2010-10-18    <guravage@caterpie.sen.cwi.nl>

	* mainbase.cpp (Save): QDir::toNativeSeparators(fname). Invoke

	save with format argument set to zero to force QImage to guess the

	format by looking at fileName's suffix.

	* VirtualLeaf-install.nsi: Put uninstaller in top directory.

	* modelcatalogue.cpp (InstallModel): For all OS-es. Move from "bin" directory to root application folder.

	* VirtualLeaf.pro: MAXOSX, look for gpl3.txt in the ../doc directory.

	* Makefile (Makefile.libplugin): Removed -makefile qmake option.

	* VirtualLeaf.cpp (TIMESTEP): Removed getIterations().

	* mesh.h (Mesh): Removed {increment,get}Iterations().

	* canvas.cpp (TimeStepWrap): Replaced getIterations() with getTime().

2010-10-15    <guravage@caterpie.sen.cwi.nl>

	* mesh.h (Mesh): Added iterations. incrementIterations() and

	getIterations().

	* VirtualLeaf.cpp (Plot): Replaced local frame counter with

	mesh.incrementIterations().

	* canvas.cpp (TimeStepWrap): Replaced local counter with

	mesh.incrementIterations().

2010-10-14    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Turned debug off to make all profiles must be

	consistant.

	* VirtualLeaf-install.nsi: Tweaked paths to coincide with UNIX

	distribution, i.e. VirtualLeaf.exe, its libraries, models, and the

	uninstaller all go in the bin directory. And leaves directory

	placed under data directory.

	* canvas.cpp (exportCellData): Added a check to inquire before

	overwritting an existing file.

2010-10-14    <merks@cwi.nl>

	* mesh.cpp: In response to referees' comments, added new parameter

	"yield_threshold" instead of fixed parameter '4' for yield

	threshold.

	* wallitem.cpp: when clicking a wall, both the wall type was

	cycled and the transporterdialog popped up. Corrected this - for

	wall type cycling, hold the Control button while left

	clicking. TransporterDialog only pops up for left click. Also made

	sure the wall is redrawn after changing the transporter values.

	* cell.cpp (DivideWalls): accomodated for rename of Circumference -> WallCircumference

	* hull.h: added an operator< to sort Points

	* hull.cpp: added an operator< to sort Points

	* cellbase.cpp (ExactCircumference): I added a new function

	ExactCircumference, yielding the circumference of the cell along

	its wall_elements

	* VirtualLeaf.cpp: adjust info_string to accomodate for new name

	of function CellBase::Circumference -> CellBase::WallCircumference

	* mesh.cpp: corrected Mesh::Compactness, the boundary coordinates

	need to be sorted in x,y order for the convex hull algorithm

	(thanks Margriet!). I updated CSVExportCellData so it exports the

	circumferences of hull and boundary_polygon.

2010-10-14    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeafpar.tmpl (export_fn_prefix): changed to 'cell.'

	* canvas.cpp (TimeStepWrap): Removed TimeStamp(). Cell data

	filename now incorporates iteration number.

	* canvas.h (MainBase): Removed TimeStamp().

2010-10-08    <guravage@caterpie.sen.cwi.nl>

	* pardialog.h:

	* pardialog.cpp:

	* parameter.h:

	* parameter.cpp: Regenerated to include export_interval and export_fn_prefix.

	* VirtualLeafpar.tmpl: Appended export_interval and export_fn_prefix.

	* canvas.h (MainBase): Declared polymorphic exportCellData() functions.

	* canvas.cpp:

	(TimeStamp): New private TimeStamp() function.

	(TimeStepWrap): Added invocation of exportCellData().

	(exportCellData): Created two polymorphic functions: one with a

	single QString argument, the other with no argument. The former is

	called from TimeStepWrap() while the latter is called from the

	"Export cell areas" item in the file menu.

2010-10-07    <guravage@caterpie.sen.cwi.nl>

	* canvas.cpp (exportCellData): Added a Q3FileDialog to inquire

	where to write the exportCellData.

