static int t;

  stringstream fname;

  TimeStep();

  t = (int)mesh.getTime();

  if ((par.export_interval > 0) && !(t%par.export_interval)){

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

    fname.fill('0');

    fname.width(6);

    fname << t << ".csv";

    this->exportCellData(QString(fname.str().c_str()));

  }

  // check number of timesteps

  if (t == par.nit) {

    emit SimulationDone();

  }

}

void Main::RestartSim(void)

{

  stopSimulation();

  if ( QMessageBox::question(

			     this,

			     tr("Restart simulation?"),

			     tr("Restart simulation.\n"

				"Are you sure?"),

			     QMessageBox::Yes | QMessageBox::No, QMessageBox::NoButton ) == QMessageBox::Yes ) {

    cerr << "Restarting simulation" << endl;

    //    extern Mesh mesh;

    mesh.Clear();

    Init();

    Plot();

    editor->FullRedraw();

  } 

  //startSimulation();

}

void Main::FitCanvasToWindow(void)

{

  double scale_factor_x = (double)editor->width()/(double)canvas.width();

  double scale_factor_y = (double)editor->height()/(double)canvas.height();

  double scale_factor = scale_factor_x > scale_factor_y ? scale_factor_x : scale_factor_y;

  QMatrix m = editor->matrix();

#ifdef QDEBUG  

  qDebug() << "editor->width() = " << editor->width() << endl;

  qDebug() << "editor->height() = " << editor->height() << endl;

  qDebug() << "scale_factor = " << scale_factor << endl;

  qDebug() << "scale_factor_x = " << scale_factor_x << endl;

  qDebug() << "scale_factor_y = " << scale_factor_y << endl;

#endif

  m.scale( scale_factor, scale_factor );

  editor->setMatrix( m );

  editor->show();

}

void Main::PauseIfRunning(void)

{

  if (running) {

    timer->stop();

  }

}

void Main::ContIfRunning(void)

{

  if (running) {

    timer->start( 0 );

  }

}

void Main::FitLeafToCanvas(void) 

{

  Vector ll,ur;

  mesh.BoundingBox(ll, ur);

  ll*=Cell::Magnification(); ur*=Cell::Magnification();

  // give the leaf some space

  Vector border = ((ur-ll)/5.);

  QRectF bb( ll.x - border.x, ll.y - border.y, ur.x-ll.x + 2*border.x, ur.y-ll.y + 2*border.y );

  // cerr << ur << ", " << ll << endl;

  // editor->fitInView(bb, Qt::KeepAspectRatio);

  editor->ensureVisible(bb);

  //editor->setTransform(viewport);

}

void Main::CleanMesh(void) 

{

  vector<double> clean_chem(Cell::NChem());

  vector<double> clean_transporters(Cell::NChem());

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

    clean_chem[i]=par.initval[i];

    clean_transporters[i]=0.;		

  }

  mesh.CleanChemicals(clean_chem);

  mesh.CleanTransporters(clean_transporters);

  mesh.setTime(0);

  Plot();

  editor->FullRedraw();

}

void Main::CleanMeshChemicals(void) 

{

  vector<double> clean_chem(Cell::NChem());

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

    clean_chem[i]=par.initval[i];

  }

  mesh.CleanChemicals(clean_chem);

  mesh.setTime(0);

  Plot();

  editor->FullRedraw();

}

void Main::CleanMeshTransporters(void) 

{

  vector<double> clean_transporters(Cell::NChem());

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

    clean_transporters[i]=0.;

  }

  mesh.CleanTransporters(clean_transporters);

  mesh.setTime(0);

  Plot();

  editor->FullRedraw();

}

void Main::RandomizeMesh(void) 

{

  vector<double> max_chem(Cell::NChem());

  vector<double> max_transporters(Cell::NChem());

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

    max_transporters[i]=0.;

    max_chem[i]=par.initval[i];

  }

  // Amount of PIN1 at walls

  max_transporters[1] = 0.01;

  mesh.RandomizeChemicals(max_chem, max_transporters);

  Plot();

}

void Main::XMLReadSettings(xmlNode *settings) 

{

  MainBase::XMLReadSettings(settings);

  view->setItemChecked(com_id, showcentersp);

  view->setItemChecked(mesh_id, showmeshp);

  view->setItemChecked(border_id, showbordercellp);

  view->setItemChecked(node_number_id, shownodenumbersp);

  view->setItemChecked(cell_number_id, showcellnumbersp);

  view->setItemChecked(cell_axes_id, showcellsaxesp);

  view->setItemChecked(cell_strain_id, showcellstrainp);

  view->setItemChecked(movie_frames_id, movieframesp);

  view->setItemChecked(only_boundary_id, showboundaryonlyp);

  view->setItemChecked(fluxes_id, showfluxesp);

  view->setItemChecked(hide_cells_id, hidecellsp);

  options->setItemChecked(dyn_cells_id, dynamicscellsp);

  view->setItemChecked( cell_walls_id, showwallsp);

 // view->setItemChecked( apoplasts_id, showapoplastsp);

  editor->setTransform(viewport);

}

xmlNode *Main::XMLSettingsTree(void)