug() << "Random seed is " << seed << endl;
+#endif
   return seed;
 }
 
-/** TESTING random generator 
-#include <vector>
-#include <fstream>
-int main(void) {
-  
-  MyUrand r(-1);
-  
-  vector<int> bucket(100);
-  for (int i = 0; i<1000000 ; i++) {
-    bucket[r(100)]++;
-  }
-  ofstream out("randomtest.dat");
-  for (int i = 0; i<=100; i++) {
-    out << i << " " << bucket[i] << endl;
-  }
-}
-***/
diff --git a/src/random.h b/src/random.h
--- a/src/random.h
+++ b/src/random.h
@@ -1,66 +1,66 @@
-/*
- *
- *  $Id$
- *
- *  This file is part of the Virtual Leaf.
- *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
- *  it under the terms of the GNU General Public License as published by
- *  the Free Software Foundation, either version 3 of the License, or
- *  (at your option) any later version.
- *
- *  The Virtual Leaf is distributed in the hope that it will be useful,
- *  but WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *  GNU General Public License for more details.
- *
- *  You should have received a copy of the GNU General Public License
- *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
- *
- *  Copyright 2010 Roeland Merks.
- *
- */
-
-
-#ifndef _RANDOM_H_
-#define _RANDOM_H_
-
-#define MBIG 1000000000
-#define MSEED 161803398
-#define MZ 0
-#define FAC (1.0/MBIG)
-
-double RANDOM();
-int Seed(int seed);
-long RandomNumber(long max);
-void AskSeed();
-int Randomize(void);
-int RandomCounter(void);
-
-
-
-// Class MyUrand, so we can pass the random generator to STL's random_shuffle,
-// and get identical simulations for a given random seed.
-class MyUrand {
- 
-  long n;
- public:
-  MyUrand(long nn) {
-    n=nn;
-  }
-  MyUrand(void){};
- 
-  void seed(long s) {
-    Seed(s);
-  }
-  
-  long operator()(long nn) { return RandomNumber(nn)-1; }
-  long operator()(void) { return RandomNumber(n); }
-};
-
-
-
-
-
-
-#endif
+/*
+ *
+ *  $Id$
+ *
+ *  This file is part of the Virtual Leaf.
+ *
+ *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *
+ *  The Virtual Leaf is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ *  Copyright 2010 Roeland Merks.
+ *
+ */
+
+
+#ifndef _RANDOM_H_
+#define _RANDOM_H_
+
+#define MBIG 1000000000
+#define MSEED 161803398
+#define MZ 0
+#define FAC (1.0/MBIG)
+
+double RANDOM();
+int Seed(int seed);
+long RandomNumber(long max);
+void AskSeed();
+int Randomize(void);
+int RandomCounter(void);
+
+
+
+// Class MyUrand, so we can pass the random generator to STL's random_shuffle,
+// and get identical simulations for a given random seed.
+class MyUrand {
+ 
+  long n;
+ public:
+  MyUrand(long nn) {
+    n=nn;
+  }
+  MyUrand(void){};
+ 
+  void seed(long s) {
+    Seed(s);
+  }
+  
+  long operator()(long nn) { return RandomNumber(nn)-1; }
+  long operator()(void) { return RandomNumber(n); }
+};
+
+
+
+
+
+
+#endif
diff --git a/src/sqr.h b/src/sqr.h
--- a/src/sqr.h
+++ b/src/sqr.h
@@ -26,13 +26,6 @@
 #ifndef _SQR_H_
 #define _SQR_H_
 
-/* static float sqrarg;
-#define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 : sqrarg*sqrarg)
-
-static double dsqrarg;
-#define DSQR(a) ((dsqrarg=(a)) == 0.0 ? 0.0 : dsqrarg*dsqrarg)
-*/
-
 
 // redefine these macros as inline functions, to prevent scary
 // behavior.  (According to compiler warnings, the above macros from
diff --git a/src/vector.h b/src/vector.h
--- a/src/vector.h
+++ b/src/vector.h
@@ -118,7 +118,6 @@ public:
   Vector operator*(const Vector &v) const; // cross product
   bool operator==(const Vector &v) const; // comparison
   bool operator< (const Vector &v) const; // order x,y,z
-  //double Norm(void) const; // gives the "norm" (| v |) of v
   inline double Norm(void) const {
   
     return sqrt(DSQR(x)+DSQR(y)+DSQR(z));
diff --git a/src/vleafmodel.h b/src/vleafmodel.h
--- a/src/vleafmodel.h
+++ b/src/vleafmodel.h
@@ -1,12 +1,29 @@
 /*
- *  vleafmodel.h
- *  mymodel
+ *
+ *  $Id$
+ *
+ *  This file is part of the Virtual Leaf.
+ *
+ *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
  *
- *  Created by Roeland Merks on 08-06-10.
- *  Copyright 2010 __MyCompanyName__. All rights reserved.
+ *  The Virtual Leaf is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ *  Copyright 2010 Roeland Merks.
  *
  */
 
