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Location: EI/VirtualLeaf/src/build_models/meinhardtplugin.h - annotation
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In response to referee's comment:
"However, (although it is probably not important for model developers), I was
still unable to load the model ‘Meinhardt 1976 with growth’ example from the
‘Models’ drop down menu, I got the ‘Fatal error’ message ‘stepwise underflow in
rkqs, with h=0.000000 and htry = 0.100000’. The model did work when I selected
the Meinhardt model in both the Models and the File -> Read leaf menus together,
it would be preferable if the models loaded from the Models menu worked
automatically. I am not sure that the update referred to in the author’s
response permits the loading of ‘My First Model in Virtual Leaf’ from the
‘Models’ drop down menu; I only got a cell that wiggled."
I made the following changes:
- meinhardt_plugin now reads "meinhardt_init.xml" by default
- changed the name of 'My First Model in Virtual Leaf’ to '0: Empty model template (does nothing)' to make it clear that the wiggle cell is the intended behavior for this model example.
- Added default parameter files for Tutorial1A-D and Tutorial2 to prevent variable behavior depending on the last parameter settings used.
--
user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
added data/leaves/tutorial1_init.xml
added data/leaves/tutorial2_init.xml
changed data/leaves/auxin_growth.xml
changed data/leaves/meinhardt_init.xml
changed src/TutorialCode/Tutorial0/tutorial0.cpp
changed src/TutorialCode/Tutorial1A/tutorial1A.h
changed src/TutorialCode/Tutorial1B/tutorial1B.h
changed src/TutorialCode/Tutorial1C/tutorial1C.h
changed src/TutorialCode/Tutorial1D/tutorial1D.h
changed src/TutorialCode/Tutorial2/tutorial2.h
changed src/build_models/meinhardtplugin.h
"However, (although it is probably not important for model developers), I was
still unable to load the model ‘Meinhardt 1976 with growth’ example from the
‘Models’ drop down menu, I got the ‘Fatal error’ message ‘stepwise underflow in
rkqs, with h=0.000000 and htry = 0.100000’. The model did work when I selected
the Meinhardt model in both the Models and the File -> Read leaf menus together,
it would be preferable if the models loaded from the Models menu worked
automatically. I am not sure that the update referred to in the author’s
response permits the loading of ‘My First Model in Virtual Leaf’ from the
‘Models’ drop down menu; I only got a cell that wiggled."
I made the following changes:
- meinhardt_plugin now reads "meinhardt_init.xml" by default
- changed the name of 'My First Model in Virtual Leaf’ to '0: Empty model template (does nothing)' to make it clear that the wiggle cell is the intended behavior for this model example.
- Added default parameter files for Tutorial1A-D and Tutorial2 to prevent variable behavior depending on the last parameter settings used.
--
user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
added data/leaves/tutorial1_init.xml
added data/leaves/tutorial2_init.xml
changed data/leaves/auxin_growth.xml
changed data/leaves/meinhardt_init.xml
changed src/TutorialCode/Tutorial0/tutorial0.cpp
changed src/TutorialCode/Tutorial1A/tutorial1A.h
changed src/TutorialCode/Tutorial1B/tutorial1B.h
changed src/TutorialCode/Tutorial1C/tutorial1C.h
changed src/TutorialCode/Tutorial1D/tutorial1D.h
changed src/TutorialCode/Tutorial2/tutorial2.h
changed src/build_models/meinhardtplugin.h
79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 413a4067bfff 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 782330072e62 782330072e62 79f94eaa3b9e 782330072e62 782330072e62 79f94eaa3b9e 782330072e62 782330072e62 782330072e62 782330072e62 79f94eaa3b9e 782330072e62 782330072e62 782330072e62 79f94eaa3b9e 782330072e62 782330072e62 79f94eaa3b9e 782330072e62 782330072e62 79f94eaa3b9e 782330072e62 782330072e62 782330072e62 782330072e62 6bcb69712a0e 6bcb69712a0e 6bcb69712a0e 79f94eaa3b9e 79f94eaa3b9e 79f94eaa3b9e 782330072e62 782330072e62 | /*
* $Id$
*
* 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 _MEINHARDTPLUGIN_H_
#define _MEINHARDTPLUGIN_H_
#include <QObject>
#include <QtGui>
#include <QString>
#include "../simplugin.h"
class MeinhardtPlugin : public QObject, SimPluginInterface {
Q_OBJECT
Q_INTERFACES(SimPluginInterface);
public:
virtual QString ModelID(void) { return QString( "Meinhardt 1976, with growth" ); }
// Executed after the cellular mechanics steps have equillibrized
virtual void CellHouseKeeping (CellBase *c);
// Differential equations describing transport of chemicals from cell to cell
virtual void CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2);
// Differential equations describing chemical reactions taking place at or near the cell walls
// (e.g. PIN accumulation)
virtual void WallDynamics(Wall *w, double *dw1, double *dw2);
// Differential equations describing chemical reactions inside the cells
virtual void CellDynamics(CellBase *c, double *dchem);
// to be executed after a cell division
virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);
// to be executed for coloring a cell
virtual void SetCellColor(CellBase *c, QColor *color);
// return number of chemicals
virtual int NChem(void) { return 4; }
// default XML file to be loaded on startup
virtual QString DefaultLeafML(void) { return QString("meinhardt_init.xml"); }
};
#endif
/* finis */
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