 |
Mesh Oriented datABase
(version 5.4.1)
Array-based unstructured mesh datastructure
|
|
Mesh Oriented datABase
(version 5.4.1)
Array-based unstructured mesh datastructure
|
#include <iostream>#include <sstream>#include "moab/Core.hpp"#include "moab/Skinner.hpp"#include "moab/CN.hpp"#include "moab/ProgOptions.hpp"#include "moab/CartVect.hpp"#include "moab/NestedRefine.hpp"#include "moab/VerdictWrapper.hpp"#include "matrix.h"
Include dependency graph for LaplacianSmoother.cpp:Go to the source code of this file.
Defines | |
| #define | WRITE_DEBUG_FILES |
| #define | RC MB_CHK_ERR( rval ) |
| #define | dbgprint(MSG) |
Functions | |
| ErrorCode | perform_laplacian_smoothing (Core *mb, Range &cells, Range &verts, int dim, Tag fixed, bool use_hc=false, bool use_acc=false, int acc_method=1, int num_its=10, double rel_eps=1e-5, double alpha=0.0, double beta=0.5, int report_its=1) |
| ErrorCode | hcFilter (Core *mb, moab::ParallelComm *pcomm, moab::Range &verts, int dim, Tag fixed, std::vector< double > &verts_o, std::vector< double > &verts_n, double alpha, double beta) |
| ErrorCode | laplacianFilter (Core *mb, moab::ParallelComm *pcomm, moab::Range &verts, int dim, Tag fixed, std::vector< double > &verts_o, std::vector< double > &verts_n, bool use_updated=true) |
| int | main (int argc, char **argv) |
Variables | |
| string | test_file_name = string( "input/surfrandomtris-4part.h5m" ) |
| #define dbgprint | ( | MSG | ) |
do \
{ \
if( !global_rank ) std::cerr << ( MSG ) << std::endl; \
} while( false )
Definition at line 50 of file LaplacianSmoother.cpp.
Referenced by moab::TempestRemapper::ComputeOverlapMesh(), moab::TempestRemapper::convert_tempest_mesh_private(), moab::TempestRemapper::ConvertMeshToTempest(), moab::TempestOnlineMap::GenerateRemappingWeights(), moab::TempestOnlineMap::LinearRemapFVtoFV_Tempest_MOAB(), moab::TempestOnlineMap::LinearRemapGLLtoGLL2_MOAB(), moab::TempestOnlineMap::LinearRemapGLLtoGLL2_Pointwise_MOAB(), moab::TempestOnlineMap::LinearRemapSE4_Tempest_MOAB(), main(), and perform_laplacian_smoothing().
| #define RC MB_CHK_ERR( rval ) |
Definition at line 49 of file LaplacianSmoother.cpp.
Referenced by hcFilter(), laplacianFilter(), main(), and perform_laplacian_smoothing().
| #define WRITE_DEBUG_FILES |
Definition at line 41 of file LaplacianSmoother.cpp.
| ErrorCode hcFilter | ( | Core * | mb, |
| moab::ParallelComm * | pcomm, | ||
| moab::Range & | verts, | ||
| int | dim, | ||
| Tag | fixed, | ||
| std::vector< double > & | verts_o, | ||
| std::vector< double > & | verts_n, | ||
| double | alpha, | ||
| double | beta | ||
| ) |
Definition at line 717 of file LaplacianSmoother.cpp.
References moab::Range::begin(), moab::Range::end(), moab::Range::erase(), ErrorCode, moab::ParallelComm::filter_pstatus(), moab::Core::get_adjacencies(), moab::Core::get_connectivity(), moab::Range::index(), laplacianFilter(), MB_SUCCESS, PSTATUS_NOT, PSTATUS_NOT_OWNED, RC, moab::Range::size(), moab::ParallelComm::size(), and moab::Core::tag_get_data().
Referenced by perform_laplacian_smoothing().
