diff --git a/.gitignore b/.gitignore index 9f608ea048ac93738e263dd975216e5c9de79998..54b93cb4250605efc11db4977bec6aa791a6db8b 100644 --- a/.gitignore +++ b/.gitignore @@ -19,3 +19,5 @@ ThirdParty # Sublime project files *.sublime-project *.sublime-workspace +# CLion build directories +cmake-build-* diff --git a/CHANGELOG.md b/CHANGELOG.md index 9a821f4b9cff6f07ba95aa26c0617856264071f4..5096bef3149769f386eb30621ee1d7f8487eca06 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,19 @@ v5.3.0 - Added float and restore avx512 back-end for SimdLib (!1387) - Fix namespace pollution which causes boost 1.74+ errors (!1389) - Fix missing copy assignment operator warnings in clang 13+ (!1391) +- Add an integral filter for the time-evolution of integrals on composites, + supports dimension equal to or one lower than the mesh dimension (!1323) +- Overload PhysEvaluate to give first derivatives using barycentric + interpolation (!1323) +- Non-conformal interface support (!1323) + +**FieldConvert** +- Added conditional to select the eNearestNeighbour method for 3D interpolation (!1335) +- Fixed the output field names of WSS module of FieldConvert +- Added float to scalar and avx2 back-end, disable avx512, sse2, sve (!1255) +- Change MPI initialisation to allow MPI_Init call outside Nektar++ (!1376) +- Added float and restore avx512 back-end for SimdLib (!1387) +- Fix namespace pollution which causes boost 1.74+ errors (!1389) **Python** - Add wrappers for Interpreter and Equation classes (!1329) @@ -16,12 +29,12 @@ v5.3.0 - Added Laplacian (NonSmooth) AV to the explicit Navier Stokes solver (!1372) - Added Physical AV to the implicit Navier Stokes solver (!1372) - Fixed Segmentation Fault when using C0 Smoother with Shock Capturing (!1394) - -**CompressibleFlowSolver** - The Incomplete IP method was made the default method for the IP method (!1377). +- Add additional parameters for the Isentropic Vortex equation system (!1323) - Improve performance of the perconditioner and diffusion operator (!1393) **NekMesh** +- Multi domain input/output for Nekpp and HDF5 file formats (!1323) - Replace VTK pointers with VTK smart-pointers to avoid memory leaking, when exporting in .vtu format (!1386) - Preserve CAD face labels and save in to session file as a "NAME=" tag on the composites (!1396) diff --git a/cmake/ThirdPartyHDF5.cmake b/cmake/ThirdPartyHDF5.cmake index c062dd833495fc843370aaccf348aa3a4a7b4d05..6d53afadbd9d244d09d69426fd569001cf7b2d01 100644 --- a/cmake/ThirdPartyHDF5.cmake +++ b/cmake/ThirdPartyHDF5.cmake @@ -69,6 +69,12 @@ IF (NEKTAR_USE_HDF5) MESSAGE(STATUS "Found HDF5: ${HDF5_LIBRARIES}") SET(HDF5_CONFIG_INCLUDE_DIR ${HDF5_INCLUDE_DIRS}) ADD_CUSTOM_TARGET(hdf5-1.8.16 ALL) + + # Newer HDF5 versions have changed the API + # We compile deprecated symbols using the old API if newer than 1.10.0 + IF(HDF5_VERSION VERSION_GREATER_EQUAL 1.10.0) + ADD_DEFINITIONS(-DH5_USE_110_API) + ENDIF() ENDIF() MARK_AS_ADVANCED(HDF5_LIBRARIES) diff --git a/docs/user-guide/xml/xml-filters.tex b/docs/user-guide/xml/xml-filters.tex index 4faa16c0cc86d6caf2e688c1133961907d51b213..c93c3845842db46f41df567fee9028c7f4b05228 100644 --- a/docs/user-guide/xml/xml-filters.tex +++ b/docs/user-guide/xml/xml-filters.tex @@ -353,6 +353,8 @@ The following parameters are supported: Prefix of the output filename to which the errors are written.\\ \inltt{OutputFrequency} & \xmark & 1 & Number of timesteps after which output is written.\\ + \inltt{ConsoleOutput} & \xmark & 0 & + Also output error in the console when writing to file.\\ \bottomrule \end{tabularx} \end{center} @@ -363,6 +365,49 @@ An example syntax is given below: ErrorFile 10 + 1 + +\end{lstlisting} + +\subsection{Integral}\label{filters:Integral} + +This filter produces a file containing the time-evolution of the integral of +the solver variables on user defined composites. By default this file is called +\inltt{session.int} where \inltt{session} is the session name. + +The following parameters are supported: + +\begin{center} + \begin{tabularx}{0.99\textwidth}{lllX} + \toprule + \textbf{Option name} & \textbf{Required} & \textbf{Default} & + \textbf{Description} \\ + \midrule + \inltt{OutputFile} & \xmark & \inltt{session} & + Prefix of the output filename to which the integrals are written.\\ + \inltt{OutputFrequency} & \xmark & 1 & + Number of timesteps after which output is written.\\ + \inltt{OutputPrecision} & \xmark & 7 & + Decimal precision with which the output is written.\\ + \inltt{Composites} & \cmark & - & + Composites on which to calculate the integral.\\ + \bottomrule + \end{tabularx} +\end{center} + +Multiple composites can be defined together by using ranges with each composite +grouping producing a summed output for each variable in the \inltt{OutputFile}. +For example \inltt{C[1,3,5-7]} would produce a single integral output for each +variable whilst \inltt{C[1-3], C[4]} would produce two. + +An example syntax is given below: + +\begin{lstlisting}[style=XMLStyle,gobble=2] + + IntegralFile + 10 + 12 + C[1], C[2-4,6] \end{lstlisting} diff --git a/docs/user-guide/xml/xml-movement.tex b/docs/user-guide/xml/xml-movement.tex new file mode 100644 index 0000000000000000000000000000000000000000..6b11bb33fa28b3577ef76d460816395c41dd763e --- /dev/null +++ b/docs/user-guide/xml/xml-movement.tex @@ -0,0 +1,64 @@ +\section{Movement} +This section defines the movement of the mesh. Currently only static +non-conformal interfaces are supported. + +\subsection{Non-conformal meshes}\label{subsec:non-conformal-meshes} +Non-conformal meshes are defined using \inltt{ZONES} and \inltt{INTERFACES}. +Each zone is a domain as defined in the \inltt{GEOMETRY} section. For a mesh to +be non-conformal it must consist of at least two zones with different domain +tags. These two zones can then be split by an interface where every interface is +defined by two composite entities, we use \inltt{LEFT} and \inltt{RIGHT} +notation to distinguish between these. Each zone must contain either the left or +the right interface edge. Zones can contain multiple edges across different +interfaces but must not contain both edges for the same interface. These left +and right interface edges have to be geometrically identical but topologically +disconnected i.e.\ occupy the same space physically but consist of independent +geometry objects. + +Non-conformal interfaces are defined enclosed in the \inltt{NEKTAR} tag. An +example showing two non-conformal interfaces on a single mesh is below: + +\begin{lstlisting}[style=XMLStyle] + + + + + + + + + + + + + + + + + +\end{lstlisting} + +Zones must have a type specified, at the moment only `FIXED' interfaces are +supported however in the future there are plans to implement rotating, sliding, +and prescribed motion using the ALE method. It is important for the zone IDs to +correspond with the relevant interface IDs present on the zone, that is if there +is an interface with ID 0 there must also be a zone with ID 0 too. Zone IDs must +be unique but interfaces can have the same ID, e.g. in the example above zone ID +1 has two interfaces attached to it. The inclusion of an +\inltt{"INTERFACE NAME="..."} allows for specifying a name, which is used for +the debug output when the verbose flag `-v' is specified. This is for user +reference to ensure the non-conformal interfaces are set up correctly, and shows +zone/interface IDs, number of elements in each zone and interface, and +connections between each zone/interface. An example debug output for the above +XML is shown below: + +\begin{lstlisting} +Movement Info: + Num zones: 3 + - 0 Fixed: 8 Quadrilaterals + - 1 Fixed: 24 Quadrilaterals + - 2 Fixed: 4 Quadrilaterals + Num interfaces: 2 + - "First": 0 (4 Segments) <-> 1 (6 Segments) + - "Second": 1 (6 Segments) <-> 2 (2 Segments) +\end{lstlisting} \ No newline at end of file diff --git a/docs/user-guide/xml/xml.tex b/docs/user-guide/xml/xml.tex index 3f913bed3c89d7315aea521827ab62be2230839f..471fa45f4adb2fdc537a1cfb5b4fb2973ecb0458 100644 --- a/docs/user-guide/xml/xml.tex +++ b/docs/user-guide/xml/xml.tex @@ -77,3 +77,5 @@ files as illustrated below: \input{xml/xml-coupling.tex} \input{xml/xml-expressions.tex} + +\input{xml/xml-movement.tex} diff --git a/library/Demos/StdRegions/CMakeLists.txt b/library/Demos/StdRegions/CMakeLists.txt index 895c4a0400a5583f06ca4276ac9f8ecd00cec312..1c431ffbdd789918a0a749930fe65a033891322a 100644 --- a/library/Demos/StdRegions/CMakeLists.txt +++ b/library/Demos/StdRegions/CMakeLists.txt @@ -2,6 +2,8 @@ ADD_NEKTAR_EXECUTABLE(StdProject COMPONENT demos DEPENDS StdRegions SOURCES StdProject.cpp) ADD_NEKTAR_EXECUTABLE(StdInterp COMPONENT demos DEPENDS StdRegions SOURCES StdInterp.cpp) +ADD_NEKTAR_EXECUTABLE(StdInterpDeriv + COMPONENT demos DEPENDS StdRegions SOURCES StdInterpDeriv.cpp) ADD_NEKTAR_EXECUTABLE(StdInterpBasis COMPONENT demos DEPENDS StdRegions SOURCES StdInterpBasis.cpp) ADD_NEKTAR_EXECUTABLE(StdEquiToCoeff2D @@ -25,6 +27,26 @@ ADD_NEKTAR_TEST(StdInterpBasis_Tet_Mod_P4_Q5) ADD_NEKTAR_TEST(StdInterpBasis_Tri_Mod_P7_Q8) ADD_NEKTAR_TEST(StdInterpBasis_Hex_Mod_P7_Q8) ADD_NEKTAR_TEST(StdInterpBasis_Pyr_Mod_P7_Q8) +ADD_NEKTAR_TEST(StdInterpBasis_Tri_Orth_P7_Q8) + +# interpolation tests for derivatives. +ADD_NEKTAR_TEST(StdInterpDeriv_Seg_Lagrange_P7_Q8) +ADD_NEKTAR_TEST(StdInterpDeriv_Seg_Mod_P7_Q8) +ADD_NEKTAR_TEST(StdInterpDeriv_Seg_Orth_P7_Q8) +ADD_NEKTAR_TEST(StdInterpDeriv_Quad_Mod_P7_Q8) +ADD_NEKTAR_TEST(StdInterpDeriv_Quad_Orth_P7_Q8) +ADD_NEKTAR_TEST(StdInterpDeriv_Quad_Lagrange_P7_Q8) +ADD_NEKTAR_TEST(StdInterpDeriv_Tri_Mod_P7_Q8) +ADD_NEKTAR_TEST(StdInterpDeriv_Tri_Orth_P7_Q8) +ADD_NEKTAR_TEST(StdInterpDeriv_Pyr_Mod_P7_Q8) +ADD_NEKTAR_TEST(StdInterpDeriv_Pyr_Orth_P7_Q8) +ADD_NEKTAR_TEST(StdInterpDeriv_Prism_Mod_P7_Q8) +ADD_NEKTAR_TEST(StdInterpDeriv_Prism_Orth_P7_Q8) +ADD_NEKTAR_TEST(StdInterpDeriv_Hex_Mod_P7_Q8) +ADD_NEKTAR_TEST(StdInterpDeriv_Hex_Orth_P7_Q8) +ADD_NEKTAR_TEST(StdInterpDeriv_Hex_Lagrange_P7_Q8) +ADD_NEKTAR_TEST(StdInterpDeriv_Tet_Mod_P8_Q9) +ADD_NEKTAR_TEST(StdInterpDeriv_Tet_Orth_P8_Q9) # Projection tests. diff --git a/library/Demos/StdRegions/StdDemoSupport.hpp b/library/Demos/StdRegions/StdDemoSupport.hpp index 4f6aad7cacb885b684a8818af605fa59cd548b2a..882184d05a91b4ff979459525c06ec0a6c1474a4 100644 --- a/library/Demos/StdRegions/StdDemoSupport.hpp +++ b/library/Demos/StdRegions/StdDemoSupport.hpp @@ -435,6 +435,16 @@ public: return m_pointstype; } + std::vector &GetBasisType() + { + return m_basis; + } + + std::string &GetShape() + { + return m_shape; + } + Array> GetCoords(StdExpansion *E) { int dimension = E->GetShapeDimension(); diff --git a/library/Demos/StdRegions/StdInterpDeriv.cpp b/library/Demos/StdRegions/StdInterpDeriv.cpp new file mode 100644 index 0000000000000000000000000000000000000000..96da6440442465666dd64e94a29177d4ba76ebdd --- /dev/null +++ b/library/Demos/StdRegions/StdInterpDeriv.cpp @@ -0,0 +1,180 @@ +/////////////////////////////////////////////////////////////////////////////// +// +// File: StdInterpDeriv.cpp +// +// For more information, please see: http://www.nektar.info +// +// The MIT License +// +// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA), +// Department of Aeronautics, Imperial College London (UK), and Scientific +// Computing and Imaging Institute, University of Utah (USA). +// +// Permission is hereby granted, free of charge, to any person obtaining a +// copy of this software and associated documentation files (the "Software"), +// to deal in the Software without restriction, including without limitation +// the rights to use, copy, modify, merge, publish, distribute, sublicense, +// and/or sell copies of the Software, and to permit persons to whom the +// Software is furnished to do so, subject to the following conditions: +// +// The above copyright notice and this permission notice shall be included +// in all copies or substantial portions of the Software. +// +// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +// DEALINGS IN THE SOFTWARE. +// +// Description: Demo for testing functionality of PhysEvaluateDeriv +// +/////////////////////////////////////////////////////////////////////////////// + +#include +#include + +#include "StdDemoSupport.hpp" + +// polynomial = 4x^4 + 3y^3 + 2z^2 + 1 +Array EvalPoly( + const Array> &pts) +{ + Array ret(pts[0].size()); + unsigned dim = pts.size(); + for (int i = 0; i < pts[0].size(); i++) + { + ret[i] = (4 * pts[0][i] * pts[0][i] * pts[0][i] * pts[0][i]) + + (dim >= 2 ? (3 * pts[1][i] * pts[1][i] * pts[1][i]) : 0.0) + + (dim >= 3 ? (2 * pts[2][i] * pts[2][i]) : 0.0) + 1; + } + + return ret; +} + +// derivative in x = 16x^3 +Array EvalPolyDerivx( + const Array> &pts) +{ + Array ret(pts[0].size()); + for (int i = 0; i < pts[0].size(); i++) + { + ret[i] = 16 * pts[0][i] * pts[0][i] * pts[0][i]; + } + + return ret; +} + +// derivative in y = 9y^2 +Array EvalPolyDerivy( + const Array> &pts) +{ + Array ret(pts[0].size()); + for (int i = 0; i < pts[0].size(); i++) + { + ret[i] = 9 * pts[1][i] * pts[1][i]; + } + + return ret; +} + +// derivative in z = 4z +Array EvalPolyDerivz( + const Array> &pts) +{ + Array ret(pts[0].size()); + for (int i = 0; i < pts[0].size(); i++) + { + ret[i] = 4 * pts[2][i]; + } + + return ret; +} + +int main(int argc, char *argv[]) +{ + DemoSupport demo; + demo.ParseArguments(argc, argv); + StdExpansion *E = demo.CreateStdExpansion(); + + const auto dimension = (unsigned)E->GetShapeDimension(); + + const auto totPoints = (unsigned)E->GetTotPoints(); + Array physIn(totPoints, 0.0), physOut(totPoints, 0.0), + sol(totPoints, 0.0), sol0(totPoints, 0.0), sol1(totPoints, 0.0), + sol2(totPoints, 0.0); + + Array> physOutDeriv(totPoints); + + Array> coordsE = demo.GetCoords(E); + physIn = EvalPoly(coordsE); + + // Create a new element but with GaussGaussChebyshev points so that we + // perform a PhysEvaluateDeriv at a different set of nodal points + // (i.e. non-collocated interpolation), all tests use default types + // initially + vector &ptypes = demo.GetPointsType(); + for (int i = 0; i < dimension; ++i) + { + ptypes[i] = "PolyEvenlySpaced"; + } + + StdExpansion *F = demo.CreateStdExpansion(); + const Array> coordsF = demo.GetCoords(F); + + for (int i = 0; i < totPoints; ++i) + { + // Fill coords array + Array coordIn(dimension, 0.0); + for (int j = 0; j < dimension; ++j) + { + coordIn[j] = coordsF[j][i]; + } + + // Operating on expansion E so using physIn from E, and coordIn from F + physOut[i] = E->PhysEvaluate(coordIn, physIn, physOutDeriv[i]); + } + + // Extract derivatives in to array for error calculation + Array physOut0(totPoints, 0.0), physOut1(totPoints, 0.0), + physOut2(totPoints, 0.0); + switch (dimension) + { + case 3: + for (int j = 0; j < totPoints; ++j) + { + physOut2[j] = physOutDeriv[j][2]; + } + sol2 = EvalPolyDerivz(coordsF); + /* fall through */ + case 2: + for (int j = 0; j < totPoints; ++j) + { + physOut1[j] = physOutDeriv[j][1]; + } + sol1 = EvalPolyDerivy(coordsF); + /* fall through */ + case 1: + for (int j = 0; j < totPoints; ++j) + { + physOut0[j] = physOutDeriv[j][0]; + } + sol0 = EvalPolyDerivx(coordsF); + /* fall through */ + default: + sol = EvalPoly(coordsF); + break; + } + + cout << "\nL infinity error: " << scientific + << E->Linf(physOut, sol) + E->Linf(physOut0, sol0) + + E->Linf(physOut1, sol1) + E->Linf(physOut2, sol2) + << endl; + cout << "L 2 error : " << scientific + << E->L2(physOut, sol) + E->L2(physOut0, sol0) + + E->L2(physOut1, sol1) + E->L2(physOut2, sol2) + << endl; + + return 0; +} diff --git a/library/Demos/StdRegions/Tests/StdInterpBasis_Pyr_Mod_P7_Q8.tst b/library/Demos/StdRegions/Tests/StdInterpBasis_Pyr_Mod_P7_Q8.tst index a7a9775bd491b98ccee1aee526a79c015e9b0d35..65450b5158d325a2ee0ca19a067f6d73ae5108a1 100644 --- a/library/Demos/StdRegions/Tests/StdInterpBasis_Pyr_Mod_P7_Q8.tst +++ b/library/Demos/StdRegions/Tests/StdInterpBasis_Pyr_Mod_P7_Q8.tst @@ -1,6 +1,6 @@ - StdInterpBasis Triangle Modified basis P=7 Q=8 + StdInterpBasis Pyramid Modified basis P=7 Q=8 StdInterpBasis -s pyramid -b Modified_A Modified_A ModifiedPyr_C -o 7 7 7 -p 8 8 8 diff --git a/library/Demos/StdRegions/Tests/StdInterpBasis_Tri_Orth_P7_Q8.tst b/library/Demos/StdRegions/Tests/StdInterpBasis_Tri_Orth_P7_Q8.tst new file mode 100644 index 0000000000000000000000000000000000000000..768c389df41c319e0d15b0bfe8ec7aeac7b2c048 --- /dev/null +++ b/library/Demos/StdRegions/Tests/StdInterpBasis_Tri_Orth_P7_Q8.tst @@ -0,0 +1,14 @@ + + + StdInterpBasis Triangle Ortho basis P=7 Q=8 + StdInterpBasis + -s triangle -b Ortho_A Ortho_B -o 7 7 -p 8 8 + + + 0 + + + 0 + + + diff --git a/library/Demos/StdRegions/Tests/StdInterpDeriv_Hex_Lagrange_P7_Q8.tst b/library/Demos/StdRegions/Tests/StdInterpDeriv_Hex_Lagrange_P7_Q8.tst new file mode 100644 index 0000000000000000000000000000000000000000..424c123d9d47bde4c4e5438fd23a3a0e65a12a22 --- /dev/null +++ b/library/Demos/StdRegions/Tests/StdInterpDeriv_Hex_Lagrange_P7_Q8.tst @@ -0,0 +1,14 @@ + + + StdInterpDeriv Hex Lagrange basis P=7 Q=8 + StdInterpDeriv + -s hexahedron -b GLL_Lagrange GLL_Lagrange GLL_Lagrange -o 7 7 7 -p 8 8 8 -P GaussLobattoLegendre GaussLobattoLegendre GaussLobattoLegendre + + + 0 + + + 0 + + + \ No newline at end of file diff --git a/library/Demos/StdRegions/Tests/StdInterpDeriv_Hex_Mod_P7_Q8.tst b/library/Demos/StdRegions/Tests/StdInterpDeriv_Hex_Mod_P7_Q8.tst new file mode 100644 index 0000000000000000000000000000000000000000..c7818794ed4856128df3219fbb5fc973ccb441bf --- /dev/null +++ b/library/Demos/StdRegions/Tests/StdInterpDeriv_Hex_Mod_P7_Q8.tst @@ -0,0 +1,14 @@ + + + StdInterpDeriv Hex Mod basis P=7 Q=8 + StdInterpDeriv + -s hexahedron -b Modified_A Modified_A Modified_A -o 7 7 7 -p 8 8 8 -P GaussLobattoLegendre GaussLobattoLegendre GaussLobattoLegendre + + + 0 + + + 0 + + + \ No newline at end of file diff --git a/library/Demos/StdRegions/Tests/StdInterpDeriv_Hex_Orth_P7_Q8.tst b/library/Demos/StdRegions/Tests/StdInterpDeriv_Hex_Orth_P7_Q8.tst new file mode 100644 index 0000000000000000000000000000000000000000..2e48201a0115ff44e7ef7720c86ad7cc9cc7fb21 --- /dev/null +++ b/library/Demos/StdRegions/Tests/StdInterpDeriv_Hex_Orth_P7_Q8.tst @@ -0,0 +1,14 @@ + + + StdInterpDeriv Hex Ortho basis P=7 Q=8 + StdInterpDeriv + -s hexahedron -b Ortho_A Ortho_A Ortho_A -o 7 7 7 -p 8 8 8 -P GaussLobattoLegendre GaussLobattoLegendre GaussLobattoLegendre + + + 0 + + + 0 + + + \ No newline at end of file diff --git a/library/Demos/StdRegions/Tests/StdInterpDeriv_Prism_Mod_P7_Q8.tst b/library/Demos/StdRegions/Tests/StdInterpDeriv_Prism_Mod_P7_Q8.tst new file mode 100644 index 0000000000000000000000000000000000000000..e9359ba26b2508b71bd8267dfcdefae4b3460c69 --- /dev/null +++ b/library/Demos/StdRegions/Tests/StdInterpDeriv_Prism_Mod_P7_Q8.tst @@ -0,0 +1,14 @@ + + + StdInterpDeriv Prism Mod basis P=7 Q=8 + StdInterpDeriv + -s prism -b Modified_A Modified_A Modified_B -o 7 7 7 -p 8 8 8 -P GaussLobattoLegendre GaussLobattoLegendre GaussRadauMAlpha1Beta0 + + + 0 + + + 0 + + + \ No newline at end of file diff --git a/library/Demos/StdRegions/Tests/StdInterpDeriv_Prism_Orth_P7_Q8.tst b/library/Demos/StdRegions/Tests/StdInterpDeriv_Prism_Orth_P7_Q8.tst new file mode 100644 index 0000000000000000000000000000000000000000..af1142f10d52ab0067dfb92612d233c5becf73d8 --- /dev/null +++ b/library/Demos/StdRegions/Tests/StdInterpDeriv_Prism_Orth_P7_Q8.tst @@ -0,0 +1,14 @@ + + + StdInterpDeriv Prism Ortho basis P=7 Q=8 + StdInterpDeriv + -s prism -b Ortho_A Ortho_A Ortho_B -o 7 7 7 -p 8 8 8 -P GaussLobattoLegendre GaussLobattoLegendre GaussRadauMAlpha1Beta0 + + + 0 + + + 0 + + + \ No newline at end of file diff --git a/library/Demos/StdRegions/Tests/StdInterpDeriv_Pyr_Mod_P7_Q8.tst b/library/Demos/StdRegions/Tests/StdInterpDeriv_Pyr_Mod_P7_Q8.tst new file mode 100644 index 0000000000000000000000000000000000000000..1fd9820aad10e282b65d6d5235729daed576ef70 --- /dev/null +++ b/library/Demos/StdRegions/Tests/StdInterpDeriv_Pyr_Mod_P7_Q8.tst @@ -0,0 +1,14 @@ + + + StdInterpDeriv Pyr Mod basis P=7 Q=8 + StdInterpDeriv + -s pyramid -b Modified_A Modified_A ModifiedPyr_C -o 7 7 7 -p 8 8 8 -P GaussLobattoLegendre GaussLobattoLegendre GaussRadauMAlpha2Beta0 + + + 0 + + + 0 + + + \ No newline at end of file diff --git a/library/Demos/StdRegions/Tests/StdInterpDeriv_Pyr_Orth_P7_Q8.tst b/library/Demos/StdRegions/Tests/StdInterpDeriv_Pyr_Orth_P7_Q8.tst new file mode 100644 index 0000000000000000000000000000000000000000..1d2fad7f2bb82f7585300fac0792cc0bedec99b1 --- /dev/null +++ b/library/Demos/StdRegions/Tests/StdInterpDeriv_Pyr_Orth_P7_Q8.tst @@ -0,0 +1,14 @@ + + + StdInterpDeriv Pyramid Ortho basis P=7 Q=8 + StdInterpDeriv + -s pyramid -b Ortho_A Ortho_A OrthoPyr_C -o 7 7 7 -p 8 8 8 -P GaussLobattoLegendre GaussLobattoLegendre GaussRadauMAlpha2Beta0 + + + 0 + + + 0 + + + \ No newline at end of file diff --git a/library/Demos/StdRegions/Tests/StdInterpDeriv_Quad_Lagrange_P7_Q8.tst b/library/Demos/StdRegions/Tests/StdInterpDeriv_Quad_Lagrange_P7_Q8.tst new file mode 100644 index 0000000000000000000000000000000000000000..b84886cba12e80ebe854c971b9736944fd9a0cb1 --- /dev/null +++ b/library/Demos/StdRegions/Tests/StdInterpDeriv_Quad_Lagrange_P7_Q8.tst @@ -0,0 +1,14 @@ + + + StdInterpDeriv Quadrilateral Lagrange basis P=7 Q=8 + StdInterpDeriv + -s quadrilateral -b GLL_Lagrange GLL_Lagrange -o 7 7 -p 8 8 -P GaussLobattoLegendre GaussLobattoLegendre + + + 0 + + + 0 + + + \ No newline at end of file diff --git a/library/Demos/StdRegions/Tests/StdInterpDeriv_Quad_Mod_P7_Q8.tst b/library/Demos/StdRegions/Tests/StdInterpDeriv_Quad_Mod_P7_Q8.tst new file mode 100644 index 0000000000000000000000000000000000000000..f65efc0a9d584de9b369c9d1d72d38b6b06a3eb7 --- /dev/null +++ b/library/Demos/StdRegions/Tests/StdInterpDeriv_Quad_Mod_P7_Q8.tst @@ -0,0 +1,14 @@ + + + StdInterpDeriv Quadrilateral Modified basis P=7 Q=8 + StdInterpDeriv + -s quadrilateral -b Modified_A Modified_A -o 7 7 -p 8 8 -P GaussLobattoLegendre GaussLobattoLegendre + + + 0 + + + 0 + + + \ No newline at end of file diff --git a/library/Demos/StdRegions/Tests/StdInterpDeriv_Quad_Orth_P7_Q8.tst