[MOAB-dev] commit/MOAB: 2 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Sun Jun 8 02:03:39 CDT 2014
2 new commits in MOAB:
https://bitbucket.org/fathomteam/moab/commits/32f2f6cac2e1/
Changeset: 32f2f6cac2e1
Branch: None
User: iulian07
Date: 2014-06-08 08:40:26
Summary: fix issue #8
there are 2 important modifications
1) merging of higher dimensional entities is done differently:
merging of faces between 2 solids should work better now
at this point, the vertices are merged, but eventual edges,
faces are not yet merged
we will not skin again, as skinning does not work well, exactly for those
entities that are on top of each other
instead, we will keep track of vertices that were merged, and retrieve
entities adjacent to those vertices; we will look for matches like this:
loop over entities adjacent to those vertices
retrieve connected vertices
get all ents adjacent to those vertices; if a match is found, put it
in a list
delete the merged higher dim entities
2) hdf5 writing: adjacencies information can contain sets that are adjacent to
entities;
start counting adjacencies after sets are assigned file ids, because otherwise
adjacencies are not counted correctly
This was the major source of problems for issue 8
Now, for writing in parallel and serial, write first sets and then adjacencies
Affected #: 6 files
diff --git a/src/MergeMesh.cpp b/src/MergeMesh.cpp
index 4978f79..6c9c632 100644
--- a/src/MergeMesh.cpp
+++ b/src/MergeMesh.cpp
@@ -5,6 +5,7 @@
#include "moab/Range.hpp"
#include "moab/CartVect.hpp"
+#include "Internals.hpp"
#include <vector>
#include <algorithm>
#include <string>
@@ -15,108 +16,120 @@
namespace moab {
- moab::ErrorCode MergeMesh::merge_entities(moab::EntityHandle *elems,
- int elems_size,
- const double merge_tol,
- const int do_merge,
- const int update_sets,
- moab::Tag merge_tag,
- bool do_higher_dim)
+ErrorCode MergeMesh::merge_entities(EntityHandle *elems,
+ int elems_size, const double merge_tol, const int do_merge,
+ const int update_sets, Tag merge_tag, bool do_higher_dim)
{
mergeTol = merge_tol;
- mergeTolSq = merge_tol*merge_tol;
- moab::Range tmp_elems;
- tmp_elems.insert( elems, elems + elems_size);
- moab::ErrorCode result = merge_entities(tmp_elems, merge_tol, do_merge, update_sets,
- (moab::Tag)merge_tag, do_higher_dim);
+ mergeTolSq = merge_tol * merge_tol;
+ Range tmp_elems;
+ tmp_elems.insert(elems, elems + elems_size);
+ ErrorCode result = merge_entities(tmp_elems, merge_tol, do_merge,
+ update_sets, (Tag) merge_tag, do_higher_dim);
return result;
}
/* This function appears to be not necessary after MOAB conversion
-void MergeMesh::perform_merge(iBase_TagHandle merge_tag)
-{
- // put into a range
- moab::ErrorCode result = perform_merge((moab::Tag) merge_tag);
- if (result != moab::MB_SUCCESS)
- throw MKException(iBase_FAILURE, "");
-}*/
-
-moab::ErrorCode MergeMesh::merge_entities(moab::Range &elems,
- const double merge_tol,
- const int do_merge,
- const int ,
- moab::Tag merge_tag,
- bool merge_higher_dim)
+ void MergeMesh::perform_merge(iBase_TagHandle merge_tag)
+ {
+ // put into a range
+ ErrorCode result = perform_merge((Tag) merge_tag);
+ if (result != MB_SUCCESS)
+ throw MKException(iBase_FAILURE, "");
+ }*/
+
+ErrorCode MergeMesh::merge_entities(Range &elems,
+ const double merge_tol, const int do_merge, const int, Tag merge_tag,
+ bool merge_higher_dim)
{
//If merge_higher_dim is true, do_merge must also be true
