GEOS
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The InternalMeshGenerator class is a class handling GEOSX generated meshes. More...
#include <InternalMeshGenerator.hpp>
Public Member Functions | |
InternalMeshGenerator (const string &name, Group *const parent) | |
Main constructor for InternalMeshGenerator. More... | |
void | importFieldOnArray (Block block, string const &blockName, string const &meshFieldName, bool isMaterialField, dataRepository::WrapperBase &wrapper) const override |
import field from the mesh on the array accessible via the given wrapper. More... | |
virtual bool | isCartesian () const |
virtual void | reduceNumNodesForPeriodicBoundary (SpatialPartition &partition, integer(&numNodes)[3]) |
Reduce the number of nodes in a block coordinate direction for. More... | |
virtual void | setNodeGlobalIndicesOnPeriodicBoundary (SpatialPartition &partition, int(&index)[3]) |
Alter the directional indices for when the ending index should be set to the beginning of the index as is the case with periodic boundaries. More... | |
virtual void | setConnectivityForPeriodicBoundaries (int(&globalIJK)[3], integer const (&numNodesInDir)[3], int const (&firstElemIndexInPartition)[3], localIndex(&nodeOfBox)[8]) |
Alter connectivity to adhere to a specific periodic type boundary. More... | |
void | setConnectivityForPeriodicBoundary (int const component, int const (&globalIJK)[3], integer const (&numNodesInDir)[3], int const (&firstElemIndexInPartition)[3], localIndex(&nodeOfBox)[8]) |
Alter connectivity to adhere to a periodic type boundary. More... | |
virtual void | coordinateTransformation (arrayView2d< real64, nodes::REFERENCE_POSITION_USD > X, std::map< string, SortedArray< localIndex > > &nodeSets) |
Performs a coordinate transformation of all nodes. More... | |
Public Member Functions inherited from geos::MeshGeneratorBase | |
MeshGeneratorBase (string const &name, Group *const parent) | |
Main constructor for MeshGenerator base class. More... | |
virtual void | expandObjectCatalogs () override |
This function is used to expand any catalogs in the data structure. | |
virtual Group * | createChild (string const &childKey, string const &childName) override |
Create a new geometric object (box, plane, etc) as a child of this group. More... | |
void | generateMesh (Group &parent, SpatialPartition &partition) |
Generate the mesh object the input mesh object. More... | |
virtual void | freeResources () |
Free internal resources associated with mesh/data import. More... | |
std::map< string, string > const & | getVolumicFieldsMapping () const |
Get the name mapping between mesh volumic field names and internal GEOS volumic field names. More... | |
std::map< string, string > const & | getSurfacicFieldsMapping () const |
Get the name mapping between mesh surfacic field names and internal GEOS surfacic field names. More... | |
Public Member Functions inherited from geos::dataRepository::Group | |
template<typename LOG_LEVEL_INFO > | |
std::enable_if_t< geos::is_log_level_info< LOG_LEVEL_INFO >, void > | addLogLevel () |
Append a levelCondition and a log description to the description of the wrapped object given a log info struct. Must be called in constructor. More... | |
virtual bool | registerCallback (void *func, const std::type_info &funcType) |
Register a callback function on the group. More... | |
virtual void | reinit () |
Performs re-initialization of certain variable depending on the solver being used. | |
Group (string const &name, Group *const parent) | |
Constructor. More... | |
Group (string const &name, conduit::Node &rootNode) | |
Constructor. More... | |
Group (Group &&source)=default | |
Move constructor. More... | |
virtual | ~Group () |
Destructor, deletes all Groups and Wrappers owned by this Group. | |
Group ()=delete | |
Deleted default constructor. | |
Group (Group const &)=delete | |
Deleted copy constructor. | |
Group & | operator= (Group const &)=delete |
Deleted copy assignment operator. More... | |
Group & | operator= (Group &&)=delete |
Deleted move assignment operator. More... | |
void | printDataHierarchy (integer indent=0) const |
Prints the data hierarchy recursively. More... | |
string | dumpInputOptions () const |
string | dumpSubGroupsNames () const |
