libMesh::DofObject Class Reference

#include <dof_object.h>

Inheritance diagram for libMesh::DofObject:

Public Member Functions

void clear_old_dof_object ()
 
void set_old_dof_object ()
 
void clear_dofs ()
 
void invalidate_dofs (const unsigned int sys_num=libMesh::invalid_uint)
 
void invalidate_id ()
 
void invalidate_processor_id ()
 
void invalidate ()
 
unsigned int n_dofs (const unsigned int s, const unsigned int var=libMesh::invalid_uint) const
 
dof_id_type id () const
 
dof_id_typeset_id ()
 
unique_id_type unique_id () const
 
unique_id_typeset_unique_id ()
 
void set_id (const dof_id_type dofid)
 
bool valid_id () const
 
bool valid_unique_id () const
 
processor_id_type processor_id () const
 
processor_id_typeprocessor_id ()
 
void processor_id (const processor_id_type pid)
 
bool valid_processor_id () const
 
unsigned int n_systems () const
 
void set_n_systems (const unsigned int s)
 
void add_system ()
 
unsigned int n_var_groups (const unsigned int s) const
 
unsigned int n_vars (const unsigned int s, const unsigned int vg) const
 
unsigned int n_vars (const unsigned int s) const
 
void set_n_vars_per_group (const unsigned int s, const std::vector< unsigned int > &nvpg)
 
unsigned int n_comp (const unsigned int s, const unsigned int var) const
 
unsigned int n_comp_group (const unsigned int s, const unsigned int vg) const
 
void set_n_comp (const unsigned int s, const unsigned int var, const unsigned int ncomp)
 
void set_n_comp_group (const unsigned int s, const unsigned int vg, const unsigned int ncomp)
 
dof_id_type dof_number (const unsigned int s, const unsigned int var, const unsigned int comp) const
 
void set_dof_number (const unsigned int s, const unsigned int var, const unsigned int comp, const dof_id_type dn)
 
bool has_dofs (const unsigned int s=libMesh::invalid_uint) const
 
void set_vg_dof_base (const unsigned int s, const unsigned int vg, const dof_id_type db)
 
dof_id_type vg_dof_base (const unsigned int s, const unsigned int vg) const
 
unsigned int packed_indexing_size () const
 
void unpack_indexing (std::vector< largest_id_type >::const_iterator begin)
 
void pack_indexing (std::back_insert_iterator< std::vector< largest_id_type > > target) const
 
void debug_buffer () const
 
void print_dof_info () const
 
void set_buffer (const std::vector< dof_id_type > &buf)
 

Static Public Member Functions

static unsigned int unpackable_indexing_size (std::vector< largest_id_type >::const_iterator begin)
 
static std::string get_info ()
 
static void print_info (std::ostream &out=libMesh::out)
 
static unsigned int n_objects ()
 
static void enable_print_counter_info ()
 
static void disable_print_counter_info ()
 

Public Attributes

DofObjectold_dof_object
 

Static Public Attributes

static const dof_id_type invalid_id = static_cast<dof_id_type>(-1)
 
static const unique_id_type invalid_unique_id = static_cast<unique_id_type>(-1)
 
static const processor_id_type invalid_processor_id = static_cast<processor_id_type>(-1)
 

Protected Types

typedef std::map< std::string, std::pair< unsigned int, unsigned int > > Counts
 

Protected Member Functions

 DofObject ()
 
 ~DofObject ()
 
 DofObject (const DofObject &)
 
DofObjectoperator= (const DofObject &dof_obj)
 
void increment_constructor_count (const std::string &name)
 
void increment_destructor_count (const std::string &name)
 

Static Protected Attributes

static Counts _counts
 
static Threads::atomic< unsigned int > _n_objects
 
static Threads::spin_mutex _mutex
 
static bool _enable_print_counter = true
 

Private Types

typedef dof_id_type index_t
 
typedef std::vector< index_tindex_buffer_t
 

Private Member Functions

unsigned int var_to_vg (const unsigned int s, const unsigned int var) const
 
unsigned int system_var_to_vg_var (const unsigned int s, const unsigned int vg, const unsigned int var) const
 
unsigned int start_idx (const unsigned int s) const
 
unsigned int end_idx (const unsigned int s) const
 

Private Attributes

unique_id_type _unique_id
 
dof_id_type _id
 
processor_id_type _processor_id
 
index_buffer_t _idx_buf
 

Static Private Attributes

static const index_t ncv_magic = 256
 
static const index_t ncv_magic_exp = 8
 

Detailed Description

The DofObject defines an abstract base class for objects that have degrees of freedom associated with them. Examples of such objects are the Node and Elem classes. This class can not be instantiated, only derived from.

Author
Benjamin S. Kirk
Date
2003, 2011

Definition at line 51 of file dof_object.h.

Member Typedef Documentation

typedef std::map<std::string, std::pair<unsigned int, unsigned int> > libMesh::ReferenceCounter::Counts
protectedinherited

Data structure to log the information. The log is identified by the class name.

Definition at line 119 of file reference_counter.h.

typedef std::vector<index_t> libMesh::DofObject::index_buffer_t
private

Definition at line 476 of file dof_object.h.

DoF index information. This is packed into a contiguous buffer of the following format:

* [ns end_0 end_1 ... end_{ns-1} (ncv_0 idx_0 ncv_1 idx_1 ... ncv_nv idx_nv)_0
*                                (ncv_0 idx_0 ncv_1 idx_1 ... ncv_nv idx_nv)_1
*                                ...
*                                (ncv_0 idx_0 ncv_1 idx_1 ... ncv_nv idx_nv)_ns ]
* 

where 'end_s' is the index past the end of the variable group storage for system s.

Note
We specifically do not store the end for the last system - this always _idx_buf.size().

Specifically, consider the case of 4 systems, with 3, 0, 1, 2 variable groups, respectively. The _idx_buf then looks like:

* [4 10 10 12 () (ncv_0 idx_0 ncv_1 idx_1 ncv_2 idx_2) () (ncv_0 idx_0) (ncv_0 idx_0 ncv_1 idx_1)]
* [0  1  2  3         4     5     6     7     8     9         10    11      12    13    14    15]
* 

The ending index is then given by:

* end_s = _idx_buf.size(), s == (ns-1),
*       = _idx_buf[s+1]    otherwise.
* 

The starting indices are not specifically stored, but rather inferred as follows:

start_s = _idx_buf[s];

Now, the defining characteristic of the VariableGroup is that it supports an arbitrary number of variables of the same type. At the DofObject level, what that means is that each Variable in the VariableGroup will have the same number of nonzero components, and they can all be indexed from the same base number. We use this information in the ncv_# and idx_# entries as follows:

ncv_# = n_vars*ncv_magic + n_comp for variable group # idx_# = base_offset for variable group #

the DoF index for a particular component c of variable v within that group is then given by

idx_var = idx_# + n_comp*v + c

Note
There is a subtlety here - "variable v within that group" usually means nothing to the user. This class is either indexed with variable group numbers, or variable numbers counted within the system. So for a system with 2 variable groups, 4 and 8 variables each, the 5th variable in the system is the 1st variable in 2nd variable group. (Now of course 0-base everything... but you get the idea.)

Definition at line 475 of file dof_object.h.

Constructor & Destructor Documentation

libMesh::DofObject::DofObject ( )
inlineprotected

Constructor. Protected so that you can't instantiate one of these except as a part of a Node or Elem.

Definition at line 514 of file dof_object.h.

References invalidate().

Referenced by libMesh::Node::Node(), operator=(), set_old_dof_object(), and unpack_indexing().

514  :
515 #ifdef LIBMESH_ENABLE_AMR
517 #endif
518 #ifdef LIBMESH_ENABLE_UNIQUE_ID
520 #endif
521  _id (invalid_id),
523 {
524  this->invalidate();
525 }
const class libmesh_nullptr_t libmesh_nullptr
dof_id_type _id
Definition: dof_object.h:411
unique_id_type _unique_id
Definition: dof_object.h:405
static const unique_id_type invalid_unique_id
Definition: dof_object.h:339
static const processor_id_type invalid_processor_id
Definition: dof_object.h:345
static const dof_id_type invalid_id
Definition: dof_object.h:334
DofObject * old_dof_object
Definition: dof_object.h:89
processor_id_type _processor_id
Definition: dof_object.h:422
libMesh::DofObject::~DofObject ( )
inlineprotected

Destructor. Protected so that you can't destroy one of these except as a part of a Node or Elem.

Definition at line 532 of file dof_object.h.

References clear_dofs(), and clear_old_dof_object().

533 {
534  // Free all memory.
535 #ifdef LIBMESH_ENABLE_AMR
536  this->clear_old_dof_object ();
537 #endif
538  this->clear_dofs ();
539 }
void clear_old_dof_object()
Definition: dof_object.C:134
libMesh::DofObject::DofObject ( const DofObject dof_obj)
protected

Copy-constructor.

Definition at line 42 of file dof_object.C.

References dof_number(), n_comp(), n_systems(), n_var_groups(), and n_vars().

42  :
43  ReferenceCountedObject<DofObject>(),
44 #ifdef LIBMESH_ENABLE_AMR
46 #endif
47 #ifdef LIBMESH_ENABLE_UNIQUE_ID
48  _unique_id (dof_obj._unique_id),
49 #endif
50  _id (dof_obj._id),
51  _processor_id (dof_obj._processor_id),
52  _idx_buf (dof_obj._idx_buf)
53 {
54 
55  // Check that everything worked
56 #ifdef DEBUG
57 
58  libmesh_assert_equal_to (this->n_systems(), dof_obj.n_systems());
59 
60  for (unsigned int s=0; s<this->n_systems(); s++)
61  {
62  libmesh_assert_equal_to (this->n_vars(s), dof_obj.n_vars(s));
63  libmesh_assert_equal_to (this->n_var_groups(s), dof_obj.n_var_groups(s));
64 
65  for (unsigned int vg=0; vg<this->n_var_groups(s); vg++)
66  libmesh_assert_equal_to (this->n_vars(s,vg), dof_obj.n_vars(s,vg));
67 
68  for (unsigned int v=0; v<this->n_vars(s); v++)
69  {
70  libmesh_assert_equal_to (this->n_comp(s,v), dof_obj.n_comp(s,v));
71 
72  for (unsigned int c=0; c<this->n_comp(s,v); c++)
73  libmesh_assert_equal_to (this->dof_number(s,v,c), dof_obj.dof_number(s,v,c));
74  }
75  }
76 
77 #endif
78 }
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:737
const class libmesh_nullptr_t libmesh_nullptr
dof_id_type dof_number(const unsigned int s, const unsigned int var, const unsigned int comp) const
Definition: dof_object.h:802
dof_id_type _id
Definition: dof_object.h:411
unique_id_type _unique_id
Definition: dof_object.h:405
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:727
DofObject * old_dof_object
Definition: dof_object.h:89
index_buffer_t _idx_buf
Definition: dof_object.h:477
unsigned int n_comp(const unsigned int s, const unsigned int var) const
Definition: dof_object.h:772
unsigned int n_systems() const
Definition: dof_object.h:718
processor_id_type _processor_id
Definition: dof_object.h:422

Member Function Documentation

void libMesh::DofObject::add_system ( )

Adds an additional system to the DofObject

Definition at line 187 of file dof_object.C.

