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Merge branch 'vol_bin_format' into 'master'

Browse Source 
.vol.bin format using archiver

See merge request jschoeberl/netgen!385
This commit is contained in:
Matthias Hochsteger 2021-06-02 12:05:47 +00:00
commit 32522368b9
9 changed files with 82 additions and 55 deletions
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2
libsrc/general/ngarray.hpp
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@ -242,7 +242,7 @@ namespace netgen
using NgFlatArray<T,BASE,TIND>::data;
/// physical size of array
size_t allocsize;
size_t allocsize = 0;
/// memory is responsibility of container
bool ownmem;

4
libsrc/include/nginterface_v2.hpp
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@ -358,8 +358,8 @@ namespace netgen
int GetParentSElement (int ei) const;
bool HasParentEdges() const;
tuple<int, std::array<int,3>> GetParentEdges (int enr) const;
tuple<int, std::array<int,4>> GetParentFaces (int fnr) const;
std::tuple<int, std::array<int,3>> GetParentEdges (int enr) const;
std::tuple<int, std::array<int,4>> GetParentFaces (int fnr) const;
int GetNIdentifications() const;
int GetIdentificationType(int idnr) const;

20
libsrc/meshing/delaunay.cpp
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@ -864,6 +864,8 @@ namespace netgen
// remove degenerated
static Timer tdegenerated("Delaunay - remove degenerated");
tdegenerated.Start();
NgBitArray badnode(mesh.GetNP());
badnode.Clear();
@ -914,6 +916,10 @@ namespace netgen
PrintMessage (3, ndeg, " degenerated elements removed");
tdegenerated.Stop();
static Timer topenel("Delaunay - find openel");
topenel.Start();
// find surface triangles which are no face of any tet
@ -1073,6 +1079,10 @@ namespace netgen
}
topenel.Stop();
static Timer trem_intersect("Delaunay - remove intersecting");
trem_intersect.Start();
// find intersecting:
@ -1190,6 +1200,10 @@ namespace netgen
}
trem_intersect.Stop();
static Timer trem_outer("Delaunay - remove outer");
trem_outer.Start();
PrintMessage (3, "Remove outer");
@ -1400,15 +1414,17 @@ namespace netgen
}
*/
int lowest_undefined_el = 1;
while (1)
{
int inside;
bool done = 1;
int i;
for (i = 1; i <= ne; i++)
for (i = lowest_undefined_el; i <= ne; i++)
if (!inner.Test(i) && !outer.Test(i))
{
lowest_undefined_el = i+1;
done = 0;
break;
}
@ -1643,6 +1659,8 @@ namespace netgen
PrintMessage (5, "outer removed");
trem_outer.Stop();
mesh.FindOpenElements(domainnr);
mesh.Compress();

2
libsrc/meshing/improve2.hpp
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@ -10,7 +10,7 @@ void BuildEdgeList( const Mesh & mesh, const Table<TINDEX, PointIndex> & element
{ { 0, 1 }, { 0, 2 }, { 0, 3 },
{ 1, 2 }, { 1, 3 }, { 2, 3 } };
int ntasks = 2*ngcore::TaskManager::GetMaxThreads();
int ntasks = 4*ngcore::TaskManager::GetMaxThreads();
Array<Array<std::tuple<PointIndex,PointIndex>>> task_edges(ntasks);
ParallelFor(IntRange(ntasks), [&] (int ti)

2
libsrc/meshing/improve3.cpp
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@ -2768,7 +2768,7 @@ void MeshOptimize3d :: SwapImprove (Mesh & mesh, OPTIMIZEGOAL goal,
candidate_edges[index] = make_tuple(d_badness, i);
}
}
});
}, TasksPerThread (4));
auto edges_with_improvement = candidate_edges.Part(0, improvement_counter.load());
QuickSort(edges_with_improvement);