+#ifndef _VLEAFMODEL_H_
+#define _VLEAFMODEL_H_
+
 #include <QObject>
 #include <QtGui>
 #include <fstream>
@@ -18,3 +35,5 @@
 #include "cellbase.h"
 #include "mymodel.h"
 #include "flux_function.h"
+
+#endif
diff --git a/src/wall.cpp b/src/wall.cpp
--- a/src/wall.cpp
+++ b/src/wall.cpp
@@ -49,13 +49,6 @@ bool Wall::CorrectWall( void ) {
 	duplicates_copy( owners.begin(), owners.end(), back_inserter(wall_owners) );
 	
 	// duplicates are the cells to which the Wall belongs
-	/* cerr << "Wall belongs to Cells: ";
-     transform(wall_owners.begin(), wall_owners.end(), ostream_iterator<int>(cerr, ", "), mem_fun(&Cell::Index));
-	 cerr << endl;
-	 */
-	
-	//list<Cell *>::iterator f = adjacent_find (++e,owners.end());
-	
 	// For the first division, wall finds three "owners", including the boundary_polygon.
 	// Remove that one from the list.
 	//cerr << "wall_owners.size() = " << wall_owners.size() << endl;
@@ -214,9 +207,6 @@ void Wall::ShowStructure(QGraphicsScene 
     
 	text1->setPen ( QColor(par.textcolor) );
 	text2->setPen ( text1->pen() );
-    
-	//text1->setTextFlags(Qt::AlignCenter);
-	//text2->setTextFlags(Qt::AlignCenter);
 	text1->show(); text2->show();
 	
 }
diff --git a/src/wallbase.cpp b/src/wallbase.cpp
--- a/src/wallbase.cpp
+++ b/src/wallbase.cpp
@@ -78,7 +78,6 @@ WallBase::WallBase(Node *sn1, Node *sn2,
 	
 	apoplast = new double[CellBase::NChem()]; // not yet in use.
     
-	//length = 0;
 	SetLength();
 	
 	// to visualize flux through WallBase
@@ -170,10 +169,6 @@ bool WallBase::SAM_P(void) {
 
 #include <fstream>
 
-/* double WallBase::Length(void){ 
- return (*n2 - *n1).Norm();
- }*/
-
 void WallBase::SetLength(void) {
 	
 	//static bool show_nodes = true;
@@ -203,11 +198,6 @@ void WallBase::SetLength(void) {
 		 n!=second_node_edge_plus_1;
 		 (++n == c1->nodes.end()) ? (n=c1->nodes.begin()):n  ) {
 		
-		/* if (n==c1->nodes.end()) { 
-		 
-		 n=c1->nodes.begin(); // wrap around
-		 }*/
-		
 		list<Node *>::const_iterator prev_n = n; 
 		if (prev_n==c1->nodes.begin()) prev_n=c1->nodes.end();
 		--prev_n;
@@ -222,25 +212,12 @@ void WallBase::SetLength(void) {
 		length += (*(*prev_n) - *(*n)).Norm(); 
 		
 	}
-	
-	/*  if (length > 100) {
-	 ostringstream warn;
-	 warn << "Strange, length is " << length << "...: " << deb_str.str() << endl;
-	 warn << "Strangeness in WallBase: " << *this << endl << endl << deb_str.str() << endl;
-	 MyWarning::warning (warn.str().c_str());
-	 }*/
-	
-	//cerr << deb_str .str() << ", length is " << length << endl;
-	//of << length << " " << ((*n2)-(*n1)).Norm() << endl;
-	
-	
 }
 
 void WallBase::CorrectTransporters(double orig_length) {
 	
 	double length_factor = length / orig_length;
-	// cerr << "[ lf = " << length_factor << "]";
-	//cerr << "Correcting amount of transporters on WallBase "  << *this << ", length factor is "  << orig_length << " / " << length << endl;
+
 	for (int ch=0;ch<CellBase::NChem();ch++) {
 		transporters1[ch] *= length_factor;
 		transporters2[ch] *= length_factor;
@@ -253,19 +230,8 @@ void WallBase::CorrectTransporters(doubl
 