References _idx_buf, n_systems(), n_var_groups(), n_vars(), and set_n_systems().

Referenced by set_id().

188 {
189  // quick return?
190  if (this->n_systems() == 0)
191  {
192  this->set_n_systems(1);
193  return;
194  }
195 
196  DofObject::index_buffer_t::iterator it = _idx_buf.begin();
197 
198  std::advance(it, this->n_systems());
199 
200  // this inserts the current vector size at the position for the new system - creating the
201  // entry we need for the new system indicating there are 0 variables.
202  _idx_buf.insert(it, cast_int<dof_id_type>(_idx_buf.size()));
203 
204  // cache this value before we screw it up!
205  const unsigned int ns_orig = this->n_systems();
206 
207  // increment the number of systems and the offsets for each of
208  // the systems including the new one we just added.
209  for (unsigned int i=0; i<ns_orig+1; i++)
210  _idx_buf[i]++;
211 
212  libmesh_assert_equal_to (this->n_systems(), (ns_orig+1));
213  libmesh_assert_equal_to (this->n_vars(ns_orig), 0);
214  libmesh_assert_equal_to (this->n_var_groups(ns_orig), 0);
215 }
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:737
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:727
void set_n_systems(const unsigned int s)
Definition: dof_object.C:157
index_buffer_t _idx_buf
Definition: dof_object.h:477
unsigned int n_systems() const
Definition: dof_object.h:718
void libMesh::DofObject::clear_dofs ( )
inline

Clear the DofMap data structures and return to a pristine state.

Definition at line 590 of file dof_object.h.

References _idx_buf, libMesh::libmesh_assert(), and n_systems().

Referenced by set_n_systems(), and ~DofObject().

591 {
592  // vector swap trick to force deallocation
593  index_buffer_t().swap(_idx_buf);
594 
595  libmesh_assert_equal_to (this->n_systems(), 0);
596  libmesh_assert (_idx_buf.empty());
597 }
libmesh_assert(j)
std::vector< index_t > index_buffer_t
Definition: dof_object.h:476
index_buffer_t _idx_buf
Definition: dof_object.h:477
unsigned int n_systems() const
Definition: dof_object.h:718
void libMesh::DofObject::clear_old_dof_object ( )

Sets the old_dof_object to libmesh_nullptr

Definition at line 134 of file dof_object.C.

References libmesh_nullptr, and old_dof_object.

Referenced by operator=(), set_old_dof_object(), unpack_indexing(), and ~DofObject().

135 {
136  delete this->old_dof_object;
138 }
const class libmesh_nullptr_t libmesh_nullptr
DofObject * old_dof_object
Definition: dof_object.h:89
void libMesh::DofObject::debug_buffer ( ) const

Print our buffer for debugging.

Definition at line 542 of file dof_object.C.

References _idx_buf, and libMesh::out.

543 {
544  libMesh::out << " [ ";
545  for (std::size_t i=0; i<_idx_buf.size(); i++)
546  libMesh::out << _idx_buf[i] << " ";
547  libMesh::out << "]\n";
548 }
index_buffer_t _idx_buf
Definition: dof_object.h:477
OStreamProxy out(std::cout)
void libMesh::ReferenceCounter::disable_print_counter_info ( )
staticinherited
dof_id_type libMesh::DofObject::dof_number ( const unsigned int  s,
const unsigned int  var,
const unsigned int  comp 
) const
inline
Returns
The global degree of freedom number for variable var, component comp for system s associated with this DofObject

When partitioning and DoF numbering have been performed by libMesh, every current DoF on this DofObject will belong to its processor.

Definition at line 802 of file dof_object.h.

References _idx_buf, invalid_id, n_comp(), n_comp_group(), n_systems(), n_vars(), start_idx(), system_var_to_vg_var(), and var_to_vg().

Referenced by libMesh::DofMap::_dof_indices(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::FEGenericBase< OutputType >::compute_periodic_constraints(), libMesh::DofMap::constrain_p_dofs(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::dof_indices(), DofObject(), libMesh::OldSolutionValue< Output, point_output >::eval_at_node(), libMesh::Node::get_info(), libMesh::Elem::get_info(), libMesh::DofMap::local_variable_indices(), libMesh::DofMap::old_dof_indices(), libMesh::BuildProjectionList::operator()(), operator=(), print_dof_info(), libMesh::HPCoarsenTest::select_refinement(), set_dof_number(), set_id(), libMesh::DofMap::set_nonlocal_dof_objects(), and libMesh::System::zero_variable().

805 {
806  libmesh_assert_less (s, this->n_systems());
807  libmesh_assert_less (var, this->n_vars(s));
808  libmesh_assert_less (comp, this->n_comp(s,var));
809 
810  const unsigned int
811  vg = this->var_to_vg(s,var),
812  start_idx_sys = this->start_idx(s);
813 
814  libmesh_assert_less ((start_idx_sys + 2*vg + 1), _idx_buf.size());
815 
816  const dof_id_type
817  base_idx = _idx_buf[start_idx_sys + 2*vg + 1];
818 
819  // if the first component is invalid, they
820  // are all invalid
821  if (base_idx == invalid_id)
822  return invalid_id;
823 
824  // otherwise the index is the first component
825  // index augmented by the component number
826  else
827  {
828  const unsigned int
829  ncg = this->n_comp_group(s,vg),
830  vig = this->system_var_to_vg_var(s,vg,var);
831 
832  // std::cout << "base_idx, var, vg, vig, ncg, comp="
833  // << base_idx << " "
834  // << var << " "
835  // << vg << " "
836  // << vig << " "
837  // << ncg << " "
838  // << comp << '\n';
839 
840  return cast_int<dof_id_type>(base_idx + vig*ncg + comp);
841  }
842 }
unsigned int n_comp_group(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:785
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:737
unsigned int system_var_to_vg_var(const unsigned int s, const unsigned int vg, const unsigned int var) const
Definition: dof_object.h:957
static const dof_id_type invalid_id
Definition: dof_object.h:334
unsigned int start_idx(const unsigned int s) const
Definition: dof_object.h:870
unsigned int var_to_vg(const unsigned int s, const unsigned int var) const
Definition: dof_object.h:938
index_buffer_t _idx_buf
Definition: dof_object.h:477
unsigned int n_comp(const unsigned int s, const unsigned int var) const
Definition: dof_object.h:772
unsigned int n_systems() const
Definition: dof_object.h:718
uint8_t dof_id_type
Definition: id_types.h:64
void libMesh::ReferenceCounter::enable_print_counter_info ( )
staticinherited

Methods to enable/disable the reference counter output from print_info()

Definition at line 101 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

Referenced by libMesh::ReferenceCounter::n_objects().

102 {
103  _enable_print_counter = true;
104  return;
105 }
unsigned int libMesh::DofObject::end_idx ( const unsigned int  s) const
inlineprivate

The ending index for system s.

Definition at line 881 of file dof_object.h.

References _idx_buf, and n_systems().

Referenced by n_var_groups(), and set_n_vars_per_group().

882 {
883  libmesh_assert_less (s, this->n_systems());
884  libmesh_assert_less (s, _idx_buf.size());
885 
886  return ((s+1) == this->n_systems()) ?
887  cast_int<unsigned int>(_idx_buf.size()) :
888  cast_int<unsigned int>(_idx_buf[s+1]);
889 }
index_buffer_t _idx_buf
Definition: dof_object.h:477
unsigned int n_systems() const
Definition: dof_object.h:718
std::string libMesh::ReferenceCounter::get_info ( )
staticinherited

Gets a string containing the reference information.

Definition at line 47 of file reference_counter.C.

References libMesh::ReferenceCounter::_counts, and libMesh::Quality::name().

Referenced by libMesh::ReferenceCounter::print_info().

48 {
49 #if defined(LIBMESH_ENABLE_REFERENCE_COUNTING) && defined(DEBUG)
50 
51  std::ostringstream oss;
52 
53  oss << '\n'
54  << " ---------------------------------------------------------------------------- \n"
55  << "| Reference count information |\n"
56  << " ---------------------------------------------------------------------------- \n";
57 
58  for (Counts::iterator it = _counts.begin();
59  it != _counts.end(); ++it)
60  {
61  const std::string name(it->first);
62  const unsigned int creations = it->second.first;
63  const unsigned int destructions = it->second.second;
64 
65  oss << "| " << name << " reference count information:\n"
66  << "| Creations: " << creations << '\n'
67  << "| Destructions: " << destructions << '\n';
68  }
69 
70  oss << " ---------------------------------------------------------------------------- \n";
71 
72  return oss.str();
73 
74 #else
75 
76  return "";
77 
78 #endif
79 }
std::string name(const ElemQuality q)
Definition: elem_quality.C:39
bool libMesh::DofObject::has_dofs ( const unsigned int  s = libMesh::invalid_uint) const
inline
Returns
true if any system has variables which have been assigned, false otherwise.

Definition at line 847 of file dof_object.h.

References libMesh::invalid_uint, n_systems(), and n_vars().

Referenced by libMesh::MeshTools::libmesh_assert_old_dof_objects(), libMesh::DofMap::old_dof_indices(), libMesh::DofMap::reinit(), and set_id().

