vtk_export_ho.h

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/*
 * Copyright (c) 2010-2015:  G-CSC, Goethe University Frankfurt
 * Author: Markus Breit
 *
 * This file is part of UG4.
 *
 * UG4 is free software: you can redistribute it and/or modify it under the
 * terms of the GNU Lesser General Public License version 3 (as published by the
 * Free Software Foundation) with the following additional attribution
 * requirements (according to LGPL/GPL v3 §7):
 *
 * (1) The following notice must be displayed in the Appropriate Legal Notices
 * of covered and combined works: "Based on UG4 (www.ug4.org/license)".
 *
 * (2) The following notice must be displayed at a prominent place in the
 * terminal output of covered works: "Based on UG4 (www.ug4.org/license)".
 *
 * (3) The following bibliography is recommended for citation and must be
 * preserved in all covered files:
 * "Reiter, S., Vogel, A., Heppner, I., Rupp, M., and Wittum, G. A massively
 *   parallel geometric multigrid solver on hierarchically distributed grids.
 *   Computing and visualization in science 16, 4 (2013), 151-164"
 * "Vogel, A., Reiter, S., Rupp, M., Nägel, A., and Wittum, G. UG4 -- a novel
 *   flexible software system for simulating pde based models on high performance
 *   computers. Computing and visualization in science 16, 4 (2013), 165-179"
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU Lesser General Public License for more details.
 */
 
#ifndef __H__UG__LIB_DISC__IO__VTK_EXPORT_HO__
#define __H__UG__LIB_DISC__IO__VTK_EXPORT_HO__
 
#include <cmath>                                                                   // for ceil, log2
#include <cstddef>                                                                 // for size_t
#include <limits>                                                                  // for numeric_limits
#include <ostream>                                                                 // for string, operator<<, basic_ostream, endl
#include <string>                                                                  // for char_traits, allocator, operator+, basic_string
#include <vector>                                                                  // for vector
 
#include "common/assert.h"                                                         // for UG_ASSERT
#include "common/error.h"                                                          // for UG_CATCH_THROW, UG_COND_THROW
#include "common/types.h"                                                          // for number
#include "common/math/math_vector_matrix/math_vector.h"                            // for MathVector
#include "common/util/smart_pointer.h"                                             // for SmartPtr, ConstSmartPtr, make_sp
#include "lib_disc/common/function_group.h"                                        // for FunctionGroup
#include "lib_disc/common/multi_index.h"                                           // for DoFIndex, DoFRef
#include "lib_disc/dof_manager/dof_distribution.h"                                 // for DoFDistribution, DoFDistribution::traits
#include "lib_disc/function_spaces/dof_position_util.h"                            // for InnerDoFPosition
#include "lib_disc/function_spaces/grid_function_global_user_data.h"               // for GlobalGridFunctionNumberData
#include "lib_disc/io/vtkoutput.h"                                                 // for VTKOutput
#include "lib_disc/local_finite_element/local_finite_element_id.h"                 // for LFEID
#include "lib_grid/algorithms/debug_util.h"                                        // for ElementDebugInfo
#include "lib_grid/algorithms/selection_util.h"                                     // for SelectAssociatedGridObjects
#include "lib_grid/attachments/attachment_pipe.h"                                  // for AttachmentAccessor
#include "lib_grid/common_attachments.h"                                           // for AVertex
#include "lib_grid/grid/grid.h"                                                    // for Grid::VertexAttachmentAccessor::VertexAttachmentAccessor<TAt...
#include "lib_grid/grid/grid_base_object_traits.h"                                 // for VertexIterator
#include "lib_grid/grid/grid_base_objects.h"                                       // for CustomVertexGroup, Vertex, Edge (ptr only), Face (ptr only)
#ifdef UG_PARALLEL
  #include "lib_grid/parallelization/parallel_refinement/parallel_refinement.h"  // for ParallelGlobalRefiner_MultiGrid
#else
  #include "lib_grid/refinement/global_multi_grid_refiner.h"                     // for GlobalMultiGridRefiner
#endif
#include "lib_grid/multi_grid.h"                                                   // for MultiGrid
#include "lib_grid/tools/selector_grid.h"                                          // for Selector
#include "lib_grid/tools/subset_group.h"                                           // for SubsetGroup
 
