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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 _MATRIX_H_
#define _MATRIX_H_

// three by three matrix (mostly for changes of basis of the vector object)
class Vector;

class Matrix {

 public:
  Matrix(const Vector &v1,const Vector &v2, const Vector &v3); // constructor
  Matrix(void);
  ~Matrix(); // destructor

  void print(ostream *os);
  Matrix(const Matrix &source); // copy constructor
  void operator=(const Matrix &source); // assignment operator

  Vector operator*(const Vector &v) const; // matrix * vector
  bool operator==(Matrix &v) const; // comparison
  double Det(void) const; // gives the "determinant" (| m |) of m
  Matrix Inverse(void) const; // gives the inverse of m
  void Rot2D(double theta); // make a matrix doing a 2D rotation over theta
  // data members 
  double **mat;

 private:

  void Alloc(void);
};

ostream &operator<<(ostream &os, Matrix &v);

#endif

/* finis */