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Commit aec9bc57 authored by David Moxey's avatar David Moxey
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Merge branch 'master' into feature/dump-mesh-on-failure

parents 76927fc7 d61fc059
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Showing with 67 additions and 60 deletions
CHANGELOG.md
View file @ aec9bc57
......@@ -6,16 +6,21 @@ v4.5.0
**NekMesh**:
- Add periodic boundary condition meshing in 2D (!733)
- Adjust boundary layer thickness in corners in 2D (!739)
- Rework meshing control so that if possible viewable meshes will be dumped
when some part of the system fails (!756)
- Add manifold meshing option (!756)
**Documentation**:
- Added the developer-guide repository as a submodule (!751)
v4.4.1
------
**Library**
- Remove the duplicate output of errorutil (!756)
**NekMesh**:
- Fix memory consumption issue with Gmsh output (!747)
- Rework meshing control so that if possible viewable meshes will be dumped
when some part of the system fails (!756)
- Add manifold meshing option (!756)
v4.4.0
------
**Library**:
......@@ -57,6 +62,7 @@ v4.4.0
- Fix bug in FieldUtils when using half mode expansions (!734)
- Do not read the same fld/pts files again for every variable (!670)
- Fix bug in CMake PETSc detection for Ubuntu 16.04/Debian 9 (!735)
- Fix warnings with Intel compiler (!742)
**ADRSolver:**
- Add a projection equation system for C^0 projections (!675)
......
library/LibUtilities/LinearAlgebra/SparseMatrix.cpp
View file @ aec9bc57
......@@ -75,19 +75,19 @@ namespace Nektar
template<typename SparseStorageType>
const IndexType NekSparseMatrix<SparseStorageType>::GetRows() const
IndexType NekSparseMatrix<SparseStorageType>::GetRows() const
{
return m_sparseStorage->GetRows();
}
template<typename SparseStorageType>
const IndexType NekSparseMatrix<SparseStorageType>::GetColumns() const
IndexType NekSparseMatrix<SparseStorageType>::GetColumns() const
{
return m_sparseStorage->GetColumns();
}
template<typename SparseStorageType>
const IndexType NekSparseMatrix<SparseStorageType>::GetNumNonZeroEntries() const
IndexType NekSparseMatrix<SparseStorageType>::GetNumNonZeroEntries() const
{
return m_sparseStorage->GetNumNonZeroEntries();
}
......@@ -137,7 +137,7 @@ namespace Nektar
}
template<typename SparseStorageType>
const size_t NekSparseMatrix<SparseStorageType>::GetMemoryFootprint() const
size_t NekSparseMatrix<SparseStorageType>::GetMemoryFootprint() const
{
return m_sparseStorage->GetMemoryUsage(
m_sparseStorage->GetNumNonZeroEntries(),
......@@ -148,7 +148,7 @@ namespace Nektar
}
template<typename SparseStorageType>
const unsigned long NekSparseMatrix<SparseStorageType>::GetMulCallsCounter() const
unsigned long NekSparseMatrix<SparseStorageType>::GetMulCallsCounter() const
{
return m_mulCallsCounter;
}
......@@ -161,7 +161,7 @@ namespace Nektar
}
template<typename SparseStorageType>
const IndexType NekSparseMatrix<SparseStorageType>::GetBandwidth()
IndexType NekSparseMatrix<SparseStorageType>::GetBandwidth()
{
int bandwidth = 0;
......
library/LibUtilities/LinearAlgebra/SparseMatrix.hpp
View file @ aec9bc57
......@@ -73,15 +73,15 @@ namespace Nektar
LIB_UTILITIES_EXPORT NekSparseMatrix(const NekSparseMatrix& src);
LIB_UTILITIES_EXPORT ~NekSparseMatrix();
LIB_UTILITIES_EXPORT const IndexType GetRows() const;
LIB_UTILITIES_EXPORT const IndexType GetColumns() const;
LIB_UTILITIES_EXPORT const IndexType GetNumNonZeroEntries() const;
LIB_UTILITIES_EXPORT IndexType GetRows() const;
LIB_UTILITIES_EXPORT IndexType GetColumns() const;
LIB_UTILITIES_EXPORT IndexType GetNumNonZeroEntries() const;
LIB_UTILITIES_EXPORT const DataType GetFillInRatio() const;
LIB_UTILITIES_EXPORT const size_t GetMemoryFootprint() const;
LIB_UTILITIES_EXPORT const unsigned long GetMulCallsCounter() const;
LIB_UTILITIES_EXPORT size_t GetMemoryFootprint() const;
LIB_UTILITIES_EXPORT unsigned long GetMulCallsCounter() const;
LIB_UTILITIES_EXPORT const DataType GetAvgRowDensity() const;
LIB_UTILITIES_EXPORT const IndexType GetBandwidth();
LIB_UTILITIES_EXPORT IndexType GetBandwidth();
LIB_UTILITIES_EXPORT COOMatTypeSharedPtr GetCooStorage();
......