- if(merge_higher_dim && !do_merge){
- return moab::MB_FAILURE;
+ if (merge_higher_dim && !do_merge)
+ {
+ return MB_FAILURE;
}
mergeTol = merge_tol;
- mergeTolSq = merge_tol*merge_tol;
+ mergeTolSq = merge_tol * merge_tol;
// get the skin of the entities
- moab::Skinner skinner(mbImpl);
- moab::Range skin_range;
- moab::ErrorCode result = skinner.find_skin(0, elems, 0, skin_range, false, false);
- if (moab::MB_SUCCESS != result) return result;
+ Skinner skinner(mbImpl);
+ Range skin_range;
+ ErrorCode result = skinner.find_skin(0, elems, 0, skin_range, false,
+ false);
+ if (MB_SUCCESS != result)
+ return result;
// create a tag to mark merged-to entity; reuse tree_root
- moab::EntityHandle tree_root = 0;
- if (0 == merge_tag) {
- result = mbImpl->tag_get_handle("__merge_tag", 1, moab::MB_TYPE_HANDLE,
- mbMergeTag,
- moab::MB_TAG_DENSE|moab::MB_TAG_EXCL,
- &tree_root);
- if (moab::MB_SUCCESS != result) return result;
+ EntityHandle tree_root = 0;
+ if (0 == merge_tag)
+ {
+ result = mbImpl->tag_get_handle("__merge_tag", 1, MB_TYPE_HANDLE,
+ mbMergeTag, MB_TAG_DENSE | MB_TAG_EXCL, &tree_root);
+ if (MB_SUCCESS != result)
+ return result;
}
- else mbMergeTag = merge_tag;
-
+ else
+ mbMergeTag = merge_tag;
+
// build a kd tree with the vertices
- moab::AdaptiveKDTree kd(mbImpl);
+ AdaptiveKDTree kd(mbImpl);
result = kd.build_tree(skin_range, &tree_root);
- if (moab::MB_SUCCESS != result) return result;
+ if (MB_SUCCESS != result)
+ return result;
// find matching vertices, mark them
result = find_merged_to(tree_root, kd, mbMergeTag);
- if (moab::MB_SUCCESS != result) return result;
+ if (MB_SUCCESS != result)
+ return result;
// merge them if requested
- if (do_merge) {
+ if (do_merge)
+ {
result = perform_merge(mbMergeTag);
- if (moab::MB_SUCCESS != result) return result;
+ if (MB_SUCCESS != result)
+ return result;
}
- if(merge_higher_dim && deadEnts.size() != 0){
+ if (merge_higher_dim && deadEnts.size() != 0)
+ {
result = merge_higher_dimensions(elems);
- if(moab::MB_SUCCESS != result) return result;
+ if (MB_SUCCESS != result)
+ return result;
}
-
- return moab::MB_SUCCESS;
+
+ return MB_SUCCESS;
}
-moab::ErrorCode MergeMesh::perform_merge(moab::Tag merge_tag)
+ErrorCode MergeMesh::perform_merge(Tag merge_tag)
{
- moab::ErrorCode result;
- if (deadEnts.size()==0){
- if(printError)std::cout << "\nWarning: Geometries don't have a common face; Nothing to merge" << std::endl;
- return moab::MB_SUCCESS; //nothing to merge carry on with the program
+ ErrorCode result;
+ if (deadEnts.size() == 0)
+ {
+ if (printError)
+ std::cout
+ << "\nWarning: Geometries don't have a common face; Nothing to merge"
+ << std::endl;
+ return MB_SUCCESS; //nothing to merge carry on with the program
}
- if (mbImpl->type_from_handle(*deadEnts.rbegin()) != moab::MBVERTEX)
- return moab::MB_FAILURE;
- std::vector<moab::EntityHandle> merge_tag_val(deadEnts.size());
+ if (mbImpl->type_from_handle(*deadEnts.rbegin()) != MBVERTEX)
+ return MB_FAILURE;
+ std::vector<EntityHandle> merge_tag_val(deadEnts.size());
result = mbImpl->tag_get_data(merge_tag, deadEnts, &merge_tag_val[0]);
- if (moab::MB_SUCCESS != result) return result;
-
- moab::Range::iterator rit;
+ if (MB_SUCCESS != result)
+ return result;
+
+ Range::iterator rit;
unsigned int i;
- for (rit = deadEnts.begin(), i = 0; rit != deadEnts.end(); rit++, i++) {
+ for (rit = deadEnts.begin(), i = 0; rit != deadEnts.end(); rit++, i++)
