[MOAB-dev] commit/MOAB: 9 new changesets

commits-noreply at bitbucket.org commits-noreply at bitbucket.org
Thu Feb 13 13:18:09 CST 2014


9 new commits in MOAB:

https://bitbucket.org/fathomteam/moab/commits/3c38dd0e07af/
Changeset:   3c38dd0e07af
Branch:      None
User:        tautges
Date:        2014-02-13 20:13:14
Summary:     Changes to allow specification of existing displacement tag(s), which can be either single name corresponding to xyz[3]
or 3 names x, y, z.  Handle either case in deform_master.

Affected #:  1 file

diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp
index 5442d1d..23ad554 100644
--- a/examples/DeformMeshRemap.cpp
+++ b/examples/DeformMeshRemap.cpp
@@ -91,6 +91,10 @@ public:
   
     //! get/set the file name
   void set_file_name(int m_or_s, const std::string &name);
+
+    //! get/set the x displacement tag names
+  std::string xdisp_name(int idx = 0);
+  void xdisp_name(const std::string &nm, int idx = 0);
   
 private:
     //! apply a known deformation to the solid elements, putting the results in the xNew tag; also
@@ -132,9 +136,15 @@ private:
     //! filenames for master/slave meshes
   std::string masterFileName, slaveFileName;
 
+    //! tag from file, might be 3
+  Tag xDisp[3];
+
     //! tag used for new positions
   Tag xNew;
   
+    //! tag name used to read disps from file
+  std::string xDispNames[3];
+  
     //! tag name used for new positions
   std::string xNewName;
 };
@@ -199,6 +209,16 @@ inline ErrorCode DeformMeshRemap::get_set_nos(int f_or_s, std::set<int> &set_nos
   return MB_SUCCESS;
 }
 
+inline std::string DeformMeshRemap::xdisp_name(int idx) 
+{
+  return xDispNames[idx];
+}
+
+void DeformMeshRemap::xdisp_name(const std::string &nm, int idx) 
+{
+  xDispNames[idx] = nm;
+}
+
 ErrorCode DeformMeshRemap::execute() 
 {
     // read master/slave files and get fluid/solid material sets
@@ -296,14 +316,14 @@ void DeformMeshRemap::set_file_name(int m_or_s, const std::string &name)
 DeformMeshRemap::DeformMeshRemap(Interface *impl, ParallelComm *master, ParallelComm *slave)  
         : mbImpl(impl), pcMaster(master), pcSlave(slave), masterSet(0), slaveSet(0), xNew(0), xNewName("xnew") 
 {
+  xDisp[0] = xDisp[1] = xDisp[2] = 0;
+
   if (!pcSlave && pcMaster)
     pcSlave = pcMaster;
 }
   
 DeformMeshRemap::~DeformMeshRemap() 
 {
-    // delete the tag
-  mbImpl->tag_delete(xNew);
 }
 
 int main(int argc, char **argv) {
@@ -312,14 +332,14 @@ int main(int argc, char **argv) {
 
   ProgOptions po("Deformed mesh options");
   po.addOpt<std::string> ("master,m", "Specify the master meshfile name" );
-  po.addOpt<std::string> ("slave,s", "Specify the slave meshfile name" );
+  po.addOpt<std::string> ("worker,w", "Specify the slave/worker meshfile name" );
+  po.addOpt<std::string> ("d1,", "Tag name for displacement x or xyz" );
+  po.addOpt<std::string> ("d2,", "Tag name for displacement y" );
+  po.addOpt<std::string> ("d3,", "Tag name for displacement z" );
+  po.addOpt<int> ("fluid,f", "Specify fluid material set number(s).");
+  po.addOpt<int> ("solid,s", "Specify fluid material set number(s).");
+  
   po.parseCommandLine(argc, argv);
-  std::string foo;
-  string masterf, slavef;
-  if(!po.getOpt("master", &masterf))
-    masterf = string(MESH_DIR) + string("/rodquad.g");
-  if(!po.getOpt("slave", &slavef))
-    slavef = string(MESH_DIR) + string("/rodtri.g");
 
   mb = new Core();
 
@@ -330,10 +350,43 @@ int main(int argc, char **argv) {
 #else  
   dfr = new DeformMeshRemap(mb);
 #endif
+
+
+  std::string masterf, slavef;
+  if(!po.getOpt("master", &masterf))
+    masterf = string(MESH_DIR) + string("/rodquad.g");
   dfr->set_file_name(DeformMeshRemap::MASTER, masterf);
+
+  if(!po.getOpt("worker", &slavef))
+    slavef = string(MESH_DIR) + string("/rodtri.g");
   dfr->set_file_name(DeformMeshRemap::SLAVE, slavef);
-  rval = dfr->add_set_no(DeformMeshRemap::SOLID, SOLID_SETNO); RR("Failed to add solid set no.");
-  rval = dfr->add_set_no(DeformMeshRemap::FLUID, FLUID_SETNO); RR("Failed to add fluid set no.");
+
+  std::vector<int> set_nos;
+  po.getOptAllArgs("fluid", set_nos);
+  if (set_nos.empty()) {
+    rval = dfr->add_set_no(DeformMeshRemap::FLUID, FLUID_SETNO); RR("Failed to add solid set no.");
+  }
+  else {
+    for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) 
+      dfr->add_set_no(DeformMeshRemap::FLUID, *vit);
+  }
+  set_nos.clear();
+  
+  po.getOptAllArgs("solid", set_nos);
+  if (set_nos.empty()) {
+    rval = dfr->add_set_no(DeformMeshRemap::SOLID, SOLID_SETNO); RR("Failed to add solid set no.");
+  }
+  else {
+    for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) 
+      dfr->add_set_no(DeformMeshRemap::SOLID, *vit);
+  }
+
+  std::string tnames[3];
+  po.getOpt("d1", &tnames[0]);
+  po.getOpt("d2", &tnames[1]);
+  po.getOpt("d3", &tnames[2]);
+  for (int i = 0; i < 3; i++) 
+    if (!tnames[i].empty()) dfr->xdisp_name(tnames[i], i);
   
   rval = dfr->execute();
   
@@ -387,40 +440,71 @@ void deform_func(const BoundBox &bbox, double *xold, double *xnew)
 ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems, const char *tag_name) 
 {
     // deform elements with an analytic function
+  ErrorCode rval;
 
-    // create the tag
-  ErrorCode rval = mbImpl->tag_get_handle((tag_name ? tag_name : ""), 3, MB_TYPE_DOUBLE, xNew, MB_TAG_CREAT|MB_TAG_DENSE);
-  RR("Failed to create xnew tag.");
-  
-    // get all the vertices and coords in the fluid, set xnew to them
-  Range verts;
-  rval = mbImpl->get_adjacencies(fluid_elems, 0, false, verts, Interface::UNION);
-  RR("Failed to get vertices.");
-  std::vector<double> coords(3*verts.size(), 0.0);
-  rval = mbImpl->get_coords(verts, &coords[0]);
-  RR("Failed to get vertex coords.");
-  rval = mbImpl->tag_set_data(xNew, verts, &coords[0]);
-  RR("Failed to set xnew tag on fluid verts.");
-
-    // get the bounding box of the solid mesh
-  BoundBox bbox;
-  bbox.update(*mbImpl, solid_elems);
-  
     // get all the vertices and coords in the solid
-  verts.clear();
+  Range verts;
   rval = mbImpl->get_adjacencies(solid_elems, 0, false, verts, Interface::UNION);
   RR("Failed to get vertices.");
-  coords.resize(3*verts.size(), 0.0);
+  std::vector<double> coords(3*verts.size());
   rval = mbImpl->get_coords(verts, &coords[0]);
   RR("Failed to get vertex coords.");
   unsigned int num_verts = verts.size();
-  for (unsigned int i = 0; i < num_verts; i++)
-    deform_func(bbox, &coords[3*i], &coords[3*i]);
+
+    // get or create the tag
+
+  if (!xDispNames[0].empty() && !xDispNames[1].empty() && !xDispNames[2].empty()) {
+      // 3 tags, specifying xyz individual data, integrate into one tag
+    rval = mbImpl->tag_get_handle((tag_name ? tag_name : ""), 3, MB_TYPE_DOUBLE, xNew, MB_TAG_CREAT|MB_TAG_DENSE);
+    RR("Failed to create xnew tag.");
+    std::vector<double> disps(num_verts);
+    for (int i = 0; i < 3; i++) {
+      rval = mbImpl->tag_get_handle(xDispNames[0].c_str(), 1, MB_TYPE_DOUBLE, xDisp[i]);
+      RR("Failed to get xDisp tag.");
+      rval = mbImpl->tag_get_data(xDisp[i], verts, &disps[0]);
+      RR("Failed to get xDisp tag values.");
+      for (unsigned int j = 0; j < num_verts; j++)
+        coords[3*j+i] = disps[j];
+    }
+  }
+  else if (!xDispNames[0].empty()) {
+    rval = mbImpl->tag_get_handle(xDispNames[0].c_str(), 3, MB_TYPE_DOUBLE, xDisp[0]);
+    RR("Failed to get first xDisp tag.");
+    xNew = xDisp[0];
+    std::vector<double> disps(3*num_verts);
+    rval = mbImpl->tag_get_data(xDisp[0], verts, &disps[0]);
+    for (unsigned int j = 0; j < 3*num_verts; j++)
+      coords[j] += disps[j];
+  }
+  else {
+      // get the bounding box of the solid mesh
+    BoundBox bbox;
+    bbox.update(*mbImpl, solid_elems);
+  
+    for (unsigned int j = 0; j < num_verts; j++)
+      deform_func(bbox, &coords[3*j], &coords[3*j]);
+  }
+
+  if (!xNew) {
+    rval = mbImpl->tag_get_handle((tag_name ? tag_name : ""), 3, MB_TYPE_DOUBLE, 
+                                  xDisp[0], MB_TAG_CREAT|MB_TAG_DENSE);
+    RR("Failed to get xNew tag.");
+  }
     
     // set the new tag to those coords
   rval = mbImpl->tag_set_data(xNew, verts, &coords[0]);
   RR("Failed to set tag data.");
   
+    // get all the vertices and coords in the fluid, set xnew to them
+  verts.clear();
+  rval = mbImpl->get_adjacencies(fluid_elems, 0, false, verts, Interface::UNION);
+  RR("Failed to get vertices.");
+  coords.resize(3*verts.size());
+  rval = mbImpl->get_coords(verts, &coords[0]);
+  RR("Failed to get vertex coords.");
+  rval = mbImpl->tag_set_data(xNew, verts, &coords[0]);
+  RR("Failed to set xnew tag on fluid verts.");
+    
   return MB_SUCCESS;
 }
 


https://bitbucket.org/fathomteam/moab/commits/eac19c077abe/
Changeset:   eac19c077abe
Branch:      None
User:        tautges
Date:        2014-02-13 20:13:14
Summary:     - add ability to specify master and slave mesh solid/fluid set numbers separately, so set numbers don't need to agree
- add ability to specify only fluid or solid sets, with other sets derived from that and all material sets in a file
- add DeformMeshRemap to list of examples in makefile

Affected #:  2 files

diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp
index 23ad554..b92d994 100644
--- a/examples/DeformMeshRemap.cpp
+++ b/examples/DeformMeshRemap.cpp
@@ -69,13 +69,13 @@ public:
   ErrorCode execute();
   