library/NekMeshUtils/MeshElements/Mesh.cpp
View file @ aec9bc57
......@@ -33,9 +33,9 @@
//
////////////////////////////////////////////////////////////////////////////////
#include <NekMeshUtils/MeshElements/Mesh.h>
#include <LibUtilities/Foundations/ManagerAccess.h>
#include <LibUtilities/BasicUtils/Progressbar.hpp>
#include <LibUtilities/Foundations/ManagerAccess.h>
#include <NekMeshUtils/MeshElements/Mesh.h>
using namespace std;
......@@ -96,17 +96,22 @@ unsigned int Mesh::GetNumEntities()
* - Finally, any boundary elements are updated so that they have the same
* interior degrees of freedom as their corresponding edge or face links.
*/
void Mesh::MakeOrder(int order,
LibUtilities::PointsType distType)
void Mesh::MakeOrder(int order, LibUtilities::PointsType distType)
{
// going to make a copy of the curavture information
// cheaper that geom objects
// currently the geometry objects which make up a 3D element
// dont use the volume nodes, they are just stored,
// so we can get away without copying them
int id = m_vertexSet.size();
EdgeSet::iterator eit;
FaceSet::iterator fit;
boost::unordered_map<int, SpatialDomains::Geometry1DSharedPtr> edgeGeoms;
boost::unordered_map<int, SpatialDomains::Geometry2DSharedPtr> faceGeoms;
boost::unordered_map<int, SpatialDomains::GeometrySharedPtr> volGeoms;
boost::unordered_map<int, EdgeSharedPtr> edgeCopies;
boost::unordered_map<int, FaceSharedPtr> faceCopies;
// Decide on distribution of points to use for each shape type based on the
// input we've been supplied.
......@@ -127,7 +132,7 @@ void Mesh::MakeOrder(int order,
pTypes[LibUtilities::eTriangle] = LibUtilities::eNodalTriElec;
pTypes[LibUtilities::eQuadrilateral] =
LibUtilities::eGaussLobattoLegendre;
pTypes[LibUtilities::ePrism] = LibUtilities::eNodalPrismElec;
pTypes[LibUtilities::ePrism] = LibUtilities::eNodalPrismElec;
pTypes[LibUtilities::eTetrahedron] = LibUtilities::eNodalTetElec;
pTypes[LibUtilities::eHexahedron] = LibUtilities::eGaussLobattoLegendre;
}
......@@ -136,32 +141,20 @@ void Mesh::MakeOrder(int order,
ASSERTL1(false, "Mesh::MakeOrder does not support this points type.");
}
// Begin by generating Nektar++ geometry objects for edges, faces and
// elements so that we don't affect any neighbouring elements in the mesh as
// Begin by coping mesh objects for edges, faces
// so that we don't affect any neighbouring elements in the mesh as
// we process each element.