{
ErrorCode rval;
std::vector< double > verts_hc( verts_o.size() );
std::vector< int > fix_tag( verts.size() );
// Perform Laplacian Smooth
rval = laplacianFilter( mb, pcomm, verts, dim, fixed, verts_o, verts_n );
RC;
// Compute Differences
for( unsigned index = 0; index < verts_o.size(); ++index )
{
verts_hc[index] = verts_n[index] - ( alpha * verts_n[index] + ( 1.0 - alpha ) * verts_o[index] );
}
// filter verts down to owned ones and get fixed tag for them
Range owned_verts;
#ifdef MOAB_HAVE_MPI
if( pcomm->size() > 1 )
{
rval = pcomm->filter_pstatus( verts, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &owned_verts );
if( rval != MB_SUCCESS ) return rval;
}
else
#endif
owned_verts = verts;
rval = mb->tag_get_data( fixed, owned_verts, &fix_tag[0] );
RC;
int vindex = 0;
for( Range::const_iterator vit = owned_verts.begin(); vit != owned_verts.end(); ++vit, vindex++ )
{
// if !fixed
if( fix_tag[vindex] ) continue;
const int index = verts.index( *vit ) * 3;
moab::Range adjverts, adjelems;
// Find the neighboring vertices (1-ring neighborhood)
rval = mb->get_adjacencies( &( *vit ), 1, dim, false, adjelems );
RC;
rval = mb->get_connectivity( adjelems, adjverts );
RC;
adjverts.erase( *vit );
const int nadjs = adjverts.size();
double delta[3] = { 0.0, 0.0, 0.0 };
for( int j = 0; j < nadjs; ++j )
{
const int joffset = verts.index( adjverts[j] ) * 3;
delta[0] += verts_hc[joffset + 0];
delta[1] += verts_hc[joffset + 1];
delta[2] += verts_hc[joffset + 2];
}
verts_n[index + 0] -= beta * verts_hc[index + 0] + ( ( 1.0 - beta ) / nadjs ) * delta[0];
verts_n[index + 1] -= beta * verts_hc[index + 1] + ( ( 1.0 - beta ) / nadjs ) * delta[1];
verts_n[index + 2] -= beta * verts_hc[index + 2] + ( ( 1.0 - beta ) / nadjs ) * delta[2];
}
return MB_SUCCESS;
}
| ErrorCode laplacianFilter | ( | Core * | mb, |
| moab::ParallelComm * | pcomm, | ||
| moab::Range & | verts, | ||
| int | dim, | ||
| Tag | fixed, | ||
| std::vector< double > & | verts_o, | ||
| std::vector< double > & | verts_n, | ||
| bool | use_updated = true |
||
| ) |
Definition at line 632 of file LaplacianSmoother.cpp.
References moab::Range::begin(), moab::Range::end(), moab::Range::erase(), ErrorCode, moab::ParallelComm::filter_pstatus(), moab::Core::get_adjacencies(), moab::Core::get_connectivity(), moab::Range::index(), MB_SUCCESS, PSTATUS_NOT, PSTATUS_NOT_OWNED, RC, moab::Range::size(), moab::ParallelComm::size(), and moab::Core::tag_get_data().
Referenced by hcFilter(), and perform_laplacian_smoothing().
{
ErrorCode rval;
std::vector< int > fix_tag( verts.size() );
double* data;
memcpy( &verts_n[0], &verts_o[0], sizeof( double ) * verts_o.size() );
if( use_updated )
data = &verts_n[0];
else
data = &verts_o[0];
// filter verts down to owned ones and get fixed tag for them
Range owned_verts;
if( pcomm->size() > 1 )
{
#ifdef MOAB_HAVE_MPI
rval = pcomm->filter_pstatus( verts, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &owned_verts );
if( rval != MB_SUCCESS ) return rval;
#endif
}
else
owned_verts = verts;
rval = mb->tag_get_data( fixed, owned_verts, &fix_tag[0] );
RC;
int vindex = 0;
for( Range::const_iterator vit = owned_verts.begin(); vit != owned_verts.end(); ++vit, vindex++ )
{
// if !fixed
if( fix_tag[vindex] ) continue;
const int index = verts.index( *vit ) * 3;
moab::Range adjverts, adjelems;
// Find the neighboring vertices (1-ring neighborhood)
rval = mb->get_adjacencies( &( *vit ), 1, dim, false, adjelems );
RC;
rval = mb->get_connectivity( adjelems, adjverts );
RC;
adjverts.erase( *vit );
const int nadjs = adjverts.size();
if( nadjs )
{
double delta[3] = { 0.0, 0.0, 0.0 };
// Add the vertices and divide by the number of vertices
for( int j = 0; j < nadjs; ++j )
{
const int joffset = verts.index( adjverts[j] ) * 3;
delta[0] += data[joffset + 0];
delta[1] += data[joffset + 1];
delta[2] += data[joffset + 2];
}
verts_n[index + 0] = delta[0] / nadjs;
verts_n[index + 1] = delta[1] / nadjs;
verts_n[index + 2] = delta[2] / nadjs;
}
}
return MB_SUCCESS;
}
| int main | ( | int | argc, |
| char ** | argv | ||
| ) |
Definition at line 89 of file LaplacianSmoother.cpp.