+ {
assert(merge_tag_val[i]);
+ if (MBVERTEX==TYPE_FROM_HANDLE(merge_tag_val[i]) )
+ mergedToVertices.insert(merge_tag_val[i]);
result = mbImpl->merge_entities(merge_tag_val[i], *rit, false, false);
- if (moab::MB_SUCCESS != result) {
+ if (MB_SUCCESS != result)
+ {
return result;
}
}
@@ -124,142 +137,249 @@ moab::ErrorCode MergeMesh::perform_merge(moab::Tag merge_tag)
return result;
}
-moab::ErrorCode MergeMesh::find_merged_to(moab::EntityHandle &tree_root,
- moab::AdaptiveKDTree &tree,
- moab::Tag merge_tag)
+ErrorCode MergeMesh::find_merged_to(EntityHandle &tree_root,
+ AdaptiveKDTree &tree, Tag merge_tag)
{
- moab::AdaptiveKDTreeIter iter;
-
+ AdaptiveKDTreeIter iter;
+
// evaluate vertices in this leaf
- moab::Range leaf_range, leaf_range2;
- std::vector<moab::EntityHandle> sorted_leaves;
+ Range leaf_range, leaf_range2;
+ std::vector<EntityHandle> sorted_leaves;
std::vector<double> coords;
- std::vector<moab::EntityHandle> merge_tag_val, leaves_out;
-
- moab::ErrorCode result = tree.get_tree_iterator(tree_root, iter);
- if (moab::MB_SUCCESS != result) return result;
- while (result == moab::MB_SUCCESS) {
- sorted_leaves.push_back( iter.handle() );
+ std::vector<EntityHandle> merge_tag_val, leaves_out;
+
+ ErrorCode result = tree.get_tree_iterator(tree_root, iter);
+ if (MB_SUCCESS != result)
+ return result;
+ while (result == MB_SUCCESS)
+ {
+ sorted_leaves.push_back(iter.handle());
result = iter.step();
}
- if (result != moab::MB_ENTITY_NOT_FOUND)
+ if (result != MB_ENTITY_NOT_FOUND)
return result;
- std::sort( sorted_leaves.begin(), sorted_leaves.end() );
-
- std::vector<moab::EntityHandle>::iterator it;
- for (it = sorted_leaves.begin(); it != sorted_leaves.end(); ++it) {
+ std::sort(sorted_leaves.begin(), sorted_leaves.end());
+
+ std::vector<EntityHandle>::iterator it;
+ for (it = sorted_leaves.begin(); it != sorted_leaves.end(); ++it)
+ {
leaf_range.clear();
result = mbImpl->get_entities_by_handle(*it, leaf_range);
- if (moab::MB_SUCCESS != result) return result;
- coords.resize(3*leaf_range.size());
+ if (MB_SUCCESS != result)
+ return result;
+ coords.resize(3 * leaf_range.size());
merge_tag_val.resize(leaf_range.size());
result = mbImpl->get_coords(leaf_range, &coords[0]);
- if (moab::MB_SUCCESS != result) return result;
+ if (MB_SUCCESS != result)
+ return result;
result = mbImpl->tag_get_data(merge_tag, leaf_range, &merge_tag_val[0]);
- if (moab::MB_SUCCESS != result) return result;
- moab::Range::iterator rit;
+ if (MB_SUCCESS != result)
+ return result;
+ Range::iterator rit;
unsigned int i;
bool inleaf_merged, outleaf_merged = false;
unsigned int lr_size = leaf_range.size();
-
- for (i = 0, rit = leaf_range.begin(); i != lr_size; rit++, i++) {
- if (0 != merge_tag_val[i]) continue;
- moab::CartVect from(&coords[3*i]);
+
+ for (i = 0, rit = leaf_range.begin(); i != lr_size; rit++, i++)
+ {
+ if (0 != merge_tag_val[i])
+ continue;
+ CartVect from(&coords[3 * i]);
inleaf_merged = false;
// check close-by leaves too
leaves_out.clear();
- result = tree.distance_search(from.array(), mergeTol,
- leaves_out, mergeTol, 1.0e-6, NULL, NULL, &tree_root);
+ result = tree.distance_search(from.array(), mergeTol, leaves_out,
+ mergeTol, 1.0e-6, NULL, NULL, &tree_root);
leaf_range2.clear();
- for (std::vector<moab::EntityHandle>::iterator vit = leaves_out.begin();
- vit != leaves_out.end(); vit++) {
- if (*vit > *it) { // if we haven't visited this leaf yet in the outer loop
