[MOAB-dev] commit/MOAB: danwu: Merged master into error_handling_enhancement
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Thu Mar 13 16:10:33 CDT 2014
1 new commit in MOAB:
https://bitbucket.org/fathomteam/moab/commits/81ab0dc8e8c2/
Changeset: 81ab0dc8e8c2
Branch: error_handling_enhancement
User: danwu
Date: 2014-03-13 22:10:27
Summary: Merged master into error_handling_enhancement
Affected #: 31 files
diff --git a/.gitignore b/.gitignore
index 94df472..c80a80a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -31,14 +31,13 @@ doc/config.tex
doc/dev.dox
doc/user/*
doc/user.dox
+examples/CrystalRouterExample
examples/DeformMeshRemap
examples/DirectAccessNoHoles
examples/DirectAccessNoHolesF90
examples/DirectAccessWithHoles
examples/examples.make
examples/freem.mod
-examples/FileRead
-examples/GeomSetHierarchy
examples/GetEntities
examples/*.h5m
examples/HelloMOAB
@@ -48,14 +47,12 @@ examples/itaps/ListSetsNTagsCXX
examples/itaps/ListSetsNTagsF90
examples/itaps/TagIterateC
examples/itaps/TagIterateF
-examples/KDTree
examples/LloydRelaxation
-examples/ObbTree
+examples/LoadPartial
examples/point_in_elem_search
examples/PushParMeshIntoMoabF90
examples/ReduceExchangeTags
examples/SetsNTags
-examples/SkinMesh
examples/structuredmesh
examples/StructuredMeshSimple
examples/TestExodusII
diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp
index 5442d1d..55dac45 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"
@@ -19,6 +20,10 @@
#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
@@ -69,13 +74,13 @@ 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;}
@@ -91,6 +96,10 @@ 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
@@ -101,24 +110,32 @@ private:
ErrorCode read_file(int m_or_s, string &fname, EntityHandle &seth);
//! write the input tag to the coordinates for the vertices in the input elems
- ErrorCode write_to_coords(Range &elems, Tag tagh);
+ //! if non-zero tmp_tag is input, save coords to tmp_tag before over-writing with tag value
+ ErrorCode write_to_coords(Range &elems, Tag tagh, Tag tmp_tag = 0);
//! 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);
+ //! if restore_coords is true, coords are restored to their initial state after file is written
+ ErrorCode write_and_save(Range &ents, EntityHandle seth, Tag tagh, const char *filename,
+ bool restore_coords = false);
+ //! 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;
+ Error *mError;
+
#ifdef USE_MPI
//! ParallelComm for master, slave meshes
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;
@@ -132,22 +149,31 @@ 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;
};
//! 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;
@@ -159,14 +185,16 @@ 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;
@@ -181,14 +209,16 @@ 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;
@@ -199,56 +229,108 @@ 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
ErrorCode rval = read_file(MASTER, masterFileName, masterSet);
if (MB_SUCCESS != rval) return rval;
-
- rval = read_file(SLAVE, slaveFileName, slaveSet);
- if (MB_SUCCESS != rval) return rval;
+ if (solidSetNos[MASTER].empty() || fluidSetNos[MASTER].empty()) {
+ rval = find_other_sets(MASTER, masterSet); RR("Failed to find other sets in master mesh.");
+ }
+
+ bool have_slave = !(slaveFileName == "none");
+ if (have_slave) {
+ rval = read_file(SLAVE, slaveFileName, slaveSet);
+ if (MB_SUCCESS != rval) return rval;
+
+ if (solidSetNos[SLAVE].empty() || fluidSetNos[SLAVE].empty()) {
+ 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]);
- // 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;
+ DataCoupler dc_master(mbImpl, src_elems, 0, NULL);
+
+ 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
+ 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()) {
+ 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
+ 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
+ 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;
LloydSmoother ll(mbImpl, NULL, fluidElems[MASTER], xNew);
rval = ll.perform_smooth();
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
+ if (debug) std::cout << "Transferring coords tag to vertex coordinates in master mesh..." << std::endl;
