void _Mesh_Build( void* mesh, void* data ) {
Mesh* self = (Mesh*)mesh;
unsigned nDims;
unsigned d_i;
assert( self );
if( self->generator ) {
Stg_Component_Build( self->generator, data, False );
MeshGenerator_Generate( self->generator, self, data );
}
if( self->algorithms ) Stg_Component_Build( self->algorithms, data, False );
nDims = Mesh_GetDimSize( self );
if( !nDims ){
self->isBuilt = False;
return;
}
self->topoDataInfos = Memory_Alloc_Array( ExtensionManager*, nDims, "mesh::topoDataInfos" );
self->topoDatas = Memory_Alloc_Array( void*, nDims, "mesh::topoDatas" );
for( d_i = 0; d_i < nDims; d_i++ ) {
char name[20];
unsigned size;
if( !UIntMap_Map( self->topoDataSizes, d_i, &size ) || !size ||
!Mesh_GetDomainSize( self, d_i ) )
{
self->topoDataInfos[d_i] = NULL;
self->topoDatas[d_i] = NULL;
continue;
}
sprintf( name, "topoData(%d)", d_i );
self->topoDataInfos[d_i] = ExtensionManager_New_OfStruct( name, size );
self->topoDatas[d_i] = (void*)ExtensionManager_Malloc( self->topoDataInfos[d_i], Mesh_GetDomainSize( self, d_i ) );
}
/*
** Set up the geometric information.
*/
self->minAxialSep = Memory_Alloc_Array( double, nDims, "Mesh::minAxialSep" );
self->minLocalCrd = Memory_Alloc_Array( double, nDims, "Mesh::minLocalCrd" );
self->maxLocalCrd = Memory_Alloc_Array( double, nDims, "Mesh::maxLocalCrd" );
self->minDomainCrd = Memory_Alloc_Array( double, nDims, "Mesh::minLocalCrd" );
self->maxDomainCrd = Memory_Alloc_Array( double, nDims, "Mesh::maxLocalCrd" );
self->minGlobalCrd = Memory_Alloc_Array( double, nDims, "Mesh::minGlobalCrd" );
self->maxGlobalCrd = Memory_Alloc_Array( double, nDims, "Mesh::maxGlobalCrd" );
Mesh_DeformationUpdate( self );
}
Cell_Index _ElementCellLayout_MapElementIdToCellId( void* elementCellLayout, unsigned element_dI ) {
#ifdef CAUTIOUS
{
ElementCellLayout* self = (ElementCellLayout*)elementCellLayout;
Stream* errorStr = Journal_Register( Error_Type, (Name)self->type );
Journal_Firewall( element_dI < Mesh_GetDomainSize( self->mesh, Mesh_GetDimSize( self->mesh ) ), errorStr, "Error - in %s(): User asked "
"for cell corresponding to element %d, but the mesh that this cell layout is based on only "
"has %d elements.\n", __func__, element_dI, Mesh_GetDomainSize( self->mesh, Mesh_GetDimSize( self->mesh ) ) );
}
#endif
return element_dI;
}
void Mesh_Sync( void* mesh ) {
Mesh* self = (Mesh*)mesh;
const Sync* sync;
int nDims, nLocals, nDomains;
assert( self );
sync = Mesh_GetSync( self, 0 );
nDims = Mesh_GetDimSize( self );
nLocals = Mesh_GetLocalSize( self, 0 );
nDomains = Mesh_GetDomainSize( self, 0 );
if (nDomains > nLocals) // only perform this where where the domain size is greater than the local size... ie running in parallel
Sync_SyncArray( sync, Mesh_GetVertex( self, 0 ), nDims * sizeof(double), Mesh_GetVertex( self, nLocals ), nDims * sizeof(double), nDims * sizeof(double) );
/* TODO
if( self->dataSyncArrays ) {
unsigned d_i;
for( d_i = 0; d_i < Mesh_GetDimSize( self ); d_i++ ) {
if( self->dataSyncArrays[d_i] )
Decomp_Sync_Array_Sync( self->dataSyncArrays[d_i] );