- result = mbImpl->get_entities_by_handle(*vit, leaf_range2, moab::Interface::UNION);
- if (moab::MB_SUCCESS != result) return result;
+ for (std::vector<EntityHandle>::iterator vit = leaves_out.begin();
+ vit != leaves_out.end(); vit++)
+ {
+ if (*vit > *it)
+ { // if we haven't visited this leaf yet in the outer loop
+ result = mbImpl->get_entities_by_handle(*vit, leaf_range2,
+ Interface::UNION);
+ if (MB_SUCCESS != result)
+ return result;
}
}
- if (!leaf_range2.empty()) {
- coords.resize(3*(lr_size+leaf_range2.size()));
- merge_tag_val.resize(lr_size+leaf_range2.size());
- result = mbImpl->get_coords(leaf_range2, &coords[3*lr_size]);
- if (moab::MB_SUCCESS != result) return result;
- result = mbImpl->tag_get_data(merge_tag, leaf_range2, &merge_tag_val[lr_size]);
- if (moab::MB_SUCCESS != result) return result;
+ if (!leaf_range2.empty())
+ {
+ coords.resize(3 * (lr_size + leaf_range2.size()));
+ merge_tag_val.resize(lr_size + leaf_range2.size());
+ result = mbImpl->get_coords(leaf_range2, &coords[3 * lr_size]);
+ if (MB_SUCCESS != result)
+ return result;
+ result = mbImpl->tag_get_data(merge_tag, leaf_range2,
+ &merge_tag_val[lr_size]);
+ if (MB_SUCCESS != result)
+ return result;
outleaf_merged = false;
}
// check other verts in this leaf
- for (unsigned int j = i+1; j < merge_tag_val.size(); j++) {
- moab::EntityHandle to_ent = j >= lr_size ? leaf_range2[j-lr_size] :
- leaf_range[j];
-
- if (*rit == to_ent) continue;
-
- if ((from - moab::CartVect(&coords[3*j])).length_squared() < mergeTolSq) {
+ for (unsigned int j = i + 1; j < merge_tag_val.size(); j++)
+ {
+ EntityHandle to_ent =
+ j >= lr_size ? leaf_range2[j - lr_size] : leaf_range[j];
+
+ if (*rit == to_ent)
+ continue;
+
+ if ((from - CartVect(&coords[3 * j])).length_squared()
+ < mergeTolSq)
+ {
merge_tag_val[j] = *rit;
- if (j < lr_size){
- inleaf_merged = true;}
- else{
- outleaf_merged = true;}
+ if (j < lr_size)
+ {
+ inleaf_merged = true;
+ }
+ else
+ {
+ outleaf_merged = true;
+ }
deadEnts.insert(to_ent);
}
}
- if (outleaf_merged) {
- result = mbImpl->tag_set_data(merge_tag, leaf_range2, &merge_tag_val[leaf_range.size()]);
- if (moab::MB_SUCCESS != result) return result;
- outleaf_merged = false;
+ if (outleaf_merged)
+ {
+ result = mbImpl->tag_set_data(merge_tag, leaf_range2,
+ &merge_tag_val[leaf_range.size()]);
+ if (MB_SUCCESS != result)
+ return result;
+ outleaf_merged = false;
}
- if (inleaf_merged) {
- result = mbImpl->tag_set_data(merge_tag, leaf_range, &merge_tag_val[0]);
- if (moab::MB_SUCCESS != result) return result;
+ if (inleaf_merged)
+ {
+ result = mbImpl->tag_set_data(merge_tag, leaf_range, &merge_tag_val[0]);
+ if (MB_SUCCESS != result)
+ return result;
}
}
}
- return moab::MB_SUCCESS;
+ return MB_SUCCESS;
}
-
//Determine which higher dimensional entities should be merged
-moab::ErrorCode MergeMesh::merge_higher_dimensions(moab::Range &elems)
-{
- Range skinEnts, adj, matches, moreDeadEnts; moab::ErrorCode result;
- moab::Skinner skinner(mbImpl);
+ErrorCode MergeMesh::merge_higher_dimensions(Range &elems)
+{
+ // apply a different strategy
+ // look at the vertices that were merged to, earlier, and find all entities adjacent to them
+ // elems (input) are used just for initial connectivity
+ ErrorCode result;
+ Range verts;
+ result = mbImpl->get_connectivity(elems, verts);
+ if (MB_SUCCESS!=result)
+ return result;
+