848 {
849  if (sys == libMesh::invalid_uint)
850  {
851  for (unsigned int s=0; s<this->n_systems(); s++)
852  if (this->n_vars(s))
853  return true;
854  }
855 
856  else
857  {
858  libmesh_assert_less (sys, this->n_systems());
859 
860  if (this->n_vars(sys))
861  return true;
862  }
863 
864  return false;
865 }
const unsigned int invalid_uint
Definition: libmesh.h:184
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:737
ImplicitSystem & sys
unsigned int n_systems() const
Definition: dof_object.h:718
dof_id_type libMesh::DofObject::id ( ) const
inline
Returns
The id for this DofObject

Definition at line 624 of file dof_object.h.

References _id, libMesh::libmesh_assert(), and valid_id().

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::BoundaryInfo::_find_id_maps(), libMesh::MeshTools::Subdivision::add_boundary_ghosts(), libMesh::ReplicatedMesh::add_elem(), libMesh::DistributedMesh::add_elem(), libMesh::BoundaryInfo::add_elements(), libMesh::TopologyMap::add_node(), libMesh::ReplicatedMesh::add_node(), libMesh::DistributedMesh::add_node(), libMesh::DistributedMesh::add_point(), libMesh::UnstructuredMesh::all_first_order(), libMesh::UnstructuredMesh::all_second_order(), libMesh::MeshTools::Subdivision::all_subdivision(), libMesh::MeshTools::Modification::all_tri(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::ParmetisPartitioner::assign_partitioning(), libMesh::MeshTools::Generation::build_delaunay_square(), libMesh::Nemesis_IO_Helper::build_element_and_node_maps(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::ParmetisPartitioner::build_graph(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::VTKIO::cells_to_vtk(), libMesh::Nemesis_IO_Helper::compute_internal_and_border_elems_and_internal_nodes(), libMesh::FEGenericBase< OutputType >::compute_periodic_constraints(), libMesh::FEMap::compute_single_point_map(), libMesh::UnstructuredMesh::copy_nodes_and_elements(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::MeshRefinement::create_parent_error_vector(), libMesh::UnstructuredMesh::create_submesh(), libMesh::ReplicatedMesh::delete_elem(), libMesh::DistributedMesh::delete_elem(), libMesh::ReplicatedMesh::delete_node(), libMesh::DistributedMesh::delete_node(), libMesh::MeshBase::detect_interior_parents(), libMesh::UNVIO::elements_out(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::UnstructuredMesh::find_neighbors(), libMesh::MeshTools::find_nodal_neighbors(), libMesh::MeshRefinement::flag_elements_by_elem_fraction(), libMesh::MeshRefinement::flag_elements_by_error_fraction(), libMesh::MeshRefinement::flag_elements_by_error_tolerance(), libMesh::MeshRefinement::flag_elements_by_mean_stddev(), libMesh::MeshTools::Modification::flatten(), libMesh::Node::get_info(), libMesh::Elem::get_info(), libMesh::DofMap::get_local_constraints(), libMesh::BoundaryInfo::get_side_and_node_maps(), libMesh::EquationSystems::get_solution(), libMesh::LaplaceMeshSmoother::init(), libMesh::ParmetisPartitioner::initialize(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::TreeNode< N >::insert(), libMesh::ReplicatedMesh::insert_elem(), libMesh::DistributedMesh::insert_elem(), libMesh::ReplicatedMesh::insert_node(), libMesh::FE< Dim, T >::inverse_map(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_topology_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_valid_amr_elem_ids(), libMesh::MeshTools::libmesh_assert_valid_elem_ids(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::MeshTools::libmesh_assert_valid_refinement_flags(), libMesh::Tri3Subdivision::local_node_number(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::Elem::node_id(), libMesh::UNVIO::nodes_out(), libMesh::VTKIO::nodes_to_vtk(), libMesh::CompareElemIdsByLevel::operator()(), libMesh::WeightedPatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::PatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::BoundaryInfo::operator=(), libMesh::Parallel::Packing< const Node * >::pack(), libMesh::Parallel::Packing< const Elem * >::pack(), libMesh::MetisPartitioner::partition_range(), libMesh::SFCPartitioner::partition_range(), libMesh::ErrorVector::plot_error(), print_dof_info(), libMesh::DistributedMesh::query_elem_ptr(), libMesh::DistributedMesh::query_node_ptr(), libMesh::Nemesis_IO::read(), libMesh::ExodusII_IO::read(), libMesh::AbaqusIO::read_elements(), libMesh::DistributedMesh::renumber_elem(), libMesh::DistributedMesh::renumber_node(), libMesh::DistributedMesh::renumber_nodes_and_elements(), libMesh::DofMap::scatter_constraints(), libMesh::HPCoarsenTest::select_refinement(), libMesh::Partitioner::set_node_processor_ids(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::Partitioner::set_parent_processor_ids(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::MeshTools::Modification::smooth(), libMesh::ReplicatedMesh::stitching_helper(), libMesh::BoundaryInfo::sync(), libMesh::Parallel::sync_dofobject_data_by_id(), libMesh::Parallel::sync_element_data_by_parent_id(), libMesh::Parallel::sync_node_data_by_element_id(), libMesh::TetGenMeshInterface::triangulate_conformingDelaunayMesh_carvehole(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::Parallel::Packing< Elem * >::unpack(), libMesh::GMVIO::write_ascii_new_impl(), libMesh::GMVIO::write_ascii_old_impl(), libMesh::CheckpointIO::write_connectivity(), libMesh::ExodusII_IO_Helper::write_element_values(), libMesh::ExodusII_IO_Helper::write_elements(), libMesh::GmshIO::write_mesh(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), libMesh::CheckpointIO::write_nodes(), libMesh::CheckpointIO::write_remote_elem(), and libMesh::XdrIO::write_serialized_connectivity().

625 {
626  libmesh_assert (this->valid_id());
627  return _id;
628 }
bool valid_id() const
Definition: dof_object.h:666
dof_id_type _id
Definition: dof_object.h:411
libmesh_assert(j)
void libMesh::ReferenceCounter::increment_constructor_count ( const std::string &  name)
inlineprotectedinherited

Increments the construction counter. Should be called in the constructor of any derived class that will be reference counted.

Definition at line 185 of file reference_counter.h.

References libMesh::ReferenceCounter::_counts, libMesh::Quality::name(), and libMesh::Threads::spin_mtx.

Referenced by libMesh::ReferenceCounter::n_objects(), and libMesh::ReferenceCountedObject< RBParametrized >::ReferenceCountedObject().

186 {
187  Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
188  std::pair<unsigned int, unsigned int> & p = _counts[name];
189 
190  p.first++;
191 }
std::string name(const ElemQuality q)
Definition: elem_quality.C:39
spin_mutex spin_mtx
Definition: threads.C:29
void libMesh::ReferenceCounter::increment_destructor_count ( const std::string &  name)
inlineprotectedinherited

Increments the destruction counter. Should be called in the destructor of any derived class that will be reference counted.

Definition at line 198 of file reference_counter.h.

References libMesh::ReferenceCounter::_counts, libMesh::Quality::name(), and libMesh::Threads::spin_mtx.

Referenced by libMesh::ReferenceCounter::n_objects(), and libMesh::ReferenceCountedObject< RBParametrized >::~ReferenceCountedObject().

199 {
200  Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
201  std::pair<unsigned int, unsigned int> & p = _counts[name];
202 
203  p.second++;
204 }
std::string name(const ElemQuality q)
Definition: elem_quality.C:39
spin_mutex spin_mtx
Definition: threads.C:29
void libMesh::DofObject::invalidate ( )
inline

Invalidates all the indices for this DofObject

Definition at line 580 of file dof_object.h.

References invalidate_dofs(), invalidate_id(), and invalidate_processor_id().

Referenced by DofObject().

581 {
582  this->invalidate_dofs ();
583  this->invalidate_id ();
584  this->invalidate_processor_id ();
585 }
void invalidate_processor_id()
Definition: dof_object.h:572
void invalidate_dofs(const unsigned int sys_num=libMesh::invalid_uint)
Definition: dof_object.h:544
void libMesh::DofObject::invalidate_dofs ( const unsigned int  sys_num = libMesh::invalid_uint)
inline

Sets all degree of freedom numbers to invalid_id

Definition at line 544 of file dof_object.h.

References invalid_id, n_comp_group(), n_systems(), n_var_groups(), and set_vg_dof_base().

Referenced by invalidate().

545 {
546  // If the user does not specify the system number...
547  if (sys_num >= this->n_systems())
548  {
549  for (unsigned int s=0; s<this->n_systems(); s++)
550  for (unsigned int vg=0; vg<this->n_var_groups(s); vg++)
551  if (this->n_comp_group(s,vg))
552  this->set_vg_dof_base(s,vg,invalid_id);
553  }
554  // ...otherwise invalidate the dofs for all systems
555  else
556  for (unsigned int vg=0; vg<this->n_var_groups(sys_num); vg++)
557  if (this->n_comp_group(sys_num,vg))
558  this->set_vg_dof_base(sys_num,vg,invalid_id);
559 }
unsigned int n_comp_group(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:785
void set_vg_dof_base(const unsigned int s, const unsigned int vg, const dof_id_type db)
Definition: dof_object.h:894
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:727
static const dof_id_type invalid_id
Definition: dof_object.h:334
unsigned int n_systems() const
Definition: dof_object.h:718
void libMesh::DofObject::invalidate_id ( )
inline

Sets the id to invalid_id

Definition at line 564 of file dof_object.h.

References invalid_id, and set_id().

Referenced by invalidate().

565 {
566  this->set_id (invalid_id);
567 }
dof_id_type & set_id()
Definition: dof_object.h:633
static const dof_id_type invalid_id
Definition: dof_object.h:334
void libMesh::DofObject::invalidate_processor_id ( )
inline

Sets the processor id to invalid_processor_id

Definition at line 572 of file dof_object.h.

References invalid_processor_id, and processor_id().

Referenced by invalidate(), libMesh::Partitioner::set_node_processor_ids(), and libMesh::Partitioner::set_parent_processor_ids().

