libMesh
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libMesh::DofObject Class Reference

The DofObject defines an abstract base class for objects that have degrees of freedom associated with them. More...

#include <dof_object.h>

Inheritance diagram for libMesh::DofObject:
[legend]

Public Member Functions

void clear_old_dof_object ()
 Sets the old_dof_object to libmesh_nullptr. More...
 
void set_old_dof_object ()
 Sets the old_dof_object to a copy of this. More...
 
void clear_dofs ()
 Clear the DofMap data structures and return to a pristine state. More...
 
void invalidate_dofs (const unsigned int sys_num=libMesh::invalid_uint)
 Sets all degree of freedom numbers to invalid_id. More...
 
void invalidate_id ()
 Sets the id to invalid_id. More...
 
void invalidate_processor_id ()
 Sets the processor id to invalid_processor_id. More...
 
void invalidate ()
 Invalidates all the indices for this DofObject. More...
 
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)
 Sets the id for this DofObject. More...
 
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)
 Sets the processor_id for this DofObject. More...
 
bool valid_processor_id () const
 
unsigned int n_systems () const
 
void set_n_systems (const unsigned int s)
 Sets the number of systems for this DofObject. More...
 
void add_system ()
 Adds an additional system to the DofObject. More...
 
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)
 Sets number of variables in each group associated with system s for this DofObject. More...
 
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)
 Sets the number of components for Variable var of system s associated with this DofObject. More...
 
void 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. More...
 
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)
 Sets the global degree of freedom number for variable var, component comp for system s associated with this DofObject. More...
 
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)
 VariableGroup DoF indices are indexed as id = base + var_in_vg*ncomp + comp This method allows for direct access to the base. More...
 
dof_id_type vg_dof_base (const unsigned int s, const unsigned int vg) const
 VariableGroup DoF indices are indexed as id = base + var_in_vg*ncomp + comp This method allows for direct access to the base. More...
 
unsigned int packed_indexing_size () const
 If we pack our indices into an buffer for communications, how many ints do we need? More...
 
void 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. More...
 
void 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. More...
 
void debug_buffer () const
 Print our buffer for debugging. More...
 
void print_dof_info () const
 Print out info for debugging. More...
 
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)
 If we have indices packed into an buffer for communications, how much of that buffer applies to this dof object? More...
 
static std::string get_info ()
 Gets a string containing the reference information. More...
 
static void print_info (std::ostream &out=libMesh::out)
 Prints the reference information, by default to libMesh::out. More...
 
static unsigned int n_objects ()
 Prints the number of outstanding (created, but not yet destroyed) objects. More...
 
static void enable_print_counter_info ()
 Methods to enable/disable the reference counter output from print_info() More...
 
static void disable_print_counter_info ()
 

Public Attributes

DofObjectold_dof_object
 This object on the last mesh. More...
 

Static Public Attributes

static const dof_id_type invalid_id = static_cast<dof_id_type>(-1)
 An invalid id to distinguish an uninitialized DofObject. More...
 
static const unique_id_type invalid_unique_id = static_cast<unique_id_type>(-1)
 An invalid unique_id to distinguish an uninitialized DofObject. More...
 
static const processor_id_type invalid_processor_id = static_cast<processor_id_type>(-1)
 An invalid processor_id to distinguish DoFs that have not been assigned to a processor. More...
 

Protected Types

typedef std::map< std::string, std::pair< unsigned int, unsigned int > > Counts
 Data structure to log the information. More...
 

Protected Member Functions

 DofObject ()
 Constructor. More...
 
 ~DofObject ()
 Destructor. More...
 
void increment_constructor_count (const std::string &name)
 Increments the construction counter. More...
 
void increment_destructor_count (const std::string &name)
 Increments the destruction counter. More...
 

Static Protected Attributes

static Counts _counts
 Actually holds the data. More...
 
static Threads::atomic< unsigned int_n_objects
 The number of objects. More...
 
static Threads::spin_mutex _mutex
 Mutual exclusion object to enable thread-safe reference counting. More...
 
static bool _enable_print_counter = true
 Flag to control whether reference count information is printed when print_info is called. More...
 

Private Types

typedef dof_id_type index_t
 DoF index information. More...
 
typedef std::vector< index_tindex_buffer_t
 

Private Member Functions

 DofObject (const DofObject &)
 "Copy"-constructor. More...
 
DofObjectoperator= (const DofObject &dof_obj)
 Deep-copying assignment operator. More...
 
unsigned int var_to_vg (const unsigned int s, const unsigned int var) const
 Utility function - for variable var in system s, figure out what variable group it lives in. More...
 
unsigned int system_var_to_vg_var (const unsigned int s, const unsigned int vg, const unsigned int var) const
 Utility function - for variable var in system s, figure out what variable group it lives in. More...
 
unsigned int start_idx (const unsigned int s) const
 The starting index for system s. More...
 
unsigned int end_idx (const unsigned int s) const
 The ending index for system s. More...
 

Private Attributes

unique_id_type _unique_id
 A globally unique id, guaranteed not to change as the mesh is repartitioned or adapted. More...
 
dof_id_type _id
 The id of the DofObject. More...
 
processor_id_type _processor_id
 The processor_id of the DofObject. More...
 
index_buffer_t _idx_buf
 

Static Private Attributes

static const index_t ncv_magic = 256
 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. More...
 
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 484 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 483 of file dof_object.h.

Constructor & Destructor Documentation

libMesh::DofObject::DofObject ( )
protected

Constructor.

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

Definition at line 522 of file dof_object.h.

References invalidate().

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

522  :
523 #ifdef LIBMESH_ENABLE_AMR
525 #endif
526 #ifdef LIBMESH_ENABLE_UNIQUE_ID
528 #endif
529  _id (invalid_id),
531 {
532  this->invalidate();
533 }
const class libmesh_nullptr_t libmesh_nullptr
dof_id_type _id
The id of the DofObject.
Definition: dof_object.h:419
void invalidate()
Invalidates all the indices for this DofObject.
Definition: dof_object.h:588
unique_id_type _unique_id
A globally unique id, guaranteed not to change as the mesh is repartitioned or adapted.
Definition: dof_object.h:413
static const unique_id_type invalid_unique_id
An invalid unique_id to distinguish an uninitialized DofObject.
Definition: dof_object.h:329
static const processor_id_type invalid_processor_id
An invalid processor_id to distinguish DoFs that have not been assigned to a processor.
Definition: dof_object.h:335
static const dof_id_type invalid_id
An invalid id to distinguish an uninitialized DofObject.
Definition: dof_object.h:324
DofObject * old_dof_object
This object on the last mesh.
Definition: dof_object.h:79
processor_id_type _processor_id
The processor_id of the DofObject.
Definition: dof_object.h:430
libMesh::DofObject::~DofObject ( )
protected

Destructor.

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

Definition at line 540 of file dof_object.h.

References clear_dofs(), and clear_old_dof_object().

541 {
542  // Free all memory.
543 #ifdef LIBMESH_ENABLE_AMR
544  this->clear_old_dof_object ();
545 #endif
546  this->clear_dofs ();
547 }
void clear_dofs()
Clear the DofMap data structures and return to a pristine state.
Definition: dof_object.h:598
void clear_old_dof_object()
Sets the old_dof_object to libmesh_nullptr.
Definition: dof_object.C:142
libMesh::DofObject::DofObject ( const DofObject dof_obj)
private

"Copy"-constructor.

Does not copy old_dof_object, but leaves it null in the new object.