     //! add a set number
-  ErrorCode add_set_no(int fluid_or_solid, int set_no);
+  ErrorCode add_set_no(int m_or_s, int fluid_or_solid, int set_no);
   
     //! remove a set number
-  ErrorCode remove_set_no(int fluid_or_solid, int set_no);
+  ErrorCode remove_set_no(int m_or_s, int fluid_or_solid, int set_no);
   
     //! get the set numbers
-  ErrorCode get_set_nos(int fluid_or_solid, std::set<int> &set_nos) const;
+  ErrorCode get_set_nos(int m_or_s, int fluid_or_solid, std::set<int> &set_nos) const;
 
     //! get the xNew tag handle
   inline Tag x_new() const {return xNew;}
@@ -110,6 +110,9 @@ private:
     //! write the tag to the vertices, then save to the specified file
   ErrorCode write_and_save(Range &ents, EntityHandle seth, Tag tagh, const char *filename);
 
+    //! find fluid/solid sets from complement of solid/fluid sets 
+  ErrorCode find_other_sets(int m_or_s, EntityHandle file_set);
+  
     //! moab interface
   Interface *mbImpl;
 
@@ -118,11 +121,11 @@ private:
   ParallelComm *pcMaster, *pcSlave;
 #endif
   
-    //! material set numbers for fluid materials
-  std::set<int> fluidSetNos;
+    //! material set numbers for fluid materials, for master/slave
+  std::set<int> fluidSetNos[2];
 
-    //! material set numbers for solid materials
-  std::set<int> solidSetNos;
+    //! material set numbers for solid materials, for master/slave
+  std::set<int> solidSetNos[2];
 
     //! sets defining master/slave meshes
   EntityHandle masterSet, slaveSet;
@@ -150,14 +153,17 @@ private:
 };
 
   //! add a set number
-inline ErrorCode DeformMeshRemap::add_set_no(int f_or_s, int set_no) 
+inline ErrorCode DeformMeshRemap::add_set_no(int m_or_s, int f_or_s, int set_no) 
 {
   std::set<int> *this_set;
+  assert ((m_or_s == MASTER || m_or_s == SLAVE) && "m_or_s should be MASTER or SLAVE.");
+  if (m_or_s != MASTER && m_or_s != SLAVE) return MB_INDEX_OUT_OF_RANGE;
+  
   switch (f_or_s) {
     case FLUID:
-        this_set = &fluidSetNos; break;
+        this_set = &fluidSetNos[m_or_s]; break;
     case SOLID:
-        this_set = &solidSetNos; break;
+        this_set = &solidSetNos[m_or_s]; break;
     default:
         assert(false && "f_or_s should be FLUID or SOLID.");
         return MB_FAILURE;
@@ -169,14 +175,16 @@ inline ErrorCode DeformMeshRemap::add_set_no(int f_or_s, int set_no)
 }
   
   //! remove a set number
-inline ErrorCode DeformMeshRemap::remove_set_no(int f_or_s, int set_no) 
+inline ErrorCode DeformMeshRemap::remove_set_no(int m_or_s, int f_or_s, int set_no) 
 {
   std::set<int> *this_set;
+  assert ((m_or_s == MASTER || m_or_s == SLAVE) && "m_or_s should be MASTER or SLAVE.");
+  if (m_or_s != MASTER && m_or_s != SLAVE) return MB_INDEX_OUT_OF_RANGE;
   switch (f_or_s) {
     case FLUID:
-        this_set = &fluidSetNos; break;
+        this_set = &fluidSetNos[m_or_s]; break;
     case SOLID:
-        this_set = &solidSetNos; break;
+        this_set = &solidSetNos[m_or_s]; break;
     default:
         assert(false && "f_or_s should be FLUID or SOLID.");
         return MB_FAILURE;
@@ -191,14 +199,16 @@ inline ErrorCode DeformMeshRemap::remove_set_no(int f_or_s, int set_no)
 }
   
   //! get the set numbers
-inline ErrorCode DeformMeshRemap::get_set_nos(int f_or_s, std::set<int> &set_nos) const
+inline ErrorCode DeformMeshRemap::get_set_nos(int m_or_s, int f_or_s, std::set<int> &set_nos) const
 {
   const std::set<int> *this_set;
+  assert ((m_or_s == MASTER || m_or_s == SLAVE) && "m_or_s should be MASTER or SLAVE.");
+  if (m_or_s != MASTER && m_or_s != SLAVE) return MB_INDEX_OUT_OF_RANGE;
   switch (f_or_s) {
     case FLUID:
-        this_set = &fluidSetNos; break;
+        this_set = &fluidSetNos[m_or_s]; break;
     case SOLID:
-        this_set = &solidSetNos; break;
+        this_set = &solidSetNos[m_or_s]; break;
     default:
         assert(false && "f_or_s should be FLUID or SOLID.");
         return MB_FAILURE;
@@ -224,10 +234,18 @@ ErrorCode DeformMeshRemap::execute()
     // read master/slave files and get fluid/solid material sets
   ErrorCode rval = read_file(MASTER, masterFileName, masterSet);
   if (MB_SUCCESS != rval) return rval;
+
+  if (*solidSetNos[MASTER].begin() == -1 || *fluidSetNos[MASTER].begin() == -1) {
+    rval = find_other_sets(MASTER, masterSet); RR("Failed to find other sets in master mesh.");
+  }
   
   rval = read_file(SLAVE, slaveFileName, slaveSet);
   if (MB_SUCCESS != rval) return rval;
 
+  if (*solidSetNos[SLAVE].begin() == -1 || *fluidSetNos[SLAVE].begin() == -1) {
+    rval = find_other_sets(SLAVE, slaveSet); RR("Failed to find other sets in slave mesh.");
+  }
+  
   Range src_elems = solidElems[MASTER];
   src_elems.merge(fluidElems[MASTER]);
     // locate slave vertices in master, orig coords; do this with a data coupler, so you can
@@ -288,6 +306,50 @@ ErrorCode DeformMeshRemap::execute()
   return MB_SUCCESS;
 }
 
+ErrorCode DeformMeshRemap::find_other_sets(int m_or_s, EntityHandle file_set) 
+{
+    // solid or fluid sets are missing; find the other
+  Range *filled_sets = NULL, *unfilled_sets = NULL, *unfilled_elems = NULL;
+  
+  if (fluidSets[m_or_s].empty() && !solidSets[m_or_s].empty()) {
+    unfilled_sets = &fluidSets[m_or_s];
+    filled_sets = &solidSets[m_or_s];
+    unfilled_elems = &fluidElems[m_or_s];
+  }
+  else if (!fluidSets[m_or_s].empty() && solidSets[m_or_s].empty()) {
+    filled_sets = &fluidSets[m_or_s];
+    unfilled_sets = &solidSets[m_or_s];
+    unfilled_elems = &solidElems[m_or_s];
+  }
+  
+    // ok, we know the filled sets, now fill the unfilled sets, and the elems from those
+  Tag tagh;
+  ErrorCode rval = mbImpl->tag_get_handle(MATERIAL_SET_TAG_NAME, tagh); RR("Couldn't get material set tag name.");
+  Range matsets;
+  rval = mbImpl->get_entities_by_type_and_tag(file_set, MBENTITYSET, &tagh, NULL, 1, matsets);
+  if (matsets.empty()) rval = MB_FAILURE;
+  RR("Couldn't get any material sets.");
+  *unfilled_sets = subtract(matsets, *filled_sets);
+  if (unfilled_sets->empty()) {
+    rval = MB_FAILURE;
+    RR("Failed to find any unfilled material sets.");
+  }
+  Range tmp_range;
+  for (Range::iterator rit = unfilled_sets->begin(); rit != unfilled_sets->end(); rit++) {
+    rval = mbImpl->get_entities_by_handle(*rit, tmp_range, true);
+    RR("Failed to get entities in unfilled set.");
+  }
+  int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin());
+  assert(dim > 0 && dim < 4);  
+  *unfilled_elems = tmp_range.subset_by_dimension(dim);
+  if (unfilled_elems->empty()) {
+    rval = MB_FAILURE;
+    RR("Failed to find any unfilled set entities.");
+  }
+  
+  return MB_SUCCESS;
+}
+
 std::string DeformMeshRemap::get_file_name(int m_or_s) const
 {
   switch (m_or_s) {
@@ -336,8 +398,10 @@ int main(int argc, char **argv) {
   po.addOpt<std::string> ("d1,", "Tag name for displacement x or xyz" );
   po.addOpt<std::string> ("d2,", "Tag name for displacement y" );
   po.addOpt<std::string> ("d3,", "Tag name for displacement z" );
-  po.addOpt<int> ("fluid,f", "Specify fluid material set number(s).");
-  po.addOpt<int> ("solid,s", "Specify fluid material set number(s).");
+  po.addOpt<int> ("fm,", "Specify master fluid material set number(s). If -1 specified, fluid sets derived from complement of solid sets.");
+  po.addOpt<int> ("fs,", "Specify master solid material set number(s). If -1 specified, fluid sets derived from complement of solid sets.");
+  po.addOpt<int> ("sm,", "Specify slave fluid material set number(s). If -1 specified, fluid sets derived from complement of solid sets.");
+  po.addOpt<int> ("ss,", "Specify slave solid material set number(s). If -1 specified, fluid sets derived from complement of solid sets.");
   
   po.parseCommandLine(argc, argv);
 
@@ -362,23 +426,44 @@ int main(int argc, char **argv) {
   dfr->set_file_name(DeformMeshRemap::SLAVE, slavef);
 
   std::vector<int> set_nos;
-  po.getOptAllArgs("fluid", set_nos);
+  po.getOptAllArgs("fm", set_nos);
   if (set_nos.empty()) {
-    rval = dfr->add_set_no(DeformMeshRemap::FLUID, FLUID_SETNO); RR("Failed to add solid set no.");
+    rval = dfr->add_set_no(DeformMeshRemap::MASTER, DeformMeshRemap::FLUID, FLUID_SETNO); 
+    RR("Failed to add solid set no.");
   }
   else {
     for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) 
-      dfr->add_set_no(DeformMeshRemap::FLUID, *vit);
+      dfr->add_set_no(DeformMeshRemap::MASTER, DeformMeshRemap::FLUID, *vit);
   }
   set_nos.clear();
   
-  po.getOptAllArgs("solid", set_nos);
+  po.getOptAllArgs("fs", set_nos);
   if (set_nos.empty()) {
-    rval = dfr->add_set_no(DeformMeshRemap::SOLID, SOLID_SETNO); RR("Failed to add solid set no.");
+    rval = dfr->add_set_no(DeformMeshRemap::SLAVE, DeformMeshRemap::FLUID, FLUID_SETNO); 
+    RR("Failed to add solid set no.");
   }
   else {
     for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) 
-      dfr->add_set_no(DeformMeshRemap::SOLID, *vit);
+      dfr->add_set_no(DeformMeshRemap::SLAVE, DeformMeshRemap::FLUID, *vit);
+  }
+  set_nos.clear();
+  
+  po.getOptAllArgs("sm", set_nos);
+  if (set_nos.empty()) {
+    rval = dfr->add_set_no(DeformMeshRemap::MASTER, DeformMeshRemap::SOLID, SOLID_SETNO); RR("Failed to add solid set no.");
+  }
+  else {
+    for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) 
+      dfr->add_set_no(DeformMeshRemap::MASTER, DeformMeshRemap::SOLID, *vit);
+  }
+
+  po.getOptAllArgs("ss", set_nos);
+  if (set_nos.empty()) {
+    rval = dfr->add_set_no(DeformMeshRemap::SLAVE, DeformMeshRemap::SOLID, SOLID_SETNO); RR("Failed to add solid set no.");
+  }
+  else {
+    for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) 
+      dfr->add_set_no(DeformMeshRemap::SLAVE, DeformMeshRemap::SOLID, *vit);
   }
 
   std::string tnames[3];
@@ -489,6 +574,7 @@ ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems,
     rval = mbImpl->tag_get_handle((tag_name ? tag_name : ""), 3, MB_TYPE_DOUBLE, 
                                   xDisp[0], MB_TAG_CREAT|MB_TAG_DENSE);
     RR("Failed to get xNew tag.");
+    xNew = xDisp[0];
   }
     