}
}
*/
}
void _SphericalGenerator_GenElementTypes( void* meshGenerator, Mesh* mesh )
{
SphericalGenerator* self = (SphericalGenerator*)meshGenerator;
Stream* stream;
unsigned nDomainEls;
unsigned e_i;
assert( self && Stg_CheckType( self, SphericalGenerator ) );
stream = Journal_Register( Info_Type, (Name)self->type );
Journal_Printf( stream, "Generating element types...\n" );
Stream_Indent( stream );
mesh->nElTypes = 1;
mesh->elTypes = Memory_Alloc_Array( Mesh_ElementType*, mesh->nElTypes, "Mesh::elTypes" );
mesh->elTypes[0] = (Mesh_ElementType*)Mesh_HexType_New();
Mesh_ElementType_SetMesh( mesh->elTypes[0], mesh );
nDomainEls = Mesh_GetDomainSize( mesh, Mesh_GetDimSize( mesh ) );
mesh->elTypeMap = Memory_Alloc_Array( unsigned, nDomainEls, "Mesh::elTypeMap" );
for( e_i = 0; e_i < nDomainEls; e_i++ )
mesh->elTypeMap[e_i] = 0;
Mesh_SetAlgorithms( mesh, Mesh_SphericalAlgorithms_New( "", NULL ) );
MPI_Barrier( self->mpiComm );
Journal_Printf( stream, "... element types are '%s',\n", mesh->elTypes[0]->type );
Journal_Printf( stream, "... mesh algorithm type is '%s',\n", mesh->algorithms->type );
Journal_Printf( stream, "... done.\n" );
Stream_UnIndent( stream );
}
void _AnalyticFeVariable_Build( void* analyticFeVariable, void* data ) {
AnalyticFeVariable* self = (AnalyticFeVariable*)analyticFeVariable;
DomainContext* context = self->context;
DofLayout* dofLayout = NULL;
Name name, varName[9];
Variable* variable = NULL;
Variable* baseVariable = NULL;
FeMesh* referenceMesh = NULL;
unsigned nDomainVerts;
Index var_I, node_I;
double* arrayPtr;
Dof_Index componentsCount;
Variable_Register* variable_Register = NULL;;
_FeVariable_Build( self, data );
context = self->context;
variable_Register = context->variable_Register;
referenceMesh = self->numericField->feMesh;
componentsCount = self->numericField->fieldComponentCount;
name = Stg_Object_AppendSuffix( self->numericField, (Name)"AnalyticVariable" );
nDomainVerts = Mesh_GetDomainSize( referenceMesh, MT_VERTEX );
if( componentsCount == 1 ) {
arrayPtr = Memory_Alloc_Array_Unnamed( double, nDomainVerts );
baseVariable = Variable_NewScalar( name,
(AbstractContext*)context, Variable_DataType_Double, (Index*)&nDomainVerts,
NULL, (void**)&arrayPtr, variable_Register );
}
void SROpGenerator_GenLevelEqNums( SROpGenerator* self, unsigned level ) {
Mesh* cMesh;
unsigned* nNodalDofs;
unsigned nDomainNodes, nLocalNodes;
DofLayout* dofLayout;
unsigned** dstArray;
unsigned curEqNum;
unsigned maxDofs;
unsigned topNode;
unsigned base, subTotal;
MPI_Comm comm;
unsigned nProcs, rank;
MPI_Status status;
unsigned* tuples;
Sync* sync;
unsigned n_i, dof_i;
assert( self && Stg_CheckType( self, SROpGenerator ) );
assert( self->meshes && self->topMaps && self->eqNums );
assert( level < self->nLevels );
cMesh = self->meshes[level];
nDomainNodes = Mesh_GetDomainSize( cMesh, MT_VERTEX );
nLocalNodes = Mesh_GetLocalSize( cMesh, MT_VERTEX );
dofLayout = self->fineEqNum->dofLayout;
comm = Comm_GetMPIComm( Mesh_GetCommTopology( cMesh, MT_VERTEX ) );
