void Spherical_MaxVel_Output( UnderworldContext* context ) {
Spherical_CubedSphereNusselt* self = (Spherical_CubedSphereNusselt*)LiveComponentRegister_Get( context->CF->LCRegister, (Name)Spherical_CubedSphereNusselt_Type );
FeVariable* velocityField = self->velocityField;
FeMesh* mesh = velocityField->feMesh;
Grid* grid = NULL;
unsigned* sizes = NULL;
int vertId, dId;
unsigned dT_i, dT_j, nDomainSize, ijk[3];
double vel[3], velMax[2], gVelMax[2], velMag;
//set 'em big and negative
velMax[0] = velMax[1] = -1*HUGE_VAL;
// get vert grid
RegularMeshUtils_ErrorCheckAndGetDetails( (Mesh*)mesh, MT_VERTEX, &nDomainSize, &grid );
sizes = grid->sizes;
// go around
for( dT_i = 0; dT_i < sizes[1]; dT_i++ ) {
for( dT_j = 0; dT_j < sizes[2]; dT_j++ ) {
// find inner vertex
ijk[0] = 0;
// angular discretisation
ijk[1] = dT_i;
ijk[2] = dT_j;
vertId = Grid_Project( grid, ijk );
// if the node is local
if( Mesh_GlobalToDomain( mesh, MT_VERTEX, vertId, &dId ) == True ) {
FeVariable_GetValueAtNode( velocityField, dId, vel );
velMag = sqrt( vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2] );
if( velMag > velMax[0] ) velMax[0] = velMag;
}
// find outer vertex
ijk[0] = grid->sizes[0]-1;
vertId = Grid_Project( grid, ijk );
// if the node is local
if( Mesh_GlobalToDomain( mesh, MT_VERTEX, vertId, &dId ) == True ) {
FeVariable_GetValueAtNode( velocityField, dId, vel );
velMag = sqrt( vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2] );
if( velMag > velMax[1] ) velMax[1] = velMag;
}
}
}
(void)MPI_Allreduce( velMax, gVelMax, 2, MPI_DOUBLE, MPI_MAX, context->communicator );
StgFEM_FrequentOutput_PrintValue( context, gVelMax[1] ); // print outer velocity max
StgFEM_FrequentOutput_PrintValue( context, gVelMax[0] ); // print inner velocity max
}
double AdvectionDiffusionSLE_AdvectiveTimestep( void* advectionDiffusionSLE ) {
AdvectionDiffusionSLE* self = (AdvectionDiffusionSLE*) advectionDiffusionSLE;
AdvDiffResidualForceTerm* residualForceTerm = self->advDiffResidualForceTerm;
FeVariable* velocityField = residualForceTerm->velocityField;
Node_LocalIndex nodeLocalCount = FeMesh_GetNodeLocalSize( self->phiField->feMesh );
Node_LocalIndex node_I;
Dimension_Index dim = self->dim;
Dimension_Index dim_I;
double timestep = HUGE_VAL;
XYZ velocity;
double minSeparation;
double minSeparationEachDim[3];
double* meshCoord;
Journal_DPrintf( self->debug, "In func: %s\n", __func__ );
FeVariable_GetMinimumSeparation( self->phiField, &minSeparation, minSeparationEachDim );
for( node_I = 0 ; node_I < nodeLocalCount ; node_I++ ){
if( self->phiField->feMesh == velocityField->feMesh){
FeVariable_GetValueAtNode( velocityField, node_I, velocity );
} else {
meshCoord = Mesh_GetVertex( self->phiField->feMesh, node_I );
FieldVariable_InterpolateValueAt( velocityField, meshCoord, velocity );
}
for ( dim_I = 0 ; dim_I < dim ; dim_I++ ) {
if( velocity[ dim_I ] == 0.0 )
continue;
timestep = MIN( timestep, fabs( minSeparationEachDim[ dim_I ]/velocity[ dim_I ] ) );
}
}
return self->courantFactor * timestep;
