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IBAMR
IBAMR version 0.19.
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Class OuternodeData<DIM> provides an implementation for data defined at cell nodes on the boundaries of AMR patches. It is derived from the hier::PatchData interface common to all SAMRAI patch data types. Given a CELL-centered AMR index space box, an outernode data object represents data of some template TYPE and depth on the cell nodes on the boundary of the box. Here, depth indicates the number of data values at each node index location. The OuternodnodeGeometry class provides the translation between the standard SAMRAI cell-centered AMR index space and outernode-centered data. More...
#include <OuternodeData.h>

Public Member Functions | |
| OuternodeData (const hier::Box< DIM > &box, int depth, tbox::Pointer< tbox::Arena > pool=tbox::Pointer< tbox::Arena >(NULL)) | |
| Constructor for an outernode data object. More... | |
| virtual | ~OuternodeData () |
| Virtual destructor for a outernode data object. More... | |
| int | getDepth () const |
| Return the depth (e.g., the number of components at each spatial location) of the array. More... | |
| bool | dataExists (int face_normal) const |
| Returns true if outernode data exists for the given face normal direction; false otherwise. More... | |
| hier::Box< DIM > | getDataBox (int face_normal, int side) |
| Return the box of valid node indices for outernode data. Note: the returned box will reside in the node index space. More... | |
| TYPE * | getPointer (int face_normal, int side, int depth=0) |
| Get a pointer to the beginning of a particular face normal, side, and depth component of the outernode centered array. More... | |
| const TYPE * | getPointer (int face_normal, int side, int depth=0) const |
| Get a const pointer to the beginning of a particular face normal, side, and depth component of the outernode centered array. More... | |
| TYPE & | operator() (const NodeIndex< DIM > &i, int depth=0) |
| Return a reference to data entry corresponding to a given node index and depth. More... | |
| const TYPE & | operator() (const NodeIndex< DIM > &i, int depth=0) const |
| Return a const reference to data entry corresponding to a given node index and depth. More... | |
| ArrayData< DIM, TYPE > & | getArrayData (int face_normal, int side) |
| Return a reference to the array data object for face normal, and side index of the outernode centered array. More... | |
| const ArrayData< DIM, TYPE > & | getArrayData (int face_normal, int side) const |
| Return a const reference to the array data object for face normal, and side index of the outernode centered array. More... | |
| virtual void | copy (const hier::PatchData< DIM > &src) |
| A fast copy from source to destination (i.e., this) patch data object. More... | |
| virtual void | copy2 (hier::PatchData< DIM > &dst) const |
| A fast copy from source (i.e., this) to destination patch data object. More... | |
| virtual void | copy (const hier::PatchData< DIM > &src, const hier::BoxOverlap< DIM > &overlap) |
| Copy data from source to destination (i.e., this) patch data object on the given overlap. More... | |
| virtual void | copy2 (hier::PatchData< DIM > &dst, const hier::BoxOverlap< DIM > &overlap) const |
| Copy data from source (i.e., this) to destination patch data object on the given overlap. More... | |
| void | copyDepth (int dst_depth, const NodeData< DIM, TYPE > &src, int src_depth) |
| Fast copy (i.e., assumes node and outernode data objects are defined over the same box) from the given node source data object to this destination outernode data object at the specified depths. More... | |
| void | copyDepth2 (int dst_depth, NodeData< DIM, TYPE > &dst, int src_depth) const |
| Fast copy (i.e., assumes node and outernode data objects are defined over the same box) to the given node destination data object from this source outernode data object at the specified depths. More... | |
| virtual void | sum (const hier::PatchData< DIM > &src, const hier::BoxOverlap< DIM > &overlap) |
| Add data from source to destination (i.e., this) patch data object on the given overlap. More... | |
| virtual bool | canEstimateStreamSizeFromBox () const |
| Return true if the patch data object can estimate the stream size required to fit its data using only index space information (i.e., a box). More... | |
| virtual int | getDataStreamSize (const hier::BoxOverlap< DIM > &overlap) const |
| Return the number of bytes needed to stream the data in this patch data object lying in the specified box overlap region. More... | |
| virtual void | packStream (tbox::AbstractStream &stream, const hier::BoxOverlap< DIM > &overlap) const |
| Pack data in this patch data object lying in the specified box overlap region into the stream. The overlap must be an NodeOverlap of the same DIM. More... | |
| virtual void | unpackStream (tbox::AbstractStream &stream, const hier::BoxOverlap< DIM > &overlap) |