MPI_Comm_size( comm, (int*)&nProcs );
MPI_Comm_rank( comm, (int*)&rank );
/* Allocate for destination array. */
nNodalDofs = AllocArray( unsigned, nDomainNodes );
for( n_i = 0; n_i < nDomainNodes; n_i++ )
nNodalDofs[n_i] = dofLayout->dofCounts[self->topMaps[level][n_i]];
dstArray = AllocComplex2D( unsigned, nDomainNodes, nNodalDofs );
/* Build initial destination array and store max dofs. */
curEqNum = 0;
maxDofs = 0;
for( n_i = 0; n_i < nLocalNodes; n_i++ ) {
if( nNodalDofs[n_i] > maxDofs )
maxDofs = nNodalDofs[n_i];
topNode = self->topMaps[level][n_i];
for( dof_i = 0; dof_i < nNodalDofs[n_i]; dof_i++ ) {
if( self->fineEqNum->mapNodeDof2Eq[topNode][dof_i] != (unsigned)-1 )
dstArray[n_i][dof_i] = curEqNum++;
else
dstArray[n_i][dof_i] = (unsigned)-1;
}
}
/* Order the equation numbers based on processor rank; cascade counts forward. */
base = 0;
subTotal = curEqNum;
if( rank > 0 ) {
insist( MPI_Recv( &base, 1, MPI_UNSIGNED, rank - 1, 6669, comm, &status ), == MPI_SUCCESS );
subTotal = base + curEqNum;
}
double* Mesh_GetVertex( void* mesh, unsigned domain ) {
Mesh* self = (Mesh*)mesh;
assert( self );
assert( domain < Mesh_GetDomainSize( self, MT_VERTEX ) );
assert( self->vertices );
return self->vertices + domain*Mesh_GetDimSize(self);
}
Cell_Index _ElementCellLayout_CellOf( void* elementCellLayout, void* _particle ) {
ElementCellLayout* self = (ElementCellLayout*)elementCellLayout;
GlobalParticle* particle = (GlobalParticle*)_particle;
unsigned elInd;
if( !Mesh_SearchElements( self->mesh, particle->coord, &elInd ) )
elInd = Mesh_GetDomainSize( self->mesh, Mesh_GetDimSize( self->mesh ) );
return elInd;
}
Cell_Index _ElementCellLayout_CellOf_Irregular( void* elementCellLayout, void* _particle ) {
/* algorithm for irregular searches, this method uses the existing particle information to
optimise the search
*/
ElementCellLayout* self = (ElementCellLayout*)elementCellLayout;
GlobalParticle* particle = (GlobalParticle*)_particle;
unsigned elInd, elDim, cell_id;
Mesh* mesh = self->mesh;
cell_id = particle->owningCell;
/* check if particle already has an owning cell, for search optimisation */
if( cell_id < Mesh_GetDomainSize( mesh, Mesh_GetDimSize( mesh ) ) ) {
IArray *inc = self->incArray;
int el_i;
unsigned nEls;
int *neighbourEls;
/* search current cell */
if( Mesh_ElementHasPoint( mesh, cell_id, particle->coord, &elDim, &elInd ) ) {
return elInd;
}
/* search neighbouring cells */
Mesh_GetIncidence( mesh, Mesh_GetDimSize( mesh ), cell_id, Mesh_GetDimSize(mesh), inc );
nEls = IArray_GetSize( inc );
neighbourEls = IArray_GetPtr( inc );
for( el_i = 0; el_i<nEls; el_i++ ) {
if( Mesh_ElementHasPoint( mesh, neighbourEls[el_i], particle->coord, &elDim, &elInd ) ) {
return elInd;
}
}
}
// brute force search
if( !Mesh_SearchElements( self->mesh, particle->coord, &elInd ) )
elInd = Mesh_GetDomainSize( self->mesh, Mesh_GetDimSize( self->mesh ) );
return elInd;
}
Mesh_ElementType* Mesh_GetElementType( void* mesh, unsigned element ) {
Mesh* self = (Mesh*)mesh;
assert( self );