+ rval = write_to_coords(solidElems[MASTER], xNew); RR("Failed writing tag to master fluid verts.");
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
+ 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.");
+ }
if (debug) {
std::string str;
@@ -256,14 +338,22 @@ ErrorCode DeformMeshRemap::execute()
if (pcMaster && pcMaster->size() > 1)
str = "PARALLEL=WRITE_PART";
#endif
- rval = mbImpl->write_file("smoothed_master.vtk", NULL, str.c_str(), &masterSet, 1);
+ if (debug) std::cout << "Writing smoothed_master.h5m..." << std::endl;
+ rval = mbImpl->write_file("smoothed_master.h5m", 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);
- }
+ if (debug) std::cout << "Writing slave_interp.h5m..." << std::endl;
+ rval = mbImpl->write_file("slave_interp.h5m", NULL, str.c_str(), &slaveSet, 1);
+ } // if have_slave
+ } // if debug
+
+ if (debug)
+ dc_master.spatial_locator()->get_tree()->tree_stats().print();
return MB_SUCCESS;
}
@@ -296,14 +386,16 @@ 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)
pcSlave = pcMaster;
}
DeformMeshRemap::~DeformMeshRemap()
{
- // delete the tag
- mbImpl->tag_delete(xNew);
+ mbImpl->release_interface(mError);
}
int main(int argc, char **argv) {
@@ -312,14 +404,16 @@ 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, 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" );
+ 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);
- 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 +424,46 @@ 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.");
+ 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);
+ 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);
+ 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);
+ 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);
+ 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]);
+ 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();
@@ -343,20 +473,38 @@ int main(int argc, char **argv) {
return rval;
}
-ErrorCode DeformMeshRemap::write_and_save(Range &ents, EntityHandle seth, Tag tagh, const char *filename)
+ErrorCode DeformMeshRemap::write_and_save(Range &ents, EntityHandle seth, Tag tagh, const char *filename,
+ bool restore_coords)
{
- ErrorCode rval = write_to_coords(ents, tagh); RR("");
+ Tag tmp_tag = 0;
+ ErrorCode rval;
+ if (restore_coords)
+ rval = mbImpl->tag_get_handle("", 3, MB_TYPE_DOUBLE, tmp_tag, MB_TAG_CREAT|MB_TAG_DENSE);
+
+ rval = write_to_coords(ents, tagh, tmp_tag); RR("");
rval = mbImpl->write_file(filename, NULL, NULL, &seth, 1); RR("");
+ if (restore_coords) {
+ rval = write_to_coords(ents, tmp_tag); RR("");
+ rval = mbImpl->tag_delete(tmp_tag);
+ }
+
return rval;
}
-ErrorCode DeformMeshRemap::write_to_coords(Range &elems, Tag tagh)
+ErrorCode DeformMeshRemap::write_to_coords(Range &elems, Tag tagh, Tag tmp_tag)
{
// write the tag to coordinates
Range verts;
ErrorCode rval = mbImpl->get_adjacencies(elems, 0, false, verts, Interface::UNION);
RR("Failed to get adj vertices.");
std::vector<double> coords(3*verts.size());
+
+ if (tmp_tag) {
+ // save the coords to tmp_tag first
+ rval = mbImpl->get_coords(verts, &coords[0]); RR("Failed to get tmp copy of coords.");
+ rval = mbImpl->tag_set_data(tmp_tag, verts, &coords[0]); RR("Failed to save tmp copy of coords.");
+ }
+
rval = mbImpl->tag_get_data(tagh, verts, &coords[0]);
RR("Failed to get tag data.");
rval = mbImpl->set_coords(verts, &coords[0]);
@@ -376,7 +524,6 @@ void deform_func(const BoundBox &bbox, double *xold, double *xnew)
xnew[0] = xold[0] + yfrac * delx;
xnew[1] = xold[1] + yfrac * (1.0 + xfrac) * 0.05;
*/
-
/* Deformation function based on fraction of bounding box dimension in each direction */
double frac = 0.01; // taken from approximate relative deformation from LLNL Diablo of XX09 assys
CartVect *xo = reinterpret_cast<CartVect*>(xold), *xn = reinterpret_cast<CartVect*>(xnew);
@@ -387,40 +534,95 @@ 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);
+ // get all the vertices and coords in the solid
+ Range solid_verts, fluid_verts;
+ rval = mbImpl->get_adjacencies(solid_elems, 0, false, solid_verts, Interface::UNION);
RR("Failed to get vertices.");
- std::vector<double> coords(3*verts.size(), 0.0);