+ // all higher dim entities that will be merged will be connected to the vertices that were
+ // merged earlier; we will look at these vertices only
+ Range vertsOfInterest=intersect(this->mergedToVertices, verts);
//Go through each dimension
- for(int dim = 1; dim <3; dim++){
+ Range possibleEntsToMerge, conn, matches, moreDeadEnts;
+
+ for (int dim = 1; dim < 3; dim++)
+ {
+ moreDeadEnts.clear();
+ possibleEntsToMerge.clear();
+ result = mbImpl->get_adjacencies(vertsOfInterest,
+ dim, false, possibleEntsToMerge,
+ Interface::UNION);
+ if (MB_SUCCESS!=result)
+ return result;
+ //Go through each possible entity and see if it shares vertices with another entity of same dimension
+ for (Range::iterator pit = possibleEntsToMerge.begin();
+ pit != possibleEntsToMerge.end(); pit++)
+ {
+ EntityHandle eh=*pit;//possible entity to be matched
+ conn.clear();
+ //Get the vertices connected to it in a range
+
+ result = mbImpl->get_connectivity(&eh, 1, conn);
+ if (MB_SUCCESS!=result)
+ return result;
+ matches.clear();
+ // now retrieve all entities connected to all conn vertices
+ result = mbImpl->get_adjacencies(conn, dim, false, matches,
+ Interface::INTERSECT);
+ if (MB_SUCCESS!=result)
+ return result;
+ if (matches.size() > 1)
+ {
+ for (Range::iterator matchIt = matches.begin();
+ matchIt != matches.end(); matchIt++)
+ {
+ EntityHandle to_remove=*matchIt;
+ if (to_remove != eh)
+ {
+ moreDeadEnts.insert(to_remove);
+ result = mbImpl->merge_entities(eh, to_remove, false, false);
+ if (result != MB_SUCCESS)
+ return result;
+ possibleEntsToMerge.erase(to_remove);
+ }
+ }
+ }
+
+ }
+ //Delete the entities of dimension dim
+ result = mbImpl->delete_entities(moreDeadEnts);
+ if (result != MB_SUCCESS)
+ return result;
+ }
+ return MB_SUCCESS;
+#if 0
+ Range skinEnts, adj, matches, moreDeadEnts;
+ ErrorCode result;
+ Skinner skinner(mbImpl);
+ //Go through each dimension
+ for (int dim = 1; dim < 3; dim++)
+ {
skinEnts.clear();
moreDeadEnts.clear();
result = skinner.find_skin(0, elems, dim, skinEnts, false, false);
//Go through each skin entity and see if it shares adjacancies with another entity
- for(moab::Range::iterator skinIt = skinEnts.begin(); skinIt != skinEnts.end(); skinIt++){
+ for (Range::iterator skinIt = skinEnts.begin();
+ skinIt != skinEnts.end(); skinIt++)
+ {
adj.clear();
//Get the adjacencies 1 dimension lower
- result = mbImpl->get_adjacencies(&(*skinIt), 1, dim-1, false, adj);
- if(result != moab::MB_SUCCESS) return result;
+ result = mbImpl->get_adjacencies(&(*skinIt), 1, dim - 1, false, adj);
+ if (result != MB_SUCCESS)
+ return result;
//See what other entities share these adjacencies
matches.clear();
- result = mbImpl->get_adjacencies(adj, dim, false, matches, moab::Interface::INTERSECT);
- if(result != moab::MB_SUCCESS) return result;
+ result = mbImpl->get_adjacencies(adj, dim, false, matches,
+ Interface::INTERSECT);
+ if (result != MB_SUCCESS)
+ return result;
//If there is more than one entity, then we have some to merge and erase
- if(matches.size() > 1){
- for(moab::Range::iterator matchIt = matches.begin(); matchIt != matches.end(); matchIt++){
- if(*matchIt != *skinIt){
- moreDeadEnts.insert(*matchIt);
- result = mbImpl->merge_entities(*skinIt, *matchIt, false, false);
- if(result != moab::MB_SUCCESS) return result;
- skinEnts.erase(*matchIt);
- }
- }
- }
+ if (matches.size() > 1)
+ {
+ for (Range::iterator matchIt = matches.begin();
+ matchIt != matches.end(); matchIt++)
+ {