assert( element < Mesh_GetDomainSize( self, Mesh_GetDimSize( self ) ) );
assert( self->elTypeMap );
assert( self->elTypeMap[element] < self->nElTypes );
assert( self->elTypes );
return self->elTypes[self->elTypeMap[element]];
}
void _HeatingForce_Build( void* heatingForce, void* data ) {
HeatingForce* self = (HeatingForce*)heatingForce;
unsigned nDomainVerts;
Stg_Component_Build( self->feMesh, data, False );
nDomainVerts = Mesh_GetDomainSize( self->feMesh, MT_VERTEX );
self->dataVariable = Variable_NewScalar( "dataVariable", self->context, Variable_DataType_Double,
&nDomainVerts, NULL, (void**)&self->data, self->context->variable_Register );
_ParticleFeVariable_Build( self, data );
DofLayout_AddAllFromVariableArray( self->dofLayout, 1, &self->dataVariable );
}
Bool Mesh_ElementHasPoint( void* mesh, unsigned element, double* point,
MeshTopology_Dim* topodim, unsigned* ind )
{
Mesh* self = (Mesh*)mesh;
assert( self );
assert( element < Mesh_GetDomainSize( self, Mesh_GetDimSize( self ) ) );
assert( self->elTypeMap );
assert( self->elTypeMap[element] < self->nElTypes );
assert( self->elTypes[self->elTypeMap[element]] );
return Mesh_ElementType_ElementHasPoint( self->elTypes[self->elTypeMap[element]], element, point,
topodim, ind );
}
void Mesh_DeformationUpdate( void* mesh ) {
Mesh* self = (Mesh*)mesh;
assert( self );
if( Mesh_GetDomainSize( self, 0 ) ) {
self->minSep = Mesh_Algorithms_GetMinimumSeparation( self->algorithms, self->minAxialSep );
Mesh_Algorithms_GetLocalCoordRange( self->algorithms, self->minLocalCrd, self->maxLocalCrd );
Mesh_Algorithms_GetDomainCoordRange( self->algorithms, self->minDomainCrd, self->maxDomainCrd );
Mesh_Algorithms_GetGlobalCoordRange( self->algorithms, self->minGlobalCrd, self->maxGlobalCrd );
Mesh_Algorithms_Update( self->algorithms );
Mesh_ElementType_Update( self->elTypes[0] );
}
}
void TrilinearElementTypeSuite_TestShape( TrilinearElementTypeSuiteData* data ) {
FeMesh* mesh = NULL;
int nEls, nVerts, nDims;
const int *verts;
double* vert = NULL;
double lCrd[3] = { 0.0, 0.0, 0.0 };
double basis[8] = { 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 };
IArray* inc;
int e_i, v_i, v_j;
mesh = buildMesh();
pcu_check_true( mesh );
Stg_Component_Initialise( mesh, data, True );
nDims = Mesh_GetDimSize( mesh );
nEls = Mesh_GetDomainSize( mesh, nDims );
inc = IArray_New();
for( e_i = 0; e_i < nEls; e_i++ ) {
Mesh_GetIncidence( mesh, nDims, e_i, 0, inc );
nVerts = IArray_GetSize( inc );
verts = IArray_GetPtr( inc );
for( v_i = 0; v_i < nVerts; v_i++ ) {
vert = Mesh_GetVertex( mesh, verts[v_i] );
FeMesh_CoordGlobalToLocal( mesh, e_i, vert, lCrd );
FeMesh_EvalBasis( mesh, e_i, lCrd, basis );
for( v_j = 0; v_j < nVerts; v_j++ ) {
if( (v_i == v_j && !Num_Approx( basis[v_j], 1.0 )) || (v_i != v_j && !Num_Approx( basis[v_j], 0.0 )) ) {
break;
}
}
if( v_j < nVerts )
break;
}
if( v_i < nVerts )
break;
}
pcu_check_true( e_i == nEls );
Stg_Class_Delete( inc );
_Stg_Component_Delete( mesh );
}
void SROpGenerator_GenLevelTopMap( SROpGenerator* self, unsigned level ) {