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  // DO NOT copy old_dof_object, because this isn't a *real* copy
55  // constructor, it's a "copy almost everything" constructor that
56  // is intended to be used solely for internal construction of
57  // old_dof_object, never for a true deep copy where the newly
58  // created object really matches the source object.
59  //
60  // if (dof_obj.old_dof_object)
61  // this->old_dof_object = new DofObject(*(dof_obj.old_dof_object));
62 
63  // Check that everything worked
64 #ifdef DEBUG
65 
66  libmesh_assert_equal_to (this->n_systems(), dof_obj.n_systems());
67 
68  for (unsigned int s=0; s<this->n_systems(); s++)
69  {
70  libmesh_assert_equal_to (this->n_vars(s), dof_obj.n_vars(s));
71  libmesh_assert_equal_to (this->n_var_groups(s), dof_obj.n_var_groups(s));
72 
73  for (unsigned int vg=0; vg<this->n_var_groups(s); vg++)
74  libmesh_assert_equal_to (this->n_vars(s,vg), dof_obj.n_vars(s,vg));
75 
76  for (unsigned int v=0; v<this->n_vars(s); v++)
77  {
78  libmesh_assert_equal_to (this->n_comp(s,v), dof_obj.n_comp(s,v));
79 
80  for (unsigned int c=0; c<this->n_comp(s,v); c++)
81  libmesh_assert_equal_to (this->dof_number(s,v,c), dof_obj.dof_number(s,v,c));
82  }
83  }
84 
85 #endif
86 }
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:745
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:810
dof_id_type _id
The id of the DofObject.
Definition: dof_object.h:419
unique_id_type _unique_id
A globally unique id, guaranteed not to change as the mesh is repartitioned or adapted.
Definition: dof_object.h:413
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:735
DofObject * old_dof_object
This object on the last mesh.
Definition: dof_object.h:79
index_buffer_t _idx_buf
Definition: dof_object.h:485
unsigned int n_comp(const unsigned int s, const unsigned int var) const
Definition: dof_object.h:780
unsigned int n_systems() const
Definition: dof_object.h:726
processor_id_type _processor_id
The processor_id of the DofObject.
Definition: dof_object.h:430

Member Function Documentation

void libMesh::DofObject::add_system ( )

Adds an additional system to the DofObject.

Definition at line 195 of file dof_object.C.

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

Referenced by set_id().

196 {
197  // quick return?
198  if (this->n_systems() == 0)
199  {
200  this->set_n_systems(1);
201  return;
202  }
203 
204  DofObject::index_buffer_t::iterator it = _idx_buf.begin();
205 
206  std::advance(it, this->n_systems());
207 
208  // this inserts the current vector size at the position for the new system - creating the
209  // entry we need for the new system indicating there are 0 variables.
210  _idx_buf.insert(it, cast_int<dof_id_type>(_idx_buf.size()));
211 
212  // cache this value before we screw it up!
213  const unsigned int ns_orig = this->n_systems();
214 
215  // increment the number of systems and the offsets for each of
216  // the systems including the new one we just added.
217  for (unsigned int i=0; i<ns_orig+1; i++)
218  _idx_buf[i]++;
219 
220  libmesh_assert_equal_to (this->n_systems(), (ns_orig+1));
221  libmesh_assert_equal_to (this->n_vars(ns_orig), 0);
222  libmesh_assert_equal_to (this->n_var_groups(ns_orig), 0);
223 }
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:745
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:735
void set_n_systems(const unsigned int s)
Sets the number of systems for this DofObject.
Definition: dof_object.C:165
index_buffer_t _idx_buf
Definition: dof_object.h:485
unsigned int n_systems() const
Definition: dof_object.h:726
void libMesh::DofObject::clear_dofs ( )

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

Definition at line 598 of file dof_object.h.

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

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

599 {
600  // vector swap trick to force deallocation
601  index_buffer_t().swap(_idx_buf);
602 
603  libmesh_assert_equal_to (this->n_systems(), 0);
604  libmesh_assert (_idx_buf.empty());
605 }
libmesh_assert(j)
std::vector< index_t > index_buffer_t
Definition: dof_object.h:484
index_buffer_t _idx_buf
Definition: dof_object.h:485
unsigned int n_systems() const
Definition: dof_object.h:726
void libMesh::DofObject::clear_old_dof_object ( )

Sets the old_dof_object to libmesh_nullptr.

Definition at line 142 of file dof_object.C.

References libmesh_nullptr, and old_dof_object.

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

143 {
144  delete this->old_dof_object;
146 }
const class libmesh_nullptr_t libmesh_nullptr
DofObject * old_dof_object
This object on the last mesh.
Definition: dof_object.h:79
void libMesh::DofObject::debug_buffer ( ) const

Print our buffer for debugging.

Definition at line 550 of file dof_object.C.

References _idx_buf, and libMesh::out.

551 {
552  libMesh::out << " [ ";
553  for (std::size_t i=0; i<_idx_buf.size(); i++)
554  libMesh::out << _idx_buf[i] << " ";
555  libMesh::out << "]\n";
556 }
OStreamProxy out
index_buffer_t _idx_buf
Definition: dof_object.h:485
void libMesh::ReferenceCounter::disable_print_counter_info ( )
staticinherited

Definition at line 107 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

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

108 {
109  _enable_print_counter = false;
110  return;
111 }
static bool _enable_print_counter
Flag to control whether reference count information is printed when print_info is called...
dof_id_type libMesh::DofObject::dof_number ( const unsigned int  s,
const unsigned int  var,
const unsigned int  comp 
) const
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 810 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(), assemble_shell(), 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(), fill_dirichlet_bc(), libMesh::Node::get_info(), libMesh::Elem::get_info(), libMesh::DofMap::local_variable_indices(), main(), libMesh::DofMap::old_dof_indices(), libMesh::BuildProjectionList::operator()(), operator=(), print_dof_info(), LinearElasticityWithContact::residual_and_jacobian(), libMesh::HPCoarsenTest::select_refinement(), set_dof_number(), set_id(), libMesh::DofMap::set_nonlocal_dof_objects(), ParsedFEMFunctionTest::setUp(), DofObjectTest< Node >::testJensEftangBug(), DofObjectTest< Node >::testManualDofCalculation(), libMesh::BoundaryVolumeSolutionTransfer::transfer_boundary_volume(), libMesh::BoundaryVolumeSolutionTransfer::transfer_volume_boundary(), and libMesh::DTKAdapter::update_variable_values().

813 {
814  libmesh_assert_less (s, this->n_systems());
815  libmesh_assert_less (var, this->n_vars(s));
816  libmesh_assert_less (comp, this->n_comp(s,var));
817 
818  const unsigned int
819  vg = this->var_to_vg(s,var),
820  start_idx_sys = this->start_idx(s);
821 
822  libmesh_assert_less ((start_idx_sys + 2*vg + 1), _idx_buf.size());
823 
824  const dof_id_type
825  base_idx = _idx_buf[start_idx_sys + 2*vg + 1];
826 
827  // if the first component is invalid, they
828  // are all invalid
829  if (base_idx == invalid_id)
830  return invalid_id;
831 
832  // otherwise the index is the first component
833  // index augmented by the component number
834  else
835  {
836  const unsigned int
837  ncg = this->n_comp_group(s,vg),
838  vig = this->system_var_to_vg_var(s,vg,var);
839 
840  // std::cout << "base_idx, var, vg, vig, ncg, comp="
841  // << base_idx << " "
842  // << var << " "
843  // << vg << " "
844  // << vig << " "
845  // << ncg << " "
846  // << comp << '\n';
847 
848  return cast_int<dof_id_type>(base_idx + vig*ncg + comp);
849  }
850 }
unsigned int n_comp_group(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:793
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:745
unsigned int system_var_to_vg_var(const unsigned int s, const unsigned int vg, const unsigned int var) const
Utility function - for variable var in system s, figure out what variable group it lives in...
Definition: dof_object.h:965
static const dof_id_type invalid_id
An invalid id to distinguish an uninitialized DofObject.
Definition: dof_object.h:324
unsigned int start_idx(const unsigned int s) const
The starting index for system s.
Definition: dof_object.h:878
unsigned int var_to_vg(const unsigned int s, const unsigned int var) const
Utility function - for variable var in system s, figure out what variable group it lives in...
Definition: dof_object.h:946
index_buffer_t _idx_buf
Definition: dof_object.h:485
unsigned int n_comp(const unsigned int s, const unsigned int var) const
Definition: dof_object.h:780
unsigned int n_systems() const
Definition: dof_object.h:726
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 }
static bool _enable_print_counter
Flag to control whether reference count information is printed when print_info is called...
unsigned int libMesh::DofObject::end_idx ( const unsigned int  s) const
private

The ending index for system s.

