Files
@ 6bcb69712a0e
Branch filter:
Location: EI/VirtualLeaf/src/matrix.cpp
6bcb69712a0e
3.8 KiB
text/x-c++src
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 | /*
*
* 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.
*
*/
#include <string>
#include <ostream>
#include <cmath>
#include "vector.h"
#include "matrix.h"
#include "tiny.h"
static const std::string _module_id("$Id$");
Matrix::Matrix(const Vector &c1, const Vector &c2, const Vector &c3) {
Alloc();
mat[0][0]=c1.x; mat[0][1]=c2.x; mat[0][2]=c3.x;
mat[1][0]=c1.y; mat[1][1]=c2.y; mat[1][2]=c3.y;
mat[2][0]=c1.z; mat[2][1]=c2.z; mat[2][2]=c3.z;
}
void Matrix::Alloc(void)
{
// constructor
mat = new double*[3];
mat[0] = new double[9];
for (int i=1;i<3;i++)
mat[i]=mat[i-1]+3;
}
Matrix::~Matrix()
{
// destructor
delete[] mat[0];
delete[] mat;
}
Matrix::Matrix(void)
{
// constructor
Alloc();
// clear matrix
for (int i=0;i<9;i++) {
mat[0][i]=0.;
}
}
Matrix::Matrix(const Matrix &source)
{
// copy constructor
Alloc();
for (int i=0;i<9;i++) {
mat[0][i]=source.mat[0][i];
}
}
void Matrix::operator=(const Matrix &source)
{
// assignment
// don't assign to self
if (this==&source) return;
// copy
for (int i=0;i<9;i++)
mat[0][i]=source.mat[0][i];
}
void Matrix::print(ostream *os)
{
*os << "{ { " << mat[0][0] << "," << mat[0][1] << "," << mat[0][2]
<< "},{" << mat[1][0] << "," << mat[1][1] << "," << mat[1][2]
<< "},{" << mat[2][0] << "," << mat[2][1] << "," << mat[2][2] << "} }";
}
ostream &operator<<(ostream &os, Matrix &v) {
v.print(&os);
return os;
}
Vector Matrix::operator*(const Vector &v) const
{
// matrix * vector
Vector result;
result.x = mat[0][0]*v.x+mat[0][1]*v.y+mat[0][2]*v.z;
result.y = mat[1][0]*v.x+mat[1][1]*v.y+mat[1][2]*v.z;
result.z = mat[2][0]*v.x+mat[2][1]*v.y+mat[2][2]*v.z;
return result;
}
bool Matrix::operator==(Matrix &m) const
{
for (int i=0;i<9;i++) {
if ((mat[0][i]-m.mat[0][i])>TINY)
return false;
}
return true;
}
double Matrix::Det(void) const
{
return
- mat[0][2]*mat[0][4]*mat[0][6]
+ mat[0][1]*mat[0][5]*mat[0][6]
+ mat[0][2]*mat[0][3]*mat[0][7]
- mat[0][0]*mat[0][5]*mat[0][7]
- mat[0][1]*mat[0][3]*mat[0][8]
+ mat[0][0]*mat[0][4]*mat[0][8];
}
Matrix Matrix::Inverse(void) const
{
// return the Inverse of this matrix
double rd=1./Det(); // Reciproce Det;
Matrix inverse;
inverse.mat[0][0]=rd*(-mat[0][5]*mat[0][7]+mat[0][4]*mat[0][8]);
inverse.mat[0][1]=rd*( mat[0][2]*mat[0][7]-mat[0][1]*mat[0][8]);
inverse.mat[0][2]=rd*(-mat[0][2]*mat[0][4]+mat[0][1]*mat[0][5]);
inverse.mat[0][3]=rd*( mat[0][5]*mat[0][6]-mat[0][3]*mat[0][8]);
inverse.mat[0][4]=rd*(-mat[0][2]*mat[0][6]+mat[0][0]*mat[0][8]);
inverse.mat[0][5]=rd*( mat[0][2]*mat[0][3]-mat[0][0]*mat[0][5]);
inverse.mat[0][6]=rd*(-mat[0][4]*mat[0][6]+mat[0][3]*mat[0][7]);
inverse.mat[0][7]=rd*( mat[0][1]*mat[0][6]-mat[0][0]*mat[0][7]);
inverse.mat[0][8]=rd*(-mat[0][1]*mat[0][3]+mat[0][0]*mat[0][4]);
return inverse;
}
void Matrix::Rot2D(double theta)
{
// make this matrix a rotation matrix over theta
// see http://mathworld.wolfram.com/RotationMatrix.html
mat[0][0] = cos(theta); mat[0][1]=sin(theta);
mat[1][0] = -sin(theta); mat[1][1]=cos(theta);
mat[0][2] = mat[1][2] = mat[2][0] = mat[2][1] = mat[2][2] = 0.;
}
/* finis */
|