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netgen/libsrc/interface/rw_cgns.cpp
mhochsteger@cerbsim.com cf59f297a7 use std::filesystem::path
2022-02-23 11:56:00 +01:00

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#include <meshing.hpp>
#include "writeuser.hpp"
#ifdef NG_CGNS
#include <variant>
#include <cgnslib.h>
namespace netgen::cg
{
typedef ngcore::ClosedHashTable<ngcore::INT<3,size_t>, size_t> PointTable;
int getDim(ElementType_t type)
{
switch(type)
{
case BAR_2:
case BAR_3:
return 1;
case TRI_3:
case TRI_6:
case QUAD_4:
case QUAD_8:
return 2;
case TETRA_4:
case TETRA_10:
case PYRA_5:
case PYRA_13:
case HEXA_8:
case HEXA_20:
case PENTA_6:
case PENTA_15:
return 3;
default:
throw Exception("Read CGNS: unknown element type " + string(cg_ElementTypeName(type)));
}
}
Segment ReadCGNSElement1D( ElementType_t type, FlatArray<cgsize_t> verts )
{
int np;
cg_npe(type, &np);
Segment s;
for (auto i : Range(np))
s[i] = verts[i];
return s;
}
Element2d ReadCGNSElement2D( ElementType_t type, FlatArray<cgsize_t> verts )
{
// static constexpr int map_tri3[] = {0,2,1};
static constexpr int map_tri6[] = {0,2,1,3,5,4}; // untested
// static constexpr int map_quad4[] = {0,3,2,1};
static constexpr int map_quad8[] = {0,3,2,1,4,7,6,5}; // untested
const int * map = nullptr;
switch(type)
{
case TRI_3:
// map = map_tri3;
break;
case QUAD_4:
// map = map_quad4;
break;
case TRI_6:
map = map_tri6;
break;
case QUAD_8:
map = map_quad8;
break;
default:
throw Exception("Read CGNS: unknown element type " + string(cg_ElementTypeName(type)));
}
int np;
cg_npe(type, &np);
Element2d el(np);
for (auto i : Range(np))
el[i] = verts[i];
return el;
}
Element ReadCGNSElement3D( ElementType_t type, FlatArray<cgsize_t> verts )
{
static constexpr int map_tet4[] = {0,2,1,3};
static constexpr int map_prism6[] = {0,2,1,3,5,4};
static constexpr int map_pyra5[] = {0,3,2,1,4};
static constexpr int map_hexa8[] = {0,3,2,1,4,7,6,5};
int np;
cg_npe(type, &np);
const int * map = nullptr;
switch(type)
{
case TETRA_4:
map = map_tet4; break;
case PYRA_5:
map = map_pyra5; break;
case PENTA_6:
map = map_prism6; break;
case HEXA_8:
map = map_hexa8; break;
// TODO: Second order elements
case TETRA_10:
case PYRA_13:
case HEXA_20:
case PENTA_15:
default:
throw Exception("Read CGNS: unknown element type " + string(cg_ElementTypeName(type)));
}
Element el(np);
for (auto i : Range(np))
el[i] = verts[map[i]];
return el;
}
void WriteCGNSElement( const Segment & el, Array<cgsize_t> & verts )
{
verts.Append(BAR_2);
verts.Append(el[0]);
verts.Append(el[1]);
}
void WriteCGNSElement( const Element2d & el, Array<cgsize_t> & verts )
{
static constexpr int map_tri6[] = {0,2,1,3,5,4}; // untested
static constexpr int map_quad8[] = {0,3,2,1,4,7,6,5}; // untested
ElementType_t type;
const int * map = nullptr;
switch(el.GetType())
{
case TRIG:
type = TRI_3;
break;
case QUAD:
type = QUAD_4;
break;
case TRIG6:
type = TRI_6;
map = map_tri6;
break;
case QUAD8:
type = QUAD_8;
map = map_quad8;
break;
// TODO: Second order elements
default:
throw Exception("Write CGNS: unknown element type " + ToString(el.GetType()));