- rval = mbImpl->get_coords(verts, &coords[0]);
+ std::vector<double> coords(3*solid_verts.size()), new_coords(3*solid_verts.size());
+ rval = mbImpl->get_coords(solid_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.");
+ unsigned int num_verts = solid_verts.size();
+
+ // 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], solid_verts, &disps[0]);
+ RR("Failed to get xDisp tag values.");
+ for (unsigned int j = 0; j < num_verts; j++)
+ new_coords[3*j+i] = 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], solid_verts, &disps[0]);
+ for (unsigned int j = 0; j < 3*num_verts; j++)
+ new_coords[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], &new_coords[3*j]);
+ }
- // get the bounding box of the solid mesh
- BoundBox bbox;
- bbox.update(*mbImpl, solid_elems);
+ 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;
+ }
+ 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;
+ }
- // get all the vertices and coords in the solid
- verts.clear();
- rval = mbImpl->get_adjacencies(solid_elems, 0, false, verts, Interface::UNION);
- RR("Failed to get vertices.");
- coords.resize(3*verts.size(), 0.0);
- 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]);
+ 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.");
+ xNew = xDisp[0];
+ }
// set the new tag to those coords
- rval = mbImpl->tag_set_data(xNew, verts, &coords[0]);
+ rval = mbImpl->tag_set_data(xNew, solid_verts, &new_coords[0]);
RR("Failed to set tag data.");
+ // get all the vertices and coords in the fluid, set xnew to them
+ rval = mbImpl->get_adjacencies(fluid_elems, 0, false, fluid_verts, Interface::UNION);
+ RR("Failed to get vertices.");
+ fluid_verts = subtract(fluid_verts, solid_verts);
+
+ if (coords.size() < 3*fluid_verts.size()) coords.resize(3*fluid_verts.size());
+ rval = mbImpl->get_coords(fluid_verts, &coords[0]);
+ RR("Failed to get vertex coords.");
+ rval = mbImpl->tag_set_data(xNew, fluid_verts, &coords[0]);
+ RR("Failed to set xnew tag on fluid verts.");
+
+ if (debug) {
+ // save deformed mesh coords to new file for visualizing
+ Range tmp_range(fluidElems[MASTER]);
+ tmp_range.merge(solidElems[MASTER]);
+ rval = write_and_save(tmp_range, masterSet, xNew, "deformed_master.h5m", true); RR("");
+ }
+
return MB_SUCCESS;
}
@@ -441,17 +643,22 @@ 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;
- 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
@@ -460,19 +667,26 @@ 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.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;
- 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
@@ -481,8 +695,66 @@ 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);
+ }
+
+ 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...";
+ }
- fluidElems[m_or_s] = tmp_range.subset_by_dimension(dim);
+ // 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/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/LloydSmoother.cpp b/src/LloydSmoother.cpp
index b1614d2..ba8169a 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};
@@ -221,7 +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/LocalDiscretization/moab/ElemEvaluator.hpp b/src/LocalDiscretization/moab/ElemEvaluator.hpp
index 866388c..6a1efd0 100644
--- a/src/LocalDiscretization/moab/ElemEvaluator.hpp
+++ b/src/LocalDiscretization/moab/ElemEvaluator.hpp
@@ -339,8 +339,13 @@ namespace moab {
std::vector<EntityHandle> dum_vec;
ErrorCode rval = mbImpl->get_connectivity(ent, vertHandles, numVerts, false, &dum_vec);
if (MB_SUCCESS != rval) return rval;
+
+ if (!evalSets[entType].evalFcn)
+ EvalSet::get_eval_set(entType, numVerts, evalSets[entType]);
+
rval = mbImpl->get_coords(vertHandles, numVerts, vertPos[0].array());
if (MB_SUCCESS != rval) return rval;
+
if (tagHandle) {
rval = set_tag_handle(tagHandle);
if (MB_SUCCESS != rval) return rval;
diff --git a/src/SpatialLocator.cpp b/src/SpatialLocator.cpp
index f976ae7..702399e 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() ||
@@ -40,7 +53,9 @@ 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
@@ -352,90 +367,29 @@ namespace moab
// relative epsilon given, translate to absolute epsilon using box dimensions
tmp_abs_iter_tol = rel_iter_tol * localBox.diagonal_length();
}
-
