Chaste  Release::3.4
Hdf5ToTxtConverter.cpp
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35 
36 #include "UblasCustomFunctions.hpp"
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 
46 template <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
95  PetscTools::Destroy(data);
96 }
97 
99 // Explicit instantiation
101 
102 template class Hdf5ToTxtConverter<1,1>;
103 template class Hdf5ToTxtConverter<1,2>;
104 template class Hdf5ToTxtConverter<2,2>;
105 template class Hdf5ToTxtConverter<1,3>;
106 template class Hdf5ToTxtConverter<2,3>;
107 template class Hdf5ToTxtConverter<3,3>;
virtual DistributedVectorFactory * GetDistributedVectorFactory()
boost::shared_ptr< Hdf5DataReader > mpReader
static bool AmMaster()
Definition: PetscTools.cpp:120
virtual unsigned GetNumNodes() const
out_stream OpenOutputFile(const std::string &rFileName, std::ios_base::openmode mode=std::ios::out|std::ios::trunc) const
static void Destroy(Vec &rVec)
Definition: PetscTools.hpp:351
void ReplicatePetscVector(Vec vec)
Hdf5ToTxtConverter(const FileFinder &rInputDirectory, const std::string &rFileBaseName, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)