69
libsrc/meshing/meshclass.cpp
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@ -413,6 +413,13 @@ namespace netgen
void Mesh :: Save (const string & filename) const
{
if (filename.find(".vol.bin") != string::npos)
{
BinaryOutArchive in(filename);
in & const_cast<Mesh&>(*this);
return;
}
ostream * outfile;
if (filename.find(".vol.gz")!=string::npos)
outfile = new ogzstream(filename.c_str());
@ -872,6 +879,14 @@ namespace netgen
void Mesh :: Load (const string & filename)
{
cout << "filename = " << filename << endl;
if (filename.find(".vol.bin") != string::npos)
{
BinaryInArchive in(filename);
in & (*this);
return;
}
istream * infile = NULL;
if (filename.find(".vol.gz") != string::npos)
@ -2100,37 +2115,27 @@ namespace netgen
t_table.Start();
TableCreator<ElementIndex, PointIndex> creator(np);
auto elsonpoint = ngcore::CreateSortedTable<ElementIndex, PointIndex>( volelements.Range(),
[&](auto & table, ElementIndex ei)
{
const Element & el = (*this)[ei];
if (dom == 0 || dom == el.GetIndex())
{
if (el.GetNP() == 4)
{
INDEX_4 i4(el[0], el[1], el[2], el[3]);
i4.Sort();
table.Add (PointIndex(i4.I1()), ei);
table.Add (PointIndex(i4.I2()), ei);
}
else
{
for (PointIndex pi : el.PNums())
table.Add(pi, ei);
}
}
}, GetNP());
for ( ; !creator.Done(); creator++)
// for (ElementIndex ei : Range(VolumeElements()))
ParallelFor
(Range(VolumeElements()), [&] (ElementIndex ei)
{
const Element & el = (*this)[ei];
if (dom == 0 || dom == el.GetIndex())
{
if (el.GetNP() == 4)
{
INDEX_4 i4(el[0], el[1], el[2], el[3]);
i4.Sort();
creator.Add (PointIndex(i4.I1()), ei);
creator.Add (PointIndex(i4.I2()), ei);
}
else
{
for (PointIndex pi : el.PNums())
creator.Add(pi, ei);
}
}
});
auto elsonpoint = creator.MoveTable();
ParallelFor (Range(elsonpoint), [&] (auto i)
{
QuickSort(elsonpoint[i]);
});
NgArray<int,PointIndex::BASE> numonpoint(np);
/*
@ -2381,7 +2386,7 @@ namespace netgen
*/
size_t numtasks = ngcore::TaskManager::GetNumThreads();
size_t numtasks = 4*ngcore::TaskManager::GetNumThreads();
Array<Array<Element2d>> thread_openelements(numtasks);
ParallelJob
( [&](TaskInfo & ti)
@ -2506,7 +2511,7 @@ namespace netgen
thread_openelements[ti.task_nr].Append (tri);
}
}
}});
}}, numtasks);
for (auto & a : thread_openelements)
for (auto & el : a)

2
libsrc/meshing/meshtype.hpp
View File

@ -446,7 +446,7 @@ namespace netgen
pnum[cnt++] = val;
return *this;
}
Element2d & operator= (initializer_list<tuple<PointIndex,PointGeomInfo>> list)
Element2d & operator= (initializer_list<std::tuple<PointIndex,PointGeomInfo>> list)
{
size_t cnt = 0;
for (auto val : list)

32
libsrc/meshing/python_mesh.cpp
View File

@ -685,29 +685,33 @@ DLL_HEADER void ExportNetgenMeshing(py::module &m)
return;
}
istream * infile;
istream * infile = nullptr;
NgArray<char> buf; // for distributing geometry!
int strs;
if( id == 0) {
if (filename.substr (filename.length()-3, 3) == ".gz")
if (filename.substr (filename.length()-8, 8) == ".vol.bin")
mesh -> Load(filename);
else if (filename.substr (filename.length()-3, 3) == ".gz")
infile = new igzstream (filename.c_str());
else
infile = new ifstream (filename.c_str());
mesh -> Load(*infile);
// make string from rest of file (for geometry info!)
// (this might be empty, in which case we take the global ng_geometry)
stringstream geom_part;
geom_part << infile->rdbuf();
string geom_part_string = geom_part.str();
strs = geom_part_string.size();
// buf = new char[strs];
buf.SetSize(strs);
memcpy(&buf[0], geom_part_string.c_str(), strs*sizeof(char));
if(infile)
{
mesh -> Load(*infile);
// make string from rest of file (for geometry info!)
// (this might be empty, in which case we take the global ng_geometry)
stringstream geom_part;
geom_part << infile->rdbuf();
string geom_part_string = geom_part.str();
strs = geom_part_string.size();
// buf = new char[strs];
buf.SetSize(strs);
memcpy(&buf[0], geom_part_string.c_str(), strs*sizeof(char));
delete infile;
}
delete infile;
if (ntasks > 1)
{

4
libsrc/meshing/topology.hpp
View File

@ -195,10 +195,10 @@ public:
private:
Array<tuple<int, std::array<int,3>>> parent_edges;
Array<std::tuple<int, std::array<int,3>>> parent_edges;
void BuildParentEdges ();
Array<tuple<int, std::array<int,4>>> parent_faces;
Array<std::tuple<int, std::array<int,4>>> parent_faces;
void BuildParentFaces ();
public:
auto GetParentEdges (int enr) const { return parent_edges[enr]; }