     // set the new tag to those coords
@@ -525,10 +611,12 @@ ErrorCode DeformMeshRemap::read_file(int m_or_s, string &fname, EntityHandle &se
   rval = mbImpl->load_file(fname.c_str(), &seth, ostr.str().c_str());
   RR("Couldn't load master/slave mesh.");
 
+  if (*solidSetNos[m_or_s].begin() == -1 || *fluidSetNos[m_or_s].begin() == -1) return MB_SUCCESS;
+  
     // get material sets for solid/fluid
   Tag tagh;
   rval = mbImpl->tag_get_handle(MATERIAL_SET_TAG_NAME, tagh); RR("Couldn't get material set tag name.");
-  for (std::set<int>::iterator sit = solidSetNos.begin(); sit != solidSetNos.end(); sit++) {
+  for (std::set<int>::iterator sit = solidSetNos[m_or_s].begin(); sit != solidSetNos[m_or_s].end(); sit++) {
     Range sets;
     int set_no = *sit;
     const void *setno_ptr = &set_no;
@@ -549,7 +637,7 @@ ErrorCode DeformMeshRemap::read_file(int m_or_s, string &fname, EntityHandle &se
   
   solidElems[m_or_s] = tmp_range.subset_by_dimension(dim);
 
-  for (std::set<int>::iterator sit = fluidSetNos.begin(); sit != fluidSetNos.end(); sit++) {
+  for (std::set<int>::iterator sit = fluidSetNos[m_or_s].begin(); sit != fluidSetNos[m_or_s].end(); sit++) {
     Range sets;
     int set_no = *sit;
     const void *setno_ptr = &set_no;

diff --git a/examples/makefile b/examples/makefile
index 6c1ed9a..26e3592 100644
--- a/examples/makefile
+++ b/examples/makefile
@@ -7,7 +7,7 @@ include ${MOAB_DIR}/lib/iMesh-Defs.inc
 # MESH_DIR is the directory containing mesh files that come with MOAB source
 MESH_DIR="../MeshFiles/unittest"
 
-EXAMPLES = HelloMOAB GetEntities SetsNTags StructuredMeshSimple DirectAccessWithHoles DirectAccessNoHoles 
+EXAMPLES = HelloMOAB GetEntities SetsNTags StructuredMeshSimple DirectAccessWithHoles DirectAccessNoHoles DeformMeshRemap
 PAREXAMPLES = HelloParMOAB ReduceExchangeTags LloydRelaxation
 F90EXAMPLES = DirectAccessNoHolesF90 PushParMeshIntoMoabF90
 EXOIIEXAMPLES = TestExodusII


https://bitbucket.org/fathomteam/moab/commits/49fa3844f339/
Changeset:   49fa3844f339
Branch:      None
User:        tautges
Date:        2014-02-13 20:13:14
Summary:     Adding the ability to compute on master only.

Affected #:  1 file

diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp
index b92d994..ac3ca39 100644
--- a/examples/DeformMeshRemap.cpp
+++ b/examples/DeformMeshRemap.cpp
@@ -238,36 +238,42 @@ ErrorCode DeformMeshRemap::execute()
   if (*solidSetNos[MASTER].begin() == -1 || *fluidSetNos[MASTER].begin() == -1) {
     rval = find_other_sets(MASTER, masterSet); RR("Failed to find other sets in master mesh.");
   }
-  
-  rval = read_file(SLAVE, slaveFileName, slaveSet);
-  if (MB_SUCCESS != rval) return rval;
 
-  if (*solidSetNos[SLAVE].begin() == -1 || *fluidSetNos[SLAVE].begin() == -1) {
-    rval = find_other_sets(SLAVE, slaveSet); RR("Failed to find other sets in slave mesh.");
+  bool have_slave = !(slaveFileName == "none");
+  if (have_slave) {
+    rval = read_file(SLAVE, slaveFileName, slaveSet);
+    if (MB_SUCCESS != rval) return rval;
+
+    if (*solidSetNos[SLAVE].begin() == -1 || *fluidSetNos[SLAVE].begin() == -1) {
+      rval = find_other_sets(SLAVE, slaveSet); RR("Failed to find other sets in slave mesh.");
+    }
   }
   
   Range src_elems = solidElems[MASTER];
   src_elems.merge(fluidElems[MASTER]);
-    // locate slave vertices in master, orig coords; do this with a data coupler, so you can
-    // later interpolate
-  Range tgt_verts, tmp_range = solidElems[SLAVE];
-  tmp_range.merge(fluidElems[SLAVE]);
-  rval = mbImpl->get_adjacencies(tmp_range, 0, false, tgt_verts, Interface::UNION);
-  RR("Failed to get target verts.");
-  
 
     // initialize data coupler on source elements
   DataCoupler dc_master(mbImpl, NULL, src_elems, 0);
-  
-    // locate slave vertices, caching results in dc
-  rval = dc_master.locate_points(tgt_verts); RR("Point location of tgt verts failed.");
-  int num_located = dc_master.spatial_locator()->local_num_located();
-  if (num_located != (int)tgt_verts.size()) {
-    rval = MB_FAILURE;
-    std::cout << "Only " << num_located << " out of " << tgt_verts.size() << " target points successfully located." << std::endl;
-    return rval;
-  }
 
+  Range tgt_verts;
+  if (have_slave) {
+      // locate slave vertices in master, orig coords; do this with a data coupler, so you can
+      // later interpolate
+    Range tmp_range = solidElems[SLAVE];
+    tmp_range.merge(fluidElems[SLAVE]);
+    rval = mbImpl->get_adjacencies(tmp_range, 0, false, tgt_verts, Interface::UNION);
+    RR("Failed to get target verts.");
+
+      // locate slave vertices, caching results in dc
+    rval = dc_master.locate_points(tgt_verts); RR("Point location of tgt verts failed.");
+    int num_located = dc_master.spatial_locator()->local_num_located();
+    if (num_located != (int)tgt_verts.size()) {
+      rval = MB_FAILURE;
+      std::cout << "Only " << num_located << " out of " << tgt_verts.size() << " target points successfully located." << std::endl;
+      return rval;
+    }
+  }
+  
     // deform the master's solid mesh, put results in a new tag
   rval = deform_master(fluidElems[MASTER], solidElems[MASTER], "xnew"); RR("");
 
@@ -279,14 +285,17 @@ ErrorCode DeformMeshRemap::execute()
     RR("Failed in lloyd smoothing.");
     cout << "Lloyd smoothing required " << ll.num_its() << " iterations." << endl;
   }
-  
-    // map new locations to slave
-    // interpolate xNew to slave points
-  rval = dc_master.interpolate((int)DataCoupler::VOLUME, "xnew"); RR("Failed to interpolate target solution.");
 
-    // transfer xNew to coords, for master and slave
+    // transfer xNew to coords, for master
   rval = write_to_coords(fluidElems[MASTER], xNew); RR("Failed writing tag to master fluid verts.");
-  rval = write_to_coords(tgt_verts, xNew); RR("Failed writing tag to slave verts.");
+
+  if (have_slave) {
+      // map new locations to slave
+      // interpolate xNew to slave points
+    rval = dc_master.interpolate((int)DataCoupler::VOLUME, "xnew"); RR("Failed to interpolate target solution.");
+      // transfer xNew to coords, for slave
+    rval = write_to_coords(tgt_verts, xNew); RR("Failed writing tag to slave verts.");
+  }
 
   if (debug) {
     std::string str;
@@ -295,13 +304,16 @@ ErrorCode DeformMeshRemap::execute()
       str = "PARALLEL=WRITE_PART";
 #endif
     rval = mbImpl->write_file("smoothed_master.vtk", NULL, str.c_str(), &masterSet, 1);
+
+    if (have_slave) {
 #ifdef USE_MPI
-    str.clear();
-    if (pcSlave && pcSlave->size() > 1) 
-      str = "PARALLEL=WRITE_PART";
+      str.clear();
+      if (pcSlave && pcSlave->size() > 1) 
+        str = "PARALLEL=WRITE_PART";
 #endif
-    rval = mbImpl->write_file("slave_interp.vtk", NULL, str.c_str(), &slaveSet, 1);
-  }
+      rval = mbImpl->write_file("slave_interp.vtk", NULL, str.c_str(), &slaveSet, 1);
+    } // if have_slave
+  } // if debug
 
   return MB_SUCCESS;
 }
@@ -394,7 +406,7 @@ int main(int argc, char **argv) {
 
   ProgOptions po("Deformed mesh options");
   po.addOpt<std::string> ("master,m", "Specify the master meshfile name" );
-  po.addOpt<std::string> ("worker,w", "Specify the slave/worker meshfile name" );
+  po.addOpt<std::string> ("worker,w", "Specify the slave/worker meshfile name, or 'none' (no quotes) if master only" );
   po.addOpt<std::string> ("d1,", "Tag name for displacement x or xyz" );
   po.addOpt<std::string> ("d2,", "Tag name for displacement y" );
   po.addOpt<std::string> ("d3,", "Tag name for displacement z" );


https://bitbucket.org/fathomteam/moab/commits/ac01dfaf6feb/
Changeset:   ac01dfaf6feb
Branch:      None
User:        tautges
Date:        2014-02-13 20:13:14
Summary:     Better error handling & debug printing.
In Tree, handle legacy tag on tree root by deleting and re-creating (legacy files have old-sized tag).