| Unpack data from stream into this patch data object over the specified box overlap region. The overlap must be an NodeOverlap of the same DIM. More... | |
| virtual void | unpackStreamAndSum (tbox::AbstractStream &stream, const hier::BoxOverlap< DIM > &overlap) |
| Unpack data from stream and add into this patch data object over the specified box overlap region. The overlap must be an NodeOverlap of the same DIM. More... | |
| void | fill (const TYPE &t, int d=0) |
| Fill all values at depth d with the value t. More... | |
| void | fill (const TYPE &t, const hier::Box< DIM > &box, int d=0) |
| Fill all values at depth d within the box with the value t. More... | |
| void | fillAll (const TYPE &t) |
| Fill all depth components with value t. More... | |
| void | fillAll (const TYPE &t, const hier::Box< DIM > &box) |
| Fill all depth components within the box with value t. More... | |
| void | print (const hier::Box< DIM > &box, std::ostream &os=tbox::plog, int prec=12) const |
| Print all outernode data values residing in the specified box. If the depth of the array is greater than one, all depths are printed. More... | |
| void | print (const hier::Box< DIM > &box, int depth, std::ostream &os=tbox::plog, int prec=12) const |
| Print all outernode data values at the given array depth in the specified box. More... | |
| void | printAxisSide (int face_normal, int side, const hier::Box< DIM > &box, std::ostream &os=tbox::plog, int prec=12) const |
| Print all outernode centered data values for specified face_normal and side residing in the specified box. If the depth of the data is greater than one, all depths are printed. More... | |
| void | printAxisSide (int face_normal, int side, const hier::Box< DIM > &box, int depth, std::ostream &os=tbox::plog, int prec=12) const |
| Print all outernode centered data values for specified face_normal, side, and depth residing in the specified box. More... | |
| virtual void | getSpecializedFromDatabase (tbox::Pointer< tbox::Database > database) |
| Check that class version and restart file version are equal. If so, read data members from the database. More... | |
| virtual void | putSpecializedToDatabase (tbox::Pointer< tbox::Database > database) |
| Write out the class version number and other data members to the database. More... | |
| const Box< DIM > & | getBox () const |
| const Box< DIM > & | getGhostBox () const |
| const IntVector< DIM > & | getGhostCellWidth () const |
| void | setTime (const double timestamp) |
| double | getTime () const |
| virtual void | getFromDatabase (tbox::Pointer< tbox::Database > database) |
| virtual void | putToDatabase (tbox::Pointer< tbox::Database > database) |
Static Public Member Functions | |
| static size_t | getSizeOfData (const hier::Box< DIM > &box, int depth) |
| Calculate the amount of memory needed to represent outernode- centered data over a CELL-centered AMR index space box. More... | |
Protected Member Functions | |
| void | setGhostBox (const Box< DIM > &ghost_box) |
Private Member Functions | |
| OuternodeData (const OuternodeData< DIM, TYPE > &) | |
| void | operator= (const OuternodeData< DIM, TYPE > &) |
Private Attributes | |
| Box< DIM > | d_box |
| Box< DIM > | d_ghost_box |
| IntVector< DIM > | d_ghosts |
| double | d_timestamp |
Internal implementations of data copy operations. | |
| int | d_depth |
| ArrayData< DIM, TYPE > | d_data [DIM][2] |
| void | copyFromNode (const NodeData< DIM, TYPE > &src) |
| void | copyFromNode (const NodeData< DIM, TYPE > &src, const NodeOverlap< DIM > &overlap) |
| void | copyToNode (NodeData< DIM, TYPE > &dst) const |
| void | copyToNode (NodeData< DIM, TYPE > &dst, const NodeOverlap< DIM > &overlap) const |
| void | copyFromOuternode (const OuternodeData< DIM, TYPE > &src) |
| void | copyFromOuternode (const OuternodeData< DIM, TYPE > &src, const NodeOverlap< DIM > &overlap) |
| void | copyToOuternode (OuternodeData< DIM, TYPE > &dst) const |
| void | copyToOuternode (OuternodeData< DIM, TYPE > &dst, const NodeOverlap< DIM > &overlap) const |
Outernode data is stored in 2*DIM arrays, each of which contains data associated with node indices on an upper or lower box face in some corrdinate direction. The data layout in the outernode data arrays matches the corresponding array sections provided by the node data implementation. Where a node index falls on more than one box face (patch boundary edges and corners), the outernode data value belongs to only one data array so that there are no redundant data values. Specifically, when DIM > 1, outernode data boxes are "trimmed" so that each node index that lives on more than one face on the box boundary will be associated with the face of the largest coordinate direction and only that face. Within each array, data is stored in (i,...,k,d) order, where i,...,k indicates a spatial index and the d indicates the component depth at that location. Memory allocation is in column-major ordering (e.g., Fortran style) so that the leftmost index runs fastest in memory.
