first commit

CMakeLists.txt

@@ -3,20 +3,20 @@
 
 # You can set which Chaste components (or other projects) your project depends on by editing the
 # find_package() call for Chaste.  E.g.
-#   find_package(Chaste COMPONENTS cell_based)
+   find_package(Chaste COMPONENTS cell_based)
 # for a project just using the cell_based component (and its dependencies), or
 #   find_package(Chaste COMPONENTS heart lung)
 # for a project combining heart & lung simulations.
 #
 # Note that the order in which components are specified does not matter.
 
 # Here we just depend on core components (nothing application-specific).
-find_package(Chaste COMPONENTS continuum_mechanics global io linalg mesh ode pde)
+#find_package(Chaste COMPONENTS cell_based global io linalg mesh ode pde)
 
 # Alternatively, to specify a Chaste installation directory use a line like that below.
 # This is needed if your project is not contained in the projects folder within a Chaste source tree.
 #find_package(Chaste COMPONENTS heart crypt PATHS /path/to/chaste-install NO_DEFAULT_PATH)
 
 # Change the project name in the line below to match the folder this file is in,
 # i.e. the name of your project.
-chaste_do_project(template_project)
+chaste_do_project(matteo_chaste)

apps/CMakeLists.txt

@@ -3,4 +3,4 @@
 
 # This allows us to build executables (apps) using the project.
 # Simply set the project name in the line below.
-chaste_do_apps_project(template_project)
+chaste_do_apps_project(matteo_chaste)

src/ConstantTargetAreaModifier.cpp

@@ -0,0 +1,73 @@
+/*
+
+Copyright (c) 2005-2016, University of Oxford.
+All rights reserved.
+
+University of Oxford means the Chancellor, Masters and Scholars of the
+University of Oxford, having an administrative office at Wellington
+Square, Oxford OX1 2JD, UK.
+
+This file is part of Chaste.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+ * Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+ * Neither the name of the University of Oxford nor the names of its
+   contributors may be used to endorse or promote products derived from this
+   software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+*/
+
+#include "ConstantTargetAreaModifier.hpp"
+
+template<unsigned DIM>
+ConstantTargetAreaModifier<DIM>::ConstantTargetAreaModifier()
+    : AbstractTargetAreaModifier<DIM>()
+{
+}
+
+template<unsigned DIM>
+ConstantTargetAreaModifier<DIM>::~ConstantTargetAreaModifier()
+{
+}
+
+template<unsigned DIM>
+void ConstantTargetAreaModifier<DIM>::UpdateTargetAreaOfCell(CellPtr pCell)
+{
+    // Get target area A of a healthy cell in S, G2 or M phase
+    double cell_target_area = this->mReferenceTargetArea;
+
+    // Set cell data
+    pCell->GetCellData()->SetItem("target area", cell_target_area);
+}
+
+template<unsigned DIM>
+void ConstantTargetAreaModifier<DIM>::OutputSimulationModifierParameters(out_stream& rParamsFile)
+{
+    // No parameters to output, so just call method on direct parent class
+    AbstractTargetAreaModifier<DIM>::OutputSimulationModifierParameters(rParamsFile);
+}
+
+// Explicit instantiation
+template class ConstantTargetAreaModifier<1>;
+template class ConstantTargetAreaModifier<2>;
+template class ConstantTargetAreaModifier<3>;
+
+// Serialization for Boost >= 1.36
+#include "SerializationExportWrapperForCpp.hpp"
+EXPORT_TEMPLATE_CLASS_SAME_DIMS(ConstantTargetAreaModifier)

