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Location: EI/VirtualLeaf/src/nodeset.h
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* Added functionality for numerical output (CSV) format. See functions starting with "CSV" in mesh.cpp. External code hull.cpp is responsible for convex hull calculations.
- ToDo: adopt menu item "File->export cell areas" so user can choose a file name or set up periodic output of numerical data.
- ToDo: add parameters re: periodic numeric output to "<settings>" block of LeafML-file, so it becomes possible to set up numeric output interactively, then write the LeafML file and run the program in batch mode to retrieve periodic numeric output.
* Added new functionality to plugin interface. It becomes possible to define a default LeafML init file for a plugin. It is read whenever the model plugin is loaded.
- ToDo: define default LeafML files for all plugins, according to the LeafML files mentioned in the Plant Phys. tutorial.
user: Roeland Merks <merks@cwi.nl>
branch 'default'
added src/hull.cpp
added src/hull.h
changed src/TutorialCode/Tutorial0/tutorial0.pro
changed src/VirtualLeaf.cpp
changed src/VirtualLeaf.pro
changed src/build_models/auxingrowthplugin.cpp
changed src/build_models/auxingrowthplugin.h
changed src/canvas.cpp
changed src/canvas.h
changed src/mainbase.h
changed src/mesh.cpp
changed src/mesh.h
changed src/modelcatalogue.cpp
changed src/simplugin.cpp
changed src/simplugin.h
changed src/xmlwrite.cpp
- ToDo: adopt menu item "File->export cell areas" so user can choose a file name or set up periodic output of numerical data.
- ToDo: add parameters re: periodic numeric output to "<settings>" block of LeafML-file, so it becomes possible to set up numeric output interactively, then write the LeafML file and run the program in batch mode to retrieve periodic numeric output.
* Added new functionality to plugin interface. It becomes possible to define a default LeafML init file for a plugin. It is read whenever the model plugin is loaded.
- ToDo: define default LeafML files for all plugins, according to the LeafML files mentioned in the Plant Phys. tutorial.
user: Roeland Merks <merks@cwi.nl>
branch 'default'
added src/hull.cpp
added src/hull.h
changed src/TutorialCode/Tutorial0/tutorial0.pro
changed src/VirtualLeaf.cpp
changed src/VirtualLeaf.pro
changed src/build_models/auxingrowthplugin.cpp
changed src/build_models/auxingrowthplugin.h
changed src/canvas.cpp
changed src/canvas.h
changed src/mainbase.h
changed src/mesh.cpp
changed src/mesh.h
changed src/modelcatalogue.cpp
changed src/simplugin.cpp
changed src/simplugin.h
changed src/xmlwrite.cpp
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 | /*
*
* $Id$
*
* 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.
*
*/
#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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