Definition at line 889 of file dof_object.h.

References _idx_buf, and n_systems().

Referenced by n_var_groups(), and set_n_vars_per_group().

890 {
891  libmesh_assert_less (s, this->n_systems());
892  libmesh_assert_less (s, _idx_buf.size());
893 
894  return ((s+1) == this->n_systems()) ?
895  cast_int<unsigned int>(_idx_buf.size()) :
896  cast_int<unsigned int>(_idx_buf[s+1]);
897 }
index_buffer_t _idx_buf
Definition: dof_object.h:485
unsigned int n_systems() const
Definition: dof_object.h:726
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)
This function returns a string containing some name for q.
Definition: elem_quality.C:39
static Counts _counts
Actually holds the data.
bool libMesh::DofObject::has_dofs ( const unsigned int  s = libMesh::invalid_uint) const
Returns
true if any system has variables which have been assigned, false otherwise.

Definition at line 855 of file dof_object.h.

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

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

856 {
857  if (sys == libMesh::invalid_uint)
858  {
859  for (unsigned int s=0; s<this->n_systems(); s++)
860  if (this->n_vars(s))
861  return true;
862  }
863 
864  else
865  {
866  libmesh_assert_less (sys, this->n_systems());
867 
868  if (this->n_vars(sys))
869  return true;
870  }
871 
872  return false;
873 }
const unsigned int invalid_uint
A number which is used quite often to represent an invalid or uninitialized value.
Definition: libmesh.h:184
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:745
ImplicitSystem & sys
unsigned int n_systems() const
Definition: dof_object.h:726
dof_id_type libMesh::DofObject::id ( ) const
Returns
The id for this DofObject

Definition at line 632 of file dof_object.h.

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

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::BoundaryInfo::_find_id_maps(), add_cube_convex_hull_to_mesh(), 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::RBConstruction::add_scaled_matrix_and_vector(), libMesh::UnstructuredMesh::all_first_order(), libMesh::UnstructuredMesh::all_second_order(), libMesh::MeshTools::Modification::all_tri(), libMesh::DofMap::allgather_recursive_constraints(), assemble_ellipticdg(), libMesh::ParmetisPartitioner::build_graph(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::FEGenericBase< OutputType >::compute_periodic_constraints(), libMesh::FEMap::compute_single_point_map(), 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::DTKAdapter::DTKAdapter(), 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::MeshTools::Modification::flatten(), libMesh::Node::get_info(), libMesh::Elem::get_info(), libMesh::DofMap::get_local_constraints(), libMesh::ParmetisPartitioner::initialize(), libMesh::TreeNode< N >::insert(), libMesh::ReplicatedMesh::insert_elem(), libMesh::DistributedMesh::insert_elem(), libMesh::ReplicatedMesh::insert_node(), libMesh::FE< Dim, T >::inverse_map(), libMesh::RBEIMEvaluation::legacy_write_out_interpolation_points_elem(), libMesh::MeshTools::libmesh_assert_valid_amr_elem_ids(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), main(), libMesh::MeshRefinement::make_coarsening_compatible(), LinearElasticityWithContact::move_mesh(), libMesh::Elem::node_id(), 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(), 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::DofMap::set_nonlocal_dof_objects(), libMesh::Partitioner::set_parent_processor_ids(), 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(), MixedDimensionMeshTest::testPointLocatorTree(), DofObjectTest< Node >::testSetId(), libMesh::TetGenMeshInterface::triangulate_conformingDelaunayMesh_carvehole(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::Parallel::Packing< Elem * >::unpack(), libMesh::CheckpointIO::write_connectivity(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), libMesh::CheckpointIO::write_nodes(), libMesh::CheckpointIO::write_remote_elem(), and libMesh::XdrIO::write_serialized_connectivity().

633 {
634  libmesh_assert (this->valid_id());
635  return _id;
636 }
bool valid_id() const
Definition: dof_object.h:674
dof_id_type _id
The id of the DofObject.
Definition: dof_object.h:419
libmesh_assert(j)
void libMesh::ReferenceCounter::increment_constructor_count ( const std::string &  name)
protectedinherited

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)
This function returns a string containing some name for q.
Definition: elem_quality.C:39
spin_mutex spin_mtx
A convenient spin mutex object which can be used for obtaining locks.
Definition: threads.C:29
static Counts _counts
Actually holds the data.
void libMesh::ReferenceCounter::increment_destructor_count ( const std::string &  name)
protectedinherited

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)
This function returns a string containing some name for q.
Definition: elem_quality.C:39
spin_mutex spin_mtx
A convenient spin mutex object which can be used for obtaining locks.
Definition: threads.C:29
static Counts _counts
Actually holds the data.
void libMesh::DofObject::invalidate ( )

Invalidates all the indices for this DofObject.

Definition at line 588 of file dof_object.h.

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

Referenced by DofObject().

589 {
590  this->invalidate_dofs ();
591  this->invalidate_id ();
592  this->invalidate_processor_id ();
593 }
void invalidate_id()
Sets the id to invalid_id.
Definition: dof_object.h:572
void invalidate_processor_id()
Sets the processor id to invalid_processor_id.
Definition: dof_object.h:580
void invalidate_dofs(const unsigned int sys_num=libMesh::invalid_uint)
Sets all degree of freedom numbers to invalid_id.
Definition: dof_object.h:552
void libMesh::DofObject::invalidate_dofs ( const unsigned int  sys_num = libMesh::invalid_uint)

Sets all degree of freedom numbers to invalid_id.

Definition at line 552 of file dof_object.h.

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

Referenced by invalidate().

553 {
554  // If the user does not specify the system number...
555  if (sys_num >= this->n_systems())
556  {
557  for (unsigned int s=0; s<this->n_systems(); s++)
558  for (unsigned int vg=0; vg<this->n_var_groups(s); vg++)
559  if (this->n_comp_group(s,vg))
560  this->set_vg_dof_base(s,vg,invalid_id);
561  }
562  // ...otherwise invalidate the dofs for all systems
563  else
564  for (unsigned int vg=0; vg<this->n_var_groups(sys_num); vg++)
565  if (this->n_comp_group(sys_num,vg))
566  this->set_vg_dof_base(sys_num,vg,invalid_id);
567 }
unsigned int n_comp_group(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:793
void set_vg_dof_base(const unsigned int s, const unsigned int vg, const dof_id_type db)
VariableGroup DoF indices are indexed as id = base + var_in_vg*ncomp + comp This method allows for di...
Definition: dof_object.h:902
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:735
static const dof_id_type invalid_id
An invalid id to distinguish an uninitialized DofObject.
Definition: dof_object.h:324
unsigned int n_systems() const
Definition: dof_object.h:726
void libMesh::DofObject::invalidate_id ( )

Sets the id to invalid_id.

Definition at line 572 of file dof_object.h.

References invalid_id, and set_id().

Referenced by invalidate(), and DofObjectTest< Node >::testInvalidateId().

573 {
574  this->set_id (invalid_id);
575 }
dof_id_type & set_id()
Definition: dof_object.h:641
static const dof_id_type invalid_id
An invalid id to distinguish an uninitialized DofObject.
Definition: dof_object.h:324
void libMesh::DofObject::invalidate_processor_id ( )

Sets the processor id to invalid_processor_id.

Definition at line 580 of file dof_object.h.

