void sefield::TetMesh::fill_ve_vec(set<VertexElement*> & veset, vector<VertexElement*> & vevec, queue<VertexElement*> & vequeue, uint ncons, VertexElement ** nbrs)
{
//cout << "Veset size: " << veset.size();
vector<uint>newindcs=std::vector<uint>();
for (uint i=0; i < ncons; ++i)
{
bool inserted = veset.insert(nbrs[i]).second;
if (inserted)
{
newindcs.push_back(i);
// This is the important one- in a vector to keep the ordering
vevec.push_back(nbrs[i]);
// And add to the queue too, to find their neighbours:
vequeue.push(nbrs[i]);
}
}
// Go to the next element in the queue
if (vequeue.empty() == true) return;
else
{
VertexElement * nextve = vequeue.front();
vequeue.pop();
VertexElement ** newneighbs = nextve->getNeighbours();
uint nextcons = nextve->getNCon();
fill_ve_vec(veset, vevec, vequeue, nextcons, newneighbs);
}
/*
for (uint i=0; i < newindcs.size(); ++i)
{
VertexElement ** newneighbs = nbrs[newindcs[i]]->getNeighbours();
uint newcons = nbrs[newindcs[i]]->getNCon();
fill_ve_vec(veset, vevec, newcons, newneighbs, false);
}
*/
}
void sefield::TetMesh::axisOrderElements(uint opt_method, std::string const & opt_file_name)
{
// Now this method provides a choice between Stefan and Robert's method
// and the new method by Iain. The original method is fast and suffices for
// simple geometries, Iain's method is superior and important for complex
// geometries, but slow.
if (opt_file_name != "")
{
std::fstream opt_file;
opt_file.open(opt_file_name.c_str(),
std::fstream::in | std::fstream::binary);
opt_file.seekg(0);
uint nelems = 0;
opt_file.read((char*)&nelems, sizeof(uint));
if (pElements.size() != nelems) {
std::ostringstream os;
os << "optimal data mismatch with simulator parameters: sefield::Tetmesh::nelems, ";
os << nelems << ":" << pElements.size();
throw steps::ArgErr(os.str());
}
opt_file.read((char*)pVertexPerm, sizeof(uint) * nelems);
VertexElementPVec elements_temp = pElements;
for (uint vidx = 0; vidx < nelems; ++vidx)
{
VertexElementP vep = elements_temp[vidx];
// sanity check
assert(vep->getIDX() == vidx);
uint new_idx = pVertexPerm[vidx];
pElements[new_idx] = vep;
}
reindexElements();
reordered();
opt_file.close();
return;
}
if (opt_method == 2)
{
// / / / / / / / / / / / / / / NEW / / / / / / / / / / / / / / / / / / //
// LOOPING OVER ALL VERTICES, APPLYING THE WALK METHOD AND FINDING WHICH
// STARTING VERTEX GIVES THE LOWEST MATRIX WIDTH.
uint pNVerts = pElements.size();
// the best vertex(narrowest width)
uint bestone = 0;
uint bestwidth = pNVerts;
std::vector<VertexElement*> orig_indices = pElements;
stringstream ss;
ss << "\nFinding optimal vertex indexing. This can take some time...";
cout << ss.str() << endl;
for (uint vidx = 0; vidx < pNVerts; ++vidx)
{
set<VertexElement*> verteleset = set<VertexElement*>();
vector<VertexElement*> vertelevec = vector<VertexElement*>();
queue<VertexElement*> vertelqueue = queue<VertexElement*>();
verteleset.insert(orig_indices[vidx]);
vertelevec.push_back(orig_indices[vidx]);
uint ve0ncons = orig_indices[vidx]->getNCon();
VertexElement ** ve0neighbs = orig_indices[vidx]->getNeighbours();
fill_ve_vec(verteleset, vertelevec, vertelqueue, ve0ncons, ve0neighbs);
pElements.clear();
vector<VertexElement*>::iterator vertele_end = vertelevec.end();
uint ielt = 0;
for (vector<VertexElement*>::iterator vertele = vertelevec.begin(); vertele != vertele_end; ++vertele)
{
pElements.push_back(*vertele);
pVertexPerm[(*vertele)->getIDX()]=ielt;
ielt++;
}
