Files @ 6bcb69712a0e
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Location: EI/VirtualLeaf/src/simplugin.h

Roeland Merks
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
/*
 *
 *  $Id$
 *
 *  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 _SIMPLUGIN_H_
#define _SIMPLUGIN_H_

#include <QtPlugin>
#include <QMetaType>
#include "cellbase.h"
#include "wallbase.h"

class Parameter;

#include <QColor>
#include <QString>


class SimPluginInterface {

 public:
  virtual QString ModelID(void) = 0; 

  virtual ~SimPluginInterface() { }

  // Executed after the cellular mechanics steps have equillibrized
  virtual void CellHouseKeeping(CellBase *c) = 0;

  // Differential equations describing transport of chemicals from cell to cell
  virtual void CelltoCellTransport(Wall *, double *dchem_c1, double *dchem_c2) = 0;

  // 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 *dw)  = 0;

  // Differential equations describing chemical reactions inside the cells
  virtual void CellDynamics(CellBase *c, double *dchem) = 0;

  // to be executed after a cell division
  virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) = 0;

  // to be executed for coloring a cell
  virtual void SetCellColor(CellBase *c, QColor *color) = 0;

  // Number of chemicals
  virtual int NChem(void) = 0;

  // Default LeafML-file to be read after model startup
  virtual QString DefaultLeafML(void);
  
  // For internal use; not to be redefined by end users
  virtual void SetParameters(Parameter *pass_pars);// { par = pass_pars; }
  virtual void SetCellsStaticDatamembers (CellsStaticDatamembers *cells_static_data_members_of_main);

 protected:
  class Parameter *par;
};

Q_DECLARE_INTERFACE(SimPluginInterface, "nl.cwi.VirtualLeaf.SimPluginInterface/1.3") 
Q_DECLARE_METATYPE(SimPluginInterface *)

#endif

/* finis */