References invalid_processor_id, and processor_id().

Referenced by invalidate(), libMesh::Partitioner::set_parent_processor_ids(), and DofObjectTest< Node >::testInvalidateProcId().

581 {
583 }
static const processor_id_type invalid_processor_id
An invalid processor_id to distinguish DoFs that have not been assigned to a processor.
Definition: dof_object.h:335
processor_id_type processor_id() const
Definition: dof_object.h:694
unsigned int libMesh::DofObject::n_comp ( const unsigned int  s,
const unsigned int  var 
) const
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 780 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::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(), main(), n_dofs(), libMesh::DofMap::old_dof_indices(), libMesh::BuildProjectionList::operator()(), operator=(), print_dof_info(), set_dof_number(), set_id(), set_n_vars_per_group(), and libMesh::DofMap::set_nonlocal_dof_objects().

782 {
783  libmesh_assert_less (s, this->n_systems());
784  libmesh_assert_less (var, this->n_vars(s));
785 
786  return this->n_comp_group(s,this->var_to_vg(s,var));
787 }
unsigned int n_comp_group(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:793
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:745
unsigned int var_to_vg(const unsigned int s, const unsigned int var) const
Utility function - for variable var in system s, figure out what variable group it lives in...
Definition: dof_object.h:946
unsigned int n_systems() const
Definition: dof_object.h:726
unsigned int libMesh::DofObject::n_comp_group ( const unsigned int  s,
const unsigned int  vg 
) const
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 793 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().

795 {
796  libmesh_assert_less (s, this->n_systems());
797  libmesh_assert_less (vg, this->n_var_groups(s));
798 
799  const unsigned int
800  start_idx_sys = this->start_idx(s);
801 
802  libmesh_assert_less ((start_idx_sys + 2*vg), _idx_buf.size());
803 
804  return (_idx_buf[start_idx_sys + 2*vg] % ncv_magic);
805 }
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:735
unsigned int start_idx(const unsigned int s) const
The starting index for system s.
Definition: dof_object.h:878
index_buffer_t _idx_buf
Definition: dof_object.h:485
unsigned int n_systems() const
Definition: dof_object.h:726
static const index_t ncv_magic
Above we introduced the chimera ncv, which is a hybrid of the form ncv = ncv_magic*nv + nc where nv a...
Definition: dof_object.h:496
unsigned int libMesh::DofObject::n_dofs ( const unsigned int  s,
const unsigned int  var = libMesh::invalid_uint 
) const
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 610 of file dof_object.h.

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

612 {
613  libmesh_assert_less (s, this->n_systems());
614 
615  unsigned int num = 0;
616 
617  // Count all variables
618  if (var == libMesh::invalid_uint)
619  for (unsigned int v=0; v<this->n_vars(s); v++)
620  num += this->n_comp(s,v);
621 
622  // Only count specified variable
623  else
624  num = this->n_comp(s,var);
625 
626  return num;
627 }
const unsigned int invalid_uint
A number which is used quite often to represent an invalid or uninitialized value.
Definition: libmesh.h:184
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:745
unsigned int n_comp(const unsigned int s, const unsigned int var) const
Definition: dof_object.h:780
unsigned int n_systems() const
Definition: dof_object.h:726
static unsigned int libMesh::ReferenceCounter::n_objects ( )
staticinherited
unsigned int libMesh::DofObject::n_systems ( ) const
unsigned int libMesh::DofObject::n_var_groups ( const unsigned int  s) const
Returns
The number of VariableGroup variable groups associated with system s for this DofObject

Definition at line 735 of file dof_object.h.

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

Referenced by add_system(), 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(), DofObjectTest< Node >::testSetNVariableGroups(), var_to_vg(), and vg_dof_base().

736 {
737  libmesh_assert_less (s, this->n_systems());
738 
739  return (this->end_idx(s) - this->start_idx(s)) / 2;
740 }
unsigned int end_idx(const unsigned int s) const
The ending index for system s.
Definition: dof_object.h:889
unsigned int start_idx(const unsigned int s) const
The starting index for system s.
Definition: dof_object.h:878
unsigned int n_systems() const
Definition: dof_object.h:726
unsigned int libMesh::DofObject::n_vars ( const unsigned int  s,
const unsigned int  vg 
) const
Returns
The number of Variable variables associated with VariableGroup vg in system s for this DofObject

Definition at line 745 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(), DofObjectTest< Node >::testSetNVariableGroups(), and var_to_vg().

747 {
748  libmesh_assert_less (s, this->n_systems());
749  libmesh_assert_less (vg, this->n_var_groups(s));
750 
751  const unsigned int start_idx_sys = this->start_idx(s);
752 
753  libmesh_assert_less ((start_idx_sys + 2*vg), _idx_buf.size());
754 
755  return (cast_int<unsigned int>
756  (_idx_buf[start_idx_sys + 2*vg]) >> ncv_magic_exp);
757 }
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:735
unsigned int start_idx(const unsigned int s) const
The starting index for system s.
Definition: dof_object.h:878
index_buffer_t _idx_buf
Definition: dof_object.h:485
unsigned int n_systems() const
Definition: dof_object.h:726
static const index_t ncv_magic_exp
Definition: dof_object.h:497
unsigned int libMesh::DofObject::n_vars ( const unsigned int  s) const
Returns
The number of Variable variables associated with system s for this DofObject

Definition at line 762 of file dof_object.h.

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

763 {
764  libmesh_assert_less (s, this->n_systems());
765 
766  const unsigned int nvg = this->n_var_groups(s);
767 
768  unsigned int val=0;
769 
770  for (unsigned int vg=0; vg<nvg; vg++)
771  val += this->n_vars(s,vg);
772 
773  return val;
774 }
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:745
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:735
unsigned int n_systems() const
Definition: dof_object.h:726
DofObject & libMesh::DofObject::operator= ( const DofObject dof_obj)
private

Deep-copying assignment operator.

Definition at line 90 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.

91 {
92  if (&dof_obj == this)
93  return *this;
94 
95 #ifdef LIBMESH_ENABLE_AMR
96  this->clear_old_dof_object();
97 
98  this->old_dof_object = new DofObject(*(dof_obj.old_dof_object));
99 #endif
100 
101  _id = dof_obj._id;
102 #ifdef LIBMESH_ENABLE_UNIQUE_ID
103  _unique_id = dof_obj._unique_id;
104 #endif
105  _processor_id = dof_obj._processor_id;
106  _idx_buf = dof_obj._idx_buf;
107 
108 
109  // Check that everything worked
110 #ifdef DEBUG
111 
112  libmesh_assert_equal_to (this->n_systems(), dof_obj.n_systems());
113 
114  for (unsigned int s=0; s<this->n_systems(); s++)
115  {
116  libmesh_assert_equal_to (this->n_vars(s), dof_obj.n_vars(s));
117  libmesh_assert_equal_to (this->n_var_groups(s), dof_obj.n_var_groups(s));
118 
119  for (unsigned int vg=0; vg<this->n_var_groups(s); vg++)
120  libmesh_assert_equal_to (this->n_vars(s,vg), dof_obj.n_vars(s,vg));
121 
122  for (unsigned int v=0; v<this->n_vars(s); v++)
123  {
124  libmesh_assert_equal_to (this->n_comp(s,v), dof_obj.n_comp(s,v));
125 
126  for (unsigned int c=0; c<this->n_comp(s,v); c++)
127  libmesh_assert_equal_to (this->dof_number(s,v,c), dof_obj.dof_number(s,v,c));
128  }
129  }
130 
131 #endif
132 
133  return *this;
134 }
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:745
dof_id_type dof_number(const unsigned int s, const unsigned int var, const unsigned int comp) const
Definition: dof_object.h:810
dof_id_type _id
The id of the DofObject.
Definition: dof_object.h:419
DofObject()
Constructor.
Definition: dof_object.h:522
unique_id_type _unique_id
A globally unique id, guaranteed not to change as the mesh is repartitioned or adapted.
Definition: dof_object.h:413
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:735
void clear_old_dof_object()
Sets the old_dof_object to libmesh_nullptr.
Definition: dof_object.C:142
DofObject * old_dof_object
This object on the last mesh.
Definition: dof_object.h:79
index_buffer_t _idx_buf
Definition: dof_object.h:485
unsigned int n_comp(const unsigned int s, const unsigned int var) const
Definition: dof_object.h:780
unsigned int n_systems() const
Definition: dof_object.h:726
processor_id_type _processor_id
The processor_id of the DofObject.
Definition: dof_object.h:430
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 532 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().