 Vector WallBase::VizFlux(void) {
 	return viz_flux * ( (*n2) - (*n1) ).Normalised().Perp2D();    
-	//return transporters1[1] * ( (*n2) - (*n1) ).Normalised().Perp2D();    
 }
 
-/* TransportFunction::TransportFunction( void ) {  
-	
-	//chem_change_c1 = new double[Cell::NChem()];
-	//chem_change_c2 = new double[Cell::NChem()];
-	
-	//for (int i=0;i<Cell::NChem();i++) {
-	// chem_change_c1[i] = chem_change_c2[i] = 0.;
-	//}
-}*/
-
 
 void WallBase::SetTransToNewTrans( void ){ 
 	for (int i=0;i<CellBase::NChem();i++) { 
@@ -301,7 +267,6 @@ bool WallBase::IntersectsWithDivisionPla
 	double x4 = p2.x, y4 = p2.y;
 	
 	double ua = ( (x4 - x3) * (y1-y3) - (y4 - y3)*(x1-x3) ) / ( (y4 -y3) * (x2 -x1) - (x4-x3)*(y2-y1));
-	//	double ub = ( (x2 - x1) * (y1 - y3)  - (y2 - y1) * (x1 -x3) ) / ( ( y4-y3) * (x2-x1) - (x4-x3)*(y2-y1)) ;
 	
 	// If ua is between 0 and 1, line p1 intersects the line segment
 	if ( ua >=0. && ua <=1.) return true;
@@ -309,5 +274,3 @@ bool WallBase::IntersectsWithDivisionPla
 	
 }
 
-
-
diff --git a/src/wallbase.h b/src/wallbase.h
--- a/src/wallbase.h
+++ b/src/wallbase.h
@@ -191,57 +191,11 @@ public:
 	 */
 	Vector VizFlux(void);
 	bool IntersectsWithDivisionPlaneP(const Vector &p1, const Vector &p2);
-	
-	/*! Function to be defined in leaf.cpp */
-	//void OnWallInsert(void);
-	
-	
-
 	void SetTransToNewTrans( void );
 	
-	// implemented in xmlwrite.cpp
-	//void XMLAdd(xmlNode *parent) const;
 private:
 	
 };
 
-/* class TransportFunction {
-	
-	friend class Mesh;
-public:
-	TransportFunction( void );
-	virtual ~TransportFunction() {
-		//delete[] chem_change_c1;
-		//delete[] chem_change_c2;
-	}
-	virtual void operator()(WallBase *w, double *dchem_c1, double *dchem_c2) = 0;// { cerr << "This is base class TransportFunction.\n"; }
-	//virtual void operator()(WallBase *w, double *dchem_c1, double *dchem_c2, double *dapo) =0;
-protected:
-	int wall_index; //double *chem_change_c1;
-	//double *chem_change_c2;
-};
-
-class CellReaction {
-	
-public:
-	CellReaction(void) {};
-	virtual ~CellReaction() {};
-	
-	//! Implements the actual, intracellular chemical reactions.
-	virtual void operator()(CellBase * c, double *dchem ) = 0;
-	
-};
-
-class WallReaction {
-	
-public:
-	WallReaction(void) {};
-	virtual ~WallReaction() {};
-	
-	//! Implements the actual, biochemical reactions occuring at the wall.
-	virtual void operator()(WallBase *, double *dw1, double *dw2) = 0;
-	
-};*/
-
 ostream &operator<<(ostream &os, const WallBase &w);
 #endif
diff --git a/src/wallitem.cpp b/src/wallitem.cpp
--- a/src/wallitem.cpp
+++ b/src/wallitem.cpp
@@ -37,22 +37,7 @@ WallItem::WallItem( Wall *w, int wallnum
   wn = wallnumber;
 
   extern Parameter par;
-  //Wall *w=&getWall();
-  
-  // Draw amount of "PIN1"
-  //double val = wn==1?(w->Transporters1(1)/par.Pi_tot)*255.:(w->Transporters2(1)/par.Pi_tot)*255.;
-  
-  /* if (val > 255 || val < 0 ) { 
-     std::cerr << "val = " << val << endl;
-     if (wn == 1) {
-     std::cerr << "Transporters1(1) = " << w->Transporters1(1) << endl;
-     } else {
-     std::cerr << "Transporters2(1) = " << w->Transporters2(1) << endl;
-     }
-    
-     }*/
-  
-  
+
 	  setColor();
   