To illustrate the outernode data layout, in particular the "box trimming" that prevents redundant data values, we describe the data for a three-dimensional outernode data object instantiated over a box [l0:u0,l1:u1,l2:u2] in the standard SAMRAI cell-centered AMR index space.
Here face normal directions 0, 1, and 2 can be thought of as X, Y, Z
respectively, and d is the data depth.
face normal 0:
lower [ l0 : l0 , l1+1 : u1 , l2+1 : u2 , d ]
upper [ u0+1 : u0+1 , l1+1 : u1 , l2+1 : u2 , d ]
Note: Boxes are trimmed at edges intersecting faces with
normal directions 1 and 2 so that node indices shared
with those faces appear in data arrays associated with
higher dimension faces.
face normal 1:
lower [ l0 : u0+1 , l1 : l1 , l2+1 : u2 , d ]
upper [ l0 : u0+1 , u1+1 : u1+1 , l2+1 : u2 , d ]
Note: Boxes are trimmed at edges intersecting faces with
normal direction 2 so that node indices shared
with those faces appear in data arrays associated with
higher dimension faces.
face normal 2:
lower [ l0 : u0+1 , l1 : u1+1 , l2 : l2 , d ]
upper [ l0 : u0+1 , l1 : u1+1 , u2+1 : u2+1 , d ]
Note: Boxes are not trimmed.
* Other spatial dimensions are represented similarly.
The data type TYPE must define a default constructor (that takes no arguments) and also the assignment operator.
| SAMRAI::pdat::OuternodeData< DIM, TYPE >::OuternodeData | ( | const hier::Box< DIM > & | box, |
| int | depth, | ||
| tbox::Pointer< tbox::Arena > | pool = tbox::Pointer< tbox::Arena >(NULL) |
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| ) |
Note: Outernode data always has ghost cell width of zero.
| box | const Box reference describing the interior of the standard CELL-centered index box over which the outernode data object will be created. |
| depth | gives the number of data values for each spatial location in the array. |
| pool | memory arena. If not given, then the standard arena is used. |
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This function assumes that the amount of memory needed for TYPE is sizeof(TYPE). If this is not the case, then a specialized function must be defined.
| box | const Box reference describing the interior of the standard CELL-centered index box over which the outernode data object will be created. Note: the ghost cell width is assumed to be zero. |
| depth | gives the number of data values for each spatial location in the array. |
| int SAMRAI::pdat::OuternodeData< DIM, TYPE >::getDepth | ( | ) | const |
| bool SAMRAI::pdat::OuternodeData< DIM, TYPE >::dataExists | ( | int | face_normal | ) | const |
| face_normal | integer face normal direction for data, must satisfy 0 <= face_normal < DIM |
| hier::Box<DIM> SAMRAI::pdat::OuternodeData< DIM, TYPE >::getDataBox | ( | int | face_normal, |
| int | side | ||
| ) |
| face_normal | integer face normal direction for data, must satisfy 0 <= face_normal < DIM |
| side | integer lower (0) or upper (1) side of outernode data array |
| TYPE* SAMRAI::pdat::OuternodeData< DIM, TYPE >::getPointer | ( | int | face_normal, |
| int | side, | ||
| int | depth = 0 |
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| ) |
| face_normal | integer face normal direction for data, must satisfy 0 <= face_normal < DIM |
| side | integer lower (0) or upper (1) side of outernode data array |
| depth | integer depth component, must satisfy 0 <= depth < actual depth of data array |
| const TYPE* SAMRAI::pdat::OuternodeData< DIM, TYPE >::getPointer | ( | int | face_normal, |
| int | side, | ||
| int | depth = 0 |
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| ) | const |
| face_normal | integer face normal direction for data, must satisfy 0 <= face_normal < DIM |
| side | integer lower (0) or upper (1) side of outernode data array |
| depth | integer depth component, must satisfy 0 <= depth < actual depth of data array |