Stream* errorStream = Journal_Register( ErrorStream_Type, (Name)"SROpGenerator::GenLevelTopMap" );
Mesh *fMesh, *cMesh;
unsigned nDomainNodes;
unsigned nLevels;
unsigned nDims;
unsigned nearest;
double *cVert, *fVert;
unsigned d_i, n_i;
assert( self && Stg_CheckType( self, SROpGenerator ) );
assert( self->meshes );
assert( level < self->nLevels );
fMesh = self->meshes[level + 1];
cMesh = self->meshes[level];
nDims = Mesh_GetDimSize( fMesh );
nLevels = self->nLevels;
nDomainNodes = Mesh_GetDomainSize( cMesh, MT_VERTEX );
self->topMaps[level] = ReallocArray( self->topMaps[level], unsigned, nDomainNodes );
for( n_i = 0; n_i < nDomainNodes; n_i++ ) {
cVert = Mesh_GetVertex( cMesh, n_i );
nearest = Mesh_NearestVertex( fMesh, cVert );
fVert = Mesh_GetVertex( fMesh, nearest );
for( d_i = 0; d_i < nDims; d_i++ ) {
if( !Num_Approx( cVert[d_i], fVert[d_i] ) )
break;
}
Journal_Firewall( d_i == nDims,
errorStream,
"\n" \
"*****************************************************************\n" \
"* Error: The finest grid could not be sub-sampled to all coarse *\n" \
"* levels. This is due to the size of the finest grid. *\n" \
"*****************************************************************\n" \
"\n" );
if( level < nLevels - 2 )
self->topMaps[level][n_i] = self->topMaps[level + 1][nearest];
else
self->topMaps[level][n_i] = nearest;
}
}
Index _MeshVariable_GetMeshArraySize( void* meshVariable ) {
MeshVariable* self = (MeshVariable*)meshVariable;
return Mesh_GetDomainSize( self->mesh, self->topoDim );
}
void WallVCSuite_TestWallVC( WallVCSuiteData* data ) {
unsigned nDomains;
unsigned nDims = 3;
unsigned meshSize[3] = {3, 3, 3};
int procToWatch;
double minCrds[3] = {0.0, 0.0, 0.0};
double maxCrds[3] = {1.0, 1.0, 1.0};
char* vcKey[] = {"WallVC_Front", "WallVC_Back", "WallVC_Left", "WallVC_Right",
"WallVC_Top", "WallVC_Bottom"};
char* vcKeyName[] = {"WallVC_FrontName", "WallVC_BackName", "WallVC_LeftName", "WallVC_RightName",
"WallVC_TopName", "WallVC_BottomName"};
char* varName[] = {"x", "y", "z", "vx", "vy", "vz", "temp"};
char input_file[PCU_PATH_MAX];
char expected_file[PCU_PATH_MAX];
Mesh* mesh;
Variable_Register* variable_Register;
ConditionFunction* quadCF;
ConditionFunction* expCF;
ConditionFunction_Register* conFunc_Register;
ExtensionManager_Register* extensionMgr_Register;
Dictionary* dictionary;
Dictionary* sources;
Stream* stream;
XML_IO_Handler* io_handler;
Variable* var[7];
double* array[7];
VariableCondition* vc;
Index i;
procToWatch = data->nProcs >=2 ? 1 : 0;
io_handler = XML_IO_Handler_New();
stream = Journal_Register( Info_Type, (Name)"WallVCStream" );
Stream_RedirectFile( stream, "testWallVC.dat" );
dictionary = Dictionary_New();
sources = Dictionary_New();
Dictionary_Add( dictionary, (Dictionary_Entry_Key)"outputPath", Dictionary_Entry_Value_FromString("./output") );
/* Input file */
pcu_filename_input( "wallVC.xml", input_file );
IO_Handler_ReadAllFromFile( io_handler, input_file, dictionary, sources );
fflush( stdout );
extensionMgr_Register = ExtensionManager_Register_New();
/* Create a mesh. */