533 {
534 #ifdef LIBMESH_ENABLE_AMR
535  // We might need to pack old_dof_object too
536  *target++ = (old_dof_object == libmesh_nullptr) ? 0 : 1;
537 #endif
538 
539  *target++ = _idx_buf.size();
540  std::copy(_idx_buf.begin(), _idx_buf.end(), target);
541 
542 #ifdef LIBMESH_ENABLE_AMR
543  if (old_dof_object)
544  old_dof_object->pack_indexing(target);
545 #endif
546 }
const class libmesh_nullptr_t libmesh_nullptr
void 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 o...
Definition: dof_object.C:532
DofObject * old_dof_object
This object on the last mesh.
Definition: dof_object.h:79
index_buffer_t _idx_buf
Definition: dof_object.h:485
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 457 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().

458 {
459  return
460  cast_int<unsigned int> (
461 #ifdef LIBMESH_ENABLE_AMR
462  ((old_dof_object == libmesh_nullptr) ? 0 : old_dof_object->packed_indexing_size()) + 2 +
463 #else
464  1 +
465 #endif
466  _idx_buf.size());
467 }
const class libmesh_nullptr_t libmesh_nullptr
DofObject * old_dof_object
This object on the last mesh.
Definition: dof_object.h:79
index_buffer_t _idx_buf
Definition: dof_object.h:485
void libMesh::DofObject::print_dof_info ( ) const

Print out info for debugging.

Definition at line 560 of file dof_object.C.

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

561 {
562  libMesh::out << this->id() << " [ ";
563 
564  for (unsigned int s=0; s<this->n_systems(); s++)
565  {
566  libMesh::out << "s:" << s << " ";
567  for (unsigned int var=0; var<this->n_vars(s); var++)
568  {
569  libMesh::out << "v:" << var << " ";
570  for (unsigned int comp=0; comp<this->n_comp(s,var); comp++)
571  {
572  libMesh::out << "c:" << comp << " dof:" << this->dof_number(s,var,comp) << " ";
573  }
574  }
575  }
576 
577  libMesh::out << "]\n";
578 }
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:745
dof_id_type dof_number(const unsigned int s, const unsigned int var, const unsigned int comp) const
Definition: dof_object.h:810
OStreamProxy out
unsigned int n_comp(const unsigned int s, const unsigned int var) const
Definition: dof_object.h:780
dof_id_type id() const
Definition: dof_object.h:632
unsigned int n_systems() const
Definition: dof_object.h:726
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()
Gets a string containing the reference information.
static bool _enable_print_counter
Flag to control whether reference count information is printed when print_info is called...
processor_id_type libMesh::DofObject::processor_id ( ) const
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 694 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::RBConstruction::add_scaled_matrix_and_vector(), libMesh::UnstructuredMesh::all_first_order(), libMesh::UnstructuredMesh::all_second_order(), libMesh::MeshTools::Modification::all_tri(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::Patch::build_around_element(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::InfElemBuilder::build_inf_elem(), 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::RBEIMEvaluation::legacy_write_out_interpolation_points_elem(), 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_neighbors(), libMesh::DofMap::local_variable_indices(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshCommunication::make_p_levels_parallel_consistent(), AugmentSparsityOnInterface::mesh_reinit(), libMesh::GhostPointNeighbors::operator()(), libMesh::SiblingCoupling::operator()(), AugmentSparsityOnInterface::operator()(), libMesh::PointNeighborCoupling::operator()(), libMesh::DefaultCoupling::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(), BoundaryMeshTest::sanityCheck(), 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(), ParsedFEMFunctionTest::setUp(), libMesh::Partitioner::single_partition_range(), libMesh::Parallel::sync_dofobject_data_by_id(), libMesh::Parallel::sync_element_data_by_parent_id(), libMesh::Parallel::sync_node_data_by_element_id(), DefaultCouplingTest::testCoupling(), PointNeighborCouplingTest::testCoupling(), DofObjectTest< Node >::testInvalidateProcId(), EquationSystemsTest::testPostInitAddElem(), DofObjectTest< Node >::testSetProcId(), BoundaryInfoTest::testShellFaceConstraints(), DofObjectTest< Node >::testValidProcId(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::Parallel::Packing< Elem * >::unpack(), libMesh::DTKAdapter::update_variable_values(), libMesh::CheckpointIO::write_connectivity(), libMesh::GmshIO::write_mesh(), libMesh::CheckpointIO::write_nodes(), and libMesh::Nemesis_IO_Helper::write_sidesets().

695 {
696  return _processor_id;
697 }
processor_id_type _processor_id
The processor_id of the DofObject.
Definition: dof_object.h:430
processor_id_type & libMesh::DofObject::processor_id ( )
Returns
The processor that this DofObject belongs to as a writable reference.

Definition at line 702 of file dof_object.h.

References _processor_id.

703 {
704  return _processor_id;
705 }
processor_id_type _processor_id
The processor_id of the DofObject.
Definition: dof_object.h:430
void libMesh::DofObject::processor_id ( const processor_id_type  pid)

Sets the processor_id for this DofObject.

Definition at line 710 of file dof_object.h.

References processor_id().

711 {
712  this->processor_id() = pid;
713 }
processor_id_type processor_id() const
Definition: dof_object.h:694
void libMesh::DofObject::set_buffer ( const std::vector< dof_id_type > &  buf)

Definition at line 512 of file dof_object.h.

Referenced by DofObjectTest< Node >::testJensEftangBug().

513  { _idx_buf = buf; }
index_buffer_t _idx_buf
Definition: dof_object.h:485
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 414 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().

418 {
419  libmesh_assert_less (s, this->n_systems());
420  libmesh_assert_less (var, this->n_vars(s));
421  libmesh_assert_less (comp, this->n_comp(s,var));
422 
423  const unsigned int
424  vg = this->var_to_vg(s,var),
425 #ifndef NDEBUG
426  ncg = this->n_comp_group(s,vg),
427 #endif
428  vig = this->system_var_to_vg_var(s,vg,var),
429  start_idx_sys = this->start_idx(s);
430 
431  libmesh_assert_less ((start_idx_sys + 2*vg + 1), _idx_buf.size());
432 
433  dof_id_type & base_idx = _idx_buf[start_idx_sys + 2*vg + 1];
434 
435  // We intend to change all dof numbers together or not at all
436  if (comp || vig)
437  libmesh_assert ((dn == invalid_id && base_idx == invalid_id) ||
438  (dn == base_idx + vig*ncg + comp));
439 
440  // only explicitly store the base index for vig==0, comp==0
441  else
442  base_idx = dn;
443 
444  // #ifdef DEBUG
445  // libMesh::out << " [ ";
446  // for (std::size_t i=0; i<_idx_buf.size(); i++)
447  // libMesh::out << _idx_buf[i] << " ";
448  // libMesh::out << "]\n";
449  // #endif
450 
451  libmesh_assert_equal_to (this->dof_number(s, var, comp), dn);
452 }
unsigned int n_comp_group(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:793
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:745
dof_id_type dof_number(const unsigned int s, const unsigned int var, const unsigned int comp) const
Definition: dof_object.h:810
unsigned int system_var_to_vg_var(const unsigned int s, const unsigned int vg, const unsigned int var) const
Utility function - for variable var in system s, figure out what variable group it lives in...
Definition: dof_object.h:965
libmesh_assert(j)
static const dof_id_type invalid_id
An invalid id to distinguish an uninitialized DofObject.
Definition: dof_object.h:324
unsigned int start_idx(const unsigned int s) const
The starting index for system s.
Definition: dof_object.h:878
unsigned int var_to_vg(const unsigned int s, const unsigned int var) const
Utility function - for variable var in system s, figure out what variable group it lives in...
Definition: dof_object.h:946
index_buffer_t _idx_buf
Definition: dof_object.h:485
unsigned int n_comp(const unsigned int s, const unsigned int var) const
Definition: dof_object.h:780
unsigned int n_systems() const
Definition: dof_object.h:726
uint8_t dof_id_type
Definition: id_types.h:64
dof_id_type & libMesh::DofObject::set_id ( )
Returns
The id for this DofObject as a writable reference.