 	  // line with "PIN1"is a bit inside the cell wall
@@ -70,18 +55,6 @@ WallItem::WallItem( Wall *w, int wallnum
 	  Vector centroid = ( offs + tmp_centroid ) * factor;
 	  
 	  QString text=QString("%1").arg(w->Index());
-
-	  /*  if (0) {
-		  QGraphicsSimpleTextItem *ctext = new QGraphicsSimpleTextItem ( text, 0, canvas );
-		  ctext->setPen( QPen(QColor("orange")) );
-		  ctext->setZValue(20);
-		  ctext->setFont( QFont( "Helvetica", par.nodenumsize, QFont::Bold) );
-		  //ctext->setTextFlags(Qt::AlignCenter);
-		  ctext->show();
-		  ctext ->setPos(centroid.x,
-						 centroid.y );
-	  }*/
-	  
 	  setLine(( from.x ),
 			  ( from.y ),
 			  ( to.x ),
@@ -100,13 +73,6 @@ void WallItem::setColor(void) {
   double tr = wn==1?w->Transporters1(1):w->Transporters2(1);
   CellBase *c = wn==1?w->C1():w->C2();
   diffcolor.setRgb( (int)( ( tr / (1 + tr) )*255.), 0, 0);
-  //diffcolor.setRgb( (int)( ((wn==1?w->Transporters1(1):w->Transporters2(1)))*255.), 0, 0);
-  /* if (wn==1) {
-     cerr << "Transporter: " << w->Transporters1(1) << endl;
-     } else {
-     cerr << "Transporter: " << w->Transporters2(1) << endl;
-     }*/
-  
   if (w->AuxinSource() && c->BoundaryPolP()) {
     setPen( QPen(purple , par.outlinewidth) );
   } else {
@@ -116,10 +82,6 @@ void WallItem::setColor(void) {
       setPen (QPen(diffcolor, par.outlinewidth) );
     }
   }
-  
-//   if (c->BoundaryPolP()) {
-//     setPen(QPen(QColor("red"), 20));
-//   }
 }
 
 void WallItem::OnClick(QMouseEvent *e) {
@@ -132,7 +94,6 @@ void WallItem::OnClick(QMouseEvent *e) {
 	qDebug() << "C1 = " << w->C1()->Index() << ", C2 = " << w->C2()->Index() << endl;
 	qDebug() << "N1 = " << w->N1()->Index() << ", N2 = " << w->N2()->Index() << endl;
 	#endif
-	//double tr = wn==1?w->Transporters1(1):w->Transporters2(1);
 	CellBase *c = wn==1?w->C1():w->C2();
 
 	TransporterDialog dialog(w, c, wn);
@@ -147,7 +108,6 @@ void WallItem::OnClick(QMouseEvent *e) {
 		}
 		
 		//extern MainBase *main_window;
-		//((Main *)main_window)->UserMessage(message);
 		
 	} else {
 		if (e->button() == Qt::LeftButton) {
@@ -166,11 +126,5 @@ void WallItem::OnClick(QMouseEvent *e) {
 			setColor();
 			update(boundingRect());
 		} 
-		/* else {
-			if (e->button() == Qt::MidButton && (e->modifiers == Qt::ShiftModifier & Qt::ControlModifier)) {
-				// hidden feature for correcting 
-			}*/
-		
-	
 	}
 }
diff --git a/src/wallitem.h b/src/wallitem.h
--- a/src/wallitem.h
+++ b/src/wallitem.h
@@ -42,8 +42,6 @@ public:
   virtual ~WallItem() {}
   Wall &getWall(void) const { return *class_cast<Wall*>(obj); }
   void OnClick(QMouseEvent *e);  
-  //virtual void userMove(double dx, double dy);  
-  //virtual void paint( QPainter * painter, const QStyleOptionGraphicsItem * option, QWidget * widget = 0);
   void setColor(void);
  private:
   int wn;
diff --git a/src/warning.cpp b/src/warning.cpp
--- a/src/warning.cpp
+++ b/src/warning.cpp
@@ -66,8 +66,6 @@ void MyWarning::error(const char *fmt, .
   