string | dumpWrappersNames () const |
template<typename T = Group> | |
T & | registerGroup (string const &name, std::unique_ptr< T > newObject) |
Register a new Group as a sub-group of current Group. More... | |
template<typename T = Group> | |
T & | registerGroup (string const &name, T *newObject) |
Register a new Group as a sub-group of current Group. More... | |
template<typename T = Group> | |
T & | registerGroup (string const &name) |
Register a new Group as a sub-group of current Group. More... | |
template<typename T = Group> | |
T & | registerGroup (subGroupMap::KeyIndex const &keyIndex) |
Register a new Group as a sub-group of current Group. More... | |
template<typename T = Group, typename TBASE = Group> | |
T & | registerGroup (string const &name, string const &catalogName) |
Register a new Group as a sub-group of current Group. More... | |
void | deregisterGroup (string const &name) |
Removes a child group from this group. More... | |
template<typename T = Group, typename KEY = void> | |
T * | getGroupPointer (KEY const &key) |
Return a pointer to a sub-group of the current Group. More... | |
template<typename T = Group, typename KEY = void> | |
T const * | getGroupPointer (KEY const &key) const |
Return a pointer to a sub-group of the current Group. More... | |
template<typename T = Group, typename KEY = void> | |
T & | getGroup (KEY const &key) |
Return a reference to a sub-group of the current Group. More... | |
template<typename T = Group, typename KEY = void> | |
T const & | getGroup (KEY const &key) const |
Return a reference to a sub-group of the current Group. More... | |
template<typename T = Group> | |
T & | getGroupByPath (string const &path) |
Retrieve a group from the hierarchy using a path. More... | |
template<typename T = Group> | |
T const & | getGroupByPath (string const &path) const |
Retrieve a group from the hierarchy using a path. More... | |
subGroupMap & | getSubGroups () |
Get the subgroups object. More... | |
subGroupMap const & | getSubGroups () const |
Get the subgroups object. More... | |
localIndex | numSubGroups () const |
return the number of sub groups in this Group More... | |
std::vector< string > | getSubGroupsNames () const |
template<typename T = Group> | |
bool | hasGroup (string const &name) const |
Check whether a sub-group exists. More... | |
template<typename T > | |
bool | hasSubGroupOfType () const |
Check whether a sub-group exists by type. More... | |
template<typename GROUPTYPE = Group, typename ... GROUPTYPES, typename LAMBDA > | |
void | forSubGroups (LAMBDA &&lambda) |
Apply the given functor to subgroups that can be casted to one of specified types. More... | |
template<typename GROUPTYPE = Group, typename ... GROUPTYPES, typename LAMBDA > | |
void | forSubGroups (LAMBDA &&lambda) const |
Apply the given functor to subgroups that can be casted to one of specified types. More... | |
template<typename GROUPTYPE = Group, typename ... GROUPTYPES, typename LAMBDA > | |
void | forSubGroupsIndex (LAMBDA &&lambda) |
Apply the given functor to subgroups that can be casted to one of specified types. More... | |
template<typename GROUPTYPE = Group, typename ... GROUPTYPES, typename LAMBDA > | |
void | forSubGroupsIndex (LAMBDA &&lambda) const |
Apply the given functor to subgroups that can be casted to one of specified types. More... | |
template<typename GROUPTYPE = Group, typename ... GROUPTYPES, typename LOOKUP_CONTAINER , typename LAMBDA > | |
void | forSubGroups (LOOKUP_CONTAINER const &subGroupKeys, LAMBDA &&lambda) |
Apply the given functor to subgroups that can be casted to one of specified types. More... | |
template<typename GROUPTYPE = Group, typename ... GROUPTYPES, typename LOOKUP_CONTAINER , typename LAMBDA > | |
void | forSubGroups (LOOKUP_CONTAINER const &subGroupKeys, LAMBDA &&lambda) const |
Apply the given functor to subgroups that can be casted to one of specified types. More... | |
template<typename LAMBDA > | |
void | forWrappers (LAMBDA &&lambda) |
Apply the given functor to wrappers. More... | |
template<typename LAMBDA > | |
void | forWrappers (LAMBDA &&lambda) const |
Apply the given functor to wrappers. More... | |
template<typename TYPE , typename ... TYPES, typename LAMBDA > | |
