From c526c8b63d8f0653886f02adef2db85d68e4d951 Mon Sep 17 00:00:00 2001
From: Simon Praetorius <simon.praetorius@tu-dresden.de>
Date: Mon, 24 Jun 2019 12:42:39 +0200
Subject: [PATCH] add vtk sequence writer and modified the default filewriter
settings accordingly
---
src/amdis/CMakeLists.txt | 1 +
src/amdis/FileWriter.hpp | 13 +--
src/amdis/io/CMakeLists.txt | 3 +
src/amdis/io/VTKSequenceWriter.hpp | 154 +++++++++++++++++++++++++++++
4 files changed, 165 insertions(+), 6 deletions(-)
create mode 100644 src/amdis/io/CMakeLists.txt
create mode 100644 src/amdis/io/VTKSequenceWriter.hpp
diff --git a/src/amdis/CMakeLists.txt b/src/amdis/CMakeLists.txt
index 1237bbc9..261e70af 100644
--- a/src/amdis/CMakeLists.txt
+++ b/src/amdis/CMakeLists.txt
@@ -71,6 +71,7 @@ DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/amdis)
add_subdirectory("common")
add_subdirectory("functions")
add_subdirectory("gridfunctions")
+add_subdirectory("io")
add_subdirectory("linearalgebra")
add_subdirectory("localoperators")
add_subdirectory("operations")
diff --git a/src/amdis/FileWriter.hpp b/src/amdis/FileWriter.hpp
index d45a086e..50ee4bb5 100644
--- a/src/amdis/FileWriter.hpp
+++ b/src/amdis/FileWriter.hpp
@@ -5,8 +5,7 @@
#include <dune/functions/functionspacebases/lagrangebasis.hh>
#include <dune/grid/io/file/vtk/vtkwriter.hh>
-#include <dune/grid/io/file/vtk/vtksequencewriter.hh>
-//#include <dune/geometry/referenceelements.hh>
+#include <dune/grid/io/file/vtk/subsamplingvtkwriter.hh>
#include <dune/typetree/childextraction.hh>
#include <amdis/FileWriterInterface.hpp>
@@ -15,6 +14,7 @@
#include <amdis/common/StaticSize.hpp>
#include <amdis/common/ValueCategory.hpp>
#include <amdis/gridfunctions/DiscreteFunction.hpp>
+#include <amdis/io/VTKSequenceWriter.hpp>
namespace AMDiS
{
@@ -86,7 +86,7 @@ namespace AMDiS
vtkWriter_ = std::make_shared<Dune::VTKWriter<GridView>>(gridView());
if (animation_)
- vtkSeqWriter_ = std::make_shared<Dune::VTKSequenceWriter<GridView>>(vtkWriter_, filename_, dir_, "");
+ vtkSeqWriter_ = std::make_shared<VTKSequenceWriter<GridView>>(vtkWriter_);
vtkWriter_->addVertexData(discreteFct_, Dune::VTK::FieldInfo(name_, VTKFieldType<Range>, VTKFieldSize<Range>));
}
@@ -97,11 +97,12 @@ namespace AMDiS
void writeFiles(AdaptInfo& adaptInfo, bool force) override
{
test_exit(dir_ == "." || filesystem::exists(dir_), "Output directory '{}' does not exist!",dir_);
+ filesystem::create_directories(dir_ + "/_piecefiles");
if (vtkSeqWriter_)
- vtkSeqWriter_->write(adaptInfo.time(), mode_);
+ vtkSeqWriter_->pwrite(adaptInfo.time(), filename_, dir_, "_piecefiles", mode_);
else if (vtkWriter_)
- vtkWriter_->write(filesystem::path({dir_, filename_}).string(), mode_);
+ vtkWriter_->pwrite(filename_, dir_, "_piecefiles", mode_);
}
protected:
@@ -114,7 +115,7 @@ namespace AMDiS
DiscreteFunction<GB,VT,TP> discreteFct_;
std::shared_ptr<Dune::VTKWriter<GridView>> vtkWriter_;
- std::shared_ptr<Dune::VTKSequenceWriter<GridView>> vtkSeqWriter_;
+ std::shared_ptr<VTKSequenceWriter<GridView>> vtkSeqWriter_;
// write .pvd if animation=true, otherwise write only .vtu
bool animation_;
diff --git a/src/amdis/io/CMakeLists.txt b/src/amdis/io/CMakeLists.txt
new file mode 100644
index 00000000..09203370
--- /dev/null
+++ b/src/amdis/io/CMakeLists.txt
@@ -0,0 +1,3 @@
+install(FILES
+ VtkSequenceWriter.hpp
+DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/amdis/io)
diff --git a/src/amdis/io/VTKSequenceWriter.hpp b/src/amdis/io/VTKSequenceWriter.hpp
new file mode 100644
index 00000000..e8be67ce
--- /dev/null
+++ b/src/amdis/io/VTKSequenceWriter.hpp
@@ -0,0 +1,154 @@
+#pragma once
+
+#include <vector>
+#include <iostream>
+#include <sstream>
+#include <fstream>
+#include <iomanip>
+#include <memory>
+
+#include <dune/grid/io/file/vtk/common.hh>
+#include <dune/common/path.hh>
+
+#include <dune/grid/io/file/vtk/vtkwriter.hh>
+
+namespace AMDiS
+{
+ /// \brief class to write pvd-files which contains a list of all collected vtk-files
+ /**
+ * Write pvd-file suitable for easy visualization with
+ * <a href="http://www.vtk.org/">The Visualization Toolkit (VTK)</a>.