Affected #:  2 files

diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp
index ac3ca39..afb4d9d 100644
--- a/examples/DeformMeshRemap.cpp
+++ b/examples/DeformMeshRemap.cpp
@@ -19,6 +19,10 @@
 #include "MBTagConventions.hpp"
 #include "DataCoupler.hpp"
 
+#define IS_BUILDING_MB
+#include "moab/Error.hpp"
+#undef IS_BUILDING_MB
+
 #ifdef USE_MPI
 #  include "moab/ParallelComm.hpp"
 #endif
@@ -116,6 +120,8 @@ private:
     //! moab interface
   Interface *mbImpl;
 
+  Error *mError;
+  
 #ifdef USE_MPI
     //! ParallelComm for master, slave meshes
   ParallelComm *pcMaster, *pcSlave;
@@ -235,7 +241,7 @@ ErrorCode DeformMeshRemap::execute()
   ErrorCode rval = read_file(MASTER, masterFileName, masterSet);
   if (MB_SUCCESS != rval) return rval;
 
-  if (*solidSetNos[MASTER].begin() == -1 || *fluidSetNos[MASTER].begin() == -1) {
+  if (solidSetNos[MASTER].empty() || fluidSetNos[MASTER].empty()) {
     rval = find_other_sets(MASTER, masterSet); RR("Failed to find other sets in master mesh.");
   }
 
@@ -244,7 +250,7 @@ ErrorCode DeformMeshRemap::execute()
     rval = read_file(SLAVE, slaveFileName, slaveSet);
     if (MB_SUCCESS != rval) return rval;
 
-    if (*solidSetNos[SLAVE].begin() == -1 || *fluidSetNos[SLAVE].begin() == -1) {
+    if (solidSetNos[SLAVE].empty() || fluidSetNos[SLAVE].empty()) {
       rval = find_other_sets(SLAVE, slaveSet); RR("Failed to find other sets in slave mesh.");
     }
   }
@@ -318,50 +324,6 @@ ErrorCode DeformMeshRemap::execute()
   return MB_SUCCESS;
 }
 
-ErrorCode DeformMeshRemap::find_other_sets(int m_or_s, EntityHandle file_set) 
-{
-    // solid or fluid sets are missing; find the other
-  Range *filled_sets = NULL, *unfilled_sets = NULL, *unfilled_elems = NULL;
-  
-  if (fluidSets[m_or_s].empty() && !solidSets[m_or_s].empty()) {
-    unfilled_sets = &fluidSets[m_or_s];
-    filled_sets = &solidSets[m_or_s];
-    unfilled_elems = &fluidElems[m_or_s];
-  }
-  else if (!fluidSets[m_or_s].empty() && solidSets[m_or_s].empty()) {
-    filled_sets = &fluidSets[m_or_s];
-    unfilled_sets = &solidSets[m_or_s];
-    unfilled_elems = &solidElems[m_or_s];
-  }
-  
-    // ok, we know the filled sets, now fill the unfilled sets, and the elems from those
-  Tag tagh;
-  ErrorCode rval = mbImpl->tag_get_handle(MATERIAL_SET_TAG_NAME, tagh); RR("Couldn't get material set tag name.");
-  Range matsets;
-  rval = mbImpl->get_entities_by_type_and_tag(file_set, MBENTITYSET, &tagh, NULL, 1, matsets);
-  if (matsets.empty()) rval = MB_FAILURE;
-  RR("Couldn't get any material sets.");
-  *unfilled_sets = subtract(matsets, *filled_sets);
-  if (unfilled_sets->empty()) {
-    rval = MB_FAILURE;
-    RR("Failed to find any unfilled material sets.");
-  }
-  Range tmp_range;
-  for (Range::iterator rit = unfilled_sets->begin(); rit != unfilled_sets->end(); rit++) {
-    rval = mbImpl->get_entities_by_handle(*rit, tmp_range, true);
-    RR("Failed to get entities in unfilled set.");
-  }
-  int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin());
-  assert(dim > 0 && dim < 4);  
-  *unfilled_elems = tmp_range.subset_by_dimension(dim);
-  if (unfilled_elems->empty()) {
-    rval = MB_FAILURE;
-    RR("Failed to find any unfilled set entities.");
-  }
-  
-  return MB_SUCCESS;
-}
-
 std::string DeformMeshRemap::get_file_name(int m_or_s) const
 {
   switch (m_or_s) {
@@ -390,6 +352,8 @@ void DeformMeshRemap::set_file_name(int m_or_s, const std::string &name)
 DeformMeshRemap::DeformMeshRemap(Interface *impl, ParallelComm *master, ParallelComm *slave)  
         : mbImpl(impl), pcMaster(master), pcSlave(slave), masterSet(0), slaveSet(0), xNew(0), xNewName("xnew") 
 {
+  mbImpl->query_interface(mError);
+  
   xDisp[0] = xDisp[1] = xDisp[2] = 0;
 
   if (!pcSlave && pcMaster)
@@ -398,6 +362,7 @@ DeformMeshRemap::DeformMeshRemap(Interface *impl, ParallelComm *master, Parallel
   
 DeformMeshRemap::~DeformMeshRemap() 
 {
+  mbImpl->release_interface(mError);
 }
 
 int main(int argc, char **argv) {
@@ -436,47 +401,29 @@ int main(int argc, char **argv) {
   if(!po.getOpt("worker", &slavef))
     slavef = string(MESH_DIR) + string("/rodtri.g");
   dfr->set_file_name(DeformMeshRemap::SLAVE, slavef);
+  if (slavef.empty()) {
+    std::cerr << "Empty slave file name; if no slave, use filename 'none' (no quotes)." << std::endl;
+    return 1;
+  }
 
   std::vector<int> set_nos;
   po.getOptAllArgs("fm", set_nos);
-  if (set_nos.empty()) {
-    rval = dfr->add_set_no(DeformMeshRemap::MASTER, DeformMeshRemap::FLUID, FLUID_SETNO); 
-    RR("Failed to add solid set no.");
-  }
-  else {
-    for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) 
-      dfr->add_set_no(DeformMeshRemap::MASTER, DeformMeshRemap::FLUID, *vit);
-  }
+  for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) 
+    dfr->add_set_no(DeformMeshRemap::MASTER, DeformMeshRemap::FLUID, *vit);
   set_nos.clear();
   
   po.getOptAllArgs("fs", set_nos);
-  if (set_nos.empty()) {
-    rval = dfr->add_set_no(DeformMeshRemap::SLAVE, DeformMeshRemap::FLUID, FLUID_SETNO); 
-    RR("Failed to add solid set no.");
-  }
-  else {
-    for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) 
-      dfr->add_set_no(DeformMeshRemap::SLAVE, DeformMeshRemap::FLUID, *vit);
-  }
+  for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) 
+    dfr->add_set_no(DeformMeshRemap::SLAVE, DeformMeshRemap::FLUID, *vit);
   set_nos.clear();
   
   po.getOptAllArgs("sm", set_nos);
-  if (set_nos.empty()) {
-    rval = dfr->add_set_no(DeformMeshRemap::MASTER, DeformMeshRemap::SOLID, SOLID_SETNO); RR("Failed to add solid set no.");
-  }
-  else {
-    for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) 
-      dfr->add_set_no(DeformMeshRemap::MASTER, DeformMeshRemap::SOLID, *vit);
-  }
+  for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) 
+    dfr->add_set_no(DeformMeshRemap::MASTER, DeformMeshRemap::SOLID, *vit);
 
   po.getOptAllArgs("ss", set_nos);
-  if (set_nos.empty()) {
-    rval = dfr->add_set_no(DeformMeshRemap::SLAVE, DeformMeshRemap::SOLID, SOLID_SETNO); RR("Failed to add solid set no.");
-  }
-  else {
-    for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) 
-      dfr->add_set_no(DeformMeshRemap::SLAVE, DeformMeshRemap::SOLID, *vit);
-  }
+  for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) 
+    dfr->add_set_no(DeformMeshRemap::SLAVE, DeformMeshRemap::SOLID, *vit);
 
   std::string tnames[3];
   po.getOpt("d1", &tnames[0]);
@@ -632,10 +579,13 @@ ErrorCode DeformMeshRemap::read_file(int m_or_s, string &fname, EntityHandle &se
     Range sets;
     int set_no = *sit;
     const void *setno_ptr = &set_no;
-    rval = mbImpl->get_entities_by_type_and_tag(seth, MBENTITYSET, &tagh, &setno_ptr, 1, sets);
-    if (sets.empty()) rval = MB_FAILURE;
-    RR("Couldn't get any solid sets.");
-    solidSets[m_or_s].merge(sets);
+    ErrorCode tmp_rval = mbImpl->get_entities_by_type_and_tag(seth, MBENTITYSET, &tagh, &setno_ptr, 1, sets);
+    if (sets.empty() || MB_SUCCESS != tmp_rval) {
+      rval = MB_FAILURE;
+      mError->set_last_error("Couldn't find solid set #%d.\n", *sit);
+    }
+    else
+      solidSets[m_or_s].merge(sets);
   }
 
     // get solid entities, and dimension
@@ -644,19 +594,26 @@ ErrorCode DeformMeshRemap::read_file(int m_or_s, string &fname, EntityHandle &se
     rval = mbImpl->get_entities_by_handle(*rit, tmp_range, true);
     RR("Failed to get entities in solid.");
   }
-  int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin());
-  assert(dim > 0 && dim < 4);
-  
-  solidElems[m_or_s] = tmp_range.subset_by_dimension(dim);
+  if (!tmp_range.empty()) {
+    int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin());
+    assert(dim > 0 && dim < 4);
+    solidElems[m_or_s] = tmp_range.subset_by_dimension(dim);
+  }
+
+  if (debug)
+    std::cout << "Read " << solidElems[m_or_s].size() << " solid elements from " << solidSets[m_or_s].size() << " sets in " << (m_or_s == MASTER ? "master" : "slave") << " mesh." << std::endl;    
 
   for (std::set<int>::iterator sit = fluidSetNos[m_or_s].begin(); sit != fluidSetNos[m_or_s].end(); sit++) {
     Range sets;
     int set_no = *sit;
     const void *setno_ptr = &set_no;
-    rval = mbImpl->get_entities_by_type_and_tag(seth, MBENTITYSET, &tagh, &setno_ptr, 1, sets);
-    if (sets.empty()) rval = MB_FAILURE;
-    RR("Couldn't get any fluid sets.");
-    fluidSets[m_or_s].merge(sets);
+    ErrorCode tmp_rval = mbImpl->get_entities_by_type_and_tag(seth, MBENTITYSET, &tagh, &setno_ptr, 1, sets);
+    if (sets.empty() || MB_SUCCESS != tmp_rval) {
+      rval = MB_FAILURE;
+      mError->set_last_error("Couldn't find fluid set #%d.\n", *sit);
+    }
+    else
+      fluidSets[m_or_s].merge(sets);
   }
 
     // get fluid entities, and dimension
@@ -665,8 +622,66 @@ ErrorCode DeformMeshRemap::read_file(int m_or_s, string &fname, EntityHandle &se
     rval = mbImpl->get_entities_by_handle(*rit, tmp_range, true);
     RR("Failed to get entities in fluid.");
   }
+  if (!tmp_range.empty()) {
+    int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin());
+    assert(dim > 0 && dim < 4);
+    fluidElems[m_or_s] = tmp_range.subset_by_dimension(dim);
+  }
   