// Note: this will reorder the vertex indices as we go- not a problem in this loop
// but they must be reset for the final index setting to work
reindexElements();
uint maxdi = 0;
for (int iv = 0; iv < pNVerts; ++iv)
{
VertexElement* ve = getVertex(iv);
int ind = ve->getIDX();
for (int i = 0; i < ve->getNCon(); ++i)
{
int inbr = ve->nbrIdx(i);
int di = ind - inbr;
if (di < 0)
{
di = -di;
}
if (di > maxdi)
{
maxdi = di;
}
}
}
if (maxdi < bestwidth)
{
bestone = vidx;
bestwidth = maxdi;
//cout << "\nOriginal vertex "<< vidx << " gives banded matrix half-width " << maxdi;
}
}
// reset the vertex indices to their original value: important
for (uint v = 0; v < pNVerts; ++v)
{
orig_indices[v]->setIDX(v);
}
set<VertexElement*> verteleset = set<VertexElement*>();
vector<VertexElement*> vertelevec = vector<VertexElement*>();
queue<VertexElement*> vertelqueue = queue<VertexElement*>();
verteleset.insert(orig_indices[bestone]);
vertelevec.push_back(orig_indices[bestone]);
uint ve0ncons = orig_indices[bestone]->getNCon();
VertexElement ** ve0neighbs = orig_indices[bestone]->getNeighbours();
fill_ve_vec(verteleset, vertelevec, vertelqueue, ve0ncons, ve0neighbs);
pElements.clear();
vector<VertexElement*>::iterator vertele_end = vertelevec.end();
uint ielt = 0;
for (vector<VertexElement*>::iterator vertele = vertelevec.begin(); vertele != vertele_end; ++vertele)
{
pElements.push_back(*vertele);
pVertexPerm[(*vertele)->getIDX()]=ielt;
ielt++;
}
}
// / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / //
else if (opt_method == 1)
{
/*
THIS ORIGINAL CODE REPLACED WITH NEW 'WALKING' METHOD. A DRAMATIC
REDUCTION IN BAND HALF-WIDTHS FOR COMPLEX 3D MESHES.
This is not the end of the story: TODO investigate whether reordering
a vertices neighbour's for the queue by distance will improve again.
*/
std::vector<double> com = centerOfMass();
double ** m = new double*[3];
for (uint i = 0; i < 3; i++)
{
m[i] = new double[3];
m[i][0] = 0.0;
m[i][1] = 0.0;
m[i][2] = 0.0;
}
for (uint ivert = 0; ivert < countVertices(); ivert++)
{
VertexElement* ve = getVertex(ivert);
double x = ve->getX() - com[0];
double y = ve->getY() - com[1];
double z = ve->getZ() - com[2];
m[0][0] += x * x;
m[0][1] += x * y;
m[0][2] += x * z;
m[1][0] += y * x;
m[1][1] += y * y;
m[1][2] += y * z;
m[2][0] += z * x;
m[2][1] += z * y;
m[2][2] += z * z;
}
uint iret;
double gamma;
double evec[3];
mainEvec(3, m, &iret, &gamma, evec);
if (iret != 1)
{
cout << "\nWarning - eigenvalue faliure " << endl;
}
for (uint i = 0; i < 3; i++)
{
delete[] m[i];
}
delete[] m;
double vx = evec[0];
double vy = evec[1];
double vz = evec[2];
vx += 1.e-8;
vy += 1.e-9;
vz += 1.e-10;
stringstream ss;
ss << "aligning to axis " << vx << " " << vy << " " << vz << endl;
//cout << ss.str();
map<double, VertexElement*> hm;
//vector<double> da;
for (uint ielt = 0; ielt < countVertices(); ielt++)
{
VertexElement * ve = getVertex(ielt);
double d = vx * ve->getX() + vy * ve->getY() + vz * ve->getZ();
hm[d] = ve;
//da.push_back(d);
}
//sort(da.begin(), da.end());
pElements.clear();
uint ielt = 0;
map<double, VertexElement*>::const_iterator iter = hm.begin();
while (iter != hm.end())
{
double d = iter->first;
pElements.push_back(hm[d]);
++iter;
// pVertexPerm[i] contains the new index in the elements array
// for the vertex that was originally at index i
pVertexPerm[hm[d]->getIDX()] = ielt;
ielt++;
}
}
else
{
std::ostringstream os;
os << "Unknown optimization method.\n";
throw steps::ArgErr(os.str());
}
reindexElements();
reordered();
}