573 {
575 }
static const processor_id_type invalid_processor_id
Definition: dof_object.h:345
processor_id_type processor_id() const
Definition: dof_object.h:686
unsigned int libMesh::DofObject::n_comp ( const unsigned int  s,
const unsigned int  var 
) const
inline
Returns
The number of components for variable var of system s associated with this DofObject. For example, the HIERARCHIC shape functions may have multiple DoFs associated with one node. Another example is the MONOMIALs, where only the elements hold the DoFs. For the different spatial directions, and orders, see FE.

Definition at line 772 of file dof_object.h.

References n_comp_group(), n_systems(), n_vars(), and var_to_vg().

Referenced by libMesh::DofMap::_dof_indices(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::FEGenericBase< OutputType >::compute_periodic_constraints(), libMesh::DofMap::constrain_p_dofs(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::dof_indices(), dof_number(), DofObject(), libMesh::OldSolutionValue< Output, point_output >::eval_at_node(), libMesh::Node::get_info(), libMesh::Elem::get_info(), libMesh::DofMap::local_variable_indices(), n_dofs(), libMesh::DofMap::old_dof_indices(), libMesh::BuildProjectionList::operator()(), operator=(), print_dof_info(), set_dof_number(), set_id(), set_n_vars_per_group(), libMesh::DofMap::set_nonlocal_dof_objects(), and libMesh::System::zero_variable().

774 {
775  libmesh_assert_less (s, this->n_systems());
776  libmesh_assert_less (var, this->n_vars(s));
777 
778  return this->n_comp_group(s,this->var_to_vg(s,var));
779 }
unsigned int n_comp_group(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:785
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:737
unsigned int var_to_vg(const unsigned int s, const unsigned int var) const
Definition: dof_object.h:938
unsigned int n_systems() const
Definition: dof_object.h:718
unsigned int libMesh::DofObject::n_comp_group ( const unsigned int  s,
const unsigned int  vg 
) const
inline
Returns
The number of components for VariableGroup vg of system s associated with this DofObject. For example, the HIERARCHIC shape functions may have multiple DoFs associated with one node. Another example is the MONOMIALs, where only the elements hold the DoFs. For the different spatial directions, and orders, see FE.

Definition at line 785 of file dof_object.h.

References _idx_buf, n_systems(), n_var_groups(), ncv_magic, and start_idx().

Referenced by libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::distribute_local_dofs_var_major(), dof_number(), invalidate_dofs(), n_comp(), libMesh::DofMap::reinit(), set_dof_number(), set_id(), set_n_comp_group(), set_n_vars_per_group(), and libMesh::DofMap::set_nonlocal_dof_objects().

787 {
788  libmesh_assert_less (s, this->n_systems());
789  libmesh_assert_less (vg, this->n_var_groups(s));
790 
791  const unsigned int
792  start_idx_sys = this->start_idx(s);
793 
794  libmesh_assert_less ((start_idx_sys + 2*vg), _idx_buf.size());
795 
796  return (_idx_buf[start_idx_sys + 2*vg] % ncv_magic);
797 }
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:727
unsigned int start_idx(const unsigned int s) const
Definition: dof_object.h:870
index_buffer_t _idx_buf
Definition: dof_object.h:477
unsigned int n_systems() const
Definition: dof_object.h:718
static const index_t ncv_magic
Definition: dof_object.h:488
unsigned int libMesh::DofObject::n_dofs ( const unsigned int  s,
const unsigned int  var = libMesh::invalid_uint 
) const
inline
Returns
The number of degrees of freedom associated with system s for this object. Optionally only counts degrees of freedom for variable number var

Definition at line 602 of file dof_object.h.

References libMesh::invalid_uint, n_comp(), n_systems(), and n_vars().

Referenced by libMesh::EquationSystems::build_parallel_solution_vector().

604 {
605  libmesh_assert_less (s, this->n_systems());
606 
607  unsigned int num = 0;
608 
609  // Count all variables
610  if (var == libMesh::invalid_uint)
611  for (unsigned int v=0; v<this->n_vars(s); v++)
612  num += this->n_comp(s,v);
613 
614  // Only count specified variable
615  else
616  num = this->n_comp(s,var);
617 
618  return num;
619 }
const unsigned int invalid_uint
Definition: libmesh.h:184
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:737
unsigned int n_comp(const unsigned int s, const unsigned int var) const
Definition: dof_object.h:772
unsigned int n_systems() const
Definition: dof_object.h:718
static unsigned int libMesh::ReferenceCounter::n_objects ( )
inlinestaticinherited
unsigned int libMesh::DofObject::n_var_groups ( const unsigned int  s) const
inline
Returns
The number of VariableGroup variable groups associated with system s for this DofObject

Definition at line 727 of file dof_object.h.

References end_idx(), n_systems(), and start_idx().

Referenced by add_system(), libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::distribute_local_dofs_var_major(), DofObject(), invalidate_dofs(), n_comp_group(), n_vars(), operator=(), set_id(), set_n_comp_group(), set_n_systems(), set_n_vars_per_group(), libMesh::DofMap::set_nonlocal_dof_objects(), set_vg_dof_base(), var_to_vg(), and vg_dof_base().

728 {
729  libmesh_assert_less (s, this->n_systems());
730 
731  return (this->end_idx(s) - this->start_idx(s)) / 2;
732 }
unsigned int end_idx(const unsigned int s) const
Definition: dof_object.h:881
unsigned int start_idx(const unsigned int s) const
Definition: dof_object.h:870
unsigned int n_systems() const
Definition: dof_object.h:718
unsigned int libMesh::DofObject::n_vars ( const unsigned int  s,
const unsigned int  vg 
) const
inline
Returns
The number of Variable variables associated with VariableGroup vg in system s for this DofObject

Definition at line 737 of file dof_object.h.

References _idx_buf, n_systems(), n_var_groups(), ncv_magic_exp, and start_idx().

Referenced by add_system(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::DofMap::distribute_dofs(), dof_number(), DofObject(), libMesh::OldSolutionValue< Output, point_output >::eval_at_node(), libMesh::Node::get_info(), libMesh::Elem::get_info(), has_dofs(), n_comp(), n_dofs(), n_vars(), libMesh::BuildProjectionList::operator()(), operator=(), print_dof_info(), set_dof_number(), set_id(), set_n_comp(), set_n_comp_group(), set_n_systems(), set_n_vars_per_group(), libMesh::DofMap::set_nonlocal_dof_objects(), system_var_to_vg_var(), and var_to_vg().

739 {
740  libmesh_assert_less (s, this->n_systems());
741  libmesh_assert_less (vg, this->n_var_groups(s));
742 
743  const unsigned int start_idx_sys = this->start_idx(s);
744 
745  libmesh_assert_less ((start_idx_sys + 2*vg), _idx_buf.size());
746 
747  return (cast_int<unsigned int>
748  (_idx_buf[start_idx_sys + 2*vg]) >> ncv_magic_exp);
749 }
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:727
unsigned int start_idx(const unsigned int s) const
Definition: dof_object.h:870
index_buffer_t _idx_buf
Definition: dof_object.h:477
unsigned int n_systems() const
Definition: dof_object.h:718
static const index_t ncv_magic_exp
Definition: dof_object.h:489
unsigned int libMesh::DofObject::n_vars ( const unsigned int  s) const
inline
Returns
The number of Variable variables associated with system s for this DofObject

Definition at line 754 of file dof_object.h.

References n_systems(), n_var_groups(), and n_vars().

755 {
756  libmesh_assert_less (s, this->n_systems());
757 
758  const unsigned int nvg = this->n_var_groups(s);
759 
760  unsigned int val=0;
761 
762  for (unsigned int vg=0; vg<nvg; vg++)
763  val += this->n_vars(s,vg);
764 
765  return val;
766 }
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:737
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:727
unsigned int n_systems() const
Definition: dof_object.h:718
DofObject & libMesh::DofObject::operator= ( const DofObject dof_obj)
protected

Deep-copying assignment operator

Definition at line 82 of file dof_object.C.

References _id, _idx_buf, _processor_id, _unique_id, clear_old_dof_object(), dof_number(), DofObject(), n_comp(), n_systems(), n_var_groups(), n_vars(), and old_dof_object.

83 {
84  if (&dof_obj == this)
85  return *this;
86 
87 #ifdef LIBMESH_ENABLE_AMR
88  this->clear_old_dof_object();
89 
90  this->old_dof_object = new DofObject(*(dof_obj.old_dof_object));
91 #endif
92 
93  _id = dof_obj._id;
94 #ifdef LIBMESH_ENABLE_UNIQUE_ID
95  _unique_id = dof_obj._unique_id;
96 #endif
97  _processor_id = dof_obj._processor_id;
98  _idx_buf = dof_obj._idx_buf;
99 
100 
101  // Check that everything worked
102 #ifdef DEBUG
103 
104  libmesh_assert_equal_to (this->n_systems(), dof_obj.n_systems());
105 
106  for (unsigned int s=0; s<this->n_systems(); s++)
107  {
108  libmesh_assert_equal_to (this->n_vars(s), dof_obj.n_vars(s));
109  libmesh_assert_equal_to (this->n_var_groups(s), dof_obj.n_var_groups(s));
110 
111  for (unsigned int vg=0; vg<this->n_var_groups(s); vg++)
112  libmesh_assert_equal_to (this->n_vars(s,vg), dof_obj.n_vars(s,vg));
113 
114  for (unsigned int v=0; v<this->n_vars(s); v++)
115  {
116  libmesh_assert_equal_to (this->n_comp(s,v), dof_obj.n_comp(s,v));
117 
118  for (unsigned int c=0; c<this->n_comp(s,v); c++)
119  libmesh_assert_equal_to (this->dof_number(s,v,c), dof_obj.dof_number(s,v,c));
120  }
121  }
122 
123 #endif
124 
125  return *this;
126 }
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:737
dof_id_type dof_number(const unsigned int s, const unsigned int var, const unsigned int comp) const
Definition: dof_object.h:802
dof_id_type _id
Definition: dof_object.h:411
unique_id_type _unique_id
Definition: dof_object.h:405
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:727
void clear_old_dof_object()
Definition: dof_object.C:134
DofObject * old_dof_object
Definition: dof_object.h:89
index_buffer_t _idx_buf
Definition: dof_object.h:477
unsigned int n_comp(const unsigned int s, const unsigned int var) const
Definition: dof_object.h:772
unsigned int n_systems() const
Definition: dof_object.h:718
processor_id_type _processor_id
Definition: dof_object.h:422
void libMesh::DofObject::pack_indexing ( std::back_insert_iterator< std::vector< largest_id_type > >  target) const

A method for creating packed data from our index buffer - basically a copy with prepended size with our current implementation.