-  fluidElems[m_or_s] = tmp_range.subset_by_dimension(dim);
+  if (debug)
+    std::cout << "Read " << fluidElems[m_or_s].size() << " fluid elements from " << fluidSets[m_or_s].size() << " sets in " << (m_or_s == MASTER ? "master" : "slave") << " mesh." << std::endl;
+
+  return rval;
+}
+
+ErrorCode DeformMeshRemap::find_other_sets(int m_or_s, EntityHandle file_set) 
+{
+    // solid or fluid sets are missing; find the other
+  Range *filled_sets = NULL, *unfilled_sets = NULL, *unfilled_elems = NULL;
+  
+  if (fluidSets[m_or_s].empty() && !solidSets[m_or_s].empty()) {
+    unfilled_sets = &fluidSets[m_or_s];
+    filled_sets = &solidSets[m_or_s];
+    unfilled_elems = &fluidElems[m_or_s];
+    if (debug)
+      std::cout << "Finding unspecified fluid elements in " << (m_or_s == MASTER ? "master" : "slave") << " mesh...";
+  }
+  else if (!fluidSets[m_or_s].empty() && solidSets[m_or_s].empty()) {
+    filled_sets = &fluidSets[m_or_s];
+    unfilled_sets = &solidSets[m_or_s];
+    unfilled_elems = &solidElems[m_or_s];
+    if (debug)
+      std::cout << "Finding unspecified solid elements in " << (m_or_s == MASTER ? "master" : "slave") << " mesh...";
+  }
+  
+    // ok, we know the filled sets, now fill the unfilled sets, and the elems from those
+  Tag tagh;
+  ErrorCode rval = mbImpl->tag_get_handle(MATERIAL_SET_TAG_NAME, tagh); RR("Couldn't get material set tag name.");
+  Range matsets;
+  rval = mbImpl->get_entities_by_type_and_tag(file_set, MBENTITYSET, &tagh, NULL, 1, matsets);
+  if (matsets.empty()) rval = MB_FAILURE;
+  RR("Couldn't get any material sets.");
+  *unfilled_sets = subtract(matsets, *filled_sets);
+  if (unfilled_sets->empty()) {
+    rval = MB_FAILURE;
+    RR("Failed to find any unfilled material sets.");
+  }
+  Range tmp_range;
+  for (Range::iterator rit = unfilled_sets->begin(); rit != unfilled_sets->end(); rit++) {
+    rval = mbImpl->get_entities_by_handle(*rit, tmp_range, true);
+    RR("Failed to get entities in unfilled set.");
+  }
+  int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin());
+  assert(dim > 0 && dim < 4);  
+  *unfilled_elems = tmp_range.subset_by_dimension(dim);
+  if (unfilled_elems->empty()) {
+    rval = MB_FAILURE;
+    RR("Failed to find any unfilled set entities.");
+  }
+
+  if (debug) 
+    std::cout << "found " << unfilled_sets->size() << " sets and " << unfilled_elems->size() << " elements." << std::endl;
   
   return MB_SUCCESS;
 }
+

diff --git a/src/moab/Tree.hpp b/src/moab/Tree.hpp
index 4d2694a..67b67f9 100644
--- a/src/moab/Tree.hpp
+++ b/src/moab/Tree.hpp
@@ -264,6 +264,14 @@ namespace moab {
       if (!boxTag && create_if_missing) {
         assert(boxTagName.length() > 0);
         ErrorCode rval = moab()->tag_get_handle(boxTagName.c_str(), 6, MB_TYPE_DOUBLE, boxTag, MB_TAG_CREAT | MB_TAG_SPARSE);
+        if (MB_INVALID_SIZE == rval) {
+            // delete the tag and get it again, legacy file...
+          rval = moab()->tag_delete(boxTag);
+          if (MB_SUCCESS != rval) return 0;
+          boxTag = 0;
+          return get_box_tag(true);
+        }
+        
         if (MB_SUCCESS != rval) return 0;
       }
       


https://bitbucket.org/fathomteam/moab/commits/c1531822339e/
Changeset:   c1531822339e
Branch:      None
User:        tautges
Date:        2014-02-13 20:13:14
Summary:     Adding progress-type debug messages.
Was assuming faces in Lloyd smoother, now getting dimension from elements.

Affected #:  2 files

diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp
index afb4d9d..6357df9 100644
--- a/examples/DeformMeshRemap.cpp
+++ b/examples/DeformMeshRemap.cpp
@@ -254,6 +254,8 @@ ErrorCode DeformMeshRemap::execute()
       rval = find_other_sets(SLAVE, slaveSet); RR("Failed to find other sets in slave mesh.");
     }
   }
+ 
+  if (debug) std::cout << "Constructing data coupler/search tree on master mesh..." << std::endl;
   
   Range src_elems = solidElems[MASTER];
   src_elems.merge(fluidElems[MASTER]);
@@ -271,6 +273,7 @@ ErrorCode DeformMeshRemap::execute()
     RR("Failed to get target verts.");
 
       // locate slave vertices, caching results in dc
+    if (debug) std::cout << "Locating slave vertices in master mesh..." << std::endl;
     rval = dc_master.locate_points(tgt_verts); RR("Point location of tgt verts failed.");
     int num_located = dc_master.spatial_locator()->local_num_located();
     if (num_located != (int)tgt_verts.size()) {
@@ -281,11 +284,13 @@ ErrorCode DeformMeshRemap::execute()
   }
   
     // deform the master's solid mesh, put results in a new tag
+  if (debug) std::cout << "Deforming fluid elements in master mesh..." << std::endl;
   rval = deform_master(fluidElems[MASTER], solidElems[MASTER], "xnew"); RR("");
 
   { // to isolate the lloyd smoother & delete when done
 
       // smooth the master mesh
+    if (debug) std::cout << "Smoothing fluid elements in master mesh..." << std::endl;
     LloydSmoother ll(mbImpl, NULL, fluidElems[MASTER], xNew);
     rval = ll.perform_smooth();
     RR("Failed in lloyd smoothing.");
@@ -293,13 +298,16 @@ ErrorCode DeformMeshRemap::execute()
   }
 
     // transfer xNew to coords, for master
+  if (debug) std::cout << "Transferring coords tag to vertex coordinates in master mesh..." << std::endl;
   rval = write_to_coords(fluidElems[MASTER], xNew); RR("Failed writing tag to master fluid verts.");
 
   if (have_slave) {
       // map new locations to slave
       // interpolate xNew to slave points
+    if (debug) std::cout << "Interpolating new coordinates to slave vertices..." << std::endl;
     rval = dc_master.interpolate((int)DataCoupler::VOLUME, "xnew"); RR("Failed to interpolate target solution.");
       // transfer xNew to coords, for slave
+    if (debug) std::cout << "Transferring coords tag to vertex coordinates in slave mesh..." << std::endl;
     rval = write_to_coords(tgt_verts, xNew); RR("Failed writing tag to slave verts.");
   }
 
@@ -309,6 +317,7 @@ ErrorCode DeformMeshRemap::execute()
     if (pcMaster && pcMaster->size() > 1) 
       str = "PARALLEL=WRITE_PART";
 #endif
+    if (debug) std::cout << "Writing smoothed_master.vtk..." << std::endl;
     rval = mbImpl->write_file("smoothed_master.vtk", NULL, str.c_str(), &masterSet, 1);
 
     if (have_slave) {
@@ -317,6 +326,7 @@ ErrorCode DeformMeshRemap::execute()
       if (pcSlave && pcSlave->size() > 1) 
         str = "PARALLEL=WRITE_PART";
 #endif
+      if (debug) std::cout << "Writing slave_interp.vtk..." << std::endl;
       rval = mbImpl->write_file("slave_interp.vtk", NULL, str.c_str(), &slaveSet, 1);
     } // if have_slave
   } // if debug

diff --git a/src/LloydSmoother.cpp b/src/LloydSmoother.cpp
index b1614d2..e9cce82 100644
--- a/src/LloydSmoother.cpp
+++ b/src/LloydSmoother.cpp
@@ -39,6 +39,17 @@ ErrorCode LloydSmoother::perform_smooth()
 {
   ErrorCode rval;
 
+  if (myElems.empty()) {
+    rval = MB_FAILURE;
+    RR("No elements specified to Lloyd smoother.");
+  }
+  else if (mbImpl->dimension_from_handle(*myElems.begin()) != mbImpl->dimension_from_handle(*myElems.rbegin())) {
+    rval = MB_FAILURE;
+    RR("Elements of unequal dimension specified to Lloyd smoother.");
+  }    
+
+  int dim = mbImpl->dimension_from_handle(*myElems.begin());
+  
     // first figure out tolerance to use
   if (0 > absTol) {
       // no tolerance set - get one relative to bounding box around elements
@@ -140,7 +151,7 @@ ErrorCode LloydSmoother::perform_smooth()
       if (fix_tag[v]) continue;
         // vertex centroid = sum(cell centroids)/ncells
       adj_elems.clear();
-      rval = mbImpl->get_adjacencies(&(*vit), 1, 2, false, adj_elems); RR("Failed getting adjs.");
+      rval = mbImpl->get_adjacencies(&(*vit), 1, dim, false, adj_elems); RR("Failed getting adjs.");
       rval = mbImpl->tag_get_data(centroid, &adj_elems[0], adj_elems.size(), &fcentroids[0]); 
       RR("Failed to get elem centroid.");
       double vnew[] = {0.0, 0.0, 0.0};


https://bitbucket.org/fathomteam/moab/commits/019f42d7cc64/
Changeset:   019f42d7cc64
Branch:      None
User:        tautges
Date:        2014-02-13 20:13:14
Summary:     DeformMeshRemap: more debugging output, and handle coord displacements properly (add to prev coords)
LloydSmoother: fix a bug with fixed tag entity handles size
SpatialLocator: if an element range is specified, build the tree too

Affected #:  3 files

diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp
index 6357df9..f0d55fa 100644
--- a/examples/DeformMeshRemap.cpp
+++ b/examples/DeformMeshRemap.cpp
@@ -12,6 +12,7 @@
 
 #include "moab/Core.hpp"
 #include "moab/Range.hpp"
+#include "moab/Skinner.hpp"
 #include "moab/LloydSmoother.hpp"
 #include "moab/ProgOptions.hpp"
 #include "moab/BoundBox.hpp"
@@ -288,6 +289,22 @@ ErrorCode DeformMeshRemap::execute()
   rval = deform_master(fluidElems[MASTER], solidElems[MASTER], "xnew"); RR("");
 
   { // to isolate the lloyd smoother & delete when done
+    if (debug) {
+        // output the skin of smoothed elems, as a check
+        // get the skin; get facets, because we might need to filter on shared entities
+      Skinner skinner(mbImpl);
+      Range skin;
+      rval = skinner.find_skin(0, fluidElems[MASTER], false, skin); RR("Unable to find skin.");
+      EntityHandle skin_set;
+      std::cout << "Writing skin_mesh.g and fluid_mesh.g." << std::endl;
+      rval = mbImpl->create_meshset(MESHSET_SET, skin_set); RR("Failed to create skin set.");
+      rval = mbImpl->add_entities(skin_set, skin); RR("Failed to add skin entities to set.");
+      rval = mbImpl->write_file("skin_mesh.vtk", NULL, NULL, &skin_set, 1); RR("Failure to write skin set.");
+      rval = mbImpl->remove_entities(skin_set, skin); RR("Failed to remove skin entities from set.");
+      rval = mbImpl->add_entities(skin_set, fluidElems[MASTER]); RR("Failed to add fluid entities to set.");
+      rval = mbImpl->write_file("fluid_mesh.vtk", NULL, NULL, &skin_set, 1); RR("Failure to write fluid set.");
+      rval = mbImpl->delete_entities(&skin_set, 1); RR("Failed to delete skin set.");
+    }
 
