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

	* auxin_growth.xml: Changed export_fn_prefix to 'cell.'

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

	* auxin_growth.xml: Added export_interval and export_fn_prefix parameters.

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

	* Added: tutorial3_init.xml

	tutorial4_init.xml

	tutorial5_init.xml

	* Removed: bend.xml

	circ.xml

	explant.xml

	init.xml

	one_acc_point_van3.xml

	one_acc_point_van3_growth.xml

	one_acc_point_van3_growth2.xml

	tissue.xml

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

<!-- 

  $Rev$:  Revision of last commit

  $Author$:  Author of last commit

  $Source$:  Source file

  $Date$:  Date of last commit

  This file is part of the Virtual Leaf.

  The Virtual Leaf is free software: you can redistribute it and/or modify

  it under the terms of the GNU General Public License as published by

  the Free Software Foundation, either version 3 of the License, or

  (at your option) any later version.

  The Virtual Leaf is distributed in the hope that it will be useful,

  but WITHOUT ANY WARRANTY; without even the implied warranty of

  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

  GNU General Public License for more details.

  You should have received a copy of the GNU General Public License

  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.

  Copyright 2010 Roeland Merks.

-->

<leaf name="/Users/roel/VLeafClean_plugin/Snapshot/VLeafMacOSX/auxin_growth.xml" date="Sat Aug 29 18:28:19 2009" simtime="11660">

  <parameter>

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

    <par name="export_fn_prefix" val="cell."/>

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    <par name="D">

      <valarray>

        <val v="1e-06"/>

        <val v="0"/>

        <val v="0"/>

        <val v="0"/>

      </valarray>

    </par>

    <par name="initval">

      <valarray>

        <val v="0"/>

        <val v="1"/>

        <val v="0"/>

        <val v="0"/>

      </valarray>

    </par>

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    <par name="maxt" val="1e+06"/>

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  </parameter>

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

#include <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;