Merge branch 'feature/vtk_writer' into 'master'

Filewriter abstraction

See merge request !61

dune.module

@@ -6,4 +6,4 @@ Module: amdis
 Version: 0.2
 Maintainer: simon.praetorius@tu-dresden.de
 Depends: dune-common (>= 2.6) dune-geometry (>= 2.6) dune-localfunctions (>= 2.6) dune-typetree (>= 2.6) dune-grid (>= 2.6) dune-functions (>= 2.6)
-Suggests: dune-uggrid dune-alugrid dune-foamgrid dune-spgrid dune-istl
+Suggests: dune-uggrid dune-alugrid dune-foamgrid dune-spgrid dune-istl dune-vtk

examples/boundary.cc

@@ -89,7 +89,7 @@ void run_periodic()
 
   prob.assemble(adaptInfo);
   prob.solve(adaptInfo);
-  prob.writeFiles(adaptInfo, true);
+  prob.writeFiles(adaptInfo);
 }
 
 

examples/convection_diffusion.cc

@@ -37,7 +37,7 @@ int main(int argc, char** argv)
   AdaptInfo adaptInfo("adapt");
   prob.assemble(adaptInfo);
   prob.solve(adaptInfo);
-  prob.writeFiles(adaptInfo, true);
+  prob.writeFiles(adaptInfo);
 
   return 0;
 }

examples/ellipt.cc

@@ -69,14 +69,11 @@ int main(int argc, char** argv)
     errL2.push_back(std::sqrt(errorL2));
     double errorH1 = errorL2 + integrate(unary_dot(grad_g - gradientAtQP(prob.solution(0))), prob.gridView(), 6);
     errH1.push_back(std::sqrt(errorH1));
-
-#if WRITE_FILES
-    Dune::VTKWriter<typename ElliptProblem::GridView> vtkWriter(gridView);
-    vtkWriter.addVertexData(prob.solution(0), Dune::VTK::FieldInfo("u", Dune::VTK::FieldInfo::Type::scalar, 1));
-    vtkWriter.write("u_" + std::to_string(l));
-#endif
   }
 
+  // write last solution to file
+  prob.writeFiles(adaptInfo);
+
   msg("");
   msg("{:5} | {:12} | {:12} | {:12} | {:12} | {:12}",
       "level", "h", "|u - u*|_L2","|u - u*|_H1","eoc_L2","eoc_H1");

examples/init/boundary.dat.2d

@@ -8,6 +8,7 @@ ellipt->solver->relative tolerance: 1.e-10
 ellipt->solver->info:           1
 ellipt->solver->precon:         ilu
 
+ellipt->output[0]->format:      vtk
 ellipt->output[0]->filename:    boundary.2d
 ellipt->output[0]->name:        u
 ellipt->output[0]->output directory: ./output

examples/init/cahn_hilliard.dat.2d

@@ -18,19 +18,19 @@ ch->solver->relative tolerance: 1e-6
 ch->solver->break if tolerance not reached: 1
 ch->solver->info: 2
 
+ch->output[0]->format:             vtk
 ch->output[0]->filename:           phi.2d
 ch->output[0]->output directory:   output
 ch->output[0]->name:               phi
-ch->output[0]->ParaView format:    1
-ch->output[0]->ParaView mode:      1
-ch->output[0]->ParaView animation: 1
+ch->output[0]->mode:               1
+ch->output[0]->animation:          1
 
+ch->output[1]->format:             vtk
 ch->output[1]->filename:           mu.2d
 ch->output[1]->output directory:   output
 ch->output[1]->name:               mu
-ch->output[1]->ParaView format:    1
-ch->output[1]->ParaView mode:      1
-ch->output[1]->ParaView animation: 1
+ch->output[1]->mode:               1
+ch->output[1]->animation:          1
 
 adapt->timestep:    0.001
 adapt->start time:  0.0

examples/init/ellipt.dat.2d

@@ -13,6 +13,7 @@ ellipt->solver->max iteration: 10000
 ellipt->solver->relative tolerance: 1.e-10
 ellipt->solver->precon: ilu
 
