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Location: EI/VirtualLeaf/src/TutorialCode/Tutorial0/tutorial0.cpp - 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
21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 6bcb69712a0e 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 21afbd2a2c01 | /*
*
* 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.
*
*/
#include <QObject>
#include <QtGui>
#include "simplugin.h"
#include "parameter.h"
#include "wallbase.h"
#include "cellbase.h"
#include "tutorial0.h"
static const std::string _module_id("$Id$");
QString Tutorial0::ModelID(void) {
// specify the name of your model here
return QString( "0: Empty model template (does nothing)" );
}
// return the number of chemicals your model uses
int Tutorial0::NChem(void) { return 0; }
// To be executed after cell division
void Tutorial0::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
// rules to be executed after cell division go here
// (e.g., cell differentiation rules)
}
void Tutorial0::SetCellColor(CellBase *c, QColor *color) {
// add cell coloring rules here
}
void Tutorial0::CellHouseKeeping(CellBase *c) {
// add cell behavioral rules here
}
void Tutorial0::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
// add biochemical transport rules here
}
void Tutorial0::WallDynamics(Wall *w, double *dw1, double *dw2) {
// add biochemical networks for reactions occuring at walls here
}
void Tutorial0::CellDynamics(CellBase *c, double *dchem) {
// add biochemical networks for intracellular reactions here
}
Q_EXPORT_PLUGIN2(tutorial0, Tutorial0)
|