Definition at line 524 of file dof_object.C.

References _idx_buf, libmesh_nullptr, old_dof_object, and pack_indexing().

Referenced by libMesh::Parallel::Packing< const Node * >::pack(), libMesh::Parallel::Packing< const Elem * >::pack(), and pack_indexing().

525 {
526 #ifdef LIBMESH_ENABLE_AMR
527  // We might need to pack old_dof_object too
528  *target++ = (old_dof_object == libmesh_nullptr) ? 0 : 1;
529 #endif
530 
531  *target++ = _idx_buf.size();
532  std::copy(_idx_buf.begin(), _idx_buf.end(), target);
533 
534 #ifdef LIBMESH_ENABLE_AMR
535  if (old_dof_object)
536  old_dof_object->pack_indexing(target);
537 #endif
538 }
const class libmesh_nullptr_t libmesh_nullptr
DofObject * old_dof_object
Definition: dof_object.h:89
index_buffer_t _idx_buf
Definition: dof_object.h:477
void pack_indexing(std::back_insert_iterator< std::vector< largest_id_type > > target) const
Definition: dof_object.C:524
unsigned int libMesh::DofObject::packed_indexing_size ( ) const

If we pack our indices into an buffer for communications, how many ints do we need?

Definition at line 449 of file dof_object.C.

References _idx_buf, libmesh_nullptr, and old_dof_object.

Referenced by libMesh::Parallel::Packing< const Node * >::packable_size(), libMesh::Parallel::Packing< const Elem * >::packable_size(), libMesh::Node::packed_size(), and libMesh::Parallel::Packing< Elem * >::unpack().

450 {
451  return
452  cast_int<unsigned int> (
453 #ifdef LIBMESH_ENABLE_AMR
454  ((old_dof_object == libmesh_nullptr) ? 0 : old_dof_object->packed_indexing_size()) + 2 +
455 #else
456  1 +
457 #endif
458  _idx_buf.size());
459 }
const class libmesh_nullptr_t libmesh_nullptr
DofObject * old_dof_object
Definition: dof_object.h:89
index_buffer_t _idx_buf
Definition: dof_object.h:477
void libMesh::DofObject::print_dof_info ( ) const

Print out info for debugging.

Definition at line 552 of file dof_object.C.

References dof_number(), id(), n_comp(), n_systems(), n_vars(), and libMesh::out.

553 {
554  libMesh::out << this->id() << " [ ";
555 
556  for (unsigned int s=0; s<this->n_systems(); s++)
557  {
558  libMesh::out << "s:" << s << " ";
559  for (unsigned int var=0; var<this->n_vars(s); var++)
560  {
561  libMesh::out << "v:" << var << " ";
562  for (unsigned int comp=0; comp<this->n_comp(s,var); comp++)
563  {
564  libMesh::out << "c:" << comp << " dof:" << this->dof_number(s,var,comp) << " ";
565  }
566  }
567  }
568 
569  libMesh::out << "]\n";
570 }
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:737
dof_id_type dof_number(const unsigned int s, const unsigned int var, const unsigned int comp) const
Definition: dof_object.h:802
unsigned int n_comp(const unsigned int s, const unsigned int var) const
Definition: dof_object.h:772
dof_id_type id() const
Definition: dof_object.h:624
unsigned int n_systems() const
Definition: dof_object.h:718
OStreamProxy out(std::cout)
void libMesh::ReferenceCounter::print_info ( std::ostream &  out = libMesh::out)
staticinherited

Prints the reference information, by default to libMesh::out.

Definition at line 88 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter, and libMesh::ReferenceCounter::get_info().

Referenced by libMesh::LibMeshInit::LibMeshInit().

89 {
91  out_stream << ReferenceCounter::get_info();
92 }
static std::string get_info()
processor_id_type libMesh::DofObject::processor_id ( ) const
inline
Returns
The processor that this DofObject belongs to.

When partitioning and DoF numbering have been performed by libMesh, every current DoF on this DofObject will belong to its processor.

Definition at line 686 of file dof_object.h.

References _processor_id.

Referenced by libMesh::BoundaryInfo::_find_id_maps(), libMesh::DistributedMesh::add_elem(), libMesh::BoundaryInfo::add_elements(), libMesh::Patch::add_local_face_neighbors(), libMesh::Patch::add_local_point_neighbors(), libMesh::DofMap::add_neighbors_to_send_list(), libMesh::DistributedMesh::add_node(), libMesh::MeshRefinement::add_node(), libMesh::ReplicatedMesh::add_point(), libMesh::DistributedMesh::add_point(), libMesh::UnstructuredMesh::all_first_order(), libMesh::UnstructuredMesh::all_second_order(), libMesh::MeshTools::Modification::all_tri(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::ParmetisPartitioner::assign_partitioning(), libMesh::Patch::build_around_element(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::VTKIO::cells_to_vtk(), libMesh::Nemesis_IO_Helper::compute_border_node_ids(), libMesh::Nemesis_IO_Helper::compute_internal_and_border_elems_and_internal_nodes(), libMesh::Nemesis_IO_Helper::compute_num_global_nodesets(), libMesh::Nemesis_IO_Helper::compute_num_global_sidesets(), libMesh::UnstructuredMesh::copy_nodes_and_elements(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::UnstructuredMesh::create_submesh(), libMesh::DistributedMesh::delete_elem(), libMesh::DistributedMesh::delete_node(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::distribute_local_dofs_var_major(), libMesh::Elem::Elem(), libMesh::MeshFunction::find_element(), libMesh::MeshFunction::find_elements(), libMesh::UnstructuredMesh::find_neighbors(), libMesh::MeshTools::Modification::flatten(), libMesh::Node::get_info(), libMesh::Elem::get_info(), libMesh::DofMap::get_info(), libMesh::DofMap::get_local_constraints(), libMesh::DistributedMesh::insert_elem(), invalidate_processor_id(), libMesh::Elem::is_semilocal(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_topology_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_valid_amr_elem_ids(), libMesh::MeshTools::libmesh_assert_valid_elem_ids(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DofMap::local_variable_indices(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshCommunication::make_p_levels_parallel_consistent(), libMesh::GhostPointNeighbors::operator()(), libMesh::SiblingCoupling::operator()(), libMesh::DefaultCoupling::operator()(), libMesh::PointNeighborCoupling::operator()(), libMesh::Parallel::Packing< const Node * >::pack(), libMesh::Parallel::Packing< const Elem * >::pack(), libMesh::XdrIO::pack_element(), libMesh::LinearPartitioner::partition_range(), libMesh::MetisPartitioner::partition_range(), libMesh::SFCPartitioner::partition_range(), libMesh::MappedSubdomainPartitioner::partition_range(), libMesh::CentroidPartitioner::partition_range(), libMesh::Partitioner::partition_unpartitioned_elements(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), processor_id(), libMesh::Nemesis_IO::read(), libMesh::CheckpointIO::read_connectivity(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::Elem::refine(), libMesh::DofMap::scatter_constraints(), libMesh::MeshCommunication::send_coarse_ghosts(), set_id(), libMesh::Partitioner::set_node_processor_ids(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::Partitioner::set_parent_processor_ids(), libMesh::Partitioner::single_partition_range(), libMesh::BoundaryInfo::sync(), libMesh::Parallel::sync_dofobject_data_by_id(), libMesh::Parallel::sync_element_data_by_parent_id(), libMesh::Parallel::sync_node_data_by_element_id(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::Parallel::Packing< Elem * >::unpack(), libMesh::GMVIO::write_binary(), libMesh::CheckpointIO::write_connectivity(), libMesh::GmshIO::write_mesh(), libMesh::CheckpointIO::write_nodes(), libMesh::XdrIO::write_serialized_connectivity(), and libMesh::Nemesis_IO_Helper::write_sidesets().

687 {
688  return _processor_id;
689 }
processor_id_type _processor_id
Definition: dof_object.h:422
processor_id_type & libMesh::DofObject::processor_id ( )
inline
Returns
The processor that this DofObject belongs to as a writable reference.

Definition at line 694 of file dof_object.h.

References _processor_id.

695 {
696  return _processor_id;
697 }
processor_id_type _processor_id
Definition: dof_object.h:422
void libMesh::DofObject::processor_id ( const processor_id_type  pid)
inline

Sets the processor_id for this DofObject.

Definition at line 702 of file dof_object.h.

References processor_id().

703 {
704  this->processor_id() = pid;
705 }
processor_id_type processor_id() const
Definition: dof_object.h:686
void libMesh::DofObject::set_buffer ( const std::vector< dof_id_type > &  buf)
inline

Definition at line 504 of file dof_object.h.

505  { _idx_buf = buf; }
index_buffer_t _idx_buf
Definition: dof_object.h:477
void libMesh::DofObject::set_dof_number ( const unsigned int  s,
const unsigned int  var,
const unsigned int  comp,
const dof_id_type  dn 
)

Sets the global degree of freedom number for variable var, component comp for system s associated with this DofObject

Definition at line 406 of file dof_object.C.

References _idx_buf, dof_number(), invalid_id, libMesh::libmesh_assert(), n_comp(), n_comp_group(), n_systems(), n_vars(), start_idx(), system_var_to_vg_var(), and var_to_vg().

Referenced by set_id().