Definition at line 641 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::MeshTools::Generation::build_cube(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::InfElemBuilder::build_inf_elem(), SlitMeshTest::build_mesh(), libMesh::UnstructuredMesh::create_submesh(), libMesh::UNVIO::elements_in(), libMesh::MeshTools::Modification::flatten(), invalidate_id(), libMesh::RBEIMEvaluation::legacy_write_out_interpolation_points_elem(), 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(), DofObjectTest< Node >::testInvalidateId(), EquationSystemsTest::testPostInitAddElem(), DofObjectTest< Node >::testSetId(), DofObjectTest< Node >::testValidId(), and libMesh::Parallel::Packing< Elem * >::unpack().

642 {
643  return _id;
644 }
dof_id_type _id
The id of the DofObject.
Definition: dof_object.h:419
void libMesh::DofObject::set_id ( const dof_id_type  dofid)
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 345 of file dof_object.C.

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

Referenced by set_id().

348 {
349  libmesh_assert_less (s, this->n_systems());
350  libmesh_assert_less (var, this->n_vars(s));
351 
352  this->set_n_comp_group(s, this->var_to_vg(s,var), ncomp);
353 }
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:745
void 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: dof_object.C:357
unsigned int var_to_vg(const unsigned int s, const unsigned int var) const
Utility function - for variable var in system s, figure out what variable group it lives in...
Definition: dof_object.h:946
unsigned int n_systems() const
Definition: dof_object.h:726
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 357 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(), libMesh::DofMap::set_nonlocal_dof_objects(), and DofObjectTest< Node >::testManualDofCalculation().

360 {
361  libmesh_assert_less (s, this->n_systems());
362  libmesh_assert_less (vg, this->n_var_groups(s));
363 
364  // Check for trivial return
365  if (ncomp == this->n_comp_group(s,vg)) return;
366 
367 #ifndef NDEBUG
368  if (ncomp >= ncv_magic)
369  {
370  const index_t ncvm = ncv_magic;
371  libmesh_error_msg("ERROR: ncomp must be less than DofObject::ncv_magic!\n" \
372  << "ncomp = " \
373  << ncomp \
374  << ", ncv_magic = " \
375  << ncvm \
376  << "\nrecompile and try again!");
377  }
378 #endif
379 
380  const unsigned int
381  start_idx_sys = this->start_idx(s),
382  n_vars_group = this->n_vars(s,vg),
383  base_offset = start_idx_sys + 2*vg;
384 
385  libmesh_assert_less ((base_offset + 1), _idx_buf.size());
386 
387  // if (ncomp)
388  // libMesh::out << "s,vg,ncomp="
389  // << s << ","
390  // << vg << ","
391  // << ncomp << '\n';
392 
393  // set the number of components, maintaining the number
394  // of variables in the group
395  _idx_buf[base_offset] = ncv_magic*n_vars_group + ncomp;
396 
397  // We use (invalid_id - 1) to signify no
398  // components for this object
399  _idx_buf[base_offset + 1] = (ncomp == 0) ? invalid_id - 1 : invalid_id;
400 
401  // this->debug_buffer();
402  // libMesh::out << "s,vg = " << s << "," << vg << '\n'
403  // << "base_offset=" << base_offset << '\n'
404  // << "this->n_comp(s,vg)=" << this->n_comp(s,vg) << '\n'
405  // << "this->n_comp_group(s,vg)=" << this->n_comp_group(s,vg) << '\n'
406  // << "this->n_vars(s,vg)=" << this->n_vars(s,vg) << '\n'
407  // << "this->n_var_groups(s)=" << this->n_var_groups(s) << '\n';
408 
409  libmesh_assert_equal_to (ncomp, this->n_comp_group(s,vg));
410 }
unsigned int n_comp_group(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:793
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:745
dof_id_type index_t
DoF index information.
Definition: dof_object.h:483
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:735
static const dof_id_type invalid_id
An invalid id to distinguish an uninitialized DofObject.
Definition: dof_object.h:324
unsigned int start_idx(const unsigned int s) const
The starting index for system s.
Definition: dof_object.h:878
index_buffer_t _idx_buf
Definition: dof_object.h:485
unsigned int n_systems() const
Definition: dof_object.h:726
static const index_t ncv_magic
Above we introduced the chimera ncv, which is a hybrid of the form ncv = ncv_magic*nv + nc where nv a...
Definition: dof_object.h:496
void libMesh::DofObject::set_n_systems ( const unsigned int  s)

Sets the number of systems for this DofObject.

Definition at line 165 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(), set_id(), DofObjectTest< Node >::testManualDofCalculation(), DofObjectTest< Node >::testSetNSystems(), and DofObjectTest< Node >::testSetNVariableGroups().

166 {
167  // Check for trivial return
168  if (ns == this->n_systems())
169  return;
170 
171  // Clear any existing data. This is safe to call
172  // even if we don't have any data.
173  this->clear_dofs();
174 
175  // Set the new number of systems
176  _idx_buf.resize(ns, ns);
177  _idx_buf[0] = ns;
178 
179 
180 #ifdef DEBUG
181 
182  // check that all systems now exist and that they have 0 size
183  libmesh_assert_equal_to (ns, this->n_systems());
184  for (unsigned int s=0; s<this->n_systems(); s++)
185  {
186  libmesh_assert_equal_to (this->n_vars(s), 0);
187  libmesh_assert_equal_to (this->n_var_groups(s), 0);
188  }
189 
190 #endif
191 }
void clear_dofs()
Clear the DofMap data structures and return to a pristine state.
Definition: dof_object.h:598
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:745
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:735
index_buffer_t _idx_buf
Definition: dof_object.h:485
unsigned int n_systems() const
Definition: dof_object.h:726
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 227 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(), DofObjectTest< Node >::testManualDofCalculation(), and DofObjectTest< Node >::testSetNVariableGroups().