+ellipt->output[0]->format: vtk backup
 ellipt->output[0]->filename: ellipt.2d
 ellipt->output[0]->name: u
 ellipt->output[0]->output directory: ./output

examples/init/ellipt.dat.3d

@@ -13,6 +13,7 @@ ellipt->solver->max iteration: 10000
 ellipt->solver->relative tolerance: 1.e-10
 ellipt->solver->precon: ilu
 
+ellipt->output[0]->format: vtk
 ellipt->output[0]->filename: ellipt.3d
 ellipt->output[0]->name: u
 ellipt->output[0]->output directory: ./output

examples/init/heat.dat.2d

@@ -12,10 +12,12 @@ heat->solver->absolute tolerance: 1e-6
 heat->solver->info: 1
 heat->solver->precon: ilu
 
+heat->output[0]->format: vtk backup
+heat->output[0]->name: u
 heat->output[0]->filename: heat.2d
 heat->output[0]->output directory: output
-heat->output[0]->ParaView mode: 1
-heat->output[0]->ParaView animation: 1
+heat->output[0]->mode: 1
+heat->output[0]->animation: 1
 
 adapt->timestep:    0.1
 adapt->start time:  0.0

examples/init/stokes.dat.2d

@@ -10,18 +10,18 @@ stokes->solver->relative tolerance: 1e-8
 stokes->solver->precon: ilu
 stokes->solver->info:	2
 
+stokes->output[0]->format: vtk
 stokes->output[0]->filename: stokes_u.2d
 stokes->output[0]->name: u
 stokes->output[0]->subsampling: 2
 stokes->output[0]->output directory: ./output
-stokes->output[0]->ParaView format: 1
-stokes->output[0]->ParaView mode: 1
+stokes->output[0]->mode: 1
 
+stokes->output[1]->format: vtk
 stokes->output[1]->filename: stokes_p.2d
 stokes->output[1]->name: p
 stokes->output[1]->output directory: ./output
-stokes->output[1]->ParaView format: 1
-stokes->output[1]->ParaView mode: 1
+stokes->output[1]->mode: 1
 
 stokes->viscosity: 1.0
 stokes->density: 1.0

examples/init/surface.dat.2d

@@ -9,6 +9,7 @@ surface->solver->relative tolerance: 1.e-6
 surface->solver->info:           1
 surface->solver->precon:         ilu
 
+surface->output[0]->format:      vtk
 surface->output[0]->filename:    surface.2d
 surface->output[0]->name:        u
 surface->output[0]->output directory: ./output

examples/neumann.cc

@@ -45,7 +45,7 @@ void run(Grid& grid)
 
   prob.assemble(adaptInfo);
   prob.solve(adaptInfo);
-  prob.writeFiles(adaptInfo, true);
+  prob.writeFiles(adaptInfo);
 }
 
 

examples/vecellipt.cc

@@ -51,7 +51,7 @@ int main(int argc, char** argv)
 #endif
 
   prob.solve(adaptInfo);
-  prob.writeFiles(adaptInfo, true);
+  prob.writeFiles(adaptInfo);
 
   return 0;
 }

src/amdis/AdaptInfo.hpp

@@ -733,10 +733,10 @@ namespace AMDiS
     double lastProcessedTimestep_ = 0.0;
 
     /// Minimal step size
-    double minTimestep_ = 0.0;
+    double minTimestep_ = std::sqrt(std::numeric_limits<double>::epsilon());
 
     /// Maximal step size
-    double maxTimestep_ = 1.0;
+    double maxTimestep_ = std::sqrt(std::numeric_limits<double>::max());
 
     /// Number of current time step
     int timestepNumber_ = 0;

src/amdis/BoundaryManager.hpp

@@ -25,6 +25,11 @@ namespace AMDiS
       return boundaryIds_[intersection.boundarySegmentIndex()];
     }
 
+    std::vector<BoundaryType> const boundaryIds() const
+    {
+      return boundaryIds_;
+    }
+
   protected:
     std::vector<BoundaryType> boundaryIds_; // maps a boundarySegementIndex to an ID
   };

src/amdis/CMakeLists.txt

@@ -39,8 +39,6 @@ install(FILES
     DOFVector.inc.hpp
     DOFVectorInterface.hpp
     Environment.hpp
-    FileWriter.hpp
-    FileWriterInterface.hpp
     Flag.hpp
     GridFunctionOperator.hpp
     GridFunctions.hpp

src/amdis/FileWriterInterface.hpp

-#pragma once
-
-#include <string>
-
-#include <amdis/Initfile.hpp>
-#include <amdis/Output.hpp>
-#include <amdis/common/Filesystem.hpp>
-
-namespace AMDiS
-{
-  // forward declaration
-  class AdaptInfo;
-
-  class FileWriterInterface
-  {
-  public:
-    explicit FileWriterInterface(std::string const& base)
-    {
-      Parameters::get(base + "->filename", filename_);
-      Parameters::get(base + "->output directory", dir_);
-      Parameters::get(base + "->name", name_);
-    }
-
-    virtual ~FileWriterInterface() = default;
-
-
-    // pure virtual method to be implemented by derived classes
-    virtual void writeFiles(AdaptInfo& adaptInfo, bool force) = 0;
-
-  public: // getter and setter
-
-    std::string const& filename() const
-    {
-      return filename_;
-    }
-
-    std::string const& dir() const
-    {
-      return dir_;
-    }
-
-    std::string const& name() const
-    {
-      return name_;
-    }
-
-    void setFilename(std::string const& filename)
-    {
-      filename_ = filename;
-    }
-
-    void setDir(std::string const& dir)
-    {
-      dir_ = dir;
-    }
-
-    void setName(std::string const& name)
-    {
-      name_ = name;
-    }
-
-  protected:
-    std::string filename_ = "solution";
-    std::string dir_ = ".";
-    std::string name_ = "solution";
-  };
-
-} // end namespace AMDiS

src/amdis/ProblemStat.hpp

@@ -37,7 +37,7 @@
 #include <amdis/gridfunctions/DiscreteFunction.hpp>
 #include <amdis/gridfunctions/DOFVectorView.hpp>
 
-#include <amdis/FileWriterInterface.hpp>
+#include <amdis/io/FileWriterBase.hpp>
 
 #include <amdis/typetree/TreeData.hpp>
 #include <amdis/typetree/TreePath.hpp>
@@ -106,14 +106,21 @@ namespace AMDiS
     }
 
 
+    /// \brief Initialisation of the problem.
     /**
-     * \brief Initialisation of the problem.
-     *
-     * Parameters read in initialize() for problem with name 'PROB'
-     *   MESH[0]->global refinements:  nr of initial global refinements
+     * Parameters read in initialize()
+     *   - `[GRID_NAME]->global refinements`:  nr of initial global refinements
      **/
     void initialize(Flag initFlag, Self* adoptProblem = nullptr, Flag adoptFlag = INIT_NOTHING);
 
+    /// \brief Read the grid and solution from backup files and initialize the problem
+    /**
+     * Parameters read in restore() for problem with name 'PROB'
+     *   - `[PROB]->restore->grid`:      name of the grid backup file
+     *   - `[PROB]->restore->solution`:  name of the solution backup file
+     **/
+    void restore(Flag initFlag);
+
 
     /// Add an operator to \ref A.
     /** @{ */
@@ -296,21 +303,9 @@ namespace AMDiS
     /// Uniform global refinement by n level
     Flag globalRefine(int n) override;
 
-    /// Writes output files.
+    /// Writes output files. If force=true write even if timestep out of write rhythm.
     void writeFiles(AdaptInfo& adaptInfo, bool force = false);
 
-    /// Backup the grid
-    void backup(std::string const& filename) const;
-
-    /// Implements \ref ProblemStatBase::backup
-    void backup(AdaptInfo& adaptInfo) override;
-
-    /// Retore the grid
-    auto restore(std::string const& filename);
-
-    /// Implements \ref ProblemStatBase::restore
-    void restore(Flag initFlag) override;
-
 
   public: // get-methods
 

src/amdis/ProblemStat.inc.hpp

@@ -12,10 +12,10 @@
 
 #include <amdis/AdaptInfo.hpp>
 #include <amdis/BackupRestore.hpp>
-#include <amdis/FileWriter.hpp>
 #include <amdis/Assembler.hpp>
 #include <amdis/GridFunctionOperator.hpp>
 #include <amdis/GridTransferManager.hpp>
+#include <amdis/io/FileWriterCreator.hpp>
 #include <amdis/linearalgebra/SymmetryStructure.hpp>
 
