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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
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 | /*
*
* $Id$
*
* 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 _VECTOR_H_
#define _VECTOR_H_
#include <iostream>
#include <cmath>
#include "sqr.h"
#ifdef QTGRAPHICS
#include <QPointF>
#endif
// three dimensional vector
using namespace std;
class Vector {
public:
inline Vector(const double cx=0,const double cy=0,const double cz=0) {
x=cx;
y=cy;
z=cz;
};
explicit inline Vector(const double m[3]) {
x=m[0];
y=m[1];
z=m[2];
}
inline Vector(const Vector &source) {
// copy constructor
x=source.x;
y=source.y;
z=source.z;
}
// type conversion from and to QPointF (2D vector class from Qt library; we throw away "z" here!!)
#ifdef QTGRAPHICS
inline operator QPointF() const {
return QPointF( x, y );
}
inline Vector(const QPointF &p) {
x = p.x();
y = p.y();
z = 0.;
}
#endif
virtual ~Vector() {
};
virtual ostream& print(ostream &os) const;
void operator=(const Vector &source); // assignment operator
void operator=(const double &s) {
x=s;
y=s;
z=s;
}
Vector operator+(const Vector &v) const; // addition
inline Vector operator-(const Vector &v) const {
Vector result;
result.x=x-v.x;
result.y=y-v.y;
result.z=z-v.z;
return result;
}
Vector &operator-=(const Vector &v);
inline Vector &operator+=(const Vector &v) {
x+=v.x;
y+=v.y;
z+=v.z;
return *this;
}
Vector operator/(const double divisor) const; // division by a double
Vector operator*(const double multiplier) const; // multiply by a scalar (double)
Vector &operator/=(const double divisor);
Vector &operator*=(const double multiplier);
Vector operator*(const Vector &v) const; // cross product
bool operator==(const Vector &v) const; // comparison
bool operator< (const Vector &v) const; // order x,y,z
inline double Norm(void) const {
return sqrt(DSQR(x)+DSQR(y)+DSQR(z));
}
// Quick and dirty Norm (i.e. Manhattan distance)
// (e.g. useful if we want to see if the vec is (0,0,0);
inline double ManhattanNorm(void) const {
return x+y+z;
}
double SqrNorm(void) const; // gives the square of |v|
void Normalise(void); // normalise myself
Vector Normalised(void) const; // return me normalised
double Angle(const Vector &angle) const; // gives the angle between me and another vector
double SignedAngle(const Vector &v) const;
bool SameDirP(const Vector &v);
double Max(void); // Find max, resp. min value of vector
double Min(void);
Vector Perp2D(void) const {
return Vector(y,-x,0);
}
// data members
double x,y,z;
void Dump(ostream &os) const {
os << x << " " << y << " " << z << " ";
}
void ReadDump(istream &is) {
is >> x >> y >> z;
}
private:
};
ostream &operator<<(ostream &os, const Vector &v);
Vector operator*(const double multiplier, const Vector &v);
double InnerProduct(const Vector &v1, const Vector &v2);
#endif
/* finis */
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