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Commit 4b560009 authored by Spencer Sherwin's avatar Spencer Sherwin
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Merge branch 'master' into fix/GetOffsetElmtId

parents e5fa5e00 9738e4ae
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CHANGELOG.md
View file @ 4b560009
......@@ -4,10 +4,13 @@ Changelog
v4.5.0
------
**NekMesh**:
- Add periodic boundary condition meshing in 2D (!733)
- Adjust boundary layer thickness in corners in 2D (!739)
**Library**
- Added in sum factorisation version for pyramid expansions and orthogonal
expansion in pyramids (!750)
**Documentation**:
- Added the developer-guide repository as a submodule (!751)
......@@ -16,6 +19,20 @@ v4.4.1
**Library**
- Remove m_offset_elmt_id and GetOffsetElmtId which fixed problems in 2D when
quad elements are listed before tri elements (!758)
- Remove the duplicate output of errorutil (!756)
- Fix interpolation issue with Lagrange basis functions (!768)
**FieldConvert**:
- Fix issue with FieldConvert when range flag used (!761)
**NekMesh**:
- Fix memory consumption issue with Gmsh output (!747, !762)
- 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)
**FieldConvert:**
- Fix issue with field ordering in the interppointdatatofld module (!754)
v4.4.0
------
......
docs/doxygen/Doxyfile.in
View file @ 4b560009
......@@ -757,6 +757,7 @@ INPUT = @CMAKE_SOURCE_DIR@/docs/doxygen/ \
@CMAKE_SOURCE_DIR@/library/LibUtilities/ \
@CMAKE_SOURCE_DIR@/library/StdRegions/ \
@CMAKE_SOURCE_DIR@/library/SpatialDomains/ \
@CMAKE_SOURCE_DIR@/library/Collections/ \
@CMAKE_SOURCE_DIR@/library/LocalRegions/ \
@CMAKE_SOURCE_DIR@/library/MultiRegions/ \
@CMAKE_SOURCE_DIR@/library/GlobalMapping/ \
......
library/Collections/BwdTrans.cpp
View file @ 4b560009
......@@ -918,7 +918,7 @@ class BwdTrans_SumFac_Prism : public Operator
{
Blas::Dgemm('N', 'N', m_nquad2, m_numElmt, m_nmodes2-i,
1.0, m_base2.get()+mode*m_nquad2, m_nquad2,
&input[0]+mode1, totmodes, 0.0,
input.get()+mode1, totmodes, 0.0,
&wsp[j*m_nquad2*m_numElmt*m_nmodes0+ cnt],
m_nquad2);
mode1 += m_nmodes2-i;
......@@ -1018,5 +1018,168 @@ OperatorKey BwdTrans_SumFac_Prism::m_type = GetOperatorFactory().
OperatorKey(ePrism, eBwdTrans, eSumFac,false),
BwdTrans_SumFac_Prism::create, "BwdTrans_SumFac_Prism");
/**
* @brief Backward transform operator using sum-factorisation (Pyr)
*/
class BwdTrans_SumFac_Pyr : public Operator
{
public:
OPERATOR_CREATE(BwdTrans_SumFac_Pyr)
virtual ~BwdTrans_SumFac_Pyr()
{
}
virtual void operator()(
const Array<OneD, const NekDouble> &input,
Array<OneD, NekDouble> &output,
Array<OneD, NekDouble> &output1,
Array<OneD, NekDouble> &output2,
Array<OneD, NekDouble> &wsp)
{
ASSERTL1(wsp.num_elements() == m_wspSize,
"Incorrect workspace size");
// Assign second half of workspace for 2nd DGEMM operation.
