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Added Reference models 2 Monolayer growth and 3 Wound healing
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| /* | ||
| Copyright (c) 2005-2018, 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. | ||
| */ | ||
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| // ------ NOTE!!! ---- | ||
| // Must be used in conjuction with VoidAreaModifier or CircularityCalcModifier, as that is where this property is set. | ||
| // ----------------------- | ||
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| #include "BoundaryCellWriter.hpp" | ||
| #include "AbstractCellPopulation.hpp" | ||
| #include "Debug.hpp" | ||
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| template<unsigned ELEMENT_DIM, unsigned SPACE_DIM> | ||
| BoundaryCellWriter<ELEMENT_DIM, SPACE_DIM>::BoundaryCellWriter() | ||
| : AbstractCellWriter<ELEMENT_DIM, SPACE_DIM>("BoundaryCells.dat") | ||
| { | ||
| this->mVtkCellDataName = "Boundary Cells"; | ||
| } | ||
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| template<unsigned ELEMENT_DIM, unsigned SPACE_DIM> | ||
| double BoundaryCellWriter<ELEMENT_DIM, SPACE_DIM>::GetCellDataForVtkOutput(CellPtr pCell, AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>* pCellPopulation) | ||
| { | ||
| // double cell_id = pCell->GetCellId(); | ||
| double isBoundary = pCell->GetCellData()->GetItem("is_boundary"); | ||
| return isBoundary; | ||
| } | ||
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| template<unsigned ELEMENT_DIM, unsigned SPACE_DIM> | ||
| void BoundaryCellWriter<ELEMENT_DIM, SPACE_DIM>::VisitCell(CellPtr pCell, AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>* pCellPopulation) | ||
| { | ||
| unsigned cell_id = pCell->GetCellId(); | ||
| double isBoundary = pCell->GetCellData()->GetItem("is_boundary"); | ||
| unsigned location_index = pCellPopulation->GetLocationIndexUsingCell(pCell); | ||
| *this->mpOutStream << " " << cell_id << " " << location_index << " " << isBoundary; | ||
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| c_vector<double, SPACE_DIM> coords = pCellPopulation->GetLocationOfCellCentre(pCell); | ||
| for (unsigned i=0; i<SPACE_DIM; i++) | ||
| { | ||
| *this->mpOutStream << " " << coords[i]; | ||
| } | ||
| } | ||
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| // Explicit instantiation | ||
| template class BoundaryCellWriter<1,1>; | ||
| template class BoundaryCellWriter<1,2>; | ||
| template class BoundaryCellWriter<2,2>; | ||
| template class BoundaryCellWriter<1,3>; | ||
| template class BoundaryCellWriter<2,3>; | ||
| template class BoundaryCellWriter<3,3>; | ||
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| #include "SerializationExportWrapperForCpp.hpp" | ||
| // Declare identifier for the serializer | ||
| EXPORT_TEMPLATE_CLASS_ALL_DIMS(BoundaryCellWriter) |
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| Original file line number | Diff line number | Diff line change |
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| /* | ||
| Copyright (c) 2005-2018, 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. | ||
| */ | ||
|
|
||
|
|
||
| // ------ NOTE!!! ---- | ||
| // Must be used in conjuction with VoidAreaModifier or CircularityCalcModifier, as that is where this property is set. | ||
| // ----------------------- | ||
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| #ifndef BoundaryCellWriter_HPP_ | ||
| #define BoundaryCellWriter_HPP_ | ||
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| #include "ChasteSerialization.hpp" | ||
| #include <boost/serialization/base_object.hpp> | ||
| #include "AbstractCellWriter.hpp" | ||
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| /** | ||
| * A class written using the visitor pattern for writing cell IDs to file. | ||
| * | ||
| * The output file is called loggedcell.dat by default. If VTK is switched on, | ||
| * then the writer also specifies the VTK output for each cell, which is stored in | ||
| * the VTK cell data "Cell IDs" by default. | ||
| */ | ||
| template<unsigned ELEMENT_DIM, unsigned SPACE_DIM> | ||
| class BoundaryCellWriter : public AbstractCellWriter<ELEMENT_DIM, SPACE_DIM> | ||
| { | ||
| private: | ||
| /** Needed for serialization. */ | ||
| friend class boost::serialization::access; | ||
| /** | ||
| * Serialize the object and its member variables. | ||
| * | ||
| * @param archive the 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<AbstractCellWriter<ELEMENT_DIM, SPACE_DIM> >(*this); | ||
| } | ||
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| public: | ||
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| /** | ||
| * Default constructor. | ||
| */ | ||
| BoundaryCellWriter(); | ||
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| /** | ||
| * Overridden GetCellDataForVtkOutput() method. | ||
| * | ||
| * Get a double associated with a cell. This method reduces duplication | ||
| * of code between the methods VisitCell() and AddVtkData(). | ||
| * | ||
| * @param pCell a cell | ||
| * @param pCellPopulation a pointer to the cell population owning the cell | ||
| * | ||
| * @return data associated with the cell | ||
| */ | ||
| double GetCellDataForVtkOutput(CellPtr pCell, AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>* pCellPopulation); | ||
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| /** | ||
| * Overridden VisitCell() method. | ||
| * | ||
| * Visit a cell and write its ID. | ||
| * | ||
| * Outputs a line of space-separated values of the form: | ||
| * ...[cell id] [location index] [x-pos] [y-pos] [z-pos] ... | ||
| * with [y-pos] and [z-pos] included for 2 and 3 dimensional simulations, respectively. | ||
| * | ||
| * This is appended to the output written by AbstractCellBasedWriter, which is a single | ||
| * value [present simulation time], followed by a tab. | ||
| * | ||
| * @param pCell a cell | ||
| * @param pCellPopulation a pointer to the cell population owning the cell | ||
| */ | ||
| virtual void VisitCell(CellPtr pCell, AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>* pCellPopulation); | ||
| }; | ||
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| #include "SerializationExportWrapper.hpp" | ||
| EXPORT_TEMPLATE_CLASS_ALL_DIMS(BoundaryCellWriter) | ||
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| #endif /* BoundaryCellWriter_HPP_ */ |
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