}
void SemiLagrangianIntegratorSuite_Test( SemiLagrangianIntegratorSuiteData* data ) {
Stg_ComponentFactory* cf;
ConditionFunction* condFunc;
//char xml_input[PCU_PATH_MAX];
double l2Error;
FeVariable* phiField;
FeVariable* phiOldField;
Swarm* gaussSwarm;
double phi[3];
unsigned node_i;
AbstractContext* context;
//pcu_filename_input( "testSemiLagrangianIntegrator.xml", xml_input );
cf = stgMainInitFromXML( "StgFEM/Utils/input/testSemiLagrangianIntegrator.xml", MPI_COMM_WORLD, NULL );
context = Stg_ComponentFactory_ConstructByName( cf, (Name)"context", AbstractContext, True, NULL );
condFunc = ConditionFunction_New( SemiLagrangianIntegratorSuite_Line, (Name)"Line", NULL );
ConditionFunction_Register_Add( condFunc_Register, condFunc );
condFunc = ConditionFunction_New( SemiLagrangianIntegratorSuite_ShearCellX, (Name)"ShearCellX", NULL );
ConditionFunction_Register_Add( condFunc_Register, condFunc );
condFunc = ConditionFunction_New( SemiLagrangianIntegratorSuite_ShearCellY, (Name)"ShearCellY", NULL );
ConditionFunction_Register_Add( condFunc_Register, condFunc );
/* manually set the timestep */
ContextEP_ReplaceAll( context, AbstractContext_EP_Dt, Dt );
ContextEP_Append( context, AbstractContext_EP_UpdateClass, SemiLagrangianIntegratorSuite_UpdatePositions );
stgMainBuildAndInitialise( cf );
phiField = (FeVariable*)LiveComponentRegister_Get( cf->LCRegister, (Name)"PhiField" );
phiOldField = (FeVariable* )LiveComponentRegister_Get( cf->LCRegister, (Name)"PhiFieldInitial" );
gaussSwarm = (Swarm* )LiveComponentRegister_Get( cf->LCRegister, (Name)"gaussSwarm" );
for( node_i = 0; node_i < Mesh_GetLocalSize( phiField->feMesh, MT_VERTEX ); node_i++ ) {
FeVariable_GetValueAtNode( phiField, node_i, phi );
FeVariable_SetValueAtNode( phiOldField, node_i, phi );
}
stgMainLoop( cf );
l2Error = SemiLagrangianIntegratorSuite_EvaluateError( phiField, phiOldField, gaussSwarm );
pcu_check_true( l2Error < TOLERANCE );
stgMainDestroy( cf );
}
void SemiLagrangianIntegratorSuite_UpdatePositions( void* data, FiniteElementContext* context ) {
Index reverseTimeStep = Dictionary_GetUnsignedInt_WithDefault( context->dictionary, "reverseTimeStep", 100 );
FeVariable* velocityField = (FeVariable*) LiveComponentRegister_Get( context->CF->LCRegister, (Name)"VelocityField" );
FeMesh* mesh = velocityField->feMesh;
unsigned node_I;
Index dim_I;
unsigned nDims = Mesh_GetDimSize( mesh );
double velocity[3];
double phi;
SemiLagrangianIntegrator* slIntegrator;
FeVariable* phiField;
FeVariable* phiStarField;
_FeVariable_SyncShadowValues( velocityField );
/* reverse the numerically advected particles (& the semi lagrangian field also) */
if( context->timeStep == reverseTimeStep + 1 ) {
for( node_I = 0; node_I < Mesh_GetLocalSize( mesh, MT_VERTEX ); node_I++ ) {
_FeVariable_GetValueAtNode( velocityField, node_I, velocity );
for( dim_I = 0; dim_I < nDims; dim_I++ ) {
velocity[dim_I] *= -1;
}
FeVariable_SetValueAtNode( velocityField, node_I, velocity );
}
}