int totmodes = m_stdExp->GetNcoeffs();
Array<OneD, NekDouble> wsp2
= wsp + m_nmodes0*m_nmodes1*m_nquad2*m_numElmt;
Vmath::Zero(m_nmodes0*m_nmodes1*m_nquad2*m_numElmt, wsp, 1);
int i = 0;
int j = 0;
int mode = 0;
int mode1 = 0;
int cnt = 0;
for (i = 0; i < m_nmodes0; ++i)
{
for (j = 0; j < m_nmodes1; ++j, ++cnt)
{
int ijmax = max(i,j);
Blas::Dgemm('N', 'N', m_nquad2, m_numElmt, m_nmodes2-ijmax,
1.0, m_base2.get()+mode*m_nquad2, m_nquad2,
input.get()+mode1, totmodes, 0.0,
wsp.get() + cnt*m_nquad2*m_numElmt, m_nquad2);
mode += m_nmodes2-ijmax;
mode1 += m_nmodes2-ijmax;
}
//increment mode in case order1!=order2
for(j = m_nmodes1; j < m_nmodes2-i; ++j)
{
int ijmax = max(i,j);
mode += m_nmodes2-ijmax;
}
}
// vertex mode - currently (1+c)/2 x (1-b)/2 x (1-a)/2
// component is evaluated
if(m_sortTopVertex)
{
for(i = 0; i < m_numElmt; ++i)
{
// top singular vertex
// (1+c)/2 x (1+b)/2 x (1-a)/2 component
Blas::Daxpy(m_nquad2, input[1+i*totmodes],
m_base2.get() + m_nquad2, 1,
&wsp[m_nquad2*m_numElmt] + i*m_nquad2, 1);
// top singular vertex
// (1+c)/2 x (1-b)/2 x (1+a)/2 component
Blas::Daxpy(m_nquad2, input[1+i*totmodes],
m_base2.get() + m_nquad2, 1,
&wsp[m_nmodes1*m_nquad2*m_numElmt]
+ i*m_nquad2, 1);
// top singular vertex
// (1+c)/2 x (1+b)/2 x (1+a)/2 component
Blas::Daxpy(m_nquad2, input[1+i*totmodes],
m_base2.get() + m_nquad2, 1,
&wsp[(m_nmodes1+1)*m_nquad2*m_numElmt]
+ i*m_nquad2, 1);
}
}
// Perform summation over '1' direction
mode = 0;
for(i = 0; i < m_nmodes0; ++i)
{
Blas::Dgemm('N', 'T', m_nquad1, m_nquad2*m_numElmt, m_nmodes1,
1.0, m_base1.get(), m_nquad1,
wsp.get() + mode*m_nquad2*m_numElmt,
m_nquad2*m_numElmt,
0.0, wsp2.get() + i*m_nquad1*m_nquad2*m_numElmt,
m_nquad1);
mode += m_nmodes1;
}
// Perform summation over '0' direction
Blas::Dgemm('N', 'T', m_nquad0, m_nquad1*m_nquad2*m_numElmt,
m_nmodes0, 1.0, m_base0.get(), m_nquad0,
wsp2.get(), m_nquad1*m_nquad2*m_numElmt,
0.0, output.get(), m_nquad0);
}
virtual void operator()(
int dir,
const Array<OneD, const NekDouble> &input,
Array<OneD, NekDouble> &output,
Array<OneD, NekDouble> &wsp)
{
ASSERTL0(false, "Not valid for this operator.");
}
protected:
const int m_nquad0;
const int m_nquad1;
const int m_nquad2;
const int m_nmodes0;
const int m_nmodes1;
const int m_nmodes2;
Array<OneD, const NekDouble> m_base0;
Array<OneD, const NekDouble> m_base1;
Array<OneD, const NekDouble> m_base2;
bool m_sortTopVertex;
private:
BwdTrans_SumFac_Pyr(
vector<StdRegions::StdExpansionSharedPtr> pCollExp,
CoalescedGeomDataSharedPtr pGeomData)
: Operator (pCollExp, pGeomData),
m_nquad0 (m_stdExp->GetNumPoints(0)),
m_nquad1 (m_stdExp->GetNumPoints(1)),
m_nquad2 (m_stdExp->GetNumPoints(2)),
m_nmodes0 (m_stdExp->GetBasisNumModes(0)),
m_nmodes1 (m_stdExp->GetBasisNumModes(1)),
m_nmodes2 (m_stdExp->GetBasisNumModes(2)),
m_base0 (m_stdExp->GetBasis(0)->GetBdata()),
m_base1 (m_stdExp->GetBasis(1)->GetBdata()),
m_base2 (m_stdExp->GetBasis(2)->GetBdata())
{
m_wspSize = m_numElmt*m_nmodes0*m_nquad2*(m_nmodes1 + m_nquad1);
if(m_stdExp->GetBasis(0)->GetBasisType()
== LibUtilities::eModified_A)
{
m_sortTopVertex = true;
}
else
{
m_sortTopVertex = false;
}
}
};
/// Factory initialisation for the BwdTrans_SumFac_Pyr operator
OperatorKey BwdTrans_SumFac_Pyr::m_type = GetOperatorFactory().