+ if (*matchIt != *skinIt)
+ {
+ moreDeadEnts.insert(*matchIt);
+ result = mbImpl->merge_entities(*skinIt, *matchIt, false, false);
+ if (result != MB_SUCCESS)
+ return result;
+ skinEnts.erase(*matchIt);
+ }
+ }
+ }
}
//Delete the entities
result = mbImpl->delete_entities(moreDeadEnts);
- if(result != moab::MB_SUCCESS)return result;
+ if (result != MB_SUCCESS)
+ return result;
}
- return moab::MB_SUCCESS;
+ return MB_SUCCESS;
+#endif
}
-}//End namespace moab
+} //End namespace moab
diff --git a/src/io/WriteHDF5.cpp b/src/io/WriteHDF5.cpp
index 337cb96..b53508e 100644
--- a/src/io/WriteHDF5.cpp
+++ b/src/io/WriteHDF5.cpp
@@ -2567,7 +2567,43 @@ ErrorCode WriteHDF5::serial_create_file( const char* filename,
rval = assign_ids( ex_itor->range, ex_itor->first_id );
CHK_MB_ERR_0(rval);
}
+ // create set tables
+ writeSets = !setSet.range.empty();
+ if (writeSets)
+ {
+ long contents_len, children_len, parents_len;
+
+ setSet.total_num_ents = setSet.range.size();
+ setSet.max_num_ents = setSet.total_num_ents;
+ rval = create_set_meta(setSet.total_num_ents, first_id);
+ CHK_MB_ERR_0(rval);
+
+ setSet.first_id = (id_t) first_id;
+ rval = assign_ids(setSet.range, setSet.first_id);
+ CHK_MB_ERR_0(rval);
+
+ rval = count_set_size(setSet.range, contents_len, children_len,
+ parents_len);
+ CHK_MB_ERR_0(rval);
+
+ rval = create_set_tables(contents_len, children_len, parents_len);
+ CHK_MB_ERR_0(rval);
+
+ setSet.offset = 0;
+ setContentsOffset = 0;
+ setChildrenOffset = 0;
+ setParentsOffset = 0;
+ writeSetContents = !!contents_len;
+ writeSetChildren = !!children_len;
+ writeSetParents = !!parents_len;
+
+ maxNumSetContents = contents_len;
+ maxNumSetChildren = children_len;
+ maxNumSetParents = parents_len;
+ } // if(!setSet.range.empty())
+ // create adjacency table after set table, because sets do not have yet an id
+ // some entities are adjacent to sets (exodus?)
// create node adjacency table
id_t num_adjacencies;
#ifdef MB_H5M_WRITE_NODE_ADJACENCIES
@@ -2605,39 +2641,6 @@ ErrorCode WriteHDF5::serial_create_file( const char* filename,
}
}
- // create set tables
- writeSets = !setSet.range.empty();
- if (writeSets)
- {
- long contents_len, children_len, parents_len;
-
- setSet.total_num_ents = setSet.range.size();
- setSet.max_num_ents = setSet.total_num_ents;
- rval = create_set_meta( setSet.total_num_ents, first_id );
- CHK_MB_ERR_0(rval);
-
- setSet.first_id = (id_t)first_id;
- rval = assign_ids( setSet.range, setSet.first_id );
- CHK_MB_ERR_0(rval);
-
- rval = count_set_size( setSet.range, contents_len, children_len, parents_len );
- CHK_MB_ERR_0(rval);
-
- rval = create_set_tables( contents_len, children_len, parents_len );
- CHK_MB_ERR_0(rval);
-
- setSet.offset = 0;
- setContentsOffset = 0;
- setChildrenOffset = 0;
- setParentsOffset = 0;
- writeSetContents = !!contents_len;
- writeSetChildren = !!children_len;
- writeSetParents = !!parents_len;
-
- maxNumSetContents = contents_len;
- maxNumSetChildren = children_len;
- maxNumSetParents = parents_len;
- } // if(!setSet.range.empty())
dbgOut.tprint( 1, "Gathering Tags\n" );
diff --git a/src/io/WriteHDF5.hpp b/src/io/WriteHDF5.hpp
index 256a217..555d4ca 100644
--- a/src/io/WriteHDF5.hpp
+++ b/src/io/WriteHDF5.hpp
@@ -104,7 +104,7 @@ public:
Range range;
//! The first Id allocated by the mhdf library. Entities in range have sequential IDs.
id_t first_id;
- //! The offset at which to begin writting this processor's data.