 
namespace ug {
 
 
template <typename TDomain, class TElem>
inline void CopySelectedElements
(
  SmartPtr<TDomain> destDom,
  SmartPtr<TDomain> srcDom,
  Selector& sel,
  AVertex& aNewVrt
)
{
  typedef typename TDomain::subset_handler_type SH_type;
 
  MultiGrid& srcGrid = *srcDom->grid();
  MultiGrid& destGrid = *destDom->grid();
 
  ConstSmartPtr<SH_type> srcSH = srcDom->subset_handler();
  SmartPtr<SH_type> destSH = destDom->subset_handler();
 
  Grid::VertexAttachmentAccessor<AVertex> aaNewVrt(srcGrid, aNewVrt);
 
  CustomVertexGroup vrts;
  typedef typename Grid::traits<TElem>::iterator iter_t;
 
  for (iter_t eiter = sel.begin<TElem>(); eiter != sel.end<TElem>(); ++eiter)
  {
    TElem* e = *eiter;
    vrts.resize(e->num_vertices());
    for (size_t iv = 0; iv < e->num_vertices(); ++iv)
      vrts.set_vertex(iv, aaNewVrt[e->vertex(iv)]);
 
    TElem* ne;
    try {ne = *destGrid.create_by_cloning(e, vrts);}
    UG_CATCH_THROW("New element could not be created.");
    destSH->assign_subset(ne, srcSH->get_subset_index(e));
  }
}
inline void CopySelectedElements {…}
 
template <typename TDomain>
inline void CopySelected
(
  SmartPtr<TDomain> destDom,
  SmartPtr<TDomain> srcDom,
  Selector& sel
)
{
  typedef typename TDomain::position_attachment_type APos_type;
  typedef typename TDomain::subset_handler_type SH_type;
 
  MultiGrid& srcGrid = *srcDom->grid();
  MultiGrid& destGrid = *destDom->grid();
 
  ConstSmartPtr<SH_type> srcSH = srcDom->subset_handler();
  SmartPtr<SH_type> destSH = destDom->subset_handler();
 
  APos_type& aPos = srcDom->position_attachment();
  UG_COND_THROW(!srcGrid.has_vertex_attachment(aPos), "Position attachment required.");
  Grid::VertexAttachmentAccessor<APos_type> aaPosSrc(srcGrid, aPos);
  if (!destGrid.has_vertex_attachment(aPos))
    destGrid.attach_to_vertices(aPos);
  Grid::VertexAttachmentAccessor<APos_type> aaPosDest(destGrid, aPos);
 
  AVertex aNewVrt;
  srcGrid.attach_to_vertices(aNewVrt);
  Grid::VertexAttachmentAccessor<AVertex> aaNewVrt(srcGrid, aNewVrt);
 
  for (int si = destSH->num_subsets(); si < srcSH->num_subsets(); ++si)
    destSH->subset_info(si) = srcSH->subset_info(si);
 
  SelectAssociatedGridObjects(sel);
 
  // create new vertices in destGrid
  for (VertexIterator viter = sel.begin<Vertex>(); viter != sel.end<Vertex>(); ++viter)
  {
    Vertex* v = *viter;
    Vertex* nv;
    try {nv = *destGrid.create_by_cloning(v);}
    UG_CATCH_THROW("New vertex could not be created.");
    aaNewVrt[v] = nv;
    aaPosDest[nv] = aaPosSrc[v];
    destSH->assign_subset(nv, srcSH->get_subset_index(v));
  }
 