       // smooth the master mesh
     if (debug) std::cout << "Smoothing fluid elements in master mesh..." << std::endl;
@@ -385,10 +402,10 @@ int main(int argc, char **argv) {
   po.addOpt<std::string> ("d1,", "Tag name for displacement x or xyz" );
   po.addOpt<std::string> ("d2,", "Tag name for displacement y" );
   po.addOpt<std::string> ("d3,", "Tag name for displacement z" );
-  po.addOpt<int> ("fm,", "Specify master fluid material set number(s). If -1 specified, fluid sets derived from complement of solid sets.");
-  po.addOpt<int> ("fs,", "Specify master solid material set number(s). If -1 specified, fluid sets derived from complement of solid sets.");
-  po.addOpt<int> ("sm,", "Specify slave fluid material set number(s). If -1 specified, fluid sets derived from complement of solid sets.");
-  po.addOpt<int> ("ss,", "Specify slave solid material set number(s). If -1 specified, fluid sets derived from complement of solid sets.");
+  po.addOpt<int> ("fm,", "Specify master fluid material set number(s). If none specified, fluid sets derived from complement of solid sets.");
+  po.addOpt<int> ("fs,", "Specify master solid material set number(s). If none specified, solid sets derived from complement of fluid sets.");
+  po.addOpt<int> ("sm,", "Specify slave fluid material set number(s). If none specified, fluid sets derived from complement of solid sets.");
+  po.addOpt<int> ("ss,", "Specify slave solid material set number(s). If none specified, solid sets derived from complement of fluid sets.");
   
   po.parseCommandLine(argc, argv);
 
@@ -500,7 +517,7 @@ ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems,
   Range verts;
   rval = mbImpl->get_adjacencies(solid_elems, 0, false, verts, Interface::UNION);
   RR("Failed to get vertices.");
-  std::vector<double> coords(3*verts.size());
+  std::vector<double> coords(3*verts.size()), new_coords(3*verts.size());
   rval = mbImpl->get_coords(verts, &coords[0]);
   RR("Failed to get vertex coords.");
   unsigned int num_verts = verts.size();
@@ -512,13 +529,14 @@ ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems,
     rval = mbImpl->tag_get_handle((tag_name ? tag_name : ""), 3, MB_TYPE_DOUBLE, xNew, MB_TAG_CREAT|MB_TAG_DENSE);
     RR("Failed to create xnew tag.");
     std::vector<double> disps(num_verts);
+    
     for (int i = 0; i < 3; i++) {
       rval = mbImpl->tag_get_handle(xDispNames[0].c_str(), 1, MB_TYPE_DOUBLE, xDisp[i]);
       RR("Failed to get xDisp tag.");
       rval = mbImpl->tag_get_data(xDisp[i], verts, &disps[0]);
       RR("Failed to get xDisp tag values.");
       for (unsigned int j = 0; j < num_verts; j++)
-        coords[3*j+i] = disps[j];
+        new_coords[3*j+i] = coords[3*j+i] + disps[j];
     }
   }
   else if (!xDispNames[0].empty()) {
@@ -528,7 +546,7 @@ ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems,
     std::vector<double> disps(3*num_verts);
     rval = mbImpl->tag_get_data(xDisp[0], verts, &disps[0]);
     for (unsigned int j = 0; j < 3*num_verts; j++)
-      coords[j] += disps[j];
+      new_coords[j] = coords[j] + disps[j];
   }
   else {
       // get the bounding box of the solid mesh
@@ -536,9 +554,19 @@ ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems,
     bbox.update(*mbImpl, solid_elems);
   
     for (unsigned int j = 0; j < num_verts; j++)
-      deform_func(bbox, &coords[3*j], &coords[3*j]);
+      deform_func(bbox, &coords[3*j], &new_coords[3*j]);
   }
 
+  if (debug) {
+    double len = 0.0;
+    for (unsigned int i = 0; i < num_verts; i++) {
+      CartVect dx = CartVect(&new_coords[3*i]) - CartVect(&coords[3*i]);
+      double tmp_len = dx.length_squared();
+      if (tmp_len > len) len = tmp_len;
+    }
+    std::cout << "Max displacement = " << len << std::endl;
+  }
+  
   if (!xNew) {
     rval = mbImpl->tag_get_handle((tag_name ? tag_name : ""), 3, MB_TYPE_DOUBLE, 
                                   xDisp[0], MB_TAG_CREAT|MB_TAG_DENSE);

diff --git a/src/LloydSmoother.cpp b/src/LloydSmoother.cpp
index e9cce82..ba8169a 100644
--- a/src/LloydSmoother.cpp
+++ b/src/LloydSmoother.cpp
@@ -232,7 +232,7 @@ ErrorCode LloydSmoother::initialize()
     RR("Trouble getting vertices.");
     
       // mark them fixed
-    std::vector<unsigned char> marks(skin.size(), 0x1);
+    std::vector<unsigned char> marks(skin_verts.size(), 0x1);
     rval = mbImpl->tag_set_data(fixedTag, skin_verts, &marks[0]);
     RR("Unable to set tag on skin.");
   }

diff --git a/src/SpatialLocator.cpp b/src/SpatialLocator.cpp
index 694122c..d699d36 100644
--- a/src/SpatialLocator.cpp
+++ b/src/SpatialLocator.cpp
@@ -40,7 +40,9 @@ namespace moab
   
       myDim = mbImpl->dimension_from_handle(*elems.begin());
       myElems = elems;
-      return MB_SUCCESS;
+
+      ErrorCode rval = myTree->build_tree(myElems);
+      return rval;
     }
     
 #ifdef USE_MPI


https://bitbucket.org/fathomteam/moab/commits/acb83a85da96/
Changeset:   acb83a85da96
Branch:      None
User:        tautges
Date:        2014-02-13 20:13:14
Summary:     Adding % change to max displacement debug output.

Affected #:  1 file

diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp
index f0d55fa..667904b 100644
--- a/examples/DeformMeshRemap.cpp
+++ b/examples/DeformMeshRemap.cpp
@@ -564,7 +564,13 @@ ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems,
       double tmp_len = dx.length_squared();
       if (tmp_len > len) len = tmp_len;
     }
-    std::cout << "Max displacement = " << len << std::endl;
+    Range tmp_elems(fluid_elems);
+    tmp_elems.merge(solid_elems);
+    BoundBox box;
+    box.update(*mbImpl, tmp_elems);
+    double max_len = std::max(box.bMax[2]-box.bMin[2], std::max(box.bMax[1]-box.bMin[1], box.bMax[0]-box.bMin[0]));
+    
+    std::cout << "Max displacement = " << len << " (" << 100.0 * len / max_len << "% of max box length)" << std::endl;
   }
   
   if (!xNew) {


https://bitbucket.org/fathomteam/moab/commits/cfbe0e273d55/
Changeset:   cfbe0e273d55
Branch:      None
User:        tautges
Date:        2014-02-13 20:15:03
Summary:     DeformMeshRemap: add some tree statistics output
AdaptiveKDTree: make several functions non-static so they show up in profiling; also use BoundBox a bit more
BVHTree: account for BoundBox change
SpatialLocator: choose tree type based on contents of myElems, and move tree construction to a separate function
BoundBox: change name of contains_box to intersects_box, and fix logic that was broken there
TreeStats.hpp: improve statistics output
test_boundbox: fix tests for changes to BoundBox

Affected #:  9 files

diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp
index 667904b..f752b4e 100644
--- a/examples/DeformMeshRemap.cpp
+++ b/examples/DeformMeshRemap.cpp
@@ -348,6 +348,9 @@ ErrorCode DeformMeshRemap::execute()
     } // if have_slave
   } // if debug
 
+  if (debug) 
+    dc_master.spatial_locator()->get_tree()->tree_stats().print();
+
   return MB_SUCCESS;
 }
 

diff --git a/src/AdaptiveKDTree.cpp b/src/AdaptiveKDTree.cpp
index 1324c30..8aafdd1 100644
--- a/src/AdaptiveKDTree.cpp
+++ b/src/AdaptiveKDTree.cpp
@@ -176,7 +176,6 @@ namespace moab {
         else {
           rval = iter.step();
           if (MB_ENTITY_NOT_FOUND == rval) {
-            treeStats.reset();
             rval = treeStats.compute_stats(mbImpl, myRoot);
             treeStats.initTime = cp.time_elapsed();
             return rval;  // at end
@@ -807,8 +806,7 @@ namespace moab {
                                           t_enter, t_exit );
     }
 
-    static ErrorCode intersect_children_with_elems(
-        AdaptiveKDTree* tool,
+    ErrorCode AdaptiveKDTree::intersect_children_with_elems(
         const Range& elems,
         AdaptiveKDTree::Plane plane,
         double eps,
@@ -823,15 +821,16 @@ namespace moab {
       right_tris.clear();
       both_tris.clear();
       CartVect coords[16];
-      Interface *const moab = tool->moab();
   
         // get extents of boxes for left and right sides
-      CartVect right_min( box_min ), left_max( box_max );
-      right_min[plane.norm] = left_max[plane.norm] = plane.coord;
-      const CartVect left_cen = 0.5*(left_max + box_min);
-      const CartVect left_dim = 0.5*(left_max - box_min);
-      const CartVect right_cen = 0.5*(box_max + right_min);
-      const CartVect right_dim = 0.5*(box_max - right_min);
+      BoundBox left_box(box_min, box_max), right_box(box_min, box_max);
+      right_box.bMin = box_min;
+      left_box.bMax = box_max;
+      right_box.bMin[plane.norm] = left_box.bMax[plane.norm] = plane.coord;
+      const CartVect left_cen = 0.5*(left_box.bMax + box_min);
+      const CartVect left_dim = 0.5*(left_box.bMax - box_min);
+      const CartVect right_cen = 0.5*(box_max + right_box.bMin);
+      const CartVect right_dim = 0.5*(box_max - right_box.bMin);
       const CartVect dim = box_max - box_min;
       const double max_tol = std::max(dim[0], std::max(dim[1], dim[2]))/10;
   
@@ -851,8 +850,8 @@ namespace moab {
   
         // vertices
       for (i = elems.begin(); i != elem_begin; ++i) {
-        tool->tree_stats().leafObjectTests++;
-        rval = moab->get_coords( &*i, 1, coords[0].array() );
+        tree_stats().leafObjectTests++;
+        rval = moab()->get_coords( &*i, 1, coords[0].array() );
         if (MB_SUCCESS != rval)
           return rval;
     
@@ -873,13 +872,13 @@ namespace moab {
         // non-polyhedron elements
       std::vector<EntityHandle> dum_vector;
       for (i = elem_begin; i != poly_begin; ++i) {
-        tool->tree_stats().leafObjectTests++;
-        rval = moab->get_connectivity( *i, conn, count, true, &dum_vector);
+        tree_stats().leafObjectTests++;
+        rval = moab()->get_connectivity( *i, conn, count, true, &dum_vector);
         if (MB_SUCCESS != rval) 
           return rval;
         if (count > (int)(sizeof(coords)/sizeof(coords[0])))
           return MB_FAILURE;
-        rval = moab->get_coords( &conn[0], count, coords[0].array() );
+        rval = moab()->get_coords( &conn[0], count, coords[0].array() );
         if (MB_SUCCESS != rval) return rval;
     
         bool lo = false, ro = false;
@@ -894,12 +893,16 @@ namespace moab {
           // identified that leaf, then we're done.  If triangle is on both
           // sides of plane, do more precise test to ensure that it is really
           // in both.
+//        BoundBox box;
+//        box.update(*moab(), *i);
         if (lo && ro) {
           double tol = eps;
           lo = ro = false;
           while (!lo && !ro && tol <= max_tol) {
-            lo = GeomUtil::box_elem_overlap( coords, TYPE_FROM_HANDLE(*i), left_cen, left_dim+CartVect(tol) );
-            ro = GeomUtil::box_elem_overlap( coords, TYPE_FROM_HANDLE(*i),right_cen,right_dim+CartVect(tol) );
+            tree_stats().boxElemTests+= 2;
+            lo = GeomUtil::box_elem_overlap( coords, TYPE_FROM_HANDLE(*i), left_cen, left_dim+CartVect(tol));
+            ro = GeomUtil::box_elem_overlap( coords, TYPE_FROM_HANDLE(*i), right_cen, right_dim+CartVect(tol));
+            
             tol *= 10.0;
           }
         }
@@ -913,20 +916,20 @@ namespace moab {
   