2010-06-28    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf-install.nsi: Grab gpl3.txt from doc directory.

	* canvas.cpp (gpl): gpl3.txt can be either in an ancestor doc

	directory (Linux) or a decedent doc directory (Windows, via the

	binary installer).

	* VirtualLeaf-install.nsi: Add VirtualLeaf doc directory.

2010-06-25    <guravage@caterpie.sen.cwi.nl>

	* gpl3.txt: Moved gpl3.txt from doc to src directory.

	* VirtualLeaf.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

	* libplugin.pro: Ditto.

	* parameter.cpp: Result of adding datadir changes to make_parameter_source.pl.

	* parameter.h: Ditto.

	* output.h: Declared new function (AppendHomeDirIfPathRelative).

	* output.cpp (AppendHomeDirIfPathRelative): Added new function.

	* canvas.cpp (gpl): Moving gpl3.txt from doc to src obviates the need to docDir.cd("../doc").

	* VirtualLeaf-install.nsi: Grab gpl3.txt from src directory.

	Add missing libiconv/bin, libxml2bin and libz/bin directories.

	Copy libiconv-2.dll, libxml2.dll and zlib1.dll from relative paths.

	* VirtualLeaf.pro: copy gpl3.txt as part of QMAKE_POST_LINK.

2010-06-24    <guravage@caterpie.sen.cwi.nl>

	* libplugin.pro: Use correct library path.

	* VirtualLeaf.pro: Ditto.

	* VirtualLeaf.cpp (DrawCell): Iterate over NChem to construct info_string.

2010-06-23    <guravage@caterpie.sen.cwi.nl>

	* simitembase.cpp: Removed NULL assignments to unused variables.

	* VirtualLeaf.cpp: Ditto.

	* apoplastitem.cpp: Ditto.

	* canvas.cpp: Ditto.

	* cell.cpp: Ditto.

	* cellbase.h: Ditto.

	* forwardeuler.cpp: Ditto.

	* mainbase.h: Ditto.

	* nodeitem.cpp: Ditto.

	* qcanvasarrow.h: Ditto.

	* simitembase.cpp: Ditto.

	* Makefile (clean): Add -f Makefile argument to each make invocation.

	* VirtualLeaf-install.nsi: New gpl license text.

	* VirtualLeaf.pro: Disabled console mode.

	* mesh.cpp (Clear): Added parentheses to qDebug statments.

	(TestIllegalWalls): Replaced qDebug().

	* canvas.cpp (mouseReleaseEvent): Replaced qDebug() with cerr since qDebug complains about *node_set.

	* wall.cpp (CorrectWall): Rplaced gDebug() with cerr in transform call and when printing *this.

2010-06-22    <guravage@caterpie.sen.cwi.nl>

	* Makefile (tutorials): Add tutorials target.

2010-06-21    <guravage@caterpie.sen.cwi.nl>

	* parameter.cpp: Added particular reassignment of datadir.

	* canvas.cpp (gpl): Added GPL3 License text. Display detail text only if the source text file exists.

2010-06-18    <guravage@caterpie.sen.cwi.nl>

	* canvas.cpp (gpl): Added gpl slot to display GPL license.

	* VirtualLeaf.pro: Changed default LIBXML2DIR, LIBICONVDIR and LIBZDIR to corresponding distribution lib directories.

	* libplugin.pro: Ditto.

	* Makefile (clean): add if stmt not to `touch` on windows.

2010-06-17    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Removed perl references.

	* libplugin.pro: Ditto.

2010-06-15    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Removed xmlwritecode.cpp from SOURCES list.

	* xmlwrite.cpp (XMLSave): Removed references to XMLWriteLeafSourceCode and XMLWriteReactionsCode.

	* xmlwrite.h (XMLIO): Ditto!