  CopySelectedElements<TDomain,Edge>(destDom, srcDom, sel, aNewVrt);
  CopySelectedElements<TDomain,Face>(destDom, srcDom, sel, aNewVrt);
  CopySelectedElements<TDomain,Volume>(destDom, srcDom, sel, aNewVrt);
 
  srcGrid.detach_from_vertices(aNewVrt);
}
inline void CopySelected {…}
 
 
template <typename TElem, typename TGridFunction, typename TGGFND>
inline void interpolate_from_original_fct
(
  SmartPtr<TGridFunction> u_new,
  const TGGFND& u_orig,
  size_t fct,
  const LFEID& lfeid
)
{
  typedef typename TGridFunction::domain_type dom_type;
  static const int dim = dom_type::dim;
  typedef typename DoFDistribution::traits<TElem>::const_iterator const_iter_type;
 
  // interpolate subset-wise
  size_t numSubsets = u_new->num_subsets();
  for (size_t si = 0; si < numSubsets; ++si)
  {
    if (!u_new->is_def_in_subset(fct, si)) continue;
 
    const_iter_type elem_iter = u_new->template begin<TElem>(si);
    const_iter_type iterEnd = u_new->template end<TElem>(si);
 
    std::vector<DoFIndex> ind;
    for (; elem_iter != iterEnd; ++elem_iter)
    {
      u_new->inner_dof_indices(*elem_iter, fct, ind);
 
      // get dof positions
      std::vector<MathVector<dim> > globPos;
      InnerDoFPosition<dom_type>(globPos, *elem_iter, *u_new->domain(), lfeid);
 
      UG_ASSERT(globPos.size() == ind.size(),
        "#DoF mismatch: InnerDoFPosition() found " << globPos.size()
        << ", but grid function has " << ind.size() << std::endl
        << "on " << ElementDebugInfo(*u_new->domain()->grid(), *elem_iter) << ".");
 
      // write values in new grid function
      for (size_t dof = 0; dof < ind.size(); ++dof)
      {
        if (!u_orig.evaluate(DoFRef(*u_new, ind[dof]), globPos[dof]))
        {
          DoFRef(*u_new, ind[dof]) = std::numeric_limits<number>::quiet_NaN();
          //UG_THROW("Interpolation onto new grid did not succeed.\n"
          //     "DoF with coords " << globPos[dof] << " is out of range.");
        }
      }
    }
  }
}
inline void interpolate_from_original_fct {…}
 
 
template <typename TGridFunction, int trueDim>
void vtk_export_ho
(
  SmartPtr<TGridFunction> u,
  const std::vector<std::string>& vFct,
  size_t order,
  SmartPtr<VTKOutput<TGridFunction::domain_type::dim> > vtkOutput,
  const char* filename,
  size_t step,
  number time,
  const SubsetGroup& ssg
)
{
  // for order 1, use the given grid function as is
  if (order == 1)
  {
    // print out new grid function on desired subsets
    bool printAll = ssg.size() == (size_t) u->subset_handler()->num_subsets();
    if (printAll)
      vtkOutput->print(filename, *u, step, time);
    else
    {
      for (size_t s = 0; s < ssg.size(); ++s)
        vtkOutput->print_subset(filename, *u, ssg[s], step, time);
    }
 
    return;
  }
 
  typedef typename TGridFunction::domain_type dom_type;
  typedef typename TGridFunction::algebra_type algebra_type;
  typedef typename dom_type::position_attachment_type position_attachment_type;
  typedef typename TGridFunction::approximation_space_type approx_space_type;
  typedef typename TGridFunction::template dim_traits<trueDim>::grid_base_object elem_type;
 
  SmartPtr<approx_space_type> srcApproxSpace = u->approx_space();
  SmartPtr<dom_type> srcDom = srcApproxSpace->domain();
 
  // select surface elements in old grid
  MultiGrid& srcGrid = *srcDom->grid();
  Selector srcSel(srcGrid);
  srcSel.select(u->template begin<elem_type>(), u->template end<elem_type>());
 
