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MOAB: Mesh Oriented datABase
(version 5.4.1)
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MOAB: Mesh Oriented datABase
(version 5.4.1)
|
#include <iostream>#include <set>#include <limits>#include <ctime>#include <vector>#include <cstdlib>#include <cstdio>#include <cassert>#include <unistd.h>#include <sys/types.h>#include <sys/stat.h>#include <fcntl.h>#include "moab/Interface.hpp"#include "MBTagConventions.hpp"#include "moab/Core.hpp"#include "moab/Range.hpp"#include "moab/Skinner.hpp"#include "moab/AdaptiveKDTree.hpp"#include "moab/CN.hpp"#include <sys/resource.h>
Include dependency graph for skin.cpp:Go to the source code of this file.
Defines | |
| #define | CHKERROR(A) |
Functions | |
| static void | get_time_mem (double &tot_time, double &tot_mem) |
| static ErrorCode | merge_duplicate_vertices (Interface &, double epsilon) |
| static ErrorCode | min_edge_length (Interface &, double &result) |
| static void | usage (const char *argv0, bool help=false) |
| int | main (int argc, char *argv[]) |
Variables | |
| const char | DEFAULT_FIXED_TAG [] = "fixed" |
| const int | MIN_EDGE_LEN_DENOM = 4 |
| #define CHKERROR | ( | A | ) |
do \ { \ if( MB_SUCCESS != ( A ) ) \ { \ std::cerr << "Internal error at line " << __LINE__ << std::endl; \ return 3; \ } \ } while( false )
Definition at line 41 of file skin.cpp.
Referenced by main().
| void get_time_mem | ( | double & | tot_time, |
| double & | tot_mem | ||
| ) | [static] |
Definition at line 465 of file skin.cpp.
Referenced by main().
{
struct rusage r_usage;
getrusage( RUSAGE_SELF, &r_usage );
double utime = (double)r_usage.ru_utime.tv_sec + ( (double)r_usage.ru_utime.tv_usec / 1.e6 );
double stime = (double)r_usage.ru_stime.tv_sec + ( (double)r_usage.ru_stime.tv_usec / 1.e6 );
tot_time = utime + stime;
tot_mem = 0;
if( 0 != r_usage.ru_maxrss )
{
tot_mem = (double)r_usage.ru_maxrss;
}
else
{
// this machine doesn't return rss - try going to /proc
// print the file name to open
char file_str[4096], dum_str[4096];
int file_ptr = open( "/proc/self/stat", O_RDONLY );
int file_len = read( file_ptr, file_str, sizeof( file_str ) - 1 );
if( file_len <= 0 )
{
close( file_ptr );
return;
}
close( file_ptr );
file_str[file_len] = '\0';
// read the preceding fields and the ones we really want...
int dum_int;
unsigned int dum_uint, vm_size, rss;
int num_fields = sscanf( file_str,
"%d " // pid
"%s " // comm
"%c " // state
"%d %d %d %d %d " // ppid, pgrp, session, tty, tpgid
"%u %u %u %u %u " // flags, minflt, cminflt, majflt, cmajflt
"%d %d %d %d %d %d " // utime, stime, cutime, cstime, counter, priority
"%u %u " // timeout, itrealvalue
"%d " // starttime
"%u %u", // vsize, rss
&dum_int, dum_str, dum_str, &dum_int, &dum_int, &dum_int, &dum_int, &dum_int,
&dum_uint, &dum_uint, &dum_uint, &dum_uint, &dum_uint, &dum_int, &dum_int, &dum_int,
&dum_int, &dum_int, &dum_int, &dum_uint, &dum_uint, &dum_int, &vm_size, &rss );
if( num_fields == 24 ) tot_mem = ( (double)vm_size );
}
}
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
Definition at line 82 of file skin.cpp.