void | forWrappers (LAMBDA &&lambda) |
Apply the given functor to wrappers that can be cast to one of specified types. More... | |
template<typename TYPE , typename ... TYPES, typename LAMBDA > | |
void | forWrappers (LAMBDA &&lambda) const |
Apply the given functor to wrappers that can be cast to one of specified types. More... | |
virtual void | initialize_postMeshGeneration () |
initialization post generation of the mesh. | |
void | initialize () |
Run initialization functions on this and all subgroups. More... | |
virtual void | initializationOrder (string_array &order) |
Sets the initialization order for sub-Groups. More... | |
void | initializePostInitialConditions () |
Initialization routine to be called after calling ApplyInitialConditions(). More... | |
void | postRestartInitializationRecursive () |
Initialization routine to be called after calling reading a restart file. More... | |
void | processInputFileRecursive (xmlWrapper::xmlDocument &xmlDocument, xmlWrapper::xmlNode &targetNode) |
Recursively read values using ProcessInputFile() from the input file and put them into the wrapped values for this group. Also add the includes content to the xmlDocument when Include nodes are encountered. More... | |
void | processInputFileRecursive (xmlWrapper::xmlDocument &xmlDocument, xmlWrapper::xmlNode &targetNode, xmlWrapper::xmlNodePos const &nodePos) |
Same as processInputFileRecursive(xmlWrapper::xmlDocument &, xmlWrapper::xmlNode &) but allow to reuse an existing xmlNodePos. More... | |
void | postInputInitializationRecursive () |
Recursively call postInputInitialization() to apply post processing after reading input values. | |
template<typename T , typename TBASE = T> | |
Wrapper< TBASE > & | registerWrapper (string const &name, wrapperMap::KeyIndex::index_type *const rkey=nullptr) |
Create and register a Wrapper around a new object. More... | |
template<typename T , typename TBASE = T> | |
Wrapper< TBASE > & | registerWrapper (Group::wrapperMap::KeyIndex const &viewKey) |
Create and register a Wrapper around a new object. More... | |
template<typename T > | |
Wrapper< T > & | registerWrapper (string const &name, std::unique_ptr< T > newObject) |
Register a Wrapper around a given object and take ownership. More... | |
template<typename T > | |
Wrapper< T > & | registerWrapper (string const &name, T *newObject) |
Register a Wrapper around an existing object, does not take ownership of the object. More... | |
WrapperBase & | registerWrapper (std::unique_ptr< WrapperBase > wrapper) |
Register and take ownership of an existing Wrapper. More... | |
void | deregisterWrapper (string const &name) |
Removes a Wrapper from this group. More... | |
void | generateDataStructureSkeleton (integer const level) |
Build a complete datastructure for schema generation. More... | |
virtual void | setSchemaDeviations (xmlWrapper::xmlNode schemaRoot, xmlWrapper::xmlNode schemaParent, integer documentationType) |
Inform the schema generator of any deviations between the xml and GEOS data structures. More... | |
virtual void | registerDataOnMeshRecursive (Group &meshBodies) |
Calls RegisterDataOnMesh() recursively. More... | |
virtual void | registerDataOnMesh (Group &meshBodies) |
Register data on mesh entities. More... | |
virtual localIndex | packSize (string_array const &wrapperNames, integer const recursive, bool onDevice, parallelDeviceEvents &events) const |
Get the size required to pack a list of wrappers. More... | |
virtual localIndex | packSize (string_array const &wrapperNames, arrayView1d< localIndex const > const &packList, integer const recursive, bool onDevice, parallelDeviceEvents &events) const |
Get the size required to pack a list of indices within a list of wrappers. More... | |
localIndex | packSize (arrayView1d< localIndex const > const &packList, integer const recursive, bool onDevice, parallelDeviceEvents &events) const |
Get the size required to pack a list of indices for all registered wrappers. More... | |
virtual localIndex | pack (buffer_unit_type *&buffer, string_array const &wrapperNames, integer const recursive, bool onDevice, parallelDeviceEvents &events) const |
Pack a list of wrappers to a buffer. More... | |