410 {
411  libmesh_assert_less (s, this->n_systems());
412  libmesh_assert_less (var, this->n_vars(s));
413  libmesh_assert_less (comp, this->n_comp(s,var));
414 
415  const unsigned int
416  vg = this->var_to_vg(s,var),
417 #ifndef NDEBUG
418  ncg = this->n_comp_group(s,vg),
419 #endif
420  vig = this->system_var_to_vg_var(s,vg,var),
421  start_idx_sys = this->start_idx(s);
422 
423  libmesh_assert_less ((start_idx_sys + 2*vg + 1), _idx_buf.size());
424 
425  dof_id_type & base_idx = _idx_buf[start_idx_sys + 2*vg + 1];
426 
427  // We intend to change all dof numbers together or not at all
428  if (comp || vig)
429  libmesh_assert ((dn == invalid_id && base_idx == invalid_id) ||
430  (dn == base_idx + vig*ncg + comp));
431 
432  // only explicitly store the base index for vig==0, comp==0
433  else
434  base_idx = dn;
435 
436  // #ifdef DEBUG
437  // libMesh::out << " [ ";
438  // for (std::size_t i=0; i<_idx_buf.size(); i++)
439  // libMesh::out << _idx_buf[i] << " ";
440  // libMesh::out << "]\n";
441  // #endif
442 
443  libmesh_assert_equal_to (this->dof_number(s, var, comp), dn);
444 }
unsigned int n_comp_group(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:785
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:737
dof_id_type dof_number(const unsigned int s, const unsigned int var, const unsigned int comp) const
Definition: dof_object.h:802
unsigned int system_var_to_vg_var(const unsigned int s, const unsigned int vg, const unsigned int var) const
Definition: dof_object.h:957
libmesh_assert(j)
static const dof_id_type invalid_id
Definition: dof_object.h:334
unsigned int start_idx(const unsigned int s) const
Definition: dof_object.h:870
unsigned int var_to_vg(const unsigned int s, const unsigned int var) const
Definition: dof_object.h:938
index_buffer_t _idx_buf
Definition: dof_object.h:477
unsigned int n_comp(const unsigned int s, const unsigned int var) const
Definition: dof_object.h:772
unsigned int n_systems() const
Definition: dof_object.h:718
uint8_t dof_id_type
Definition: id_types.h:64
dof_id_type & libMesh::DofObject::set_id ( )
inline
Returns
The id for this DofObject as a writable reference.

Definition at line 633 of file dof_object.h.

References _id.

Referenced by libMesh::GMVIO::_read_one_cell(), libMesh::ReplicatedMesh::add_elem(), libMesh::DistributedMesh::add_elem(), libMesh::ReplicatedMesh::add_node(), libMesh::DistributedMesh::add_node(), libMesh::UnstructuredMesh::all_first_order(), libMesh::MeshTools::Subdivision::all_subdivision(), libMesh::MeshCommunication::assign_global_indices(), libMesh::MeshTools::Generation::build_cube(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::UnstructuredMesh::create_submesh(), libMesh::UNVIO::elements_in(), libMesh::MeshTools::Modification::flatten(), invalidate_id(), libMesh::Node::Node(), libMesh::Nemesis_IO::read(), libMesh::ExodusII_IO::read(), libMesh::VTKIO::read(), libMesh::CheckpointIO::read_connectivity(), libMesh::UCDIO::read_implementation(), libMesh::GmshIO::read_mesh(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::OFFIO::read_stream(), libMesh::MatlabIO::read_stream(), libMesh::RemoteElem::RemoteElem(), libMesh::ReplicatedMesh::renumber_elem(), libMesh::DistributedMesh::renumber_elem(), libMesh::ReplicatedMesh::renumber_node(), libMesh::DistributedMesh::renumber_node(), libMesh::ReplicatedMesh::renumber_nodes_and_elements(), set_id(), libMesh::ReplicatedMesh::stitching_helper(), and libMesh::Parallel::Packing< Elem * >::unpack().

634 {
635  return _id;
636 }
dof_id_type _id
Definition: dof_object.h:411
void libMesh::DofObject::set_n_comp ( const unsigned int  s,
const unsigned int  var,
const unsigned int  ncomp 
)

Sets the number of components for Variable var of system s associated with this DofObject

Definition at line 337 of file dof_object.C.

References n_systems(), n_vars(), set_n_comp_group(), and var_to_vg().

Referenced by set_id().

340 {
341  libmesh_assert_less (s, this->n_systems());
342  libmesh_assert_less (var, this->n_vars(s));
343 
344  this->set_n_comp_group(s, this->var_to_vg(s,var), ncomp);
345 }
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:737
void set_n_comp_group(const unsigned int s, const unsigned int vg, const unsigned int ncomp)
Definition: dof_object.C:349
unsigned int var_to_vg(const unsigned int s, const unsigned int var) const
Definition: dof_object.h:938
unsigned int n_systems() const
Definition: dof_object.h:718
void libMesh::DofObject::set_n_comp_group ( const unsigned int  s,
const unsigned int  vg,
const unsigned int  ncomp 
)

Sets the number of components for VariableGroup vg of system s associated with this DofObject

Definition at line 349 of file dof_object.C.

References _idx_buf, invalid_id, n_comp_group(), n_systems(), n_var_groups(), n_vars(), ncv_magic, and start_idx().

Referenced by libMesh::DofMap::reinit(), set_id(), set_n_comp(), set_n_vars_per_group(), and libMesh::DofMap::set_nonlocal_dof_objects().

352 {
353  libmesh_assert_less (s, this->n_systems());
354  libmesh_assert_less (vg, this->n_var_groups(s));
355 
356  // Check for trivial return
357  if (ncomp == this->n_comp_group(s,vg)) return;
358 
359 #ifndef NDEBUG
360  if (ncomp >= ncv_magic)
361  {
362  const index_t ncvm = ncv_magic;
363  libmesh_error_msg("ERROR: ncomp must be less than DofObject::ncv_magic!\n" \
364  << "ncomp = " \
365  << ncomp \
366  << ", ncv_magic = " \
367  << ncvm \
368  << "\nrecompile and try again!");
369  }
370 #endif
371 
372  const unsigned int
373  start_idx_sys = this->start_idx(s),
374  n_vars_group = this->n_vars(s,vg),
375  base_offset = start_idx_sys + 2*vg;
376 
377  libmesh_assert_less ((base_offset + 1), _idx_buf.size());
378 
379  // if (ncomp)
380  // libMesh::out << "s,vg,ncomp="
381  // << s << ","
382  // << vg << ","
383  // << ncomp << '\n';
384 
385  // set the number of components, maintaining the number
386  // of variables in the group
387  _idx_buf[base_offset] = ncv_magic*n_vars_group + ncomp;
388 
389  // We use (invalid_id - 1) to signify no
390  // components for this object
391  _idx_buf[base_offset + 1] = (ncomp == 0) ? invalid_id - 1 : invalid_id;
392 
393  // this->debug_buffer();
394  // libMesh::out << "s,vg = " << s << "," << vg << '\n'
395  // << "base_offset=" << base_offset << '\n'
396  // << "this->n_comp(s,vg)=" << this->n_comp(s,vg) << '\n'
397  // << "this->n_comp_group(s,vg)=" << this->n_comp_group(s,vg) << '\n'
398  // << "this->n_vars(s,vg)=" << this->n_vars(s,vg) << '\n'
399  // << "this->n_var_groups(s)=" << this->n_var_groups(s) << '\n';
400 
401  libmesh_assert_equal_to (ncomp, this->n_comp_group(s,vg));
402 }
unsigned int n_comp_group(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:785
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:737
dof_id_type index_t
Definition: dof_object.h:475
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:727
static const dof_id_type invalid_id
Definition: dof_object.h:334
unsigned int start_idx(const unsigned int s) const
Definition: dof_object.h:870
index_buffer_t _idx_buf
Definition: dof_object.h:477
unsigned int n_systems() const
Definition: dof_object.h:718
static const index_t ncv_magic
Definition: dof_object.h:488
void libMesh::DofObject::set_n_systems ( const unsigned int  s)

Sets the number of systems for this DofObject

Definition at line 157 of file dof_object.C.

References _idx_buf, clear_dofs(), n_systems(), n_var_groups(), and n_vars().

Referenced by add_system(), libMesh::Elem::refine(), libMesh::EquationSystems::reinit(), and set_id().

158 {
159  // Check for trivial return
160  if (ns == this->n_systems())
161  return;
162 
163  // Clear any existing data. This is safe to call
164  // even if we don't have any data.
165  this->clear_dofs();
166 
167  // Set the new number of systems
168  _idx_buf.resize(ns, ns);
169  _idx_buf[0] = ns;
170 
171 
172 #ifdef DEBUG
173 
174  // check that all systems now exist and that they have 0 size
175  libmesh_assert_equal_to (ns, this->n_systems());
176  for (unsigned int s=0; s<this->n_systems(); s++)
177  {
178  libmesh_assert_equal_to (this->n_vars(s), 0);
179  libmesh_assert_equal_to (this->n_var_groups(s), 0);
180  }
181 
182 #endif
183 }
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:737
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:727
index_buffer_t _idx_buf
Definition: dof_object.h:477
unsigned int n_systems() const
Definition: dof_object.h:718
void libMesh::DofObject::set_n_vars_per_group ( const unsigned int  s,
const std::vector< unsigned int > &  nvpg 
)

Sets number of variables in each group associated with system s for this DofObject. Implicit in this is also setting the number of VariableGroup variable groups for the system. Has the effect of setting the number of components to 0 even when called even with (nvg == this->n_var_groups(s)).

Definition at line 219 of file dof_object.C.

References _idx_buf, end, end_idx(), invalid_id, n_comp(), n_comp_group(), n_systems(), n_var_groups(), n_vars(), ncv_magic, set_n_comp_group(), and start_idx().

Referenced by set_id().