  // create new domain
  dom_type* dom_ptr;
  try {dom_ptr = new dom_type();}
  UG_CATCH_THROW("Temporary domain could not be created.");
  SmartPtr<dom_type> destDom = make_sp(dom_ptr);
 
  // copy grid from old domain to new domain (into a flat grid!)
  try {CopySelected(destDom, srcDom, srcSel);}
  UG_CATCH_THROW("Temporary grid could not be created.");
 
  // refine
#ifdef UG_PARALLEL
  ParallelGlobalRefiner_MultiGrid refiner(*destDom->distributed_grid_manager());
#else
  MultiGrid& destGrid = *destDom->grid();
  GlobalMultiGridRefiner refiner(destGrid);
#endif
  size_t numRefs = (size_t) ceil(log2(order));
  for (size_t iref = 0; iref < numRefs; ++iref)
  {
    try {refiner.refine();}
    UG_CATCH_THROW("Refinement step " << iref << " could not be carried out.");
  }
 
  // retain function group for functions being exported
  FunctionGroup fg(srcApproxSpace->dof_distribution_info(), vFct);
 
  // create approx space and add functions
  approx_space_type* approx_ptr;
  try {approx_ptr = new approx_space_type(destDom, algebra_type::get_type());}
  UG_CATCH_THROW("Temporary approximation space could not be created.");
  SmartPtr<approx_space_type> destApproxSpace = make_sp(approx_ptr);
 
  for (size_t fct = 0; fct < fg.size(); ++fct)
  {
    if (fg.function_pattern()->is_def_everywhere(fg.unique_id(fct)))
      destApproxSpace->add(fg.name(fct), "Lagrange", 1);
    else
    {
      int num_subsets = fg.function_pattern()->num_subsets();
      std::string subsets;
      for (int si = 0; si < num_subsets; ++si)
      {
        if (fg.function_pattern()->is_def_in_subset(fct, si))
          subsets += std::string(",") + fg.function_pattern()->subset_name(si);
      }
      if (!subsets.empty())
        subsets.erase(0,1); // delete leading ","
 
      destApproxSpace->add(fg.name(fct), "Lagrange", 1, subsets.c_str());
    }
  }
  destApproxSpace->init_top_surface();
 
  TGridFunction* gridFct_ptr;
  try {gridFct_ptr = new TGridFunction(destApproxSpace);}
  UG_CATCH_THROW("Temporary grid function could not be created.");
  SmartPtr<TGridFunction> u_new = make_sp(gridFct_ptr);
 
  // interpolate onto new grid
  for (size_t fct = 0; fct < fg.size(); ++fct)
  {
    const LFEID lfeid = u_new->dof_distribution()->lfeid(fct);
 
    GlobalGridFunctionNumberData<TGridFunction, trueDim> ggfnd =
      GlobalGridFunctionNumberData<TGridFunction, trueDim>(u, fg.name(fct));
 
    // iterate over DoFs in new function and evaluate
    // should be vertices only for Lagrange-1
    if (u_new->max_dofs(VERTEX))
      interpolate_from_original_fct<Vertex, TGridFunction, GlobalGridFunctionNumberData<TGridFunction, trueDim> >
        (u_new, ggfnd, fct, lfeid);
    /*
    if (u_new->max_dofs(EDGE))
      interpolate_from_original_fct<Edge, TGridFunction, GlobalGridFunctionNumberData<TGridFunction, trueDim> >
        (u_new, ggfnd, fct, lfeid);
    if (u_new->max_dofs(FACE))
      interpolate_from_original_fct<Face, TGridFunction, GlobalGridFunctionNumberData<TGridFunction, trueDim> >
        (u_new, ggfnd, fct, lfeid);
    if (u_new->max_dofs(VOLUME))
      interpolate_from_original_fct<Volume, TGridFunction, GlobalGridFunctionNumberData<TGridFunction, trueDim> >
        (u_new, ggfnd, fct, lfeid);
    */
  }
 