}
verts.Append(type);
for (auto i : Range(el.GetNP()))
verts.Append(el[i]);
}
void WriteCGNSElement( const Element & el, Array<cgsize_t> & verts )
{
static constexpr int map_tet4[] = {0,2,1,3};
static constexpr int map_prism6[] = {0,2,1,3,5,4};
static constexpr int map_pyra5[] = {0,3,2,1,4};
static constexpr int map_hexa8[] = {0,3,2,1,4,7,6,5};
ElementType_t type;
const int * map = nullptr;
switch(el.GetType())
{
case TET:
map = map_tet4;
type = TETRA_4;
break;
case PYRAMID:
type = PYRA_5;
map = map_pyra5;
break;
case PRISM:
type = PENTA_6;
map = map_prism6;
break;
case HEX:
type = HEXA_8;
map = map_hexa8;
break;
// TODO: Second order elements
default:
throw Exception("Write CGNS: unknown element type " + ToString(el.GetType()));
}
verts.Append(type);
for (auto i : Range(el.GetNP()))
verts.Append(el[map[i]]);
}
int WriteCGNSRegion( const Mesh & mesh, int dim, int index, int fn, int base, int zone, int ne_before )
{
int meshdim = mesh.GetDimension();
int codim = meshdim-dim;
if(codim < 0 || codim > 2)
return 0;
// make sure that each material/boundary name is unique
string prefix[] = { "dom_", "bnd_", "bbnd_" };
string name = prefix[meshdim-dim] + ToString(index) + "_";
if(codim==0) name += mesh.GetMaterial(index+1);
if(codim==1) name += *mesh.GetBCNamePtr(index);
if(codim==2) name += mesh.GetCD2Name(index);
int ne = 0;
Array<int> data;
if(dim==3)
for(const auto el : mesh.VolumeElements())
if(el.GetIndex()==index)
{
ne++;
WriteCGNSElement(el, data);
}
if(dim==2)
for(const auto el : mesh.SurfaceElements())
if(el.GetIndex()==index)
{
ne++;
WriteCGNSElement(el, data);
}
if(dim==1)
for(const auto el : mesh.LineSegments())
if(el.si==index)
{
ne++;
WriteCGNSElement(el, data);
}
if(ne==0)
return 0;
int section;
// int start = 1;
// int end = ne;
#if CGNS_VERSION < 3400
cg_section_write(fn,base,zone, name.c_str(), MIXED, ne_before+1, ne_before+ne, 0, &data[0], &section);
#else
cg_poly_section_write(fn,base,zone, name.c_str(), MIXED, ne_before+1, ne_before+ne, 0, &data[0], nullptr, &section);
#endif
return ne;
}
// maps cgns node type to ngsolve node type
// enum NODE_TYPE { NT_VERTEX = 0, NT_EDGE = 1, NT_FACE = 2, NT_CELL = 3, NT_ELEMENT = 4, NT_FACET = 5 };
int getNodeType( GridLocation_t location )
{
switch(location)
{
case Vertex:
return 0;
case CellCenter:
return 3;
case FaceCenter:
return 2;
case EdgeCenter:
return 1;
default:
throw Exception("Read CGNS: unknown grid location " + string(cg_GridLocationName(location)));
}
}
GridLocation_t getCGNodeType( int node_type )
{
switch(node_type)
{
case 0:
return Vertex;
case 1:
return EdgeCenter;
case 2:
return FaceCenter;
case 3:
return CellCenter;
default:
throw Exception("Write CGNS: unknown node type " + ToString(node_type));
}
}
struct Solution
{
int fn, base, zone, solution;
string name;
GridLocation_t location; // solution is defined on either cells, faces, edges or vertices
PointSetType_t point_type;
cgsize_t n_points;
Array<string> field_names;
Array<DataType_t> field_datatypes;
Solution() = default;
Solution(int fn_, int base_, int zone_, int solution_)