References ProgOptions::addOpt(), moab::Core::create_meshset(), dbgprint, ErrorCode, moab::NestedRefine::exchange_ghosts(), moab::ParallelComm::exchange_tags(), moab::NestedRefine::generate_mesh_hierarchy(), moab::Core::get_entities_by_dimension(), moab::Core::get_entities_by_type(), moab::Core::load_file(), mb, MB_TAG_CREAT, MB_TAG_DENSE, MB_TYPE_INTEGER, MBVERTEX, MESHSET_SET, ProgOptions::parseCommandLine(), perform_laplacian_smoothing(), RC, moab::Range::size(), moab::ParallelComm::size(), moab::Core::tag_delete(), moab::Core::tag_get_handle(), moab::Core::tag_set_data(), test_file_name, and moab::Core::write_file().
{
int num_its = 10;
int num_ref = 0;
int num_dim = 2;
int report_its = 1;
int num_degree = 2;
bool use_hc = false;
bool use_acc = false;
int acc_method = 1;
double alpha = 0.5, beta = 0.0;
double rel_eps = 1e-5;
const int nghostrings = 1;
ProgOptions opts;
ErrorCode rval;
std::stringstream sstr;
int global_rank;
MPI_Init( &argc, &argv );
MPI_Comm_rank( MPI_COMM_WORLD, &global_rank );
// Decipher program options from user
opts.addOpt< int >( std::string( "niter,n" ),
std::string( "Number of Laplacian smoothing iterations (default=10)" ), &num_its );
opts.addOpt< double >( std::string( "eps,e" ),
std::string( "Tolerance for the Laplacian smoothing error (default=1e-5)" ), &rel_eps );
opts.addOpt< double >( std::string( "alpha" ),
std::string( "Tolerance for the Laplacian smoothing error (default=0.0)" ), &alpha );
opts.addOpt< double >( std::string( "beta" ),
std::string( "Tolerance for the Laplacian smoothing error (default=0.5)" ), &beta );
opts.addOpt< int >( std::string( "dim,d" ), std::string( "Topological dimension of the mesh (default=2)" ),
&num_dim );
opts.addOpt< std::string >( std::string( "file,f" ),
std::string( "Input mesh file to smoothen (default=surfrandomtris-4part.h5m)" ),
&test_file_name );
opts.addOpt< int >(
std::string( "nrefine,r" ),
std::string( "Number of uniform refinements to perform and apply smoothing cycles (default=1)" ), &num_ref );
opts.addOpt< int >( std::string( "ndegree,p" ), std::string( "Degree of uniform refinement (default=2)" ),
&num_degree );
opts.addOpt< void >( std::string( "humphrey,c" ),
std::string( "Use Humphrey’s Classes algorithm to reduce shrinkage of "
"Laplacian smoother (default=false)" ),
&use_hc );
opts.addOpt< void >( std::string( "aitken,d" ),
std::string( "Use Aitken \\delta^2 acceleration to improve convergence of "
"Lapalace smoothing algorithm (default=false)" ),
&use_acc );
opts.addOpt< int >( std::string( "acc,a" ),
std::string( "Type of vector Aitken process to use for acceleration (default=1)" ),
&acc_method );
opts.parseCommandLine( argc, argv );
// get MOAB and ParallelComm instances
Core* mb = new Core;
if( NULL == mb ) return 1;
int global_size = 1;
// get the ParallelComm instance
ParallelComm* pcomm = new ParallelComm( mb, MPI_COMM_WORLD );
global_size = pcomm->size();
string roptions, woptions;
if( global_size > 1 )
{ // if reading in parallel, need to tell it how
sstr.str( "" );
sstr << "PARALLEL=READ_PART;PARTITION=PARALLEL_PARTITION;PARALLEL_RESOLVE_SHARED_ENTS;"
"PARALLEL_GHOSTS="
<< num_dim << ".0." << nghostrings << ";DEBUG_IO=0;DEBUG_PIO=0";
roptions = sstr.str();
woptions = "PARALLEL=WRITE_PART";
}
// read the file
moab::EntityHandle fileset, currset;
rval = mb->create_meshset( MESHSET_SET, fileset );
RC;
currset = fileset;
rval = mb->load_file( test_file_name.c_str(), &fileset, roptions.c_str() );
RC;
std::vector< EntityHandle > hsets( num_ref + 1, fileset );
if( num_ref )
{
// Perform uniform refinement of the smoothed mesh
#ifdef MOAB_HAVE_MPI
NestedRefine* uref = new NestedRefine( mb, pcomm, currset );
#else
NestedRefine* uref = new NestedRefine( mb, 0, currset );
#endif
std::vector< int > num_degrees( num_ref, num_degree );
rval = uref->generate_mesh_hierarchy( num_ref, &num_degrees[0], hsets );
RC;
// Now exchange 1 layer of ghost elements, using vertices as bridge
// (we could have done this as part of reading process, using the PARALLEL_GHOSTS read
// option)
rval = uref->exchange_ghosts( hsets, nghostrings );
RC;
delete uref;
}
for( int iref = 0; iref <= num_ref; ++iref )
{
// specify which set we are currently working on
currset = hsets[iref];
// make tag to specify fixed vertices, since it's input to the algorithm; use a default
// value of non-fixed so we only need to set the fixed tag for skin vertices
Tag fixed;
int def_val = 0;
rval = mb->tag_get_handle( "fixed", 1, MB_TYPE_INTEGER, fixed, MB_TAG_CREAT | MB_TAG_DENSE, &def_val );
RC;
// get all vertices and cells
Range verts, cells, skin_verts;
rval = mb->get_entities_by_type( currset, MBVERTEX, verts );
RC;
rval = mb->get_entities_by_dimension( currset, num_dim, cells );
RC;
dbgprint( "Found " << verts.size() << " vertices and " << cells.size() << " elements" );
// get the skin vertices of those cells and mark them as fixed; we don't want to fix the
// vertices on a part boundary, but since we exchanged a layer of ghost cells, those
// vertices aren't on the skin locally ok to mark non-owned skin vertices too, I won't move
// those anyway use MOAB's skinner class to find the skin
Skinner skinner( mb );
rval = skinner.find_skin( currset, cells, true, skin_verts );
RC; // 'true' param indicates we want vertices back, not cells
std::vector< int > fix_tag( skin_verts.size(), 1 ); // initialized to 1 to indicate fixed
rval = mb->tag_set_data( fixed, skin_verts, &fix_tag[0] );
RC;
// exchange tags on owned verts for fixed points
if( global_size > 1 )
{
#ifdef MOAB_HAVE_MPI
rval = pcomm->exchange_tags( fixed, skin_verts );
RC;
#endif
}
// now perform the Laplacian relaxation
rval = perform_laplacian_smoothing( mb, cells, verts, num_dim, fixed, use_hc, use_acc, acc_method, num_its,
rel_eps, alpha, beta, report_its );
RC;
// output file, using parallel write
sstr.str( "" );
sstr << "LaplacianSmoother_" << iref << ".h5m";
rval = mb->write_file( sstr.str().c_str(), "H5M", woptions.c_str(), &currset, 1 );
RC;
// delete fixed tag, since we created it here
rval = mb->tag_delete( fixed );
RC;
}
delete pcomm;
// delete MOAB instance
delete mb;
MPI_Finalize();
return 0;
}
| ErrorCode perform_laplacian_smoothing | ( | Core * | mb, |
| Range & | cells, | ||
| Range & | verts, | ||
| int | dim, | ||
| Tag | fixed, | ||
| bool | use_hc = false, |
||
| bool | use_acc = false, |
||
| int | acc_method = 1, |
||
| int | num_its = 10, |
||
| double | rel_eps = 1e-5, |
||
| double | alpha = 0.0, |
||
| double | beta = 0.5, |
||
| int | report_its = 1 |
||
| ) |
Definition at line 259 of file LaplacianSmoother.cpp.
References moab::Range::begin(), moab::ParallelComm::comm(), dbgprint, moab::Range::empty(), moab::Range::end(), ErrorCode, moab::ParallelComm::exchange_tags(), moab::ParallelComm::filter_pstatus(), moab::Core::get_connectivity(), moab::Core::get_coords(), moab::ParallelComm::get_pcomm(), moab::ParallelComm::get_shared_entities(), hcFilter(), moab::Core::id_from_handle(), moab::Range::insert(), laplacianFilter(), length(), moab::CartVect::length_squared(), MB_CHK_ERR, moab::MB_SHAPE, MB_SUCCESS, MB_TAG_CREAT, MB_TAG_DENSE, MB_TYPE_DOUBLE, PSTATUS_NOT, PSTATUS_NOT_OWNED, moab::VerdictWrapper::quality_measure(), moab::ParallelComm::rank(), RC, moab::CartVect::scale(), moab::Core::set_coords(), moab::VerdictWrapper::set_size(), moab::Range::size(), moab::ParallelComm::size(), moab::Core::tag_get_data(), moab::Core::tag_get_handle(), moab::Core::tag_set_data(), moab::Core::type_from_handle(), and moab::Core::write_file().
Referenced by main().
{
ErrorCode rval;
int global_rank = 0, global_size = 1;
int nacc = 2; /* nacc_method: 1 = Method 2 from [1], 2 = Method 3 from [1] */
std::vector< double > verts_acc1, verts_acc2, verts_acc3;
double rat_theta = rel_eps, rat_alpha = rel_eps, rat_alphaprev = rel_eps;
#ifdef MOAB_HAVE_MPI
const char* woptions = "PARALLEL=WRITE_PART";
#else
const char* woptions = "";
#endif
std::vector< int > fix_tag( verts.size() );
rval = mb->tag_get_data( fixed, verts, &fix_tag[0] );
RC;
#ifdef MOAB_HAVE_MPI
ParallelComm* pcomm = ParallelComm::get_pcomm( mb, 0 );
global_rank = pcomm->rank();
global_size = pcomm->size();
#endif
dbgprint( "-- Starting smoothing cycle --" );
// perform Laplacian relaxation:
// 1. setup: set vertex centroids from vertex coords; filter to owned verts; get fixed tags
// get all verts coords into tag; don't need to worry about filtering out fixed verts,
// we'll just be setting to their fixed coords
std::vector< double > verts_o, verts_n;
verts_o.resize( 3 * verts.size(), 0.0 );
verts_n.resize( 3 * verts.size(), 0.0 );
// std::vector<const void*> vdata(1);
// vdata[0] = &verts_n[0];
// const int vdatasize = verts_n.size();
void* vdata = &verts_n[0];
rval = mb->get_coords( verts, &verts_o[0] );
RC;
const int nbytes = sizeof( double ) * verts_o.size();
Tag errt, vpost;
double def_val[3] = { 0.0, 0.0, 0.0 };
rval = mb->tag_get_handle( "error", 1, MB_TYPE_DOUBLE, errt, MB_TAG_CREAT | MB_TAG_DENSE, def_val );
RC;
rval = mb->tag_get_handle( "vpos", 3, MB_TYPE_DOUBLE, vpost, MB_TAG_CREAT | MB_TAG_DENSE, def_val );
RC;
// rval = mb->tag_set_by_ptr(vpost, verts, vdata); RC;
if( use_acc )
{
verts_acc1.resize( verts_o.size(), 0.0 );
verts_acc2.resize( verts_o.size(), 0.0 );
verts_acc3.resize( verts_o.size(), 0.0 );
memcpy( &verts_acc1[0], &verts_o[0], nbytes );
memcpy( &verts_acc2[0], &verts_o[0], nbytes );
memcpy( &verts_acc3[0], &verts_o[0], nbytes );
}
// Filter verts down to owned ones and get fixed tag for them