221 {
222 
223  libmesh_assert_less (s, this->n_systems());
224 
225  // number of variable groups for this system - inferred
226  const unsigned int nvg = cast_int<unsigned int>(nvpg.size());
227 
228  // BSK - note that for compatibility with the previous implementation
229  // calling this method when (nvars == this->n_vars()) requires that
230  // we invalidate the DOF indices and set the number of components to 0.
231  // Note this was a bit of a surprise to me - there was no quick return in
232  // the old method, which caused removal and readdition of the DOF indices
233  // even in the case of (nvars == this->n_vars()), resulting in n_comp(s,v)
234  // implicitly becoming 0 regardless of any previous value.
235  // quick return?
236  if (nvg == this->n_var_groups(s))
237  {
238  for (unsigned int vg=0; vg<nvg; vg++)
239  {
240  this->set_n_comp_group(s,vg,0);
241  libmesh_assert_equal_to (this->n_vars(s,vg), nvpg[vg]);
242  }
243  return;
244  }
245 
246  // since there is ample opportunity to screw up other systems, let us
247  // cache their current sizes and later assert that they are unchanged.
248 #ifdef DEBUG
249  DofObject::index_buffer_t old_system_sizes;
250  old_system_sizes.reserve(this->n_systems());
251 
252  for (unsigned int s_ctr=0; s_ctr<this->n_systems(); s_ctr++)
253  old_system_sizes.push_back(this->n_var_groups(s_ctr));
254 #endif
255 
256  // remove current indices if we have some
257  if (this->n_var_groups(s) != 0)
258  {
259  const unsigned int old_nvg_s = this->n_var_groups(s);
260 
261  DofObject::index_buffer_t::iterator
262  it = _idx_buf.begin(),
263  end = _idx_buf.begin();
264 
265  std::advance(it, this->start_idx(s));
266  std::advance(end, this->end_idx(s));
267  _idx_buf.erase(it,end);
268 
269  for (unsigned int ctr=(s+1); ctr<this->n_systems(); ctr++)
270  _idx_buf[ctr] -= 2*old_nvg_s;
271  }
272 
273  // better not have any now!
274  libmesh_assert_equal_to (this->n_var_groups(s), 0);
275 
276  // Make sure we didn't screw up any of our sizes!
277 #ifdef DEBUG
278  for (unsigned int s_ctr=0; s_ctr<this->n_systems(); s_ctr++)
279  if (s_ctr != s)
280  libmesh_assert_equal_to (this->n_var_groups(s_ctr), old_system_sizes[s_ctr]);
281 #endif
282 
283  // OK, if the user requested 0 that is what we have
284  if (nvg == 0)
285  return;
286 
287  {
288  // array to hold new indices
289  DofObject::index_buffer_t var_idxs(2*nvg);
290  for (unsigned int vg=0; vg<nvg; vg++)
291  {
292  var_idxs[2*vg ] = ncv_magic*nvpg[vg] + 0;
293  var_idxs[2*vg + 1] = invalid_id - 1;
294  }
295 
296  DofObject::index_buffer_t::iterator it = _idx_buf.begin();
297  std::advance(it, this->end_idx(s));
298  _idx_buf.insert(it, var_idxs.begin(), var_idxs.end());
299 
300  for (unsigned int ctr=(s+1); ctr<this->n_systems(); ctr++)
301  _idx_buf[ctr] += 2*nvg;
302 
303  // resize _idx_buf to fit so no memory is wasted.
305  }
306 
307  libmesh_assert_equal_to (nvg, this->n_var_groups(s));
308 
309 #ifdef DEBUG
310 
311  // libMesh::out << " [ ";
312  // for (std::size_t i=0; i<_idx_buf.size(); i++)
313  // libMesh::out << _idx_buf[i] << " ";
314  // libMesh::out << "]\n";
315 
316  libmesh_assert_equal_to (this->n_var_groups(s), nvpg.size());
317 
318  for (unsigned int vg=0; vg<this->n_var_groups(s); vg++)
319  {
320  libmesh_assert_equal_to (this->n_vars(s,vg), nvpg[vg]);
321  libmesh_assert_equal_to (this->n_comp_group(s,vg), 0);
322  }
323 
324  for (unsigned int v=0; v<this->n_vars(s); v++)
325  libmesh_assert_equal_to (this->n_comp(s,v), 0);
326 
327  // again, all other system sizes should be unchanged!
328  for (unsigned int s_ctr=0; s_ctr<this->n_systems(); s_ctr++)
329  if (s_ctr != s)
330  libmesh_assert_equal_to (this->n_var_groups(s_ctr), old_system_sizes[s_ctr]);
331 
332 #endif
333 }
unsigned int n_comp_group(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:785
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:737
IterBase * end
unsigned int end_idx(const unsigned int s) const
Definition: dof_object.h:881
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:727
static const dof_id_type invalid_id
Definition: dof_object.h:334
unsigned int start_idx(const unsigned int s) const
Definition: dof_object.h:870
std::vector< index_t > index_buffer_t
Definition: dof_object.h:476
void set_n_comp_group(const unsigned int s, const unsigned int vg, const unsigned int ncomp)
Definition: dof_object.C:349
index_buffer_t _idx_buf
Definition: dof_object.h:477
unsigned int n_comp(const unsigned int s, const unsigned int var) const
Definition: dof_object.h:772
unsigned int n_systems() const
Definition: dof_object.h:718
static const index_t ncv_magic
Definition: dof_object.h:488
void libMesh::DofObject::set_old_dof_object ( )

Sets the old_dof_object to a copy of this

Definition at line 142 of file dof_object.C.

References clear_old_dof_object(), DofObject(), libMesh::libmesh_assert(), and old_dof_object.

Referenced by libMesh::DofMap::reinit().

143 {
144  this->clear_old_dof_object();
145 
147 
148  // Make a new DofObject, assign a copy of \p this.
149  // Make sure the copy ctor for DofObject works!!
150  this->old_dof_object = new DofObject(*this);
151 }
libmesh_assert(j)
void clear_old_dof_object()
Definition: dof_object.C:134
DofObject * old_dof_object
Definition: dof_object.h:89
void libMesh::DofObject::set_vg_dof_base ( const unsigned int  s,
const unsigned int  vg,
const dof_id_type  db 
)
inline

VariableGroup DoF indices are indexed as id = base + var_in_vg*ncomp + comp This method allows for direct access to the base.

Definition at line 894 of file dof_object.h.

References _idx_buf, n_systems(), n_var_groups(), start_idx(), and vg_dof_base().

Referenced by libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::distribute_local_dofs_var_major(), invalidate_dofs(), libMesh::DofMap::reinit(), set_id(), and libMesh::DofMap::set_nonlocal_dof_objects().

897 {
898  libmesh_assert_less (s, this->n_systems());
899  libmesh_assert_less (vg, this->n_var_groups(s));
900 
901  const unsigned int
902  start_idx_sys = this->start_idx(s);
903 
904  libmesh_assert_less ((start_idx_sys + 2*vg + 1), _idx_buf.size());
905 
906  _idx_buf[start_idx_sys + 2*vg + 1] = db;
907 
908  libmesh_assert_equal_to (this->vg_dof_base(s,vg), db);
909 }
dof_id_type vg_dof_base(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:914
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:727
unsigned int start_idx(const unsigned int s) const
Definition: dof_object.h:870
index_buffer_t _idx_buf
Definition: dof_object.h:477
unsigned int n_systems() const
Definition: dof_object.h:718
unsigned int libMesh::DofObject::start_idx ( const unsigned int  s) const
inlineprivate

The starting index for system s.

Definition at line 870 of file dof_object.h.

References _idx_buf, and n_systems().

Referenced by dof_number(), n_comp_group(), n_var_groups(), n_vars(), set_dof_number(), set_n_comp_group(), set_n_vars_per_group(), set_vg_dof_base(), and vg_dof_base().

871 {
872  libmesh_assert_less (s, this->n_systems());
873  libmesh_assert_less (s, _idx_buf.size());
874 
875  return cast_int<unsigned int>(_idx_buf[s]);
876 }
index_buffer_t _idx_buf
Definition: dof_object.h:477
unsigned int n_systems() const
Definition: dof_object.h:718
unsigned int libMesh::DofObject::system_var_to_vg_var ( const unsigned int  s,
const unsigned int  vg,
const unsigned int  var 
) const
inlineprivate

Utility function - for variable var in system s, figure out what variable group it lives in.

Definition at line 957 of file dof_object.h.

References n_vars().

Referenced by dof_number(), and set_dof_number().

960 {
961  unsigned int accumulated_sum=0;
962 
963  for (unsigned int vgc=0; vgc<vg; vgc++)
964  accumulated_sum += this->n_vars(s,vgc);
965 
966  libmesh_assert_less_equal (accumulated_sum, var);
967 
968  return (var - accumulated_sum);
969 }
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:737
void libMesh::DofObject::unpack_indexing ( std::vector< largest_id_type >::const_iterator  begin)

A method for creating our index buffer from packed data - basically with our current implementation we investigate the size term and then copy.

Definition at line 486 of file dof_object.C.

References _idx_buf, clear_old_dof_object(), DofObject(), libMesh::libmesh_assert(), old_dof_object, and unpack_indexing().

Referenced by libMesh::Parallel::Packing< Elem * >::unpack(), and unpack_indexing().

487 {
488  _idx_buf.clear();
489 
490 #ifdef LIBMESH_ENABLE_AMR
491  this->clear_old_dof_object();
492  const bool has_old_dof_object = cast_int<bool>(*begin++);
493 #endif
494 
495  const largest_id_type size = *begin++;
496  _idx_buf.reserve(size);
497  std::copy(begin, begin+size, back_inserter(_idx_buf));
498 
499  // Check as best we can for internal consistency now
500  libmesh_assert(_idx_buf.empty() ||
501  (_idx_buf[0] <= _idx_buf.size()));
502 #ifdef DEBUG
503  if (!_idx_buf.empty())
504  for (unsigned int i=1; i < _idx_buf[0]; ++i)
505  {
506  libmesh_assert_greater_equal (_idx_buf[i], _idx_buf[i-1]);
507  libmesh_assert_equal_to ((_idx_buf[i] - _idx_buf[i-1])%2, 0);
508  libmesh_assert_less_equal (_idx_buf[i], _idx_buf.size());
509  }
510 #endif
511 
512 #ifdef LIBMESH_ENABLE_AMR
513  if (has_old_dof_object)
514  {
515  this->old_dof_object = new DofObject();
516  this->old_dof_object->unpack_indexing(begin+size);
517  }
518 #endif
519 }
uint64_t largest_id_type
Definition: id_types.h:139
libmesh_assert(j)
void clear_old_dof_object()
Definition: dof_object.C:134
DofObject * old_dof_object
Definition: dof_object.h:89
void unpack_indexing(std::vector< largest_id_type >::const_iterator begin)
Definition: dof_object.C:486
index_buffer_t _idx_buf
Definition: dof_object.h:477
unsigned int libMesh::DofObject::unpackable_indexing_size ( std::vector< largest_id_type >::const_iterator  begin)
static

If we have indices packed into an buffer for communications, how much of that buffer applies to this dof object?