 namespace AMDiS {
@@ -131,6 +131,48 @@ void ProblemStat<Traits>::initialize(
 }
 
 
+template <class Traits>
+void ProblemStat<Traits>::
+restore(Flag initFlag)
+{
+  std::string grid_filename = Parameters::get<std::string>(name_ + "->restore->grid").value();
+  std::string solution_filename = Parameters::get<std::string>(name_ + "->restore->solution").value();
+  test_exit(filesystem::exists(grid_filename), "Restore file '{}' not found.", grid_filename);
+  test_exit(filesystem::exists(solution_filename), "Restore file '{}' not found.", solution_filename);
+
+  // restore grid from file
+  if (Dune::Capabilities::hasBackupRestoreFacilities<Grid>::v)
+    adoptGrid(std::unique_ptr<Grid>(Dune::BackupRestoreFacility<Grid>::restore(grid_filename)));
+  else
+    adoptGrid(std::unique_ptr<Grid>(BackupRestoreByGridFactory<Grid>::restore(grid_filename)));
+
+  // create fespace
+  if (initFlag.isSet(INIT_FE_SPACE) || initFlag.isSet(INIT_SYSTEM))
+    createGlobalBasis();
+
+  // create system
+  if (initFlag.isSet(INIT_SYSTEM))
+    createMatricesAndVectors();
+
+  // create solver
+  if (linearSolver_)
+    warning("solver already created\n");
+  else if (initFlag.isSet(INIT_SOLVER))
+    createSolver();
+
+  // create marker
+  if (initFlag.isSet(INIT_MARKER))
+    createMarker();
+
+  // create file writer
+  if (initFlag.isSet(INIT_FILEWRITER))
+    createFileWriter();
+
+  solution_->resize();
+  solution_->restore(solution_filename);
+}
+
+
 template <class Traits>
 void ProblemStat<Traits>::createGrid()
 {
@@ -256,17 +298,29 @@ void ProblemStat<Traits>::createMarker()
 template <class Traits>
 void ProblemStat<Traits>::createFileWriter()
 {
+  FileWriterCreator<CoefficientVector> creator(solution_, boundaryManager_);
+
   filewriter_.clear();
   auto localView = globalBasis_->localView();
-  for_each_node(localView.tree(), [&,this](auto const& node, auto treePath) -> void
+  for_each_node(localView.tree(), [&](auto const& /*node*/, auto treePath) -> void
   {
     std::string componentName = name_ + "->output[" + to_string(treePath) + "]";
+    auto format = Parameters::get<std::vector<std::string>>(componentName + "->format");
+
+    if (!format && to_string(treePath).empty()) {
+      // alternative for root treepath
+      componentName = name_ + "->output";
+      format = Parameters::get<std::vector<std::string>>(componentName + "->format");
+    }
 
-    if (!Parameters::get<std::string>(componentName + "->filename"))
+    if (!format)
       return;
 
-    auto writer = makeFileWriterPtr(componentName, this->solution(treePath));
-    filewriter_.push_back(std::move(writer));
+    for (std::string const& type : format.value()) {
+      auto writer = creator.create(type, componentName, treePath);
+      if (writer)
+        filewriter_.push_back(std::move(writer));
+    }
   });
 }
 
@@ -518,112 +572,8 @@ writeFiles(AdaptInfo& adaptInfo, bool force)
 {
   Dune::Timer t;
   for (auto writer : filewriter_)
-    writer->writeFiles(adaptInfo, force);
+    writer->write(adaptInfo, force);
   msg("writeFiles needed {} seconds", t.elapsed());
 }
 