	* mesh.cpp (findNextBoundaryNode): Initialize Node *next_boundary_node = NULL;

	* xmlwrite.cpp (XMLReadSimtime): Removed unused variable cur

	(XMLReadWalls): viz_flux need not be declared twice; default value of 0.0.

	(XMLReadCells): Removed unused count variable.

	(XMLReadSimtime): Removed unused cur variable.

	(XMLRead): Removed unused v_str variable.

	* simitembase.cpp (userMove): Use assignment merely to obviate compilation warning.

	(SimItemBase) Ditto.

	* qcanvasarrow.h (QGraphicsLineItem): Use assignment merely to obviate compilation warning.

	* output.cpp (OpenWriteFile): Removed unused par variable.

	* nodeitem.cpp (paint): Use assignment merely to obviate compilation warning.

	* forwardeuler.cpp (odeint): Use assignment merely to obviate compilation warning.

	* cell.cpp (DivideOverGivenLine): Use assignment merely to obviate compilation warning.

	* canvas.cpp (FigureEditor): Use assignments merely to obviate compilation errors.

	(mousePressEvent): Removed unused item variable.

	* apoplastitem.cpp

	(ApoplastItem): Removed unused par variable.

	(OnClick): Use NULL assignment merely to obviate compilation warning.

	* mainbase.h (MainBase): Use assignment merely to obviate compilation warning.

	* cellbase.h (CellsStaticDatamembers): Use assignment merely to obviate compilation warning.

	* cell.cpp: Wrapped diagnostic output in QDEBUG blocks.

	* VirtualLeaf.cpp ditto.

	* canvas.cpp ditto.

	* cell.cpp ditto.

	* data_plot.cpp ditto.

	* forwardeuler.cpp ditto.

	* mesh.cpp ditto.

	* mesh.h

	* random.cpp ditto.

	* wall.cpp ditto.

	* wallbase.cpp ditto.

	* wallitem.cpp ditto.

2010-06-07    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Removed explicit perl invocation to regerenerate parameter files.

	* libplugin.pro: ditto.

2010-06-03    <guravage@caterpie.sen.cwi.nl>

	* pardialog.h: Added default versions of this automatically generated file.

	* pardialog.cpp: ditto.

	* parameter.h: ditto.

	* parameter.cpp: ditto.

	* VirtualLeaf.pro: delete/generate  parameter.{h,cpp}and pardialog.{h,cpp} only if perl is installed.

 	* libplugin.pro: dito.

	* Makefile: Added top-level Makefile

2010-05-10    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Added -fPIC option to QMAKE_CXXFLAGS.

2010-10-18    <guravage@caterpie.sen.cwi.nl>

	* Makefile (Makefile.tutorial3): Removed -makefile qmake option.

2010-10-14    <guravage@caterpie.sen.cwi.nl>

	* tutorial3.h (SimPluginInterface): Added default LeafML file.

2010-06-25    <guravage@caterpie.sen.cwi.nl>

	* tutorial3.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

2010-06-23    <guravage@caterpie.sen.cwi.nl>

	* tutorial3.pro: Corrected windows library path.

<?xml version="1.0" encoding="UTF-8"?>

<leaf name="/Users/roel/VLeaf1.0/V1.0/bin/auxinfluxinit.xml" date="Mon Jun  7 15:40:43 2010" simtime="0">