RegisterCreatorFunction(
OperatorKey(ePyramid, eBwdTrans, eSumFac,false),
BwdTrans_SumFac_Pyr::create, "BwdTrans_SumFac_Pyr");
}
}
library/Collections/IProduct.cpp
View file @ 4b560009
......@@ -422,6 +422,101 @@ void PrismIProduct(bool sortTopVertex, int numElmt,
}
/**
*
*/
void PyrIProduct(bool sortTopVertex, int numElmt,
int nquad0, int nquad1, int nquad2,
int nmodes0, int nmodes1, int nmodes2,
const Array<OneD, const NekDouble> &base0,
const Array<OneD, const NekDouble> &base1,
const Array<OneD, const NekDouble> &base2,
const Array<OneD, const NekDouble> &jac,
const Array<OneD, const NekDouble> &input,
Array<OneD, NekDouble> &output,
Array<OneD, NekDouble> &wsp)
{
int totmodes = LibUtilities::StdPyrData::getNumberOfCoefficients(
nmodes0,nmodes1,nmodes2);
int totpoints = nquad0*nquad1*nquad2;
int cnt;
int mode, mode1;
ASSERTL1(wsp.num_elements() >= numElmt*(nquad1*nquad2*nmodes0 +
nquad2*max(nquad0*nquad1,nmodes0*nmodes1)),
"Insufficient workspace size");
Vmath::Vmul(numElmt*totpoints,jac,1,input,1,wsp,1);
Array<OneD, NekDouble> wsp1 = wsp + numElmt * nquad2
* (max(nquad0*nquad1,
nmodes0*nmodes1));
// Perform iproduct with respect to the '0' direction
Blas::Dgemm('T', 'N', nquad1*nquad2*numElmt, nmodes0, nquad0,
1.0, wsp.get(), nquad0, base0.get(),
nquad0, 0.0, wsp1.get(), nquad1*nquad2*numElmt);
// Inner product with respect to the '1' direction
mode = 0;
for(int i=0; i < nmodes0; ++i)
{
Blas::Dgemm('T', 'N', nquad2*numElmt, nmodes1, nquad1,
1.0, wsp1.get()+ i*nquad1*nquad2*numElmt, nquad1,
base1.get(), nquad1,
0.0, wsp.get() + mode*nquad2*numElmt,nquad2*numElmt);
mode += nmodes1;
}
// Inner product with respect to the '2' direction
mode = mode1 = cnt = 0;
for(int i = 0; i < nmodes0; ++i)
{
for(int j = 0; j < nmodes1; ++j, ++cnt)
{
int ijmax = max(i,j);
Blas::Dgemm('T', 'N', nmodes2-ijmax, numElmt, nquad2,
1.0, base2.get()+mode*nquad2, nquad2,
wsp.get()+cnt*nquad2*numElmt, nquad2,
0.0, output.get()+mode1, totmodes);
mode += nmodes2-ijmax;
mode1 += nmodes2-ijmax;
}
//increment mode in case order1!=order2
for(int j = nmodes1; j < nmodes2; ++j)
{
int ijmax = max(i,j);
mode += nmodes2-ijmax;
}
}
// fix for modified basis for top singular vertex component
// Already have evaluated (1+c)/2 (1-b)/2 (1-a)/2
if(sortTopVertex)
{
for(int n = 0; n < numElmt; ++n)
{
// add in (1+c)/2 (1+b)/2 component
output[1+n*totmodes] += Blas::Ddot(nquad2,
base2.get()+nquad2,1,
&wsp[nquad2*numElmt + n*nquad2],1);
// add in (1+c)/2 (1-b)/2 (1+a)/2 component
output[1+n*totmodes] += Blas::Ddot(nquad2,
base2.get()+nquad2,1,
&wsp[nquad2*nmodes1*numElmt+n*nquad2],1);
// add in (1+c)/2 (1+b)/2 (1+a)/2 component
output[1+n*totmodes] += Blas::Ddot(nquad2,
base2.get()+nquad2,1,
&wsp[nquad2*(nmodes1+1)*numElmt+n*nquad2],1);
}
}
}
/**
*
*/
......