virtual localIndex | pack (buffer_unit_type *&buffer, string_array const &wrapperNames, arrayView1d< localIndex const > const &packList, integer const recursive, bool onDevice, parallelDeviceEvents &events) const |
Pack a list of indices within a list of wrappers. More... | |
localIndex | pack (buffer_unit_type *&buffer, arrayView1d< localIndex const > const &packList, integer const recursive, bool onDevice, parallelDeviceEvents &events) const |
Pack a list of indices for all registered wrappers. More... | |
virtual localIndex | unpack (buffer_unit_type const *&buffer, arrayView1d< localIndex > &packList, integer const recursive, bool onDevice, parallelDeviceEvents &events, MPI_Op op=MPI_REPLACE) |
Unpack a buffer. More... | |
template<typename KEY > | |
WrapperBase const & | getWrapperBase (KEY const &key) const |
Return a reference to a WrapperBase stored in this group. More... | |
template<typename KEY > | |
WrapperBase & | getWrapperBase (KEY const &key) |
Return a reference to a WrapperBase stored in this group. More... | |
indexType | getWrapperIndex (string const &name) const |
wrapperMap const & | wrappers () const |
Get access to the internal wrapper storage. More... | |
wrapperMap & | wrappers () |
Get access to the internal wrapper storage. More... | |
indexType | numWrappers () const |
Return the number of wrappers. More... | |
std::vector< string > | getWrappersNames () const |
template<typename LOOKUP_TYPE > | |
bool | hasWrapper (LOOKUP_TYPE const &lookup) const |
Check if a wrapper exists. More... | |
template<typename T , typename LOOKUP_TYPE > | |
Wrapper< T > const & | getWrapper (LOOKUP_TYPE const &index) const |
Retrieve a Wrapper stored in this group. More... | |
template<typename T , typename LOOKUP_TYPE > | |
Wrapper< T > & | getWrapper (LOOKUP_TYPE const &index) |
Retrieve a Wrapper stored in this group. More... | |
template<typename T , typename LOOKUP_TYPE > | |
Wrapper< T > const * | getWrapperPointer (LOOKUP_TYPE const &index) const |
Retrieve a Wrapper stored in this group. More... | |
template<typename T , typename LOOKUP_TYPE > | |
Wrapper< T > * | getWrapperPointer (LOOKUP_TYPE const &index) |
Retrieve a Wrapper stored in this group. More... | |
template<typename T , typename LOOKUP_TYPE > | |
GEOS_DECLTYPE_AUTO_RETURN | getReference (LOOKUP_TYPE const &lookup) const |
Look up a wrapper and get reference to wrapped object. More... | |
template<typename T , typename LOOKUP_TYPE > | |
T & | getReference (LOOKUP_TYPE const &lookup) |
Look up a wrapper and get reference to wrapped object. More... | |
virtual void | resize (localIndex const newSize) |
Resize the group and all contained wrappers that resize with parent. More... | |
virtual void | reserve (indexType const newsize) |
Set the new capacity and reserve it in all wrappers that resize with parent. More... | |
localIndex | capacity () const |
Get the "capacity" of the group, which determines the capacity of resizable wrappers. More... | |
localIndex | size () const |
Get the "size" of the group, which determines the number of elements in resizable wrappers. More... | |
string const & | getName () const |
Get group name. More... | |
string | getPath () const |
Return the path of this Group in the data repository. Starts with '/' followed by the hierarchy of the children of the "Problem" in which the Group is. More... | |
DataContext const & | getDataContext () const |
template<typename KEY > | |
DataContext const & | getWrapperDataContext (KEY key) const |
Group & | getParent () |
Access the group's parent. More... | |
Group const & | getParent () const |
Access the group's parent. More... | |
bool | hasParent () const |
localIndex | getIndexInParent () const |
Get the group's index within its parent group. More... | |
localIndex | getSubGroupIndex (keyType const &key) const |
Get the index of a sub-Group within this group. More... | |
int | sizedFromParent () const |
Check whether this Group is resized when its parent is resized. More... | |
Group & | setSizedFromParent (int val) |
Set whether this wrapper is resized when its parent is resized. More... | |
RestartFlags | getRestartFlags () const |
Get flags that control restart output of this group. More... | |
void | setRestartFlags (RestartFlags flags) |
Set flags that control restart output of this group. More... | |