- EntityHandle closest_leaf;
- std::vector<double> dists;
- std::vector<EntityHandle> leaves;
- ErrorCode rval = MB_SUCCESS;
+ if (elemEval && myTree->get_eval() != elemEval)
+ myTree->set_eval(elemEval);
+
+ ErrorCode rval = MB_SUCCESS;
for (int i = 0; i < num_points; i++) {
int i3 = 3*i;
- ents[i] = 0;
- if (tmp_abs_iter_tol) {
- rval = myTree->distance_search(pos+i3, tmp_abs_iter_tol, leaves, tmp_abs_iter_tol, inside_tol, &dists);
- if (MB_SUCCESS != rval) return rval;
- if (!leaves.empty()) {
- // get closest leaf
- double min_dist = *dists.begin();
- closest_leaf = *leaves.begin();
- std::vector<EntityHandle>::iterator vit = leaves.begin()+1;
- std::vector<double>::iterator dit = dists.begin()+1;
- for (; vit != leaves.end() && min_dist; vit++, dit++) {
- if (*dit < min_dist) {
- min_dist = *dit;
- closest_leaf = *vit;
- }
- }
- dists.clear();
- leaves.clear();
- }
- }
- else {
- rval = myTree->point_search(pos+i3, closest_leaf);
- if (MB_ENTITY_NOT_FOUND == rval) closest_leaf = 0;
- else if (MB_SUCCESS != rval) return rval;
- }
-
- // if no ElemEvaluator, just return the box
- if (!elemEval) {
- ents[i] = closest_leaf;
- params[i3] = params[i3+1] = params[i3+2] = -2;
- if (is_inside && closest_leaf) is_inside[i] = true;
+ ErrorCode tmp_rval = myTree->point_search(pos+i3, ents[i], abs_iter_tol, inside_tol, NULL, NULL,
+ (CartVect*)(params+i3));
+ if (MB_SUCCESS != tmp_rval) {
+ rval = tmp_rval;
continue;
}
-
- // find natural coordinates of point in element(s) in that leaf
- CartVect tmp_nat_coords;
- Range range_leaf;
- rval = mbImpl->get_entities_by_dimension(closest_leaf, myDim, range_leaf, false);
- if(rval != MB_SUCCESS) return rval;
-
- // loop over the range_leaf
- int tmp_inside;
- int *is_ptr = (is_inside ? is_inside+i : &tmp_inside);
- *is_ptr = false;
- EntityHandle ent = 0;
- for(Range::iterator rit = range_leaf.begin(); rit != range_leaf.end(); rit++)
- {
- rval = elemEval->set_ent_handle(*rit);
- if (MB_SUCCESS != rval) return rval;
- rval = elemEval->reverse_eval(pos+i3, tmp_abs_iter_tol, inside_tol, params+i3, is_ptr);
- if (MB_SUCCESS != rval) return rval;
- if (*is_ptr) {
- ent = *rit;
- break;
- }
- }
- if (debug && !ent) {
+
+ if (debug && !ents[i]) {
std::cout << "Point " << i << " not found; point: ("
<< pos[i3] << "," << pos[i3+1] << "," << pos[i3+2] << ")" << std::endl;
- std::cout << "Source element candidates: " << std::endl;
- range_leaf.print(" ");
- for(Range::iterator rit = range_leaf.begin(); rit != range_leaf.end(); rit++)
- {
- std::cout << "Candidate " << CN::EntityTypeName(mbImpl->type_from_handle(*rit)) << " " << mbImpl->id_from_handle(*rit) << ": ";
- rval = elemEval->set_ent_handle(*rit);
- if (MB_SUCCESS != rval) return rval;
- rval = elemEval->reverse_eval(pos+i3, tmp_abs_iter_tol, inside_tol, params+i3, is_ptr);
- if (MB_SUCCESS != rval) return rval;
- std::cout << "Parameters: (" << params[i3] << "," << params[i3+1] << "," << params[i3+2] << ")"
- << " inside = " << *is_ptr << std::endl;
- }
}
- ents[i] = ent;
- }
- return MB_SUCCESS;
+ if (is_inside) is_inside[i] = (ents[i] ? true : false);
+ }
+
+ return rval;
}
/* Count the number of located points in locTable
diff --git a/src/io/Tqdcfr.cpp b/src/io/Tqdcfr.cpp
index 701ff15..7416164 100644
--- a/src/io/Tqdcfr.cpp
+++ b/src/io/Tqdcfr.cpp
@@ -959,7 +959,7 @@ ErrorCode Tqdcfr::read_block(const unsigned int blindex,
FREADD(blockh->attribOrder); num_read += sizeof(double);
void const* tag_data[] = { &dbl_buf[0] };
- int tag_sizes[] = { blockh->attribOrder };
+ int tag_sizes[] = { static_cast<int>(blockh->attribOrder) };
result = mdbImpl->tag_set_by_ptr(block_attribs,&(blockh->setHandle),1,tag_data,tag_sizes);
if (MB_SUCCESS != result) return result;
}
@@ -1932,7 +1932,8 @@ ErrorCode Tqdcfr::BlockHeader::read_info_header(const double data_version,
result = instance->mdbImpl->tag_get_handle(BLOCK_HEADER,3*sizeof(unsigned int),MB_TYPE_INTEGER,
bhTag_header,MB_TAG_CREAT|MB_TAG_SPARSE|MB_TAG_BYTES,&def_uint_zero[0]);
if (MB_SUCCESS != result) return result;
- int block_header_data[] = { block_headers[i].blockCol, block_headers[i].blockMat, block_headers[i].blockDim };