| TYPE& SAMRAI::pdat::OuternodeData< DIM, TYPE >::operator() | ( | const NodeIndex< DIM > & | i, |
| int | depth = 0 |
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| ) |
| i | const reference to NodeIndex, MUST be an index on the outernode of the box. |
| depth | integer depth component, must satisfy 0 <= depth < actual depth of data array |
| const TYPE& SAMRAI::pdat::OuternodeData< DIM, TYPE >::operator() | ( | const NodeIndex< DIM > & | i, |
| int | depth = 0 |
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| ) | const |
| i | const reference to NodeIndex, MUST be an index on the outernode of the box. |
| depth | integer depth component, must satisfy 0 <= depth < actual depth of data array |
| ArrayData<DIM,TYPE>& SAMRAI::pdat::OuternodeData< DIM, TYPE >::getArrayData | ( | int | face_normal, |
| int | side | ||
| ) |
| face_normal | integer face normal direction for data, must satisfy 0 <= face_normal < DIM |
| side | integer lower (0) or upper (1) side of outeredge data array |
| const ArrayData<DIM,TYPE>& SAMRAI::pdat::OuternodeData< DIM, TYPE >::getArrayData | ( | int | face_normal, |
| int | side | ||
| ) | const |
| face_normal | integer face normal direction for data, must satisfy 0 <= face_normal < DIM |
| side | integer lower (0) or upper (1) side of outeredge data array |
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Data is copied where there is overlap in the underlying index space. The copy is performed on the interior plus the ghost cell width (for both the source and destination). Currently, source data must be either NodeData or OuternodeData of the same DIM and TYPE. If not, then an unrecoverable error results.
Implements SAMRAI::hier::PatchData< DIM >.
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Data is copied where there is overlap in the underlying index space. The copy is performed on the interior plus the ghost cell width (for both the source and destination). Currently, destination data must be either NodeData or OuternodeData of the same DIM and TYPE. If not, then an unrecoverable error results.
Implements SAMRAI::hier::PatchData< DIM >.
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Currently, source data must be either NodeData or OuternodeData of the same DIM and TYPE and the overlap must be an NodeOverlap of the same DIM. If not, then an unrecoverable error
results.
Implements SAMRAI::hier::PatchData< DIM >.
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Currently, destination data must be either NodeData or OuternodeData
of the same DIM and TYPE and the overlap must be an NodeOverlap of the same DIM. If not, then an unrecoverable error
results.
Implements SAMRAI::hier::PatchData< DIM >.
| void SAMRAI::pdat::OuternodeData< DIM, TYPE >::copyDepth | ( | int | dst_depth, |
| const NodeData< DIM, TYPE > & | src, | ||
| int | src_depth | ||
| ) |
| void SAMRAI::pdat::OuternodeData< DIM, TYPE >::copyDepth2 | ( | int | dst_depth, |
| NodeData< DIM, TYPE > & | dst, | ||
| int | src_depth | ||
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Currently, source data must be OuternodeData of the same DIM and TYPE and the overlap must be an EdgeOverlap of the same DIM.
If not, then an unrecoverable error results.
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This routine is defined for the standard types (bool, char,
double, float, int, and dcomplex).
Implements SAMRAI::hier::PatchData< DIM >.
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This routine is defined for the standard types (bool, char,
double, float, int, and dcomplex).
Implements SAMRAI::hier::PatchData< DIM >.
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Implements SAMRAI::hier::PatchData< DIM >.
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Implements SAMRAI::hier::PatchData< DIM >.