b/library/Demos/StdRegions/Tests/StdInterpDeriv_Quad_Orth_P7_Q8.tst new file mode 100644 index 0000000000000000000000000000000000000000..bb6c7c165d49ddb093e76f64c6a7636d08a0f706 --- /dev/null +++ b/library/Demos/StdRegions/Tests/StdInterpDeriv_Quad_Orth_P7_Q8.tst @@ -0,0 +1,14 @@ + + + StdInterpDeriv Quadrilateral Orth basis P=7 Q=8 + StdInterpDeriv + -s quadrilateral -b Ortho_A Ortho_A -o 7 7 -p 8 8 -P GaussLobattoLegendre GaussLobattoLegendre + + + 0 + + + 0 + + + \ No newline at end of file diff --git a/library/Demos/StdRegions/Tests/StdInterpDeriv_Seg_Lagrange_P7_Q8.tst b/library/Demos/StdRegions/Tests/StdInterpDeriv_Seg_Lagrange_P7_Q8.tst new file mode 100644 index 0000000000000000000000000000000000000000..4845a2c94da78c8b47389b38279bd2e411d8da43 --- /dev/null +++ b/library/Demos/StdRegions/Tests/StdInterpDeriv_Seg_Lagrange_P7_Q8.tst @@ -0,0 +1,14 @@ + + + StdInterpDeriv Seg Lagrange basis P=7 Q=8 + StdInterpDeriv + -s segment -b GLL_Lagrange -o 7 -p 8 -P GaussLobattoLegendre + + + 0 + + + 0 + + + \ No newline at end of file diff --git a/library/Demos/StdRegions/Tests/StdInterpDeriv_Seg_Mod_P7_Q8.tst b/library/Demos/StdRegions/Tests/StdInterpDeriv_Seg_Mod_P7_Q8.tst new file mode 100644 index 0000000000000000000000000000000000000000..a30b5982b7ce0bdcf9a412db0a9d5c968f2716b6 --- /dev/null +++ b/library/Demos/StdRegions/Tests/StdInterpDeriv_Seg_Mod_P7_Q8.tst @@ -0,0 +1,14 @@ + + + StdInterpDeriv Seg Mod basis P=7 Q=8 + StdInterpDeriv + -s segment -b Modified_A -o 7 -p 8 -P GaussLobattoLegendre + + + 0 + + + 0 + + + \ No newline at end of file diff --git a/library/Demos/StdRegions/Tests/StdInterpDeriv_Seg_Orth_P7_Q8.tst b/library/Demos/StdRegions/Tests/StdInterpDeriv_Seg_Orth_P7_Q8.tst new file mode 100644 index 0000000000000000000000000000000000000000..90e2aed0634cd4788c8093ecd4ca7ed3b2023d52 --- /dev/null +++ b/library/Demos/StdRegions/Tests/StdInterpDeriv_Seg_Orth_P7_Q8.tst @@ -0,0 +1,14 @@ + + + StdInterpDeriv Seg Orth basis P=7 Q=8 + StdInterpDeriv + -s segment -b Ortho_A -o 7 -p 8 -P GaussLobattoLegendre + + + 0 + + + 0 + + + \ No newline at end of file diff --git a/library/Demos/StdRegions/Tests/StdInterpDeriv_Tet_Mod_P8_Q9.tst b/library/Demos/StdRegions/Tests/StdInterpDeriv_Tet_Mod_P8_Q9.tst new file mode 100644 index 0000000000000000000000000000000000000000..7fe69f0ea1b832c165ee0573029b21ea8a4c6c6f --- /dev/null +++ b/library/Demos/StdRegions/Tests/StdInterpDeriv_Tet_Mod_P8_Q9.tst @@ -0,0 +1,14 @@ + + + StdInterpDeriv Tet Mod basis P=8 Q=9 + StdInterpDeriv + -s tetrahedron -b Modified_A Modified_B Modified_C -o 8 8 8 -p 9 9 9 -P GaussLobattoLegendre GaussRadauMAlpha1Beta0 GaussRadauMAlpha2Beta0 + + + 0 + + + 0 + + + \ No newline at end of file diff --git a/library/Demos/StdRegions/Tests/StdInterpDeriv_Tet_Orth_P8_Q9.tst b/library/Demos/StdRegions/Tests/StdInterpDeriv_Tet_Orth_P8_Q9.tst new file mode 100644 index 0000000000000000000000000000000000000000..43227919b8114bc81813597e01f4afa15cf1ec59 --- /dev/null +++ b/library/Demos/StdRegions/Tests/StdInterpDeriv_Tet_Orth_P8_Q9.tst @@ -0,0 +1,14 @@ + + + StdInterpDeriv Tet Orth basis P=8 Q=9 + StdInterpDeriv + -s tetrahedron -b Ortho_A Ortho_B Ortho_C -o 8 8 8 -p 9 9 9 -P GaussLobattoLegendre GaussRadauMAlpha1Beta0 GaussRadauMAlpha2Beta0 + + + 0 + + + 0 + + + \ No newline at end of file diff --git a/library/Demos/StdRegions/Tests/StdInterpDeriv_Tri_Mod_P7_Q8.tst b/library/Demos/StdRegions/Tests/StdInterpDeriv_Tri_Mod_P7_Q8.tst new file mode 100644 index 0000000000000000000000000000000000000000..bd187def1a1c6a644732c7ecadc00b41a65ab3c9 --- /dev/null +++ b/library/Demos/StdRegions/Tests/StdInterpDeriv_Tri_Mod_P7_Q8.tst @@ -0,0 +1,14 @@ + + + StdInterpDeriv Tri Modified basis P=7 Q=8 + StdInterpDeriv + -s triangle -b Modified_A Modified_B -o 7 7 -p 8 8 -P GaussLobattoLegendre GaussRadauMAlpha1Beta0 + + + 0 + + + 0 + + + diff --git a/library/Demos/StdRegions/Tests/StdInterpDeriv_Tri_Orth_P7_Q8.tst b/library/Demos/StdRegions/Tests/StdInterpDeriv_Tri_Orth_P7_Q8.tst new file mode 100644 index 0000000000000000000000000000000000000000..8701632b79276250a797738991b28bc7711c9c3d --- /dev/null +++ b/library/Demos/StdRegions/Tests/StdInterpDeriv_Tri_Orth_P7_Q8.tst @@ -0,0 +1,14 @@ + + + StdInterpDeriv Tri Ortho basis P=7 Q=8 + StdInterpDeriv + -s triangle -b Ortho_A Ortho_B -o 7 7 -p 8 8 -P GaussLobattoLegendre GaussRadauMAlpha1Beta0 + + + 0 + + + 0 + + + \ No newline at end of file diff --git a/library/FieldUtils/OutputModules/OutputVtk.cpp b/library/FieldUtils/OutputModules/OutputVtk.cpp index 57215bc6e02e863ed6af0ebde0757160bac46d6c..8e53c34614e0e11f2a7b9f8f3daa521e12df8f99 100644 --- a/library/FieldUtils/OutputModules/OutputVtk.cpp +++ b/library/FieldUtils/OutputModules/OutputVtk.cpp @@ -1605,6 +1605,22 @@ void OutputVtk::OutputFromPts(po::variables_map &vm) void OutputVtk::OutputFromExp(po::variables_map &vm) { + // Move geometry based on zones data in .xml and time in .fld metadatamap + // Perform movement of zones based on time in field files metadata map + if (m_f->m_graph->GetMovement()->GetMoveFlag()) + { + if (!m_f->m_fieldMetaDataMap["Time"].empty()) + { + m_f->m_graph->GetMovement()->PerformMovement( + boost::lexical_cast( + m_f->m_fieldMetaDataMap["Time"])); + for (auto &i : m_f->m_exp) + { + i->Reset(); + } + } + } + if (m_config["legacy"].m_beenSet) { ASSERTL0(!m_config["multiblock"].m_beenSet, @@ -1623,8 +1639,11 @@ void OutputVtk::OutputFromExp(po::variables_map &vm) // Save mesh state (if using filter this allows us to only ProcessEquispaced // if needed) - m_cachedMesh = m_vtkMesh; - + if (!m_f->m_graph->GetMovement()->GetMoveFlag()) + { + m_cachedMesh = m_vtkMesh; + } + if (m_config["highorder"].m_beenSet) { ASSERTL0(!m_config["multiblock"].m_beenSet, diff --git a/library/FieldUtils/OutputModules/OutputVtk.h b/library/FieldUtils/OutputModules/OutputVtk.h index b75c7c7706ac64ee33e1bfe7b422f265387b55ae..dc0a5577117fe17b7e7aa5055a8d360dae55e784 100644 --- a/library/FieldUtils/OutputModules/OutputVtk.h +++ b/library/FieldUtils/OutputModules/OutputVtk.h @@ -90,6 +90,8 @@ protected: /// Flag if mesh has been cached bool m_cachedMesh = false; + std::string PrepareOutput(po::variables_map &vm); + private: /// Prepare high order Lagrange VTK output vtkSmartPointer OutputFromExpHighOrder( diff --git a/library/LibUtilities/BasicConst/NektarUnivConsts.hpp b/library/LibUtilities/BasicConst/NektarUnivConsts.hpp index e606427cd9c2a73a14533cb80730d9e57943d1bb..23485a0784205219373f2cc78a82594028fdb030 100644 --- a/library/LibUtilities/BasicConst/NektarUnivConsts.hpp +++ b/library/LibUtilities/BasicConst/NektarUnivConsts.hpp @@ -62,6 +62,10 @@ static const NekDouble CoinTol = 1E-6; // Factor for tolerance for floating point comparison static const unsigned int kNekFloatCompFact = 4; + +// Constants for minimisation functions +static const NekDouble kFindDistanceMin = 5e-05; +static const unsigned int kNewtonIterations = 51; } // namespace NekConstants } // namespace Nektar diff --git a/library/LibUtilities/BasicUtils/FieldIO.h b/library/LibUtilities/BasicUtils/FieldIO.h index 43b7a86452aa52c015a0a263b48a25e09f37a6ec..b0aec9a601af9f5b8cc406c658dc10aa7ff92484 100644 --- a/library/LibUtilities/BasicUtils/FieldIO.h +++ b/library/LibUtilities/BasicUtils/FieldIO.h @@ -256,6 +256,10 @@ public: LIB_UTILITIES_EXPORT static void AddInfoTag( TagWriterSharedPtr root, const FieldMetaDataMap &fieldmetadatamap); + LIB_UTILITIES_EXPORT std::string SetUpOutput(const std::string outname, + bool perRank, + bool backup = false); + protected: /// Communicator to use when writing parallel format LibUtilities::CommSharedPtr m_comm; @@ -273,10 +277,6 @@ protected: return "fld"; } - LIB_UTILITIES_EXPORT std::string SetUpOutput(const std::string outname, - bool perRank, - bool backup = false); - /// @copydoc FieldIO::Write LIB_UTILITIES_EXPORT virtual void v_Write( const std::string &outFile, diff --git a/library/LibUtilities/BasicUtils/VmathArray.hpp b/library/LibUtilities/BasicUtils/VmathArray.hpp index d2d332a1b0efe2a7a81223d5d30bce671f47576d..ab55408255ab1753a423644ba8c025e4926ae3df 100644 --- a/library/LibUtilities/BasicUtils/VmathArray.hpp +++ b/library/LibUtilities/BasicUtils/VmathArray.hpp @@ -358,7 +358,7 @@ void Vvtvm(int n, const Array &w, const int incw, #endif } -/// \brief vvtvvtp (vector times vector plus vector times vector): z = v*w + y*z +/// \brief vvtvvtp (vector times vector plus vector times vector): z = v*w + x*y template void Vvtvvtp(int n, const Array &v, int incv, const Array &w, int incw, @@ -384,6 +384,24 @@ void Vvtvvtp(int n, const Array &v, int incv, #endif } +/// \brief vvtvvtm (vector times vector minus vector times vector): z = v*w - +/// x*y +template +void Vvtvvtm(int n, const Array &v, int incv, + const Array &w, int incw, + const Array &x, int incx, + const Array &y, int incy, Array &z, + int incz) +{ + ASSERTL1(n * incv <= v.size() + v.GetOffset(), "Array out of bounds"); + ASSERTL1(n * incw <= w.size() + w.GetOffset(), "Array out of bounds"); + ASSERTL1(n * incx <= x.size() + x.GetOffset(), "Array out of bounds"); + ASSERTL1(n * incy <= y.size() + y.GetOffset(), "Array out of bounds"); + ASSERTL1(n * incz <= z.size() + z.GetOffset(), "Array out of bounds"); + + Vvtvvtm(n, &v[0], incv, &w[0], incw, &x[0], incx, &y[0], incy, &z[0], incz); +} + /// \brief svtsvtp (scalar times vector plus scalar times vector): z = alpha*x + /// beta*y template diff --git a/library/LibUtilities/Communication/Comm.h b/library/LibUtilities/Communication/Comm.h index 7ec0b32911ba6787315a5a190e229835b0a7d303..86c64d5571dd058fedae3baeab5928b92ff2da52 100644 --- a/library/LibUtilities/Communication/Comm.h +++ b/library/LibUtilities/Communication/Comm.h @@ -145,6 +145,9 @@ public: void Irsend(int pProc, T &pData, int count, const CommRequestSharedPtr &request, int loc); template + void Isend(int pProc, T &pData, int count, + const CommRequestSharedPtr &request, int loc); + template void SendInit(int pProc, T &pData, int count, const CommRequestSharedPtr &request, int loc); template @@ -235,6 +238,8 @@ protected: virtual void v_Irsend(void *buf, int count, CommDataType dt, int dest, CommRequestSharedPtr request, int loc) = 0; + virtual void v_Isend(void *buf, int count, CommDataType dt, int dest, + CommRequestSharedPtr request, int loc) = 0; virtual void v_SendInit(void *buf, int count, CommDataType dt, int dest, CommRequestSharedPtr request, int loc) = 0; virtual void v_Irecv(void *buf, int count, CommDataType dt, int source, @@ -600,6 +605,23 @@ void Comm::Irsend(int pProc, T &pData, int count, CommDataTypeTraits::GetDataType(), pProc, request, loc); } +/** + * Starts a nonblocking send + * + * @param pProc Rank of destination + * @param pData Array/vector to send + * @param count Number of elements to send in pData + * @param request Communication request object + * @param loc Location in request to use + */ +template +void Comm::Isend(int pProc, T &pData, int count, + const CommRequestSharedPtr &request, int loc) +{ + v_Isend(CommDataTypeTraits::GetPointer(pData), count, + CommDataTypeTraits::GetDataType(), pProc, request, loc); +} + /** * Creates a persistent request for a send * diff --git a/library/LibUtilities/Communication/CommMpi.cpp b/library/LibUtilities/Communication/CommMpi.cpp index bc93c2bf2b9b93acc1ddc7f7a378d653147a0b27..8080e6dc8f5bdf449357483725fa82643b1c6123 100644 --- a/library/LibUtilities/Communication/CommMpi.cpp +++ b/library/LibUtilities/Communication/CommMpi.cpp @@ -416,6 +416,14 @@ void CommMpi::v_Irsend(void *buf, int count, CommDataType dt, int dest, MPI_Irsend(buf, count, dt, dest, 0, m_comm, req->GetRequest(loc)); } +void CommMpi::v_Isend(void *buf, int count, CommDataType dt, int dest, + CommRequestSharedPtr request, int loc) +{ + CommRequestMpiSharedPtr req = + std::static_pointer_cast(request); + MPI_Isend(buf, count, dt, dest, 0, m_comm, req->GetRequest(loc)); +} + void CommMpi::v_SendInit(void *buf, int count, CommDataType dt, int dest, CommRequestSharedPtr request, int loc) { @@ -444,14 +452,21 @@ void CommMpi::v_StartAll(CommRequestSharedPtr request) { CommRequestMpiSharedPtr req = std::static_pointer_cast(request); - MPI_Startall(req->GetNumRequest(), req->GetRequest(0)); + if (req->GetNumRequest() != 0) + { + MPI_Startall(req->GetNumRequest(), req->GetRequest(0)); + } } void CommMpi::v_WaitAll(CommRequestSharedPtr request) { CommRequestMpiSharedPtr req = std::static_pointer_cast(request); - MPI_Waitall(req->GetNumRequest(), req->GetRequest(0), MPI_STATUSES_IGNORE); + if (req->GetNumRequest() != 0) + { + MPI_Waitall(req->GetNumRequest(), req->GetRequest(0), + MPI_STATUSES_IGNORE); + } } CommRequestSharedPtr CommMpi::v_CreateRequest(int num) diff --git a/library/LibUtilities/Communication/CommMpi.h b/library/LibUtilities/Communication/CommMpi.h index 111da7a91fb133ad78d6973a0e28d44df1132540..f86e62241961d566f04d5fb4a14c938b4224b8bf 100644 --- a/library/LibUtilities/Communication/CommMpi.h +++ b/library/LibUtilities/Communication/CommMpi.h @@ -168,6 +168,8 @@ protected: CommDataType recvtype) final; virtual void v_Irsend(void *buf, int count, CommDataType dt, int dest, CommRequestSharedPtr request, int loc) final; + virtual void v_Isend(void *buf, int count, CommDataType dt, int dest, + CommRequestSharedPtr request, int loc) final; virtual void v_SendInit(void *buf, int count, CommDataType dt, int dest, CommRequestSharedPtr request, int loc) final; virtual void v_Irecv(void *buf, int count, CommDataType dt, int source, diff --git a/library/LibUtilities/Communication/CommSerial.cpp b/library/LibUtilities/Communication/CommSerial.cpp index e4e3f8a8e6a8754eca1b5a6b573acdb26deda4ed..550ec304a5f209c02ddad74aadd35f1b4e024274 100644 --- a/library/LibUtilities/Communication/CommSerial.cpp +++ b/library/LibUtilities/Communication/CommSerial.cpp @@ -255,6 +255,12 @@ void CommSerial::v_Irsend(void *buf, int count, CommDataType dt, int dest, boost::ignore_unused(buf, count, dt, dest, request, loc); } +void CommSerial::v_Isend(void *buf, int count, CommDataType dt, int dest, + CommRequestSharedPtr request, int loc) +{ + boost::ignore_unused(buf, count, dt, dest, request, loc); +} + void CommSerial::v_SendInit(void *buf, int count, CommDataType dt, int dest, CommRequestSharedPtr request, int loc) { diff --git a/library/LibUtilities/Communication/CommSerial.h b/library/LibUtilities/Communication/CommSerial.h index 6adec3774146ac832986100c5cf3d945766dee45..9823319cc7c03d224f16a6bd455ec378801ad14b 100644 --- a/library/LibUtilities/Communication/CommSerial.h +++ b/library/LibUtilities/Communication/CommSerial.h @@ -137,6 +137,11 @@ protected: CommRequestSharedPtr request, int loc) final; + LIB_UTILITIES_EXPORT virtual void v_Isend(void *buf, int count, + CommDataType dt, int dest, + CommRequestSharedPtr request, + int loc) final; + LIB_UTILITIES_EXPORT virtual void v_SendInit(void *buf, int count, CommDataType dt, int dest, CommRequestSharedPtr request, diff --git a/library/LocalRegions/HexExp.cpp b/library/LocalRegions/HexExp.cpp index de07729da56983cce29ec5ac7b0c75b8b95b71a1..f72bd3251a5f2f298fc67da6ec80a23ae56d2269 100644 --- a/library/LocalRegions/HexExp.cpp +++ b/library/LocalRegions/HexExp.cpp @@ -86,13 +86,6 @@ HexExp::HexExp(const HexExp &T) { } -/** - * \brief Destructor - */ -HexExp::~HexExp() -{ -} - //----------------------------- // Integration Methods //----------------------------- @@ -410,7 +403,7 @@ void HexExp::v_IProductWRTDerivBase(const int dir, const Array &inarray, Array &outarray) { - HexExp::IProductWRTDerivBase_SumFac(dir, inarray, outarray); + HexExp::v_IProductWRTDerivBase_SumFac(dir, inarray, outarray); } /** @@ -433,7 +426,7 @@ void HexExp::v_IProductWRTDerivBase(const int dir, * @param inarray The function \f$ u \f$. * @param outarray Value of the inner product. */ -void HexExp::IProductWRTDerivBase_SumFac( +void HexExp::v_IProductWRTDerivBase_SumFac( const int dir, const Array &inarray, Array &outarray) { @@ -559,7 +552,7 @@ void HexExp::IProductWRTDerivBase_MatOp( * @param inarray The function \f$ u \f$. * @param outarray Value of the inner product. */ -void HexExp::IProductWRTDirectionalDerivBase_SumFac( +void HexExp::v_IProductWRTDirectionalDerivBase_SumFac( const Array &direction, const Array &inarray, Array &outarray) @@ -623,7 +616,7 @@ NekDouble HexExp::v_StdPhysEvaluate( const Array &physvals) { // Evaluate point in local coordinates. - return StdHexExp::v_PhysEvaluate(Lcoord, physvals); + return StdExpansion3D::v_PhysEvaluate(Lcoord, physvals); } NekDouble HexExp::v_PhysEvaluate(const Array &coord, @@ -633,7 +626,17 @@ NekDouble HexExp::v_PhysEvaluate(const Array &coord, ASSERTL0(m_geom, "m_geom not defined"); m_geom->GetLocCoords(coord, Lcoord); - return StdHexExp::v_PhysEvaluate(Lcoord, physvals); + return StdExpansion3D::v_PhysEvaluate(Lcoord, physvals); +} + +NekDouble HexExp::v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) +{ + Array Lcoord(3); + ASSERTL0(m_geom, "m_geom not defined"); + m_geom->GetLocCoords(coord, Lcoord); + return StdHexExp::v_PhysEvaluate(Lcoord, inarray, firstOrderDerivs); } StdRegions::StdExpansionSharedPtr HexExp::v_GetStdExp(void) const diff --git a/library/LocalRegions/HexExp.h b/library/LocalRegions/HexExp.h index e6265174ecbd99e69cda679fee384e2b4664ea31..320665ad61eaa7ea80d534ab8156fa8be2586b02 100644 --- a/library/LocalRegions/HexExp.h +++ b/library/LocalRegions/HexExp.h @@ -45,20 +45,10 @@ namespace Nektar { -namespace SpatialDomains -{ -class HexGeom; -typedef std::shared_ptr HexGeomSharedPtr; -} // namespace SpatialDomains - namespace LocalRegions { -class HexExp; - -typedef std::shared_ptr HexExpSharedPtr; -typedef std::vector HexExpVector; - -class HexExp : virtual public StdRegions::StdHexExp, virtual public Expansion3D +class HexExp final : virtual public StdRegions::StdHexExp, + virtual public Expansion3D { public: LOCAL_REGIONS_EXPORT HexExp(const LibUtilities::BasisKey &Ba, @@ -68,61 +58,61 @@ public: LOCAL_REGIONS_EXPORT HexExp(const HexExp &T); - LOCAL_REGIONS_EXPORT ~HexExp(); + LOCAL_REGIONS_EXPORT ~HexExp() final = default; protected: //------------------------------ // Integration Method //------------------------------ - LOCAL_REGIONS_EXPORT virtual NekDouble v_Integral( - const Array &inarray); + LOCAL_REGIONS_EXPORT NekDouble + v_Integral(const Array &inarray) final; //----------------------------- // Differentiation Methods //----------------------------- - LOCAL_REGIONS_EXPORT virtual void v_PhysDeriv( + LOCAL_REGIONS_EXPORT void v_PhysDeriv( const Array &inarray, Array &out_d0, Array &out_d1, - Array &out_d2); + Array &out_d2) final; - LOCAL_REGIONS_EXPORT virtual void v_PhysDeriv( - const int dir, const Array &inarray, - Array &outarray); + LOCAL_REGIONS_EXPORT void v_PhysDeriv( + int dir, const Array &inarray, + Array &outarray) final; LOCAL_REGIONS_EXPORT void v_PhysDirectionalDeriv( const Array &inarray, const Array &direction, - Array &out); + Array &out) final; //--------------------------------------- // Transforms //--------------------------------------- - LOCAL_REGIONS_EXPORT virtual void v_FwdTrans( + LOCAL_REGIONS_EXPORT void v_FwdTrans( const Array &inarray, - Array &outarray); + Array &outarray) final; //--------------------------------------- // Inner product functions //--------------------------------------- - LOCAL_REGIONS_EXPORT virtual void v_IProductWRTBase( + LOCAL_REGIONS_EXPORT void v_IProductWRTBase( const Array &inarray, - Array &outarray); + Array &outarray) final; - LOCAL_REGIONS_EXPORT virtual void v_IProductWRTBase_SumFac( + LOCAL_REGIONS_EXPORT void v_IProductWRTBase_SumFac( const Array &inarray, - Array &outarray, bool multiplybyweights = true); + Array &outarray, bool multiplybyweights = true) final; - LOCAL_REGIONS_EXPORT virtual void v_IProductWRTDerivBase( + LOCAL_REGIONS_EXPORT void v_IProductWRTDerivBase( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) final; - LOCAL_REGIONS_EXPORT void IProductWRTDerivBase_SumFac( + LOCAL_REGIONS_EXPORT void v_IProductWRTDerivBase_SumFac( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) final; - LOCAL_REGIONS_EXPORT virtual void v_AlignVectorToCollapsedDir( + LOCAL_REGIONS_EXPORT void v_AlignVectorToCollapsedDir( const int dir, const Array &inarray, - Array> &outarray); + Array> &outarray) final; LOCAL_REGIONS_EXPORT void IProductWRTDerivBase_MatOp( const int dir, const Array &inarray, @@ -136,113 +126,130 @@ protected: IProductWRTDirectionalDerivBase_SumFac(direction, inarray, outarray); } - LOCAL_REGIONS_EXPORT void IProductWRTDirectionalDerivBase_SumFac( + LOCAL_REGIONS_EXPORT void v_IProductWRTDirectionalDerivBase_SumFac( const Array &direction, const Array &inarray, - Array &outarray); + Array &outarray) final; //--------------------------------------- // Evaluation functions //--------------------------------------- - LOCAL_REGIONS_EXPORT virtual NekDouble v_StdPhysEvaluate( - const Array &Lcoord, - const Array &physvals); + LOCAL_REGIONS_EXPORT NekDouble + v_StdPhysEvaluate(const Array &Lcoord, + const Array &physvals) final; + + LOCAL_REGIONS_EXPORT NekDouble + v_PhysEvaluate(const Array &coords, + const Array &physvals) final; - LOCAL_REGIONS_EXPORT virtual NekDouble v_PhysEvaluate( - const Array &coords, - const Array &physvals); + STD_REGIONS_EXPORT NekDouble + v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) final; - LOCAL_REGIONS_EXPORT virtual void v_GetCoord( + LOCAL_REGIONS_EXPORT void v_GetCoord( const Array &Lcoords, - Array &coords); + Array &coords) final; - LOCAL_REGIONS_EXPORT virtual void v_GetCoords( + LOCAL_REGIONS_EXPORT void v_GetCoords( Array &coords_1, Array &coords_2, - Array &coords_3); + Array &coords_3) final; //--------------------------------------- // Helper functions //--------------------------------------- - LOCAL_REGIONS_EXPORT virtual LibUtilities::ShapeType v_DetShapeType() const; + LOCAL_REGIONS_EXPORT + LibUtilities::ShapeType v_DetShapeType() const final; - LOCAL_REGIONS_EXPORT virtual StdRegions::StdExpansionSharedPtr v_GetStdExp( - void) const; + LOCAL_REGIONS_EXPORT + StdRegions::StdExpansionSharedPtr v_GetStdExp(void) const final; - LOCAL_REGIONS_EXPORT virtual StdRegions::StdExpansionSharedPtr