+ int block_header_data[] = { static_cast<int>(block_headers[i].blockCol), static_cast<int>(block_headers[i].blockMat),
+ static_cast<int>(block_headers[i].blockDim) };
result = instance->mdbImpl->tag_set_data(bhTag_header,&(block_headers[i].setHandle), 1,
block_header_data);
}
diff --git a/src/moab/AdaptiveKDTree.hpp b/src/moab/AdaptiveKDTree.hpp
index c77bdbc..e4c5078 100644
--- a/src/moab/AdaptiveKDTree.hpp
+++ b/src/moab/AdaptiveKDTree.hpp
@@ -38,6 +38,13 @@ namespace moab {
~AdaptiveKDTree();
+ /** \brief Parse options for tree creation
+ * \param options Options passed in by application
+ * \return Failure is returned if any options were passed in and not interpreted; could mean
+ * inappropriate options for a particular tree type
+ */
+ ErrorCode parse_options(FileOptions &options);
+
/** Build the tree
* Build a tree with the entities input. If a non-NULL tree_root_set pointer is input,
* use the pointed-to set as the root of this tree (*tree_root_set!=0) otherwise construct
@@ -251,16 +258,8 @@ namespace moab {
virtual ErrorCode print();
private:
-
friend class AdaptiveKDTreeIter;
- /** \brief Parse options for tree creation
- * \param options Options passed in by application
- * \return Failure is returned if any options were passed in and not interpreted; could mean
- * inappropriate options for a particular tree type
- */
- ErrorCode parse_options(FileOptions &options);
-
ErrorCode init();
/**\brief find a triangle near the input point */
@@ -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/BVHTree.hpp b/src/moab/BVHTree.hpp
index d435ebf..354d3a1 100644
--- a/src/moab/BVHTree.hpp
+++ b/src/moab/BVHTree.hpp
@@ -272,7 +272,6 @@ namespace moab {
Range entityHandles;
std::vector<TreeNode> myTree;
- ElemEvaluator *myEval;
int splitsPerDir;
EntityHandle startSetHandle;
static const char *treeName;
@@ -305,7 +304,7 @@ namespace moab {
}
inline BVHTree::BVHTree(Interface *impl) :
- Tree(impl), myEval(NULL), splitsPerDir(3), startSetHandle(0) {boxTagName = treeName;}
+ Tree(impl), splitsPerDir(3), startSetHandle(0) {boxTagName = treeName;}
inline unsigned int BVHTree::set_interval(BoundBox &interval,
std::vector<Bucket>::const_iterator begin,
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 ¢er);
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 3d29c55..2690058 100644
--- a/src/moab/SpatialLocator.hpp
+++ b/src/moab/SpatialLocator.hpp
@@ -193,6 +193,12 @@ 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/Tree.hpp b/src/moab/Tree.hpp
index 4d2694a..0a995b4 100644
--- a/src/moab/Tree.hpp
+++ b/src/moab/Tree.hpp
@@ -236,7 +236,7 @@ namespace moab {
inline Tree::Tree(Interface* iface)
: mbImpl(iface), maxPerLeaf(6), maxDepth(30), treeDepth(-1), minWidth(1.0e-10),
- meshsetFlags(0), cleanUp(true), myRoot(0), boxTag(0)
+ meshsetFlags(0), cleanUp(true), myRoot(0), boxTag(0), myEval(0)
{}
inline Tree::~Tree()
@@ -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;
}
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/src/parallel/WriteHDF5Parallel.cpp b/src/parallel/WriteHDF5Parallel.cpp
index 20a36a3..be692ba 100644
--- a/src/parallel/WriteHDF5Parallel.cpp
+++ b/src/parallel/WriteHDF5Parallel.cpp
@@ -118,6 +118,7 @@ const char* mpi_err_str( int errorcode ) {
template <typename T> inline
void VALGRIND_MAKE_VEC_UNDEFINED( std::vector<T>& v ) {
+ if (v.size()) {}
VALGRIND_MAKE_MEM_UNDEFINED( &v[0], v.size() * sizeof(T) );
}
diff --git a/test/parallel/Makefile.am b/test/parallel/Makefile.am
index 1b9aeef..aca93e1 100644
--- a/test/parallel/Makefile.am
+++ b/test/parallel/Makefile.am
@@ -116,4 +116,6 @@ MOSTLYCLEANFILES = mhdf_ll.h5m tmp0.h5m tmp1.h5m tmp2.h5m tmp3.h5m \
initial1.vtk \
test_mpas.h5m \
dum.h5m \
- test_mpas_no_mixed_elements.h5m
+ test_mpas_no_mixed_elements.h5m \
+ test_mpas_rcbzoltan.h5m \
+ test_mpas_rcbzoltan_no_mixed_elements.h5m
diff --git a/test/parallel/par_coupler_test.cpp b/test/parallel/par_coupler_test.cpp
index 6ec3143..b0d7c06 100644
--- a/test/parallel/par_coupler_test.cpp
+++ b/test/parallel/par_coupler_test.cpp
@@ -139,8 +139,8 @@ int main(int argc, char **argv)
if (!dbgFile.empty()) {
std::stringstream dfname;
dfname << dbgFile << rank << ".txt";
- std::freopen(dfname.str().c_str(), "a", stdout);