: fn(fn_), base(base_), zone(zone_), solution(solution_)
{
char solname[100];
cg_sol_info(fn, base, zone, solution, solname, &location);
name = solname;
cg_sol_ptset_info(fn, base, zone, solution, &point_type, &n_points);
int n_fields = 0;
cg_nfields(fn, base, zone, solution, &n_fields);
field_names.SetSize(n_fields);
field_datatypes.SetSize(n_fields);
for(auto fi : Range(n_fields))
{
char buf[100];
cg_field_info(fn, base, zone, solution, fi+1, &field_datatypes[fi], buf);
field_names[fi] = buf;
}
}
};
struct Zone
{
ZoneType_t zone_type;
int fn, base, zone;
int first_index_1d, first_index_2d, first_index_3d;
int nv=0, ne_1d=0, ne_2d=0, ne_3d=0;
Array<string> names_1d, names_2d, names_3d;
string name;
cgsize_t size[3];
Array<Solution> solutions;
Zone(int fn_, int base_, int zone_)
: fn(fn_), base(base_), zone(zone_)
{
cg_zone_type(fn, base, zone, &zone_type);
char zone_name[100];
cg_zone_read(fn,base,zone, zone_name, size);
nv = size[0];
int n_solutions;
cg_nsols(fn, base, zone, &n_solutions);
solutions.SetSize(n_solutions);
for(auto si : Range(n_solutions))
solutions[si] = Solution{fn, base, zone, si+1};
}
void ReadSolutions( int meshdim, std::vector<string> & sol_names, std::vector<Array<double>> & sol_values, std::vector<int> & sol_locations )
{
static Timer tall("CGNS::ReadSolutions"); RegionTimer rtall(tall);
for (auto & sol : solutions)
{
for (auto fi : Range(sol.field_names.Size()))
{
cgsize_t size = sol.n_points;
size=0; // TODO: check if sol.point_type is a list or range, and handle appropriately
if(size==0)
{
switch(sol.location)
{
case Vertex:
size = nv;
break;
case CellCenter:
size = (meshdim == 3 ? ne_3d : ne_2d);
break;
case FaceCenter:
case IFaceCenter:
case JFaceCenter:
case KFaceCenter:
case EdgeCenter:
default:
throw Exception("Read CGNS: unknown grid location " + string(cg_GridLocationName(sol.location)));
}
}
auto values = Array<double>(size);
cgsize_t imin = 1UL;
cg_field_read(fn, base, zone, sol.solution, sol.field_names[fi].c_str(), RealDouble, &imin, &size, &values[0]);
sol_names.push_back(sol.field_names[fi]);
sol_values.emplace_back(std::move(values));
sol_locations.push_back(getNodeType(sol.location));
}
}
}
void ReadMesh( Mesh & mesh, PointTable & point_table )
{
static Timer tall("CGNS::ReadMesh-Zone"); RegionTimer rtall(tall);
static Timer tsection("CGNS::ReadMesh-Section");
first_index_1d = mesh.GetRegionNamesCD(2).Size();
first_index_2d = mesh.GetRegionNamesCD(1).Size();
first_index_3d = mesh.GetRegionNamesCD(0).Size();
Array<double> x(nv), y(nv), z(nv);
cgsize_t imin=1;
cg_coord_read(fn,base,zone, "CoordinateX", RealDouble, &imin, &nv, &x[0]);
cg_coord_read(fn,base,zone, "CoordinateY", RealDouble, &imin, &nv, &y[0]);
cg_coord_read(fn,base,zone, "CoordinateZ", RealDouble, &imin, &nv, &z[0]);
Array<cgsize_t> point_map(nv);
for(auto i : Range(nv))
{
ngcore::INT<3,size_t> hash = {*reinterpret_cast<size_t*>(&x[i]), *reinterpret_cast<size_t*>(&y[i]), *reinterpret_cast<size_t*>(&z[i])};
size_t pi_ng;
size_t pos;
// check if this point is new
if( point_table.PositionCreate (hash, pos) )
{
pi_ng = mesh.AddPoint( {x[i], y[i], z[i]} );