src/ConstantTargetAreaModifier.hpp

@@ -0,0 +1,94 @@
+/*
+
+Copyright (c) 2005-2016, University of Oxford.
+All rights reserved.
+
+University of Oxford means the Chancellor, Masters and Scholars of the
+University of Oxford, having an administrative office at Wellington
+Square, Oxford OX1 2JD, UK.
+
+This file is part of Chaste.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+ * Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+ * Neither the name of the University of Oxford nor the names of its
+   contributors may be used to endorse or promote products derived from this
+   software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+*/
+
+#ifndef CONSTANTTARGETAREAMODIFIER_HPP_
+#define CONSTANTTARGETAREAMODIFIER_HPP_
+
+#include "ChasteSerialization.hpp"
+#include "AbstractTargetAreaModifier.hpp"
+
+/**
+ * A modifier class in which the target area property of each cell is held constant over time.
+ */
+template<unsigned DIM>
+class ConstantTargetAreaModifier : public AbstractTargetAreaModifier<DIM>
+{
+    /** Needed for serialization. */
+    friend class boost::serialization::access;
+    /**
+     * Boost Serialization method for archiving/checkpointing.
+     * Archives the object and its member variables.
+     *
+     * @param archive  The boost archive.
+     * @param version  The current version of this class.
+     */
+    template<class Archive>
+    void serialize(Archive & archive, const unsigned int version)
+    {
+        archive & boost::serialization::base_object<AbstractTargetAreaModifier<DIM> >(*this);
+    }
+
+public:
+
+    /**
+     * Default constructor.
+     */
+    ConstantTargetAreaModifier();
+
+    /**
+     * Destructor.
+     */
+    virtual ~ConstantTargetAreaModifier();
+
+    /**
+     * Overridden UpdateTargetAreaOfCell() method.
+     *
+     * @param pCell pointer to the cell
+     */
+    virtual void UpdateTargetAreaOfCell(const CellPtr pCell);
+
+    /**
+     * Overridden OutputSimulationModifierParameters() method.
+     * Output any simulation modifier parameters to file.
+     *
+     * @param rParamsFile the file stream to which the parameters are output
+     */
+    void OutputSimulationModifierParameters(out_stream& rParamsFile);
+};
+
+#include "SerializationExportWrapper.hpp"
+EXPORT_TEMPLATE_CLASS_SAME_DIMS(ConstantTargetAreaModifier)
+
+#endif /*CONSTANTTARGETAREAMODIFIER_HPP_*/

src/MatteoCellCycleModel.cpp

@@ -0,0 +1,81 @@
+
+#include "MatteoCellCycleModel.hpp"
+#include "DifferentiatedCellProliferativeType.hpp"
+#include "Debug.hpp"
+
+MatteoCellCycleModel::MatteoCellCycleModel()
+    : AbstractSimpleCellCycleModel(),
+      mMinCellCycleDuration(12.0), // Hours
+      mMaxCellCycleDuration(14.0)  // Hours
+{
+}
+
+/*called every time step and tells if a cell is aready to divide (using the cell cycle model)*/
+
+bool MatteoCellCycleModel::ReadyToDivide()
+{
+   bool ready = mpCell->GetCellData()->GetItem("divide");
+    mpCell->GetCellData()->SetItem("divide", 0);
+    return ready;
+
+
+}
+
+MatteoCellCycleModel::MatteoCellCycleModel(const MatteoCellCycleModel& rModel)
+   : AbstractSimpleCellCycleModel(rModel),
+     mMinCellCycleDuration(rModel.mMinCellCycleDuration),
+     mMaxCellCycleDuration(rModel.mMaxCellCycleDuration)
+{
+}
+
+AbstractCellCycleModel* MatteoCellCycleModel::CreateCellCycleModel()
+{
+    return new MatteoCellCycleModel(*this);
+}
+
+void MatteoCellCycleModel::SetCellCycleDuration()
+{
+}
+
+double MatteoCellCycleModel::GetMinCellCycleDuration()
+{
+    return mMinCellCycleDuration;
+}
+
+void MatteoCellCycleModel::SetMinCellCycleDuration(double minCellCycleDuration)
+{
+    mMinCellCycleDuration = minCellCycleDuration;
+}
+
+double MatteoCellCycleModel::GetMaxCellCycleDuration()
+{
+    return mMaxCellCycleDuration;
+}
+
+void MatteoCellCycleModel::SetMaxCellCycleDuration(double maxCellCycleDuration)
+{
+    mMaxCellCycleDuration = maxCellCycleDuration;
+}
+
+double MatteoCellCycleModel::GetAverageTransitCellCycleTime()
+{
+    return 0.5*(mMinCellCycleDuration + mMaxCellCycleDuration);
+}
+
+double MatteoCellCycleModel::GetAverageStemCellCycleTime()
+{
+    return 0.5*(mMinCellCycleDuration + mMaxCellCycleDuration);
+}
+
+void MatteoCellCycleModel::OutputCellCycleModelParameters(out_stream& rParamsFile)
+{
+    *rParamsFile << "\t\t\t<MinCellCycleDuration>" << mMinCellCycleDuration << "</MinCellCycleDuration>\n";
+    *rParamsFile << "\t\t\t<MaxCellCycleDuration>" << mMaxCellCycleDuration << "</MaxCellCycleDuration>\n";
+
+    // Call method on direct parent class
+    AbstractSimpleCellCycleModel::OutputCellCycleModelParameters(rParamsFile);
+}
+
+// Serialization for Boost >= 1.36
+#include "SerializationExportWrapperForCpp.hpp"
+CHASTE_CLASS_EXPORT(MatteoCellCycleModel)