for(eit = m_edgeSet.begin(); eit != m_edgeSet.end(); eit++)
{
SpatialDomains::Geometry1DSharedPtr geom =
(*eit)->GetGeom(m_spaceDim);
geom->FillGeom();
edgeGeoms[(*eit)->m_id] = geom;
}
for(fit = m_faceSet.begin(); fit != m_faceSet.end(); fit++)
// at the same time we delete the curvature from the original edge
for (eit = m_edgeSet.begin(); eit != m_edgeSet.end(); eit++)
{
SpatialDomains::Geometry2DSharedPtr geom =
(*fit)->GetGeom(m_spaceDim);
geom->FillGeom();
faceGeoms[(*fit)->m_id] = geom;
edgeCopies[(*eit)->m_id] = EdgeSharedPtr(new Edge(*(*eit)));
(*eit)->m_edgeNodes.clear();
}
for(int i = 0; i < m_element[m_expDim].size(); i++)
for (fit = m_faceSet.begin(); fit != m_faceSet.end(); fit++)
{
ElementSharedPtr el = m_element[m_expDim][i];
SpatialDomains::GeometrySharedPtr geom =
el->GetGeom(m_spaceDim);
geom->FillGeom();
volGeoms[el->GetId()] = geom;
faceCopies[(*fit)->m_id] = FaceSharedPtr(new Face(*(*fit)));
(*fit)->m_faceNodes.clear();
}
boost::unordered_set<int> processedEdges, processedFaces, processedVolumes;
......@@ -176,8 +169,8 @@ void Mesh::MakeOrder(int order,
{
if (m_verbose)
{
LibUtilities::PrintProgressbar(
ct, m_edgeSet.size(), "MakeOrder: Edges: ");
LibUtilities::PrintProgressbar(ct, m_edgeSet.size(),
"MakeOrder: Edges: ");
}
int edgeId = (*eit)->m_id;
......@@ -186,8 +179,12 @@ void Mesh::MakeOrder(int order,
continue;
}
(*eit)->MakeOrder(order, edgeGeoms[edgeId],
pTypes[LibUtilities::eSegment], m_spaceDim, id);
EdgeSharedPtr cpEdge = edgeCopies[edgeId];
SpatialDomains::GeometrySharedPtr geom = cpEdge->GetGeom(m_spaceDim);
geom->FillGeom();
(*eit)->MakeOrder(order, geom, pTypes[LibUtilities::eSegment],
m_spaceDim, id);
processedEdges.insert(edgeId);
}
......@@ -198,8 +195,8 @@ void Mesh::MakeOrder(int order,
{
if (m_verbose)
{
LibUtilities::PrintProgressbar(
ct, m_faceSet.size(), "MakeOrder: Faces: ");
LibUtilities::PrintProgressbar(ct, m_faceSet.size(),
"MakeOrder: Faces: ");
}
int faceId = (*fit)->m_id;
......@@ -208,10 +205,14 @@ void Mesh::MakeOrder(int order,
continue;
}
LibUtilities::ShapeType type = (*fit)->m_vertexList.size() == 3 ?
LibUtilities::eTriangle : LibUtilities::eQuadrilateral;
(*fit)->MakeOrder(order, faceGeoms[faceId], pTypes[type], m_spaceDim,
id);
FaceSharedPtr cpFace = faceCopies[faceId];
SpatialDomains::GeometrySharedPtr geom = cpFace->GetGeom(m_spaceDim);
geom->FillGeom();
LibUtilities::ShapeType type = (*fit)->m_vertexList.size() == 3
? LibUtilities::eTriangle
: LibUtilities::eQuadrilateral;
(*fit)->MakeOrder(order, geom, pTypes[type], m_spaceDim, id);
processedFaces.insert(faceId);
}
......@@ -219,7 +220,7 @@ void Mesh::MakeOrder(int order,
for (int i = 0; i < m_element[1].size(); ++i)
{
ElementSharedPtr el = m_element[1][i];
EdgeSharedPtr edge = el->GetEdgeLink();
EdgeSharedPtr edge = el->GetEdgeLink();
if (!edge)
{
......@@ -235,7 +236,7 @@ void Mesh::MakeOrder(int order,
for (int i = 0; i < m_element[2].size(); ++i)
{
ElementSharedPtr el = m_element[2][i];
FaceSharedPtr face = el->GetFaceLink();
FaceSharedPtr face = el->GetFaceLink();
if (!face)
{
......@@ -256,9 +257,10 @@ void Mesh::MakeOrder(int order,
{
LibUtilities::PrintProgressbar(i, nElmt, "MakeOrder: Elements: ");
}
ElementSharedPtr el = m_element[m_expDim][i];
el->MakeOrder(order, volGeoms[el->GetId()], pTypes[el->GetConf().m_e],
m_spaceDim, id);
ElementSharedPtr el = m_element[m_expDim][i];
SpatialDomains::GeometrySharedPtr geom = el->GetGeom(m_spaceDim);
geom->FillGeom();
el->MakeOrder(order, geom, pTypes[el->GetConf().m_e], m_spaceDim, id);
}
if (m_verbose)
......@@ -266,6 +268,5 @@ void Mesh::MakeOrder(int order,
cout << endl;
}
}
}
}
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