  <parameter>

    <par name="arrowcolor" val="white"/>

    <par name="arrowsize" val="10"/>

    <par name="textcolor" val="red"/>

    <par name="cellnumsize" val="1"/>

    <par name="nodenumsize" val="1"/>

    <par name="node_mag" val="20"/>

    <par name="outlinewidth" val="2"/>

    <par name="cell_outline_color" val="forestgreen"/>

    <par name="resize_stride" val="10"/>

    <par name="T" val="1"/>

    <par name="lambda_length" val="100"/>

    <par name="lambda_celllength" val="0"/>

    <par name="target_length" val="60"/>

    <par name="cell_expansion_rate" val="10"/>

    <par name="cell_div_expansion_rate" val="10"/>

    <par name="auxin_dependent_growth" val="true"/>

    <par name="ode_accuracy" val="0.0001"/>

    <par name="mc_stepsize" val="0.4"/>

    <par name="mc_cell_stepsize" val="0.2"/>

    <par name="energy_threshold" val="1000"/>

    <par name="bend_lambda" val="0"/>

    <par name="alignment_lambda" val="0"/>

    <par name="rel_cell_div_threshold" val="2"/>

    <par name="rel_perimeter_stiffness" val="2"/>

    <par name="collapse_node_threshold" val="0.05"/>

    <par name="morphogen_div_threshold" val="0.2"/>

    <par name="morphogen_expansion_threshold" val="0.01"/>

    <par name="copy_wall" val="true"/>

    <par name="source" val="0"/>

    <par name="D">

      <valarray>

        <val v="0.0001"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

      </valarray>

    </par>

    <par name="initval">

      <valarray>

        <val v="1"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

      </valarray>

    </par>

    <par name="k1" val="1"/>

    <par name="k2" val="0.3"/>

    <par name="r" val="1"/>

    <par name="kr" val="1"/>

    <par name="km" val="1"/>

    <par name="Pi_tot" val="1"/>

    <par name="transport" val="0.36"/>

    <par name="ka" val="1"/>

    <par name="pin_prod" val="0"/>

    <par name="pin_prod_in_epidermis" val="0"/>

    <par name="pin_breakdown" val="0"/>

    <par name="pin_breakdown_internal" val="0.001"/>

    <par name="aux1prod" val="0.001"/>

    <par name="aux1prodmeso" val="0"/>

    <par name="aux1decay" val="0.001"/>

    <par name="aux1decaymeso" val="0.1"/>

    <par name="aux1transport" val="0.036"/>

    <par name="aux_cons" val="0"/>

    <par name="aux_breakdown" val="0"/>

    <par name="kaux1" val="1"/>

    <par name="kap" val="1"/>

    <par name="leaf_tip_source" val="0.001"/>

    <par name="sam_efflux" val="0.0001"/>

    <par name="sam_auxin" val="10"/>

    <par name="sam_auxin_breakdown" val="0"/>

    <par name="van3prod" val="0.002"/>

    <par name="van3autokat" val="0.1"/>

    <par name="van3sat" val="10"/>

    <par name="k2van3" val="0.3"/>

    <par name="dt" val="0.1"/>

    <par name="rd_dt" val="10"/>

    <par name="datadir" val="."/>

    <par name="movie" val="false"/>

    <par name="nit" val="100000"/>

    <par name="maxt" val="1000"/>

    <par name="storage_stride" val="10"/>

    <par name="xml_storage_stride" val="500"/>

    <par name="rseed" val="-1"/>

    <par name="constituous_expansion_limit" val="16"/>

    <par name="vessel_inh_level" val="1"/>

    <par name="vessel_expansion_rate" val="0.25"/>

    <par name="d" val="0"/>

    <par name="e" val="0"/>

    <par name="f" val="0"/>

    <par name="c" val="0"/>

    <par name="mu" val="0"/>

    <par name="nu" val="0"/>

    <par name="rho0" val="0"/>

    <par name="rho1" val="0"/>

    <par name="c0" val="0"/>

    <par name="gamma" val="0"/>

    <par name="eps" val="0"/>

    <par name="k">

      <valarray>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

      </valarray>

    </par>

    <par name="i1" val="0"/>

    <par name="i2" val="0"/>

    <par name="i3" val="0"/>

    <par name="i4" val="0"/>

    <par name="i5" val="0"/>

    <par name="s1" val=""/>

    <par name="s2" val=""/>

    <par name="s3" val=""/>

    <par name="b1" val="false"/>

    <par name="b2" val="false"/>

    <par name="b3" val="false"/>

    <par name="b4" val="false"/>

    <par name="dir1" val="."/>

    <par name="dir2" val="."/>

  </parameter>

  <code name="VirtualLeaf.cpp">#include &lt;fstream&gt;

