diff --git a/src/build_models/leafplugin.cpp b/src/build_models/leafplugin.cpp
deleted file mode 100644
--- a/src/build_models/leafplugin.cpp
+++ /dev/null
@@ -1,425 +0,0 @@
-/*
- *
- * 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 .
- *
- * Copyright 2010 Roeland Merks.
- *
- */
-
-#include
-#include
-
-#include "simplugin.h"
-
-#include "parameter.h"
-
-#include "wallbase.h"
-#include "cellbase.h"
-#include "leafplugin.h"
-
-#include "far_mem_5.h"
-
-static const std::string _module_id("$Id$");
-
-bool batch = false;
-
-// To be executed after cell division
-void LeafPlugin::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
- // PIN1 distributes between parent and daughter according to area
- double area = daughter1->Area(), daughter_area = daughter2->Area();
- double tot_area = area + daughter_area;
-
- //chem[1]*=(area/tot_area);
- //daughter.chem[1]*=(daughter_area/tot_area);
-
- // For lack of detailed data, or a better rule, we assume that cells remain polarized
- // after division
-
- // So the PIN1 is redistributed according to the original polarization over the walls
-
- // parent_info contains info about the parent
- // redistribute the PIN in the endosome according to area
-
- // "Fudge" rule: if one of the cells is at the boundary, remove all AUX1 in the other cell
- if (daughter1->AtBoundaryP() && !daughter2->AtBoundaryP()) {
- //daughter2->new_chem[2]=daughter2->chem[2]=0.;
- daughter2->SetNewChem(2,0);
- daughter2->SetChemical(2,0);
- //daughter.new_chem[0]=daughter.chem[0]=0.;
- //cerr << "Clearing daughter\n";
- //for (list::const_iterator w=daughter.walls.begin();
- // w!=daughter.walls.end();
- // w++) {
-
- // (*w)->setTransporter(&daughter, 1, 0.);
-
- //}
- //new_chem[2]=chem[2]=parent_info->PINendosome;
- daughter1->SetNewChem(2,parent_info->PINendosome);
- daughter1->SetChemical(2,parent_info->PINendosome);
-
- } else {
- if (daughter2->AtBoundaryP() && !daughter1->AtBoundaryP()) {
-
- //new_chem[2]=chem[2]=0.;
- daughter1->SetNewChem(2,0);
- daughter1->SetChemical(2,0);
-
- /*new_chem[0]=chem[0]=0.;
- for (list::const_iterator w=walls.begin();
- w!=walls.end();
- w++) {
-
- (*w)->setTransporter(this, 1, 0.);
- }*/
- //daughter2->chem[2]=parent_info->PINendosome;
- daughter2->SetChemical(2,parent_info->PINendosome);
- //cerr << "Clearing parent\n";
-
- } else {
- //daughter1->new_chem[2]=daughter1->chem[2] = parent_info->PINendosome*(area/tot_area);
- daughter1->SetNewChem(2,parent_info->PINendosome*(area/tot_area));
- daughter1->SetChemical(2, parent_info->PINendosome*(area/tot_area));
- //daughter2->new_chem[2]=daughter2->chem[2] = parent_info->PINendosome*(daughter_area/tot_area);
- daughter2->SetNewChem(2,parent_info->PINendosome*(daughter_area/tot_area));
- daughter2->SetChemical(2,parent_info->PINendosome*(daughter_area/tot_area));
-
- }
- }
-
- /*
- // NB: Code commented out; not yet adapted to plugin format... RM 18/12/2009
- // Now redistribute the membrane PINs according to the original polarization in the parent
- // mmm... I'd like to have a better, biologically motivated rule for this,
- // but for lack of something better... I hope I'm excused :-). Let's say the overall
- // organization of the actin fibres is not completely destroyed after division...