point_table.SetData(pos, pi_ng);
}
else
point_table.GetData(pos, pi_ng);
point_map[i] = pi_ng;
}
int nsections;
cg_nsections(fn, base, zone, &nsections);
int index_1d = first_index_1d;
int index_2d = first_index_2d;
int index_3d = first_index_3d;
for (auto section : Range(1,nsections+1))
{
RegionTimer rtsection(tsection);
char sec_name[100];
ElementType_t type;
cgsize_t start, end;
int nbndry, parent_flag;
cg_section_read(fn, base, zone, section, sec_name, &type, &start, &end, &nbndry, &parent_flag);
PrintMessage(4, "Read section ", section, " with name ", sec_name, " and element type ", cg_ElementTypeName(type));
string ngname{sec_name};
for (char & c : ngname)
if(c==' ')
c = '_';
if(type==MIXED)
{
bool have_1d_elements = false;
bool have_2d_elements = false;
bool have_3d_elements = false;
cgsize_t nv;
cg_ElementDataSize(fn, base, zone, section, &nv);
Array<cgsize_t> vertices(nv);
#if CGNS_VERSION < 3400
cg_elements_read(fn, base, zone, section, &vertices[0], nullptr);
#else
cg_poly_elements_read(fn, base, zone, section, &vertices[0], nullptr, nullptr);
#endif
size_t vi = 0;
while(vi<nv)
{
auto type = static_cast<ElementType_t>(vertices[vi++]);
int dim = getDim(type);
int np;
cg_npe(type, &np);
for (auto & v : vertices.Range(vi, vi+np))
v = point_map[v-1];
if(dim==1)
{
if(!have_1d_elements)
{
index_1d++;
have_1d_elements = true;
mesh.AddEdgeDescriptor(EdgeDescriptor{});
names_1d.Append(ngname);
}
auto el = ReadCGNSElement1D(type, vertices.Range(vi, vertices.Size()));
el.si = index_1d;
mesh.AddSegment(el);
vi += el.GetNP();
ne_1d++;
}
if(dim==2)
{
if(!have_2d_elements)
{
index_2d++;
have_2d_elements = true;
mesh.AddFaceDescriptor(FaceDescriptor(index_2d, 1, 0, 1));
names_2d.Append(ngname);
}
auto el = ReadCGNSElement2D(type, vertices.Range(vi, vertices.Size()));
el.SetIndex(index_2d);
mesh.AddSurfaceElement(el);
vi += el.GetNP();
ne_2d++;
}
if(dim==3)
{
if(!have_3d_elements)
{
index_3d++;
have_3d_elements = true;
names_3d.Append(ngname);
}
auto el = ReadCGNSElement3D(type, vertices.Range(vi, vertices.Size()));
el.SetIndex(index_3d);
mesh.AddVolumeElement(el);
vi += el.GetNP();
ne_3d++;
}
}
}
else
{
int dim = getDim(type);
cgsize_t nv;
cg_ElementDataSize(fn, base, zone, section, &nv);
int np=0;
cg_npe(type, &np);
Array<cgsize_t> vertices(nv);
cg_elements_read(fn, base, zone, section, &vertices[0], nullptr);
for (auto & v : vertices)
v = point_map[v-1];
int ne_section = nv/np;
if(dim==1)
{
index_1d++;
mesh.AddEdgeDescriptor(EdgeDescriptor{});
names_1d.Append(ngname);
for(auto i : Range(ne_section))
{
auto el = ReadCGNSElement1D(type, vertices.Range(np*i, np*(i+1)));
el.si = index_1d;
mesh.AddSegment(el);
}
ne_1d += ne_section;
}
if(dim==2)
{
index_2d++;
mesh.AddFaceDescriptor(FaceDescriptor(index_2d, 1, 0, 1));
names_2d.Append(ngname);
for(auto i : Range(ne_section))
{
auto el = ReadCGNSElement2D(type, vertices.Range(np*i, np*(i+1)));
el.SetIndex(index_2d);
mesh.AddSurfaceElement(el);
}
ne_2d += ne_section;
}
if(dim==3)
{
index_3d++;
names_3d.Append(ngname);
for(auto i : Range(ne_section))
{
auto el = ReadCGNSElement3D(type, vertices.Range(np*i, np*(i+1)));