229 {
230 
231  libmesh_assert_less (s, this->n_systems());
232 
233  // number of variable groups for this system - inferred
234  const unsigned int nvg = cast_int<unsigned int>(nvpg.size());
235 
236  // BSK - note that for compatibility with the previous implementation
237  // calling this method when (nvars == this->n_vars()) requires that
238  // we invalidate the DOF indices and set the number of components to 0.
239  // Note this was a bit of a surprise to me - there was no quick return in
240  // the old method, which caused removal and readdition of the DOF indices
241  // even in the case of (nvars == this->n_vars()), resulting in n_comp(s,v)
242  // implicitly becoming 0 regardless of any previous value.
243  // quick return?
244  if (nvg == this->n_var_groups(s))
245  {
246  for (unsigned int vg=0; vg<nvg; vg++)
247  {
248  this->set_n_comp_group(s,vg,0);
249  libmesh_assert_equal_to (this->n_vars(s,vg), nvpg[vg]);
250  }
251  return;
252  }
253 
254  // since there is ample opportunity to screw up other systems, let us
255  // cache their current sizes and later assert that they are unchanged.
256 #ifdef DEBUG
257  DofObject::index_buffer_t old_system_sizes;
258  old_system_sizes.reserve(this->n_systems());
259 
260  for (unsigned int s_ctr=0; s_ctr<this->n_systems(); s_ctr++)
261  old_system_sizes.push_back(this->n_var_groups(s_ctr));
262 #endif
263 
264  // remove current indices if we have some
265  if (this->n_var_groups(s) != 0)
266  {
267  const unsigned int old_nvg_s = this->n_var_groups(s);
268 
269  DofObject::index_buffer_t::iterator
270  it = _idx_buf.begin(),
271  end = _idx_buf.begin();
272 
273  std::advance(it, this->start_idx(s));
274  std::advance(end, this->end_idx(s));
275  _idx_buf.erase(it,end);
276 
277  for (unsigned int ctr=(s+1); ctr<this->n_systems(); ctr++)
278  _idx_buf[ctr] -= 2*old_nvg_s;
279  }
280 
281  // better not have any now!
282  libmesh_assert_equal_to (this->n_var_groups(s), 0);
283 
284  // Make sure we didn't screw up any of our sizes!
285 #ifdef DEBUG
286  for (unsigned int s_ctr=0; s_ctr<this->n_systems(); s_ctr++)
287  if (s_ctr != s)
288  libmesh_assert_equal_to (this->n_var_groups(s_ctr), old_system_sizes[s_ctr]);
289 #endif
290 
291  // OK, if the user requested 0 that is what we have
292  if (nvg == 0)
293  return;
294 
295  {
296  // array to hold new indices
297  DofObject::index_buffer_t var_idxs(2*nvg);
298  for (unsigned int vg=0; vg<nvg; vg++)
299  {
300  var_idxs[2*vg ] = ncv_magic*nvpg[vg] + 0;
301  var_idxs[2*vg + 1] = invalid_id - 1;
302  }
303 
304  DofObject::index_buffer_t::iterator it = _idx_buf.begin();
305  std::advance(it, this->end_idx(s));
306  _idx_buf.insert(it, var_idxs.begin(), var_idxs.end());
307 
308  for (unsigned int ctr=(s+1); ctr<this->n_systems(); ctr++)
309  _idx_buf[ctr] += 2*nvg;
310 
311  // resize _idx_buf to fit so no memory is wasted.
313  }
314 
315  libmesh_assert_equal_to (nvg, this->n_var_groups(s));
316 
317 #ifdef DEBUG
318 
319  // libMesh::out << " [ ";
320  // for (std::size_t i=0; i<_idx_buf.size(); i++)
321  // libMesh::out << _idx_buf[i] << " ";
322  // libMesh::out << "]\n";
323 
324  libmesh_assert_equal_to (this->n_var_groups(s), nvpg.size());
325 
326  for (unsigned int vg=0; vg<this->n_var_groups(s); vg++)
327  {
328  libmesh_assert_equal_to (this->n_vars(s,vg), nvpg[vg]);
329  libmesh_assert_equal_to (this->n_comp_group(s,vg), 0);
330  }
331 
332  for (unsigned int v=0; v<this->n_vars(s); v++)
333  libmesh_assert_equal_to (this->n_comp(s,v), 0);
334 
335  // again, all other system sizes should be unchanged!
336  for (unsigned int s_ctr=0; s_ctr<this->n_systems(); s_ctr++)
337  if (s_ctr != s)
338  libmesh_assert_equal_to (this->n_var_groups(s_ctr), old_system_sizes[s_ctr]);
339 
340 #endif
341 }
unsigned int n_comp_group(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:793
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:745
IterBase * end
Also have a polymorphic pointer to the end object, this prevents iterating past the end...
unsigned int end_idx(const unsigned int s) const
The ending index for system s.
Definition: dof_object.h:889
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:735
static const dof_id_type invalid_id
An invalid id to distinguish an uninitialized DofObject.
Definition: dof_object.h:324
unsigned int start_idx(const unsigned int s) const
The starting index for system s.
Definition: dof_object.h:878
std::vector< index_t > index_buffer_t
Definition: dof_object.h:484
void 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: dof_object.C:357
index_buffer_t _idx_buf
Definition: dof_object.h:485
unsigned int n_comp(const unsigned int s, const unsigned int var) const
Definition: dof_object.h:780
unsigned int n_systems() const
Definition: dof_object.h:726
static const index_t ncv_magic
Above we introduced the chimera ncv, which is a hybrid of the form ncv = ncv_magic*nv + nc where nv a...
Definition: dof_object.h:496
void libMesh::DofObject::set_old_dof_object ( )

Sets the old_dof_object to a copy of this.

Definition at line 150 of file dof_object.C.

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

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

151 {
152  this->clear_old_dof_object();
153 
155 
156  // Make a new DofObject, assign a copy of \p this.
157  // Make sure the copy ctor for DofObject works!!
158  this->old_dof_object = new DofObject(*this);
159 }
libmesh_assert(j)
DofObject()
Constructor.
Definition: dof_object.h:522
void clear_old_dof_object()
Sets the old_dof_object to libmesh_nullptr.
Definition: dof_object.C:142
DofObject * old_dof_object
This object on the last mesh.
Definition: dof_object.h:79
unique_id_type & libMesh::DofObject::set_unique_id ( )
void libMesh::DofObject::set_vg_dof_base ( const unsigned int  s,
const unsigned int  vg,
const dof_id_type  db 
)

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 902 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(), libMesh::DofMap::set_nonlocal_dof_objects(), and DofObjectTest< Node >::testManualDofCalculation().

905 {
906  libmesh_assert_less (s, this->n_systems());
907  libmesh_assert_less (vg, this->n_var_groups(s));
908 
909  const unsigned int
910  start_idx_sys = this->start_idx(s);
911 
912  libmesh_assert_less ((start_idx_sys + 2*vg + 1), _idx_buf.size());
913 
914  _idx_buf[start_idx_sys + 2*vg + 1] = db;
915 
916  libmesh_assert_equal_to (this->vg_dof_base(s,vg), db);
917 }
dof_id_type vg_dof_base(const unsigned int s, const unsigned int vg) const
VariableGroup DoF indices are indexed as id = base + var_in_vg*ncomp + comp This method allows for di...
Definition: dof_object.h:922
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:735
unsigned int start_idx(const unsigned int s) const
The starting index for system s.
Definition: dof_object.h:878
index_buffer_t _idx_buf
Definition: dof_object.h:485
unsigned int n_systems() const
Definition: dof_object.h:726
unsigned int libMesh::DofObject::start_idx ( const unsigned int  s) const
private

The starting index for system s.

Definition at line 878 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().

879 {
880  libmesh_assert_less (s, this->n_systems());
881  libmesh_assert_less (s, _idx_buf.size());
882 
883  return cast_int<unsigned int>(_idx_buf[s]);
884 }
index_buffer_t _idx_buf
Definition: dof_object.h:485
unsigned int n_systems() const
Definition: dof_object.h:726
unsigned int libMesh::DofObject::system_var_to_vg_var ( const unsigned int  s,
const unsigned int  vg,
const unsigned int  var 
) const
private

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

Definition at line 965 of file dof_object.h.

References n_vars().

Referenced by dof_number(), and set_dof_number().

968 {
969  unsigned int accumulated_sum=0;
970 
971  for (unsigned int vgc=0; vgc<vg; vgc++)
972  accumulated_sum += this->n_vars(s,vgc);
973 
974  libmesh_assert_less_equal (accumulated_sum, var);
975 
976  return (var - accumulated_sum);
977 }
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:745
unique_id_type libMesh::DofObject::unique_id ( ) const
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 494 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().