v_GetLinStdExp( - void) const; + LOCAL_REGIONS_EXPORT + StdRegions::StdExpansionSharedPtr v_GetLinStdExp(void) const final; - LOCAL_REGIONS_EXPORT virtual void v_ExtractDataToCoeffs( + LOCAL_REGIONS_EXPORT void v_ExtractDataToCoeffs( const NekDouble *data, const std::vector &nummodes, const int mode_offset, NekDouble *coeffs, - std::vector &fromType); + std::vector &fromType) final; - LOCAL_REGIONS_EXPORT virtual bool v_GetFaceDGForwards(const int i) const; + LOCAL_REGIONS_EXPORT bool v_GetFaceDGForwards(const int i) const; - LOCAL_REGIONS_EXPORT virtual void v_GetTracePhysMap( - const int face, Array &outarray); + LOCAL_REGIONS_EXPORT void v_GetTracePhysMap( + const int face, Array &outarray) final; - LOCAL_REGIONS_EXPORT void v_ComputeTraceNormal(const int face); + LOCAL_REGIONS_EXPORT void v_ComputeTraceNormal(const int face) final; //--------------------------------------- // Operator creation functions //--------------------------------------- - LOCAL_REGIONS_EXPORT virtual void v_MassMatrixOp( + LOCAL_REGIONS_EXPORT void v_MassMatrixOp( const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); + Array &outarray, + const StdRegions::StdMatrixKey &mkey) final; - LOCAL_REGIONS_EXPORT virtual void v_LaplacianMatrixOp( + LOCAL_REGIONS_EXPORT void v_LaplacianMatrixOp( const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); + Array &outarray, + const StdRegions::StdMatrixKey &mkey) final; - LOCAL_REGIONS_EXPORT virtual void v_LaplacianMatrixOp( + LOCAL_REGIONS_EXPORT void v_LaplacianMatrixOp( const int k1, const int k2, const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); + Array &outarray, + const StdRegions::StdMatrixKey &mkey) final; - LOCAL_REGIONS_EXPORT virtual void v_WeakDerivMatrixOp( + LOCAL_REGIONS_EXPORT void v_WeakDerivMatrixOp( const int i, const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); + Array &outarray, + const StdRegions::StdMatrixKey &mkey) final; - LOCAL_REGIONS_EXPORT virtual void v_WeakDirectionalDerivMatrixOp( + LOCAL_REGIONS_EXPORT void v_WeakDirectionalDerivMatrixOp( const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); + Array &outarray, + const StdRegions::StdMatrixKey &mkey) final; - LOCAL_REGIONS_EXPORT virtual void v_MassLevelCurvatureMatrixOp( + LOCAL_REGIONS_EXPORT void v_MassLevelCurvatureMatrixOp( const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); + Array &outarray, + const StdRegions::StdMatrixKey &mkey) final; - LOCAL_REGIONS_EXPORT virtual void v_HelmholtzMatrixOp( + LOCAL_REGIONS_EXPORT void v_HelmholtzMatrixOp( const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); + Array &outarray, + const StdRegions::StdMatrixKey &mkey) final; LOCAL_REGIONS_EXPORT void v_GeneralMatrixOp_MatOp( const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); + Array &outarray, + const StdRegions::StdMatrixKey &mkey) final; - LOCAL_REGIONS_EXPORT virtual void v_ReduceOrderCoeffs( + LOCAL_REGIONS_EXPORT void v_ReduceOrderCoeffs( int numMin, const Array &inarray, - Array &outarray); + Array &outarray) final; - LOCAL_REGIONS_EXPORT virtual void v_SVVLaplacianFilter( - Array &array, const StdRegions::StdMatrixKey &mkey); + LOCAL_REGIONS_EXPORT void v_SVVLaplacianFilter( + Array &array, + const StdRegions::StdMatrixKey &mkey) final; //--------------------------------------- // Matrix creation functions //--------------------------------------- - LOCAL_REGIONS_EXPORT virtual DNekMatSharedPtr v_GenMatrix( - const StdRegions::StdMatrixKey &mkey); + LOCAL_REGIONS_EXPORT DNekMatSharedPtr + v_GenMatrix(const StdRegions::StdMatrixKey &mkey) final; - LOCAL_REGIONS_EXPORT virtual DNekMatSharedPtr v_CreateStdMatrix( - const StdRegions::StdMatrixKey &mkey); + LOCAL_REGIONS_EXPORT DNekMatSharedPtr + v_CreateStdMatrix(const StdRegions::StdMatrixKey &mkey) final; - LOCAL_REGIONS_EXPORT virtual DNekScalMatSharedPtr v_GetLocMatrix( - const MatrixKey &mkey); + LOCAL_REGIONS_EXPORT DNekScalMatSharedPtr + v_GetLocMatrix(const MatrixKey &mkey) final; - LOCAL_REGIONS_EXPORT virtual DNekScalBlkMatSharedPtr v_GetLocStaticCondMatrix( - const MatrixKey &mkey); + LOCAL_REGIONS_EXPORT + DNekScalBlkMatSharedPtr v_GetLocStaticCondMatrix( + const MatrixKey &mkey) final; - LOCAL_REGIONS_EXPORT void v_DropLocStaticCondMatrix(const MatrixKey &mkey); + LOCAL_REGIONS_EXPORT void v_DropLocStaticCondMatrix( + const MatrixKey &mkey) final; - LOCAL_REGIONS_EXPORT virtual void v_ComputeLaplacianMetric(); + LOCAL_REGIONS_EXPORT void v_ComputeLaplacianMetric() final; private: LibUtilities::NekManager @@ -250,18 +257,18 @@ private: LibUtilities::NekManager m_staticCondMatrixManager; - HexExp(); - - virtual void v_LaplacianMatrixOp_MatFree_Kernel( + void v_LaplacianMatrixOp_MatFree_Kernel( const Array &inarray, - Array &outarray, Array &wsp); + Array &outarray, Array &wsp) final; - virtual void v_NormalTraceDerivFactors( + void v_NormalTraceDerivFactors( Array> &factors, Array> &d0factors, - Array> &d1factors); + Array> &d1factors) final; }; +typedef std::shared_ptr HexExpSharedPtr; +typedef std::vector HexExpVector; } // namespace LocalRegions } // namespace Nektar diff --git a/library/LocalRegions/NodalTetExp.h b/library/LocalRegions/NodalTetExp.h index d31c044a36ddef5097ab3c9a03f0f822ad6df7bd..4bfecbac719b4f3c9ec1e00d69bdd523b4a4e540 100644 --- a/library/LocalRegions/NodalTetExp.h +++ b/library/LocalRegions/NodalTetExp.h @@ -44,7 +44,7 @@ namespace Nektar namespace LocalRegions { -class NodalTetExp : public TetExp +class NodalTetExp final : virtual public TetExp { // public: // NodalTetExp(const StdRegions::Basis &Ba, const StdRegions::Basis @@ -68,7 +68,7 @@ class NodalTetExp : public TetExp LOCAL_REGIONS_EXPORT NodalTetExp(const NodalTetExp &T); /// Destructor - LOCAL_REGIONS_EXPORT ~NodalTetExp(); + LOCAL_REGIONS_EXPORT ~NodalTetExp() final = default; protected: private: diff --git a/library/LocalRegions/NodalTriExp.cpp b/library/LocalRegions/NodalTriExp.cpp index 048d833dd5d448d4a9d208e691d714d46e566296..6020e1959dbf4588ad1769cbd5d529b46cde1bbf 100644 --- a/library/LocalRegions/NodalTriExp.cpp +++ b/library/LocalRegions/NodalTriExp.cpp @@ -62,16 +62,14 @@ NodalTriExp::NodalTriExp(const LibUtilities::BasisKey &Ba, } NodalTriExp::NodalTriExp(const NodalTriExp &T) - : StdExpansion(T), StdExpansion2D(T), StdRegions::StdNodalTriExp(T), + : StdExpansion(T), + StdExpansion2D(T), StdRegions::StdTriExp(T), StdRegions::StdNodalTriExp( + T), Expansion(T), Expansion2D(T), m_matrixManager(T.m_matrixManager), m_staticCondMatrixManager(T.m_staticCondMatrixManager) { } -NodalTriExp::~NodalTriExp() -{ -} - //---------------------------- // Integration Methods //---------------------------- @@ -459,7 +457,18 @@ NekDouble NodalTriExp::PhysEvaluate( ASSERTL0(m_geom, "m_geom not defined"); m_geom->GetLocCoords(coord, Lcoord); - return StdNodalTriExp::v_PhysEvaluate(Lcoord, physvals); + return StdExpansion2D::v_PhysEvaluate(Lcoord, physvals); +} + +NekDouble NodalTriExp::v_PhysEvaluate( + const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) +{ + Array Lcoord(2); + ASSERTL0(m_geom, "m_geom not defined"); + m_geom->GetLocCoords(coord, Lcoord); + return StdExpansion2D::v_PhysEvaluate(Lcoord, inarray, firstOrderDerivs); } StdRegions::StdExpansionSharedPtr NodalTriExp::v_GetStdExp(void) const diff --git a/library/LocalRegions/NodalTriExp.h b/library/LocalRegions/NodalTriExp.h index ba76368ab5e2c9ffc6aa945a3edc3453a9ad0bd1..1b54489b8b7f8f3dd2c97a695917dcbd55519da0 100644 --- a/library/LocalRegions/NodalTriExp.h +++ b/library/LocalRegions/NodalTriExp.h @@ -49,8 +49,8 @@ namespace Nektar namespace LocalRegions { -class NodalTriExp : virtual public StdRegions::StdNodalTriExp, - virtual public Expansion2D +class NodalTriExp final : virtual public StdRegions::StdNodalTriExp, + virtual public Expansion2D { public: /** \brief Constructor using BasisKey class for quadrature @@ -64,7 +64,7 @@ public: LOCAL_REGIONS_EXPORT NodalTriExp(const NodalTriExp &T); /// Destructor - LOCAL_REGIONS_EXPORT ~NodalTriExp(); + LOCAL_REGIONS_EXPORT ~NodalTriExp() final = default; LOCAL_REGIONS_EXPORT void GetCoords( Array &coords_1, Array &coords_2, @@ -127,6 +127,11 @@ public: StdExpansion::MassMatrixOp_MatFree(inarray, outarray, mkey); } + LOCAL_REGIONS_EXPORT NekDouble + v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) final; + void LaplacianMatrixOp(const Array &inarray, Array &outarray, const StdRegions::StdMatrixKey &mkey) @@ -180,11 +185,11 @@ protected: Array &outarray, const StdRegions::StdMatrixKey &mkey); - virtual StdRegions::StdExpansionSharedPtr v_GetStdExp(void) const; + StdRegions::StdExpansionSharedPtr v_GetStdExp(void) const final; - virtual StdRegions::StdExpansionSharedPtr v_GetLinStdExp(void) const; + StdRegions::StdExpansionSharedPtr v_GetLinStdExp(void) const final; - virtual DNekMatSharedPtr v_GenMatrix(const StdRegions::StdMatrixKey &mkey); + DNekMatSharedPtr v_GenMatrix(const StdRegions::StdMatrixKey &mkey) final; private: LibUtilities::NekManager @@ -202,16 +207,16 @@ private: return StdNodalTriExp::GenNBasisTransMatrix(); } - virtual void v_GetCoords( + void v_GetCoords( Array &coords_0, Array &coords_1 = NullNekDouble1DArray, - Array &coords_2 = NullNekDouble1DArray) + Array &coords_2 = NullNekDouble1DArray) final { GetCoords(coords_0, coords_1, coords_2); } - virtual void v_GetCoord(const Array &lcoord, - Array &coord) + void v_GetCoord(const Array &lcoord, + Array &coord) final { GetCoord(lcoord, coord); } @@ -224,45 +229,44 @@ private: /** \brief Virtual call to integrate the physical point list \a inarray over region (see SegExp::Integral) */ - virtual NekDouble v_Integral(const Array &inarray) + NekDouble v_Integral(const Array &inarray) final { return Integral(inarray); } /** \brief Virtual call to TriExp::IProduct_WRT_B */ - virtual void v_IProductWRTBase(const Array &inarray, - Array &outarray) + void v_IProductWRTBase(const Array &inarray, + Array &outarray) final { IProductWRTBase(inarray, outarray); } - virtual void v_IProductWRTDerivBase( - const int dir, const Array &inarray, - Array &outarray) + void v_IProductWRTDerivBase(const int dir, + const Array &inarray, + Array &outarray) final { IProductWRTDerivBase(dir, inarray, outarray); } - virtual void v_StdPhysDeriv( + void v_StdPhysDeriv( const Array &inarray, Array &out_d0, Array &out_d1, - Array &out_d2 = NullNekDouble1DArray) + Array &out_d2 = NullNekDouble1DArray) final { StdTriExp::v_PhysDeriv(inarray, out_d0, out_d1, out_d2); } - virtual void v_PhysDeriv( + void v_PhysDeriv( const Array &inarray, Array &out_d0, Array &out_d1, - Array &out_d2 = NullNekDouble1DArray) + Array &out_d2 = NullNekDouble1DArray) final { boost::ignore_unused(out_d2); PhysDeriv(inarray, out_d0, out_d1); } - virtual void v_PhysDeriv(const int dir, - const Array &inarray, - Array &outarray) + void v_PhysDeriv(const int dir, const Array &inarray, + Array &outarray) final { Array tmp; switch (dir) @@ -286,28 +290,27 @@ private: } /// Virtual call to SegExp::FwdTrans - virtual void v_FwdTrans(const Array &inarray, - Array &outarray) + void v_FwdTrans(const Array &inarray, + Array &outarray) final { FwdTrans(inarray, outarray); } /// Virtual call to TriExp::Evaluate - virtual NekDouble v_PhysEvaluate( - const Array &coord, - const Array &physvals) + NekDouble v_PhysEvaluate(const Array &coord, + const Array &physvals) final { return PhysEvaluate(coord, physvals); } - virtual DNekMatSharedPtr v_CreateStdMatrix( - const StdRegions::StdMatrixKey &mkey) + DNekMatSharedPtr v_CreateStdMatrix( + const StdRegions::StdMatrixKey &mkey) final { return CreateStdMatrix(mkey); } - virtual DNekScalMatSharedPtr v_GetLocMatrix(const MatrixKey &mkey) + DNekScalMatSharedPtr v_GetLocMatrix(const MatrixKey &mkey) final { return m_matrixManager[mkey]; } @@ -321,73 +324,75 @@ private: // m_matrixManager[mkey]; // } - virtual DNekScalBlkMatSharedPtr v_GetLocStaticCondMatrix( - const MatrixKey &mkey) + DNekScalBlkMatSharedPtr v_GetLocStaticCondMatrix( + const MatrixKey &mkey) final { return m_staticCondMatrixManager[mkey]; } - virtual void v_BwdTrans_SumFac(const Array &inarray, - Array &outarray) + void v_BwdTrans_SumFac(const Array &inarray, + Array &outarray) final { StdNodalTriExp::v_BwdTrans_SumFac(inarray, outarray); } - virtual void v_IProductWRTBase_SumFac( - const Array &inarray, - Array &outarray, bool multiplybyweights = true) + void v_IProductWRTBase_SumFac(const Array &inarray, + Array &outarray, + bool multiplybyweights = true) final { boost::ignore_unused(multiplybyweights); IProductWRTBase_SumFac(inarray, outarray); } - virtual void v_IProductWRTDerivBase_SumFac( + void v_IProductWRTDerivBase_SumFac( const int dir, const Array &inarray, - Array &outarray) + Array &outarray) final { IProductWRTDerivBase_SumFac(dir, inarray, outarray); } - virtual void v_AlignVectorToCollapsedDir( + void v_AlignVectorToCollapsedDir( const int dir, const Array &inarray, - Array> &outarray); + Array> &outarray) final; - virtual void v_MassMatrixOp(const Array &inarray, - Array &outarray, - const StdRegions::StdMatrixKey &mkey) + void v_MassMatrixOp(const Array &inarray, + Array &outarray, + const StdRegions::StdMatrixKey &mkey) final { MassMatrixOp(inarray, outarray, mkey); } - virtual void v_LaplacianMatrixOp( - const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey) + void v_LaplacianMatrixOp(const Array &inarray, + Array &outarray, + const StdRegions::StdMatrixKey &mkey) final { LaplacianMatrixOp(inarray, outarray, mkey); } - virtual void v_LaplacianMatrixOp( - const int k1, const int k2, const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey) + void v_LaplacianMatrixOp(const int k1, const int k2, + const Array &inarray, + Array &outarray, + const StdRegions::StdMatrixKey &mkey) final { LaplacianMatrixOp(k1, k2, inarray, outarray, mkey); } - virtual void v_WeakDerivMatrixOp( - const int i, const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey) + void v_WeakDerivMatrixOp(const int i, + const Array &inarray, + Array &outarray, + const StdRegions::StdMatrixKey &mkey) final { WeakDerivMatrixOp(i, inarray, outarray, mkey); } - virtual void v_HelmholtzMatrixOp( - const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey) + void v_HelmholtzMatrixOp(const Array &inarray, + Array &outarray, + const StdRegions::StdMatrixKey &mkey) final { HelmholtzMatrixOp(inarray, outarray, mkey); } - void v_ComputeTraceNormal(const int edge); + void v_ComputeTraceNormal(const int edge) final; }; typedef std::shared_ptr NodalTriExpSharedPtr; diff --git a/library/LocalRegions/PointExp.cpp b/library/LocalRegions/PointExp.cpp index a42168f29cb4b71b71ebe51b3cf7e124caed78f6..f2986dbc7558a68699d126053dbe591ff535bef0 100644 --- a/library/LocalRegions/PointExp.cpp +++ b/library/LocalRegions/PointExp.cpp @@ -46,10 +46,6 @@ PointExp::PointExp(const SpatialDomains::PointGeomSharedPtr &geom) m_ncoeffs = 1; } -PointExp::~PointExp(void) -{ -} - void PointExp::v_GetCoords(Array &coords_0, Array &coords_1, Array &coords_2) diff --git a/library/LocalRegions/PointExp.h b/library/LocalRegions/PointExp.h index 2139ea6b56108f1697712d0d766d08e8d049af91..6375f67e334fca2ee965a582fe813491bad3ef23 100644 --- a/library/LocalRegions/PointExp.h +++ b/library/LocalRegions/PointExp.h @@ -44,13 +44,14 @@ namespace Nektar { namespace LocalRegions { -class PointExp : virtual public StdRegions::StdPointExp, - virtual public Expansion0D +class PointExp final : virtual public StdRegions::StdPointExp, + virtual public Expansion0D { public: LOCAL_REGIONS_EXPORT PointExp( const SpatialDomains::PointGeomSharedPtr &m_geom); - LOCAL_REGIONS_EXPORT ~PointExp(void); + + LOCAL_REGIONS_EXPORT ~PointExp() final = default; inline const Array &GetCoeffs(void) const { @@ -123,19 +124,18 @@ protected: //!< same as the coefficient but is defined for consistency (It //!< is also used in Robin boundary conditions) - virtual void v_GetCoords(Array &coords_0, - Array &coords_1, - Array &coords_2); + void v_GetCoords(Array &coords_0, + Array &coords_1, + Array &coords_2) final; - virtual void v_NormVectorIProductWRTBase( - const Array &Fx, - Array &outarray); + void v_NormVectorIProductWRTBase(const Array &Fx, + Array &outarray) final; }; typedef std::shared_ptr PointExpSharedPtr; typedef std::vector PointExpVector; -const static Array NullPointExpSharedPtrArray; +const static Array NullPointExpSharedPtrArray{}; } // namespace LocalRegions } // namespace Nektar diff --git a/library/LocalRegions/PrismExp.cpp b/library/LocalRegions/PrismExp.cpp index db94737d4a575795944cc8a41d2566de10ae09a5..c51fdbe214e19c40f1f66d68d0ae1f8194fd4d3f 100644 --- a/library/LocalRegions/PrismExp.cpp +++ b/library/LocalRegions/PrismExp.cpp @@ -73,10 +73,6 @@ PrismExp::PrismExp(const PrismExp &T) { } -PrismExp::~PrismExp() -{ -} - //------------------------------- // Integration Methods //------------------------------- @@ -521,7 +517,7 @@ NekDouble PrismExp::v_StdPhysEvaluate( const Array &physvals) { // Evaluate point in local (eta) coordinates. - return StdPrismExp::v_PhysEvaluate(Lcoord, physvals); + return StdExpansion3D::v_PhysEvaluate(Lcoord, physvals); } NekDouble PrismExp::v_PhysEvaluate(const Array &coord, @@ -533,7 +529,17 @@ NekDouble PrismExp::v_PhysEvaluate(const Array &coord, m_geom->GetLocCoords(coord, Lcoord); - return StdPrismExp::v_PhysEvaluate(Lcoord, physvals); + return StdExpansion3D::v_PhysEvaluate(Lcoord, physvals); +} + +NekDouble PrismExp::v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) +{ + Array Lcoord(3); + ASSERTL0(m_geom, "m_geom not defined"); + m_geom->GetLocCoords(coord, Lcoord); + return StdPrismExp::v_PhysEvaluate(Lcoord, inarray, firstOrderDerivs); } //--------------------------------------- diff --git a/library/LocalRegions/PrismExp.h b/library/LocalRegions/PrismExp.h index fd9571dcb403b3ab96f8e99035c4053602e8f7a8..e27947b2c291e7109060ed2c3cb2ae99ff47805e 100644 --- a/library/LocalRegions/PrismExp.h +++ b/library/LocalRegions/PrismExp.h @@ -46,8 +46,8 @@ namespace Nektar { namespace LocalRegions { -class PrismExp : virtual public StdRegions::StdPrismExp, - virtual public Expansion3D +class PrismExp final : virtual public StdRegions::StdPrismExp, + virtual public Expansion3D { public: /// \brief Constructor using BasisKey class for quadrature @@ -59,132 +59,142 @@ public: LOCAL_REGIONS_EXPORT PrismExp(const PrismExp &T); - LOCAL_REGIONS_EXPORT ~PrismExp(); + LOCAL_REGIONS_EXPORT ~PrismExp() final = default; protected: //------------------------------- // Integration Methods //------------------------------- - LOCAL_REGIONS_EXPORT virtual NekDouble v_Integral( - const Array &inarray); + LOCAL_REGIONS_EXPORT NekDouble + v_Integral(const Array &inarray) final; //---------------------------- // Differentiation Methods //---------------------------- - LOCAL_REGIONS_EXPORT virtual void v_PhysDeriv( + LOCAL_REGIONS_EXPORT void v_PhysDeriv( const Array &inarray, Array &out_d0, Array &out_d1, - Array &out_d2); + Array &out_d2) final; //--------------------------------------- // Transforms //--------------------------------------- - LOCAL_REGIONS_EXPORT virtual void v_FwdTrans( + LOCAL_REGIONS_EXPORT void v_FwdTrans( const Array &inarray, - Array &outarray); + Array &outarray) final; //--------------------------------------- // Inner product functions //--------------------------------------- - LOCAL_REGIONS_EXPORT virtual void v_IProductWRTBase( + LOCAL_REGIONS_EXPORT void v_IProductWRTBase( const Array &inarray, - Array &outarray); - LOCAL_REGIONS_EXPORT virtual void v_IProductWRTBase_SumFac( + Array &outarray) final; + LOCAL_REGIONS_EXPORT void v_IProductWRTBase_SumFac( const Array &inarray, - Array &outarray, bool multiplybyweights = true); + Array &outarray, bool multiplybyweights = true) final; LOCAL_REGIONS_EXPORT void v_IProductWRTDerivBase( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) final; LOCAL_REGIONS_EXPORT void v_IProductWRTDerivBase_SumFac( const int dir, const Array &inarray, - Array &outarray); - LOCAL_REGIONS_EXPORT virtual void v_AlignVectorToCollapsedDir( + Array &outarray) final; + LOCAL_REGIONS_EXPORT void v_AlignVectorToCollapsedDir( const int dir, const Array &inarray, - Array> &outarray); + Array> &outarray) final; //--------------------------------------- // Evaluation functions //--------------------------------------- - LOCAL_REGIONS_EXPORT virtual void v_GetCoord( + LOCAL_REGIONS_EXPORT void v_GetCoord( const Array &Lcoords, - Array &coords); + Array &coords) final; - LOCAL_REGIONS_EXPORT virtual void v_GetCoords( + LOCAL_REGIONS_EXPORT void v_GetCoords( Array &coords_1, Array &coords_2, - Array &coords_3); + Array &coords_3) final; - LOCAL_REGIONS_EXPORT virtual NekDouble v_StdPhysEvaluate( - const Array &Lcoord, - const Array &physvals); + LOCAL_REGIONS_EXPORT NekDouble + v_StdPhysEvaluate(const Array &Lcoord, + const Array &physvals) final; - LOCAL_REGIONS_EXPORT virtual NekDouble v_PhysEvaluate( - const Array &coord, - const Array &physvals); + LOCAL_REGIONS_EXPORT NekDouble + v_PhysEvaluate(const Array &coord, + const Array &physvals) final; + + LOCAL_REGIONS_EXPORT NekDouble + v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) final; //--------------------------------------- // Helper functions //--------------------------------------- - LOCAL_REGIONS_EXPORT virtual StdRegions::StdExpansionSharedPtr v_GetStdExp( - void) const; + LOCAL_REGIONS_EXPORT + StdRegions::StdExpansionSharedPtr v_GetStdExp(void) const final; - LOCAL_REGIONS_EXPORT virtual StdRegions::StdExpansionSharedPtr v_GetLinStdExp( - void) const; + LOCAL_REGIONS_EXPORT + StdRegions::StdExpansionSharedPtr v_GetLinStdExp(void) const final; - LOCAL_REGIONS_EXPORT virtual int v_GetCoordim(); - LOCAL_REGIONS_EXPORT virtual void v_ExtractDataToCoeffs( + LOCAL_REGIONS_EXPORT int v_GetCoordim() final; + LOCAL_REGIONS_EXPORT void v_ExtractDataToCoeffs( const NekDouble *data, const std::vector &nummodes, const int mode_offset, NekDouble *coeffs, - std::vector &fromType); + std::vector &fromType) final; - LOCAL_REGIONS_EXPORT virtual void v_GetTracePhysMap( - const int face, Array &outarray); + LOCAL_REGIONS_EXPORT void v_GetTracePhysMap( + const int face, Array &outarray) final; - LOCAL_REGIONS_EXPORT