#ifdef UG_PARALLEL
  // copy storage type and layouts
  u_new->set_storage_type(u->get_storage_mask());
  u_new->set_layouts(u->layouts());
#endif
 
  // print out new grid function on desired subsets
  bool printAll = ssg.size() == (size_t) u->subset_handler()->num_subsets();
  if (printAll)
    vtkOutput->print(filename, *u_new, step, time);
  else
  {
    for (size_t s = 0; s < ssg.size(); ++s)
      vtkOutput->print_subset(filename, *u_new, ssg[s], step, time);
  }
}
void vtk_export_ho {…}
 
 
 
template <typename TGridFunction>
void vtk_export_ho
(
  SmartPtr<TGridFunction> u,
  const std::vector<std::string>& vFct,
  size_t order,
  SmartPtr<VTKOutput<TGridFunction::domain_type::dim> > vtkOutput,
  const char* filename,
  size_t step,
  number time,
  const std::vector<std::string>& vSubset
)
{
  // construct subset group from given subsets
  SubsetGroup ssg(u->subset_handler());
  try
  {
    if (vSubset.empty())
      ssg.add_all();
    else
      ssg.add(vSubset);
  }
  UG_CATCH_THROW("Subsets are faulty.");
 
  // find highest dim that contains any elements
  MultiGrid& srcGrid = *u->approx_space()->domain()->grid();
  if (srcGrid.num_volumes())
    vtk_export_ho<TGridFunction, TGridFunction::dim >= 3 ? 3 : TGridFunction::dim>
      (u, vFct, order, vtkOutput, filename, step, time, ssg);
  else if (srcGrid.num_faces())
    vtk_export_ho<TGridFunction, TGridFunction::dim >= 2 ? 2 : TGridFunction::dim>
      (u, vFct, order, vtkOutput, filename, step, time, ssg);
  else if (srcGrid.num_edges())
    vtk_export_ho<TGridFunction, TGridFunction::dim >= 1 ? 1 : TGridFunction::dim>
      (u, vFct, order, vtkOutput, filename, step, time, ssg);
  else if (srcGrid.num_vertices())
    vtk_export_ho<TGridFunction, TGridFunction::dim >= 0 ? 0 : TGridFunction::dim>
      (u, vFct, order, vtkOutput, filename, step, time, ssg);
  else
    vtk_export_ho<TGridFunction, TGridFunction::dim>(u, vFct, order, vtkOutput, filename, step, time, ssg);
}
void vtk_export_ho {…}
 
 
template <typename TGridFunction>
void vtk_export_ho
(
  SmartPtr<TGridFunction> u,
  const std::vector<std::string>& vFct,
  size_t order,
  SmartPtr<VTKOutput<TGridFunction::domain_type::dim> > vtkOutput,
  const char* filename,
  const std::vector<std::string>& vSubset
  )
{
  vtk_export_ho(u, vFct, order, vtkOutput, filename, 0, 0.0, vSubset);
}
void vtk_export_ho {…}
 
 
template <typename TGridFunction>
void vtk_export_ho
(
  SmartPtr<TGridFunction> u,
  const std::vector<std::string>& vFct,
  size_t order,
  SmartPtr<VTKOutput<TGridFunction::domain_type::dim> > vtkOutput,
  const char* filename,
  size_t step,
  number time
)
{
  vtk_export_ho(u, vFct, order, vtkOutput, filename, step, time, std::vector<std::string>());
}
void vtk_export_ho {…}
 
 
template <typename TGridFunction>
void vtk_export_ho
(
  SmartPtr<TGridFunction> u,
  const std::vector<std::string>& vFct,
  size_t order,
  SmartPtr<VTKOutput<TGridFunction::domain_type::dim> > vtkOutput,
  const char* filename
  )
{
  vtk_export_ho(u, vFct, order, vtkOutput, filename, 0, 0.0, std::vector<std::string>());
}
void vtk_export_ho {…}
 
 
} // end namespace ug
 
 
#endif // __H__UG__LIB_DISC__IO__VTK_EXPORT_HO__