library/Collections/IProduct.h
View file @ 4b560009
......@@ -82,6 +82,19 @@ void PrismIProduct(bool sortTopVert, int numElmt,
Array<OneD, NekDouble> &output,
Array<OneD, NekDouble> &wsp);
void PyrIProduct(bool sortTopVert, int numElmt,
int nquad0, int nquad1, int nquad2,
int nmodes0, int nmodes1, int nmodes2,
const Array<OneD, const NekDouble> &base0,
const Array<OneD, const NekDouble> &base1,
const Array<OneD, const NekDouble> &base2,
const Array<OneD, const NekDouble> &jac,
const Array<OneD, const NekDouble> &input,
Array<OneD, NekDouble> &output,
Array<OneD, NekDouble> &wsp);
void TetIProduct(bool sortTopEdge, int numElmt,
int nquad0, int nquad1, int nquad2,
int nmodes0, int nmodes1, int nmodes2,
......
library/Collections/IProductWRTBase.cpp
View file @ 4b560009
......@@ -586,7 +586,7 @@ OperatorKey IProductWRTBase_SumFac_Tri::m_type = GetOperatorFactory().
/**
* @brief Backward transform operator using sum-factorisation (Hex)
* @brief Inner Product operator using sum-factorisation (Hex)
*/
class IProductWRTBase_SumFac_Hex : public Operator
{
......@@ -765,7 +765,7 @@ OperatorKey IProductWRTBase_SumFac_Tet::m_type = GetOperatorFactory().
/**
* @brief Backward transform operator using sum-factorisation (Prism)
* @brief Inner Product operator using sum-factorisation (Prism)
*/
class IProductWRTBase_SumFac_Prism : public Operator
{
......@@ -856,5 +856,99 @@ OperatorKey IProductWRTBase_SumFac_Prism::m_type = GetOperatorFactory().
OperatorKey(ePrism, eIProductWRTBase, eSumFac,false),
IProductWRTBase_SumFac_Prism::create, "IProductWRTBase_SumFac_Prism");
/**
* @brief Inner Product operator using sum-factorisation (Pyr)
*/
class IProductWRTBase_SumFac_Pyr : public Operator
{
public:
OPERATOR_CREATE(IProductWRTBase_SumFac_Pyr)
virtual ~IProductWRTBase_SumFac_Pyr()
{
}
virtual void operator()(
const Array<OneD, const NekDouble> &input,
Array<OneD, NekDouble> &output,
Array<OneD, NekDouble> &output1,
Array<OneD, NekDouble> &output2,
Array<OneD, NekDouble> &wsp)
{
ASSERTL1(wsp.num_elements() == m_wspSize,
"Incorrect workspace size");
PyrIProduct(m_sortTopVertex, m_numElmt,
m_nquad0, m_nquad1, m_nquad2,
m_nmodes0, m_nmodes1, m_nmodes2,
m_base0, m_base1, m_base2,
m_jac,input,output,wsp);
}
virtual void operator()(
int dir,
const Array<OneD, const NekDouble> &input,
Array<OneD, NekDouble> &output,
Array<OneD, NekDouble> &wsp)
{
ASSERTL0(false, "Not valid for this operator.");
}
protected:
const int m_nquad0;
const int m_nquad1;
const int m_nquad2;
const int m_nmodes0;
const int m_nmodes1;
const int m_nmodes2;