-
- // distribute wallPINs according to the circumference of the parent and daughter
- double circ = Circumference( );
- double daughter_circ = daughter.Circumference();
- double tot_circ = circ + daughter_circ;
-
- double wallPINs = (circ / tot_circ) * parent_info->PINmembrane;
- double daughter_wallPINs = (daughter_circ / tot_circ) * parent_info->PINmembrane;
-
- //cerr << "wallPINs = " << wallPINs << ", daughter_wallPINs = " << daughter_wallPINs << "sum = " << wallPINs + daughter_wallPINs << ", PINmembrane = " << parent_info->PINmembrane << endl;
- // distrubute it according to the overall polarity
- Vector polarization = parent_info->polarization.Normalised().Perp2D();
-
- double sum=0.;
- for (list::const_iterator w=walls.begin();
- w!=walls.end();
- w++) {
-
- // distribute according to angle (0 degrees: maximum, 180 degrees minimum)
- double tmp=InnerProduct((*w)->getWallVector(this),polarization); // move domain from [-1,1] to [0,1]
-
- cerr << "[" << tmp << "]";
- sum+=tmp;
- //(*w)->setTransporter(this, 1,
- }
-
- //cerr << "Sum is " << sum << endl;
- //double sum_wall_Pi = SumTransporters(1);
-
- // After division, cells produce PIN1 (in intracellular storage) until total amount becomes Pi_tot
- //SetChemical(1, par.Pi_tot - sum_wall_Pi );
- //SetNewChem(1, Chemical(1));
-
- //cerr << "[ " << sum_wall_Pi + Chemical(1) << "]";
- */
-}
-
-void LeafPlugin::SetCellColor(CellBase *c, QColor *color) {
-
- // Red: AUX1
- // Green: Auxin
- // Blue: van-3
- // color->setRgb(chem[2]/(1+chem[2]) * 255.,(chem[0]/(1+chem[0]) * 255.),(chem[3]/(1+chem[3]) *255.) );
- color->setRgb(c->Chemical(2)/(1+c->Chemical(2)) * 255.,(c->Chemical(0)/(1+c->Chemical(0)) * 255.),(c->Chemical(3)/(1+c->Chemical(3)) *255.) );
-
-
-}
-
-
-
-void LeafPlugin::CellHouseKeeping(CellBase *c) {
-
- if (c->Boundary()==CellBase::None) {
- if (c->Area() > par->rel_cell_div_threshold * c->BaseArea() ) {
- //c->SetChemical(0,0);
- c->Divide();
- }
-
- // expand if this is not a provascular cell
- if (c->Chemical(3) < 0.7 ) {
- c->EnlargeTargetArea(par->cell_expansion_rate);
- }
- }
-
-}
-
-void LeafPlugin::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
-
- // leaf edge is const source of auxin
- // (Neumann boundary condition: we specify the influx)
- if (w->C2()->BoundaryPolP()) {
- if (w->AuxinSource()) {
- double aux_flux = par->leaf_tip_source * w->Length();
- dchem_c1[0]+= aux_flux;
-
- // dchem_c2 is undefined..!
- return;
- } else {
- if (w->AuxinSink()) {
-
- // efflux into Shoot Apical meristem
- // we assume all PINs are directed towards shoot apical meristem
- dchem_c1[0] -= par->sam_efflux * w->C1()->Chemical(0) / (par->ka + w->C1()->Chemical(0));
-
- return;
- } else {
-
- // Active fluxes (PIN1 and AUX1 mediated transport)
-
- // (Transporters measured in moles, here)
- // efflux from cell 1 to cell 2
- double trans12 = ( par->transport * w->Transporters1(1) * w->C1()->Chemical(0) / (par->ka + w->C1()->Chemical(0))
- + par->aux1transport * w->C2()->Chemical(2) * w->C1()->Chemical(0) / (par->kaux1 + w->C1()->Chemical(0)) );
-
- // efflux from cell 2 to cell 1
- double trans21 = ( par->transport * w->Transporters2(1) * w->C2()->Chemical(0) / (par->ka + w->C2()->Chemical(0))
- + par->aux1transport * w->C1()->Chemical(2) * w->C2()->Chemical(0) / (par->kaux1 + w->C2()->Chemical(0)) );
-
- dchem_c1[0] += trans21 - trans12;
- dchem_c2[0] += trans12 - trans21;
- return;
- }
-
- }
- }
-
-
- if (w->C1()->BoundaryPolP()) {
-
- if (w->AuxinSource()) {
- double aux_flux = par->leaf_tip_source * w->Length();
- dchem_c2[0] += aux_flux;
- // dchem_c1 is undefined...!