slIntegrator = (SemiLagrangianIntegrator*)LiveComponentRegister_Get( context->CF->LCRegister, (Name)"integrator" );
phiField = (FeVariable* )LiveComponentRegister_Get( context->CF->LCRegister, (Name)"PhiField" );
phiStarField = (FeVariable* )LiveComponentRegister_Get( context->CF->LCRegister, (Name)"PhiStarField" );
SemiLagrangianIntegrator_Solve( slIntegrator, phiField, phiStarField );
for( node_I = 0; node_I < Mesh_GetLocalSize( mesh, MT_VERTEX ); node_I++ ) {
FeVariable_GetValueAtNode( phiStarField, node_I, &phi );
FeVariable_SetValueAtNode( phiField, node_I, &phi );
}
}
void lecode_tools_Isostasy_AverageSurfaces(lecode_tools_Isostasy *self,
double** _avg_sep, double** _avg_height)
{
FeMesh *mesh;
Grid *grid, *elGrid;
double *local_height, *global_height;
double *local_top_vy, *global_top_vy;
double *local_bot_vy, *global_bot_vy;
int *local_top_cnt, *global_top_cnt;
int *local_bot_cnt, *global_bot_cnt;
int param[3], elParam[3], num_nodes, n;
double vel[3];
IArray *inc;
int nDims, arrayPos, arraySize;
int ii, jj;
mesh = self->mesh;
nDims = Mesh_GetDimSize( mesh );
grid = *Mesh_GetExtension(mesh, Grid**, mesh->vertGridId );
elGrid = *Mesh_GetExtension(mesh, Grid**, mesh->elGridId );
num_nodes = FeMesh_GetNodeLocalSize(mesh);
inc = IArray_New();
/* mem alloc from bottom surface */
arraySize=0; /*to prevent warnings*/
if ( nDims == 2 ) arraySize = elGrid->sizes[0];
else if ( nDims == 3 ) arraySize = elGrid->sizes[0]*elGrid->sizes[self->zontalAxis];
else assert(0);
local_top_vy = (double*)malloc( arraySize*sizeof(double) );
memset( local_top_vy, 0, arraySize*sizeof(double) );
local_bot_vy = (double*)malloc( arraySize*sizeof(double) );
memset( local_bot_vy, 0, arraySize*sizeof(double) );
local_height = (double*)malloc( arraySize*sizeof(double) );
memset( local_height, 0, arraySize*sizeof(double) );
local_top_cnt = (int*)malloc( arraySize*sizeof(int) );
memset( local_top_cnt, 0, arraySize*sizeof(int) );
local_bot_cnt = (int*)malloc( arraySize*sizeof(int) );
memset( local_bot_cnt, 0, arraySize*sizeof(int) );
for (ii = 0; ii < num_nodes; ii++)
{
FeMesh_GetNodeElements( mesh, ii, inc );
n = FeMesh_NodeDomainToGlobal(mesh, ii);
Grid_Lift(grid, n, param);
if ((self->surfaceIdx != -1 && param[self->vertAxis] == self->surfaceIdx) ||
(self->surfaceIdx == -1 && param[self->vertAxis] == grid->sizes[self->vertAxis] - 1))
{
FeVariable_GetValueAtNode(self->vel_field, ii, vel);
if ( self->avg )
{
local_top_vy[0] += vel[self->vertAxis];
local_height[0] += Mesh_GetVertex( mesh, ii )[self->vertAxis];
local_top_cnt[0]++;
}
else
{
for (jj = 0; jj < inc->size; jj++ )
{
Grid_Lift( elGrid, FeMesh_ElementDomainToGlobal( self->mesh, inc->ptr[jj] ), elParam );
/* Make sure element is below surface. */
if ( self->surfaceIdx != -1 && elParam[self->vertAxis] >= self->surfaceIdx )
continue;
arrayPos = elParam[0];
if ( nDims == 3 ) arrayPos += elParam[self->zontalAxis]*elGrid->sizes[0];
local_top_vy[arrayPos] += vel[self->vertAxis];
local_height[arrayPos] += Mesh_GetVertex( mesh, ii )[self->vertAxis];
local_top_cnt[arrayPos]++;
}
}
}