   QString qmess(message);
   
-  //  bool batch = false;
-  
   if (qApp->type()==QApplication::Tty) {
     // batch mode: print the message to stderr
     fprintf(stderr, "Fatal error: %s\n",qmess.toStdString().c_str());
diff --git a/src/warning.h b/src/warning.h
--- a/src/warning.h
+++ b/src/warning.h
@@ -1,60 +1,47 @@
-/*
- *
- *  $Id$
- *
- *  This file is part of the Virtual Leaf.
- *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
- *  it under the terms of the GNU General Public License as published by
- *  the Free Software Foundation, either version 3 of the License, or
- *  (at your option) any later version.
- *
- *  The Virtual Leaf is distributed in the hope that it will be useful,
- *  but WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *  GNU General Public License for more details.
- *
- *  You should have received a copy of the GNU General Public License
- *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
- *
- *  Copyright 2010 Roeland Merks.
- *
- */
-
-
-#ifndef _WARNING_H_
-#define _WARNING_H_
-
-#define MEMORYCHECK(x) if ((x)==NULL) {   fprintf(stderr, "Out of Memory error in "#x" \n");  exit(0); }
-
-#define UNIDENTIFIED 2353996
-//static int last_value=UNIDENTIFIED;
-/*#define WATCH(x) if (last_value==UNIDENTIFIED) {   last_value=x; 
-} else { if (x!=last_value) { fprintf(stderr,"WATCH value changed. Suspending execution. \n Interrupt within debugger to examine position in program.\n"); 
-				 last_value=x; 
-				 while(1);
-	   } else { 
-		      last_value=x;
-	   } 
-	   }*/
-
-
-/* These functions were a gift from Josh Barnes */
-/* I changed the name "eprintf" to "warning" */
-
-#ifdef __cplusplus 
-extern "C" { 
-#endif
-  // namespace MyWarning needed because libxml2 also defines a warning token.
-    
-  namespace MyWarning {
-    void error(const char *, ...);
-    void warning(const char *, ...);
-    void unique_warning(const char *, ...);
-  }
-  
-#ifdef __cplusplus
-}
-#endif
-
-#endif
+/*
+ *
+ *  $Id$
+ *
+ *  This file is part of the Virtual Leaf.
+ *
+ *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *
+ *  The Virtual Leaf is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ *  Copyright 2010 Roeland Merks.
+ *
+ */
+
+
+#ifndef _WARNING_H_
+#define _WARNING_H_
+
+#define MEMORYCHECK(x) if ((x)==NULL) {   fprintf(stderr, "Out of Memory error in "#x" \n");  exit(0); }
+
+#define UNIDENTIFIED 2353996
+
+#ifdef __cplusplus 
+extern "C" { 
+#endif
+  // namespace MyWarning needed because libxml2 also defines a warning token.
+    
+  namespace MyWarning {
+    void error(const char *, ...);
+    void warning(const char *, ...);
+    void unique_warning(const char *, ...);
+  }
+  
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/src/xmlwrite.cpp b/src/xmlwrite.cpp
--- a/src/xmlwrite.cpp
+++ b/src/xmlwrite.cpp
@@ -187,7 +187,6 @@ void Cell::XMLAddCore(xmlNodePtr xmlcell
     {
       ostringstream text;
       xmlNodePtr wall_xml = xmlNewChild(xmlcell, NULL, BAD_CAST "wall", NULL);
-      //text <<wall_list_index( *i );
       text << XMLIO::list_index( m->walls.begin(), m->walls.end(), *i );
       xmlNewProp(wall_xml, BAD_CAST "w", BAD_CAST text.str().c_str());
     }
@@ -362,7 +361,6 @@ int Cell::XMLRead(xmlNode *cur)  {
 		  {
 		    stringstream text;
 		    text << "Exception in Mesh::XMLRead: Too many chemical values given for cell(s). Ignoring remaining values.";
-		    //ThrowStringStream(text);
 		    unique_warning(text.str().c_str());
 		    break;
 		  }
@@ -373,7 +371,6 @@ int Cell::XMLRead(xmlNode *cur)  {
 		if (nc==0) {
 		  unique_warning("Token \"v\" not found in xmlwrite.cpp at or around line no. 1002");
 		}
-		//double v = strtod( (char *)nc, 0 );
 		double v=standardlocale.toDouble((char *)nc, &ok);
 		if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(char *)nc);
 		chem[nv++]=v;
@@ -393,7 +390,6 @@ int Cell::XMLRead(xmlNode *cur)  {
 			unique_warning("Token \"area\" not found in xmlwrite.cpp at or around line no. 1018");
 		}
 		if (v_str != NULL) {
-		  //area = strtod( (char *)v_str, 0);
 			area=standardlocale.toDouble((char *)v_str, &ok);
 			if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(char *)v_str);
 			xmlFree(v_str);
@@ -407,7 +403,6 @@ int Cell::XMLRead(xmlNode *cur)  {
 			unique_warning("Token \"target_area\" not found in xmlwrite.cpp at or around line no. 1029");
 		}
     if (v_str != NULL) {
-      //target_area = strtod( (char *)v_str, 0);
       	target_area=standardlocale.toDouble((char *)v_str, &ok);
 	if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(char *)v_str);
       xmlFree(v_str);
@@ -422,7 +417,6 @@ int Cell::XMLRead(xmlNode *cur)  {
       unique_warning("Token \"target_length\" not found in xmlwrite.cpp at or around line no. 1041");
     }
     if (v_str != NULL) {
-      //target_length = strtod( (char *)v_str, 0);
       target_length=standardlocale.toDouble((char *)v_str, &ok);
       if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(char *)v_str);
       xmlFree(v_str);
@@ -436,7 +430,6 @@ int Cell::XMLRead(xmlNode *cur)  {
       unique_warning("Token \"lambda_celllength\" not found in xmlwrite.cpp at or around line no. 1052");
     }
     if (v_str != NULL) {
-      //lambda_celllength = strtod( (char *)v_str, 0);
       lambda_celllength=standardlocale.toDouble((char *)v_str, &ok);
       if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(char *)v_str);
       xmlFree(v_str);
@@ -450,7 +443,6 @@ int Cell::XMLRead(xmlNode *cur)  {
       unique_warning("Token \"stiffness\" not found in xmlwrite.cpp at or around line no. 1063");
     }
     if (v_str != NULL) {
-      //stiffness = strtod( (char *)v_str, 0);
       stiffness=standardlocale.toDouble((char *)v_str, &ok);
       if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(char *)v_str);
       xmlFree(v_str);
@@ -598,12 +590,6 @@ void Wall::XMLAdd(xmlNode *parent) const
   // Save the node to a stream so we can reconstruct its state later
   xmlNodePtr xmlwall = xmlNewChild(parent, NULL, BAD_CAST "wall",NULL);
   