+ *
+ * \tparam GridView Grid view of the grid we are writing
+ */
+ template <class GridView>
+ class VTKSequenceWriter
+ {
+ using VTKWriter = Dune::VTKWriter<GridView>;
+
+ public:
+ /// \brief Set up the VTKSequenceWriter class
+ /**
+ * \param vtkWriter Writer object used to write the individual time step data files
+ */
+ VTKSequenceWriter(std::shared_ptr<VTKWriter> vtkWriter)
+ : vtkWriter_(std::move(vtkWriter))
+ {}
+
+ /// \brief Set up the VTKSequenceWriter class by creating a timestep writer of type \ref VTKWriter
+ /**
+ * \param gridView GridView object passed to the constructor of the VTKWriter
+ * \param args... Additional arguments forwarded to the VTKWriter constructor.
+ */
+ template <class... Args>
+ VTKSequenceWriter(GridView const& gridView, Args&&... args)
+ : VTKSequenceWriter<GridView>(std::make_shared<VTKWriter>(gridView, FWD(args)...))
+ {}
+
+
+ /// accessor for the underlying VTKWriter instance
+ std::shared_ptr<VTKWriter> const& vtkWriter() const
+ {
+ return vtkWriter_;
+ }
+
+ /// \brief Adds a field of cell data to the VTK file
+ template <class... Args>
+ void addCellData(Args&&... args)
+ {
+ vtkWriter_->addCellData(FWD(args)...);
+ }
+
+ /// \brief Adds a field of vertex data to the VTK file
+ template <class... Args>
+ void addVertexData (Args&&... args)
+ {
+ vtkWriter_->addVertexData(FWD(args)...);
+ }
+
+ /// \brief Writes VTK data for the given time,
+ /**
+ * \param time The time(step) for the data to be written.
+ * \param name The basename of the .pvd file (without file extension)
+ * \param type VTK output type.
+ */
+ virtual void write(double time, std::string const& name, Dune::VTK::OutputType type = Dune::VTK::ascii)
+ {
+ pwrite(time, name, ".", "", type);
+ }
+
+ /// \brief Writes VTK data for the given time,
+ /**
+ * \param time The time(step) for the data to be written.
+ * \param name The basename of the .pvd file (without file extension)
+ * \param path The directory where to put the .pvd file
+ * \param extendpath The (relative) subdirectory to path, where to put the timestep files
+ * \param type VTK output type.
+ */
+ virtual void pwrite(double time, std::string const& name, std::string const& path, std::string const& extendpath,
+ Dune::VTK::OutputType type = Dune::VTK::ascii)
+ {
+ // remember current time step
+ unsigned int count = timesteps_.size();
+ timesteps_.push_back(time);
+
+ // write VTK file
+ vtkWriter_->pwrite(seqName(name, count), Dune::concatPaths(path, extendpath), "", type);
+
+ // write pvd file ... only on rank 0
+ if (Environment::mpiRank() == 0) {
+ std::ofstream pvdFile;
+ pvdFile.exceptions(std::ios_base::badbit | std::ios_base::failbit |
+ std::ios_base::eofbit);
+ std::string pvdname = path + "/" + name + ".pvd";
+ pvdFile.open(pvdname.c_str());
+ pvdFile << "<?xml version=\"1.0\"?>\n"
+ << "<VTKFile type=\"Collection\" version=\"0.1\" byte_order=\"" << Dune::VTK::getEndiannessString() << "\">\n"
+ << "<Collection>\n";
+ for (unsigned int i = 0; i <= count; ++i) {
+ std::string piecepath = extendpath;
+ std::string fullname = getParallelHeaderName(seqName(name,i), piecepath, Environment::mpiSize());
+ pvdFile << "<DataSet timestep=\"" << timesteps_[i]
+ << "\" part=\"0\" file=\""
+ << fullname << "\"/>\n";
+ }
+ pvdFile << "</Collection>\n"
+ << "</VTKFile>\n" << std::flush;
+ pvdFile.close();
+ }
+ }
+
+ protected:
+ // create sequence name
+ static std::string seqName(std::string const& name, unsigned int count)
+ {
+ std::stringstream n;
+ n.fill('0');
+ n << name << "-" << std::setw(5) << count;
+ return n.str();
+ }
+
+ static std::string getParallelHeaderName(std::string const& name, std::string const& path, int commSize)
+ {
+ std::ostringstream s;
+ if (path.size() > 0) {
+ s << path;
+ if (path[path.size()-1] != '/')
+ s << '/';
+ }
+ s << 's' << std::setw(4) << std::setfill('0') << commSize << '-';
+ s << name;
+ if (GridView::dimension > 1)
+ s << ".pvtu";
+ else
+ s << ".pvtp";
+ return s.str();
+ }
+
+ private:
+ std::shared_ptr<VTKWriter> vtkWriter_;
+ std::vector<double> timesteps_;
+ };
+
+} // end namespace AMDiS
+
--
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