if (param[self->vertAxis] == 0 )
{
FeVariable_GetValueAtNode(self->vel_field, ii, vel);
if ( self->avg )
{
local_bot_vy[0] += vel[self->vertAxis];
local_height[0] -= Mesh_GetVertex( mesh, ii )[self->vertAxis];
local_bot_cnt[0]++;
}
else
{
for (jj = 0; jj < inc->size; jj++ )
{
Grid_Lift( elGrid, FeMesh_ElementDomainToGlobal( self->mesh, inc->ptr[jj] ), elParam );
/* Make sure element is below surface. */
if ( self->surfaceIdx != -1 && elParam[self->vertAxis] >= self->surfaceIdx )
continue;
arrayPos = elParam[0];
if ( nDims == 3 ) arrayPos += elParam[self->zontalAxis]*elGrid->sizes[0];
local_bot_vy[arrayPos] += vel[self->vertAxis];
local_height[arrayPos] -= Mesh_GetVertex( mesh, ii )[self->vertAxis];
local_bot_cnt[arrayPos]++;
}
}
}
}
global_top_vy = (double*)malloc( arraySize*sizeof(double) );
global_bot_vy = (double*)malloc( arraySize*sizeof(double) );
global_height = (double*)malloc( arraySize*sizeof(double) );
global_top_cnt = (int*)malloc( arraySize*sizeof(int) );
global_bot_cnt = (int*)malloc( arraySize*sizeof(int) );
MPI_Allreduce(local_height, global_height, arraySize, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
MPI_Allreduce(local_top_vy, global_top_vy, arraySize, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
MPI_Allreduce(local_bot_vy, global_bot_vy, arraySize, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
MPI_Allreduce(local_top_cnt, global_top_cnt, arraySize, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
MPI_Allreduce(local_bot_cnt, global_bot_cnt, arraySize, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
free( local_height );
free( local_top_vy );
free( local_bot_vy );
free( local_top_cnt );
free( local_bot_cnt );
Stg_Class_Delete( inc );
*_avg_sep = (double*)malloc( arraySize*sizeof(double) );
*_avg_height = (double*)malloc( arraySize*sizeof(double) );
for ( ii = 0; ii < arraySize; ii++ )
{
(*_avg_sep)[ii] = global_top_vy[ii]/(double)(global_top_cnt[ii]) - global_bot_vy[ii]/(double)(global_bot_cnt[ii]);
(*_avg_height)[ii] = global_height[ii]/(double)(global_top_cnt[ii]);
if (self->avg)
break;
}
free( global_height );
free( global_top_vy );
free( global_bot_vy );
free( global_top_cnt );
free( global_bot_cnt );
}
void lucMeshCrossSection_Sample( void* drawingObject, Bool reverse)
{
lucMeshCrossSection* self = (lucMeshCrossSection*)drawingObject;
FeVariable* fieldVariable = (FeVariable*) self->fieldVariable;
Mesh* mesh = (Mesh*) fieldVariable->feMesh;
Grid* vertGrid;
Node_LocalIndex crossSection_I;
IJK node_ijk;
Node_GlobalIndex node_gI;
Node_DomainIndex node_dI;
int i,j, d, sizes[3] = {1,1,1};
Coord globalMin, globalMax, min, max;
int localcount = 0;
vertGrid = *(Grid**)ExtensionManager_Get( mesh->info, mesh, self->vertexGridHandle );
for (d=0; d<fieldVariable->dim; d++) sizes[d] = vertGrid->sizes[d];
self->dim[0] = sizes[ self->axis ];
self->dim[1] = sizes[ self->axis1 ];
self->dim[2] = sizes[ self->axis2 ];
crossSection_I = lucCrossSection_GetValue(self, 0, self->dim[0]-1);
FieldVariable_GetMinAndMaxLocalCoords( fieldVariable, min, max );
