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Two last corrections:
- Viewport was not written during automatic export of XML files, because Virtualization of XMLSettingsTree did not work due to inconsistent function definition (const vs. non-const)
- Some of the default parameter-file had "Start saving movie frames" switched on by default, dramatically slowing down the example runs. Now it is switched off in all example XML files.
user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed data/leaves/auxin_growth.xml
changed data/leaves/tutorial5_init.xml
changed src/VirtualLeaf.cpp
changed src/mainbase.cpp
changed src/mainbase.h
- Viewport was not written during automatic export of XML files, because Virtualization of XMLSettingsTree did not work due to inconsistent function definition (const vs. non-const)
- Some of the default parameter-file had "Start saving movie frames" switched on by default, dramatically slowing down the example runs. Now it is switched off in all example XML files.
user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed data/leaves/auxin_growth.xml
changed data/leaves/tutorial5_init.xml
changed src/VirtualLeaf.cpp
changed src/mainbase.cpp
changed src/mainbase.h
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*
* $Id$
*
* 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 */
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