- std::freopen(dfname.str().c_str(), "a", stderr);
+ if (!std::freopen(dfname.str().c_str(), "a", stdout)) return false;
+ if (!std::freopen(dfname.str().c_str(), "a", stderr)) return false;
}
// create MOAB instance based on that
diff --git a/test/spatial_locator_test.cpp b/test/spatial_locator_test.cpp
index 0171bf9..404e668 100644
--- a/test/spatial_locator_test.cpp
+++ b/test/spatial_locator_test.cpp
@@ -4,7 +4,9 @@
#include "moab/HomXform.hpp"
#include "moab/ScdInterface.hpp"
#include "moab/CartVect.hpp"
+#include "moab/AdaptiveKDTree.hpp"
#include "moab/BVHTree.hpp"
+#include "moab/ElemEvaluator.hpp"
#include "moab/ProgOptions.hpp"
#include "moab/CpuTimer.hpp"
@@ -69,11 +71,21 @@ void test_kd_tree()
Range elems;
rval = create_hex_mesh(mb, elems, ints, 3); CHECK_ERR(rval);
- // initialize spatial locator with the elements and the default tree type
- SpatialLocator *sl = new SpatialLocator(&mb, elems);
+ // initialize spatial locator with the elements and KDtree
+ AdaptiveKDTree kd(&mb);
+ std::ostringstream opts;
+ opts << "MAX_DEPTH=" << max_depth << ";MAX_PER_LEAF=" << leaf;
+ FileOptions fo(opts.str().c_str());
+ rval = kd.parse_options(fo);
+ SpatialLocator *sl = new SpatialLocator(&mb, elems, &kd);
test_locator(sl);
+ // test with an evaluator
+ ElemEvaluator eval(&mb);
+ kd.set_eval(&eval);
+ test_locator(sl);
+
// destroy spatial locator, and tree along with it
delete sl;
}
@@ -96,6 +108,11 @@ void test_bvh_tree()
SpatialLocator *sl = new SpatialLocator(&mb, elems, &bvh);
test_locator(sl);
+ // test with an evaluator
+ ElemEvaluator eval(&mb);
+ bvh.set_eval(&eval);
+ test_locator(sl);
+
// destroy spatial locator, and tree along with it
delete sl;
}
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
diff --git a/tools/mbcoupler/Coupler.cpp b/tools/mbcoupler/Coupler.cpp
index b496441..afee8af 100644
--- a/tools/mbcoupler/Coupler.cpp
+++ b/tools/mbcoupler/Coupler.cpp
@@ -483,10 +483,13 @@ ErrorCode Coupler::test_local_box(double *xyz,
{
std::vector<EntityHandle> entities;
std::vector<CartVect> nat_coords;
- bool canWrite;
+ bool canWrite = false;
if (tl) {
canWrite = tl->get_writeEnabled();
- if(!canWrite) tl->enableWriteAccess();
+ if(!canWrite) {
+ tl->enableWriteAccess();
+ canWrite = true;
+ }
}
if (rel_eps && !abs_eps) {
@@ -833,7 +836,7 @@ ErrorCode Coupler::interp_field(EntityHandle elem,
else
{
double vfields[27]; // will work for linear hex, quadratic hex or Tets
- moab::Element::Map *elemMap;
+ moab::Element::Map *elemMap = NULL;
int num_verts = 0;
// get the EntityType
// get the tag values at the vertices
@@ -1533,7 +1536,7 @@ int Coupler::get_group_integ_vals(std::vector< std::vector<iBase_EntityHandle> >
iMesh_getEntTopo(iMeshInst, (*iter_j), &topo_type, &err);
ERRORR("Failed to get topology for entity.", err);
- moab::Element::Map *elemMap;
+ moab::Element::Map *elemMap = NULL;
int num_verts = 0;
if (topo_type == iMesh_HEXAHEDRON) {
elemMap = new moab::Element::LinearHex();
diff --git a/tools/mbcoupler/DataCoupler.cpp b/tools/mbcoupler/DataCoupler.cpp
index a5a3ec1..06a8564 100644
--- a/tools/mbcoupler/DataCoupler.cpp
+++ b/tools/mbcoupler/DataCoupler.cpp
@@ -1,24 +1,27 @@
#include "DataCoupler.hpp"
-#include "moab/ParallelComm.hpp"
#include "moab/Tree.hpp"
#include "moab/TupleList.hpp"
#include "moab/SpatialLocator.hpp"
#include "moab/ElemEvaluator.hpp"
#include "moab/Error.hpp"
+#ifdef USE_MPI
+#include "moab/ParallelComm.hpp"
+#endif
+
#include "iostream"
-#include <stdio.h>
#include <algorithm>
#include <sstream>
+#include <stdio.h>
#include "assert.h"
namespace moab {
DataCoupler::DataCoupler(Interface *impl,
- ParallelComm *pc,
Range &source_ents,
int coupler_id,
+ ParallelComm *pc,
bool init_locator,
int dim)
: mbImpl(impl), myPcomm(pc), myId(coupler_id), myDim(dim)
@@ -64,7 +67,12 @@ ErrorCode DataCoupler::locate_points(Range &targ_ents,
const double inside_tol)
{
targetEnts = targ_ents;
-
+
+#ifdef USE_MPI
+ if (myPcomm && myPcomm->size() > 1)
+ return myLocator->par_locate_points(myPcomm, targ_ents, rel_iter_tol, abs_iter_tol, inside_tol);
+#endif
+
return myLocator->locate_points(targ_ents, rel_iter_tol, abs_iter_tol, inside_tol);
}
@@ -72,6 +80,11 @@ ErrorCode DataCoupler::locate_points(double *xyz, int num_points,