FieldVariable_GetMinAndMaxGlobalCoords( fieldVariable, globalMin, globalMax );
Journal_Printf( lucDebug, "%s called on field %s, with axis of cross section as %d, crossSection_I as %d (dims %d,%d,%d) field dim %d\n",
__func__, fieldVariable->name, self->axis, crossSection_I, self->dim[0], self->dim[1], self->dim[2], self->fieldDim);
/* Get mesh cross section self->vertices and values */
self->resolutionA = self->dim[1];
self->resolutionB = self->dim[2];
lucCrossSection_AllocateSampleData(self, self->fieldDim);
int lSize = Mesh_GetLocalSize( mesh, MT_VERTEX );
double time = MPI_Wtime();
Journal_Printf(lucInfo, "Sampling mesh (%s) %d x %d... 0%", self->name, self->dim[1], self->dim[2]);
node_ijk[ self->axis ] = crossSection_I;
for ( i = 0 ; i < self->dim[1]; i++ )
{
int percent = 100 * (i + 1) / self->dim[1];
Journal_Printf(lucInfo, "\b\b\b\b%3d%%", percent);
fflush(stdout);
/* Reverse order if requested */
int i0 = i;
if (reverse) i0 = self->dim[1] - i - 1;
node_ijk[ self->axis1 ] = i0;
for ( j = 0 ; j < self->dim[2]; j++ )
{
self->vertices[i][j][0] = HUGE_VAL;
self->vertices[i][j][2] = 0;
node_ijk[ self->axis2 ] = j;
node_gI = Grid_Project( vertGrid, node_ijk );
/* Get coord and value if node is local... */
if (Mesh_GlobalToDomain( mesh, MT_VERTEX, node_gI, &node_dI ) && node_dI < lSize)
{
/* Found on this processor */
double value[self->fieldDim];
FeVariable_GetValueAtNode( fieldVariable, node_dI, value );
double* pos = Mesh_GetVertex( mesh, node_dI );
/*fprintf(stderr, "[%d] (%d,%d) Node %d %f,%f,%f value %f\n", self->context->rank, i, j, node_gI, pos[0], pos[1], pos[2], value);*/
for (d=0; d<fieldVariable->dim; d++)
self->vertices[i][j][d] = pos[d];
for (d=0; d<self->fieldDim; d++)
self->values[i][j][d] = (float)value[d];
localcount++;
}
}
}
Journal_Printf(lucInfo, " %f sec. ", MPI_Wtime() - time);
/* Collate */
time = MPI_Wtime();
for ( i=0 ; i < self->dim[1]; i++ )
{
for ( j=0 ; j < self->dim[2]; j++ )
{
/* Receive values at root */
if (self->context->rank == 0)
{
/* Already have value? */
if (self->vertices[i][j][0] != HUGE_VAL) {localcount--; continue; }
/* Recv (pos and value together = (3 + fevar dims)*float) */
float data[3 + self->fieldDim];
(void)MPI_Recv(data, 3+self->fieldDim, MPI_FLOAT, MPI_ANY_SOURCE, i*self->dim[2]+j, self->context->communicator, MPI_STATUS_IGNORE);
/* Copy */
memcpy(self->vertices[i][j], data, 3 * sizeof(float));
memcpy(self->values[i][j], &data[3], self->fieldDim * sizeof(float));
}
else
{
/* Found on this proc? */
if (self->vertices[i][j][0] == HUGE_VAL) continue;
/* Copy */
float data[3 + self->fieldDim];
memcpy(data, self->vertices[i][j], 3 * sizeof(float));
memcpy(&data[3], self->values[i][j], self->fieldDim * sizeof(float));
/* Send values to root (pos & value = 4 * float) */
MPI_Ssend(data, 3+self->fieldDim, MPI_FLOAT, 0, i*self->dim[2]+j, self->context->communicator);
localcount--;
}
}
}
MPI_Barrier(self->context->communicator); /* Barrier required, prevent subsequent MPI calls from interfering with transfer */
