EI/VirtualLeaf Changeset - c8fbdf1e4153 · Centrum Wiskunde & Informatica (CWI)

Changeset - c8fbdf1e4153

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Michael Guravage - 15 years ago 2010-05-28 13:53:39
michael.guravage@cwi.nl

Roeland's recent improvements - especially a more robust Mesh::Derivatives().

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed src/VirtualLeaf.pro
changed src/build_models/plugin_test.pro
changed src/cell.cpp
changed src/cellbase.cpp
changed src/cellbase.h
changed src/mesh.cpp
changed src/mesh.h

7 files changed with 39 insertions and 9 deletions:

src/VirtualLeaf.pro

src/build_models/plugin_test.pro

src/cell.cpp

src/cellbase.cpp

src/cellbase.h

src/mesh.cpp

src/mesh.h

0 comments (0 inline, 0 general)

src/VirtualLeaf.pro

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@@ @@ -19,8 +19,8 @@ @@
 #  Copyright 2010 Roeland Merks.
+#
 CONFIG -= release
 CONFIG += debug
 CONFIG += release
 CONFIG -= debug
 CONFIG += qt
 QMAKE_CXXFLAGS += -fexceptions

src/build_models/plugin_test.pro

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@@ @@ -19,7 +19,6 @@ @@
 #  Copyright 2010 Roeland Merks.
+#
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin

src/cell.cpp

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@@ @@ -415,6 +415,7 @@ void Cell::DivideWalls(ItList new_node_l @@
 		daughter->chem[i]=chem[i];
+	}
 	daughter->cell_type = cell_type;
 	//extern double auxin_account;
 	//auxin_account += daughter->chem[0];

src/cellbase.cpp

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@@ @@ -101,6 +101,7 @@ Vector() @@
 	div_counter=0;
 	cell_type = 0;
 	flag_for_divide = false;
 	division_axis = 0;
+}
@@ @@ -140,6 +141,7 @@ CellBase::CellBase(double x,double y,dou @@
 	div_counter = 0;
 	cell_type = 0;
 	flag_for_divide = false;
 	division_axis = 0;
+}
@@ @@ -180,7 +182,7 @@ CellBase::CellBase(const CellBase &src) @@
 	cell_type = src.cell_type;
 	div_counter = src.div_counter;
 	flag_for_divide = src.flag_for_divide;
-	</i>
+	division_axis = src.division_axis;
+}
@@ @@ -219,6 +221,7 @@ CellBase CellBase::operator=(const CellB @@
 	cell_type = src.cell_type;
 	div_counter = src.div_counter;
 	flag_for_divide = src.flag_for_divide;
 	division_axis = src.division_axis;
 	return *this;
+}

src/cellbase.h

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@@ @@ -96,6 +96,7 @@ class CellBase : public QObject, public @@
   virtual ~CellBase() {
 	  delete[] chem;
 	  delete[] new_chem;
 	  if (division_axis) delete division_axis;
 	  //cerr << "CellBase " << index << " is dying. " << endl;
+  }
@@ @@ -217,7 +218,13 @@ class CellBase : public QObject, public @@
 	inline void Divide(void) {
 		flag_for_divide = true;
+	}
     //Vector Strain(void) const;
 	inline void DivideOverAxis(const Vector &v) {
 		division_axis = new Vector(v);
 		flag_for_divide = true;
+	}
 	//Vector Strain(void) const;
     inline double Circumference(void) const {
       double sum=0.;
@@ @@ -447,6 +454,8 @@ protected: @@
     bool dead;
 	bool flag_for_divide;
 	Vector *division_axis;
 	int cell_type;
     //double length;

src/mesh.cpp

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@@ @@ -1983,9 +1983,21 @@ void Mesh::Derivatives(double *derivs) { @@
    // (*wr)(*w, &(derivs[i]), &(derivs[i+nchems]));
 	  plugin->WallDynamics(*w,  &(derivs[i]), &(derivs[i+nchems]));
     // Transport function adds to derivatives of cell chemicals
 	  plugin->CelltoCellTransport(*w, &(derivs[(*w)->c1->Index() * nchems]),
 								  &(derivs[(*w)->c2->Index() * nchems]));
 	  double *dchem_c1 = &(derivs[(*w)->c1->Index() * nchems]);
 	  double *dchem_c2 = &(derivs[(*w)->c2->Index() * nchems]);
 	  //plugin->CelltoCellTransport(*w, &(derivs[(*w)->c1->Index() * nchems]),
 							//	  &(derivs[(*w)->c2->Index() * nchems]));
 	  // quick fix: dummy values to prevent end user from writing into outer space and causing a crash :-)
 	  // start here if you want to implement chemical input/output into environment over boundaries
 	  double dummy1, dummy2;
 	  if ((*w)->c1->Index()<0) { // tests if c1 is the boundary pol
 		  dchem_c1 = &dummy1;
+	  }
 	  if ((*w)->c2->Index()<0) {
 		  dchem_c2 = &dummy2;
+	  }
 	  plugin->CelltoCellTransport(*w, dchem_c1, dchem_c2);
 	  //(*tf)(*w, &(derivs[(*w)->c1->Index() * nchems]),
       //&(derivs[(*w)->c2->Index() * nchems] ) );
     i+=2*nchems;

src/mesh.h

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@@ @@ -242,7 +242,13 @@ public: @@
 			// Call functions of Cell that cannot be called from CellBase, including Division
 			if ((*i)->flag_for_divide) {
 				(*i)->Divide();
 				if ((*i)->division_axis) {
 					(*i)->DivideOverAxis(*(*i)->division_axis);
 					delete (*i)->division_axis;
 					(*i)->division_axis = 0;
 				} else {
 					(*i)->Divide();
+				}
 				(*i)->flag_for_divide=false;
+			}
+		}

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