#include <sstream>

#include <cstring>

#include <functional> 

#include <getopt.h>

#include <cerrno>

#include "mesh.h"

#include "parameter.h"

#include "random.h"

#include "pi.h"

#include "cellitem.h"

#include "canvas.h"

#include "cell.h"

#include "output.h"

#include <qwidget.h>

#include <q3process.h>

#include <qapplication.h>

#include <QDesktopWidget>

#include <QGraphicsScene>

#include <QMessageBox>

//Added by qt3to4:

#include <QMouseEvent>

#include <unistd.h>

#include <q3textstream.h> 

#ifdef HAVE_QWT

#include "data_plot.h"

#endif

#include <QPalette>

#include <QBrush>

#include <QToolTip>

#include "simplugin.h"

#include "testplugin.h"

/* #define _xstr_(s) _str_(s)

#define _str_(s) #s

#include _xstr_(REACTIONS_HEADER)

*/

extern Parameter par;

MainBase *main_window = 0;

double auxin_account = 0.;

TestPlugin *plugin = new TestPlugin();

#ifdef XFIGGRAPHICS

#define TIMESTEP double Graphics::TimeStep(void)

#endif

class PrintNode {

public:

  void operator() (const Node &n) const 

  {

    cerr << n.Index() << ": " << n <<  endl;

  }

};

class EdgeSource {

public:

  void operator() (Cell &c) {

    if (c.AtBoundaryP()) {

      cerr << "Cell " << c.Index() << " is a source cell.\n";

      c.SetSource(0,par.source);

    } else {

      cerr << "Cell " << c.Index() << " is _not_ a source cell.\n";

    }

  }

};

class CellInfo {

public:

  void operator() (Cell &c,std::ostream &os) const {

    os << "Cell " << c.index << " says: " << endl;

    os << "c.nodes.size() = " << c.nodes.size() << endl;

    for (list<Node *>::iterator i=c.nodes.begin();

	 i!=c.nodes.end();

	 i++) {

      cerr << (*i)->Index() << " ";

    }

    cerr << endl;

  }

};

double PINSum(Cell &c) {

	return c.Chemical(1) + c.SumTransporters(1);// + c.ReduceCellAndWalls<double>( complex_PijAj );

}

class DrawCell {

public:

  void operator() (Cell &c,QGraphicsScene &canvas, MainBase &m) const {

    if (m.ShowBorderCellsP() || c.Boundary()==Cell::None) {

      if (!m.ShowBoundaryOnlyP() && !m.HideCellsP()) 

	if (m.ShowToolTipsP()) {

	  QString info_string=QString("Cell %1, chemicals: ( %2, %3, %4, %5, %6)\n %7 of PIN1 at walls.\n Area is %8\n PIN sum is %9\n Circumference is %10\n Boundary type is %11").arg(c.Index()).arg(c.Chemical(0)).arg(c.Chemical(1)).arg(c.Chemical(2)).arg(c.Chemical(3)).arg(c.Chemical(4)).arg(c.SumTransporters(1)).arg(c.Area()).arg(PINSum(c)).arg(c.Circumference()).arg(c.BoundaryStr());

	  info_string += "\n" + c.printednodelist();

	  c.Draw(&canvas, info_string);

	} else {

	  c.Draw(&canvas);

	}

      if (m.ShowCentersP())

	c.DrawCenter(&canvas);

    if (m.ShowFluxesP())

	c.DrawFluxes(&canvas, par.arrowsize);

       }

  }

};

Mesh mesh;

bool batch=false;

void MainBase::Plot(int resize_stride) {

  clear();

  static int count=0;

  if (resize_stride) {

    if ( !((++count)%resize_stride) ) {

      FitLeafToCanvas();