Array<OneD, const NekDouble> m_jac;
Array<OneD, const NekDouble> m_base0;
Array<OneD, const NekDouble> m_base1;
Array<OneD, const NekDouble> m_base2;
bool m_sortTopVertex;
private:
IProductWRTBase_SumFac_Pyr(
vector<StdRegions::StdExpansionSharedPtr> pCollExp,
CoalescedGeomDataSharedPtr pGeomData)
: Operator (pCollExp, pGeomData),
m_nquad0 (m_stdExp->GetNumPoints(0)),
m_nquad1 (m_stdExp->GetNumPoints(1)),
m_nquad2 (m_stdExp->GetNumPoints(2)),
m_nmodes0 (m_stdExp->GetBasisNumModes(0)),
m_nmodes1 (m_stdExp->GetBasisNumModes(1)),
m_nmodes2 (m_stdExp->GetBasisNumModes(2)),
m_base0 (m_stdExp->GetBasis(0)->GetBdata()),
m_base1 (m_stdExp->GetBasis(1)->GetBdata()),
m_base2 (m_stdExp->GetBasis(2)->GetBdata())
{
m_jac = pGeomData->GetJacWithStdWeights(pCollExp);
m_wspSize = m_numElmt * m_nquad2
*(max(m_nquad0*m_nquad1,m_nmodes0*m_nmodes1))
+ m_nquad1*m_nquad2*m_numElmt*m_nmodes0;
if(m_stdExp->GetBasis(0)->GetBasisType()
== LibUtilities::eModified_A)
{
m_sortTopVertex = true;
}
else
{
m_sortTopVertex = false;
}
}
};
/// Factory initialisation for the IProductWRTBase_SumFac_Pyr operator
OperatorKey IProductWRTBase_SumFac_Pyr::m_type = GetOperatorFactory().
RegisterCreatorFunction(
OperatorKey(ePyramid, eIProductWRTBase, eSumFac,false),
IProductWRTBase_SumFac_Pyr::create, "IProductWRTBase_SumFac_Pyr");
}
}
library/Collections/PhysDeriv.cpp
View file @ 4b560009
......@@ -938,7 +938,7 @@ class PhysDeriv_SumFac_Hex : public Operator
Array<OneD, Array<OneD, NekDouble> > out(3);
out[0] = output0; out[1] = output1; out[2] = output2;
for(int i = 0; i < m_dim; ++i)
for(int i = 0; i < 3; ++i)
{
Diff[i] = wsp + i*ntot;
}
......@@ -967,10 +967,10 @@ class PhysDeriv_SumFac_Hex : public Operator
// calculate full derivative
for(int i = 0; i < m_coordim; ++i)
{
Vmath::Vmul(ntot,m_derivFac[i*m_dim],1,Diff[0],1,out[i],1);
for(int j = 1; j < m_dim; ++j)
Vmath::Vmul(ntot,m_derivFac[i*3],1,Diff[0],1,out[i],1);
for(int j = 1; j < 3; ++j)
{
Vmath::Vvtvp (ntot, m_derivFac[i*m_dim+j], 1,
Vmath::Vvtvp (ntot, m_derivFac[i*3+j], 1,
Diff[j], 1,
out[i], 1,
out[i], 1);
......@@ -989,7 +989,7 @@ class PhysDeriv_SumFac_Hex : public Operator
Array<OneD, NekDouble> tmp0,tmp1,tmp2;
Array<OneD, Array<OneD, NekDouble> > Diff(3);
for(int i = 0; i < m_dim; ++i)
for(int i = 0; i < 3; ++i)
{
Diff[i] = wsp + i*ntot;
}
......@@ -1016,10 +1016,10 @@ class PhysDeriv_SumFac_Hex : public Operator
}
// calculate full derivative
Vmath::Vmul(ntot,m_derivFac[dir*m_dim],1,Diff[0],1,output,1);
for(int j = 1; j < m_dim; ++j)
Vmath::Vmul(ntot,m_derivFac[dir*3],1,Diff[0],1,output,1);