-
-template <class Grid, class GridView,
-  class = decltype(Dune::BackupRestoreFacility<Grid>::backup(std::declval<Grid>(), std::string("")))>
-void backup_impl(Grid const& grid, GridView const& gv, std::string filename, std::true_type)
-{
-  Dune::BackupRestoreFacility<Grid>::backup(grid, filename);
-}
-
-template <class Grid, class GridView, bool B,
-  class = decltype(BackupRestoreByGridFactory<Grid>::backup(std::declval<GridView>(), std::string("")))>
-void backup_impl(Grid const& grid, GridView const& gv, std::string filename, bool_t<B>)
-{
-  warning("Falling back to backup of gridview.");
-  BackupRestoreByGridFactory<Grid>::backup(gv, filename);
-}
-
-template <class Traits>
-void ProblemStat<Traits>::
-backup(std::string const& filename) const
-{
-  backup_impl(*grid_, gridView(), filename, bool_t<Dune::Capabilities::hasBackupRestoreFacilities<Grid>::v>{});
-}
-
-
-template <class Traits>
-void ProblemStat<Traits>::
-backup(AdaptInfo& adaptInfo)
-{
-  auto param = Parameters::get<std::string>(name_ + "->backup->grid");
-  std::string grid_filename = param ? *param :
-    name_ + "_" + std::to_string(adaptInfo.timestepNumber()) + ".grid";
-
-  auto param2 = Parameters::get<std::string>(name_ + "->backup->solution");
-  std::string solution_filename = param2 ? *param2 :
-    name_ + "_" + std::to_string(adaptInfo.timestepNumber()) + ".solution";
-
-  backup(grid_filename);
-  solution_->backup(solution_filename);
-  msg("Problem backuped to files '{}' and '{}'.", grid_filename, solution_filename);
-}
-
-
-template <class Grid,
-  class = decltype(Dune::BackupRestoreFacility<Grid>::restore(std::string("")))>
-auto restore_impl(std::string filename, std::true_type)
-{
-  return Dune::BackupRestoreFacility<Grid>::restore(filename);
-}
-
-template <class Grid, bool B,
-  class = decltype(BackupRestoreByGridFactory<Grid>::restore(std::string("")))>
-auto restore_impl(std::string filename, bool_t<B>)
-{
-  return BackupRestoreByGridFactory<Grid>::restore(filename);
-}
-
-template <class Traits>
-auto ProblemStat<Traits>::
-restore(std::string const& filename)
-{
-  // restore grid from file
-  std::unique_ptr<Grid> grid(restore_impl<Grid>(filename, bool_t<Dune::Capabilities::hasBackupRestoreFacilities<Grid>::v>{}));
-  return std::move(grid);
-}
-
-
-template <class Traits>
-void ProblemStat<Traits>::
-restore(Flag initFlag)
-{
-  std::string grid_filename = Parameters::get<std::string>(name_ + "->restore->grid").value();
-  std::string solution_filename = Parameters::get<std::string>(name_ + "->restore->solution").value();
-  test_exit(filesystem::exists(grid_filename), "Restore file '{}' not found.", grid_filename);
-  test_exit(filesystem::exists(solution_filename), "Restore file '{}' not found.", solution_filename);
-
-  // restore grid from file
-  adoptGrid(restore(grid_filename));
-
-  // create fespace
-  if (initFlag.isSet(INIT_FE_SPACE) || initFlag.isSet(INIT_SYSTEM))
-    createGlobalBasis();
-
-  // create system
-  if (initFlag.isSet(INIT_SYSTEM))
-    createMatricesAndVectors();
-
-  // create solver
-  if (linearSolver_)
-    warning("solver already created\n");
-  else if (initFlag.isSet(INIT_SOLVER))
-    createSolver();
-
-  // create marker
-  if (initFlag.isSet(INIT_MARKER))
-    createMarker();
-
-  // create file writer
-  if (initFlag.isSet(INIT_FILEWRITER))
-    createFileWriter();
-
-  solution_->resizeZero();
-  solution_->restore(solution_filename);
-}
-
 } // end namespace AMDiS

src/amdis/ProblemStatBase.hpp

@@ -111,12 +111,6 @@ namespace AMDiS
      */
     virtual void estimate(AdaptInfo& adaptInfo) = 0;
 
-    /// \brief backup the grid and the solution to a file
-    virtual void backup(AdaptInfo& adaptInfo) = 0;
-
-    /// \brief restore the grid and the solution from a file
-    virtual void restore(Flag initFlag) = 0;
-
     /// Returns the name of the problem.
     virtual std::string const& name() const = 0;
   };