EI/VirtualLeaf Changeset - 6bcb69712a0e · Centrum Wiskunde & Informatica (CWI)

Changeset - 6bcb69712a0e

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Roeland Merks - 15 years ago 2010-11-24 18:02:13
roeland.merks@cwi.nl

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

11 files changed with 14 insertions and 1 deletions:

data/leaves/auxin_growth.xml

bin+mod

data/leaves/meinhardt_init.xml

bin+mod

data/leaves/tutorial1_init.xml

bin+new file

data/leaves/tutorial2_init.xml

bin+new file

src/TutorialCode/Tutorial0/tutorial0.cpp

src/TutorialCode/Tutorial1A/tutorial1A.h

src/TutorialCode/Tutorial1B/tutorial1B.h

src/TutorialCode/Tutorial1C/tutorial1C.h

src/TutorialCode/Tutorial1D/tutorial1D.h

src/TutorialCode/Tutorial2/tutorial2.h

src/build_models/meinhardtplugin.h

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data/leaves/auxin_growth.xml

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data/leaves/meinhardt_init.xml

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data/leaves/tutorial1_init.xml

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data/leaves/tutorial2_init.xml

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src/TutorialCode/Tutorial0/tutorial0.cpp

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@@ @@ -13,49 +13,49 @@ @@
  *  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( "My first model in VirtualLeaf" );
+  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) {

src/TutorialCode/Tutorial1A/tutorial1A.h

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@@ @@ -32,29 +32,32 @@ class Tutorial1A : public QObject, SimPl @@
 	Q_INTERFACES(SimPluginInterface);
 public:
 	virtual QString ModelID(void);
 	// Executed after the cellular mechanics steps have equillibrized
 	virtual void CellHouseKeeping (CellBase *c);
 	// Differential equations describing transport of chemicals from cell to cell
 	virtual void CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2);
 	// 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 *dw2);
 	// Differential equations describing chemical reactions inside the cells
 	virtual void CellDynamics(CellBase *c, double *dchem);
 	// to be executed after a cell division
 	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);
 	// to be executed for coloring a cell
 	virtual void SetCellColor(CellBase *c, QColor *color);
 	// return number of chemicals
 	virtual int NChem(void);
 	virtual QString DefaultLeafML(void) { return QString("tutorial1_init.xml"); }
 };

src/TutorialCode/Tutorial1B/tutorial1B.h

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@@ @@ -32,29 +32,31 @@ class Tutorial1B : public QObject, SimPl @@
 	Q_INTERFACES(SimPluginInterface);
 public:
 	virtual QString ModelID(void);
 	// Executed after the cellular mechanics steps have equillibrized
 	virtual void CellHouseKeeping (CellBase *c);
 	// Differential equations describing transport of chemicals from cell to cell
 	virtual void CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2);
 	// 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 *dw2);
 	// Differential equations describing chemical reactions inside the cells
 	virtual void CellDynamics(CellBase *c, double *dchem);
 	// to be executed after a cell division
 	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);
 	// to be executed for coloring a cell
 	virtual void SetCellColor(CellBase *c, QColor *color);
 	// return number of chemicals
 	virtual int NChem(void);
 	virtual QString DefaultLeafML(void) { return QString("tutorial1_init.xml"); }
 };

src/TutorialCode/Tutorial1C/tutorial1C.h

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@@ @@ -32,29 +32,30 @@ class Tutorial1C : public QObject, SimPl @@
 	Q_INTERFACES(SimPluginInterface);
 public:
 	virtual QString ModelID(void);
 	// Executed after the cellular mechanics steps have equillibrized
 	virtual void CellHouseKeeping (CellBase *c);
 	// Differential equations describing transport of chemicals from cell to cell
 	virtual void CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2);
 	// 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 *dw2);
 	// Differential equations describing chemical reactions inside the cells
 	virtual void CellDynamics(CellBase *c, double *dchem);
 	// to be executed after a cell division
 	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);
 	// to be executed for coloring a cell
 	virtual void SetCellColor(CellBase *c, QColor *color);
 	// return number of chemicals
 	virtual int NChem(void);
 	virtual QString DefaultLeafML(void) { return QString("tutorial1_init.xml"); }
 };

src/TutorialCode/Tutorial1D/tutorial1D.h

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@@ @@ -32,29 +32,30 @@ class Tutorial1D : public QObject, SimPl @@
 	Q_INTERFACES(SimPluginInterface);
 public:
 	virtual QString ModelID(void);
 	// Executed after the cellular mechanics steps have equillibrized
 	virtual void CellHouseKeeping (CellBase *c);
 	// Differential equations describing transport of chemicals from cell to cell
 	virtual void CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2);
 	// 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 *dw2);
 	// Differential equations describing chemical reactions inside the cells
 	virtual void CellDynamics(CellBase *c, double *dchem);
 	// to be executed after a cell division
 	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);
 	// to be executed for coloring a cell
 	virtual void SetCellColor(CellBase *c, QColor *color);
 	// return number of chemicals
 	virtual int NChem(void);
 	virtual QString DefaultLeafML(void) { return QString("tutorial1_init.xml"); }
 };

src/TutorialCode/Tutorial2/tutorial2.h

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@@ @@ -32,29 +32,32 @@ class Tutorial2 : public QObject, SimPlu @@
 	Q_INTERFACES(SimPluginInterface);
 public:
 	virtual QString ModelID(void);
 	// Executed after the cellular mechanics steps have equillibrized
 	virtual void CellHouseKeeping (CellBase *c);
 	// Differential equations describing transport of chemicals from cell to cell
 	virtual void CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2);
 	// 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 *dw2);
 	// Differential equations describing chemical reactions inside the cells
 	virtual void CellDynamics(CellBase *c, double *dchem);
 	// to be executed after a cell division
 	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);
 	// to be executed for coloring a cell
 	virtual void SetCellColor(CellBase *c, QColor *color);
 	// return number of chemicals
 	virtual int NChem(void);
 	// default XML file to be loaded on startup
 	virtual QString DefaultLeafML(void) { return QString("tutorial2_init.xml"); }
 };

src/build_models/meinhardtplugin.h

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@@ @@ -34,29 +34,32 @@ class MeinhardtPlugin : public QObject, @@
     Q_INTERFACES(SimPluginInterface);
  public:
   virtual QString ModelID(void) { return QString( "Meinhardt 1976, with growth" ); }
   // Executed after the cellular mechanics steps have equillibrized
   virtual void CellHouseKeeping (CellBase *c);
   // Differential equations describing transport of chemicals from cell to cell
   virtual void CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2);
   // 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 *dw2);
   // Differential equations describing chemical reactions inside the cells
   virtual void CellDynamics(CellBase *c, double *dchem);
   // to be executed after a cell division
   virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);
   // to be executed for coloring a cell
   virtual void SetCellColor(CellBase *c, QColor *color);
   // return number of chemicals
   virtual int NChem(void) { return 4; }
   // default XML file to be loaded on startup
   virtual QString DefaultLeafML(void) { return QString("meinhardt_init.xml"); }
 };
 #endif
 /* finis */

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