Files @ c6ad8e34e8eb
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Location: EI/VirtualLeaf/src/nodeset.h

Roeland Merks
In response to referee's comment:

"I am also afraid that

the ‘snapshot’ and the ‘Export cell data’ functions do not seem to work very
well in my hands, could the program be changed so that the correct file
extension (.jpg, .tif, .txt, .dat, .xls, .csv…) is given automatically."

I corrected the "export cell data" dialog (it did not actually write the file in the submitted version). Also we now assume default file extensions (.jpg for snapshot and .csv for data export) if none is given.

--
user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed src/VirtualLeaf.pro
changed src/canvas.cpp
removed src/miscq.cpp
removed src/miscq.h
/*
 *
 *  $Id$
 *
 *  This file is part of the Virtual Leaf.
 *
 *  VirtualLeaf is free software: you can redistribute it and/or modify
 *  it under the terms of the GNU General Public License as published by
 *  the Free Software Foundation, either version 3 of the License, or
 *  (at your option) any later version.
 *
 *  VirtualLeaf is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License
 *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
 *
 *  Copyright 2010 Roeland Merks.
 *
 */


#ifndef _NODESET_H_
#define _NODESET_H_

#include <algorithm>
#include <numeric>
#include <list>
#include <iterator>
#include "node.h"

class NodeSet : public list<Node *> {

 public:
  NodeSet(void) {
    done = false;
  }

  inline bool DoneP(void) { return done; }
  inline void ResetDone(void) { done = false; }

  void AddNode(Node * n) {
    push_back(n);
    n->node_set = this;
  }

  list <Cell *> getCells(void) {

    list<Cell *> cellset;

    for (list<Node *>::const_iterator i=begin();
	 i!=end();
	 i++) {
      transform ( (*i)->owners.begin(), (*i)->owners.end(), back_inserter( cellset ) , mem_fun_ref ( &Neighbor::getCell ));
    }

    cellset.sort();

    // remove all non-unique elements
    // (unique moves all unique elements to the front and returns an iterator to the end of the unique elements;
    // so we simply erase all remaining elements.
    cellset.erase(::unique(cellset.begin(), cellset.end() ), cellset.end() );

    // remove boundary_polygon
    cellset.erase( find_if ( cellset.begin(), cellset.end(), mem_fun( &Cell::BoundaryPolP  ) ) );
    return cellset;
  }

  void CleanUp(void) {

    // remove double Nodes from the set
    sort();
    erase(::unique(begin(), end() ), 
	  end() );


  }
  void print(ostream &os) const {
    transform( begin(), end(), ostream_iterator<int>( os, " " ), mem_fun( &Node::Index ) );
  }

  /*! Attempt a move over (rx, ry)
    reject if energetically unfavourable.
  */

  void AttemptMove(double rx, double ry) {

    done = true;
    // 1. Collect list of all attached to the nodes in the set
    list<Cell *> celllist = getCells();

    // 2. Sum the current energy of these cells
    double old_energy=0.;
    double sum_stiff = 0.;
    for ( list<Cell *>::const_iterator i = celllist.begin(); 
	  i!=celllist.end();
	  ++i ) {

      old_energy += (*i)->Energy();
      sum_stiff += (*i)->Stiffness();
    }

    // 3. (Temporarily) move the set's nodes.
    for ( list<Node *>::iterator n = begin();
	  n!=end();
	  ++n ) {

      (*n)->x+=rx;
      (*n)->y+=ry;
      // (*n)->z += rz;
    }

    // 4. Recalculate the energy
    double new_energy = 0.;
    for ( list<Cell *>::const_iterator i = celllist.begin(); 
	  i!=celllist.end();
	  ++i ) {

      new_energy += (*i)->Energy();
    }


    // 5. Accept or Reject DeltaH
    double dh = new_energy - old_energy;

    list<int> new_areas;

    // cerr << "Nodeset says: dh = " << dh << " ...";
    if (dh < -sum_stiff || RANDOM()<exp((-dh - sum_stiff)/par.T) ) {

      // ACCEPT
      // recalculate areas of cells
      for_each ( celllist.begin(), celllist.end(), mem_fun ( &Cell::RecalcArea ) );

      // recalculate integrals of cells
      for_each ( celllist.begin(), celllist.end(), mem_fun ( &Cell::SetIntegrals ) );


    } else {
      // REJECT

      // Move the set's nodes back to their original position
      for ( list<Node *>::iterator n = begin();
	    n!= end();
	    ++n ) {

	(*n)->x-=rx;
	(*n)->y-=ry;
      }
    }
  }

  void XMLAdd(xmlNode *root) const;
  void XMLRead(xmlNode *root, Mesh *m);
 private:
  bool done;
};

ostream &operator<<(ostream &os, const NodeSet &ns);
#endif

/* finis */