Range owned_verts, shared_owned_verts;
if( global_size > 1 )
{
#ifdef MOAB_HAVE_MPI
rval = pcomm->filter_pstatus( verts, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &owned_verts );MB_CHK_ERR( rval );
#endif
}
else
owned_verts = verts;
#ifdef MOAB_HAVE_MPI
// Get shared owned verts, for exchanging tags
rval = pcomm->get_shared_entities( -1, shared_owned_verts, 0, false, true );MB_CHK_ERR( rval );
// Workaround: if no shared owned verts, put a non-shared one in the list, to prevent exchanging
// tags for all shared entities
if( shared_owned_verts.empty() ) shared_owned_verts.insert( *verts.begin() );
#endif
#ifdef WRITE_DEBUG_FILES
{
// output file, using parallel write
std::stringstream sstr;
sstr << "LaplacianSmootherIterate_0.h5m";
rval = mb->write_file( sstr.str().c_str(), NULL, woptions );
RC;
}
#endif
bool check_metrics = true;
VerdictWrapper vw( mb );
vw.set_size( 1. ); // for relative size measures; maybe it should be user input
double mxdelta = 0.0, global_max = 0.0;
// 2. for num_its iterations:
for( int nit = 0; nit < num_its; nit++ )
{
mxdelta = 0.0;
// 2a. Apply Laplacian Smoothing Filter to Mesh
if( use_hc )
{
rval = hcFilter( mb, pcomm, verts, dim, fixed, verts_o, verts_n, alpha, beta );
RC;
}
else
{
rval = laplacianFilter( mb, pcomm, verts, dim, fixed, verts_o, verts_n );
RC;
}
if( check_metrics )
{
bool smooth_success = true;
std::vector< double > coords;
double jac = 0.0;
int num_nodes = 0;
for( unsigned ic = 0; ic < cells.size(); ++ic )
{
EntityHandle ecell = cells[ic];
EntityType etype = mb->type_from_handle( ecell );
Range everts;
rval = mb->get_connectivity( &ecell, 1, everts, num_nodes );
RC;
coords.resize( num_nodes * 3, 0.0 );
for( int iv = 0; iv < num_nodes; ++iv )
{
const int offset = mb->id_from_handle( everts[iv] ) * 3;
for( int ii = 0; ii < 3; ++ii )
coords[iv * 3 + ii] = verts_n[offset + ii];
}
rval = vw.quality_measure( ecell, MB_SHAPE, jac, num_nodes, etype, &coords[0] );
RC;
if( jac < 1e-8 )
{
dbgprint( "Inverted element " << ic << " with jacobian = " << jac << "." );
smooth_success = false;
break;
}
}
if( !smooth_success )
{
verts_o.swap( verts_n );
dbgprint( "Found element inversions during smoothing. Stopping iterations." );
break;
}
}
if( use_acc )
{
// if (acc_method < 5 || nit <= 3) {
// memcpy( &verts_acc1[0], &verts_acc2[0], nbytes );
// memcpy( &verts_acc2[0], &verts_acc3[0], nbytes );
// memcpy( &verts_acc3[0], &verts_n[0], nbytes );
// }
rat_alphaprev = rat_alpha;
for( unsigned i = 0; i < verts_n.size(); ++i )
{
rat_alpha =
std::max( rat_alpha,
std::abs( ( verts_acc3[i] - verts_acc2[i] ) * ( verts_acc2[i] - verts_acc1[i] ) ) /
( ( verts_acc2[i] - verts_acc1[i] ) * ( verts_acc2[i] - verts_acc1[i] ) ) );
}
rat_theta = std::abs( rat_alpha / rat_alphaprev - 1.0 );
if( nit > 3 && ( nit % nacc ) && rat_theta < 1.0 )
{
if( acc_method == 1 )
{ /* Method 2 from ACCELERATION OF VECTOR SEQUENCES:
http://onlinelibrary.wiley.com/doi/10.1002/cnm.1630020409/pdf */
double vnorm = 0.0, den, acc_alpha = 0.0, acc_gamma = 0.0;
for( unsigned i = 0; i < verts_n.size(); ++i )
{
den = ( verts_acc3[i] - 2.0 * verts_acc2[i] + verts_acc1[i] );
vnorm += den * den;
acc_alpha += ( verts_acc3[i] - verts_acc2[i] ) * ( verts_acc3[i] - verts_acc2[i] );
acc_gamma += ( verts_acc2[i] - verts_acc1[i] ) * ( verts_acc2[i] - verts_acc1[i] );
}
for( unsigned i = 0; i < verts_n.size(); ++i )
{
verts_n[i] = verts_acc2[i] + ( acc_gamma * ( verts_acc3[i] - verts_acc2[i] ) -
acc_alpha * ( verts_acc2[i] - verts_acc1[i] ) ) /
vnorm;
}
}
else if( acc_method == 2 )
{ /* Method 3 from ACCELERATION OF VECTOR SEQUENCES:
http://onlinelibrary.wiley.com/doi/10.1002/cnm.1630020409/pdf */
double vnorm = 0.0, num = 0.0, den = 0.0, mu = 0.0;
for( unsigned i = 0; i < verts_n.size(); ++i )
{
num +=
( verts_acc3[i] - verts_acc2[i] ) * ( verts_acc3[i] - 2.0 * verts_acc2[i] + verts_acc1[i] );
den = ( verts_acc3[i] - 2.0 * verts_acc2[i] + verts_acc1[i] );
vnorm += den * den;
}
mu = num / vnorm;
for( unsigned i = 0; i < verts_n.size(); ++i )
{
verts_n[i] = verts_acc3[i] + mu * ( verts_acc2[i] - verts_acc3[i] );
}
}
else if( acc_method == 3 )
{ /* Method 5 from ACCELERATION OF VECTOR SEQUENCES:
http://onlinelibrary.wiley.com/doi/10.1002/cnm.1630020409/pdf */
double num = 0.0, den = 0.0, mu = 0.0;
for( unsigned i = 0; i < verts_n.size(); ++i )
{
num += ( verts_acc3[i] - verts_acc2[i] ) * ( verts_acc2[i] - verts_acc1[i] );
den +=
( verts_acc2[i] - verts_acc1[i] ) * ( verts_acc3[i] - 2.0 * verts_acc2[i] + verts_acc1[i] );
}
mu = num / den;
for( unsigned i = 0; i < verts_n.size(); ++i )
{
verts_n[i] = verts_acc3[i] - mu * ( verts_acc3[i] - verts_acc2[i] );
}
}
else if( acc_method == 4 )
{ /* Method 8 from ACCELERATION OF VECTOR SEQUENCES:
http://onlinelibrary.wiley.com/doi/10.1002/cnm.1630020409/pdf */
double num = 0.0, den = 0.0, lambda = 0.0;
for( unsigned i = 0; i < verts_n.size(); ++i )
{
num += ( verts_acc3[i] - verts_acc2[i] ) * ( verts_acc3[i] - verts_acc2[i] );
den += ( verts_acc2[i] - verts_acc1[i] ) * ( verts_acc2[i] - verts_acc1[i] );
}
lambda = std::sqrt( num / den );
for( unsigned i = 0; i < verts_n.size(); ++i )
{
verts_n[i] = verts_acc3[i] - lambda / ( lambda - 1.0 ) * ( verts_acc3[i] - verts_acc2[i] );
}
}
else if( acc_method == 5 )
{ /* Minimum polynomial extrapolation of vector sequenes :
https://en.wikipedia.org/wiki/Minimum_polynomial_extrapolation */
/* Pseudo-code
U=x(:,2:end-1)-x(:,1:end-2);
c=-pinv(U)*(x(:,end)-x(:,end-1));
c(end+1,1)=1;
s=(x(:,2:end)*c)/sum(c);
*/
Matrix U( verts_n.size(), 2 );
Vector res( verts_n.size() );
for( unsigned ir = 0; ir < verts_n.size(); ir++ )
{
U( ir, 0 ) = verts_acc2[ir] - verts_acc1[ir];
U( ir, 1 ) = verts_acc3[ir] - verts_acc2[ir];
res[ir] = -( verts_n[ir] - verts_acc3[ir] );
}
// U.print();
// Vector acc = QR(U).solve(res);
Vector acc = solve( U, res );