Definition at line 465 of file dof_object.C.

Referenced by libMesh::Parallel::Packing< const Elem * >::packed_size(), libMesh::Parallel::Packing< const Node * >::packed_size(), and libMesh::Parallel::Packing< Node * >::unpack().

466 {
467 #ifdef LIBMESH_ENABLE_AMR
468  const bool has_old_dof_object = cast_int<bool>(*begin++);
469 
470  static const int dof_header_size = 2;
471 #else
472  static const bool has_old_dof_object = false;
473  static const int dof_header_size = 1;
474 #endif
475 
476  const largest_id_type this_indexing_size = *begin++;
477 
478  return cast_int<unsigned int>
479  (dof_header_size + this_indexing_size +
480  (has_old_dof_object ?
481  unpackable_indexing_size(begin+this_indexing_size) : 0));
482 }
static unsigned int unpackable_indexing_size(std::vector< largest_id_type >::const_iterator begin)
Definition: dof_object.C:465
uint64_t largest_id_type
Definition: id_types.h:139
bool libMesh::DofObject::valid_id ( ) const
inline
bool libMesh::DofObject::valid_processor_id ( ) const
inline
Returns
true if this DofObject has a valid id set, false otherwise.

Definition at line 710 of file dof_object.h.

References _processor_id, and invalid_processor_id.

Referenced by set_id().

711 {
713 }
static const processor_id_type invalid_processor_id
Definition: dof_object.h:345
processor_id_type _processor_id
Definition: dof_object.h:422
bool libMesh::DofObject::valid_unique_id ( ) const
inline
unsigned int libMesh::DofObject::var_to_vg ( const unsigned int  s,
const unsigned int  var 
) const
inlineprivate

Utility function - for variable var in system s, figure out what variable group it lives in.

Definition at line 938 of file dof_object.h.

References n_var_groups(), and n_vars().

Referenced by dof_number(), n_comp(), set_dof_number(), and set_n_comp().

940 {
941  const unsigned int
942  nvg = this->n_var_groups(s);
943 
944  for (unsigned int vg=0, vg_end=0; vg<nvg; vg++)
945  {
946  vg_end += this->n_vars(s,vg);
947  if (var < vg_end) return vg;
948  }
949 
950  libmesh_error_msg("We'll never get here!");
951  return 0;
952 }
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:737
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:727
dof_id_type libMesh::DofObject::vg_dof_base ( const unsigned int  s,
const unsigned int  vg 
) const
inline

VariableGroup DoF indices are indexed as id = base + var_in_vg*ncomp + comp This method allows for direct access to the base.

Definition at line 914 of file dof_object.h.

References _idx_buf, n_systems(), n_var_groups(), and start_idx().

Referenced by libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::distribute_local_dofs_var_major(), libMesh::DofMap::reinit(), set_id(), libMesh::DofMap::set_nonlocal_dof_objects(), and set_vg_dof_base().

916 {
917  libmesh_assert_less (s, this->n_systems());
918  libmesh_assert_less (vg, this->n_var_groups(s));
919 
920  const unsigned int
921  start_idx_sys = this->start_idx(s);
922 
923  libmesh_assert_less ((start_idx_sys + 2*vg + 1), _idx_buf.size());
924 
925  // #ifdef DEBUG
926  // std::cout << " [ ";
927  // for (std:size_t i=0; i<_idx_buf.size(); i++)
928  // std::cout << _idx_buf[i] << " ";
929  // std::cout << "]\n";
930  // #endif
931 
932  return _idx_buf[start_idx_sys + 2*vg + 1];
933 }
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:727
unsigned int start_idx(const unsigned int s) const
Definition: dof_object.h:870
index_buffer_t _idx_buf
Definition: dof_object.h:477
unsigned int n_systems() const
Definition: dof_object.h:718

Member Data Documentation

ReferenceCounter::Counts libMesh::ReferenceCounter::_counts
staticprotectedinherited
bool libMesh::ReferenceCounter::_enable_print_counter = true
staticprotectedinherited

Flag to control whether reference count information is printed when print_info is called.

Definition at line 143 of file reference_counter.h.

Referenced by libMesh::ReferenceCounter::disable_print_counter_info(), libMesh::ReferenceCounter::enable_print_counter_info(), and libMesh::ReferenceCounter::print_info().

dof_id_type libMesh::DofObject::_id
private

The id of the DofObject

Definition at line 411 of file dof_object.h.

Referenced by id(), operator=(), set_id(), and valid_id().

Threads::spin_mutex libMesh::ReferenceCounter::_mutex
staticprotectedinherited

Mutual exclusion object to enable thread-safe reference counting.

Definition at line 137 of file reference_counter.h.

Threads::atomic< unsigned int > libMesh::ReferenceCounter::_n_objects
staticprotectedinherited

The number of objects. Print the reference count information when the number returns to 0.

Definition at line 132 of file reference_counter.h.

Referenced by libMesh::ReferenceCounter::n_objects(), libMesh::ReferenceCounter::ReferenceCounter(), and libMesh::ReferenceCounter::~ReferenceCounter().

processor_id_type libMesh::DofObject::_processor_id
private

The processor_id of the DofObject. Degrees of freedom are wholly owned by processors, however they may be duplicated on other processors.

This is stored as an unsigned short int since we cannot expect to be solving on 65000+ processors any time soon, can we??

Definition at line 422 of file dof_object.h.

Referenced by operator=(), processor_id(), and valid_processor_id().

unique_id_type libMesh::DofObject::_unique_id
private

A globally unique id, guaranteed not to change as the mesh is repartitioned or adapted

Definition at line 405 of file dof_object.h.

Referenced by operator=(), set_unique_id(), unique_id(), and valid_unique_id().

const dof_id_type libMesh::DofObject::invalid_id = static_cast<dof_id_type>(-1)
static

An invalid id to distinguish an uninitialized DofObject

Definition at line 334 of file dof_object.h.

Referenced by libMesh::DofMap::_dof_indices(), libMesh::Node::active(), libMesh::TopologyMap::add_node(), libMesh::MeshRefinement::add_node(), libMesh::ReplicatedMesh::add_point(), libMesh::UnstructuredMesh::all_second_order(), libMesh::MeshTools::Modification::all_tri(), libMesh::Elem::bracketing_nodes(), libMesh::FEGenericBase< OutputType >::compute_periodic_constraints(), libMesh::FEGenericBase< OutputType >::compute_proj_constraints(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::distribute_local_dofs_var_major(), libMesh::DofMap::dof_indices(), dof_number(), libMesh::TopologyMap::find(), libMesh::ReplicatedMesh::insert_node(), invalidate_dofs(), invalidate_id(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids(), libMesh::Node::Node(), libMesh::Elem::node_id(), libMesh::DofMap::old_dof_indices(), libMesh::Parallel::Packing< const Elem * >::pack(), libMesh::XdrIO::pack_element(), libMesh::Elem::point(), libMesh::XdrIO::polynomial_level_file_name(), libMesh::MeshBase::query_elem(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::ReplicatedMesh::reserve_elem(), libMesh::DistributedMesh::reserve_elem(), libMesh::DofMap::SCALAR_dof_indices(), set_dof_number(), set_n_comp_group(), set_n_vars_per_group(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::Parallel::Packing< Elem * >::unpack(), and valid_id().

const processor_id_type libMesh::DofObject::invalid_processor_id = static_cast<processor_id_type>(-1)
static

An invalid processor_id to distinguish DoFs that have not been assigned to a processor.

Definition at line 345 of file dof_object.h.

Referenced by libMesh::BoundaryInfo::_find_id_maps(), libMesh::DistributedMesh::add_elem(), libMesh::DistributedMesh::add_node(), libMesh::MeshCommunication::allgather(), libMesh::MeshTools::create_bounding_box(), libMesh::MeshTools::create_nodal_bounding_box(), libMesh::DistributedMesh::delete_elem(), libMesh::DistributedMesh::delete_node(), libMesh::Elem::Elem(), libMesh::MeshCommunication::find_global_indices(), libMesh::DistributedMesh::insert_elem(), invalidate_processor_id(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids(), libMesh::DistributedMesh::n_active_elem(), libMesh::MeshBase::n_elem_on_proc(), libMesh::MeshBase::n_nodes_on_proc(), libMesh::MeshBase::n_unpartitioned_elem(), libMesh::MeshBase::n_unpartitioned_nodes(), libMesh::SparsityPattern::Build::operator()(), libMesh::MeshBase::query_elem(), libMesh::CheckpointIO::read_connectivity(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::ReplicatedMesh::reserve_elem(), libMesh::DistributedMesh::reserve_elem(), libMesh::Partitioner::set_node_processor_ids(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::Partitioner::set_parent_processor_ids(), libMesh::Parallel::sync_dofobject_data_by_id(), libMesh::Parallel::sync_dofobject_data_by_xyz(), libMesh::Parallel::sync_element_data_by_parent_id(), libMesh::Parallel::sync_node_data_by_element_id(), libMesh::MeshTools::total_weight(), libMesh::Parallel::Packing< Node * >::unpack(), libMesh::Parallel::Packing< Elem * >::unpack(), valid_processor_id(), libMesh::CheckpointIO::write(), and libMesh::CheckpointIO::write_connectivity().

const unique_id_type libMesh::DofObject::invalid_unique_id = static_cast<unique_id_type>(-1)
static
const index_t libMesh::DofObject::ncv_magic = 256
staticprivate

Above we introduced the chimera ncv, which is a hybrid of the form ncv = ncv_magic*nv + nc where nv are the number of identical variables of a given type, and nc is the number of components for this set of variables.

It is hoped that by setting this to a power of two, an optimizing compiler will recognize later that #/ncv_magic is simply a bitshift

Definition at line 488 of file dof_object.h.

Referenced by n_comp_group(), set_n_comp_group(), and set_n_vars_per_group().

const index_t libMesh::DofObject::ncv_magic_exp = 8
staticprivate

Definition at line 489 of file dof_object.h.

Referenced by n_vars().


The documentation for this class was generated from the following files: