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dof_object.C

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// The libMesh Finite Element Library.
// Copyright (C) 2002-2012 Benjamin S. Kirk, John W. Peterson, Roy H. Stogner

// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.

// This library 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.

// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA



// C++ includes

// Local includes
#include "libmesh/dof_object.h"


namespace libMesh
{



// ------------------------------------------------------------
// DofObject class static member -now initialized in header
const dof_id_type       DofObject::invalid_id;
const processor_id_type DofObject::invalid_processor_id;



// ------------------------------------------------------------
// DofObject class members
// Copy Constructor
DofObject::DofObject (const DofObject& dof_obj) :
  ReferenceCountedObject<DofObject>(),
#ifdef LIBMESH_ENABLE_AMR
  old_dof_object (NULL),
#endif
  _id            (dof_obj._id),
  _processor_id  (dof_obj._processor_id),
  _idx_buf       (dof_obj._idx_buf)
{

  // Check that everything worked
#ifdef DEBUG

  libmesh_assert_equal_to (this->n_systems(), dof_obj.n_systems());

  for (unsigned int s=0; s<this->n_systems(); s++)
    {
      libmesh_assert_equal_to (this->n_vars(s),       dof_obj.n_vars(s));
      libmesh_assert_equal_to (this->n_var_groups(s), dof_obj.n_var_groups(s));

      for (unsigned int vg=0; vg<this->n_var_groups(s); vg++)
        libmesh_assert_equal_to (this->n_vars(s,vg), dof_obj.n_vars(s,vg));
      
      for (unsigned int v=0; v<this->n_vars(s); v++)
        {
          libmesh_assert_equal_to (this->n_comp(s,v), dof_obj.n_comp(s,v));

          for (unsigned int c=0; c<this->n_comp(s,v); c++)
            libmesh_assert_equal_to (this->dof_number(s,v,c), dof_obj.dof_number(s,v,c));
        }
    }

#endif
}


// Deep-copying assignment operator
DofObject& DofObject::operator= (const DofObject& dof_obj)
{
#ifdef LIBMESH_ENABLE_AMR
  this->clear_old_dof_object();

  this->old_dof_object = new DofObject(*(dof_obj.old_dof_object));
#endif

  _id           = dof_obj._id;
  _processor_id = dof_obj._processor_id;
  _idx_buf      = dof_obj._idx_buf;


  // Check that everything worked
#ifdef DEBUG

  libmesh_assert_equal_to (this->n_systems(), dof_obj.n_systems());

  for (unsigned int s=0; s<this->n_systems(); s++)
    {
      libmesh_assert_equal_to (this->n_vars(s),       dof_obj.n_vars(s));
      libmesh_assert_equal_to (this->n_var_groups(s), dof_obj.n_var_groups(s));

      for (unsigned int vg=0; vg<this->n_var_groups(s); vg++)
        libmesh_assert_equal_to (this->n_vars(s,vg), dof_obj.n_vars(s,vg));
      
      for (unsigned int v=0; v<this->n_vars(s); v++)
        {
          libmesh_assert_equal_to (this->n_comp(s,v), dof_obj.n_comp(s,v));

          for (unsigned int c=0; c<this->n_comp(s,v); c++)
            libmesh_assert_equal_to (this->dof_number(s,v,c), dof_obj.dof_number(s,v,c));
        }
    }

#endif

  return *this;
}





#ifdef LIBMESH_ENABLE_AMR

void  DofObject::clear_old_dof_object ()
{
  // If we have been called before...
  // prevent a memory leak
  if (old_dof_object != NULL)
    {
      delete this->old_dof_object;
      this->old_dof_object = NULL;
    }
}



void DofObject::set_old_dof_object ()
{
  this->clear_old_dof_object();

  libmesh_assert (!this->old_dof_object);

  // Make a new DofObject, assign a copy of \p this.
  // Make sure the copy ctor for DofObject works!!
  this->old_dof_object = new DofObject(*this);
}

#endif



void DofObject::set_n_systems (const unsigned int ns)
{
  // Check for trivial return
  if (ns == this->n_systems())
    return;

  // Clear any existing data.  This is safe to call
  // even if we don't have any data.
  this->clear_dofs();

  // Set the new number of systems
  _idx_buf.resize(ns, ns);
  _idx_buf[0] = ns;