- return;
- } else {
-
- if (w->AuxinSink()) {
-
-
- // efflux into Shoot Apical meristem
- // we assume all PINs are directed towards shoot apical meristem
-
- // no passive fluxes: outside is impermeable
-
- // Active fluxes (PIN1 and AUX1 mediated transport)
-
- // (Transporters measured in moles, here)
- // efflux from cell 1 to cell 2
- // assumption: no AUX1 in shoot apical meristem
- double trans12 = ( par->transport * w->Transporters1(1) * w->C1()->Chemical(0) / (par->ka + w->C1()->Chemical(0)));
- dchem_c1[0] += - trans12;
-
- return;
-
- //dchem_c2[0] -= par->sam_efflux * w->C2()->Chemical(0) / (par->ka + w->C2()->Chemical(0));
-
- // return;
- } else {
-
- }
- }
- }
-
-
- // Passive fluxes (Fick's law)
- // only auxin flux now
- // flux depends on edge length and concentration difference
- for (int c=0;cLength() * ( par->D[c] ) * ( w->C2()->Chemical(c) - w->C1()->Chemical(c) );
- dchem_c1[c] += phi;
- dchem_c2[c] -= phi;
- }
- // Active fluxes (PIN1 and AUX1 mediated transport)
-
- // (Transporters measured in moles, here)
- // efflux from cell 1 to cell 2
- double trans12 = ( par->transport * w->Transporters1(1) * w->C1()->Chemical(0) / (par->ka + w->C1()->Chemical(0))
- + par->aux1transport * w->C2()->Chemical(2) * w->C1()->Chemical(0) / (par->kaux1 + w->C1()->Chemical(0)) );
-
- // efflux from cell 2 to cell 1
- double trans21 = ( par->transport * w->Transporters2(1) * w->C2()->Chemical(0) / (par->ka + w->C2()->Chemical(0))
- + par->aux1transport * w->C1()->Chemical(2) * w->C2()->Chemical(0) / (par->kaux1 + w->C2()->Chemical(0)) );
-
- dchem_c1[0] += trans21 - trans12;
- dchem_c2[0] += trans12 - trans21;
-
-
-
-}
-void LeafPlugin::WallDynamics(Wall *w, double *dw1, double *dw2) {
-
- // Cells polarize available PIN1 to Shoot Apical Meristem
- if (w->C2()->BoundaryPolP()) {
- if (w->AuxinSink()) {
-
- dw1[0] = 0.; dw2[0] = 0.;
- dw1[2] = 0.; dw2[2] = 0.;
-
- // assume high auxin concentration in SAM, to convince PIN1 to polarize to it
- // exocytosis regulated0
- double nb_auxin = par->sam_auxin;
- double receptor_level = nb_auxin * par->r / (par->kr + nb_auxin);
-
- dw1[1] = par->k1 * w->C1()->Chemical(1) * receptor_level /( par->km + w->C1()->Chemical(1) ) - par->k2 * w->Transporters1(1);
-
- dw2[1] = 0.;
- return;
-
- } else {
- dw1[0]=dw2[0]=dw1[1]=dw2[1]=dw1[2]=dw2[2];
- return;
- }
- }
-
- if (w->C1()->BoundaryPolP()) {
- if (w->AuxinSink()) {
-
- dw1[0] = 0.; dw2[0] = 0.;
- dw1[2] = 0.; dw2[2] = 0.;
-
- // assume high auxin concentration in SAM, to convince PIN1 to polarize to it
- // exocytosis regulated
- double nb_auxin = par->sam_auxin;
- double receptor_level = nb_auxin * par->r / (par->kr + nb_auxin);
- dw2[1] = par->k1 * w->C2()->Chemical(1) * receptor_level /( par->km + w->C2()->Chemical(1) ) - par->k2 * w->Transporters2(1);
-
- dw1[1] = 0.;
- return;
-
- } else {
- dw1[0]=dw2[0]=dw1[1]=dw2[1]=dw1[2]=dw2[2];
- return;
- }
- }
-
-
-
- // PIN1 localization at wall 1
- // Note: chemical 0 is Auxin (intracellular storage only)
- // Chemical 1 is PIN1 (walls and intracellular storage)
- //! \f$ \frac{d Pij/dt}{dt} = k_1 A_j \frac{P_i}{L_ij} - k_2 P_{ij} \f$
- // Note that Pij is measured in term of concentration (mol/L)
- // Pi in terms of quantity (mol)
-
- double dPijdt1=0., dPijdt2=0.;
-
- // normal cell
- double auxin2 = w->C2()->Chemical(0);
- double receptor_level1 = auxin2 * par->r / (par->kr + auxin2);
-
- dPijdt1 =
- // exocytosis regulated
- par->k1 * w->C1()->Chemical(1) * receptor_level1 / ( par->km + w->C1()->Chemical(1) ) - par->k2 * w->Transporters1(1);
-
- double auxin1 = w->C1()->Chemical(0);
- double receptor_level2 = auxin1 * par->r / (par->kr + auxin1);
-
- // normal cell
- dPijdt2 =
-
- // exocytosis regulated
- par->k1 * w->C2()->Chemical(1) * receptor_level2 / ( par->km + w->C2()->Chemical(1) ) - par->k2 * w->Transporters2(1);
-
- /* PIN1 of neighboring vascular cell inhibits PIN1 endocytosis */
-
- dw1[0] = 0.; dw2[0] = 0.;