el.SetIndex(index_3d);
mesh.AddVolumeElement(el);
}
ne_3d += ne_section;
}
}
}
mesh.GetRegionNamesCD(2).SetSize(index_1d);
mesh.GetRegionNamesCD(1).SetSize(index_2d);
mesh.GetRegionNamesCD(0).SetSize(index_3d);
mesh.GetRegionNamesCD(2) = nullptr;
mesh.GetRegionNamesCD(1) = nullptr;
mesh.GetRegionNamesCD(0) = nullptr;
}
void SetNames( Mesh & mesh )
{
if(mesh.GetDimension() == 2)
{
for (auto i : Range(names_1d.Size()))
mesh.SetBCName(first_index_1d + i, names_1d[i]);
for (auto i : Range(names_2d.Size()))
mesh.SetMaterial(first_index_2d + i +1, names_2d[i]);
}
else
{
for (auto i : Range(names_1d.Size()))
mesh.SetCD2Name(first_index_1d + i +1, names_1d[i]);
for (auto i : Range(names_2d.Size()))
{
mesh.SetBCName(first_index_2d + i, names_2d[i]);
mesh.GetFaceDescriptor(first_index_2d + i +1).SetDomainIn(first_index_3d+1);
}
for (auto i : Range(names_3d.Size()))
mesh.SetMaterial(first_index_3d + i +1, names_3d[i]);
}
}
};
}
namespace netgen
{
int ReadCGNSMesh (Mesh & mesh, const filesystem::path & filename, Array<unique_ptr<cg::Zone>> & zones)
{
mesh.SetDimension(3);
static Timer tall("CGNS::ReadMesh"); RegionTimer rtall(tall);
int fn;
cg_open(filename.string().c_str(),CG_MODE_READ,&fn);
int base = 1;
int nzones;
cg_nzones(fn, base, &nzones);
int n_vertices = 0;
for (auto zi : Range(1, nzones+1))
{
int size[3];
char name[100];
cg_zone_read(fn,base,zi, name, size);
n_vertices += size[0];
}
cg::PointTable points(2*n_vertices);
for (auto zi : Range(1, nzones+1))
{
ZoneType_t zone_type;
cg_zone_type(fn, base, zi, &zone_type);
if(zone_type != Unstructured )
{
PrintMessage(2, "skipping zone with type ", cg_ZoneTypeName(zone_type) );
continue;
}
auto zone = make_unique<cg::Zone>(fn, base, zi);
zone->ReadMesh( mesh, points );
zones.Append(std::move(zone));
}
if(mesh.GetNE() == 0)
mesh.SetDimension(2);
for (auto & zone : zones)
zone->SetNames(mesh);
mesh.UpdateTopology();
const auto & topo = mesh.GetTopology();
for (auto sei : Range(mesh.SurfaceElements()))
{
int ei0, ei1;
topo.GetSurface2VolumeElement (sei+1, ei0, ei1);
auto si = mesh.SurfaceElement(sei).GetIndex();
auto & fd = mesh.GetFaceDescriptor(si);
if(ei0>0)
{
int i0 = mesh.VolumeElement(ei0).GetIndex();
if(fd.DomainIn()!=i0)
fd.SetDomainOut(i0);
}
if(ei1>0)
{
int i1 = mesh.VolumeElement(ei1).GetIndex();
if(fd.DomainIn()!=i1)
fd.SetDomainOut(i1);
}
}
return fn;
}
void ReadCGNSMesh (Mesh & mesh, const filesystem::path & filename)
{
Array<unique_ptr<cg::Zone>> zones;
int fn = ReadCGNSMesh(mesh, filename, zones);
cg_close(fn);
}
// Reads mesh and solutions of .csns file
tuple<shared_ptr<Mesh>, vector<string>, vector<Array<double>>, vector<int>> ReadCGNSFile(const filesystem::path & filename, int base)
{
static Timer tall("CGNS::ReadFile"); RegionTimer rtall(tall);
auto mesh = make_shared<Mesh>();
Array<unique_ptr<cg::Zone>> zones;
int fn = ReadCGNSMesh(*mesh, filename, zones);
std::vector<string> names;
std::vector<Array<double>> values;
std::vector<int> locations;
for (auto & zone : zones)
zone->ReadSolutions( mesh->GetDimension(), names, values, locations );
cg_close(fn);