#ifdef DEBUG

  // check that all systems now exist and that they have 0 size
  libmesh_assert_equal_to (ns, this->n_systems());
  for (unsigned int s=0; s<this->n_systems(); s++)
    {
      libmesh_assert_equal_to (this->n_vars(s),       0);
      libmesh_assert_equal_to (this->n_var_groups(s), 0);
    }
  
#endif
}



void DofObject::add_system()
{
  // quick return?
  if (this->n_systems() == 0)
    {
      this->set_n_systems(1);
      return;
    }

  DofObject::index_buffer_t::iterator it = _idx_buf.begin();

  std::advance(it, this->n_systems());

  // this inserts the current vector size at the position for the new system - creating the
  // entry we need for the new system indicating there are 0 variables.
  _idx_buf.insert(it, _idx_buf.size());

  // cache this value before we screw it up!
  const unsigned int ns_orig = this->n_systems();

  // incriment the number of systems and the offsets for each of
  // the systems including the new one we just added.
  for (unsigned int i=0; i<ns_orig+1; i++)
    _idx_buf[i]++;

  libmesh_assert_equal_to (this->n_systems(), (ns_orig+1));
  libmesh_assert_equal_to (this->n_vars(ns_orig), 0);
  libmesh_assert_equal_to (this->n_var_groups(ns_orig), 0);
}



void DofObject::set_n_vars_per_group(const unsigned int s,
                                     const std::vector<unsigned int> &nvpg)
{
  
  libmesh_assert_less (s, this->n_systems());

  // number of varaible groups for this system - inferred
  const unsigned int nvg = libmesh_cast_int<unsigned int>(nvpg.size());
  
  // BSK - note that for compatibility with the previous implementation
  // calling this method when (nvars == this->n_vars()) requires that
  // we invalidate the DOF indices and set the number of components to 0.
  // Note this was a bit of a suprise to me - there was no quick return in
  // the old method, which caused removal and readdition of the DOF indices
  // even in the case of (nvars == this->n_vars()), resulting in n_comp(s,v)
  // implicitly becoming 0 regardless of any previous value.
  // quick return?
  if (nvg == this->n_var_groups(s))
    {
      for (unsigned int vg=0; vg<nvg; vg++)
        {
          this->set_n_comp_group(s,vg,0);
          libmesh_assert_equal_to (this->n_vars(s,vg), nvpg[vg]);
        }
      return;
    }

  // since there is ample opportunity to screw up other systems, let us
  // cache their current sizes and later assert that they are unchanged.
#ifdef DEBUG
  DofObject::index_buffer_t old_system_sizes;
  old_system_sizes.reserve(this->n_systems());

  for (unsigned int s_ctr=0; s_ctr<this->n_systems(); s_ctr++)
    old_system_sizes.push_back(this->n_var_groups(s_ctr));
#endif

  // remove current indices if we have some
  if (this->n_var_groups(s) != 0)
    {
      const unsigned int old_nvg_s = this->n_var_groups(s);

      DofObject::index_buffer_t::iterator
        it  = _idx_buf.begin(),
        end = _idx_buf.begin();

      std::advance(it,  this->start_idx(s));
      std::advance(end, this->end_idx(s));
      _idx_buf.erase(it,end);

      for (unsigned int ctr=(s+1); ctr<this->n_systems(); ctr++)
        _idx_buf[ctr] -= 2*old_nvg_s;
    }

  // better not have any now!
  libmesh_assert_equal_to (this->n_var_groups(s), 0);

  // had better not screwed up any of our sizes!
#ifdef DEBUG
  for (unsigned int s_ctr=0; s_ctr<this->n_systems(); s_ctr++)
    if (s_ctr != s)
      libmesh_assert_equal_to (this->n_var_groups(s_ctr), old_system_sizes[s_ctr]);
#endif

  // OK, if the user requested 0 that is what we have
  if (nvg == 0)
    return;

  {
    // array to hold new indices
    DofObject::index_buffer_t var_idxs(2*nvg);
    for (unsigned int vg=0; vg<nvg; vg++)
      { 
        var_idxs[2*vg    ] = ncv_magic*nvpg[vg] + 0;
        var_idxs[2*vg + 1] = invalid_id - 1;
      }

    DofObject::index_buffer_t::iterator it = _idx_buf.begin();
    std::advance(it, this->end_idx(s));
    _idx_buf.insert(it, var_idxs.begin(), var_idxs.end());

    for (unsigned int ctr=(s+1); ctr<this->n_systems(); ctr++)
      _idx_buf[ctr] += 2*nvg;

    // resize _idx_buf to fit so no memory is wasted.
    DofObject::index_buffer_t(_idx_buf).swap(_idx_buf);
  }

  // that better had worked.  Assert stuff.
  libmesh_assert_equal_to (nvg, this->n_var_groups(s));
  
#ifdef DEBUG

  // std::cout << " [ ";
  // for (unsigned int i=0; i<_idx_buf.size(); i++)
  //   std::cout << _idx_buf[i] << " ";
  // std::cout << "]\n";

  libmesh_assert_equal_to (this->n_var_groups(s), nvpg.size());

  for (unsigned int vg=0; vg<this->n_var_groups(s); vg++)
    {
      libmesh_assert_equal_to (this->n_vars(s,vg), nvpg[vg]);
      libmesh_assert_equal_to (this->n_comp_group(s,vg), 0);
    }

  for (unsigned int v=0; v<this->n_vars(s); v++)
    libmesh_assert_equal_to (this->n_comp(s,v), 0);
  
  // again, all other system sizes shoudl be unchanged!
  for (unsigned int s_ctr=0; s_ctr<this->n_systems(); s_ctr++)
    if (s_ctr != s)
      libmesh_assert_equal_to (this->n_var_groups(s_ctr), old_system_sizes[s_ctr]);

#endif
}



void DofObject::set_n_comp(const unsigned int s,
                           const unsigned int var,
                           const unsigned int ncomp)
{
  libmesh_assert_less (s,   this->n_systems());
  libmesh_assert_less (var, this->n_vars(s));

  this->set_n_comp_group(s, this->var_to_vg(s,var), ncomp);
}



void DofObject::set_n_comp_group(const unsigned int s,
                                 const unsigned int vg,
                                 const unsigned int ncomp)
{
  libmesh_assert_less (s,  this->n_systems());
  libmesh_assert_less (vg, this->n_var_groups(s));
  
  // Check for trivial return
  if (ncomp == this->n_comp_group(s,vg)) return;

#ifndef NDEBUG
  if (ncomp >= ncv_magic)
    {
      const index_t ncvm = ncv_magic;
      libMesh::err << "ERROR: ncomp must be less than DofObject::ncv_magic!\n"
                   << "ncomp = " << ncomp << ", ncv_magic = " << ncvm
                   << "\nrecompile and try again!\n";
      libmesh_error();
    }
#endif
  
  const unsigned int
    start_idx_sys = this->start_idx(s),
    n_vars_group  = this->n_vars(s,vg),
    base_offset   = start_idx_sys + 2*vg;

  libmesh_assert_less ((base_offset + 1), _idx_buf.size());

  // if (ncomp)
  //   std::cout << "s,vg,ncomp=" 
  //          << s  << ","
  //          << vg << ","
  //          << ncomp << '\n';

  // set the number of components, maintaining the number
  // of variables in the group
  _idx_buf[base_offset] = ncv_magic*n_vars_group + ncomp;

  // We use (invalid_id - 1) to signify no
  // components for this object
  _idx_buf[base_offset + 1] = (ncomp == 0) ? invalid_id - 1 : invalid_id;
  
  // this->debug_buffer();
  // std::cout << "s,vg = " << s << "," << vg << '\n'
  //        << "base_offset=" << base_offset << '\n'
  //        << "this->n_comp(s,vg)=" << this->n_comp(s,vg) << '\n'
  //        << "this->n_comp_group(s,vg)=" << this->n_comp_group(s,vg) << '\n'
  //        << "this->n_vars(s,vg)=" << this->n_vars(s,vg) << '\n'
  //        << "this->n_var_groups(s)=" << this->n_var_groups(s) << '\n';

  libmesh_assert_equal_to (ncomp, this->n_comp_group(s,vg));
}



void DofObject::set_dof_number(const unsigned int s,
                               const unsigned int var,
                               const unsigned int comp,
                               const dof_id_type dn)
{
  libmesh_assert_less (s,    this->n_systems());
  libmesh_assert_less (var,  this->n_vars(s));
  libmesh_assert_less (comp, this->n_comp(s,var));

  const unsigned int
    vg            = this->var_to_vg(s,var),
    ncg           = this->n_comp_group(s,vg),
    vig           = this->system_var_to_vg_var(s,vg,var),
    start_idx_sys = this->start_idx(s);

  libmesh_assert_less ((start_idx_sys + 2*vg + 1), _idx_buf.size());

  dof_id_type &base_idx = _idx_buf[start_idx_sys + 2*vg + 1];

  // We intend to change all dof numbers together or not at all
  if (comp || vig)
    libmesh_assert ((dn == invalid_id && base_idx == invalid_id) ||
                    (dn == base_idx + vig*ncg + comp));
  
  // only explicitly store the base index for vig==0, comp==0
  else
    base_idx = dn;

// #ifdef DEBUG
//   std::cout << " [ ";
//   for (unsigned int i=0; i<_idx_buf.size(); i++)
//     std::cout << _idx_buf[i] << " ";
//   std::cout << "]\n";
// #endif

  libmesh_assert_equal_to (this->dof_number(s, var, comp), dn);
}

  

// FIXME: it'll be tricky getting this to work with 64-bit dof_id_type
unsigned int DofObject::packed_indexing_size() const
{
  return 
#ifdef LIBMESH_ENABLE_AMR
    ((old_dof_object == NULL) ? 0 : old_dof_object->packed_indexing_size()) + 2 +
#else
    1 +
#endif
    _idx_buf.size();
}


  
// FIXME: it'll be tricky getting this to work with 64-bit dof_id_type
unsigned int DofObject::unpackable_indexing_size(std::vector<int>::const_iterator begin)
{
#ifdef LIBMESH_ENABLE_AMR
  const int has_old_dof_object = *begin++;

  // Either we have an old_dof_object or we don't
  libmesh_assert(has_old_dof_object == 1 || has_old_dof_object == 0);
  static const int dof_header_size = 2;
#else
  static const bool has_old_dof_object = false;
  static const int dof_header_size = 1;
#endif

  const int this_indexing_size = *begin++;

  return dof_header_size + this_indexing_size +
    (has_old_dof_object ?
      unpackable_indexing_size(begin+this_indexing_size) : 0);
}


// FIXME: it'll be tricky getting this to work with 64-bit dof_id_type
void DofObject::unpack_indexing(std::vector<int>::const_iterator begin)
{
  _idx_buf.clear();

#ifdef LIBMESH_ENABLE_AMR
  this->clear_old_dof_object();
  const int has_old_dof_object = *begin++;
  libmesh_assert(has_old_dof_object == 1 ||
                 has_old_dof_object == 0);
#endif

  const int size = *begin++;
  _idx_buf.reserve(size);
  std::copy(begin, begin+size, back_inserter(_idx_buf));

  // Check as best we can for internal consistency now
  libmesh_assert(_idx_buf.empty() ||
                 (_idx_buf[0] <= _idx_buf.size()));
#ifdef DEBUG
  if (!_idx_buf.empty())
    for (unsigned int i=1; i < _idx_buf[0]; ++i)
      {
        libmesh_assert_greater_equal (_idx_buf[i], _idx_buf[i-1]);
        libmesh_assert_equal_to ((_idx_buf[i] - _idx_buf[i-1])%2, 0);
        libmesh_assert_less_equal (_idx_buf[i], _idx_buf.size());
      }
#endif

#ifdef LIBMESH_ENABLE_AMR
  if (has_old_dof_object)
    {
      this->old_dof_object = new DofObject();
      this->old_dof_object->unpack_indexing(begin+size);
    }
#endif
}


// FIXME: it'll be tricky getting this to work with 64-bit dof_id_type
void DofObject::pack_indexing(std::back_insert_iterator<std::vector<int> > target) const
{
#ifdef LIBMESH_ENABLE_AMR
  // We might need to pack old_dof_object too
  *target++ = (old_dof_object == NULL) ? 0 : 1;
#endif

  *target++ = _idx_buf.size();
  std::copy(_idx_buf.begin(), _idx_buf.end(), target);

#ifdef LIBMESH_ENABLE_AMR
  if (old_dof_object)
    old_dof_object->pack_indexing(target);
#endif
}



void DofObject::debug_buffer () const
{
  std::cout << " [ ";
  for (unsigned int i=0; i<_idx_buf.size(); i++)
    std::cout << _idx_buf[i] << " ";
  std::cout << "]\n";
}



} // namespace libMesh

---

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Last modified: February 05 2013 19:54:46 UTC

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