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| void SAMRAI::pdat::OuternodeData< DIM, TYPE >::fill | ( | const TYPE & | t, |
| int | d = 0 |
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| void SAMRAI::pdat::OuternodeData< DIM, TYPE >::fill | ( | const TYPE & | t, |
| const hier::Box< DIM > & | box, | ||
| int | d = 0 |
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| ) |
| void SAMRAI::pdat::OuternodeData< DIM, TYPE >::fillAll | ( | const TYPE & | t | ) |
| void SAMRAI::pdat::OuternodeData< DIM, TYPE >::fillAll | ( | const TYPE & | t, |
| const hier::Box< DIM > & | box | ||
| ) |
| void SAMRAI::pdat::OuternodeData< DIM, TYPE >::print | ( | const hier::Box< DIM > & | box, |
| std::ostream & | os = tbox::plog, |
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| int | prec = 12 |
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| ) | const |
| box | const reference to box over whioch to print data. Note box is assumed to reside in standard cell-centered index space and will be converted to node index space. |
| os | reference to output stream. |
| prec | integer precision for printing floating point numbers (i.e., TYPE = float, double, or dcomplex). The default is 12 decimal places for double and complex floating point numbers, and the default is 6 decimal places floats. For other types, this value is ignored. |
| void SAMRAI::pdat::OuternodeData< DIM, TYPE >::print | ( | const hier::Box< DIM > & | box, |
| int | depth, | ||
| std::ostream & | os = tbox::plog, |
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| int | prec = 12 |
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| ) | const |
| box | const reference to box over whioch to print data. Note box is assumed to reside in standard cell-centered index space and will be converted to node index space. |
| depth | integer depth component, must satisfy 0 <= depth < actual depth of data array |
| os | reference to output stream. |
| prec | integer precision for printing floating point numbers (i.e., TYPE = float, double, or dcomplex). The default is 12 decimal places for double and complex floating point numbers, and the default is 6 decimal places floats. For other types, this value is ignored. |
| void SAMRAI::pdat::OuternodeData< DIM, TYPE >::printAxisSide | ( | int | face_normal, |
| int | side, | ||
| const hier::Box< DIM > & | box, | ||
| std::ostream & | os = tbox::plog, |
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| int | prec = 12 |
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| ) | const |
| face_normal | integer face normal direction for data, must satisfy 0 <= face_normal < DIM |
| side | integer lower (0) or upper (1) side of outernode data array |
| box | const reference to box over whioch to print data. Note box is assumed to reside in standard cell-centered index space and will be converted to node index space. |
| os | reference to output stream. |
| prec | integer precision for printing floating point numbers (i.e., TYPE = float, double, or dcomplex). The default is 12 decimal places for double and complex floating point numbers, and the default is 6 decimal places floats. For other types, this value is ignored. |
| void SAMRAI::pdat::OuternodeData< DIM, TYPE >::printAxisSide | ( | int | face_normal, |
| int | side, | ||
| const hier::Box< DIM > & | box, | ||
| int | depth, | ||
| std::ostream & | os = tbox::plog, |
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| int | prec = 12 |
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| ) | const |
| face_normal | integer face normal direction for data, must satisfy 0 <= face_normal < DIM |
| side | integer lower (0) or upper (1) side of outernode data array |
| box | const reference to box over whioch to print data. Note box is assumed to reside in standard cell-centered index space and will be converted to node index space. |
| depth | integer depth component, must satisfy 0 <= depth < actual depth of data array |
| os | reference to output stream. |
| prec | integer precision for printing floating point numbers (i.e., TYPE = float, double, or dcomplex). The default is 12 decimal places for double and complex floating point numbers, and the default is 6 decimal places floats. For other types, this value is ignored. |
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Assertions: database must be a non-null pointer.
Implements SAMRAI::hier::PatchData< DIM >.
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Assertions: database must be a non-null pointer.
Implements SAMRAI::hier::PatchData< DIM >.
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Return the box over which this patch data object is defined. All objects in the same patch are defined over the same box, although the patch data objects may interpret how to allocate storage for that box in different ways.
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Return the ghost cell box. The ghost cell box is defined to be the interior box grown by the ghost cell width.
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Get the ghost cell width associated with this patch data object.
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Set the simulation time stamp for the patch data type. The simulation time is initialized to zero when the patch data type is created.
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Get the simulation time stamp for the patch data type.
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Checks that class version and restart file version are equal. If so, reads in the data members common to all patch data types from database. This method then calls the getSpecializedFromDatabase() method to retrieve the data special to the concrete patch data type.
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Writes out the class version number to the database. Then, writes the data members common to all patch data types from database. After the common data is written to the database, the putSpecializedToDatabase() method is invoked.
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This protected method is used by concrete patch data subclasses to set the ghost box over which the patch data will be allocated. Note that this allows the ghost box to be inconsistant with its standard interpretation as the patch domain box grown by the ghost cell width (as set in the constructor).
This function is included to treat some special cases for concrete patch data types and should be used with caution.
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1.8.17