return std::make_tuple(mesh, names, values, locations);
}
void WriteCGNSMesh (const Mesh & mesh, int fn, int & base, int & zone)
{
int dim = mesh.GetDimension();
cg_base_write(fn, "mesh", dim, dim, &base);
int nv = static_cast<int>(mesh.GetNV());
int ne = mesh.GetNE();
Array<double> x, y, z;
for(auto & p : mesh.Points())
{
x.Append(p[0]);
y.Append(p[1]);
z.Append(p[2]);
}
cgsize_t isize[3] = { nv, ne, 0 };
cg_zone_write(fn,base, "mesh", isize, Unstructured, &zone);
int coord;
cg_coord_write(fn,base,zone, RealDouble, "CoordinateX", &x[0], &coord);
cg_coord_write(fn,base,zone, RealDouble, "CoordinateY", &y[0], &coord);
cg_coord_write(fn,base,zone, RealDouble, "CoordinateZ", &z[0], &coord);
int imax3 = 0;
for(const auto & el : mesh.VolumeElements())
imax3 = max(imax3, el.GetIndex());
int imax2 = 0;
for(const auto & el : mesh.SurfaceElements())
imax2 = max(imax2, el.GetIndex());
int imax1 = 0;
for(const auto & el : mesh.LineSegments())
imax1 = max(imax1, el.si);
int ne_written = 0;
// int meshdim = mesh.GetDimension();
for(const auto i : IntRange(imax3))
ne_written += cg::WriteCGNSRegion(mesh, 3, i+1, fn, base, zone, ne_written);
for(const auto i : IntRange(imax2))
ne_written += cg::WriteCGNSRegion(mesh, 2, i+1, fn, base, zone, ne_written);
for(const auto i : IntRange(imax1))
ne_written += cg::WriteCGNSRegion(mesh, 1, i+1, fn, base, zone, ne_written);
}
void WriteCGNSMesh (const Mesh & mesh, const filesystem::path & filename)
{
static Timer tall("CGNS::WriteMesh"); RegionTimer rtall(tall);
int fn, base, zone;
cg_open(filename.string().c_str(),CG_MODE_WRITE,&fn);
WriteCGNSMesh(mesh, fn, base, zone);
cg_close(fn);
}
void WriteCGNSFile(shared_ptr<Mesh> mesh, const filesystem::path & filename, vector<string> fields, vector<Array<double>> values, vector<int> locations)
{
static Timer tall("CGNS::WriteFile"); RegionTimer rtall(tall);
int fn, base, zone;
cg_open(filename.string().c_str(),CG_MODE_WRITE,&fn);
WriteCGNSMesh(*mesh, fn, base, zone);
for(auto i : IntRange(fields.size()))
{
int section, field;
string name = "solution_" + ToString(i);
cg_sol_write(fn, base, zone, name.c_str(), cg::getCGNodeType(locations[i]), &section);
cg_field_write(fn, base, zone, section, RealDouble, fields[i].c_str(), &values[i][0], &field);
}
cg_close(fn);
}
}
#else // NG_CGNS
namespace netgen
{
void ReadCGNSMesh (Mesh & mesh, const filesystem::path & filename)
{
PrintMessage(1, "Could not import CGNS mesh: Netgen was built without CGNS support");
}
tuple<shared_ptr<Mesh>, vector<string>, vector<Array<double>>, vector<int>> ReadCGNSFile(const filesystem::path & filename, int base)
{
throw Exception("Netgen was built without CGNS support");
}
void WriteCGNSMesh (const Mesh & mesh, const filesystem::path & filename)
{
PrintMessage(1, "Could not write CGNS mesh: Netgen was built without CGNS support");
}
void WriteCGNSFile(shared_ptr<Mesh> mesh, const filesystem::path & filename, vector<string> fields, vector<Array<double>> values, vector<int> locations)
{
throw Exception("Netgen was built without CGNS support");
}
}
#endif // NG_CGNS
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