mesh = (Mesh*) WallVCSuite_buildMesh( nDims, meshSize, minCrds, maxCrds, extensionMgr_Register );
nDomains = Mesh_GetDomainSize( mesh, MT_VERTEX );
/* Create CF stuff */
quadCF = ConditionFunction_New( WallVCSuite_quadratic, (Name)"quadratic", NULL );
expCF = ConditionFunction_New( WallVCSuite_exponential, (Name)"exponential", NULL);
conFunc_Register = ConditionFunction_Register_New( );
ConditionFunction_Register_Add(conFunc_Register, quadCF);
ConditionFunction_Register_Add(conFunc_Register, expCF);
/* Create variable register */
variable_Register = Variable_Register_New();
/* Create variables */
for (i = 0; i < 6; i++) {
array[i] = Memory_Alloc_Array( double, nDomains, "array[i]" );
var[i] = Variable_NewScalar( varName[i], NULL, Variable_DataType_Double, (Index*)&nDomains, NULL, (void**)&array[i], 0 );
Variable_Register_Add(variable_Register, var[i]);
}
array[6] = Memory_Alloc_Array( double, nDomains * 5, "array[6]" );
var[6] = Variable_NewVector( varName[6], NULL, Variable_DataType_Double, 5, &nDomains, NULL, (void**)&array[6], 0 );
Variable_Register_Add(variable_Register, var[6]);
Variable_Register_BuildAll(variable_Register);
for (i = 0; i < 6; i++) {
Index j, k;
vc = (VariableCondition*) WallVC_New( vcKeyName[i], NULL, vcKey[i], variable_Register, conFunc_Register, dictionary, mesh );
Stg_Component_Build( vc, 0, False );
for (j = 0; j < 6; j++)
memset(array[j], 0, sizeof(double)* nDomains );
memset(array[6], 0, sizeof(double)* nDomains * 5);
VariableCondition_Apply(vc, NULL);
if (data->rank == procToWatch) {
Journal_Printf( stream,"Testing for %s\n", vcKey[i]);
for (j = 0; j < 6; j++) {
Journal_Printf( stream,"\nvar[%u]: %.2lf", j, array[j][0]);
for (k = 1; k < nDomains; k++)
Journal_Printf( stream,", %.2lf", array[j][k]);
}
Journal_Printf( stream,"\nvar[6]: %.2lf", array[6][0]);
for (j = 1; j < nDomains*5; j++)
Journal_Printf( stream,", %.2lf", array[6][j]);
Journal_Printf( stream,"\n\n");
for (j = 0; j < 7; j++) {
for (k = 0; k < nDomains; k++)
Journal_Printf( stream,"%s ", VariableCondition_IsCondition(vc, k, j) ? "True " : "False");
Journal_Printf( stream,"\n");
} Journal_Printf( stream,"\n");
for (j = 0; j < 7; j++) {
for (k = 0; k < nDomains; k++) {
VariableCondition_ValueIndex valIndex;
valIndex = VariableCondition_GetValueIndex(vc, k, j);
if (valIndex != (unsigned)-1)
Journal_Printf( stream,"%03u ", valIndex);
else
Journal_Printf( stream,"XXX ");
} Journal_Printf( stream,"\n");
} Journal_Printf( stream,"\n");
}
Stg_Class_Delete(vc);
}
if (data->rank == procToWatch) {
pcu_filename_expected( "testWallVC.expected", expected_file );
pcu_check_fileEq( "testWallVC.dat", expected_file );
remove( "testWallVC.dat" );
}
Stg_Class_Delete(variable_Register);
for (i = 0; i < 7; i++) {
Stg_Class_Delete(var[i]);
if (array[i]) Memory_Free(array[i]);
}
Stg_Class_Delete(extensionMgr_Register);
Stg_Class_Delete(io_handler);
Stg_Class_Delete(conFunc_Register);
Stg_Class_Delete(quadCF);
Stg_Class_Delete(expCF);
Stg_Class_Delete(dictionary);
Stg_Class_Delete(sources);
FreeObject( mesh );
}