-  /* {
-     ostringstream text;
-     text << index;
-     xmlNewProp(xmlnode, BAD_CAST "index", BAD_CAST text.str().c_str());
-     }*/
-  
   {
     ostringstream text;
     text << Index();
@@ -657,12 +643,6 @@ void Wall::XMLAdd(xmlNode *parent) const
       
     
   xmlNodePtr tr1_xml = xmlNewChild(xmlwall, NULL, BAD_CAST "transporters1", NULL); 
-  //   {
-  //     ostringstream text;
-  //     text << Cell::nchem;
-  //     xmlNewProp(tr1_xml, BAD_CAST "n", BAD_CAST text.str().c_str());
-  //   }
-  
   if (transporters1) {
     for (int i=0;i<Cell::NChem();i++) {
       xmlNodePtr tr1_val_xml = xmlNewChild(tr1_xml, NULL, BAD_CAST "val", NULL);
@@ -753,7 +733,7 @@ void Mesh::XMLSave(const char *docname, 
 	
 	time_t t;
 	std::time(&t);
-	// asctime_r(localtime(&t),tstring); //Doesn't work for MinGW
+
 	char *tstring = strdup(asctime(localtime(&t))); // but this does
 	// replace "end of line character by '\0'
 	char *eol=strchr(tstring,'\n');
@@ -769,7 +749,7 @@ void Mesh::XMLSave(const char *docname, 
 	/*
 	 * Creates a DTD declaration. Isn't mandatory. 
 	 */
-	//dtd = xmlCreateIntSubset(doc, BAD_CAST "root", NULL, BAD_CAST "tree2.dtd");
+
 	par.XMLAdd(root_node);
 
 	xmlNodePtr xmlnodes = xmlNewChild(root_node, NULL, BAD_CAST "nodes",NULL);
@@ -896,7 +876,6 @@ void Mesh::XMLSave(const char *docname, 
 	/*
 	 * this is to debug memory for regression tests
 	 */
-	//xmlMemoryDump();
 }
 