const double rel_iter_tol, const double abs_iter_tol,
const double inside_tol)
{
+#ifdef USE_MPI
+ if (myPcomm && myPcomm->size() > 1)
+ return myLocator->par_locate_points(myPcomm, xyz, num_points, rel_iter_tol, abs_iter_tol, inside_tol);
+#endif
+
return myLocator->locate_points(xyz, num_points, rel_iter_tol, abs_iter_tol, inside_tol);
}
@@ -95,7 +108,7 @@ ErrorCode DataCoupler::interpolate(/*DataCoupler::Method*/ int method,
return interpolate(method, tag, interp_vals, point_indices, normalize);
}
-ErrorCode DataCoupler::interpolate(/*DataCoupler::Method*/ int *methods,
+ErrorCode DataCoupler::interpolate(/*DataCoupler::Method*/ int */* methods */,
Tag *tags,
int *points_per_method,
int num_methods,
@@ -111,7 +124,12 @@ ErrorCode DataCoupler::interpolate(/*DataCoupler::Method*/ int *methods,
for (int i = 0; i < num_methods; i++) pts_total += (points_per_method ? points_per_method[i] : targetEnts.size());
unsigned int num_indices = (point_indices ? point_indices->size() : targetEnts.size());
+ // # points and indices should be identical
+ if (pts_total != num_indices)
+ return MB_FAILURE;
+ // since each tuple contains one interpolated tag, if we're interpolating multiple tags, every tuple
+ // needs to be able to store up to max tag size
int max_tsize = -1;
for (int i = 0; i < num_methods; i++) {
int tmp_tsize;
@@ -120,75 +138,82 @@ ErrorCode DataCoupler::interpolate(/*DataCoupler::Method*/ int *methods,
max_tsize = std::max(max_tsize, tmp_tsize);
}
- // if tl was passed in non-NULL, just have those points, otherwise have targetPts plus
- // locally mapped pts
- if (pts_total != num_indices)
- return MB_FAILURE;
-
- if (myPcomm) {
- // TL to send interpolation indices to target procs
- // Tuple structure: (pto_i, ridx_i, lidx_i, meth_i, tagidx_i, interp_val[max_tsize]_d)
- TupleList tinterp;
- tinterp.initialize(5, 0, 0, max_tsize, num_indices);
- int t = 0;
- tinterp.enableWriteAccess();
- for (int i = 0; i < num_methods; i++) {
- int num_points = (points_per_method ? points_per_method[i] : targetEnts.size());
+ if (myPcomm && myPcomm->size() > 1) {
+ // build up the tuple list to distribute from my target points; assume that
+ // all procs use same method/tag input
+ TupleList TLob; // TLob structure: (pto_i, ridx_i, lidx_i, meth_tagidx_i)
+ TLob.initialize(4, 0, 0, 0, num_indices);
+ int tn = 0; // the tuple number we're currently on
+ TLob.enableWriteAccess();
+ for (int m = 0; m < num_methods; m++) {
+ int num_points = (points_per_method ? points_per_method[m] : targetEnts.size());
for (int j = 0; j < num_points; j++) {
- int idx = (point_indices ? (*point_indices)[j] : j);
+ int idx = (point_indices ? (*point_indices)[j] : j); // the index in my targetEnts for this interpolation point
// remote proc/idx from myLocator->parLocTable
- tinterp.vi_wr[5*t] = myLocator->par_loc_table().vi_rd[2*idx]; // proc
- tinterp.vi_wr[5*t+1] = myLocator->par_loc_table().vi_rd[2*idx+1]; // remote idx
+ TLob.vi_wr[4*tn] = myLocator->par_loc_table().vi_rd[2*idx]; // proc
+ TLob.vi_wr[4*tn+1] = myLocator->par_loc_table().vi_rd[2*idx+1]; // remote idx
// local entity index, tag/method index from my data
- tinterp.vi_wr[5*t+2] = idx;
- tinterp.vi_wr[5*t+3] = methods[i];
- tinterp.vi_wr[5*t+4] = i;
- tinterp.inc_n();
- t++;
+ TLob.vi_wr[4*tn+2] = idx;
+ TLob.vi_wr[4*tn+3] = m;
+ TLob.inc_n();
+ tn++;
}
}
// scatter/gather interpolation points
- myPcomm->proc_config().crystal_router()->gs_transfer(1, tinterp, 0);
-
- // perform interpolation on local source mesh; put results into
- // tinterp.vr_wr
-
- for (unsigned int i = 0; i < tinterp.get_n(); i++) {
- int lidx = tinterp.vi_rd[5*i+1];
-// /*Method*/ int method = (/*Method*/ int)tinterp.vi_rd[5*i+3];
- Tag tag = tags[tinterp.vi_rd[5*i+4]];
-
+ myPcomm->proc_config().crystal_router()->gs_transfer(1, TLob, 0);
+
+ // perform interpolation on local source mesh; put results into TLinterp
+ TupleList TLinterp; // TLinterp structure: (pto_i, ridx_i, vals[max_tsize]_d)
+ TLinterp.initialize(2, 0, 0, max_tsize, TLob.get_n());
+ TLinterp.set_n(TLob.get_n()); // set the size right away
+ TLinterp.enableWriteAccess();
+
+ for (unsigned int i = 0; i < TLob.get_n(); i++) {