double accsum = acc[0] + acc[1] + 1.0;
for( unsigned ir = 0; ir < verts_n.size(); ir++ )
{
verts_n[ir] = ( verts_acc1[ir] * acc[0] + verts_acc2[ir] * acc[1] + verts_acc3[ir] ) / accsum;
}
memcpy( &verts_acc1[0], &verts_acc2[0], nbytes );
memcpy( &verts_acc2[0], &verts_acc3[0], nbytes );
memcpy( &verts_acc3[0], &verts_n[0], nbytes );
}
else
{
int offset = 0;
for( Range::const_iterator vit = verts.begin(); vit != verts.end(); ++vit, offset += 3 )
{
// if !fixed
if( fix_tag[offset / 3] ) continue;
CartVect num1 = ( CartVect( &verts_acc3[offset] ) - CartVect( &verts_acc2[offset] ) );
CartVect num2 = ( CartVect( &verts_acc3[offset] ) - 2.0 * CartVect( &verts_acc2[offset] ) +
CartVect( &verts_acc1[offset] ) );
num1.scale( num2 );
const double mu = num1.length_squared() / num2.length_squared();
verts_n[offset + 0] =
verts_acc3[offset + 0] + mu * ( verts_acc2[offset + 0] - verts_acc3[offset + 0] );
verts_n[offset + 1] =
verts_acc3[offset + 1] + mu * ( verts_acc2[offset + 1] - verts_acc3[offset + 1] );
verts_n[offset + 2] =
verts_acc3[offset + 2] + mu * ( verts_acc2[offset + 2] - verts_acc3[offset + 2] );
}
}
}
memcpy( &verts_acc1[0], &verts_acc2[0], nbytes );
memcpy( &verts_acc2[0], &verts_acc3[0], nbytes );
memcpy( &verts_acc3[0], &verts_n[0], nbytes );
}
// 2b. foreach owned vertex: compute change in coordinate norm
for( unsigned v = 0; v < verts.size(); ++v )
{
double delta = ( CartVect( &verts_n[3 * v] ) - CartVect( &verts_o[3 * v] ) ).length();
mxdelta = std::max( delta, mxdelta );
EntityHandle vh = verts[v];
rval = mb->tag_set_data( errt, &vh, 1, &mxdelta );
RC;
}
// global reduce for maximum delta, then report it
global_max = mxdelta;
#ifdef MOAB_HAVE_MPI
if( global_size > 1 ) MPI_Allreduce( &mxdelta, &global_max, 1, MPI_DOUBLE, MPI_MAX, pcomm->comm() );
#endif
if( !( nit % report_its ) )
{
dbgprint( "\tIterate " << nit << ": Global Max delta = " << global_max << "." );
}
#ifdef WRITE_DEBUG_FILES
{
// write the tag back onto vertex coordinates
rval = mb->set_coords( verts, &verts_n[0] );
RC;
// output VTK file for debugging purposes
std::stringstream sstr;
sstr << "LaplacianSmootherIterate_" << nit + 1 << ".h5m";
rval = mb->write_file( sstr.str().c_str(), NULL, woptions );
RC;
}
#endif
#ifdef MOAB_HAVE_MPI
// 2c. exchange tags on owned verts
if( global_size > 1 )
{
rval = mb->tag_set_data( vpost, owned_verts, vdata );
RC;
rval = pcomm->exchange_tags( vpost, shared_owned_verts );
RC;
}
#endif
if( global_max < rel_eps )
break;
else
{
std::copy( verts_n.begin(), verts_n.end(), verts_o.begin() );
}
}
// write the tag back onto vertex coordinates
rval = mb->set_coords( verts, &verts_n[0] );
RC;
dbgprint( "-- Final iterate error = " << global_max << ".\n" );
return MB_SUCCESS;
}
| string test_file_name = string( "input/surfrandomtris-4part.h5m" ) |
Definition at line 46 of file LaplacianSmoother.cpp.
1.7.6.1.
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