InputFlags | getInputFlags () const |
Get input flags for schema generation. More... | |
void | setInputFlags (InputFlags flags) |
Set input flags for schema generation. More... | |
conduit::Node & | getConduitNode () |
Return the Conduit node object associated with this group. More... | |
conduit::Node const & | getConduitNode () const |
Return the Conduit node object associated with this group. More... | |
void | prepareToWrite () |
Register the group and its wrappers with Conduit. | |
void | finishWriting () |
Write the group and its wrappers into Conduit. | |
void | loadFromConduit () |
Read the group and its wrappers from Conduit. | |
void | enableLogLevelInput () |
void | setLogLevel (integer const logLevel) |
Set verbosity level. More... | |
integer | getLogLevel () const |
Static Public Member Functions | |
static string | catalogName () |
Return the name of the InternalMeshGenerator in object Catalog. More... | |
Static Public Member Functions inherited from geos::MeshGeneratorBase | |
static CatalogInterface::CatalogType & | getCatalog () |
Accessor for the singleton Catalog object. More... | |
Static Public Member Functions inherited from geos::dataRepository::Group | |
template<typename T0 , typename T1 , typename ... CASTTYPES, typename CONTAINERTYPE , typename LAMBDA > | |
static bool | applyLambdaToContainer (CONTAINERTYPE &container, LAMBDA &&lambda) |
Apply a given functor to a container if the container can be cast to one of the specified types. More... | |
static CatalogInterface::CatalogType & | getCatalog () |
Get the singleton catalog for this Group. More... | |
Protected Member Functions | |
void | postInputInitialization () override |
Protected Member Functions inherited from geos::dataRepository::Group | |
virtual void | initializePreSubGroups () |
Called by Initialize() prior to initializing sub-Groups. | |
virtual void | initializePostSubGroups () |
Called by Initialize() after to initializing sub-Groups. | |
virtual void | initializePostInitialConditionsPreSubGroups () |
Called by InitializePostInitialConditions() prior to initializing sub-Groups. | |
virtual void | initializePostInitialConditionsPostSubGroups () |
Called by InitializePostInitialConditions() after to initializing sub-Groups. | |
virtual void | postRestartInitialization () |
Performs initialization required after reading from a restart file. | |
Protected Attributes | |
int | m_dim |
Mesh number of dimension. | |
real64 | m_min [3] |
Minimum extent of mesh dimensions. | |
real64 | m_max [3] |
Maximum extent of mesh dimensions. | |
real64 | m_coordinatePrecision |
Position tolerance for adding nodes to nodesets. | |
array1d< real64 > | m_vertices [3] |
Array of vertex coordinates. | |
array1d< integer > | m_nElems [3] |
Ndim x nElem spatialized for element indexes. | |
array1d< real64 > | m_nElemBias [3] |
Ndim x nElem spatialized array of element bias. | |
array1d< real64 > | m_setCoords [3] |
Protected Attributes inherited from geos::MeshGeneratorBase | |
std::map< string, string > | m_volumicFields |
Mapping from volumic field source to GEOS field. | |
std::map< string, string > | m_surfacicFields |
Mapping from surfacic field source to GEOS field. | |
Additional Inherited Members | |
Public Types inherited from geos::MeshGeneratorBase | |
enum class | Block { VOLUMIC , SURFACIC , LINEIC } |
Describe which kind of block must be considered. | |
using | CatalogInterface = dataRepository::CatalogInterface< MeshGeneratorBase, string const &, Group *const > |
using alias for templated Catalog meshGenerator type | |
Public Types inherited from geos::dataRepository::Group | |
using | subGroupMap = MappedVector< Group, Group *, keyType, indexType > |
The template specialization of MappedVector to use for the collection of sub-Group objects. | |
using | wrapperMap = MappedVector< WrapperBase, WrapperBase *, keyType, indexType > |
The template specialization of MappedVector to use for the collection wrappers objects. | |
using | CatalogInterface = dataRepository::CatalogInterface< Group, string const &, Group *const > |
Type alias for catalog interface used by this class. See CatalogInterface. | |
The InternalMeshGenerator class is a class handling GEOSX generated meshes.