void v_ComputeTraceNormal(const int face); + LOCAL_REGIONS_EXPORT void v_ComputeTraceNormal(const int face) final; //--------------------------------------- // Operator creation functions //--------------------------------------- - LOCAL_REGIONS_EXPORT virtual void v_MassMatrixOp( + LOCAL_REGIONS_EXPORT void v_MassMatrixOp( const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual void v_LaplacianMatrixOp( + Array &outarray, + const StdRegions::StdMatrixKey &mkey) final; + LOCAL_REGIONS_EXPORT void v_LaplacianMatrixOp( const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual void v_LaplacianMatrixOp( + Array &outarray, + const StdRegions::StdMatrixKey &mkey) final; + LOCAL_REGIONS_EXPORT void v_LaplacianMatrixOp( const int k1, const int k2, const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual void v_HelmholtzMatrixOp( + Array &outarray, + const StdRegions::StdMatrixKey &mkey) final; + LOCAL_REGIONS_EXPORT void v_HelmholtzMatrixOp( const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual void v_GeneralMatrixOp_MatOp( + Array &outarray, + const StdRegions::StdMatrixKey &mkey) final; + LOCAL_REGIONS_EXPORT void v_GeneralMatrixOp_MatOp( const Array &inarray, Array &outarray, const StdRegions::StdMatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual void v_SVVLaplacianFilter( - Array &array, const StdRegions::StdMatrixKey &mkey); + LOCAL_REGIONS_EXPORT void v_SVVLaplacianFilter( + Array &array, + const StdRegions::StdMatrixKey &mkey) final; //--------------------------------------- // Matrix creation functions //--------------------------------------- - LOCAL_REGIONS_EXPORT virtual DNekMatSharedPtr v_GenMatrix( - const StdRegions::StdMatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual DNekMatSharedPtr v_CreateStdMatrix( - const StdRegions::StdMatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual DNekScalMatSharedPtr v_GetLocMatrix( - const MatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual DNekScalBlkMatSharedPtr v_GetLocStaticCondMatrix( - const MatrixKey &mkey); + LOCAL_REGIONS_EXPORT DNekMatSharedPtr + v_GenMatrix(const StdRegions::StdMatrixKey &mkey) final; + LOCAL_REGIONS_EXPORT DNekMatSharedPtr + v_CreateStdMatrix(const StdRegions::StdMatrixKey &mkey) final; + LOCAL_REGIONS_EXPORT DNekScalMatSharedPtr + v_GetLocMatrix(const MatrixKey &mkey) final; + LOCAL_REGIONS_EXPORT DNekScalBlkMatSharedPtr + v_GetLocStaticCondMatrix(const MatrixKey &mkey) final; LOCAL_REGIONS_EXPORT void v_DropLocStaticCondMatrix(const MatrixKey &mkey); LOCAL_REGIONS_EXPORT - virtual void v_GetSimplexEquiSpacedConnectivity(Array &conn, - bool standard = true); + void v_GetSimplexEquiSpacedConnectivity(Array &conn, + bool standard = true) final; LOCAL_REGIONS_EXPORT - virtual void v_NormalTraceDerivFactors( + void v_NormalTraceDerivFactors( Array> &d0factors, Array> &d1factors, - Array> &d2factors); + Array> &d2factors) final; private: LibUtilities::NekManager @@ -192,9 +202,9 @@ private: LibUtilities::NekManager m_staticCondMatrixManager; - virtual void v_LaplacianMatrixOp_MatFree_Kernel( + void v_LaplacianMatrixOp_MatFree_Kernel( const Array &inarray, - Array &outarray, Array &wsp); + Array &outarray, Array &wsp) final; }; typedef std::shared_ptr PrismExpSharedPtr; diff --git a/library/LocalRegions/PyrExp.cpp b/library/LocalRegions/PyrExp.cpp index ed723887898b397fc8e707e99920887ec7a48572..8abdfb7f097874efe8b32ff7f7d701ad466e086c 100644 --- a/library/LocalRegions/PyrExp.cpp +++ b/library/LocalRegions/PyrExp.cpp @@ -69,10 +69,6 @@ PyrExp::PyrExp(const PyrExp &T) { } -PyrExp::~PyrExp() -{ -} - //---------------------------- // Integration Methods //---------------------------- @@ -604,7 +600,7 @@ NekDouble PyrExp::v_StdPhysEvaluate( const Array &physvals) { // Evaluate point in local coordinates. - return StdPyrExp::v_PhysEvaluate(Lcoord, physvals); + return StdExpansion3D::v_PhysEvaluate(Lcoord, physvals); } NekDouble PyrExp::v_PhysEvaluate(const Array &coord, @@ -617,7 +613,17 @@ NekDouble PyrExp::v_PhysEvaluate(const Array &coord, // TODO: check GetLocCoords() m_geom->GetLocCoords(coord, Lcoord); - return StdPyrExp::v_PhysEvaluate(Lcoord, physvals); + return StdExpansion3D::v_PhysEvaluate(Lcoord, physvals); +} + +NekDouble PyrExp::v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) +{ + Array Lcoord(3); + ASSERTL0(m_geom, "m_geom not defined"); + m_geom->GetLocCoords(coord, Lcoord); + return StdPyrExp::v_PhysEvaluate(Lcoord, inarray, firstOrderDerivs); } //--------------------------------------- diff --git a/library/LocalRegions/PyrExp.h b/library/LocalRegions/PyrExp.h index 4130484f5febbf21f90ad7fc1b5f5f4201370bc8..5f8cc0af40deb07db1ef79bd92fc873f3ce2842a 100644 --- a/library/LocalRegions/PyrExp.h +++ b/library/LocalRegions/PyrExp.h @@ -47,7 +47,8 @@ namespace Nektar namespace LocalRegions { -class PyrExp : virtual public StdRegions::StdPyrExp, virtual public Expansion3D +class PyrExp final : virtual public StdRegions::StdPyrExp, + virtual public Expansion3D { public: /** \brief Constructor using BasisKey class for quadrature points and order @@ -59,110 +60,117 @@ public: LOCAL_REGIONS_EXPORT PyrExp(const PyrExp &T); - LOCAL_REGIONS_EXPORT ~PyrExp(); + LOCAL_REGIONS_EXPORT ~PyrExp() final = default; protected: //------------------------------- // Integration Methods //------------------------------- - LOCAL_REGIONS_EXPORT virtual NekDouble v_Integral( - const Array &inarray); + LOCAL_REGIONS_EXPORT NekDouble + v_Integral(const Array &inarray) final; //---------------------------- // Differentiation Methods //---------------------------- - LOCAL_REGIONS_EXPORT virtual void v_PhysDeriv( + LOCAL_REGIONS_EXPORT void v_PhysDeriv( const Array &inarray, Array &out_d0, Array &out_d1, - Array &out_d2); + Array &out_d2) final; //--------------------------------------- // Transforms //--------------------------------------- - LOCAL_REGIONS_EXPORT virtual void v_FwdTrans( + LOCAL_REGIONS_EXPORT void v_FwdTrans( const Array &inarray, - Array &outarray); + Array &outarray) final; //--------------------------------------- // Inner product functions //--------------------------------------- - LOCAL_REGIONS_EXPORT virtual void v_IProductWRTBase( + LOCAL_REGIONS_EXPORT void v_IProductWRTBase( const Array &inarray, - Array &outarray); - LOCAL_REGIONS_EXPORT virtual void v_IProductWRTBase_SumFac( + Array &outarray) final; + LOCAL_REGIONS_EXPORT void v_IProductWRTBase_SumFac( const Array &inarray, - Array &outarray, bool multiplybyweights = true); + Array &outarray, bool multiplybyweights = true) final; LOCAL_REGIONS_EXPORT void v_IProductWRTDerivBase( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) final; LOCAL_REGIONS_EXPORT void v_IProductWRTDerivBase_SumFac( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) final; - LOCAL_REGIONS_EXPORT virtual void v_AlignVectorToCollapsedDir( + LOCAL_REGIONS_EXPORT void v_AlignVectorToCollapsedDir( const int dir, const Array &inarray, - Array> &outarray); + Array> &outarray) final; //--------------------------------------- // Evaluation functions //--------------------------------------- - LOCAL_REGIONS_EXPORT virtual StdRegions::StdExpansionSharedPtr v_GetStdExp( - void) const; + LOCAL_REGIONS_EXPORT + StdRegions::StdExpansionSharedPtr v_GetStdExp(void) const final; - LOCAL_REGIONS_EXPORT virtual StdRegions::StdExpansionSharedPtr v_GetLinStdExp( - void) const; + LOCAL_REGIONS_EXPORT + StdRegions::StdExpansionSharedPtr v_GetLinStdExp(void) const final; - LOCAL_REGIONS_EXPORT virtual void v_GetCoord( + LOCAL_REGIONS_EXPORT void v_GetCoord( const Array &Lcoords, - Array &coords); + Array &coords) final; - LOCAL_REGIONS_EXPORT virtual void v_GetCoords( + LOCAL_REGIONS_EXPORT void v_GetCoords( Array &coords_1, Array &coords_2, - Array &coords_3); + Array &coords_3) final; - LOCAL_REGIONS_EXPORT virtual void v_ExtractDataToCoeffs( + LOCAL_REGIONS_EXPORT void v_ExtractDataToCoeffs( const NekDouble *data, const std::vector &nummodes, const int mode_offset, NekDouble *coeffs, - std::vector &fromType); + std::vector &fromType) final; LOCAL_REGIONS_EXPORT NekDouble v_StdPhysEvaluate(const Array &Lcoord, const Array &physvals); - LOCAL_REGIONS_EXPORT virtual NekDouble v_PhysEvaluate( - const Array &coord, - const Array &physvals); + LOCAL_REGIONS_EXPORT NekDouble + v_PhysEvaluate(const Array &coord, + const Array &physvals) final; + + LOCAL_REGIONS_EXPORT NekDouble + v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) final; //--------------------------------------- // Helper functions //--------------------------------------- - LOCAL_REGIONS_EXPORT virtual int v_GetCoordim(); + LOCAL_REGIONS_EXPORT int v_GetCoordim() final; - LOCAL_REGIONS_EXPORT virtual void v_GetTracePhysMap( - const int face, Array &outarray); + LOCAL_REGIONS_EXPORT void v_GetTracePhysMap( + const int face, Array &outarray) final; - LOCAL_REGIONS_EXPORT void v_ComputeTraceNormal(const int face); + LOCAL_REGIONS_EXPORT void v_ComputeTraceNormal(const int face) final; - LOCAL_REGIONS_EXPORT virtual void v_SVVLaplacianFilter( - Array &array, const StdRegions::StdMatrixKey &mkey); + LOCAL_REGIONS_EXPORT void v_SVVLaplacianFilter( + Array &array, + const StdRegions::StdMatrixKey &mkey) final; //--------------------------------------- // Matrix creation functions //--------------------------------------- - LOCAL_REGIONS_EXPORT virtual DNekMatSharedPtr v_GenMatrix( - const StdRegions::StdMatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual DNekMatSharedPtr v_CreateStdMatrix( - const StdRegions::StdMatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual DNekScalMatSharedPtr v_GetLocMatrix( - const MatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual DNekScalBlkMatSharedPtr v_GetLocStaticCondMatrix( - const MatrixKey &mkey); - LOCAL_REGIONS_EXPORT void v_DropLocStaticCondMatrix(const MatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual void v_ComputeLaplacianMetric(); - LOCAL_REGIONS_EXPORT virtual void v_NormalTraceDerivFactors( + LOCAL_REGIONS_EXPORT DNekMatSharedPtr + v_GenMatrix(const StdRegions::StdMatrixKey &mkey) final; + LOCAL_REGIONS_EXPORT DNekMatSharedPtr + v_CreateStdMatrix(const StdRegions::StdMatrixKey &mkey) final; + LOCAL_REGIONS_EXPORT DNekScalMatSharedPtr + v_GetLocMatrix(const MatrixKey &mkey) final; + LOCAL_REGIONS_EXPORT DNekScalBlkMatSharedPtr + v_GetLocStaticCondMatrix(const MatrixKey &mkey) final; + LOCAL_REGIONS_EXPORT void v_DropLocStaticCondMatrix( + const MatrixKey &mkey) final; + LOCAL_REGIONS_EXPORT void v_ComputeLaplacianMetric() final; + LOCAL_REGIONS_EXPORT void v_NormalTraceDerivFactors( Array> &d0factors, Array> &d1factors, - Array> &d2factors); + Array> &d2factors) final; private: LibUtilities::NekManager @@ -170,9 +178,9 @@ private: LibUtilities::NekManager m_staticCondMatrixManager; - virtual void v_LaplacianMatrixOp_MatFree_Kernel( + void v_LaplacianMatrixOp_MatFree_Kernel( const Array &inarray, - Array &outarray, Array &wsp); + Array &outarray, Array &wsp) final; }; typedef std::shared_ptr PyrExpSharedPtr; diff --git a/library/LocalRegions/QuadExp.cpp b/library/LocalRegions/QuadExp.cpp index 4920c8a7438000e973cc39621f43e2af6281c4a2..ad7c25c041bdc235f75e8cb39b795f401e7b92af 100644 --- a/library/LocalRegions/QuadExp.cpp +++ b/library/LocalRegions/QuadExp.cpp @@ -70,10 +70,6 @@ QuadExp::QuadExp(const QuadExp &T) { } -QuadExp::~QuadExp() -{ -} - NekDouble QuadExp::v_Integral(const Array &inarray) { int nquad0 = m_base[0]->GetNumPoints(); @@ -628,7 +624,7 @@ NekDouble QuadExp::v_StdPhysEvaluate( const Array &physvals) { // Evaluate point in local (eta) coordinates. - return StdQuadExp::v_PhysEvaluate(Lcoord, physvals); + return StdExpansion2D::v_PhysEvaluate(Lcoord, physvals); } NekDouble QuadExp::v_PhysEvaluate(const Array &coord, @@ -639,7 +635,17 @@ NekDouble QuadExp::v_PhysEvaluate(const Array &coord, ASSERTL0(m_geom, "m_geom not defined"); m_geom->GetLocCoords(coord, Lcoord); - return StdQuadExp::v_PhysEvaluate(Lcoord, physvals); + return StdExpansion2D::v_PhysEvaluate(Lcoord, physvals); +} + +NekDouble QuadExp::v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) +{ + Array Lcoord(2); + ASSERTL0(m_geom, "m_geom not defined"); + m_geom->GetLocCoords(coord, Lcoord); + return StdQuadExp::v_PhysEvaluate(Lcoord, inarray, firstOrderDerivs); } // Get edge values from the 2D Phys space along an edge diff --git a/library/LocalRegions/QuadExp.h b/library/LocalRegions/QuadExp.h index 128292f488305189bd6ea1c219ed81f80735b403..7d2a841719baa01b884138ef5f22f35372b75824 100644 --- a/library/LocalRegions/QuadExp.h +++ b/library/LocalRegions/QuadExp.h @@ -47,8 +47,8 @@ namespace Nektar namespace LocalRegions { -class QuadExp : virtual public StdRegions::StdQuadExp, - virtual public Expansion2D +class QuadExp final : virtual public StdRegions::StdQuadExp, + virtual public Expansion2D { public: /** @@ -61,7 +61,7 @@ public: LOCAL_REGIONS_EXPORT QuadExp(const QuadExp &T); - LOCAL_REGIONS_EXPORT virtual ~QuadExp(); + LOCAL_REGIONS_EXPORT virtual ~QuadExp() final = default; protected: //------------------------------- @@ -152,6 +152,10 @@ protected: LOCAL_REGIONS_EXPORT virtual NekDouble v_PhysEvaluate( const Array &coord, const Array &physvals); + LOCAL_REGIONS_EXPORT NekDouble + v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) final; LOCAL_REGIONS_EXPORT virtual void v_GetEdgePhysVals( const int edge, const Array &inarray, Array &outarray); @@ -225,9 +229,10 @@ protected: LOCAL_REGIONS_EXPORT virtual void v_HelmholtzMatrixOp( const Array &inarray, Array &outarray, const StdRegions::StdMatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual void v_GeneralMatrixOp_MatOp( + LOCAL_REGIONS_EXPORT void v_GeneralMatrixOp_MatOp( const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); + Array &outarray, + const StdRegions::StdMatrixKey &mkey) final; LOCAL_REGIONS_EXPORT virtual void v_LaplacianMatrixOp_MatFree_Kernel( const Array &inarray, Array &outarray, Array &wsp); @@ -249,8 +254,6 @@ private: m_matrixManager; LibUtilities::NekManager m_staticCondMatrixManager; - - QuadExp(); }; typedef std::shared_ptr QuadExpSharedPtr; diff --git a/library/LocalRegions/SegExp.cpp b/library/LocalRegions/SegExp.cpp index 20ade987739a8b6c07d38963435a2147b9389160..c46195b6c9d5d0dd4b20ba0d50de50505542caf2 100644 --- a/library/LocalRegions/SegExp.cpp +++ b/library/LocalRegions/SegExp.cpp @@ -81,13 +81,6 @@ SegExp::SegExp(const SegExp &S) { } -/** - * - */ -SegExp::~SegExp() -{ -} - //---------------------------- // Integration Methods //---------------------------- @@ -598,7 +591,7 @@ NekDouble SegExp::v_StdPhysEvaluate( const Array &physvals) { // Evaluate point in local (eta) coordinates. - return StdSegExp::v_PhysEvaluate(Lcoord, physvals); + return StdExpansion1D::v_PhysEvaluate(Lcoord, physvals); } NekDouble SegExp::v_PhysEvaluate(const Array &coord, @@ -609,7 +602,29 @@ NekDouble SegExp::v_PhysEvaluate(const Array &coord, ASSERTL0(m_geom, "m_geom not defined"); m_geom->GetLocCoords(coord, Lcoord); - return StdSegExp::v_PhysEvaluate(Lcoord, physvals); + return StdExpansion1D::v_PhysEvaluate(Lcoord, physvals); +} + +NekDouble SegExp::v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) +{ + Array Lcoord(1); + ASSERTL0(m_geom, "m_geom not defined"); + m_geom->GetLocCoords(coord, Lcoord); + return StdSegExp::v_PhysEvaluate(Lcoord, inarray, firstOrderDerivs); +} + +NekDouble SegExp::v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs, + std::array &secondOrderDerivs) +{ + Array Lcoord(1); + ASSERTL0(m_geom, "m_geom not defined"); + m_geom->GetLocCoords(coord, Lcoord); + return StdSegExp::v_PhysEvaluate(Lcoord, inarray, firstOrderDerivs, + secondOrderDerivs); } void SegExp::v_GetCoord(const Array &Lcoords, diff --git a/library/LocalRegions/SegExp.h b/library/LocalRegions/SegExp.h index 6e44cd3f693250513952d473ed5f20a5fe86fa06..2487d5565acb8823d32f32a58dfc67dadf473982 100644 --- a/library/LocalRegions/SegExp.h +++ b/library/LocalRegions/SegExp.h @@ -48,7 +48,8 @@ namespace Nektar namespace LocalRegions { -class SegExp : virtual public StdRegions::StdSegExp, virtual public Expansion1D +class SegExp final : virtual public StdRegions::StdSegExp, + virtual public Expansion1D { public: @@ -58,180 +59,189 @@ public: LOCAL_REGIONS_EXPORT SegExp(const SegExp &S); - LOCAL_REGIONS_EXPORT ~SegExp(); + LOCAL_REGIONS_EXPORT ~SegExp() final = default; protected: //---------------------------- // Integration Methods //---------------------------- - LOCAL_REGIONS_EXPORT virtual NekDouble v_Integral( - const Array &inarray) override; + LOCAL_REGIONS_EXPORT NekDouble + v_Integral(const Array &inarray) final; //----------------------------- // Differentiation Methods //----------------------------- - LOCAL_REGIONS_EXPORT virtual void v_PhysDeriv( + LOCAL_REGIONS_EXPORT void v_PhysDeriv( const Array &inarray, Array &out_d0, Array &out_d1 = NullNekDouble1DArray, - Array &out_d2 = NullNekDouble1DArray) override; + Array &out_d2 = NullNekDouble1DArray) final; - LOCAL_REGIONS_EXPORT virtual void v_PhysDeriv( + LOCAL_REGIONS_EXPORT void v_PhysDeriv( const int dir, const Array &inarray, - Array &outarray) override; + Array &outarray) final; - LOCAL_REGIONS_EXPORT virtual void v_PhysDeriv_s( + LOCAL_REGIONS_EXPORT void v_PhysDeriv_s( const Array &inarray, - Array &out_ds) override; + Array &out_ds) final; - LOCAL_REGIONS_EXPORT virtual void v_PhysDeriv_n( + LOCAL_REGIONS_EXPORT void v_PhysDeriv_n( const Array &inarray, - Array &out_dn) override; + Array &out_dn) final; //----------------------------- // Transforms //----------------------------- - LOCAL_REGIONS_EXPORT virtual void v_FwdTrans( + LOCAL_REGIONS_EXPORT void v_FwdTrans( const Array &inarray, - Array &outarray) override; + Array &outarray) final; - LOCAL_REGIONS_EXPORT virtual void v_FwdTransBndConstrained( + LOCAL_REGIONS_EXPORT void v_FwdTransBndConstrained( const Array &inarray, - Array &outarray) override; + Array &outarray) final; //----------------------------- // Inner product functions //----------------------------- - LOCAL_REGIONS_EXPORT virtual void v_IProductWRTBase( + LOCAL_REGIONS_EXPORT void v_IProductWRTBase( const Array &inarray, - Array &outarray) override; + Array &outarray) final; - LOCAL_REGIONS_EXPORT virtual void v_IProductWRTBase( + LOCAL_REGIONS_EXPORT void v_IProductWRTBase( const Array &base, const Array &inarray, - Array &outarray, int coll_check) override; + Array &outarray, int coll_check) final; - LOCAL_REGIONS_EXPORT virtual void v_IProductWRTDerivBase( + LOCAL_REGIONS_EXPORT void v_IProductWRTDerivBase( const int dir, const Array &inarray, - Array &outarray) override; + Array &outarray) final; - LOCAL_REGIONS_EXPORT virtual void v_NormVectorIProductWRTBase( + LOCAL_REGIONS_EXPORT void v_NormVectorIProductWRTBase( const Array &Fx, const Array &Fy, - Array &outarray) override; + Array &outarray) final; - LOCAL_REGIONS_EXPORT virtual void v_NormVectorIProductWRTBase( + LOCAL_REGIONS_EXPORT void v_NormVectorIProductWRTBase( const Array> &Fvec, - Array &outarray) override; + Array &outarray) final; //----------------------------- // Evaluation functions //----------------------------- - LOCAL_REGIONS_EXPORT virtual NekDouble v_StdPhysEvaluate( - const Array &Lcoord, - const Array &physvals) override; - - LOCAL_REGIONS_EXPORT virtual NekDouble v_PhysEvaluate( - const Array &coord, - const Array &physvals) override; - - LOCAL_REGIONS_EXPORT virtual void v_GetCoord( + LOCAL_REGIONS_EXPORT NekDouble + v_StdPhysEvaluate(const Array &Lcoord, + const Array &physvals) final; + + LOCAL_REGIONS_EXPORT NekDouble + v_PhysEvaluate(const Array &coord, + const Array &physvals) final; + + LOCAL_REGIONS_EXPORT NekDouble + v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) final; + + LOCAL_REGIONS_EXPORT NekDouble + v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs, + std::array &secondOrderDerivs) final; + + LOCAL_REGIONS_EXPORT void v_GetCoord( const Array &Lcoords, - Array &coords) override; + Array &coords) final; - LOCAL_REGIONS_EXPORT virtual void v_GetCoords( + LOCAL_REGIONS_EXPORT void v_GetCoords( Array &coords_1, Array &coords_2, - Array &coords_3) override; + Array &coords_3) final; - LOCAL_REGIONS_EXPORT virtual void v_GetVertexPhysVals( + LOCAL_REGIONS_EXPORT void v_GetVertexPhysVals( const int vertex, const Array &inarray, - NekDouble &outarray) override; + NekDouble &outarray) final; - LOCAL_REGIONS_EXPORT virtual void v_AddVertexPhysVals( + LOCAL_REGIONS_EXPORT void v_AddVertexPhysVals( const int vertex, const NekDouble &inarray, Array &outarray); - LOCAL_REGIONS_EXPORT virtual void v_GetTracePhysVals( + LOCAL_REGIONS_EXPORT void v_GetTracePhysVals( const int edge, const StdRegions::StdExpansionSharedPtr &EdgeExp, const Array &inarray, - Array &outarray, - StdRegions::Orientation orient) override; + Array &outarray, StdRegions::Orientation orient) final; LOCAL_REGIONS_EXPORT virtual void v_GetTracePhysMap( - const int vertex, Array &map) override; + const int vertex, Array &map) final; //----------------------------- // Helper functions //----------------------------- - LOCAL_REGIONS_EXPORT virtual StdRegions::StdExpansionSharedPtr v_GetStdExp( - void) const override; + LOCAL_REGIONS_EXPORT + StdRegions::StdExpansionSharedPtr v_GetStdExp(void) const final; - LOCAL_REGIONS_EXPORT virtual StdRegions::StdExpansionSharedPtr v_GetLinStdExp( - void) const override; + LOCAL_REGIONS_EXPORT + StdRegions::StdExpansionSharedPtr v_GetLinStdExp(void) const final; - LOCAL_REGIONS_EXPORT virtual int v_GetCoordim() override; + LOCAL_REGIONS_EXPORT int v_GetCoordim() final; - LOCAL_REGIONS_EXPORT virtual void v_SetCoeffsToOrientation( + LOCAL_REGIONS_EXPORT void v_SetCoeffsToOrientation( StdRegions::Orientation dir, Array &inarray, - Array &outarray) override; + Array &outarray) final; LOCAL_REGIONS_EXPORT virtual int v_GetNumPoints(const int dir) const; LOCAL_REGIONS_EXPORT virtual int v_GetNcoeffs(void) const; - LOCAL_REGIONS_EXPORT virtual const LibUtilities::BasisSharedPtr &v_GetBasis( + LOCAL_REGIONS_EXPORT const LibUtilities::BasisSharedPtr &v_GetBasis( int dir) const; - LOCAL_REGIONS_EXPORT virtual int v_NumBndryCoeffs() const override; + LOCAL_REGIONS_EXPORT