+ int lidx = TLob.vi_rd[4*i+1]; // index into myLocator's local table
+ // method and tag indexed with same index
+// /*Method*/ int method = methods[TLob.vi_rd[4*i+3]];
+ Tag tag = tags[TLob.vi_rd[4*i+3]];
+ // copy proc/remote index from TLob
+ TLinterp.vi_wr[2*i] = TLob.vi_rd[4*i];
+ TLinterp.vi_wr[2*i+1] = TLob.vi_rd[4*i+2];
+
+ // set up the evaluator for the tag and entity, then interpolate, putting result in TLinterp
myLocator->elem_eval()->set_tag_handle(tag);
myLocator->elem_eval()->set_ent_handle(myLocator->loc_table().vul_rd[lidx]);
- result = myLocator->elem_eval()->eval(myLocator->loc_table().vr_rd+3*lidx, tinterp.vr_rd+i*max_tsize);
+ result = myLocator->elem_eval()->eval(myLocator->loc_table().vr_rd+3*lidx, TLinterp.vr_rd+i*max_tsize);
if (MB_SUCCESS != result) return result;
}
// scatter/gather interpolation data
- myPcomm->proc_config().crystal_router()->gs_transfer(1, tinterp, 0);
+ myPcomm->proc_config().crystal_router()->gs_transfer(1, TLinterp, 0);
// copy the interpolated field as a unit
- std::copy(tinterp.vr_rd, tinterp.vr_rd+tinterp.get_n()*max_tsize, interp_vals);
+ std::copy(TLinterp.vr_rd, TLinterp.vr_rd+TLinterp.get_n()*max_tsize, interp_vals);
}
else {
+ // if called serially, interpolate directly from local locations/entities,
+ // into either interp_vals or by setting data directly on tags on those entities
std::vector<double> tmp_vals;
std::vector<EntityHandle> tmp_ents;
double *tmp_dbl = interp_vals;
for (int i = 0; i < num_methods; i++) {
int num_points = (points_per_method ? points_per_method[i] : targetEnts.size());
- // interpolated data is tsize long, which is either max size (if data passed back to caller in tinterp)
+ // interpolated data is tsize long, which is either max size (if data passed back to caller in interp_vals)
// or tag size (if data will be set on entities, in which case it shouldn't have padding)
+ // set sizes here, inside loop over methods, to reduce memory usage
int tsize = max_tsize, tsize_bytes = 0;
if (!interp_vals) {
tmp_vals.resize(num_points*max_tsize);
tmp_dbl = &tmp_vals[0];
tmp_ents.resize(num_points);
result = mbImpl->tag_get_length(tags[i], tsize);
+ if (MB_SUCCESS != result) return result;
result = mbImpl->tag_get_bytes(tags[i], tsize_bytes);
+ if (MB_SUCCESS != result) return result;
}
for (int j = 0; j < num_points; j++) {
@@ -206,7 +231,7 @@ ErrorCode DataCoupler::interpolate(/*DataCoupler::Method*/ int *methods,
result = myLocator->elem_eval()->eval(myLocator->loc_table().vr_rd+3*lidx, tmp_dbl);
tmp_dbl += tsize;
if (MB_SUCCESS != result) return result;
- } // for j
+ } // for j over points
if (!interp_vals) {
// set tags on tmp_ents; data is already w/o padding, due to tsize setting above
@@ -214,7 +239,7 @@ ErrorCode DataCoupler::interpolate(/*DataCoupler::Method*/ int *methods,
if (MB_SUCCESS != result) return result;
}
- } // for i
+ } // for i over methods
} // if myPcomm
// done
diff --git a/tools/mbcoupler/DataCoupler.hpp b/tools/mbcoupler/DataCoupler.hpp
index bfe2ba5..a9d6f5e 100644
--- a/tools/mbcoupler/DataCoupler.hpp
+++ b/tools/mbcoupler/DataCoupler.hpp
@@ -39,21 +39,23 @@ class DataCoupler
{
public:
+ enum Method {CONSTANT, LINEAR_FE, QUADRATIC_FE, SPECTRAL} ;
+
enum IntegType {VOLUME};
/* constructor
* Constructor, which also optionally initializes the coupler
+ * \param source_ents Elements in the source mesh
+ * \param coupler_id Id of this coupler, should be the same over all procs
* \param pc ParallelComm object to be used with this coupler, representing the union
* of processors containing source and target meshes
- * \param source_elems Elements in the source mesh
- * \param coupler_id Id of this coupler, should be the same over all procs
* \param init_locator If true, initializes a spatial locator inside the constructor
* \param dim Dimension of entities to be coupled; if -1, get from source_elems
*/
DataCoupler(Interface *impl,
- ParallelComm *pc,
Range &source_ents,
int coupler_id,
+ ParallelComm *pc = NULL,
bool init_locator = true,
int dim = -1);
This diff is so big that we needed to truncate the remainder.
Repository URL: https://bitbucket.org/fathomteam/moab/
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