References moab::Interface::add_entities(), moab::Range::begin(), CHKERROR, moab::Interface::create_meshset(), DEFAULT_FIXED_TAG, dim, moab::dum, moab::Range::empty(), entities, ErrorCode, moab::Skinner::find_skin(), moab::Interface::get_adjacencies(), moab::Interface::get_entities_by_dimension(), moab::Interface::get_entities_by_type_and_tag(), get_time_mem(), iface, input_file, moab::Interface::list_entities(), moab::Interface::load_mesh(), MATERIAL_SET_TAG_NAME, MB_SUCCESS, MB_TAG_CREAT, MB_TAG_DENSE, MB_TAG_SPARSE, MB_TYPE_INTEGER, MBENTITYSET, moab::Range::merge(), merge_duplicate_vertices(), MESHSET_SET, MIN_EDGE_LEN_DENOM, min_edge_length(), NEUMANN_SET_TAG_NAME, moab::Range::num_of_dimension(), moab::Range::size(), moab::Interface::tag_get_handle(), moab::Interface::tag_set_data(), moab::Interface::UNION, usage, and moab::Interface::write_mesh().
{
int i = 1;
std::vector< int > matsets;
int neuset_num = -1;
bool write_tag = false, write_whole_mesh = false;
bool print_perf = false;
bool use_vert_elem_adjs = false;
bool merge_vertices = false;
double merge_epsilon = -1;
bool list_skin = false;
bool use_scd = false;
const char* fixed_tag = DEFAULT_FIXED_TAG;
const char *input_file = 0, *output_file = 0;
bool no_more_flags = false;
char* endptr = 0;
long block = 0; // initialize to eliminate compiler warning
while( i < argc )
{
if( !no_more_flags && argv[i][0] == '-' )
{
const int f = i++;
for( int j = 1; argv[f][j]; ++j )
{
switch( argv[f][j] )
{
case 'a':
use_vert_elem_adjs = true;
break;
case 'p':
print_perf = true;
break;
case 't':
write_tag = true;
break;
case 'w':
write_whole_mesh = true;
break;
case 'm':
merge_vertices = true;
break;
case '-':
no_more_flags = true;
break;
case 'h':
usage( argv[0], true );
break;
case 'l':
list_skin = true;
break;
case 'S':
use_scd = true;
break;
case 'b':
if( i == argc || 0 >= ( block = strtol( argv[i], &endptr, 0 ) ) || *endptr )
{
std::cerr << "Expected positive integer following '-b' flag" << std::endl;
usage( argv[0] );
}
matsets.push_back( (int)block );
++i;
break;
case 's':
if( i == argc || 0 >= ( neuset_num = strtol( argv[i], &endptr, 0 ) ) || *endptr )
{
std::cerr << "Expected positive integer following '-s' flag" << std::endl;
usage( argv[0] );
}
++i;
break;
case 'T':
if( i == argc || argv[i][0] == '-' )
{
std::cerr << "Expected tag name following '-T' flag" << std::endl;
usage( argv[0] );
}
fixed_tag = argv[i++];
break;
case 'M':
if( i == argc || 0.0 > ( merge_epsilon = strtod( argv[i], &endptr ) ) || *endptr )
{
std::cerr << "Expected positive numeric value following '-M' flag" << std::endl;
usage( argv[0] );
}
merge_vertices = true;
++i;
break;
default:
std::cerr << "Unrecognized flag: '" << argv[f][j] << "'" << std::endl;
usage( argv[0] );
break;
}
}
}
else if( input_file && output_file )
{
std::cerr << "Extra argument: " << argv[i] << std::endl;
usage( argv[0] );
}
else if( input_file )
{
output_file = argv[i++];
}
else
{
input_file = argv[i++];
}
}
if( !input_file )
{
std::cerr << "No input file specified" << std::endl;
usage( argv[0] );
}
ErrorCode result;
Core mbimpl;
Interface* iface = &mbimpl;
if( print_perf )
{
double tmp_time1, tmp_mem1;
get_time_mem( tmp_time1, tmp_mem1 );
std::cout << "Before reading: cpu time = " << tmp_time1 << ", memory = " << tmp_mem1 / 1.0e6 << "MB."
<< std::endl;
}
// read input file
result = iface->load_mesh( input_file );
if( MB_SUCCESS != result )
{
std::cerr << "Failed to load \"" << input_file << "\"." << std::endl;
return 2;
}
std::cerr << "Read \"" << input_file << "\"" << std::endl;
if( print_perf )
{
double tmp_time2, tmp_mem2;
get_time_mem( tmp_time2, tmp_mem2 );
std::cout << "After reading: cpu time = " << tmp_time2 << ", memory = " << tmp_mem2 / 1.0e6 << "MB."
<< std::endl;
}
if( merge_vertices )
{
if( merge_epsilon < 0.0 )
{
if( MB_SUCCESS != min_edge_length( *iface, merge_epsilon ) )
{
std::cerr << "Error determining minimum edge length" << std::endl;
return 1;
}
merge_epsilon /= MIN_EDGE_LEN_DENOM;
}
if( MB_SUCCESS != merge_duplicate_vertices( *iface, merge_epsilon ) )
{
std::cerr << "Error merging duplicate vertices" << std::endl;
return 1;
}
}
// get entities of largest dimension
int dim = 4;
Range entities;
while( entities.empty() && dim > 1 )
{
dim--;
result = iface->get_entities_by_dimension( 0, dim, entities );CHKERROR( result );
}
Range skin_ents;
Tag matset_tag = 0, neuset_tag = 0;
result = iface->tag_get_handle( MATERIAL_SET_TAG_NAME, 1, MB_TYPE_INTEGER, matset_tag );
if( MB_SUCCESS != result ) return 1;
result = iface->tag_get_handle( NEUMANN_SET_TAG_NAME, 1, MB_TYPE_INTEGER, neuset_tag );
if( MB_SUCCESS != result ) return 1;
if( matsets.empty() )
skin_ents = entities;
else
{
// get all entities in the specified blocks
if( 0 == matset_tag )
{
std::cerr << "Couldn't find any material sets in this mesh." << std::endl;
return 1;
}
for( std::vector< int >::iterator vit = matsets.begin(); vit != matsets.end(); ++vit )
{
int this_matset = *vit;
const void* this_matset_ptr = &this_matset;
Range this_range, ent_range;
result =
iface->get_entities_by_type_and_tag( 0, MBENTITYSET, &matset_tag, &this_matset_ptr, 1, this_range );
if( MB_SUCCESS != result )
{
std::cerr << "Trouble getting material set #" << *vit << std::endl;
return 1;
}
else if( this_range.empty() )
{
std::cerr << "Warning: couldn't find material set " << *vit << std::endl;
continue;
}
result = iface->get_entities_by_dimension( *this_range.begin(), dim, ent_range, true );
if( MB_SUCCESS != result ) continue;
skin_ents.merge( ent_range );
}
}
if( skin_ents.empty() )
{
std::cerr << "No entities for which to compute skin; exiting." << std::endl;
return 1;
}
if( use_vert_elem_adjs )
{
// make a call which we know will generate vert-elem adjs
Range dum_range;
result = iface->get_adjacencies( &( *skin_ents.begin() ), 1, 1, false, dum_range );
if( MB_SUCCESS != result ) return 1;
}
double tmp_time = 0.0, tmp_mem = 0.0;
if( print_perf )
{
get_time_mem( tmp_time, tmp_mem );
std::cout << "Before skinning: cpu time = " << tmp_time << ", memory = " << tmp_mem / 1.0e6 << "MB."
<< std::endl;
}
// skin the mesh
Range forward_lower, reverse_lower;
Skinner tool( iface );
if( use_scd )
result = tool.find_skin( 0, skin_ents, false, forward_lower, NULL, false, true, true );
else
result = tool.find_skin( 0, skin_ents, false, forward_lower, &reverse_lower );
Range boundary;
boundary.merge( forward_lower );
boundary.merge( reverse_lower );
if( MB_SUCCESS != result || boundary.empty() )
{
std::cerr << "Mesh skinning failed." << std::endl;
return 3;
}
if( list_skin )
{
Range skin_verts;
result = iface->get_adjacencies( boundary, 0, true, skin_verts, Interface::UNION );
std::cout << "Skin has ";
if( skin_ents.num_of_dimension( 3 ) )
std::cout << boundary.num_of_dimension( 2 ) << " faces and ";
else if( skin_ents.num_of_dimension( 2 ) )
std::cout << boundary.num_of_dimension( 1 ) << " edges and ";
std::cout << skin_verts.size() << " vertices." << std::endl;
}
if( write_tag )
{
// get tag handle
Tag tag;
int zero = 0;
result = iface->tag_get_handle( fixed_tag, 1, MB_TYPE_INTEGER, tag, MB_TAG_DENSE | MB_TAG_CREAT, &zero );CHKERROR( result );
// Set tags
std::vector< int > ones;
Range bverts;
result = iface->get_adjacencies( boundary, 0, false, bverts, Interface::UNION );
if( MB_SUCCESS != result )
{
std::cerr << "Trouble getting vertices on boundary." << std::endl;
return 1;
}
ones.resize( bverts.size(), 1 );
result = iface->tag_set_data( tag, bverts, &ones[0] );CHKERROR( result );
}
if( -1 != neuset_num )
{
// create a neumann set with these entities
if( 0 == neuset_tag )
{
result = iface->tag_get_handle( "NEUMANN_SET_TAG_NAME", 1, MB_TYPE_INTEGER, neuset_tag,
MB_TAG_SPARSE | MB_TAG_CREAT );
if( MB_SUCCESS != result || 0 == neuset_tag ) return 1;
}
// always create a forward neumann set, assuming we have something in the set
EntityHandle forward_neuset = 0;
result = iface->create_meshset( MESHSET_SET, forward_neuset );
if( MB_SUCCESS != result || 0 == forward_neuset ) return 1;
result = iface->tag_set_data( neuset_tag, &forward_neuset, 1, &neuset_num );
if( MB_SUCCESS != result ) return 1;
if( !forward_lower.empty() )
{
result = iface->add_entities( forward_neuset, forward_lower );
if( MB_SUCCESS != result ) return 1;
}
if( !reverse_lower.empty() )
{
EntityHandle reverse_neuset = 1;
result = iface->create_meshset( MESHSET_SET, reverse_neuset );
if( MB_SUCCESS != result || 0 == forward_neuset ) return 1;
result = iface->add_entities( reverse_neuset, reverse_lower );
if( MB_SUCCESS != result ) return 1;
Tag sense_tag;
int dum_sense = 0;
result = iface->tag_get_handle( "SENSE", 1, MB_TYPE_INTEGER, sense_tag, MB_TAG_SPARSE | MB_TAG_CREAT,
&dum_sense );
if( result != MB_SUCCESS ) return 1;
int sense_val = -1;
result = iface->tag_set_data( neuset_tag, &reverse_neuset, 1, &sense_val );
if( MB_SUCCESS != result ) return 0;
result = iface->add_entities( forward_neuset, &reverse_neuset, 1 );
if( MB_SUCCESS != result ) return 0;
}
}
if( NULL != output_file && write_whole_mesh )
{
// write output file
result = iface->write_mesh( output_file );
if( MB_SUCCESS != result )
{
std::cerr << "Failed to write \"" << output_file << "\"." << std::endl;
return 2;
}
std::cerr << "Wrote \"" << output_file << "\"" << std::endl;
}
else if( NULL != output_file )
{
// write only skin; write them as one set
EntityHandle skin_set;
result = iface->create_meshset( MESHSET_SET, skin_set );
if( MB_SUCCESS != result ) return 1;
result = iface->add_entities( skin_set, forward_lower );
if( MB_SUCCESS != result ) return 1;
result = iface->add_entities( skin_set, reverse_lower );
if( MB_SUCCESS != result ) return 1;
int dum = 10000;
result = iface->tag_set_data( matset_tag, &skin_set, 1, &dum );
if( MB_SUCCESS != result ) return 1;
result = iface->write_mesh( output_file, &skin_set, 1 );
if( MB_SUCCESS != result )
{
std::cerr << "Failed to write \"" << output_file << "\"." << std::endl;
return 2;
}
std::cerr << "Wrote \"" << output_file << "\"" << std::endl;
}
if( print_perf )
{
double tot_time, tot_mem;
get_time_mem( tot_time, tot_mem );
std::cout << "Total cpu time = " << tot_time << " seconds." << std::endl;
std::cout << "Total skin cpu time = " << tot_time - tmp_time << " seconds." << std::endl;
std::cout << "Total memory = " << tot_mem / 1024 << " MB." << std::endl;
std::cout << "Total skin memory = " << ( tot_mem - tmp_mem ) / 1024 << " MB." << std::endl;
std::cout << "Entities: " << std::endl;
iface->list_entities( 0, 0 );
}
return 0;
}
| ErrorCode merge_duplicate_vertices | ( | Interface & | moab, |
| double | epsilon | ||
| ) | [static] |
Definition at line 558 of file skin.cpp.
References moab::Range::begin(), moab::AdaptiveKDTree::build_tree(), moab::AdaptiveKDTree::distance_search(), moab::Range::end(), moab::Range::erase(), ErrorCode, moab::Range::find(), moab::Interface::get_coords(), moab::Interface::get_entities_by_type(), MB_SUCCESS, MBVERTEX, moab::Range::merge(), moab::Interface::merge_entities(), and tree.
Referenced by main().
{
ErrorCode rval;
Range verts;
rval = moab.get_entities_by_type( 0, MBVERTEX, verts );
if( MB_SUCCESS != rval ) return rval;
AdaptiveKDTree tree( &moab );
EntityHandle root;
rval = tree.build_tree( verts, &root );
if( MB_SUCCESS != rval )
{
fprintf( stderr, "Failed to build kD-tree.\n" );
return rval;
}
std::set< EntityHandle > dead_verts;
std::vector< EntityHandle > leaves;
for( Range::iterator i = verts.begin(); i != verts.end(); ++i )
{
double coords[3];
rval = moab.get_coords( &*i, 1, coords );
if( MB_SUCCESS != rval ) return rval;
leaves.clear();
;
rval = tree.distance_search( coords, epsilon, leaves, epsilon, epsilon );
if( MB_SUCCESS != rval ) return rval;
Range near;
for( std::vector< EntityHandle >::iterator j = leaves.begin(); j != leaves.end(); ++j )
{
Range tmp;
rval = moab.get_entities_by_type( *j, MBVERTEX, tmp );
if( MB_SUCCESS != rval ) return rval;
near.merge( tmp.begin(), tmp.end() );
}
Range::iterator v = near.find( *i );
assert( v != near.end() );
near.erase( v );
EntityHandle merge = 0;
for( Range::iterator j = near.begin(); j != near.end(); ++j )
{
if( *j < *i && dead_verts.find( *j ) != dead_verts.end() ) continue;
double coords2[3];
rval = moab.get_coords( &*j, 1, coords2 );
if( MB_SUCCESS != rval ) return rval;
coords2[0] -= coords[0];
coords2[1] -= coords[1];
coords2[2] -= coords[2];
double dsqr = coords2[0] * coords2[0] + coords2[1] * coords2[1] + coords2[2] * coords2[2];
if( dsqr <= epsilon * epsilon )
{
merge = *j;
break;
}
}
if( merge )
{
dead_verts.insert( *i );
rval = moab.merge_entities( merge, *i, false, true );
if( MB_SUCCESS != rval ) return rval;
}
}
if( dead_verts.empty() )
std::cout << "No duplicate/coincident vertices." << std::endl;
else
std::cout << "Merged and deleted " << dead_verts.size() << " vertices "
<< "coincident within " << epsilon << std::endl;
return MB_SUCCESS;
}
| ErrorCode min_edge_length | ( | Interface & | moab, |
| double & | result | ||
| ) | [static] |
Definition at line 513 of file skin.cpp.