+ //! The offset at which to begin writing this processor's data.
//! Always zero except for parallel IO.
long offset;
//! Offset for adjacency data. Always zero except for parallel IO
diff --git a/src/moab/MergeMesh.hpp b/src/moab/MergeMesh.hpp
index 489bb3e..8eef9a8 100644
--- a/src/moab/MergeMesh.hpp
+++ b/src/moab/MergeMesh.hpp
@@ -7,73 +7,69 @@
namespace moab {
class AdaptiveKDTree;
-
-class MergeMesh
+
+class MergeMesh
{
public:
- /* \brief Constructor
- */
- MergeMesh(moab::Interface *mbImpl, bool printErrorIn = true);
-
- /* \brief Destructor
- */
+ /* \brief Constructor
+ */
+ MergeMesh(Interface *mbImpl, bool printErrorIn = true);
+
+ /* \brief Destructor
+ */
virtual ~MergeMesh();
- /* \brief Merge vertices in elements passed in
- */
- moab::ErrorCode merge_entities(moab::EntityHandle *elems,
- int elems_size,
- const double merge_tol,
- const int do_merge = true,
- const int update_sets = false,
- moab::Tag merge_tag = 0,
- bool do_higher_dim = true);
-
- moab::ErrorCode merge_entities(moab::Range &elems,
- const double merge_tol,
- const int do_merge = true,
- const int update_sets = false,
- moab::Tag merge_tag = 0,
- bool do_higher_dim = true);
-
+ /* \brief Merge vertices in elements passed in
+ */
+ ErrorCode merge_entities(EntityHandle *elems, int elems_size,
+ const double merge_tol, const int do_merge = true, const int update_sets =
+ false, Tag merge_tag = 0, bool do_higher_dim = true);
+
+ ErrorCode merge_entities(Range &elems, const double merge_tol,
+ const int do_merge = true, const int update_sets = false,
+ Tag merge_tag = 0, bool do_higher_dim = true);
+
//Identify higher dimension to be merged
- moab::ErrorCode merge_higher_dimensions(moab::Range &elems);
+ ErrorCode merge_higher_dimensions(Range &elems);
- //- perform the actual merge
- moab::ErrorCode perform_merge(moab::Tag merged_to);
+ //- perform the actual merge
+ ErrorCode perform_merge(Tag merged_to);
private:
//iMesh_Instance imeshImpl;
double mergeTol, mergeTolSq;
- moab::Tag mergeTag;
+ Tag mergeTag;
+
+ //- given a kdtree, set tag on vertices in leaf nodes with vertices
+ //- to which they should be merged
+ ErrorCode find_merged_to(EntityHandle &tree_root,
+ AdaptiveKDTree &tree, Tag merged_to);
+
+ Interface *mbImpl;
- //- given a kdtree, set tag on vertices in leaf nodes with vertices
- //- to which they should be merged
- moab::ErrorCode find_merged_to(moab::EntityHandle &tree_root,
- moab::AdaptiveKDTree &tree,
- moab::Tag merged_to);
-
- moab::Interface *mbImpl;
+ //- the tag pointing to the entity to which an entity will be merged
+ Tag mbMergeTag;
- //- the tag pointing to the entity to which an entity will be merged
- moab::Tag mbMergeTag;
+ //- entities which will go away after the merge
+ Range deadEnts;
- //- entities which will go away after the merge
- moab::Range deadEnts;
+ // vertices that were merged with other vertices, and were left in the database
+ Range mergedToVertices;
//Allow a warning to be suppressed when no merging is done
bool printError;
};
- inline MergeMesh::MergeMesh(Interface *impl, bool printErrorIn)
- : mbImpl(impl), printError(printErrorIn)
+inline MergeMesh::MergeMesh(Interface *impl, bool printErrorIn) :
+ mbImpl(impl), printError(printErrorIn)
{
}
-inline MergeMesh::~MergeMesh()
+inline MergeMesh::~MergeMesh()
{
- if (mbMergeTag) mbImpl->tag_delete(mbMergeTag);
+ if (mbMergeTag)
+ mbImpl->tag_delete(mbMergeTag);
}
}
diff --git a/src/parallel/WriteHDF5Parallel.cpp b/src/parallel/WriteHDF5Parallel.cpp
index be692ba..7bd14b8 100644
--- a/src/parallel/WriteHDF5Parallel.cpp
+++ b/src/parallel/WriteHDF5Parallel.cpp