int v_NumBndryCoeffs() const final; - LOCAL_REGIONS_EXPORT virtual int v_NumDGBndryCoeffs() const override; + LOCAL_REGIONS_EXPORT int v_NumDGBndryCoeffs() const final; - LOCAL_REGIONS_EXPORT virtual void v_ComputeTraceNormal( - const int vertex) override; + LOCAL_REGIONS_EXPORT void v_ComputeTraceNormal(const int vertex) final; - LOCAL_REGIONS_EXPORT virtual SpatialDomains::GeomType v_MetricInfoType(); + LOCAL_REGIONS_EXPORT SpatialDomains::GeomType v_MetricInfoType(); - LOCAL_REGIONS_EXPORT virtual void v_ExtractDataToCoeffs( + LOCAL_REGIONS_EXPORT void v_ExtractDataToCoeffs( const NekDouble *data, const std::vector &nummodes, const int mode_offset, NekDouble *coeffs, - std::vector &fromType) override; + std::vector &fromType) final; - LOCAL_REGIONS_EXPORT virtual const Array - &v_GetPhysNormals(void) override; + LOCAL_REGIONS_EXPORT const Array &v_GetPhysNormals( + void) final; //----------------------------- // Operator creation functions //----------------------------- - LOCAL_REGIONS_EXPORT virtual void v_LaplacianMatrixOp( + LOCAL_REGIONS_EXPORT void v_LaplacianMatrixOp( const Array &inarray, Array &outarray, - const StdRegions::StdMatrixKey &mkey) override; + const StdRegions::StdMatrixKey &mkey) final; - LOCAL_REGIONS_EXPORT virtual void v_HelmholtzMatrixOp( + LOCAL_REGIONS_EXPORT void v_HelmholtzMatrixOp( const Array &inarray, Array &outarray, - const StdRegions::StdMatrixKey &mkey) override; + const StdRegions::StdMatrixKey &mkey) final; //----------------------------- // Matrix creation functions //----------------------------- - LOCAL_REGIONS_EXPORT virtual DNekMatSharedPtr v_GenMatrix( - const StdRegions::StdMatrixKey &mkey) override; + LOCAL_REGIONS_EXPORT DNekMatSharedPtr + v_GenMatrix(const StdRegions::StdMatrixKey &mkey) final; LOCAL_REGIONS_EXPORT DNekScalMatSharedPtr CreateMatrix(const MatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual DNekMatSharedPtr v_CreateStdMatrix( - const StdRegions::StdMatrixKey &mkey) override; + LOCAL_REGIONS_EXPORT DNekMatSharedPtr + v_CreateStdMatrix(const StdRegions::StdMatrixKey &mkey) final; - LOCAL_REGIONS_EXPORT virtual DNekScalMatSharedPtr v_GetLocMatrix( - const MatrixKey &mkey) override; + LOCAL_REGIONS_EXPORT DNekScalMatSharedPtr + v_GetLocMatrix(const MatrixKey &mkey) final; - LOCAL_REGIONS_EXPORT virtual DNekScalBlkMatSharedPtr v_GetLocStaticCondMatrix( - const MatrixKey &mkey) override; + LOCAL_REGIONS_EXPORT DNekScalBlkMatSharedPtr + v_GetLocStaticCondMatrix(const MatrixKey &mkey) final; LOCAL_REGIONS_EXPORT void v_DropLocStaticCondMatrix( - const MatrixKey &mkey) override; + const MatrixKey &mkey) final; private: LibUtilities::NekManager @@ -239,8 +249,6 @@ private: LibUtilities::NekManager m_staticCondMatrixManager; - SegExp(); - LOCAL_REGIONS_EXPORT void ReverseCoeffsAndSign( const Array &inarray, Array &outarray); diff --git a/library/LocalRegions/TetExp.cpp b/library/LocalRegions/TetExp.cpp index a8444064d326a123bc23c3afa27108657716147b..574384ace7fb2ee6dc58e51bb3b26086ef6afef0 100644 --- a/library/LocalRegions/TetExp.cpp +++ b/library/LocalRegions/TetExp.cpp @@ -89,13 +89,6 @@ TetExp::TetExp(const TetExp &T) { } -/** - * \brief Destructor - */ -TetExp::~TetExp() -{ -} - //----------------------------- // Integration Methods //----------------------------- @@ -470,7 +463,7 @@ NekDouble TetExp::v_StdPhysEvaluate( const Array &physvals) { // Evaluate point in local (eta) coordinates. - return StdTetExp::v_PhysEvaluate(Lcoord, physvals); + return StdExpansion3D::v_PhysEvaluate(Lcoord, physvals); } /** @@ -488,7 +481,17 @@ NekDouble TetExp::v_PhysEvaluate(const Array &coord, m_geom->GetLocCoords(coord, Lcoord); // Evaluate point in local (eta) coordinates. - return StdTetExp::v_PhysEvaluate(Lcoord, physvals); + return StdExpansion3D::v_PhysEvaluate(Lcoord, physvals); +} + +NekDouble TetExp::v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) +{ + Array Lcoord(3); + ASSERTL0(m_geom, "m_geom not defined"); + m_geom->GetLocCoords(coord, Lcoord); + return StdTetExp::v_PhysEvaluate(Lcoord, inarray, firstOrderDerivs); } /** diff --git a/library/LocalRegions/TetExp.h b/library/LocalRegions/TetExp.h index 3e8bffe59cce7aa5bd663c7a3ed02a776c4e7a6e..6de5da6f0fe61664a92572837612d6c745fc8700 100644 --- a/library/LocalRegions/TetExp.h +++ b/library/LocalRegions/TetExp.h @@ -58,136 +58,141 @@ public: LOCAL_REGIONS_EXPORT TetExp(const TetExp &T); - LOCAL_REGIONS_EXPORT ~TetExp(); + LOCAL_REGIONS_EXPORT ~TetExp() override = default; protected: //----------------------------- // Integration Methods //----------------------------- - LOCAL_REGIONS_EXPORT virtual NekDouble v_Integral( - const Array &inarray); + LOCAL_REGIONS_EXPORT NekDouble + v_Integral(const Array &inarray) override; //----------------------------- // Differentiation Methods //----------------------------- - LOCAL_REGIONS_EXPORT virtual void v_PhysDeriv( + LOCAL_REGIONS_EXPORT void v_PhysDeriv( const Array &inarray, Array &out_d0, Array &out_d1, - Array &out_d2); + Array &out_d2) override; //----------------------------- // Transforms //----------------------------- - LOCAL_REGIONS_EXPORT virtual void v_FwdTrans( + LOCAL_REGIONS_EXPORT void v_FwdTrans( const Array &inarray, - Array &outarray); + Array &outarray) override; //----------------------------- // Inner product functions //----------------------------- - LOCAL_REGIONS_EXPORT virtual void v_IProductWRTBase( + LOCAL_REGIONS_EXPORT void v_IProductWRTBase( const Array &inarray, - Array &outarray); - LOCAL_REGIONS_EXPORT virtual void v_IProductWRTBase_SumFac( + Array &outarray) override; + LOCAL_REGIONS_EXPORT void v_IProductWRTBase_SumFac( const Array &inarray, - Array &outarray, bool multiplybyweights = true); - LOCAL_REGIONS_EXPORT virtual void v_IProductWRTDerivBase( + Array &outarray, + bool multiplybyweights = true) override; + LOCAL_REGIONS_EXPORT void v_IProductWRTDerivBase( const int dir, const Array &inarray, - Array &outarray); - LOCAL_REGIONS_EXPORT virtual void v_AlignVectorToCollapsedDir( + Array &outarray) override; + LOCAL_REGIONS_EXPORT void v_AlignVectorToCollapsedDir( const int dir, const Array &inarray, - Array> &outarray); + Array> &outarray) override; //----------------------------- // Evaluation functions //----------------------------- - LOCAL_REGIONS_EXPORT virtual NekDouble v_StdPhysEvaluate( - const Array &Lcoord, - const Array &physvals); + LOCAL_REGIONS_EXPORT NekDouble + v_StdPhysEvaluate(const Array &Lcoord, + const Array &physvals) override; - LOCAL_REGIONS_EXPORT virtual NekDouble v_PhysEvaluate( - const Array &coords, - const Array &physvals); + LOCAL_REGIONS_EXPORT NekDouble + v_PhysEvaluate(const Array &coords, + const Array &physvals) override; - LOCAL_REGIONS_EXPORT virtual void v_GetCoord( + LOCAL_REGIONS_EXPORT NekDouble + v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) final; + + LOCAL_REGIONS_EXPORT void v_GetCoord( const Array &Lcoords, - Array &coords); + Array &coords) override; - LOCAL_REGIONS_EXPORT virtual void v_GetCoords( + LOCAL_REGIONS_EXPORT void v_GetCoords( Array &coords_1, Array &coords_2, - Array &coords_3); + Array &coords_3) override; //----------------------------- // Helper functions //----------------------------- - LOCAL_REGIONS_EXPORT virtual LibUtilities::ShapeType v_DetShapeType() const; + LOCAL_REGIONS_EXPORT + LibUtilities::ShapeType v_DetShapeType() const override; - LOCAL_REGIONS_EXPORT virtual StdRegions::StdExpansionSharedPtr v_GetStdExp( - void) const; + LOCAL_REGIONS_EXPORT + StdRegions::StdExpansionSharedPtr v_GetStdExp(void) const override; - LOCAL_REGIONS_EXPORT virtual StdRegions::StdExpansionSharedPtr v_GetLinStdExp( - void) const; + LOCAL_REGIONS_EXPORT + StdRegions::StdExpansionSharedPtr v_GetLinStdExp(void) const override; - LOCAL_REGIONS_EXPORT virtual int v_GetCoordim(); + LOCAL_REGIONS_EXPORT int v_GetCoordim() override; - LOCAL_REGIONS_EXPORT virtual void v_ExtractDataToCoeffs( + LOCAL_REGIONS_EXPORT void v_ExtractDataToCoeffs( const NekDouble *data, const std::vector &nummodes, const int mode_offset, NekDouble *coeffs, - std::vector &fromType); + std::vector &fromType) override; - LOCAL_REGIONS_EXPORT virtual void v_GetTracePhysMap( - const int face, Array &outarray); + LOCAL_REGIONS_EXPORT void v_GetTracePhysMap( + const int face, Array &outarray) override; - LOCAL_REGIONS_EXPORT void v_ComputeTraceNormal(const int face); + LOCAL_REGIONS_EXPORT void v_ComputeTraceNormal(const int face) override; //----------------------------- // Operator creation functions //----------------------------- - LOCAL_REGIONS_EXPORT virtual void v_HelmholtzMatrixOp( + LOCAL_REGIONS_EXPORT void v_HelmholtzMatrixOp( const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); + Array &outarray, + const StdRegions::StdMatrixKey &mkey) override; - LOCAL_REGIONS_EXPORT virtual void v_LaplacianMatrixOp( + LOCAL_REGIONS_EXPORT void v_LaplacianMatrixOp( const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); + Array &outarray, + const StdRegions::StdMatrixKey &mkey) override; - LOCAL_REGIONS_EXPORT virtual void v_LaplacianMatrixOp( + LOCAL_REGIONS_EXPORT void v_LaplacianMatrixOp( const int k1, const int k2, const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); + Array &outarray, + const StdRegions::StdMatrixKey &mkey) override; - LOCAL_REGIONS_EXPORT virtual void v_SVVLaplacianFilter( - Array &array, const StdRegions::StdMatrixKey &mkey); + LOCAL_REGIONS_EXPORT void v_SVVLaplacianFilter( + Array &array, + const StdRegions::StdMatrixKey &mkey) override; //----------------------------- // Matrix creation functions //----------------------------- - LOCAL_REGIONS_EXPORT virtual DNekMatSharedPtr v_GenMatrix( - const StdRegions::StdMatrixKey &mkey); + LOCAL_REGIONS_EXPORT DNekMatSharedPtr + v_GenMatrix(const StdRegions::StdMatrixKey &mkey) override; - LOCAL_REGIONS_EXPORT virtual DNekMatSharedPtr v_CreateStdMatrix( - const StdRegions::StdMatrixKey &mkey); + LOCAL_REGIONS_EXPORT DNekMatSharedPtr + v_CreateStdMatrix(const StdRegions::StdMatrixKey &mkey) override; - LOCAL_REGIONS_EXPORT virtual DNekScalMatSharedPtr v_GetLocMatrix( - const MatrixKey &mkey); + LOCAL_REGIONS_EXPORT DNekScalMatSharedPtr + v_GetLocMatrix(const MatrixKey &mkey) override; - LOCAL_REGIONS_EXPORT virtual DNekScalBlkMatSharedPtr v_GetLocStaticCondMatrix( - const MatrixKey &mkey); + LOCAL_REGIONS_EXPORT + DNekScalBlkMatSharedPtr v_GetLocStaticCondMatrix( + const MatrixKey &mkey) override; - LOCAL_REGIONS_EXPORT void v_DropLocStaticCondMatrix(const MatrixKey &mkey); + LOCAL_REGIONS_EXPORT void v_DropLocStaticCondMatrix( + const MatrixKey &mkey) override; - LOCAL_REGIONS_EXPORT void SetUpInverseTransformationMatrix( - const DNekMatSharedPtr &m_transformationmatrix, - DNekMatSharedPtr m_inversetransformationmatrix, - DNekMatSharedPtr m_inversetransposedtransformationmatrix); + LOCAL_REGIONS_EXPORT void v_ComputeLaplacianMetric() override; - LOCAL_REGIONS_EXPORT void v_ComputeConditionNumberOfMatrix( - const DNekScalMatSharedPtr &mat); - - LOCAL_REGIONS_EXPORT virtual void v_ComputeLaplacianMetric(); - - LOCAL_REGIONS_EXPORT virtual void v_NormalTraceDerivFactors( + LOCAL_REGIONS_EXPORT void v_NormalTraceDerivFactors( Array> &d0factors, Array> &d1factors, - Array> &d2factors); + Array> &d2factors) override; private: LibUtilities::NekManager @@ -195,14 +200,12 @@ private: LibUtilities::NekManager m_staticCondMatrixManager; - TetExp(); - LOCAL_REGIONS_EXPORT void GeneralMatrixOp_MatOp( const Array &inarray, Array &outarray, const StdRegions::StdMatrixKey &mkey); - virtual void v_LaplacianMatrixOp_MatFree_Kernel( + void v_LaplacianMatrixOp_MatFree_Kernel( const Array &inarray, - Array &outarray, Array &wsp); + Array &outarray, Array &wsp) override; }; typedef std::shared_ptr TetExpSharedPtr; diff --git a/library/LocalRegions/TriExp.cpp b/library/LocalRegions/TriExp.cpp index 5a563183e09e2d9d19f4668b2da66fc3a95fa7a2..0ce25fd70d9a77044e857f6188a9b4f377638a97 100644 --- a/library/LocalRegions/TriExp.cpp +++ b/library/LocalRegions/TriExp.cpp @@ -72,10 +72,6 @@ TriExp::TriExp(const TriExp &T) { } -TriExp::~TriExp() -{ -} - NekDouble TriExp::v_Integral(const Array &inarray) { int nquad0 = m_base[0]->GetNumPoints(); @@ -750,7 +746,7 @@ NekDouble TriExp::v_StdPhysEvaluate( const Array &physvals) { // Evaluate point in local (eta) coordinates. - return StdTriExp::v_PhysEvaluate(Lcoord, physvals); + return StdExpansion2D::v_PhysEvaluate(Lcoord, physvals); } NekDouble TriExp::v_PhysEvaluate(const Array &coord, @@ -761,7 +757,17 @@ NekDouble TriExp::v_PhysEvaluate(const Array &coord, ASSERTL0(m_geom, "m_geom not defined"); m_geom->GetLocCoords(coord, Lcoord); - return StdTriExp::v_PhysEvaluate(Lcoord, physvals); + return StdExpansion2D::v_PhysEvaluate(Lcoord, physvals); +} + +NekDouble TriExp::v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) +{ + Array Lcoord(2); + ASSERTL0(m_geom, "m_geom not defined"); + m_geom->GetLocCoords(coord, Lcoord); + return StdTriExp::v_PhysEvaluate(Lcoord, inarray, firstOrderDerivs); } void TriExp::v_GetTracePhysVals( diff --git a/library/LocalRegions/TriExp.h b/library/LocalRegions/TriExp.h index 064e4e7ccc9ac725eb3036cf8d171c508e222112..ca4c127fac69e380ada855605b39f9eac5662b2a 100644 --- a/library/LocalRegions/TriExp.h +++ b/library/LocalRegions/TriExp.h @@ -61,196 +61,212 @@ public: LOCAL_REGIONS_EXPORT TriExp(const TriExp &T); - LOCAL_REGIONS_EXPORT ~TriExp(); + LOCAL_REGIONS_EXPORT ~TriExp() override = default; protected: //------------------------------- // Integration Methods //------------------------------- - LOCAL_REGIONS_EXPORT virtual NekDouble v_Integral( - const Array &inarray); + LOCAL_REGIONS_EXPORT NekDouble + v_Integral(const Array &inarray) override; //---------------------------- // Differentiation Methods //---------------------------- - LOCAL_REGIONS_EXPORT virtual void v_PhysDeriv( + LOCAL_REGIONS_EXPORT void v_PhysDeriv( const Array &inarray, Array &out_d0, Array &out_d1, - Array &out_d2 = NullNekDouble1DArray); - LOCAL_REGIONS_EXPORT virtual void v_PhysDeriv( + Array &out_d2 = NullNekDouble1DArray) override; + LOCAL_REGIONS_EXPORT void v_PhysDeriv( const int dir, const Array &inarray, - Array &outarray); - LOCAL_REGIONS_EXPORT virtual void v_PhysDirectionalDeriv( + Array &outarray) override; + LOCAL_REGIONS_EXPORT void v_PhysDirectionalDeriv( const Array &inarray, const Array &direction, - Array &out); + Array &out) override; //--------------------------------------- // Transforms //--------------------------------------- - LOCAL_REGIONS_EXPORT virtual void v_FwdTrans( + LOCAL_REGIONS_EXPORT void v_FwdTrans( const Array &inarray, - Array &outarray); - LOCAL_REGIONS_EXPORT virtual void v_FwdTransBndConstrained( + Array &outarray) override; + LOCAL_REGIONS_EXPORT void v_FwdTransBndConstrained( const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Inner product functions //--------------------------------------- - LOCAL_REGIONS_EXPORT virtual void v_IProductWRTBase( + LOCAL_REGIONS_EXPORT void v_IProductWRTBase( const Array &inarray, - Array &outarray); - LOCAL_REGIONS_EXPORT virtual void v_IProductWRTDerivBase( + Array &outarray) override; + LOCAL_REGIONS_EXPORT void v_IProductWRTDerivBase( const int dir, const Array &inarray, - Array &outarray); - LOCAL_REGIONS_EXPORT virtual void v_IProductWRTBase_SumFac( + Array &outarray) override; + LOCAL_REGIONS_EXPORT void v_IProductWRTBase_SumFac( const Array &inarray, - Array &outarray, bool multiplybyweights = true); - LOCAL_REGIONS_EXPORT virtual void v_IProductWRTBase_MatOp( + Array &outarray, + bool multiplybyweights = true) override; + LOCAL_REGIONS_EXPORT void v_IProductWRTBase_MatOp( const Array &inarray, - Array &outarray); - LOCAL_REGIONS_EXPORT virtual void v_IProductWRTDerivBase_SumFac( + Array &outarray) override; + LOCAL_REGIONS_EXPORT void v_IProductWRTDerivBase_SumFac( const int dir, const Array &inarray, - Array &outarray); - LOCAL_REGIONS_EXPORT virtual void v_AlignVectorToCollapsedDir( + Array &outarray) override; + LOCAL_REGIONS_EXPORT void v_AlignVectorToCollapsedDir( const int dir, const Array &inarray, - Array> &outarray); + Array> &outarray) override; - LOCAL_REGIONS_EXPORT virtual void v_IProductWRTDerivBase_MatOp( + LOCAL_REGIONS_EXPORT void v_IProductWRTDerivBase_MatOp( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; - LOCAL_REGIONS_EXPORT virtual void v_IProductWRTDirectionalDerivBase( + LOCAL_REGIONS_EXPORT void v_IProductWRTDirectionalDerivBase( const Array &direction, const Array &inarray, - Array &outarray); + Array &outarray) override; - LOCAL_REGIONS_EXPORT virtual void v_IProductWRTDirectionalDerivBase_SumFac( + LOCAL_REGIONS_EXPORT void v_IProductWRTDirectionalDerivBase_SumFac( const Array &direction, const Array &inarray, - Array &outarray); + Array &outarray) override; - LOCAL_REGIONS_EXPORT virtual void v_NormVectorIProductWRTBase( + LOCAL_REGIONS_EXPORT void v_NormVectorIProductWRTBase( const Array &Fx, const Array &Fy, const Array &Fz, - Array &outarray); + Array &outarray) override; - LOCAL_REGIONS_EXPORT virtual void v_NormVectorIProductWRTBase( + LOCAL_REGIONS_EXPORT void v_NormVectorIProductWRTBase( const Array> &Fvec, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Evaluation functions //--------------------------------------- - LOCAL_REGIONS_EXPORT virtual StdRegions::StdExpansionSharedPtr v_GetStdExp( - void) const; + LOCAL_REGIONS_EXPORT + StdRegions::StdExpansionSharedPtr v_GetStdExp(void) const override; - LOCAL_REGIONS_EXPORT virtual StdRegions::StdExpansionSharedPtr v_GetLinStdExp( - void) const; + LOCAL_REGIONS_EXPORT + StdRegions::StdExpansionSharedPtr v_GetLinStdExp(void) const override; - LOCAL_REGIONS_EXPORT virtual void v_GetCoord( + LOCAL_REGIONS_EXPORT void v_GetCoord( const Array &Lcoords, - Array &coords); - LOCAL_REGIONS_EXPORT virtual void v_GetCoords( + Array &coords) override; + LOCAL_REGIONS_EXPORT void v_GetCoords( Array &coords_1, Array &coords_2, - Array &coords_3); - LOCAL_REGIONS_EXPORT virtual NekDouble v_StdPhysEvaluate( - const Array &Lcoord, - const Array &physvals); - LOCAL_REGIONS_EXPORT virtual NekDouble v_PhysEvaluate( - const Array &coord, - const Array &physvals); - LOCAL_REGIONS_EXPORT virtual void v_GetTracePhysVals( + Array &coords_3) override; + LOCAL_REGIONS_EXPORT NekDouble + v_StdPhysEvaluate(const Array &Lcoord, + const Array &physvals) override; + LOCAL_REGIONS_EXPORT NekDouble + v_PhysEvaluate(const Array &coord, + const Array &physvals) override; + LOCAL_REGIONS_EXPORT NekDouble + v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) final; + LOCAL_REGIONS_EXPORT void v_GetTracePhysVals( const int edge, const StdRegions::StdExpansionSharedPtr &EdgeExp, const Array &inarray, - Array &outarray, StdRegions::Orientation orient); - LOCAL_REGIONS_EXPORT virtual void v_GetEdgeInterpVals( + Array &outarray, + StdRegions::Orientation orient) override; + LOCAL_REGIONS_EXPORT void v_GetEdgeInterpVals( const int edge, const Array &inarray, Array &outarray); - LOCAL_REGIONS_EXPORT virtual void v_GetTraceQFactors( - const int edge, Array &outarray); - LOCAL_REGIONS_EXPORT virtual void v_ComputeTraceNormal(const int edge); + LOCAL_REGIONS_EXPORT void v_GetTraceQFactors( + const int edge, Array &outarray) override; + LOCAL_REGIONS_EXPORT void v_ComputeTraceNormal(const int edge) override; //--------------------------------------- // Helper functions //--------------------------------------- - LOCAL_REGIONS_EXPORT virtual int v_GetCoordim(); - LOCAL_REGIONS_EXPORT virtual void v_ExtractDataToCoeffs( + LOCAL_REGIONS_EXPORT int v_GetCoordim() override; + LOCAL_REGIONS_EXPORT void v_ExtractDataToCoeffs( const NekDouble *data, const std::vector &nummodes, const int mode_offset, NekDouble *coeffs, - std::vector &fromType); - LOCAL_REGIONS_EXPORT virtual StdRegions::Orientation v_GetTraceOrient( - int edge); + std::vector &fromType) override; + LOCAL_REGIONS_EXPORT + StdRegions::Orientation v_GetTraceOrient(int edge) override; LOCAL_REGIONS_EXPORT virtual const LibUtilities::BasisSharedPtr &v_GetBasis( int dir) const; LOCAL_REGIONS_EXPORT virtual int v_GetNumPoints(const int dir) const; - LOCAL_REGIONS_EXPORT virtual void v_GetTracePhysMap( - const int edge, Array &outarray); + LOCAL_REGIONS_EXPORT void v_GetTracePhysMap( + const int edge, Array &outarray) override; //--------------------------------------- // Matrix creation functions //--------------------------------------- - LOCAL_REGIONS_EXPORT virtual DNekMatSharedPtr v_GenMatrix( - const StdRegions::StdMatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual DNekMatSharedPtr v_CreateStdMatrix( - const StdRegions::StdMatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual DNekScalMatSharedPtr v_GetLocMatrix( - const MatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual DNekScalBlkMatSharedPtr v_GetLocStaticCondMatrix( - const MatrixKey &mkey); + LOCAL_REGIONS_EXPORT + DNekMatSharedPtr v_GenMatrix(const StdRegions::StdMatrixKey &mkey) override; + LOCAL_REGIONS_EXPORT + DNekMatSharedPtr v_CreateStdMatrix( + const StdRegions::StdMatrixKey &mkey) override; + LOCAL_REGIONS_EXPORT + DNekScalMatSharedPtr v_GetLocMatrix(const MatrixKey &mkey) override; + LOCAL_REGIONS_EXPORT + DNekScalBlkMatSharedPtr v_GetLocStaticCondMatrix( + const MatrixKey &mkey) override; - LOCAL_REGIONS_EXPORT void v_DropLocStaticCondMatrix(const MatrixKey &mkey); + LOCAL_REGIONS_EXPORT void v_DropLocStaticCondMatrix( + const MatrixKey &mkey) override; - LOCAL_REGIONS_EXPORT virtual void v_MassMatrixOp( + LOCAL_REGIONS_EXPORT void v_MassMatrixOp( const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual void v_LaplacianMatrixOp( + Array &outarray, + const StdRegions::StdMatrixKey &mkey) override; + LOCAL_REGIONS_EXPORT void v_LaplacianMatrixOp( const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual void v_LaplacianMatrixOp( + Array &outarray, + const StdRegions::StdMatrixKey &mkey) override; + LOCAL_REGIONS_EXPORT void v_LaplacianMatrixOp( const int k1, const int k2, const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual void v_WeakDerivMatrixOp( + Array &outarray, + const StdRegions::StdMatrixKey &mkey) override; + LOCAL_REGIONS_EXPORT