References moab::Range::begin(), moab::Range::end(), entities, moab::Range::erase(), ErrorCode, moab::Interface::get_connectivity(), moab::Interface::get_coords(), moab::Interface::get_entities_by_handle(), moab::Range::lower_bound(), MB_SUCCESS, MBENTITYSET, MBVERTEX, moab::CN::NumSubEntities(), moab::CN::SubEntityVertexIndices(), t, moab::Interface::type_from_handle(), and moab::Range::upper_bound().
Referenced by main().
{
double sqr_result = std::numeric_limits< double >::max();
ErrorCode rval;
Range entities;
rval = moab.get_entities_by_handle( 0, entities );
if( MB_SUCCESS != rval ) return rval;
Range::iterator i = entities.upper_bound( MBVERTEX );
entities.erase( entities.begin(), i );
i = entities.lower_bound( MBENTITYSET );
entities.erase( i, entities.end() );
std::vector< EntityHandle > storage;
for( i = entities.begin(); i != entities.end(); ++i )
{
EntityType t = moab.type_from_handle( *i );
const EntityHandle* conn;
int conn_len, indices[2];
rval = moab.get_connectivity( *i, conn, conn_len, true, &storage );
if( MB_SUCCESS != rval ) return rval;
int num_edges = CN::NumSubEntities( t, 1 );
for( int j = 0; j < num_edges; ++j )
{
CN::SubEntityVertexIndices( t, 1, j, indices );
EntityHandle v[2] = { conn[indices[0]], conn[indices[1]] };
if( v[0] == v[1] ) continue;
double c[6];
rval = moab.get_coords( v, 2, c );
if( MB_SUCCESS != rval ) return rval;
c[0] -= c[3];
c[1] -= c[4];
c[2] -= c[5];
double len_sqr = c[0] * c[0] + c[1] * c[1] + c[2] * c[2];
if( len_sqr < sqr_result ) sqr_result = len_sqr;
}
}
result = sqrt( sqr_result );
return MB_SUCCESS;
}
| static void usage | ( | const char * | argv0, |
| bool | help = false |
||
| ) | [static] |
Definition at line 54 of file skin.cpp.
References DEFAULT_FIXED_TAG, help(), and MIN_EDGE_LEN_DENOM.
{
std::ostream& str = help ? std::cout : std::cerr;
str << "Usage: " << argv0
<< " [-b <block_num> [-b ...] ] [-l] [-m] [-M <n>] [-p] [-s <sideset_num>] [-S] [-t|-T "
"<name>] [-w] [-v|-V <n>]"
<< " <input_file> [<output_file>]" << std::endl;
str << "Help : " << argv0 << " -h" << std::endl;
if( !help ) exit( 1 );
str << "Options: " << std::endl;
str << "-a : Compute skin using vert-elem adjacencies (more memory, less time)." << std::endl;
str << "-b <block_num> : Compute skin only for material set/block <block_num>." << std::endl;
str << "-p : Print cpu & memory performance." << std::endl;
str << "-s <sideset_num> : Put skin in neumann set/sideset <sideset_num>." << std::endl;
str << "-S : Look for and use structured mesh information to speed up skinning." << std::endl;
str << "-t : Set '" << DEFAULT_FIXED_TAG << "' tag on skin vertices." << std::endl;
str << "-T <name> : Create tag with specified name and set to 1 on skin vertices." << std::endl;
str << "-w : Write out whole mesh (otherwise just writes skin)." << std::endl;
str << "-m : consolidate duplicate vertices" << std::endl;
str << "-M <n> : consolidate duplicate vertices with specified tolerance. "
"(Default: min_edge_length/"
<< MIN_EDGE_LEN_DENOM << ")" << std::endl;
str << "-l : List total numbers of entities and vertices in skin." << std::endl;
exit( 0 );
}
| const char DEFAULT_FIXED_TAG[] = "fixed" |
| const int MIN_EDGE_LEN_DENOM = 4 |
1.7.6.1