 
@@ -909,16 +888,20 @@ void Mesh::XMLReadSimtime(const xmlNode 
   
   
   if (strsimtime) {
-    //double simtime = strtod((const char *)strsimtime, 0);
+
     QLocale standardlocale(QLocale::C);
     bool ok;
     
     double simtime=standardlocale.toDouble((char *)strsimtime, &ok);
     if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(char *)strsimtime);
       time = simtime;
-		cerr << "Simtime = " << strsimtime << endl;
+#ifdef QDEBUG
+                qDebug() << "Simtime = " << strsimtime << endl;
+#endif
 	} else {
-		cerr << "No simtime found in file \n";
+#ifdef QDEBUG
+    qDebug() << "No simtime found in file." << endl;
+#endif
 		time =0;
 	}	
 }
@@ -964,7 +947,6 @@ void Mesh::XMLReadGeometry(const xmlNode
 		cur = cur->next;
 	}
     
-	//cur = root_node;
     
 	// allocate Cells
 	cur = root_node;
@@ -975,10 +957,10 @@ void Mesh::XMLReadGeometry(const xmlNode
 		if ((!xmlStrcmp(cur->name, (const xmlChar *)"cells"))){
 			xmlChar *offsetxc = xmlGetProp(cur, BAD_CAST "offsetx");
 			xmlChar *offsetyc = xmlGetProp(cur, BAD_CAST "offsety");
-			//double ox = strtod((const char*)offsetxc, 0);
+
 			double ox=standardlocale.toDouble((const char *)offsetxc, &ok);
 			if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)offsetxc);
-			//double oy = strtod((const char*)offsetyc, 0);
+
 			double oy=standardlocale.toDouble((const char *)offsetyc, &ok);
 			if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)offsetyc);
 			Cell::setOffset(ox, oy);
@@ -986,13 +968,13 @@ void Mesh::XMLReadGeometry(const xmlNode
 			xmlFree(offsetyc);
 			
 			xmlChar *magnificationc = xmlGetProp(cur, BAD_CAST "magnification");
-			//Cell::SetMagnification(strtod((const char*)magnificationc, 0 ));
+
 			Cell::SetMagnification(standardlocale.toDouble((const char *)magnificationc, &ok));
 			if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)magnificationc);
 			xmlFree(magnificationc);
 			
 			xmlChar *baseareac = xmlGetProp(cur, BAD_CAST "base_area");
-			//Cell::BaseArea()= strtod((const char *)baseareac, 0 );
+
 			Cell::BaseArea() = standardlocale.toDouble((const char *)baseareac, &ok);
 			if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)baseareac);
 			xmlFree(baseareac);
@@ -1071,7 +1053,7 @@ void Mesh::XMLReadNodes(xmlNode *root) {
   xmlChar *tlc = xmlGetProp(root, BAD_CAST "target_length");
 	
   if (tlc != 0) {
-    //Node::target_length = strtod( (const char *)tlc, 0 );
+
 	  
     Node::target_length = standardlocale.toDouble((const char *)tlc, &ok);
     if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)tlc);
@@ -1112,11 +1094,10 @@ void Mesh::XMLReadNodes(xmlNode *root) {
 	unique_warning("Token \"sam\" not found in xmlwrite.cpp at or around line.");
       }
 			
-      //double x = strtod( (char *)xc , 0);
+
       double x = standardlocale.toDouble((const char *)xc, &ok);
       if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)xc);
 		
-      //double y = strtod( (char *)yc , 0 );
       double y = standardlocale.toDouble((const char *)yc, &ok);
       if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)yc);
 			
@@ -1162,8 +1143,6 @@ void Mesh::XMLReadWalls(xmlNode *root, v
   walls.clear();
   Wall::nwalls = 0;
   tmp_walls->clear();
-  //Node::nnodes=0;
-	
 	
   QLocale standardlocale(QLocale::C);
   bool ok;
@@ -1211,7 +1190,7 @@ void Mesh::XMLReadWalls(xmlNode *root, v
 	if (	nc==0) {
 	  unique_warning("Token \"length\" not found in xmlwrite.cpp at or around line no. 809");
 	}
-	//double length = strtod( (char *)nc, 0);
+
 	double length = standardlocale.toDouble((const char *)nc, &ok);
 	if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)nc);
 
