69 ConfigOption(
false,
"-1",
"Tag identifying first surface.");
71 ConfigOption(
false,
"-1",
"Tag identifying first surface.");
73 false,
"",
"Direction in which to align (either x, y, or z)");
75 ConfigOption(
true,
"0",
"Attempt to reorient tets and prisms");
87 int surf1 =
m_config[
"surf1"].as<
int>();
88 int surf2 =
m_config[
"surf2"].as<
int>();
89 string dir =
m_config[
"dir"].as<
string>();
90 bool orient =
m_config[
"orient"].as<
bool>();
94 cerr <<
"WARNING: surf1 must be set to a positive integer. "
95 <<
"Skipping periodic alignment." << endl;
101 cerr <<
"WARNING: surf2 must be set to a positive integer. "
102 <<
"Skipping periodic alignment." << endl;
106 if (dir !=
"x" && dir !=
"y" && dir !=
"z")
108 cerr <<
"WARNING: dir must be set to either x, y or z. "
109 <<
"Skipping periodic alignment." << endl;
114 vec[0] = dir ==
"x" ? 1.0 : 0.0;
115 vec[1] = dir ==
"y" ? 1.0 : 0.0;
116 vec[2] = dir ==
"z" ? 1.0 : 0.0;
121 if (it1 ==
m_mesh->m_composite.end())
123 cerr <<
"WARNING: Couldn't find surface " << surf1
124 <<
". Skipping periodic alignment." << endl;
128 if (it2 ==
m_mesh->m_composite.end())
130 cerr <<
"WARNING: Couldn't find surface " << surf2 <<
", "
131 <<
"skipping periodic alignment." << endl;
138 if (c1->m_items.size() != c2->m_items.size())
140 cerr <<
"WARNING: Surfaces " << surf1 <<
" and " << surf2
141 <<
" have different numbers of elements. Skipping periodic"
142 <<
" alignment." << endl;
146 c1->m_reorder =
false;
147 c2->m_reorder =
false;
149 map<int, pair<FaceSharedPtr, vector<int> > > perFaces;
152 map<int, Node> centroidMap;
154 for (
int i = 0; i < c2->m_items.size(); ++i)
157 for (
int j = 0; j < c2->m_items[i]->GetVertexCount(); ++j)
159 centroid += *(c2->m_items[i]->GetVertex(j));
161 centroid /= (
NekDouble)c2->m_items[i]->GetVertexCount();
162 centroidMap[i] = centroid;
165 boost::unordered_set<int> elmtDone;
166 map<int, int> elmtPairs;
167 map<int, int> vertCheck;
169 for (
int i = 0; i < c1->m_items.size(); ++i)
172 for (
int j = 0; j < c1->m_items[i]->GetVertexCount(); ++j)
174 centroid += *(c1->m_items[i]->GetVertex(j));
176 centroid /= (
NekDouble)c1->m_items[i]->GetVertexCount();
178 for (it = centroidMap.begin(); it != centroidMap.end(); ++it)
180 if (elmtDone.count(it->first) > 0)
185 Node dx = it->second - centroid;
186 if (fabs(fabs(dx.
m_x * vec[0] + dx.
m_y * vec[1] + dx.
m_z * vec[2]) /
195 id1 = c1->m_items[i]->GetEdgeLink()->
m_id;
196 id2 = c2->m_items[it->first]->GetEdgeLink()->m_id;
200 id1 = c1->m_items[i]->GetFaceLink()->m_id;
201 id2 = c2->m_items[it->first]->GetFaceLink()->m_id;
204 elmtDone.insert(it->first);
205 elmtPairs[i] = it->first;
208 int nVerts = c1->m_items[i]->GetVertexCount();
209 vector<int> perVerts(nVerts, 0), perVertsInv(nVerts, 0);
213 for (
int k = 0; k < nVerts; ++k)
216 c1->m_items[i]->GetFaceLink()->m_vertexList[k];
219 for (l = 0; l < nVerts; ++l)
226 if (fabs(fabs(dn.
m_x * vec[0] + dn.
m_y * vec[1] +
236 if (vertCheck.count(id1) == 0)
238 vertCheck[id1] = id2;
243 "Periodic vertex already "
250 "Could not identify periodic vertices.");
253 int tot1 = 0, tot2 = 0;
254 for (
int k = 0; k < nVerts; ++k)
257 tot2 += perVertsInv[k];
259 ASSERTL0(tot1 == nVerts * (nVerts - 1) / 2 &&
260 tot2 == nVerts * (nVerts - 1) / 2,
261 "Error identifying periodic vertices");
266 perFaces[id1] = make_pair(
267 c2->m_items[it->first]->GetFaceLink(), perVerts);
269 make_pair(c1->m_items[i]->GetFaceLink(), perVertsInv);
275 if (it == centroidMap.end())
277 cerr <<
"WARNING: Could not find matching edge for surface "
278 <<
"element " << c1->m_items[i]->GetId() <<
". "
279 <<
"Skipping periodic alignment." << endl;
285 vector<ElementSharedPtr> tmp = c2->m_items;
289 for (
int i = 0; i < tmp.size(); ++i)
291 c2->m_items[i] = tmp[elmtPairs[i]];
#define ASSERTL0(condition, msg)
pair< ModuleType, string > ModuleKey
map< string, ConfigOption > m_config
List of configuration values.
MeshSharedPtr m_mesh
Mesh object.
NekDouble m_y
Y-coordinate.
Represents a point in the domain.
NEKMESHUTILS_EXPORT NekDouble abs2() const
boost::shared_ptr< Composite > CompositeSharedPtr
Shared pointer to a composite.
boost::shared_ptr< Node > NodeSharedPtr
Represents a command-line configuration option.
StandardMatrixTag boost::call_traits< LhsDataType >::const_reference rhs typedef NekMatrix< LhsDataType, StandardMatrixTag >::iterator iterator
NekDouble m_x
X-coordinate.
boost::shared_ptr< Mesh > MeshSharedPtr
Shared pointer to a mesh.
virtual void Process()
Write mesh to output file.
virtual ~ProcessPerAlign()
Destructor.
void ReorderPrisms(PerMap &perFaces)
Reorder node IDs so that prisms and tetrahedra are aligned correctly.
NekDouble m_z
Z-coordinate.
#define ASSERTL1(condition, msg)
Assert Level 1 – Debugging which is used whether in FULLDEBUG or DEBUG compilation mode...
ModuleFactory & GetModuleFactory()
Abstract base class for processing modules.
tKey RegisterCreatorFunction(tKey idKey, CreatorFunction classCreator, tDescription pDesc="")
Register a class with the factory.