Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
Hdf5ToMeshalyzerConverter.cpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
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10This file is part of Chaste.
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12Redistribution and use in source and binary forms, with or without
13modification, are permitted provided that the following conditions are met:
14 * Redistributions of source code must retain the above copyright notice,
15 this list of conditions and the following disclaimer.
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19 * Neither the name of the University of Oxford nor the names of its
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21 software without specific prior written permission.
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23THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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33
34*/
35
36#include "Hdf5ToMeshalyzerConverter.hpp"
37#include "MeshalyzerMeshWriter.hpp"
38#include "GenericMeshReader.hpp"
40#include "PetscTools.hpp"
41#include "Exception.hpp"
42#include "ReplicatableVector.hpp"
43#include "DistributedVector.hpp"
44#include "DistributedVectorFactory.hpp"
45#include "Version.hpp"
46
47template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
49{
50
51 std::string filename = "";
52 if (this->mDatasetNames[this->mOpenDatasetIndex] == "Data")
53 {
54 filename += this->mFileBaseName + "_";
55 }
56 filename += type + ".dat";
57
58 out_stream p_file = out_stream(nullptr);
60 {
61 p_file = this->mpOutputFileHandler->OpenOutputFile(filename);
62
63 // Check how many digits are to be output in the solution (0 goes to default value of digits)
64 if (this->mPrecision != 0)
65 {
66 p_file->precision(this->mPrecision);
67 }
68 }
69
70 unsigned num_nodes = this->mpReader->GetNumberOfRows();
71 unsigned num_timesteps = this->mpReader->GetUnlimitedDimensionValues().size();
72
73 DistributedVectorFactory factory(num_nodes);
74
75 Vec data = factory.CreateVec();
76 ReplicatableVector repl_data(num_nodes);
77 for (unsigned time_step=0; time_step<num_timesteps; time_step++)
78 {
79 this->mpReader->GetVariableOverNodes(data, type, time_step);
80 repl_data.ReplicatePetscVector(data);
81
82 assert(repl_data.GetSize() == num_nodes);
83
85 {
86 for (unsigned i=0; i<num_nodes; i++)
87 {
88 *p_file << repl_data[i] << "\n";
89 }
90 }
91 }
94 {
95 std::string comment = "# " + ChasteBuildInfo::GetProvenanceString();
96 *p_file << comment;
97 p_file->close();
98 }
99}
100
101template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
103 const std::string& rFileBaseName,
105 bool usingOriginalNodeOrdering,
106 unsigned precision)
107 : AbstractHdf5Converter<ELEMENT_DIM,SPACE_DIM>(rInputDirectory, rFileBaseName, pMesh, "output", precision)
108{
109 do
110 {
111 std::vector<std::string> variable_names = this->mpReader->GetVariableNames();
112 for (unsigned i=0; i<variable_names.size(); i++)
113 {
114 Write(variable_names[i]);
115 }
116 }
117 while ( this->MoveOntoNextDataset() );
118
119 // Now we might call this class more than once, so we don't always need to write the mesh out.
120 // so check to see if it is there already.
122 std::string output_directory = rInputDirectory.GetRelativePath(test_output) + "/" + this->mRelativeSubdirectory;
123 FileFinder mesh_file(output_directory + "/" + rFileBaseName + "_mesh.pts", RelativeTo::ChasteTestOutput);
124
125 if (!mesh_file.IsFile())
126 {
127 // Write mesh in a suitable form for meshalyzer
128 MeshalyzerMeshWriter<ELEMENT_DIM,SPACE_DIM> mesh_writer(output_directory, rFileBaseName + "_mesh", false);
129
130 // Normal case is that the in-memory mesh is converted
131 if (!usingOriginalNodeOrdering || !this->mpMesh->IsMeshOnDisk())
132 {
133 // The second argument tells the writer to not follow original element ordering for performance reasons.
134 mesh_writer.WriteFilesUsingMesh(*(this->mpMesh), false);
135 }
136 else
137 {
138 // In this case we expect the mesh to have been read in from file
140 // Note that the next line will throw if the mesh has not been read from file
141 std::string original_file = this->mpMesh->GetMeshFileBaseName();
142 std::shared_ptr<AbstractMeshReader<ELEMENT_DIM, SPACE_DIM> > p_original_mesh_reader
143 = GenericMeshReader<ELEMENT_DIM, SPACE_DIM>(original_file);
144 mesh_writer.WriteFilesUsingMeshReader(*p_original_mesh_reader);
145 }
146 }
147 PetscTools::Barrier("Hdf5ToMeshalyzerConverter");
148}
149
150// Explicit instantiation
151template class Hdf5ToMeshalyzerConverter<1,1>;
152template class Hdf5ToMeshalyzerConverter<1,2>;
153template class Hdf5ToMeshalyzerConverter<2,2>;
154template class Hdf5ToMeshalyzerConverter<1,3>;
155template class Hdf5ToMeshalyzerConverter<2,3>;
156template class Hdf5ToMeshalyzerConverter<3,3>;
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * mpMesh
boost::shared_ptr< Hdf5DataReader > mpReader
void WriteFilesUsingMeshReader(AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader)
virtual void WriteFilesUsingMesh(AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, bool keepOriginalElementIndexing=true)
static std::string GetProvenanceString()
std::string GetRelativePath(const FileFinder &rBasePath) const
bool IsFile() const
Hdf5ToMeshalyzerConverter(const FileFinder &rInputDirectory, const std::string &rFileBaseName, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, bool usingOriginalNodeOrdering, unsigned precision=0)
static void Destroy(Vec &rVec)
static bool AmMaster()
static void Barrier(const std::string callerId="")
void ReplicatePetscVector(Vec vec)