@@ -1222,7 +1201,7 @@ void Mesh::XMLReadWalls(xmlNode *root, v
 				
 	double viz_flux = 0.0;
 	if (nc!=0) {
-	  //viz_flux = strtod( (char *)nc, 0);
+
 	  viz_flux = standardlocale.toDouble((const char *)nc, &ok);
 	  if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)nc);
 	}
@@ -1288,7 +1267,7 @@ void Mesh::XMLReadWalls(xmlNode *root, v
 		  {
 		    stringstream text;
 		    text << "Exception in Mesh::XMLRead: Too many transporter values given for wall(s). Ignoring remaining values.";
-		    //ThrowStringStream(text);
+
 		    unique_warning(text.str().c_str());
 		    break;
 		  }
@@ -1298,7 +1277,7 @@ void Mesh::XMLReadWalls(xmlNode *root, v
 		if (nc==0) {
 		  unique_warning("Token \"v\" not found in xmlwrite.cpp at or around line no. 835");
 		}
-		//double v = strtod( (char *)nc, 0 );
+
 		double v = standardlocale.toDouble((const char *)nc, &ok);
 		if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)nc);
 
@@ -1324,7 +1303,7 @@ void Mesh::XMLReadWalls(xmlNode *root, v
 		    text << "Exception in Mesh::XMLRead: Too many transporter values given for wall(s). Ignoring remaining values.";
 		    unique_warning(text.str().c_str());
 		    break;
-		    // ThrowStringStream(text);
+
 		  }
 		}
 								
@@ -1333,7 +1312,7 @@ void Mesh::XMLReadWalls(xmlNode *root, v
 		if (nc==0) {
 		  unique_warning("Token \"v\" not found in xmlwrite.cpp at or around line no. 861");
 		}
-		//double v = strtod( (char *)nc, 0 );
+
 		double v = standardlocale.toDouble((const char *)nc, &ok);
 		if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)nc);
 
@@ -1356,7 +1335,7 @@ void Mesh::XMLReadWalls(xmlNode *root, v
 		  {
 		    stringstream text;
 		    text << "Exception in Mesh::XMLRead: Too many transporter values given for wall(s). Ignoring remaining values.";
-		    //ThrowStringStream(text);
+
 		    unique_warning(text.str().c_str());
 		    break;
 		  }
@@ -1366,7 +1345,7 @@ void Mesh::XMLReadWalls(xmlNode *root, v
 		if (nc==0) {
 		  unique_warning("Token \"v\" not found in xmlwrite.cpp at or around line no. 887");
 		}
-		//double v = strtod( (char *)nc, 0 );
+
 		double v = standardlocale.toDouble((const char *)nc, &ok);
 		if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)nc);
 
@@ -1375,17 +1354,13 @@ void Mesh::XMLReadWalls(xmlNode *root, v
 	      }
 	      v_node = v_node->next; 
 	    }
-						
 	  }
 	  w_node=w_node->next;
 	}
-				
       }
       cur = cur->next;
     }
-		
   }
-  //  CleanUpWalls();
 }
 
 
@@ -1402,8 +1377,6 @@ void Mesh::XMLReadWallsToCells(xmlNode *
 	
 	while (cur!=NULL) {
 		
-		//Cell *new_cell=0;
-		
 		if ((!xmlStrcmp(cur->name, (const xmlChar *)"cell")) ||
 			(!xmlStrcmp(cur->name, (const xmlChar *)"boundary_polygon" ))) {
 			
@@ -1584,12 +1557,10 @@ void Mesh::XMLRead(const char *docname, 
 	
 	/*Get the root element node */
 	xmlNode *root_element = xmlDocGetRootElement(doc);
-	
-	//XMLParseTree(root_element);
+
 	if (geometry) XMLReadGeometry(root_element);
 	if (pars) XMLReadPars(root_element);
 	if (simtime) XMLReadSimtime(root_element);
-	//print_element_names(root_element);
 	
 	// If pointer settings defined, return a copy of the settings tree
 	if (settings) {
@@ -1617,11 +1588,6 @@ void Mesh::XMLRead(const char *docname, 
 }
 
 
-/*  int Mesh::XMLReadWall(xmlNode *cur)  {
-  
-
-    return w;
-    }*/
 void Parameter::XMLRead(xmlNode *root) {
 	
 	xmlNode *cur = root->xmlChildrenNode;