void v_WeakDerivMatrixOp( const int i, const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual void v_WeakDirectionalDerivMatrixOp( + Array &outarray, + const StdRegions::StdMatrixKey &mkey) override; + LOCAL_REGIONS_EXPORT void v_WeakDirectionalDerivMatrixOp( const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual void v_MassLevelCurvatureMatrixOp( + Array &outarray, + const StdRegions::StdMatrixKey &mkey) override; + LOCAL_REGIONS_EXPORT void v_MassLevelCurvatureMatrixOp( const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual void v_HelmholtzMatrixOp( + Array &outarray, + const StdRegions::StdMatrixKey &mkey) override; + LOCAL_REGIONS_EXPORT void v_HelmholtzMatrixOp( const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual void v_GeneralMatrixOp_MatOp( + Array &outarray, + const StdRegions::StdMatrixKey &mkey) override; + LOCAL_REGIONS_EXPORT void v_GeneralMatrixOp_MatOp( const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); - LOCAL_REGIONS_EXPORT virtual void v_LaplacianMatrixOp_MatFree_Kernel( + Array &outarray, + const StdRegions::StdMatrixKey &mkey) final; + LOCAL_REGIONS_EXPORT void v_LaplacianMatrixOp_MatFree_Kernel( const Array &inarray, - Array &outarray, Array &wsp); - LOCAL_REGIONS_EXPORT virtual void v_ReduceOrderCoeffs( + Array &outarray, Array &wsp) override; + LOCAL_REGIONS_EXPORT void v_ReduceOrderCoeffs( int numMin, const Array &inarray, - Array &outarray); + Array &outarray) override; - LOCAL_REGIONS_EXPORT virtual void v_ComputeLaplacianMetric(); + LOCAL_REGIONS_EXPORT void v_ComputeLaplacianMetric() override; - LOCAL_REGIONS_EXPORT virtual void v_SVVLaplacianFilter( - Array &array, const StdRegions::StdMatrixKey &mkey); + LOCAL_REGIONS_EXPORT void v_SVVLaplacianFilter( + Array &array, + const StdRegions::StdMatrixKey &mkey) override; - LOCAL_REGIONS_EXPORT virtual void v_NormalTraceDerivFactors( + LOCAL_REGIONS_EXPORT void v_NormalTraceDerivFactors( Array> &factors, Array> &d0factors, - Array> &d1factors); + Array> &d1factors) override; private: LibUtilities::NekManager m_matrixManager; LibUtilities::NekManager m_staticCondMatrixManager; - - TriExp(); }; typedef std::shared_ptr TriExpSharedPtr; diff --git a/library/MultiRegions/AssemblyMap/AssemblyCommDG.cpp b/library/MultiRegions/AssemblyMap/AssemblyCommDG.cpp index ff962bdbef9752a180a19f381eeeac0466d6be2a..d4deae6eeadd220dff809227432335a0ff44f3c4 100644 --- a/library/MultiRegions/AssemblyMap/AssemblyCommDG.cpp +++ b/library/MultiRegions/AssemblyMap/AssemblyCommDG.cpp @@ -400,21 +400,33 @@ AssemblyCommDG::AssemblyCommDG( std::vector avg(MPIFuncs.size(), -1); bool verbose = locExp.GetSession()->DefinesCmdLineArgument("verbose"); - if (verbose && comm->GetRank() == 0) + if (verbose && comm->TreatAsRankZero()) { std::cout << "MPI setup for trace exchange: " << std::endl; } + // Padding for output + int maxStrLen = 0; + for (size_t i = 0; i < MPIFuncs.size(); ++i) + { + maxStrLen = MPIFuncsNames[i].size() > maxStrLen + ? MPIFuncsNames[i].size() + : maxStrLen; + } + for (size_t i = 0; i < MPIFuncs.size(); ++i) { Timing(comm, warmup, numPoints, MPIFuncs[i]); std::tie(avg[i], min, max) = Timing(comm, iter, numPoints, MPIFuncs[i]); - if (verbose && comm->GetRank() == 0) + if (verbose && comm->TreatAsRankZero()) { std::cout << " " << MPIFuncsNames[i] - << " times (avg, min, max): " << avg[i] << " " << min - << " " << max << std::endl; + << " times (avg, min, max)" + << std::string(maxStrLen - MPIFuncsNames[i].size(), + ' ') + << ": " << avg[i] << " " << min << " " << max + << std::endl; } } @@ -422,7 +434,7 @@ AssemblyCommDG::AssemblyCommDG( int fastestMPI = std::distance( avg.begin(), std::min_element(avg.begin(), avg.end())); - if (verbose && comm->GetRank() == 0) + if (verbose && comm->TreatAsRankZero()) { std::cout << " Chosen fastest method: " << MPIFuncsNames[fastestMPI] << std::endl; @@ -567,7 +579,7 @@ void AssemblyCommDG::InitialiseStructure( } // This creates a list of all geometry of problem dimension - 1 - // and populates the maxQuad member variable + // and populates the maxQuad member variable for AllToAll std::vector localEdgeIds; for (eid = 0; eid < locExpVector.size(); ++eid) { @@ -586,7 +598,7 @@ void AssemblyCommDG::InitialiseStructure( } } - // Find max quadrature points across all processes + // Find max quadrature points across all processes for AllToAll method comm->AllReduce(m_maxQuad, LibUtilities::ReduceMax); // Create list of boundary edge IDs @@ -675,7 +687,6 @@ void AssemblyCommDG::InitialiseStructure( // Find what edge Ids match with other ranks size_t myRank = comm->GetRank(); - Array perTraceSend(m_nRanks, 0); for (size_t i = 0; i < m_nRanks; ++i) { if (i == myRank) diff --git a/library/MultiRegions/AssemblyMap/AssemblyCommDG.h b/library/MultiRegions/AssemblyMap/AssemblyCommDG.h index c6117b53a7bb0ad40d056dda58fd65bc7e4e98ed..a54b085d6e003c9ae7f4d8fce26c6573580099df 100644 --- a/library/MultiRegions/AssemblyMap/AssemblyCommDG.h +++ b/library/MultiRegions/AssemblyMap/AssemblyCommDG.h @@ -262,7 +262,7 @@ public: * and backwards spaces. * * @param testFwd Local forwards space of the trace (which will be sent) - * @param testBwd Local bacwards space of the trace (which will receive + * @param testBwd Local backwards space of the trace (which will receive * contributions) */ MULTI_REGIONS_EXPORT inline void PerformExchange( diff --git a/library/MultiRegions/AssemblyMap/InterfaceMapDG.cpp b/library/MultiRegions/AssemblyMap/InterfaceMapDG.cpp new file mode 100644 index 0000000000000000000000000000000000000000..7d9a0d8c6e35f188fb3cf080be6d973faa474a5f --- /dev/null +++ b/library/MultiRegions/AssemblyMap/InterfaceMapDG.cpp @@ -0,0 +1,680 @@ +/////////////////////////////////////////////////////////////////////////////// +// +// File InterfaceMapDG.cpp +// +// For more information, please see: http://www.nektar.info +// +// The MIT License +// +// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA), +// Department of Aeronautics, Imperial College London (UK), and Scientific +// Computing and Imaging Institute, University of Utah (USA). +// +// Permission is hereby granted, free of charge, to any person obtaining a +// copy of this software and associated documentation files (the "Software"), +// to deal in the Software without restriction, including without limitation +// the rights to use, copy, modify, merge, publish, distribute, sublicense, +// and/or sell copies of the Software, and to permit persons to whom the +// Software is furnished to do so, subject to the following conditions: +// +// The above copyright notice and this permission notice shall be included +// in all copies or substantial portions of the Software. +// +// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +// DEALINGS IN THE SOFTWARE. +// +// Description: MPI communication for interfaces +// +/////////////////////////////////////////////////////////////////////////////// + +#include "InterfaceMapDG.h" +#include + +namespace Nektar +{ +namespace MultiRegions +{ + +InterfaceTrace::InterfaceTrace( + const ExpListSharedPtr &trace, + const SpatialDomains::InterfaceShPtr &interfaceShPtr) + : m_trace(trace), m_interface(interfaceShPtr) +{ +} + +// Creates the objects that communicates trace values across the interface in +// serial and parallel. Does this by checking all interfaces to see if they +// are contained locally (on the current rank), and checks all other ranks for +// the same interface ID and if contains the opposite interface side i.e. +// 'left' or 'right' +InterfaceMapDG::InterfaceMapDG( + const SpatialDomains::MeshGraphSharedPtr &meshGraph, + const ExpListSharedPtr &trace) + : m_graph(meshGraph), m_movement(meshGraph->GetMovement()), m_trace(trace) +{ + auto comm = m_trace->GetComm(); + auto interfaceCollection = m_movement->GetInterfaces(); + + // myIndxLR contains the info about what interface edges are present on + // current rank with each interface no, i, consisting of: + // [i] = indx + // [i + 1] = 0 (non), = 1 (left only), = 2 (right only), = 3 (both) + std::map myIndxLRMap; + + // localInterfaces contains a map of interface ID to a pair of interface + // traces, this pair is 'left' and 'right' interface and is used to + // construct and store the traces for interfaces present on the current rank + std::map> + localInterfaces; + + // Map of m_localInterfaces vector to interface ID + Array indxToInterfaceID(interfaceCollection.size()); + + // Loops over all interfaces and check if either side, 'left' or 'right' + // are empty on the current rank, if not empty then populate the local + // interface data structures and keep track using myIndxLRMap + size_t cnt = 0; + for (const auto &interface : interfaceCollection) + { + indxToInterfaceID[cnt] = interface.first.first; + myIndxLRMap[interface.first.first] = 0; + + if (!interface.second->GetLeftInterface()->IsEmpty()) + { + myIndxLRMap[interface.first.first] += 1; + + localInterfaces[interface.first.first].first = + MemoryManager::AllocateSharedPtr( + trace, interface.second->GetLeftInterface()); + m_localInterfaces.emplace_back( + localInterfaces[interface.first.first].first); + } + + if (!interface.second->GetRightInterface()->IsEmpty()) + { + myIndxLRMap[interface.first.first] += 2; + + localInterfaces[interface.first.first].second = + MemoryManager::AllocateSharedPtr( + trace, interface.second->GetRightInterface()); + m_localInterfaces.emplace_back( + localInterfaces[interface.first.first].second); + } + + cnt++; + } + + // Send num of interfaces size so all partitions can prepare buffers + int nRanks = comm->GetSize(); + + // Send all interface edges present to all partitions + Array interfaceEdges(myIndxLRMap.size()); + cnt = 0; + for (auto pres : myIndxLRMap) + { + interfaceEdges[cnt++] = pres.second; + } + Array rankLocalInterfaceIds(myIndxLRMap.size() * nRanks, 0); + comm->AllGather(interfaceEdges, rankLocalInterfaceIds); + + // Map of rank to vector of interface traces + std::map> oppRankSharedInterface; + + // Find what interface Ids match with other ranks, then check if opposite + // edge + size_t myRank = comm->GetRank(); + size_t numInterfaces = interfaceCollection.size(); + for (int i = 0; i < nRanks; ++i) + { + for (size_t j = 0; j < numInterfaces; ++j) + { + int otherId = indxToInterfaceID[j]; + + // otherCode represents for a specific interface ID what sides are + // present on rank i, 0=non, 1=left, 2=right, 3=both + int otherCode = rankLocalInterfaceIds[i * numInterfaces + j]; + + // myCode represents for a specific interface ID what sides are + // present on this rank/process 0=non, 1=left, 2=right, 3=both + int myCode = myIndxLRMap[otherId]; + + // Special case if checking current rank (this process) + if (i == myRank) + { + // If contains both edges locally then set check local to true + if (myCode == 3) + { + localInterfaces[otherId].first->SetCheckLocal(true); + localInterfaces[otherId].second->SetCheckLocal(true); + } + + continue; + } + + // Checks if this ranks 'left' matches any 'right' on other rank + if ((myCode == 1 && otherCode == 2) || + (myCode == 1 && otherCode == 3) || + (myCode == 3 && otherCode == 2)) + { + oppRankSharedInterface[i].emplace_back( + localInterfaces[otherId].first); + } + // Checks if this ranks 'right' matches any 'left' on other rank + else if ((myCode == 2 && otherCode == 1) || + (myCode == 2 && otherCode == 3) || + (myCode == 3 && otherCode == 1)) + { + oppRankSharedInterface[i].emplace_back( + localInterfaces[otherId].second); + } + // Checks if this ranks 'both' matches any 'both' on other rank + else if (myCode == 3 && otherCode == 3) + { + oppRankSharedInterface[i].emplace_back( + localInterfaces[otherId].first); + oppRankSharedInterface[i].emplace_back( + localInterfaces[otherId].second); + } + } + } + + // Create individual interface exchange objects (each object is rank -> + // rank) and contains a vector of interfaceTrace objects + for (auto &rank : oppRankSharedInterface) + { + m_exchange.emplace_back( + MemoryManager::AllocateSharedPtr( + m_movement, m_trace, comm, rank)); + } + + // Find missing coordinates on interface from other side + ExchangeCoords(); +} + +void InterfaceMapDG::ExchangeCoords() +{ + LibUtilities::Timer timer; + timer.Start(); + + auto comm = m_trace->GetComm(); + auto zones = m_movement->GetZones(); + + LibUtilities::Timer timer2; + timer2.Start(); + for (auto &interfaceTrace : m_localInterfaces) + { + interfaceTrace->CalcLocalMissing(); + } + timer2.Stop(); + timer2.AccumulateRegion("InterfaceMapDG::ExchangeCoords local", 1); + + // If parallel communication is needed + if (!m_exchange.empty()) + { + LibUtilities::Timer timer3; + timer3.Start(); + + auto requestSend = comm->CreateRequest(m_exchange.size()); + auto requestRecv = comm->CreateRequest(m_exchange.size()); + + for (int i = 0; i < m_exchange.size(); ++i) + { + m_exchange[i]->RankFillSizes(requestSend, requestRecv, i); + } + comm->WaitAll(requestSend); + comm->WaitAll(requestRecv); + + for (int i = 0; i < m_exchange.size(); ++i) + { + m_exchange[i]->SendMissing(requestSend, requestRecv, i); + } + comm->WaitAll(requestSend); + comm->WaitAll(requestRecv); + + for (auto &i : m_exchange) + { + i->CalcRankDistances(); + } + + timer3.Stop(); + timer3.AccumulateRegion("InterfaceMapDG::ExchangeCoords parallel", 1); + } + + m_movement->GetCoordExchangeFlag() = false; + + timer.Stop(); + timer.AccumulateRegion("InterfaceMapDG::ExchangeCoords"); +} + +/** + * Calculates what coordinates on the interface are missing; i.e. aren't located + * in an edge from the other side of the interface on this partition. These are + * stored in the vector #m_missingCoords, and another vector of the same index + * layout contains the location of that coordinate in the trace i.e. the + * 'offset + i' value. It checks first if the interface is flagged local, which + * denotes whether the opposite side is also present on this rank, if not then + * all coordinates are missing. If local then the same structure as + * CalcRankDistances is used to minimise computational cost. + */ +void InterfaceTrace::CalcLocalMissing() +{ + // Nuke old missing/found + m_missingCoords.clear(); + m_mapMissingCoordToTrace.clear(); + + // Store copy of found coords to optimise search before clearing + auto foundLocalCoordsCopy = m_foundLocalCoords; + m_foundLocalCoords.clear(); + + auto childEdge = m_interface->GetEdge(); + // If not flagged 'check local' then all points are missing + if (!m_checkLocal) + { + int cnt = 0; + for (auto &childId : childEdge) + { + auto childElmt = m_trace->GetExpFromGeomId(childId.first); + size_t nq = childElmt->GetTotPoints(); + Array xc(nq, 0.0), yc(nq, 0.0), zc(nq, 0.0); + childElmt->GetCoords(xc, yc, zc); + int offset = + m_trace->GetPhys_Offset(m_trace->GetElmtToExpId(childId.first)); + + for (int i = 0; i < nq; ++i, ++cnt) + { + Array xs(3); + xs[0] = xc[i]; + xs[1] = yc[i]; + xs[2] = zc[i]; + + m_missingCoords.emplace_back(xs); + m_mapMissingCoordToTrace.emplace_back(offset + i); + } + } + } + // Otherwise we need to check to see what points the other side of the + // interface on this rank contains. This is done by looping over each + // quadrature point in all the edges on this side of the interface, then + // check if this quadrature point is also in any edges on the other side + // of the interface. First use MinMaxCheck as a cheap method to eliminate + // far away edges. If it passes MinMaxCheck perform the FindDistance search + // which numerically searches for the closest local coordinate on the other + // interface side edge and returns the cartesian distance from the search + // coordinate to the found local coordinate. If determined to be close + // enough then add to found local coordinates. + else + { + for (auto &childId : childEdge) + { + auto childElmt = m_trace->GetExpFromGeomId(childId.first); + size_t nq = childElmt->GetTotPoints(); + Array xc(nq, 0.0), yc(nq, 0.0), zc(nq, 0.0); + childElmt->GetCoords(xc, yc, zc); + int offset = + m_trace->GetPhys_Offset(m_trace->GetElmtToExpId(childId.first)); + + for (int i = 0; i < nq; ++i) + { + bool found = false; + Array foundLocCoord; + Array xs(3); + xs[0] = xc[i]; + xs[1] = yc[i]; + xs[2] = zc[i]; + + // First search the edge the point was found in last timestep + if (foundLocalCoordsCopy.find(offset + i) != + foundLocalCoordsCopy.end()) + { + auto edge = m_interface->GetOppInterface()->GetEdge( + foundLocalCoordsCopy[offset + i].first); + NekDouble dist = edge->FindDistance(xs, foundLocCoord); + + if (dist < 5e-5) + { + m_foundLocalCoords[offset + i] = + std::make_pair(edge->GetGlobalID(), foundLocCoord); + continue; + } + } + + // If not in last timestep edge then loop over all interface + // edges + auto parentEdge = m_interface->GetOppInterface()->GetEdge(); + for (auto &edge : parentEdge) + { + // First check if inside the edge bounding box + if (!edge.second->MinMaxCheck(xs)) + { + continue; + } + + NekDouble dist = + edge.second->FindDistance(xs, foundLocCoord); + if (dist < NekConstants::kFindDistanceMin) + { + found = true; + m_foundLocalCoords[offset + i] = std::make_pair( + edge.second->GetGlobalID(), foundLocCoord); + break; + } + } + + if (!found) + { + m_missingCoords.emplace_back(xs); + m_mapMissingCoordToTrace.emplace_back(offset + i); + } + } + } + } + + // If running in serial there shouldn't be any missing coordinates. + // Unless we flag to ignore this check for this specific interface. + if (m_trace->GetComm()->IsSerial() && !m_interface->GetSkipCoordCheck()) + { + ASSERTL0(m_missingCoords.empty(), + "Missing " + std::to_string(m_missingCoords.size()) + + " coordinates on interface ID " + + std::to_string(m_interface->GetId()) + + " linked to interface ID " + + std::to_string(m_interface->GetOppInterface()->GetId()) + + ". Check both sides of the interface line up."); + } +} + +// This fills m_sendSize and m_recvSize with the correct sizes for the +// communication lengths for each rank when communicating the traces. I.e. +// however many quadrature points on the opposite side of the interface to +// send, and however many on this side to receive. +void InterfaceExchange::RankFillSizes( + LibUtilities::CommRequestSharedPtr &requestSend, + LibUtilities::CommRequestSharedPtr &requestRecv, int requestNum) +{ + + // Recalc size is the number of interfaces missing points that need to be + // communicated. + int recalcSize = 0; + for (auto &localInterface : m_interfaceTraces) + { + recalcSize += + m_zones[localInterface->GetInterface()->GetId()]->GetMoved(); + } + + m_sendSize[m_rank] = Array(recalcSize); + m_recvSize[m_rank] = Array(recalcSize); + + int cnt = 0; + for (auto &interface : m_interfaceTraces) + { + if (m_zones[interface->GetInterface()->GetId()]->GetMoved()) + { + // Calculates the number of missing coordinates to be communicated + // This size is 3 times the number of missing coordinates to allow + // for 3D points + m_sendSize[m_rank][cnt++] = + interface->GetMissingCoords().size() * 3; + } + } + + // Uses non-blocking send/recvs to send communication sizes to other ranks + m_comm->Isend(m_rank, m_sendSize[m_rank], m_interfaceTraces.size(), + requestSend, requestNum); + m_comm->Irecv(m_rank, m_recvSize[m_rank], m_interfaceTraces.size(), + requestRecv, requestNum); +} + +// Uses the calculated send/recv sizes to send all missing coordinates to +// other ranks. +void InterfaceExchange::SendMissing( + LibUtilities::CommRequestSharedPtr &requestSend, + LibUtilities::CommRequestSharedPtr &requestRecv, int requestNum) +{ + m_totSendSize[m_rank] = std::accumulate(m_sendSize[m_rank].begin(), + m_sendSize[m_rank].end(), 0); + m_totRecvSize[m_rank] = std::accumulate(m_recvSize[m_rank].begin(), + m_recvSize[m_rank].end(), 0); + + m_send = Array(m_totSendSize[m_rank]); + m_recv = Array(m_totRecvSize[m_rank]); + + int cnt = 0; + for (auto &interface : m_interfaceTraces) + { + if (m_zones[interface->GetInterface()->GetId()]->GetMoved()) + { + auto missing = interface->GetMissingCoords(); + for (auto coord : missing) + { + // Points are organised in blocks of three + // x coord, then y coord, then z coord. + for (int k = 0; k < 3; ++k, ++cnt) + { + m_send[cnt] = coord[k]; + } + } + } + } + + // Uses non-blocking send/recvs to send missing points to other ranks + m_comm->Isend(m_rank, m_send, m_totSendSize[m_rank], requestSend, + requestNum); + m_comm->Irecv(m_rank, m_recv, m_totRecvSize[m_rank], requestRecv, + requestNum); +} + +/** + * Performs the trace exchange across interfaces + * 1) Calculate and send the Fwd trace to other ranks with pairwise comms + * 2) While waiting for the send/recv to complete we fill the local interfaces + * Bwd trace + * 3) Fill the remaining Bwd trace with the received trace data from other ranks + */ +void InterfaceMapDG::ExchangeTrace(Array &Fwd, + Array &Bwd) +{ + if (m_movement->GetCoordExchangeFlag()) + { + ExchangeCoords(); + } + auto comm = m_trace->GetComm(); + // If no parallel exchange needed we only fill the local traces + if (m_exchange.empty()) + { + + // Fill local interface traces + for (auto &m_localInterface : m_localInterfaces) + { + m_localInterface->FillLocalBwdTrace(Fwd, Bwd); + } + } + else + { + auto requestSend = comm->CreateRequest(m_exchange.size()); + auto requestRecv = comm->CreateRequest(m_exchange.size()); + for (int i = 0; i < m_exchange.size(); ++i) + { + m_exchange[i]->SendFwdTrace(requestSend, requestRecv, i, Fwd); + } + + // Fill local interface traces + for (auto &m_localInterface : m_localInterfaces) + { + m_localInterface->FillLocalBwdTrace(Fwd, Bwd); + } + + comm->WaitAll(requestSend); + comm->WaitAll(requestRecv); + + // Fill communicated interface traces + for (auto &i : m_exchange) + { + i->FillRankBwdTraceExchange(Bwd); + } + } +} + +void InterfaceTrace::FillLocalBwdTrace(Array &Fwd, + Array &Bwd) +{ + // If flagged then fill trace from local coords + if (m_checkLocal) + { + for (auto &foundLocCoord : m_foundLocalCoords) + { + int traceId = m_trace->GetElmtToExpId(foundLocCoord.second.first); + Array locCoord = foundLocCoord.second.second; + + Array edgePhys = + Fwd + m_trace->GetPhys_Offset(traceId); + + Bwd[foundLocCoord.first] = + m_trace->GetExp(traceId)->StdPhysEvaluate(locCoord, edgePhys); + } + } +} + +void InterfaceExchange::FillRankBwdTraceExchange(Array &Bwd) +{ + int cnt = 0; + for (int i = 0; i < m_interfaceTraces.size(); ++i) + { + Array traceTmp(m_sendSize[m_rank][i] / 3, 0.0); + for (int j = 0; j < m_sendSize[m_rank][i] / 3; ++j, ++cnt) + { + traceTmp[j] = m_recvTrace[cnt]; + } + + m_interfaceTraces[i]->FillRankBwdTrace(traceTmp, Bwd); + } +} + +void InterfaceTrace::FillRankBwdTrace(Array &trace, + Array &Bwd) +{ + for (int i = 0; i < m_mapMissingCoordToTrace.size(); ++i) + { + if (!std::isnan(trace[i])) + { + Bwd[m_mapMissingCoordToTrace[i]] = trace[i]; + } + } +} + +void InterfaceExchange::SendFwdTrace( + LibUtilities::CommRequestSharedPtr &requestSend, + LibUtilities::CommRequestSharedPtr &requestRecv, int requestNum, + Array &Fwd) +{ + m_recvTrace = + Array(m_totSendSize[m_rank] / 3, std::nan("")); + m_sendTrace = + Array(m_totRecvSize[m_rank] / 3, std::nan("")); + + for (auto &i : m_foundRankCoords[m_rank]) + { + int traceId = m_trace->GetElmtToExpId(i.second.first); + Array locCoord = i.second.second; + + Array edgePhys = + Fwd + m_trace->GetPhys_Offset(traceId); + + m_sendTrace[i.first] = + m_trace->GetExp(traceId)->StdPhysEvaluate(locCoord, edgePhys); + } + + m_comm->Isend(m_rank, m_sendTrace, m_sendTrace.size(), requestSend, + requestNum); + m_comm->Irecv(m_rank, m_recvTrace, m_recvTrace.size(), requestRecv, + requestNum); +} + +/** + * Check coords in m_recv from other rank to see if present on this rank, and + * then populates m_foundRankCoords if found. + * - Loops over all interface traces present in the exchange, i.e. every + * interface needed on this rank-to-rank communication object + * - Then loops over all the quadrature points missing from the other side in + * that interface using global coordinates + * - Loop over each local edge and use MinMaxCheck on the point as a fast + * comparison on whether the point lies on the edge + * - If true then use the more expensive FindDistance function to find the + * closest local coordinate of the global 'missing' point on the local edge + * and the distance from the edge that corresponds to + * - If distance is less than 5e-5 save found coordinate in m_foundRankCoords + */ + +void InterfaceExchange::CalcRankDistances() +{ + // Clear old found coordinates + auto foundRankCoordsCopy = m_foundRankCoords; + m_foundRankCoords[m_rank] + .clear(); // @TODO: This may cause problems with 2 interfaces and one is + // fixed? With the skip below. + + Array disp(m_recvSize[m_rank].size() + 1, 0.0); + std::partial_sum(m_recvSize[m_rank].begin(), m_recvSize[m_rank].end(), + &disp[1]); + + for (int i = 0; i < m_interfaceTraces.size(); ++i) + { + if (!m_zones[m_interfaceTraces[i]->GetInterface()->GetId()]->GetMoved()) + { + // If zone is not moved then skip + continue; + } + + auto localEdge = m_interfaceTraces[i]->GetInterface()->GetEdge(); + + for (int j = disp[i]; j < disp[i + 1]; j += 3) + { + Array foundLocCoord; + Array xs(3); + xs[0] = m_recv[j]; + xs[1] = m_recv[j + 1]; + xs[2] = m_recv[j + 2]; + + // First search the edge the point was found in last timestep + if (foundRankCoordsCopy[m_rank].find(j / 3) != + foundRankCoordsCopy[m_rank].end()) + { + auto edge = m_interfaceTraces[i]->GetInterface()->GetEdge( + foundRankCoordsCopy[m_rank][j / 3].first); + NekDouble dist = edge->FindDistance(xs, foundLocCoord); + + if (dist < 5e-5) + { + m_foundRankCoords[m_rank][j / 3] = + std::make_pair(edge->GetGlobalID(), foundLocCoord); + continue; + } + } + + for (auto &edge : localEdge) + { + // First check if inside the edge bounding box + if (!edge.second->MinMaxCheck(xs)) + { + continue; + } + + NekDouble dist = edge.second->FindDistance(xs, foundLocCoord); + + if (dist < NekConstants::kFindDistanceMin) + { + m_foundRankCoords[m_rank][j / 3] = std::make_pair( + edge.second->GetGlobalID(), foundLocCoord); + break; + } + } + } + } +} + +} // namespace MultiRegions +} // namespace Nektar \ No newline at end of file diff --git a/library/MultiRegions/AssemblyMap/InterfaceMapDG.h b/library/MultiRegions/AssemblyMap/InterfaceMapDG.h new file mode 100644 index 0000000000000000000000000000000000000000..d59a89f69933f0b0ade816f1347fd8ead701345c --- /dev/null +++ b/library/MultiRegions/AssemblyMap/InterfaceMapDG.h @@ -0,0 +1,274 @@ +/////////////////////////////////////////////////////////////////////////////// +// +// File InterfaceMapDG.h +// +// For more information, please see: http://www.nektar.info +// +// The MIT License +// +// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA), +// Department of Aeronautics, Imperial College London (UK), and Scientific +// Computing and Imaging Institute, University of Utah (USA). +// +// Permission is hereby granted, free of charge, to any person obtaining a +// copy of this software and associated documentation files (the "Software"), +// to deal in the Software without restriction, including without limitation +// the rights to use, copy, modify, merge, publish, distribute, sublicense, +// and/or sell copies of the Software, and to permit persons to whom the +// Software is furnished to do so, subject to the following conditions: +// +// The above copyright notice and this permission notice shall be included +// in all copies or substantial portions of the Software. +// +// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +// DEALINGS IN THE SOFTWARE. +// +// Description: MPI communication for interfaces, header file +// +/////////////////////////////////////////////////////////////////////////////// + +#ifndef NEKTAR_INTERFACEMAPDG_H +#define NEKTAR_INTERFACEMAPDG_H + +#include +#include + +namespace Nektar +{ +namespace MultiRegions +{ + +/** + * Object for each interface present between two ranks, which are held in the + * InterfaceExchange object. + */ + +class InterfaceTrace +{ +public: + /// Constructor + MULTI_REGIONS_EXPORT InterfaceTrace( + const ExpListSharedPtr &trace, + const SpatialDomains::InterfaceShPtr &interfaceShPtr); + + /// Default destructor + MULTI_REGIONS_EXPORT virtual ~InterfaceTrace() = default; + + inline void SetCheckLocal(bool flag) + { + m_checkLocal = flag; + } + + /// Returns the missing coordinates vector + inline std::vector> GetMissingCoords() + { + return m_missingCoords; + } + + /// Returns the interface object + SpatialDomains::InterfaceShPtr GetInterface() + { + return m_interface; + } + + /// Calculates what coordinates on the interface are missing locally + void CalcLocalMissing(); + /// Fills the Bwd trace by interpolating from the Fwd for local interfaces + void FillLocalBwdTrace(Array &Fwd, + Array &Bwd); + /// Fills the Bwd trace from partitioned trace + void FillRankBwdTrace(Array &trace, + Array &Bwd); + +private: + /// Trace expansion list + ExpListSharedPtr m_trace; + /// Local interface object + SpatialDomains::InterfaceShPtr m_interface; + /// Flag whether the opposite side of the interface is present locally + bool m_checkLocal = false; + /// Vector of coordinates on interface missing from the other side locally + std::vector> m_missingCoords; + /// Map of found coordinates present locally + std::map>> m_foundLocalCoords; + /// Vector of indices corresponding to m_missingCoord locations in trace + std::vector m_mapMissingCoordToTrace; +}; + +typedef std::shared_ptr InterfaceTraceSharedPtr; + +/** + * Object for one rank-to-rank communication for all interfaces shared + * between those ranks. e.g. if on rank 1 and there are interfaces shared with + * rank 2 and 3, there will be two InterfaceExchange objects in m_exchange in + * InterfaceMapDG. This holds the InterfaceTrace objects in m_interfaceTraces. + */ +class InterfaceExchange +{ +public: + /// Default destructor + MULTI_REGIONS_EXPORT virtual ~InterfaceExchange() = default; + + /// Constructor + MULTI_REGIONS_EXPORT InterfaceExchange( + SpatialDomains::MovementSharedPtr movement, + const ExpListSharedPtr &trace, const LibUtilities::CommSharedPtr &comm, + std::pair> rankPair) + : m_movement(movement), m_zones(movement->GetZones()), m_trace(trace), + m_comm(comm), m_rank(rankPair.first), + m_interfaceTraces(rankPair.second) + { + } + + /** + * Communicates with other ranks how many missing coordinates for each + * interface to expect + * + * @param requestSend List of send requests + * @param requestRecv List of receive requests + * @param requestNum Index of request in list to use + */ + MULTI_REGIONS_EXPORT void RankFillSizes( + LibUtilities::CommRequestSharedPtr &requestSend, + LibUtilities::CommRequestSharedPtr &requestRecv, int requestNum); + + /** + * Sends/receives the missing coordinates to/from other ranks + * + * @param requestSend List of send requests + * @param requestRecv List of receive requests + * @param requestNum Index of request in list to use + */ + MULTI_REGIONS_EXPORT void SendMissing( + LibUtilities::CommRequestSharedPtr &requestSend, + LibUtilities::CommRequestSharedPtr &requestRecv, int requestNum); + + /// Populates m_foundRankCoords using the FindDistance function + MULTI_REGIONS_EXPORT void CalcRankDistances(); + + /** + * Calculates and sends the trace to other rank from the m_foundRankCoords + * structure using non-blocking pairwise communication i.e. Isend & Irecv + * + * @param requestSend List of send requests + * @param requestRecv List of receive requests + * @param requestNum Index of request in list to use + * @param Fwd The values to send across the interface + */ + MULTI_REGIONS_EXPORT void SendFwdTrace( + LibUtilities::CommRequestSharedPtr &requestSend, + LibUtilities::CommRequestSharedPtr &requestRecv, int requestNum, + Array &Fwd); + + /** + * Loops over interfaces and partitions out the received trace from the + * other ranks for insertion into Bwd using FillRankBwdTrace + * + * @param Bwd The Bwd trace to be filled from across the interface + */ + MULTI_REGIONS_EXPORT void FillRankBwdTraceExchange( + Array &Bwd); + +private: + /// Movement object associated with the non-conformal interfaces + SpatialDomains::MovementSharedPtr m_movement; + /// Map of zone IDs to zone bases + std::map m_zones; + /// Trace expansion list + const ExpListSharedPtr m_trace; + /// Communicator + const LibUtilities::CommSharedPtr m_comm; + /// Process rank + int m_rank; + /// Vector of interface traces i.e. every interface side present on m_rank + const std::vector m_interfaceTraces; + /// Send buffer for coord exchange + Array m_send; + /// Receive buffer for coord exchange + Array m_recv; + /// Receive buffer for trace exchange + Array m_recvTrace; + /// Send buffer for trace exchange + Array m_sendTrace; + /// Map of rank to total size of send buffer for all interfaces + std::map m_totSendSize; + /// Map of rank to total size of receive buffer for all interfaces + std::map m_totRecvSize; + /// Map of rank to array of size of send buffer for each interface + std::map> m_sendSize; + /// Map of rank to array of size of receive buffer for each interface + std::map> m_recvSize; + + /** + * Caches the found coordinates to reuse when exchanging the trace in a + * map of integer rank to a map of integer missing coordinate location to a + * pair of local edge ID and found local coordinate + */ + std::map>>> + m_foundRankCoords; +}; + +typedef std::shared_ptr InterfaceExchangeSharedPtr; + +/** + * Implements the communication patterns to allow for exchange of information + * across non-conformal interfaces and across different partitions. Holds all + * the InterfaceExchange objects in m_exchange. + */ +class InterfaceMapDG +{ +public: + /// Default destructor + MULTI_REGIONS_EXPORT ~InterfaceMapDG() = default; + + /** + * Sets up the InterfaceExchange objects stored in m_exchange, each object + * is rank -> rank and contains a vector of InterfaceTrace objects + * corresponding to shared interfaces between those ranks. + */ + MULTI_REGIONS_EXPORT InterfaceMapDG( + const SpatialDomains::MeshGraphSharedPtr &graph, + const ExpListSharedPtr &trace); + + /** + * @brief Perform the trace exchange between processors, given the forwards + * and backwards spaces. + * + * @param Fwd Local forwards space of the trace (which will be sent) + * @param Bwd Local backwards space of the trace (which will receive + * contributions) + */ + MULTI_REGIONS_EXPORT void ExchangeTrace(Array &Fwd, + Array &Bwd); + /** + * @brief Perform the coordinate exchange between processors. This is where + * the missing coordinates on the interface are found and sent to all other + * processors on the other side of that interface so the matching ranks can + * be found. + */ + MULTI_REGIONS_EXPORT void ExchangeCoords(); + +private: + /// Mesh associated with this expansion list. + SpatialDomains::MeshGraphSharedPtr m_graph; + /// Movement object associated with the non-conformal interfaces + SpatialDomains::MovementSharedPtr m_movement; + /// Interface sides present on current process + std::vector m_localInterfaces; + /// Trace expansion list + const ExpListSharedPtr m_trace; + /// Vector of interface exchanges, i.e. every rank-to-rank comm needed + std::vector m_exchange; +}; + +typedef std::shared_ptr InterfaceMapDGSharedPtr; + +} // namespace MultiRegions +} // namespace Nektar + +#endif \ No newline at end of file diff --git a/library/MultiRegions/CMakeLists.txt b/library/MultiRegions/CMakeLists.txt index 67daccb0e6e6b8e1954cb4b4b522f2719b20beb7..790e0cbfafc39eda6689e9f8233dfac522ca7e07 100644 --- a/library/MultiRegions/CMakeLists.txt +++ b/library/MultiRegions/CMakeLists.txt @@ -3,6 +3,7 @@ SET(MULTI_REGIONS_SOURCES ./AssemblyMap/AssemblyMap.cpp ./AssemblyMap/AssemblyMapCG.cpp ./AssemblyMap/AssemblyMapDG.cpp +./AssemblyMap/InterfaceMapDG.cpp ./AssemblyMap/LocTraceToTraceMap.cpp ContField.cpp ContField3DHomogeneous1D.cpp @@ -76,6 +77,7 @@ SET(ASSEMBLY_MAP_HEADERS ./AssemblyMap/AssemblyMap.h ./AssemblyMap/AssemblyMapCG.h ./AssemblyMap/AssemblyMapDG.h +./AssemblyMap/InterfaceMapDG.h ./AssemblyMap/LocTraceToTraceMap.h ) diff --git a/library/MultiRegions/DisContField.cpp b/library/MultiRegions/DisContField.cpp index e08894f27855f78a85e3b2d00335d76de93ea6d0..3b57a136e41355739c665b1d7794316b614e7226 100644 --- a/library/MultiRegions/DisContField.cpp +++ b/library/MultiRegions/DisContField.cpp @@ -213,6 +213,10 @@ void DisContField::SetUpDG(const std::string variable, // Set up physical normals SetUpPhysNormals(); + // Create interface exchange object + m_interfaceMap = + MemoryManager::AllocateSharedPtr(m_graph, m_trace); + int cnt, n; // Identify boundary trace @@ -736,6 +740,7 @@ DisContField::DisContField(const DisContField &In, m_globalBndMat = In.m_globalBndMat; m_trace = In.m_trace; m_traceMap = In.m_traceMap; + m_interfaceMap = In.m_interfaceMap; m_locTraceToTraceMap = In.m_locTraceToTraceMap; m_periodicVerts = In.m_periodicVerts; m_periodicEdges = In.m_periodicEdges; @@ -745,7 +750,7 @@ DisContField::DisContField(const DisContField &In, m_boundaryTraces = In.m_boundaryTraces; m_leftAdjacentTraces = In.m_leftAdjacentTraces; - if (SetUpJustDG == false) + if (!SetUpJustDG) { // set elmt edges to point to robin bc edges if required int i, cnt = 0; @@ -2893,6 +2898,11 @@ void DisContField::v_GetFwdBwdTracePhys( { // Do parallel exchange for forwards/backwards spaces. m_traceMap->GetAssemblyCommDG()->PerformExchange(Fwd, Bwd); + + // Do exchange of interface traces (local and parallel) + // We may have to split this out into separate local and + // parallel for IP method??? + m_interfaceMap->ExchangeTrace(Fwd, Bwd); } } @@ -3063,6 +3073,7 @@ void DisContField::v_ExtractTracePhys( m_locTraceToTraceMap->GetNFwdLocTracePts()); m_locTraceToTraceMap->FwdLocTracesFromField(inarray, tracevals); m_locTraceToTraceMap->InterpLocTracesToTrace(0, tracevals, outarray); + m_traceMap->GetAssemblyCommDG()->PerformExchange(outarray, outarray); } else diff --git a/library/MultiRegions/DisContField.h b/library/MultiRegions/DisContField.h index e345541f05dcc8bfc9fb21187fcab20c231e7078..6f64ff50525910f738fa39f7e27afbe6fa558deb 100644 --- a/library/MultiRegions/DisContField.h +++ b/library/MultiRegions/DisContField.h @@ -37,6 +37,7 @@ #define NEKTAR_LIBS_MULTIREGIONS_DISCONTFIELD1D_H #include +#include #include #include #include @@ -148,6 +149,9 @@ protected: /// condition on the different boundary regions. Array m_bndConditions; + /// Interfaces mapping for trace space. + InterfaceMapDGSharedPtr m_interfaceMap; + /// Global boundary matrix. GlobalLinSysMapShPtr m_globalBndMat; diff --git a/library/MultiRegions/ExpList.cpp b/library/MultiRegions/ExpList.cpp index ea3d8838fdbbb16d9e29967bc5ca4c125d5e9a8a..5bf104168d3be20444b8677a5bb04cc62fd086ce 100644 --- a/library/MultiRegions/ExpList.cpp +++ b/library/MultiRegions/ExpList.cpp @@ -126,7 +126,8 @@ ExpList::ExpList(const ExpList &in, const bool DeclareCoeffPhysArrays) m_coll_coeff_offset(in.m_coll_coeff_offset), m_coll_phys_offset(in.m_coll_phys_offset), m_coeff_offset(in.m_coeff_offset), m_phys_offset(in.m_phys_offset), - m_blockMat(in.m_blockMat), m_WaveSpace(false) + m_blockMat(in.m_blockMat), m_WaveSpace(false), + m_elmtToExpId(in.m_elmtToExpId) { // Set up m_coeffs, m_phys and offset arrays. @@ -194,7 +195,7 @@ ExpList::ExpList(const LibUtilities::SessionReaderSharedPtr &pSession, const SpatialDomains::ExpansionInfoMap &expansions = graph->GetExpansionInfo(var); - // Initialise Expansionn Vector + // Initialise Expansion Vector InitialiseExpVector(expansions); // Setup phys coeff space @@ -754,6 +755,15 @@ ExpList::ExpList( { CreateCollections(ImpType); } + + // Setup element to expansion ID maps for the trace elements + // Loop in reverse order so that in case where using a + // Homogeneous expansion it sets geometry ids to first part of + // m_exp list. Otherwise will set to second (complex) expansion + for (int i = (*m_exp).size() - 1; i >= 0; --i) + { + m_elmtToExpId[(*m_exp)[i]->GetGeom()->GetGlobalID()] = i; + } } /** @@ -1289,7 +1299,8 @@ void ExpList::InitialiseExpVector( "Dimension of basis key is greater than 3"); } - // Assign next id + // Assign next id and fill the global id -> exp id map + m_elmtToExpId[exp->GetGeom()->GetGlobalID()] = id; exp->SetElmtId(id++); // Add the expansion @@ -2675,6 +2686,9 @@ void ExpList::v_Reset() LibUtilities::NekManager::ClearManager(); + // Reset block matrix map + m_blockMat->clear(); + // Loop over all elements and reset geometry information. for (int i = 0; i < m_exp->size(); ++i) { @@ -2687,6 +2701,21 @@ void ExpList::v_Reset() { (*m_exp)[i]->Reset(); } + + CreateCollections(Collections::eNoImpType); // @TODO: Might need to pass in + // correct type here +} + +void ExpList::ResetMatrices() +{ + // Reset matrix managers. + LibUtilities::NekManager::ClearManager(); + LibUtilities::NekManager::ClearManager(); + + // Reset block matrix map + m_blockMat->clear(); } /** diff --git a/library/MultiRegions/ExpList.h b/library/MultiRegions/ExpList.h index 2dec5110da6f9816a681c3bf3f472623b8e3913c..20d5f611947fcfc3ed11359244b9140d07e4f2c2 100644 --- a/library/MultiRegions/ExpList.h +++ b/library/MultiRegions/ExpList.h @@ -51,6 +51,7 @@ #include #include #include +#include #include namespace Nektar @@ -409,6 +410,9 @@ public: v_Reset(); } + /// Reset matrices + MULTI_REGIONS_EXPORT void ResetMatrices(); + void WriteTecplotHeader(std::ostream &outfile, std::string var = "") { v_WriteTecplotHeader(outfile, var); @@ -703,6 +707,11 @@ public: /// expansion of the \f$n^{\mathrm{th}}\f$ element. inline LocalRegions::ExpansionSharedPtr &GetExp(int n) const; + /// This function returns (a shared pointer to) the local elemental + /// expansion of the \f$n^{\mathrm{th}}\f$ element given a global + /// geometry ID. + inline LocalRegions::ExpansionSharedPtr &GetExpFromGeomId(int n); + /// This function returns (a shared pointer to) the local elemental /// expansion containing the arbitrary point given by \a gloCoord. MULTI_REGIONS_EXPORT LocalRegions::ExpansionSharedPtr &GetExp( @@ -1114,8 +1123,26 @@ public: // points otwards from MULTI_REGIONS_EXPORT std::vector &GetLeftAdjacentTraces(void); + /// This function returns the map of index inside m_exp to geom id + MULTI_REGIONS_EXPORT inline const std::unordered_map + &GetElmtToExpId(void) + { + return m_elmtToExpId; + } + + /// This function returns the index inside m_exp for a given geom id + MULTI_REGIONS_EXPORT inline int GetElmtToExpId(int elmtId) + { + auto it = m_elmtToExpId.find(elmtId); + ASSERTL0(it != m_elmtToExpId.end(), "Global geometry ID " + + std::to_string(elmtId) + + " not found in element ID to " + "expansion ID map.") + return it->second; + } + protected: - /// Exapnsion type + /// Expansion type ExpansionType m_expType; std::shared_ptr GenGlobalMatrixFull( @@ -2217,6 +2244,22 @@ inline LocalRegions::ExpansionSharedPtr &ExpList::GetExp(int n) const return (*m_exp)[n]; } +/** + * @param n The global id of the element concerned. + * + * @return (A shared pointer to) the local expansion of the + * \f$n^{\mathrm{th}}\f$ element. + */ +inline LocalRegions::ExpansionSharedPtr &ExpList::GetExpFromGeomId(int n) +{ + auto it = m_elmtToExpId.find(n); + ASSERTL0(it != m_elmtToExpId.end(), "Global geometry ID " + + std::to_string(n) + + " not found in element ID to " + "expansion ID map.") + return (*m_exp)[it->second]; +} + /** * @return (A const shared pointer to) the local expansion vector #m_exp */ diff --git a/library/NekMesh/CMakeLists.txt b/library/NekMesh/CMakeLists.txt index d41b0e6a36b629e60c45af58d424cca6ed673f64..adb3d762b7deb64001c37958d115dec2011cee1e 100644 --- a/library/NekMesh/CMakeLists.txt +++ b/library/NekMesh/CMakeLists.txt @@ -13,6 +13,7 @@ SET(NEKMESH_SOURCES Module/OutputModules/OutputSTL.cpp Module/OutputModules/OutputStdOut.cpp Module/ProcessModules/ProcessBL.cpp + Module/ProcessModules/ProcessCombine.cpp Module/ProcessModules/ProcessCurve.cpp Module/ProcessModules/ProcessCurvedEdges.cpp Module/ProcessModules/ProcessCyl.cpp @@ -71,6 +72,7 @@ SET(NEKMESH_HEADERS Module/OutputModules/OutputSTL.h Module/OutputModules/OutputStdOut.h Module/ProcessModules/ProcessBL.h + Module/ProcessModules/ProcessCombine.h Module/ProcessModules/ProcessCurve.h Module/ProcessModules/ProcessCurvedEdges.h