         // polyhedra
       for (i = poly_begin; i != set_begin; ++i) {
-        tool->tree_stats().leafObjectTests++;
-        rval = moab->get_connectivity( *i, conn, count, true );
+        tree_stats().leafObjectTests++;
+        rval = moab()->get_connectivity( *i, conn, count, true );
         if (MB_SUCCESS != rval) 
           return rval;
       
           // just check the bounding box of the polyhedron
         bool lo = false, ro = false;
         for (int j = 0; j < count; ++j) {
-          rval = moab->get_connectivity( conn[j], conn2, count2, true );
+          rval = moab()->get_connectivity( conn[j], conn2, count2, true );
           if (MB_SUCCESS != rval)
             return rval;
       
           for (int k = 0; k < count2; ++k) {
-            rval = moab->get_coords( conn2 + k, 1, coords[0].array() );
+            rval = moab()->get_coords( conn2 + k, 1, coords[0].array() );
             if (MB_SUCCESS != rval)
               return rval;
             if (coords[0][plane.norm] <= plane.coord)
@@ -947,8 +950,8 @@ namespace moab {
         // sets
       BoundBox tbox;
       for (i = set_begin; i != elems.end(); ++i) {
-        tool->tree_stats().leafObjectTests++;
-        rval = tbox.update(*tool->moab(), *i);
+        tree_stats().leafObjectTests++;
+        rval = tbox.update(*moab(), *i);
         if (MB_SUCCESS != rval)
           return rval;
     
@@ -1005,8 +1008,7 @@ namespace moab {
           AdaptiveKDTree::Plane plane = { box_min[axis] + (p/(1.0+plane_count)) * diff[axis], axis };
           Range left, right, both;
           double val;
-          r = intersect_children_with_elems( iter.tool(),
-                                             entities, plane, eps,
+          r = intersect_children_with_elems( entities, plane, eps,
                                              box_min, box_max,
                                              left, right, both, 
                                              val );
@@ -1057,32 +1059,38 @@ namespace moab {
       if (MB_SUCCESS != r)
         return r;
 
-      tmp_data.resize( vertices.size() );
+      unsigned int nverts = vertices.size();
+      tmp_data.resize( 3*nverts);
+      r = iter.tool()->moab()->get_coords( vertices, &tmp_data[0], &tmp_data[nverts], &tmp_data[2*nverts] );
+      if (MB_SUCCESS != r)
+        return r;
+  
       for (int axis = 0; axis < 3; ++axis) {
         int plane_count = num_planes;
+
+          // if num_planes results in width < eps, reset the plane count
         if ((num_planes+1)*eps >= diff[axis])
           plane_count = (int)(diff[axis] / eps) - 1;
 
-        double *ptrs[] = { 0, 0, 0 };
-        ptrs[axis] = &tmp_data[0];
-        r = iter.tool()->moab()->get_coords( vertices, ptrs[0], ptrs[1], ptrs[2] );
-        if (MB_SUCCESS != r)
-          return r;
-  
         for (int p = 1; p <= plane_count; ++p) {
+
+            // coord of this plane on axis
           double coord = box_min[axis] + (p/(1.0+plane_count)) * diff[axis];
-          double closest_coord = tmp_data[0];
-          for (unsigned i = 1; i < tmp_data.size(); ++i) 
-            if (fabs(coord-tmp_data[i]) < fabs(coord-closest_coord))
-              closest_coord = tmp_data[i];
+
+            // find closest vertex coordinate to this plane position
+          unsigned int istrt = axis*nverts;
+          double closest_coord = tmp_data[istrt];
+          for (unsigned i = 1; i < nverts; ++i) 
+            if (fabs(coord-tmp_data[istrt+i]) < fabs(coord-closest_coord))
+              closest_coord = tmp_data[istrt+i];
           if (closest_coord - box_min[axis] <= eps || box_max[axis] - closest_coord <= eps)
             continue;
           
+            // seprate elems into left/right/both, and compute separating metric
           AdaptiveKDTree::Plane plane = { closest_coord, axis };
           Range left, right, both;
           double val;
-          r = intersect_children_with_elems( iter.tool(),
-                                             entities, plane, eps,
+          r = intersect_children_with_elems( entities, plane, eps,
                                              box_min, box_max,
                                              left, right, both, 
                                              val );
@@ -1160,8 +1168,7 @@ namespace moab {
           AdaptiveKDTree::Plane plane = { *citer, axis };
           Range left, right, both;
           double val;
-          r = intersect_children_with_elems( iter.tool(),
-                                             entities, plane, eps,
+          r = intersect_children_with_elems( entities, plane, eps,
                                              box_min, box_max,
                                              left, right, both, 
                                              val );
@@ -1276,8 +1283,7 @@ namespace moab {
           AdaptiveKDTree::Plane plane = { coords[indices[p]], axis };
           Range left, right, both;
           double val;
-          r = intersect_children_with_elems( iter.tool(),
-                                             entities, plane, eps,
+          r = intersect_children_with_elems( entities, plane, eps,
                                              box_min, box_max,
                                              left, right, both, 
                                              val );

diff --git a/src/BVHTree.cpp b/src/BVHTree.cpp
index d54e24d..e2592fb 100644
--- a/src/BVHTree.cpp
+++ b/src/BVHTree.cpp
@@ -48,7 +48,7 @@ namespace moab
 
 #ifndef NDEBUG
       for(std::vector<HandleData>::const_iterator i = handle_data_vec.begin(); i != handle_data_vec.end(); ++i) {
-        if(!boundBox.contains_box(i->myBox, 0)){
+        if(!boundBox.intersects_box(i->myBox, 0)){
           std::cerr << "BB:" << boundBox << "EB:" << i->myBox << std::endl;
           return MB_FAILURE;
         }
@@ -168,16 +168,16 @@ namespace moab
         for (unsigned int dim = 0; dim < 3; ++dim){
           const unsigned int index = Bucket::bucket_index(splitsPerDir, box, interval, dim);
           Bucket &bucket = buckets[dim][index];
-          if(!bucket.boundingBox.contains_box(box))
+          if(!bucket.boundingBox.intersects_box(box))
             std::cerr << "Buckets not covering elements!" << std::endl;
         }
       }
-      if(!elt_union.contains_box(interval) ){
+      if(!elt_union.intersects_box(interval) ){
         std::cout << "element union: " << std::endl << elt_union; 
         std::cout << "intervals: " << std::endl << interval;
         std::cout << "union of elts does not contain original box!" << std::endl;
       }
-      if (!interval.contains_box(elt_union) ){
+      if (!interval.intersects_box(elt_union) ){
         std::cout << "original box does not contain union of elts" << std::endl;
         std::cout << interval << std::endl << elt_union << std::endl;
       }
@@ -193,9 +193,9 @@ namespace moab
         for(unsigned int i = 0; i < nonempty.size(); ++i)
           test_box.update(buckets_[nonempty[i]].boundingBox);
 
-        if(!test_box.contains_box(interval) )
+        if(!test_box.intersects_box(interval) )
           std::cout << "union of buckets in dimension: " << d << "does not contain original box!" << std::endl;
-        if (!interval.contains_box(test_box) ) {
+        if (!interval.intersects_box(test_box) ) {
           std::cout << "original box does " << "not contain union of buckets" 
                     << "in dimension: " << d << std::endl;
           std::cout << interval << std::endl << test_box << std::endl;
@@ -234,7 +234,7 @@ namespace moab
             s != splits_end; ++s, ++left_end) {
           BoundBox test_box = s->leftBox;
           test_box.update(s->rightBox);
-          if(!data.boundingBox.contains_box(test_box)) {
+          if(!data.boundingBox.intersects_box(test_box)) {
             std::cout << "nr: " << s->nr << std::endl;
             std::cout << "Test box: " << std::endl << 
                 test_box;
@@ -247,7 +247,7 @@ namespace moab
             std::cout << "Split boxes larger than bb" 
                       << std::endl;
           }
-          if(!test_box.contains_box(data.boundingBox)) {
+          if(!test_box.intersects_box(data.boundingBox)) {
             std::cout << "bb larger than union of split boxes" << std::endl;
           }         	
         }
@@ -288,7 +288,7 @@ namespace moab
       data.Lmax = data.leftBox.bMax[data.dim];
 #ifndef NDEBUG
       BoundBox test_box(data.rightBox);
-      if(!data.boundingBox.contains_box(test_box)) {
+      if(!data.boundingBox.intersects_box(test_box)) {
         std::cerr << "MEDIAN: BB Does not contain splits" << std::endl;
         std::cerr << "test_box:         " << test_box << std::endl;
         std::cerr << "data.boundingBox: " << data.boundingBox << std::endl;
@@ -335,7 +335,7 @@ namespace moab
           else {
             right_box.update(i->myBox);
           }
-          if(!right_box.contains_box(i->myBox)) {
+          if(!right_box.intersects_box(i->myBox)) {
             if(!issue) {
               std::cerr << "Bounding right box issue!" 
                         << std::endl;
@@ -352,7 +352,7 @@ namespace moab
           else {
             left_box.update(i->myBox);
           }
-          if(!data.leftBox.contains_box(i->myBox)) {
+          if(!data.leftBox.intersects_box(i->myBox)) {
             if(!issue) {
               std::cerr << "Bounding left box issue!" 
                         << std::endl;
@@ -367,13 +367,13 @@ namespace moab
           }
         }
       }
-      if(!left_box.contains_box(data.leftBox)) 
+      if(!left_box.intersects_box(data.leftBox)) 
         std::cout << "left elts do not contain left box" << std::endl;
-      if(!data.leftBox.contains_box(left_box)) 
+      if(!data.leftBox.intersects_box(left_box)) 
         std::cout << "left box does not contain left elts" << std::endl;
-      if(!right_box.contains_box(data.rightBox))
+      if(!right_box.intersects_box(data.rightBox))
         std::cout << "right elts do not contain right box" << std::endl;
-      if(!data.rightBox.contains_box(right_box))
+      if(!data.rightBox.intersects_box(right_box))
         std::cout << "right box do not contain right elts" << std::endl;
 
       if(count_left != data.nl || count_right != data.nr) {
@@ -400,7 +400,7 @@ namespace moab
     {
 #ifndef NDEBUG
       for(HandleDataVec::const_iterator i = begin; i != end; ++i) {
-        if(!box.contains_box(i->myBox, 0)) {
+        if(!box.intersects_box(i->myBox, 0)) {
           std::cerr << "depth: " << depth << std::endl;
           std::cerr << "BB:" << box << "EB:" << i->myBox << std::endl;
           std::exit(-1);

diff --git a/src/SpatialLocator.cpp b/src/SpatialLocator.cpp
index d699d36..a8a8f07 100644
--- a/src/SpatialLocator.cpp
+++ b/src/SpatialLocator.cpp
@@ -2,6 +2,7 @@
 #include "moab/Interface.hpp"
 #include "moab/ElemEvaluator.hpp"
 #include "moab/AdaptiveKDTree.hpp"
+#include "moab/BVHTree.hpp"
 