for(int j = 1; j < 3; ++j)
{
Vmath::Vvtvp (ntot, m_derivFac[dir*m_dim+j], 1,
Vmath::Vvtvp (ntot, m_derivFac[dir*3+j], 1,
Diff[j], 1,
output, 1,
output, 1);
......@@ -1028,7 +1028,6 @@ class PhysDeriv_SumFac_Hex : public Operator
protected:
Array<TwoD, const NekDouble> m_derivFac;
int m_dim;
int m_coordim;
const int m_nquad0;
const int m_nquad1;
......@@ -1048,7 +1047,6 @@ class PhysDeriv_SumFac_Hex : public Operator
{
LibUtilities::PointsKeyVector PtsKey = m_stdExp->GetPointsKeys();
m_dim = PtsKey.size();
m_coordim = m_stdExp->GetCoordim();
m_derivFac = pGeomData->GetDerivFactors(pCollExp);
......@@ -1096,7 +1094,7 @@ class PhysDeriv_SumFac_Tet : public Operator
Array<OneD, Array<OneD, NekDouble> > out(3);
out[0] = output0; out[1] = output1; out[2] = output2;
for(int i = 0; i < m_dim; ++i)
for(int i = 0; i < 3; ++i)
{
Diff[i] = wsp + i*ntot;
}
......@@ -1161,10 +1159,10 @@ class PhysDeriv_SumFac_Tet : public Operator
// calculate full derivative
for(int i = 0; i < m_coordim; ++i)
{
Vmath::Vmul(ntot,m_derivFac[i*m_dim],1,Diff[0],1,out[i],1);
for(int j = 1; j < m_dim; ++j)
Vmath::Vmul(ntot,m_derivFac[i*3],1,Diff[0],1,out[i],1);
for(int j = 1; j < 3; ++j)
{
Vmath::Vvtvp (ntot, m_derivFac[i*m_dim+j], 1,
Vmath::Vvtvp (ntot, m_derivFac[i*3+j], 1,
Diff[j], 1, out[i], 1, out[i], 1);
}
}
......@@ -1181,7 +1179,7 @@ class PhysDeriv_SumFac_Tet : public Operator
Array<OneD, NekDouble> tmp0,tmp1,tmp2;
Array<OneD, Array<OneD, NekDouble> > Diff(3);
for(int i = 0; i < m_dim; ++i)
for(int i = 0; i < 3; ++i)
{
Diff[i] = wsp + i*ntot;
}
......@@ -1244,17 +1242,16 @@ class PhysDeriv_SumFac_Tet : public Operator
}
// calculate full derivative
Vmath::Vmul(ntot,m_derivFac[dir*m_dim],1,Diff[0],1,output,1);
for(int j = 1; j < m_dim; ++j)
Vmath::Vmul(ntot,m_derivFac[dir*3],1,Diff[0],1,output,1);
for(int j = 1; j < 3; ++j)
{
Vmath::Vvtvp (ntot, m_derivFac[dir*m_dim+j], 1,
Vmath::Vvtvp (ntot, m_derivFac[dir*3+j], 1,
Diff[j], 1, output, 1, output, 1);
}
}
protected:
Array<TwoD, const NekDouble> m_derivFac;
int m_dim;
int m_coordim;
const int m_nquad0;
const int m_nquad1;
......@@ -1278,7 +1275,6 @@ class PhysDeriv_SumFac_Tet : public Operator
{
LibUtilities::PointsKeyVector PtsKey = m_stdExp->GetPointsKeys();
m_dim = PtsKey.size();
m_coordim = m_stdExp->GetCoordim();
m_derivFac = pGeomData->GetDerivFactors(pCollExp);
......@@ -1358,7 +1354,7 @@ class PhysDeriv_SumFac_Prism : public Operator
Array<OneD, Array<OneD, NekDouble> > out(3);
out[0] = output0; out[1] = output1; out[2] = output2;
for(int i = 0; i < m_dim; ++i)
for(int i = 0; i < 3; ++i)