    }

  }

  mesh.LoopCells(DrawCell(),canvas,*this);

  if (ShowNodeNumbersP()) 

    mesh.LoopNodes( bind2nd (mem_fun_ref ( &Node::DrawIndex), &canvas ) ) ;

  if (ShowCellNumbersP()) 

    mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawIndex), &canvas ) ) ;

  if (ShowCellAxesP()) 

    mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawAxis), &canvas ) );

  if (ShowCellStrainP()) 

    mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawStrain), &canvas ) );

  if (ShowWallsP())

    mesh.LoopWalls( bind2nd( mem_fun_ref( &Wall::Draw ), &canvas ) );

	if (ShowApoplastsP()) 

		mesh.LoopWalls( bind2nd( mem_fun_ref( &Wall::DrawApoplast ), &canvas ) );

	if (ShowMeshP()) 

    mesh.DrawNodes(&canvas);

  if (ShowBoundaryOnlyP()) 

    mesh.DrawBoundary(&canvas);

	if ( ( batch || MovieFramesP() )) {

		static int frame = 0;

		// frame numbers are sequential for the most frequently written file type.

		// for the less frequently written file type they match the other type

		if (!(count%par.storage_stride) )  {

			stringstream fname;

			fname << par.datadir << "/leaf.";

			fname.fill('0');

			fname.width(6);

			/* 

			 fname << frame << ".pdf";

			if (par.storage_stride <= par.xml_storage_stride) {

				frame++;

			}

			Save(fname.str().c_str(), "PDF");

			*/

			if (par.storage_stride <= par.xml_storage_stride) {

				frame++;

			}

		}

		if (!(count%par.xml_storage_stride)) {

			stringstream fname;

			fname << par.datadir << "/leaf.";

			fname.fill('0');

			fname.width(6);

			fname << frame << ".xml";

			if (par.xml_storage_stride < par.storage_stride) {

				frame++;

			}

			// Write XML file every ten plot steps

			mesh.XMLSave(fname.str().c_str(), XMLSettingsTree());

		}

	}

}

void Cell::Flux(double *flux, double *D)  {

  // loop over cell edges

  for (int c=0;c<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->BoundaryPolP()) continue;

    // flux depends on edge length and concentration difference

    for (int c=0;c<Cell::nchem;c++) {

      double phi = (*i)->length * ( D[c] ) * ( (*i)->c2->chem[c] - chem[c] );

      if ((*i)->c1!=this) {

	cerr << "Warning, bad cells boundary: " << (*i)->c1->index << ", " << index << endl;

      }

      flux[c] += phi;

    }    

  }

}

INIT {

	if (leaffile) { 

    xmlNode *settings;

    mesh.XMLRead(leaffile, &settings);

    main_window->XMLReadSettings(settings);

    xmlFree(settings);

    main_window->UserMessage(QString("Ready. Time is %1").arg(mesh.getTimeHours().c_str()));

  } else {

	  Cell &circle=mesh.CircularCell(0,0,10,10);

    circle.SetTargetArea(circle.CalcArea());

	  mesh.SetBaseArea();

	// clean up chemicals 

	  for (int c=0; c<Cell::NChem(); c++) {

		  circle.SetChemical(c, 0.);

      }

  }

}

TIMESTEP {

  static int i=0;

  static int t=0;

  static int ncells;

  if (!batch) {

    UserMessage(QString("Time: %1").arg(mesh.getTimeHours().c_str()),0);

  }

  ncells=mesh.NCells();

  double dh;

  if(DynamicCellsP()) {

    dh = mesh.DisplaceNodes();

    // Only allow for node insertion, cell division and cell growth

    // if the system has equillibrized

    // i.e. cell wall tension equillibrization is much faster

    // than biological processes, including division, cell wall yielding

    // and cell expansion

    mesh.InsertNodes(); // (this amounts to cell wall yielding)

    if ( (-dh) < par.energy_threshold) {

      mesh.IncreaseCellCapacityIfNecessary();

		mesh.LoopCurrentCells(&TestPlugin::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(plugin, 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(plugin, par.rd_dt);

    Plot(par.resize_stride);

  }