Journal_Printf(lucInfo, " Gather in %f sec.\n", MPI_Wtime() - time);
Journal_Firewall(localcount == 0, lucError,
"Error - in %s: count of values sampled compared to sent/received by mpi on proc %d does not match (balance = %d)\n",
__func__, self->context->rank, localcount);
}
void Stokes_SLE_PenaltySolver_MakePenalty( Stokes_SLE_PenaltySolver* self, Stokes_SLE* sle, Vec* _penalty ) {
Vec fVec = sle->fForceVec->vector, hVec = sle->hForceVec->vector, penalty, lambda;
Mat kMat = sle->kStiffMat->matrix;
FeMesh *mesh = sle->kStiffMat->rowVariable->feMesh;
FeVariable *velField = sle->kStiffMat->rowVariable;
SolutionVector* uVec = sle->uSolnVec;
FeEquationNumber *eqNum = uVec->eqNum;
IArray *inc;
PetscScalar *lambdaVals, lambdaMin, *penaltyVals;
int numDofs, numLocalElems, nodeCur, numLocalNodes, rank, eq;
SolutionVector *solVec = sle->uSolnVec;
double *velBackup;
Vec vecBackup;
int ii, jj, kk;
MPI_Comm_rank( MPI_COMM_WORLD, &rank );
numDofs = Mesh_GetDimSize( mesh );
numLocalElems = FeMesh_GetElementLocalSize( mesh );
numLocalNodes = FeMesh_GetNodeLocalSize( mesh );
velBackup = (double*)malloc( numLocalNodes*numDofs*sizeof(double) );
for( ii = 0; ii < numLocalNodes; ii++ )
FeVariable_GetValueAtNode( velField, ii, velBackup + ii*numDofs );
VecDuplicate( hVec, &penalty );
VecGetArray( penalty, &penaltyVals );
VecDuplicate( fVec, &lambda );
MatGetDiagonal( kMat, lambda );
{
PetscInt idx;
PetscReal min, max;
VecMin( lambda, &idx, &min );
VecMax( lambda, &idx, &max );
if( rank == 0 ) {
printf( "LAMBDA RANGE:\n" );
printf( " MIN: %e\n", min );
printf( " MAX: %e\n", max );
}
}
vecBackup = solVec->vector;
solVec->vector = lambda;
SolutionVector_UpdateSolutionOntoNodes( solVec );
inc = IArray_New();
lambdaVals = (double*)malloc( numDofs*sizeof(double) );
for( ii = 0; ii < numLocalElems; ii++ ) {
lambdaMin = DBL_MAX;
FeMesh_GetElementNodes( mesh, ii, inc );
for( jj = 0; jj < inc->size; jj++ ) {
nodeCur = inc->ptr[jj];
FeVariable_GetValueAtNode( velField, nodeCur, lambdaVals );
for( kk = 0; kk < numDofs; kk++ ) {
eq = eqNum->mapNodeDof2Eq[nodeCur][kk];
if( eq == -1 )
continue;
/*
eq = *(int*)STreeMap_Map( eqNum->ownedMap, &eq );
VecGetValues( lambda, 1, &eq, &lambdaVal );
*/
if( lambdaVals[kk] < 0.0 )
printf( "%g\n", lambdaVals[kk] );
if( lambdaVals[kk] < lambdaMin )
lambdaMin = lambdaVals[kk];
}
}
penaltyVals[ii] = lambdaMin;
}
if( lambdaVals ) free( lambdaVals );
Stg_Class_Delete( inc );
solVec->vector = vecBackup;
for( ii = 0; ii < numLocalNodes; ii++ )
FeVariable_SetValueAtNode( velField, ii, velBackup + ii*numDofs );
if( velBackup ) free( velBackup );
FeVariable_SyncShadowValues( velField );
Stg_VecDestroy(&lambda );
VecRestoreArray( penalty, &penaltyVals );
VecAssemblyBegin( penalty );
VecAssemblyEnd( penalty );
{
PetscInt idx;
PetscReal min, max;
VecMin( penalty, &idx, &min );
VecMax( penalty, &idx, &max );
if( rank == 0 ) {
printf( "SEMI-PENALTY RANGE:\n" );
printf( " MIN: %e\n", min );
printf( " MAX: %e\n", max );
}
}
*_penalty = penalty;
}