@@ -420,8 +420,17 @@ ErrorCode WriteHDF5Parallel::parallel_create_file( const char* filename,
if (MB_SUCCESS != rval) return error(rval);
if (times) times[FILEID_EXCHANGE_TIME] = timer.elapsed();
+ /**************** Create meshset tables *********************/
- /**************** Create adjacency tables *********************/
+ debug_barrier();
+ dbgOut.tprint(1,"creating meshset table\n");
+ topState.start("creating meshset tables");
+ rval = create_meshset_tables(times);
+ topState.end(rval);
+ if (MB_SUCCESS != rval) return error(rval);
+ if (times) times[CREATE_SET_TIME] = timer.elapsed();
+
+ /**************** Create adjacency tables *********************/
debug_barrier();
dbgOut.tprint(1,"creating adjacency table\n");
@@ -431,15 +440,7 @@ ErrorCode WriteHDF5Parallel::parallel_create_file( const char* filename,
if (MB_SUCCESS != rval) return error(rval);
if (times) times[CREATE_ADJ_TIME] = timer.elapsed();
- /**************** Create meshset tables *********************/
- debug_barrier();
- dbgOut.tprint(1,"creating meshset table\n");
- topState.start("creating meshset tables");
- rval = create_meshset_tables(times);
- topState.end(rval);
- if (MB_SUCCESS != rval) return error(rval);
- if (times) times[CREATE_SET_TIME] = timer.elapsed();
/**************** Create tag data *********************/
diff --git a/test/mergemesh_test.cpp b/test/mergemesh_test.cpp
index 89c4702..8bdb158 100644
--- a/test/mergemesh_test.cpp
+++ b/test/mergemesh_test.cpp
@@ -8,16 +8,20 @@
using namespace moab;
-const char* meshfile = STRINGIFY(MESHDIR) "/16_unmerged_hex.h5m";
+ const char* meshfile = STRINGIFY(MESHDIR) "/16_unmerged_hex.h5m";
+ const char *outfile = "mm_out.h5m";
-
-int main( int , char** )
+int main( int argc, char** argv)
{
Core moab_core;
ErrorCode rval;
Interface* iface = &moab_core;
// can be generalized to load user defined input/output file
-// std::cout << "loading mesh file " << (std::string) meshfile << std::endl;
+
+ if (argc>1)
+ meshfile = argv[1];
+ if (argc>2)
+ outfile= argv[2];
rval = iface->load_mesh(meshfile);
if (MB_SUCCESS != rval) {
std::cerr << "Error reading file: " << meshfile << std::endl;
@@ -29,17 +33,16 @@ int main( int , char** )
MergeMesh mm(iface);
double merge_tol = 1e-3;
- bool merge_higher_dim_entities = true;
- rval = mm.merge_entities(ents, merge_tol, merge_higher_dim_entities);
+ rval = mm.merge_entities(ents, merge_tol);
if (MB_SUCCESS != rval) {
std::cerr << "Error in MergeMesh during merging entities" << std::endl;
exit(2);
}
// Fixed for now
- const char *outfile = "mm_out.h5m";
- rval = iface->write_mesh( outfile);
+
+ rval = iface->write_file( outfile);
if (MB_SUCCESS != rval) {
std::cerr << "Error saving file: " << outfile << std::endl;
exit(2);
https://bitbucket.org/fathomteam/moab/commits/2b4d00d533ec/
Changeset: 2b4d00d533ec
Branch: master
User: iulian07
Date: 2014-06-08 08:55:57
Summary: issue 8, merging clarification
the mergedToVertices need to be cleared before starting again a new
performing of merge
Affected #: 1 file
diff --git a/src/MergeMesh.cpp b/src/MergeMesh.cpp
index 6c9c632..cb43b85 100644
--- a/src/MergeMesh.cpp
+++ b/src/MergeMesh.cpp
@@ -104,6 +104,9 @@ ErrorCode MergeMesh::merge_entities(Range &elems,
ErrorCode MergeMesh::perform_merge(Tag merge_tag)
{
+ // we start with an empty range of vertices that are "merged to"
+ // they are used (eventually) for higher dim entities
+ mergedToVertices.clear();
ErrorCode result;
if (deadEnts.size() == 0)
{
Repository URL: https://bitbucket.org/fathomteam/moab/
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