 // include ScdInterface for box partitioning
 #include "moab/ScdInterface.hpp"
@@ -18,10 +19,8 @@ namespace moab
     SpatialLocator::SpatialLocator(Interface *impl, Range &elems, Tree *tree, ElemEvaluator *eval) 
             : mbImpl(impl), myElems(elems), myDim(-1), myTree(tree), elemEval(eval), iCreatedTree(false)
     {
-      if (!myTree) {
-        myTree = new AdaptiveKDTree(impl);
-        iCreatedTree = true;
-      }
+      create_tree();
+      
       if (!elems.empty()) {
         myDim = mbImpl->dimension_from_handle(*elems.rbegin());
         ErrorCode rval = myTree->build_tree(myElems);
@@ -32,6 +31,20 @@ namespace moab
       }
     }
 
+    void SpatialLocator::create_tree() 
+    {
+      if (myTree) return;
+      
+      if (myElems.empty() || mbImpl->type_from_handle(*myElems.rbegin()) == MBVERTEX) 
+          // create a kdtree if only vertices
+        myTree = new AdaptiveKDTree(mbImpl);
+      else
+          // otherwise a BVHtree, since it performs better for elements
+        myTree = new BVHTree(mbImpl);
+
+      iCreatedTree = true;
+    }
+
     ErrorCode SpatialLocator::add_elems(Range &elems) 
     {
       if (elems.empty() ||

diff --git a/src/moab/AdaptiveKDTree.hpp b/src/moab/AdaptiveKDTree.hpp
index c77bdbc..450a418 100644
--- a/src/moab/AdaptiveKDTree.hpp
+++ b/src/moab/AdaptiveKDTree.hpp
@@ -251,7 +251,6 @@ namespace moab {
       virtual ErrorCode print();
       
   private:
-
       friend class AdaptiveKDTreeIter;
 
         /** \brief Parse options for tree creation
@@ -273,7 +272,18 @@ namespace moab {
                           DataType type, int count, void* default_val, Tag& tag_handle,
                           std::vector<Tag>& created_tags );
   
-      static ErrorCode best_subdivision_snap_plane( int num_planes,
+      ErrorCode intersect_children_with_elems(
+          const Range& elems,
+          AdaptiveKDTree::Plane plane,
+          double eps,
+          CartVect box_min,
+          CartVect box_max,
+          Range& left_tris,
+          Range& right_tris,
+          Range& both_tris,
+          double& metric_value );
+
+      ErrorCode best_subdivision_snap_plane( int num_planes,
                                                     const AdaptiveKDTreeIter& iter,
                                                     Range& best_left,
                                                     Range& best_right,
@@ -282,7 +292,7 @@ namespace moab {
                                                     std::vector<double>& tmp_data,
                                                     double eps );
   
-      static ErrorCode best_subdivision_plane( int num_planes,
+      ErrorCode best_subdivision_plane( int num_planes,
                                                const AdaptiveKDTreeIter& iter,
                                                Range& best_left,
                                                Range& best_right,
@@ -290,7 +300,7 @@ namespace moab {
                                                AdaptiveKDTree::Plane& best_plane,
                                                double eps );
   
-      static ErrorCode best_vertex_median_plane( int num_planes,
+      ErrorCode best_vertex_median_plane( int num_planes,
                                                  const AdaptiveKDTreeIter& iter,
                                                  Range& best_left,
                                                  Range& best_right,
@@ -299,7 +309,7 @@ namespace moab {
                                                  std::vector<double>& coords,
                                                  double eps);
   
-      static ErrorCode best_vertex_sample_plane( int num_planes,
+      ErrorCode best_vertex_sample_plane( int num_planes,
                                                  const AdaptiveKDTreeIter& iter,
                                                  Range& best_left,
                                                  Range& best_right,

diff --git a/src/moab/BoundBox.hpp b/src/moab/BoundBox.hpp
index 3e525ac..c74707a 100644
--- a/src/moab/BoundBox.hpp
+++ b/src/moab/BoundBox.hpp
@@ -17,7 +17,7 @@ namespace moab {
       ~BoundBox() {}
 
       bool contains_point(const double *point, const double tol = 0.0) const;
-      bool contains_box(const BoundBox &b, const double tol = 0.0) const;
+      bool intersects_box(const BoundBox &b, const double tol = 0.0) const;
       void compute_center(CartVect &center);
       void update(const BoundBox &other_box);
       void update(const double *coords);
@@ -75,10 +75,10 @@ namespace moab {
       else return true;
     }
 
-    inline bool BoundBox::contains_box(const BoundBox &b, const double tol) const {
-      if (b.bMin[0] < bMin[0]-tol || b.bMax[0] > bMax[0]+tol ||
-          b.bMin[1] < bMin[1]-tol || b.bMax[1] > bMax[1]+tol ||
-          b.bMin[2] < bMin[2]-tol || b.bMax[2] > bMax[2]+tol) 
+    inline bool BoundBox::intersects_box(const BoundBox &b, const double tol) const {
+      if (b.bMax[0] < bMin[0]-tol || b.bMin[0] > bMax[0]+tol ||
+          b.bMax[1] < bMin[1]-tol || b.bMin[1] > bMax[1]+tol ||
+          b.bMax[2] < bMin[2]-tol || b.bMin[2] > bMax[2]+tol) 
         return false;
 
       else return true;

diff --git a/src/moab/SpatialLocator.hpp b/src/moab/SpatialLocator.hpp
index f9a1746..5fe7572 100644
--- a/src/moab/SpatialLocator.hpp
+++ b/src/moab/SpatialLocator.hpp
@@ -199,6 +199,12 @@ namespace moab {
       ErrorCode register_src_with_intermediate_procs(ParallelComm *pc, double abs_iter_tol, TupleList &TLreg_o);
       
 #endif
+
+        /** Create a tree
+         * Tree type depends on what's in myElems: if empty or all vertices, creates a kdtree,
+         * otherwise creates a BVHTree.
+         */
+      void create_tree();
       
         /* MOAB instance */
       Interface* mbImpl;

diff --git a/src/moab/TreeStats.hpp b/src/moab/TreeStats.hpp
index be619a5..4ae685b 100644
--- a/src/moab/TreeStats.hpp
+++ b/src/moab/TreeStats.hpp
@@ -59,6 +59,7 @@ namespace moab
       unsigned int leavesVisited;
       unsigned int numTraversals;
       unsigned int leafObjectTests;
+      unsigned int boxElemTests;
 
   private:
       ErrorCode traverse(Interface *impl, EntityHandle node, unsigned int &depth);
@@ -68,6 +69,8 @@ namespace moab
     inline ErrorCode TreeStats::compute_stats(Interface *impl, EntityHandle root_node) 
     {
       maxDepth = 0;
+      numNodes = 0;
+      numLeaves = 0;
       return traverse(impl, root_node, maxDepth);
     }
       
@@ -111,21 +114,27 @@ namespace moab
       leavesVisited = 0;
       numTraversals = 0;
       leafObjectTests = 0;
+      boxElemTests = 0;
     }
     
     inline void TreeStats::print() const {
       std::cout << "Tree initialization time = " << initTime << " seconds" << std::endl;
       
+      std::cout << "Num nodes         = " << numNodes << std::endl;
+      std::cout << "Num leaves        = " << numLeaves << std::endl;
+      std::cout << "Max depth         = " << maxDepth << std::endl << std::endl;
+
       std::cout << "NodesVisited      = " << nodesVisited << std::endl;
       std::cout << "LeavesVisited     = " << leavesVisited << std::endl;
       std::cout << "Num Traversals    = " << numTraversals << std::endl;
       std::cout << "Leaf Object Tests = " << leafObjectTests << std::endl;
+      std::cout << "Box-Element Tests = " << boxElemTests << std::endl;
     }
 
     inline void TreeStats::output() const 
     {
-      std::cout << initTime << " " << nodesVisited << " " << leavesVisited << " " << numTraversals << " " << leafObjectTests
-                << " # initTime, nodesVisited, leavesVisited, numTraversals, leafObjectTests" << std::endl;
+      std::cout << initTime << " " << nodesVisited << " " << leavesVisited << " " << numTraversals << " " << leafObjectTests << " " << boxElemTests
+                << " # initTime, nodesVisited, leavesVisited, numTraversals, leafObjectTests, boxElemTests" << std::endl;
     }
 }
 

diff --git a/test/test_boundbox.cpp b/test/test_boundbox.cpp
index 9fe0357..b089972 100644
--- a/test/test_boundbox.cpp
+++ b/test/test_boundbox.cpp
@@ -35,7 +35,7 @@ void test_bound_box()
     // test for contains point failure
   bool result = box.contains_point(vec.array(), tol);
   CHECK(!result);
-  result = box.contains_box(other_box, tol);
+  result = box.intersects_box(other_box, tol);
   CHECK(!result);
   
   box = other_box;
@@ -44,7 +44,7 @@ void test_bound_box()
     // test for success
   result = box.contains_point(&vals[0], tol);
   CHECK(result);
-  result = box.contains_box(other_box, tol);
+  result = box.intersects_box(other_box, tol);
   CHECK(result);
   
     // check update functions
@@ -54,9 +54,9 @@ void test_bound_box()
   CHECK(result);
   result = box.contains_point((three*1.1).array(), tol);
   CHECK(!result);
-  result = box.contains_box(BoundBox(three, three), tol);
+  result = box.intersects_box(BoundBox(three, three), tol);
   CHECK(result);
-  result = box.contains_box(BoundBox(three, 1.1*three), tol);
+  result = box.intersects_box(BoundBox(1.1*three, 3.0*three), tol);
   CHECK(!result);
   
   CartVect negthree(-3.0);
@@ -65,9 +65,9 @@ void test_bound_box()
   CHECK(result);
   result = box.contains_point((negthree*1.1).array(), tol);
   CHECK(!result);
-  result = box.contains_box(BoundBox(negthree, negthree), tol);
+  result = box.intersects_box(BoundBox(negthree, negthree), tol);
   CHECK(result);
-  result = box.contains_box(BoundBox(1.1*negthree, negthree), tol);
+  result = box.intersects_box(BoundBox(3.0*negthree, 1.1*negthree), tol);
   CHECK(!result);
   
   for (int i = 0; i < 3; i++) {
@@ -78,9 +78,9 @@ void test_bound_box()
   CHECK(result);
   result = box.contains_point((CartVect(&vals[0])*1.1).array(), tol);
   CHECK(!result);
-  result = box.contains_box(BoundBox(&vals[0]), tol);
+  result = box.intersects_box(BoundBox(&vals[0]), tol);
   CHECK(result);
-  result = box.contains_box(BoundBox(1.1*CartVect(&vals[0]), CartVect(&vals[3])), tol);
+  result = box.intersects_box(BoundBox(1.2*CartVect(&vals[0]), 1.1*CartVect(&vals[0])), tol);
   CHECK(!result);
   
     // check length functions


https://bitbucket.org/fathomteam/moab/commits/3751a47ac8f8/
Changeset:   3751a47ac8f8
Branch:      deformed-mesh-remap
User:        tautges
Date:        2014-02-13 20:17:49
Summary:     Merge branch 'deformed-mesh-remap' of bitbucket.org:fathomteam/moab into deformed-mesh-remap

Conflicts:
	src/SpatialLocator.cpp
	src/moab/SpatialLocator.hpp

Affected #:  0 files

Repository URL: https://bitbucket.org/fathomteam/moab/

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