495 {
496  _idx_buf.clear();
497 
498 #ifdef LIBMESH_ENABLE_AMR
499  this->clear_old_dof_object();
500  const bool has_old_dof_object = cast_int<bool>(*begin++);
501 #endif
502 
503  const largest_id_type size = *begin++;
504  _idx_buf.reserve(size);
505  std::copy(begin, begin+size, back_inserter(_idx_buf));
506 
507  // Check as best we can for internal consistency now
508  libmesh_assert(_idx_buf.empty() ||
509  (_idx_buf[0] <= _idx_buf.size()));
510 #ifdef DEBUG
511  if (!_idx_buf.empty())
512  for (unsigned int i=1; i < _idx_buf[0]; ++i)
513  {
514  libmesh_assert_greater_equal (_idx_buf[i], _idx_buf[i-1]);
515  libmesh_assert_equal_to ((_idx_buf[i] - _idx_buf[i-1])%2, 0);
516  libmesh_assert_less_equal (_idx_buf[i], _idx_buf.size());
517  }
518 #endif
519 
520 #ifdef LIBMESH_ENABLE_AMR
521  if (has_old_dof_object)
522  {
523  this->old_dof_object = new DofObject();
524  this->old_dof_object->unpack_indexing(begin+size);
525  }
526 #endif
527 }
uint64_t largest_id_type
Definition: id_types.h:139
libmesh_assert(j)
DofObject()
Constructor.
Definition: dof_object.h:522
void clear_old_dof_object()
Sets the old_dof_object to libmesh_nullptr.
Definition: dof_object.C:142
DofObject * old_dof_object
This object on the last mesh.
Definition: dof_object.h:79
void 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 w...
Definition: dof_object.C:494
index_buffer_t _idx_buf
Definition: dof_object.h:485
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 473 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().

474 {
475 #ifdef LIBMESH_ENABLE_AMR
476  const bool has_old_dof_object = cast_int<bool>(*begin++);
477 
478  static const int dof_header_size = 2;
479 #else
480  static const bool has_old_dof_object = false;
481  static const int dof_header_size = 1;
482 #endif
483 
484  const largest_id_type this_indexing_size = *begin++;
485 
486  return cast_int<unsigned int>
487  (dof_header_size + this_indexing_size +
488  (has_old_dof_object ?
489  unpackable_indexing_size(begin+this_indexing_size) : 0));
490 }
static unsigned int unpackable_indexing_size(std::vector< largest_id_type >::const_iterator begin)
If we have indices packed into an buffer for communications, how much of that buffer applies to this ...
Definition: dof_object.C:473
uint64_t largest_id_type
Definition: id_types.h:139
bool libMesh::DofObject::valid_id ( ) const
Returns
true if this DofObject has a valid id set, false otherwise.

Definition at line 674 of file dof_object.h.

References _id, and invalid_id.

Referenced by libMesh::ReplicatedMesh::add_elem(), libMesh::DistributedMesh::add_elem(), libMesh::ReplicatedMesh::add_node(), libMesh::DistributedMesh::add_node(), libMesh::Node::get_info(), libMesh::Elem::get_info(), id(), libMesh::Elem::libmesh_assert_valid_node_pointers(), set_id(), DofObjectTest< Node >::testInvalidateId(), and DofObjectTest< Node >::testValidId().

675 {
676  return (DofObject::invalid_id != _id);
677 }
dof_id_type _id
The id of the DofObject.
Definition: dof_object.h:419
static const dof_id_type invalid_id
An invalid id to distinguish an uninitialized DofObject.
Definition: dof_object.h:324
bool libMesh::DofObject::valid_processor_id ( ) const
Returns
true if this DofObject has a valid id set, false otherwise.

Definition at line 718 of file dof_object.h.

References _processor_id, and invalid_processor_id.

Referenced by set_id(), DofObjectTest< Node >::testInvalidateProcId(), and DofObjectTest< Node >::testValidProcId().

719 {
721 }
static const processor_id_type invalid_processor_id
An invalid processor_id to distinguish DoFs that have not been assigned to a processor.
Definition: dof_object.h:335
processor_id_type _processor_id
The processor_id of the DofObject.
Definition: dof_object.h:430
bool libMesh::DofObject::valid_unique_id ( ) const
Returns
true if this DofObject has a valid unique_id set, false otherwise.

Definition at line 682 of file dof_object.h.

References _unique_id, and invalid_unique_id.

Referenced by libMesh::ReplicatedMesh::add_elem(), libMesh::DistributedMesh::add_elem(), libMesh::ReplicatedMesh::add_node(), libMesh::DistributedMesh::add_node(), libMesh::ReplicatedMesh::add_point(), libMesh::Elem::get_info(), libMesh::ReplicatedMesh::insert_elem(), libMesh::DistributedMesh::insert_elem(), libMesh::ReplicatedMesh::insert_node(), libMesh::Parallel::Packing< const Node * >::pack(), libMesh::Parallel::Packing< const Elem * >::pack(), set_id(), and unique_id().

683 {
684 #ifdef LIBMESH_ENABLE_UNIQUE_ID
686 #else
687  return false;
688 #endif
689 }
unique_id_type _unique_id
A globally unique id, guaranteed not to change as the mesh is repartitioned or adapted.
Definition: dof_object.h:413
static const unique_id_type invalid_unique_id
An invalid unique_id to distinguish an uninitialized DofObject.
Definition: dof_object.h:329
unsigned int libMesh::DofObject::var_to_vg ( const unsigned int  s,
const unsigned int  var 
) const
private

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

Definition at line 946 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().

948 {
949  const unsigned int
950  nvg = this->n_var_groups(s);
951 
952  for (unsigned int vg=0, vg_end=0; vg<nvg; vg++)
953  {
954  vg_end += this->n_vars(s,vg);
955  if (var < vg_end) return vg;
956  }
957 
958  libmesh_error_msg("We'll never get here!");
959  return 0;
960 }
unsigned int n_vars(const unsigned int s, const unsigned int vg) const
Definition: dof_object.h:745
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:735
dof_id_type libMesh::DofObject::vg_dof_base ( const unsigned int  s,
const unsigned int  vg 
) const

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 922 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(), set_vg_dof_base(), and DofObjectTest< Node >::testManualDofCalculation().

924 {
925  libmesh_assert_less (s, this->n_systems());
926  libmesh_assert_less (vg, this->n_var_groups(s));
927 
928  const unsigned int
929  start_idx_sys = this->start_idx(s);
930 
931  libmesh_assert_less ((start_idx_sys + 2*vg + 1), _idx_buf.size());
932 
933  // #ifdef DEBUG
934  // std::cout << " [ ";
935  // for (std:size_t i=0; i<_idx_buf.size(); i++)
936  // std::cout << _idx_buf[i] << " ";
937  // std::cout << "]\n";
938  // #endif
939 
940  return _idx_buf[start_idx_sys + 2*vg + 1];
941 }
unsigned int n_var_groups(const unsigned int s) const
Definition: dof_object.h:735
unsigned int start_idx(const unsigned int s) const
The starting index for system s.
Definition: dof_object.h:878
index_buffer_t _idx_buf
Definition: dof_object.h:485
unsigned int n_systems() const
Definition: dof_object.h:726

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 419 of file dof_object.h.

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

index_buffer_t libMesh::DofObject::_idx_buf
private
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 430 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 413 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 324 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::RBEIMConstruction::enrich_RB_space(), 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(), NodalNeighborsTest::testEdge2(), NodalNeighborsTest::testEdge3(), NodalNeighborsTest::testEdge4(), DofObjectTest< Node >::testValidId(), 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 335 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::MeshCommunication::delete_remote_elements(), libMesh::Elem::Elem(), libMesh::MeshCommunication::find_global_indices(), libMesh::MeshCommunication::gather(), 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(), DofObjectTest< Node >::testValidProcId(), 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 496 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 497 of file dof_object.h.

Referenced by n_vars().

DofObject* libMesh::DofObject::old_dof_object

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