Definition at line 36 of file InternalMeshGenerator.hpp.
Main constructor for InternalMeshGenerator.
[in] | name | of the InternalMeshGenerator |
[in] | parent | point to the parent Group of the InternalMeshGenerator |
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inlinestatic |
Return the name of the InternalMeshGenerator in object Catalog.
Definition at line 53 of file InternalMeshGenerator.hpp.
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inlinevirtual |
Performs a coordinate transformation of all nodes.
[in,out] | X | The nodes coordinates. |
[in,out] | nodeSets | The name to node sets mapping. |
Reimplemented in geos::InternalWellboreGenerator.
Definition at line 137 of file InternalMeshGenerator.hpp.
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inlineoverridevirtual |
import field from the mesh on the array accessible via the given wrapper.
block | Type of block to import from. |
blockName | name of the block to copy data from. |
meshFieldName | name of the field in the meshd |
isMaterialField | Indicate if we want to import material or regular fields |
wrapper | Wrapper to access the array |
Implements geos::MeshGeneratorBase.
Definition at line 56 of file InternalMeshGenerator.hpp.
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inlinevirtual |
Reimplemented in geos::InternalWellboreGenerator.
Definition at line 72 of file InternalMeshGenerator.hpp.
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overrideprotectedvirtual |
This function provides capability to post process input values prior to any other initialization operations.
Reimplemented from geos::dataRepository::Group.
Reimplemented in geos::InternalWellboreGenerator.
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inlinevirtual |
Reduce the number of nodes in a block coordinate direction for.
partition | The partitioning object |
numNodes | The number of nodes in each coordinate direction. |
Reimplemented in geos::InternalWellboreGenerator.
Definition at line 82 of file InternalMeshGenerator.hpp.
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inlinevirtual |
Alter connectivity to adhere to a specific periodic type boundary.
globalIJK | The global ijk indices. |
numNodesInDir | The number of elements in each direction globally. |
firstElemIndexInPartition | The first index in the partition in each direction. |
nodeOfBox | The connectivity. |
Reimplemented in geos::InternalWellboreGenerator.
Definition at line 110 of file InternalMeshGenerator.hpp.
void geos::InternalMeshGenerator::setConnectivityForPeriodicBoundary | ( | int const | component, |
int const (&) | globalIJK[3], | ||
integer const (&) | numNodesInDir[3], | ||
int const (&) | firstElemIndexInPartition[3], | ||
localIndex(&) | nodeOfBox[8] | ||
) |
Alter connectivity to adhere to a periodic type boundary.
component | The direction of the periodicity. |
globalIJK | The global ijk indices. |
numNodesInDir | The number of elements in each direction globally. |
firstElemIndexInPartition | The first index in the partition in each direction. |
nodeOfBox | The connectivity. |
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inlinevirtual |
Alter the directional indices for when the ending index should be set to the beginning of the index as is the case with periodic boundaries.
partition | The partitioning object |
index | The indices to be evaluated for periodic indexing. merging. |
Reimplemented in geos::InternalWellboreGenerator.
Definition at line 97 of file InternalMeshGenerator.hpp.
Coordinates of the nodes in each direction which may be calculated based on some geometry specifications and "set" for later use when generating the mesh.
Definition at line 192 of file InternalMeshGenerator.hpp.