- dw1[2] = 0.; dw2[2] = 0.;
-
- dw1[1] = dPijdt1;
- dw2[1] = dPijdt2;
-
-}
-
-double LeafPlugin::complex_PijAj(CellBase *here, CellBase *nb, Wall *w) {
-
- // gives the amount of complex "auxinreceptor-Pin1" at the wall (at QSS)
- //return here.Chemical(1) * nb.Chemical(0) / ( par->km + here.Chemical(1));
-
- double nb_aux = (nb->BoundaryPolP() && w->AuxinSink()) ? par->sam_auxin : nb->Chemical(0);
- double receptor_level = nb_aux * par->r / (par->kr + nb_aux);
-
- return here->Chemical(1) * receptor_level / ( par->km + here->Chemical(1));
-
-}
-
-
-void LeafPlugin::CellDynamics(CellBase *c, double *dchem) {
-
- double dPidt = 0.;
-
- double sum_Pij = c->SumTransporters( 1 );
-
- // exocytosis regulated:
- // van3 expression reduces rate of PIN1 endocytosis
- dPidt = -par->k1 * c->ReduceCellAndWalls( far_3_arg_mem_fun( *this, &LeafPlugin::complex_PijAj ) ) +
- (c->Chemical(3) < 0.5 ? par->k2 : par->k2van3) * sum_Pij;
-
- // production of PIN depends on auxin concentration
- dPidt += (c->AtBoundaryP()?par->pin_prod_in_epidermis:par->pin_prod) * c->Chemical(0) - c->Chemical(1) * par->pin_breakdown;
-
- /*if (c->AtBoundaryP()) {
- dchem[2] = 0.01;
- //cerr << "Making cell blue.\n";
- } else {
- dchem[2] = -0.1 * c->Chemical(2);
- }*/
-
- // no PIN production in SAM
- if (c->Boundary() == CellBase::SAM) {
- dchem[1]=0.;
- dchem[0]= - par->sam_auxin_breakdown * c->Chemical(0);
- dchem[2]=0.;
- } else {
-
- dchem[1] = dPidt;
-
-
- // source of auxin
- dchem[0] = par->aux_cons;
-
- // auxin-induced AUX1 production, in the epidermis
- dchem[2] = ( c->AtBoundaryP() ? par->aux1prod : par->aux1prodmeso ) * ( c->Chemical(0) / ( 1. + par->kap * c->Chemical(0) ) ) - ( par->aux1decay ) * c->Chemical(2) ;//: 0.;
-
- // auxin-induced production of VAN-3? Autokatalysis?
- //dchem[3] = par->van3prod * (c->Chemical(0) / (1. + par->kvp * c-> Chemical(0) ) )
- double A = c->Chemical(0);
- double van3 = c->Chemical(3);
- dchem[3] = par->van3prod * A - par->van3autokat * van3 + van3*van3/(1 + par->van3sat * van3*van3 );
- }
-}
-
-
-
-
-
-
-Q_EXPORT_PLUGIN2(leafplugin, LeafPlugin)
diff --git a/src/build_models/leafplugin.h b/src/build_models/leafplugin.h
deleted file mode 100644
--- a/src/build_models/leafplugin.h
+++ /dev/null
@@ -1,64 +0,0 @@
-/*
- * $Id$
- *
- * 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 .
- *
- * Copyright 2010 Roeland Merks.
- *
- */
-
-#ifndef _LEAFPLUGIN_H_
-#define _LEAFPLUGIN_H_
-
-#include
-#include
-#include
-#include "../simplugin.h"
-
-
-class LeafPlugin : public QObject, SimPluginInterface {
- Q_OBJECT
- Q_INTERFACES(SimPluginInterface);
-
-public:
- virtual QString ModelID(void) { return QString( "Traveling wave model with influx carriers - Merks and Beemster, 2006-2008" ); }
-
- // 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; }
-
- private:
- double complex_PijAj(CellBase *here, CellBase *nb, Wall *w);
-
-};
-
-#endif
diff --git a/src/build_models/plugin_leaf.pro b/src/build_models/plugin_leaf.pro
deleted file mode 100644
--- a/src/build_models/plugin_leaf.pro
+++ /dev/null
@@ -1,55 +0,0 @@
-#
-# $Id$
-#
-# 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 .
-#
-# Copyright 2010 Roeland Merks.
-#
-
-CONFIG += release
-CONFIG -= debug
-CONFIG += plugin
-
-BINDIR = ../../bin
-LIBDIR = ../../lib
-DEFINES = QTGRAPHICS # VLEAFPLUGIN
-DESTDIR = $${BINDIR}/models
-TARGET = leaf
-HEADERS = ../simplugin.h $${TARGET}plugin.h
-QMAKE_CXXFLAGS += -fexceptions -I..
-QMAKE_CXXFLAGS_DEBUG += -g3
-QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
-
-QT += qt3support
-SOURCES = $${TARGET}plugin.cpp
-TEMPLATE = lib
-
-unix {
- LIBS += -L$${LIBDIR} -lvleaf
- QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
- QMAKE_LFLAGS += -fPIC
-}
-
-win32 {
- LIBXML2DIR = C:\libxml2
- LIBICONVDIR = C:\libiconv
- LIBZDIR = C:\libz
- LIBS += -L$${LIBDIR} -Llib -lvleaf
- QMAKE_CXXFLAGS += -DLIBXML_STATIC
- QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
-}
-
-# finis