Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
Hdf5ToTxtConverter.cpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
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10This file is part of Chaste.
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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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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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34*/
35
37#include "Hdf5ToTxtConverter.hpp"
38#include "PetscTools.hpp"
39#include "Exception.hpp"
40#include "ReplicatableVector.hpp"
41#include "DistributedVector.hpp"
42#include "DistributedVectorFactory.hpp"
43#include "DistributedTetrahedralMesh.hpp"
44#include "Warnings.hpp"
45
46template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
48 const std::string& rFileBaseName,
50 : AbstractHdf5Converter<ELEMENT_DIM,SPACE_DIM>(rInputDirectory, rFileBaseName, pMesh, "txt_output", 0u)
51{
52 // Make sure that we are never trying to write from an incomplete data HDF5 file
53 assert(this->mpReader->GetNumberOfRows() == pMesh->GetNumNodes());
54
55 FileFinder output_directory(this->mRelativeSubdirectory,rInputDirectory);
56 OutputFileHandler handler(output_directory);
57
58 unsigned num_nodes = pMesh->GetNumNodes();
59 unsigned num_timesteps = this->mpReader->GetUnlimitedDimensionValues().size();
60
62 Vec data = p_factory->CreateVec();
63 ReplicatableVector repl_data(num_nodes);
64
65 // Loop over time steps
66 for (unsigned time_step=0; time_step<num_timesteps; time_step++)
67 {
68 // Loop over variables
69 for (unsigned var_index=0; var_index<this->mNumVariables; var_index++)
70 {
71 std::string variable_name = this->mpReader->GetVariableNames()[var_index];
72
73 // Create a .txt file for this time step and this variable
74 std::stringstream file_name;
75 file_name << rFileBaseName << "_" << variable_name << "_" << time_step << ".txt";
76 out_stream p_file = handler.OpenOutputFile(file_name.str());
77
78 this->mpReader->GetVariableOverNodes(data, variable_name, time_step);
79 repl_data.ReplicatePetscVector(data);
80
81 assert(repl_data.GetSize() == num_nodes);
82
84 {
85 for (unsigned i=0; i<num_nodes; i++)
86 {
87 *p_file << repl_data[i] << "\n";
88 }
89 }
90 p_file->close();
91 }
92 }
93
94 // Tidy up
96}
97
98// Explicit instantiation
99template class Hdf5ToTxtConverter<1,1>;
100template class Hdf5ToTxtConverter<1,2>;
101template class Hdf5ToTxtConverter<2,2>;
102template class Hdf5ToTxtConverter<1,3>;
103template class Hdf5ToTxtConverter<2,3>;
104template class Hdf5ToTxtConverter<3,3>;
boost::shared_ptr< Hdf5DataReader > mpReader
virtual DistributedVectorFactory * GetDistributedVectorFactory()
virtual unsigned GetNumNodes() const
Hdf5ToTxtConverter(const FileFinder &rInputDirectory, const std::string &rFileBaseName, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)
out_stream OpenOutputFile(const std::string &rFileName, std::ios_base::openmode mode=std::ios::out|std::ios::trunc) const
static void Destroy(Vec &rVec)
static bool AmMaster()
void ReplicatePetscVector(Vec vec)