Module/ProcessModules/ProcessCyl.h diff --git a/library/NekMesh/MeshElements/Node.h b/library/NekMesh/MeshElements/Node.h index f9dcfa70f7e78c435b6cdca0b38b643c3f8c895c..dca34b6dbe922d5268cec57493c94f1bab51a6be 100644 --- a/library/NekMesh/MeshElements/Node.h +++ b/library/NekMesh/MeshElements/Node.h @@ -452,12 +452,18 @@ NEKMESH_EXPORT bool IsNodeClose( */ struct NodeHash : std::unary_function { + + // @TODO: Way of fixing this so it doesn't delete coincident nodes for + // non-conformal grids std::size_t operator()(NodeSharedPtr const &p) const { return hash_combine(p->m_x, p->m_y, p->m_z); } }; -typedef std::unordered_set NodeSet; + +// @TODO: Fixed by just hashing based on memory address, I feel like we +// shouldn't just delete vertices anyway... +typedef std::unordered_set NodeSet; } // namespace NekMesh } // namespace Nektar diff --git a/library/NekMesh/Module/InputModules/InputNekpp.cpp b/library/NekMesh/Module/InputModules/InputNekpp.cpp index b0a4f3211e50e94125dd8ec626fab327663e6b3d..6e378bcf8b9c4a9d6521b359ceb96b0fcfe7ade3 100644 --- a/library/NekMesh/Module/InputModules/InputNekpp.cpp +++ b/library/NekMesh/Module/InputModules/InputNekpp.cpp @@ -74,9 +74,13 @@ void InputNekpp::Process() m_log(VERBOSE) << "Reading Nektar++ XML file '" << filename[0] << "'" << endl; + LibUtilities::CommSharedPtr pComm = + m_mesh->m_comm ? m_mesh->m_comm : LibUtilities::CommSharedPtr(); + char *prgname = const_cast("NekMesh"); LibUtilities::SessionReaderSharedPtr pSession = - LibUtilities::SessionReader::CreateInstance(1, &prgname, filename); + LibUtilities::SessionReader::CreateInstance(1, &prgname, filename, + pComm); SpatialDomains::MeshGraphSharedPtr graph = SpatialDomains::MeshGraph::Read(pSession); diff --git a/library/NekMesh/Module/OutputModules/OutputNekpp.cpp b/library/NekMesh/Module/OutputModules/OutputNekpp.cpp index 799e7addf6ad9ea11d52703bf2b4956f95f96276..f930ffb4ff9eda6eceb7e9fc297f781b1fb0a44f 100644 --- a/library/NekMesh/Module/OutputModules/OutputNekpp.cpp +++ b/library/NekMesh/Module/OutputModules/OutputNekpp.cpp @@ -782,14 +782,19 @@ void OutputNekpp::TransferComposites(MeshGraphSharedPtr graph) } } +// @TODO: We currently lose domain information from input file here. This +// assumes +// every composite that is of expansion dimension is a separate domain +// and sequentially numbered. So junks multi-composite domains & IDs. void OutputNekpp::TransferDomain(MeshGraphSharedPtr graph) { - map &domain = graph->GetDomain(); - - string list; + std::map &domain = graph->GetDomain(); + int cnt = 0; for (auto &it : m_mesh->m_composite) { + + string list; if (it.second->m_items[0]->GetDim() == m_mesh->m_expDim) { if (list.length() > 0) @@ -797,12 +802,12 @@ void OutputNekpp::TransferDomain(MeshGraphSharedPtr graph) list += ","; } list += boost::lexical_cast(it.second->m_id); + + SpatialDomains::CompositeMap fullDomain; + graph->GetCompositeList(list, fullDomain); + domain[cnt++] = fullDomain; } } - - SpatialDomains::CompositeMap fullDomain; - graph->GetCompositeList(list, fullDomain); - domain[0] = fullDomain; } } // namespace NekMesh diff --git a/library/NekMesh/Module/ProcessModules/ProcessCombine.cpp b/library/NekMesh/Module/ProcessModules/ProcessCombine.cpp new file mode 100644 index 0000000000000000000000000000000000000000..d97ffb953271b927cb4d1914cb02ed5e5a7a21cc --- /dev/null +++ b/library/NekMesh/Module/ProcessModules/ProcessCombine.cpp @@ -0,0 +1,329 @@ +//////////////////////////////////////////////////////////////////////////////// +// +// File: ProcessCombine.cpp +// +// For more information, please see: http://www.nektar.info/ +// +// The MIT License +// +// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA), +// Department of Aeronautics, Imperial College London (UK), and Scientific +// Computing and Imaging Institute, University of Utah (USA). +// +// Permission is hereby granted, free of charge, to any person obtaining a +// copy of this software and associated documentation files (the "Software"), +// to deal in the Software without restriction, including without limitation +// the rights to use, copy, modify, merge, publish, distribute, sublicense, +// and/or sell copies of the Software, and to permit persons to whom the +// Software is furnished to do so, subject to the following conditions: +// +// The above copyright notice and this permission notice shall be included +// in all copies or substantial portions of the Software. +// +// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +// DEALINGS IN THE SOFTWARE. +// +// Description: Combine two mesh files into one output file. +// +//////////////////////////////////////////////////////////////////////////////// + +#include "ProcessCombine.h" +#include +#include +#include +#include + +using namespace std; +using namespace Nektar::NekMesh; + +namespace Nektar +{ +namespace NekMesh +{ + +ModuleKey ProcessCombine::className = + GetModuleFactory().RegisterCreatorFunction( + ModuleKey(eProcessModule, "combine"), ProcessCombine::create, + "Combine two mesh files into one output file."); + +ProcessCombine::ProcessCombine(MeshSharedPtr m) : ProcessModule(m) +{ + m_config["file"] = ConfigOption( + false, "", "Second mesh file to be combined with the input mesh file."); +} + +ProcessCombine::~ProcessCombine() +{ +} + +void ProcessCombine::Process() +{ + ASSERTL0(m_config["file"].beenSet, + "The 'file' module parameter must be set.") + + std::string fname = m_config["file"].as(); + + // Check to see if filename exists. + if (!boost::filesystem::exists(fname)) + { + m_log(FATAL) << "Unable to read file: '" << fname << "'" << std::endl; + } + + // Process the second mesh input + ModuleKey module; + module.first = eInputModule; + + vector tmp1; + boost::split(tmp1, fname, boost::is_any_of(":")); + if (tmp1.size() == 1) + { + int dot = tmp1[0].find_last_of('.') + 1; + string ext = tmp1[0].substr(dot, tmp1[0].length() - dot); + + if (ext == "gz") + { + string tmp = tmp1[0].substr(0, tmp1[0].length() - 3); + dot = tmp.find_last_of('.') + 1; + ext = tmp.substr(dot, tmp.length() - dot); + } + + module.second = ext; + tmp1.push_back("infile=" + tmp1[0]); + } + else + { + module.second = tmp1[1]; + tmp1.push_back("infile=" + tmp1[0]); + } + + // Copy communicator + MeshSharedPtr mesh = std::make_shared(); + mesh->m_comm = m_mesh->m_comm; + + ModuleSharedPtr mod = GetModuleFactory().CreateInstance(module, mesh); + mod->SetLogger(m_log); + mod->GetLogger().SetPrefix("ProcessCombine"); + + // Set options for this module. + for (int j = 1; j < tmp1.size(); ++j) + { + vector tmp2; + boost::split(tmp2, tmp1[j], boost::is_any_of("=")); + + if (tmp2.size() == 1) + { + mod->RegisterConfig(tmp2[0]); + } + else if (tmp2.size() == 2) + { + mod->RegisterConfig(tmp2[0], tmp2[1]); + } + else + { + NEKERROR(ErrorUtil::efatal, "ERROR: Invalid module configuration: " + "format is either :arg or :arg=val"); + } + } + + // Ensure configuration options have been set. + mod->SetDefaults(); + + // Run second input module + mod->Process(); + MeshSharedPtr mesh2 = mod->GetMesh(); + + // Check dimensions of both meshes are the same + ASSERTL0(m_mesh->m_expDim == mesh2->m_expDim, + "The expansion dimensions of the meshes being combined must be " + "the same.") + + // Renumber vertices and copy in to m_vertexSet + int vid = m_mesh->m_vertexSet.size(); + for (auto &elmt : mesh2->m_element[m_mesh->m_expDim]) + { + for (int j = 0; j < elmt->GetVertexCount(); ++j) + { + pair testIns = + m_mesh->m_vertexSet.insert(elmt->GetVertex(j)); + + if (testIns.second) + { + (*testIns.first)->m_id = vid++; + } + + elmt->SetVertex(j, *testIns.first); + } + } + + // Renumber edges and copy in to m_edgeSet + int eid = m_mesh->m_edgeSet.size(); + for (auto &elmt : mesh2->m_element[m_mesh->m_expDim]) + { + for (int j = 0; j < elmt->GetEdgeCount(); ++j) + { + EdgeSharedPtr ed = elmt->GetEdge(j); + pair testIns = + m_mesh->m_edgeSet.insert(ed); + + if (testIns.second) + { + EdgeSharedPtr ed2 = *testIns.first; + ed2->m_id = eid++; + // ed2->m_elLink.push_back( + // pair(elmt, j)); + } + else + { + EdgeSharedPtr e2 = *(testIns.first); + elmt->SetEdge(j, e2); + if (e2->m_edgeNodes.size() == 0 && ed->m_edgeNodes.size() > 0) + { + e2->m_curveType = ed->m_curveType; + e2->m_edgeNodes = ed->m_edgeNodes; + + // Reverse nodes if appropriate. + if (e2->m_n1->m_id != ed->m_n1->m_id) + { + reverse(e2->m_edgeNodes.begin(), e2->m_edgeNodes.end()); + } + } + + // if (ed->m_parentCAD) + //{ + // e2->m_parentCAD = ed->m_parentCAD; + //} + + // Update edge to element map. + // e2->m_elLink.push_back( + // pair(elmt, j)); + } + + elmt->SetEdge(j, *testIns.first); + } + } + + // @TODO: Create links for 1D elements? + + // Renumber faces and copy in to m_faceSet + int fid = m_mesh->m_faceSet.size(); + for (auto &elmt : mesh2->m_element[m_mesh->m_expDim]) + { + for (int j = 0; j < elmt->GetFaceCount(); ++j) + { + pair testIns = + m_mesh->m_faceSet.insert(elmt->GetFace(j)); + + if (testIns.second) + { + (*(testIns.first))->m_id = fid++; + // Update face to element map. + //(*(testIns.first))->m_elLink.push_back( + // pair(elmt,j)); + } + else + { + // Update face to element map. + //(*(testIns.first))->m_elLink.push_back( + // pair(elmt,j)); + } + + elmt->SetFace(j, *testIns.first); + } + } + + // @TODO: Create links for 2D elements? + + // Renumber elements and copy in to m_element + auto &elmts = mesh2->m_element; + for (int d = 0; d < 4; ++d) + { + int numEl = m_mesh->m_element[d].size(); + auto elVec = elmts[d]; + for (auto &el : elVec) + { + el->SetId(numEl++); + m_mesh->m_element[d].emplace_back(el); + } + } + + // Renumber composites and copy in to m_composite + std::map compRenumber; + for (int d = 0; d <= m_mesh->m_expDim; ++d) + { + vector &elmt = m_mesh->m_element[d]; + for (int i = elmt.size() - mesh2->m_element[d].size(); i < elmt.size(); + ++i) // for number of elements added by mesh 2 + { + CompositeMap::iterator it; + unsigned int tagid = elmt[i]->GetTagList()[0]; + + auto findKey = compRenumber.find(elmt[i]->GetTagList()[0]); + if (findKey != compRenumber.end()) + { + tagid = findKey->second; + } + else + { + // Checks if composite tag is already defined in mesh 1 + while (m_mesh->m_composite.find(tagid) != + m_mesh->m_composite.end()) + { + tagid++; + // Checks if trying to replace the tag with a tag already + // defined in mesh 2 + if (mesh2->m_composite.find(tagid) != + mesh2->m_composite.end()) + { + tagid++; + } + } + + compRenumber[elmt[i]->GetTagList()[0]] = tagid; + } + + it = m_mesh->m_composite.find(tagid); + if (it == m_mesh->m_composite.end()) + { + CompositeSharedPtr tmp = + std::shared_ptr(new Composite()); + pair testIns; + tmp->m_id = tagid; + tmp->m_tag = elmt[i]->GetTag(); + if (mesh2->m_faceLabels.count(tmp->m_id) != 0) + { + tmp->m_label = mesh2->m_faceLabels[tmp->m_id]; + } + + testIns = m_mesh->m_composite.insert( + pair(tagid, tmp)); + it = testIns.first; + } + + elmt[i]->GetTagList()[0] = tagid; + it->second->m_items.push_back(elmt[i]); + } + } + + if (!compRenumber.empty()) + { + m_log << "Duplicate composite IDs from mesh 1 detected in mesh 2." + << endl; + m_log << "These will be remapped in the output file to:" << endl; + + for (auto &cIt : compRenumber) + { + if (cIt.first != cIt.second) + { + m_log << "- C[" << cIt.first << "] => " + << "C[" << cIt.second << "]" << endl; + } + } + } +} +} // namespace NekMesh +} // namespace Nektar diff --git a/library/NekMesh/Module/ProcessModules/ProcessCombine.h b/library/NekMesh/Module/ProcessModules/ProcessCombine.h new file mode 100644 index 0000000000000000000000000000000000000000..2535f617bfab9c01ef26250f4f00ce370e3e958a --- /dev/null +++ b/library/NekMesh/Module/ProcessModules/ProcessCombine.h @@ -0,0 +1,75 @@ +//////////////////////////////////////////////////////////////////////////////// +// +// File: ProcessCombine.h +// +// For more information, please see: http://www.nektar.info/ +// +// The MIT License +// +// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA), +// Department of Aeronautics, Imperial College London (UK), and Scientific +// Computing and Imaging Institute, University of Utah (USA). +// +// Permission is hereby granted, free of charge, to any person obtaining a +// copy of this software and associated documentation files (the "Software"), +// to deal in the Software without restriction, including without limitation +// the rights to use, copy, modify, merge, publish, distribute, sublicense, +// and/or sell copies of the Software, and to permit persons to whom the +// Software is furnished to do so, subject to the following conditions: +// +// The above copyright notice and this permission notice shall be included +// in all copies or substantial portions of the Software. +// +// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +// DEALINGS IN THE SOFTWARE. +// +// Description: Combine two mesh files into one output file. +// +//////////////////////////////////////////////////////////////////////////////// + +#ifndef UTILITIES_NEKMESH_PROCESSCombine +#define UTILITIES_NEKMESH_PROCESSCombine + +#include + +namespace Nektar +{ +namespace NekMesh +{ + +/** + * @brief This processing module calculates the Jacobian of elements + * using %SpatialDomains::GeomFactors and the %Element::GetGeom + * method. For now it simply prints a list of elements which have + * negative Jacobian. + */ +class ProcessCombine : public NekMesh::ProcessModule +{ +public: + /// Creates an instance of this class + static std::shared_ptr create(NekMesh::MeshSharedPtr m) + { + return MemoryManager::AllocateSharedPtr(m); + } + static NekMesh::ModuleKey className; + + ProcessCombine(NekMesh::MeshSharedPtr m); + virtual ~ProcessCombine(); + + /// Write mesh to output file. + void Process() override; + + std::string GetModuleName() override + { + return "ProcessCombine"; + } +}; +} // namespace NekMesh +} // namespace Nektar + +#endif diff --git a/library/SolverUtils/ALEHelper.cpp b/library/SolverUtils/ALEHelper.cpp new file mode 100644 index 0000000000000000000000000000000000000000..6491c6ae056f8fc42203d50825daa95e3822520e --- /dev/null +++ b/library/SolverUtils/ALEHelper.cpp @@ -0,0 +1,429 @@ +#include "ALEHelper.h" +#include +#include + +namespace Nektar +{ + +namespace SolverUtils +{ + +void ALEHelper::InitObject(int spaceDim, + Array &fields) +{ + m_spaceDim = spaceDim; + m_fieldsALE = fields; + + // Initialise grid velocities as 0s + m_gridVelocity = Array>(m_spaceDim); + m_gridVelocityTrace = Array>(m_spaceDim); + for (int i = 0; i < spaceDim; ++i) + { + m_gridVelocity[i] = + Array(fields[0]->GetTotPoints(), 0.0); + m_gridVelocityTrace[i] = + Array(fields[0]->GetTrace()->GetTotPoints(), 0.0); + } + + // Create ALE objects for each interface zone + if (fields[0]->GetGraph() != + nullptr) // homogeneous graphs are missing the graph data + { + for (auto &zone : fields[0]->GetGraph()->GetMovement()->GetZones()) + { + switch (zone.second->GetMovementType()) + { + case SpatialDomains::MovementType::eFixed: + m_ALEs.emplace_back(ALEFixedShPtr( + MemoryManager::AllocateSharedPtr( + zone.second))); + break; + case SpatialDomains::MovementType::eTranslate: + m_ALEs.emplace_back(ALETranslateShPtr( + MemoryManager::AllocateSharedPtr( + zone.second))); + m_ALESolver = true; + break; + case SpatialDomains::MovementType::eRotate: + m_ALEs.emplace_back(ALERotateShPtr( + MemoryManager::AllocateSharedPtr( + zone.second))); + m_ALESolver = true; + break; + case SpatialDomains::MovementType::ePrescribe: + m_ALEs.emplace_back(ALEPrescribeShPtr( + MemoryManager::AllocateSharedPtr( + zone.second))); + m_ALESolver = true; + break; + case SpatialDomains::MovementType::eNone: + WARNINGL0(false, + "Zone cannot have movement type of 'None'.") + } + } + } + + // Update grid velocity + UpdateGridVelocity(0); +} + +void ALEHelper::UpdateGridVelocity(const NekDouble &time) +{ + // Reset grid velocity to 0 + for (int i = 0; i < m_spaceDim; ++i) + { + std::fill(m_gridVelocity[i].begin(), m_gridVelocity[i].end(), 0.0); + } + + // Now update for each movement zone, adding the grid velocities + for (auto &ALE : m_ALEs) + { + ALE->UpdateGridVel(time, m_fieldsALE, m_gridVelocity); + } +} + +void ALEHelper::ALEPreMultiplyMass(Array> &fields) +{ + const int nm = m_fieldsALE[0]->GetNcoeffs(); + MultiRegions::GlobalMatrixKey mkey(StdRegions::eMass); + + // Premultiply each field by the mass matrix + for (int i = 0; i < m_fieldsALE.size(); ++i) + { + fields[i] = Array(nm); + m_fieldsALE[i]->GeneralMatrixOp(mkey, m_fieldsALE[i]->GetCoeffs(), + fields[i]); + } +} + +void ALEHelper::ALEDoElmtInvMass( + Array> &traceNormals, + Array> &fields, NekDouble time) +{ + boost::ignore_unused(time, traceNormals); + // Update m_fields with u^n by multiplying by inverse mass + // matrix. That's then used in e.g. checkpoint output and L^2 error + // calculation. + + // @TODO: Look at geometric factor and junk only what is needed + // @TODO: Look at collections and see if they offer a speed up + for (int i = 0; i < m_fieldsALE.size(); ++i) + { + m_fieldsALE[i]->MultiplyByElmtInvMass( + fields[i], + m_fieldsALE[i]->UpdateCoeffs()); // @TODO: Potentially matrix free? + m_fieldsALE[i]->BwdTrans(m_fieldsALE[i]->GetCoeffs(), + m_fieldsALE[i]->UpdatePhys()); + } +} + +void ALEHelper::ALEDoElmtInvMassBwdTrans( + const Array> &inarray, + Array> &outarray) +{ + const int nc = m_fieldsALE[0]->GetNcoeffs(); + int nVariables = inarray.size(); + + // General idea is that we are time-integrating the quantity (Mu), so we + // need to multiply input by inverse mass matrix to get coefficients u, + // and then backwards transform to physical space so we can apply the DG + // operator. + Array tmp(nc); + for (int i = 0; i < nVariables; ++i) + { + outarray[i] = Array(m_fieldsALE[0]->GetNpoints()); + m_fieldsALE[i]->MultiplyByElmtInvMass(inarray[i], tmp); + m_fieldsALE[i]->BwdTrans(tmp, outarray[i]); + } +} + +void ALEHelper::MoveMesh(const NekDouble &time, + Array> &traceNormals) +{ + // Only move if timestepped + if (time == m_prevStageTime) + { + return; + } + + auto curvedEdges = m_fieldsALE[0]->GetGraph()->GetCurvedEdges(); + auto curvedFaces = m_fieldsALE[0]->GetGraph()->GetCurvedFaces(); + + LibUtilities::Timer timer; + timer.Start(); + m_fieldsALE[0]->GetGraph()->GetMovement()->PerformMovement( + time); // @TODO: Moved out of loop! + timer.Stop(); + timer.AccumulateRegion("Movement::PerformMovement"); + + // The order of the resets below is v important to avoid errors + for (auto &field : m_fieldsALE) + { + field->ResetMatrices(); + } + + // Loop over all elements and faces and edges and reset geometry + // information. Only need to do this on the first field as the geometry + // information is shared. + for (auto &zone : m_fieldsALE[0]->GetGraph()->GetMovement()->GetZones()) + { + if (zone.second->GetMoved()) + { + auto conEl = zone.second->GetConstituentElements(); + for (const auto &i : conEl) + { + for (const auto &j : i) + { + j->ResetNonRecursive(curvedEdges, curvedFaces); + } + } + + // We need to rebuild geometric factors on the trace elements + for (const auto &i : conEl[m_fieldsALE[0]->GetShapeDimension() - + 1]) // This only takes the trace elements + { + m_fieldsALE[0]->GetTrace()->GetExpFromGeomId(i->GetGlobalID()) + ->Reset(); + } + } + } + + for (auto &field : m_fieldsALE) + { + for (auto &zone : field->GetGraph()->GetMovement()->GetZones()) + { + if (zone.second->GetMoved()) + { + auto conEl = zone.second->GetConstituentElements(); + // Loop over zone elements expansions and rebuild geometric + // factors + for (const auto &i : + conEl[0]) // This only takes highest dimensioned elements + { + field->GetExpFromGeomId(i->GetGlobalID())->Reset(); + } + } + } + } + + for (auto &zone : m_fieldsALE[0]->GetGraph()->GetMovement()->GetZones()) + { + if (zone.second->GetMoved()) + { + auto conEl = zone.second->GetConstituentElements(); + // Loop over zone elements expansions and rebuild geometric factors + // and recalc trace normals + for (const auto &i : + conEl[0]) // This only takes highest dimensioned elements + { + for (int j = 0; j < m_fieldsALE[0] + ->GetExpFromGeomId(i->GetGlobalID()) + ->GetNtraces(); + ++j) + { + m_fieldsALE[0] + ->GetExpFromGeomId(i->GetGlobalID()) + ->ComputeTraceNormal(j); + } + } + } + } + + for (auto &field : m_fieldsALE) + { + // Reset collections (despite the default being eNoCollection it does + // remember the last auto-tuned values), eNoImpType gives lots of output + field->CreateCollections(Collections::eNoCollection); + } + + // Reload new trace normals in to the solver cache + m_fieldsALE[0]->GetTrace()->GetNormals(traceNormals); + + // Recompute grid velocity. + UpdateGridVelocity(time); + + // Updates trace grid velocity + for (int i = 0; i < m_gridVelocityTrace.size(); ++i) + { + m_fieldsALE[0]->ExtractTracePhys(m_gridVelocity[i], + m_gridVelocityTrace[i]); + } + + // Set the flag to exchange coords in InterfaceMapDG to true + m_fieldsALE[0]->GetGraph()->GetMovement()->GetCoordExchangeFlag() = true; + + m_prevStageTime = time; +} + +const Array> + &ALEHelper::GetGridVelocityTrace() +{ + return m_gridVelocityTrace; +} + +ALEFixed::ALEFixed(SpatialDomains::ZoneBaseShPtr zone) + : m_zone(std::static_pointer_cast(zone)) +{ +} + +void ALEFixed::v_UpdateGridVel( + NekDouble time, Array &fields, + Array> &gridVelocity) +{ + boost::ignore_unused(time, fields, gridVelocity); +} + +ALETranslate::ALETranslate(SpatialDomains::ZoneBaseShPtr zone) + : m_zone(std::static_pointer_cast(zone)) +{ +} + +void ALETranslate::v_UpdateGridVel( + NekDouble time, Array &fields, + Array> &gridVelocity) +{ + boost::ignore_unused(time); + + auto vel = m_zone->GetVel(time); + auto exp = fields[0]->GetExp(); + + auto elements = m_zone->GetElements(); + for (auto &el : elements) + { + int indx = fields[0]->GetElmtToExpId(el->GetGlobalID()); + int offset = fields[0]->GetPhys_Offset(indx); + auto expansion = (*exp)[indx]; + + int nq = expansion->GetTotPoints(); + for (int i = 0; i < nq; ++i) + { + for (int j = 0; j < gridVelocity.size(); ++j) + { + gridVelocity[j][offset + i] += vel[j]; + } + } + } +} + +ALERotate::ALERotate(SpatialDomains::ZoneBaseShPtr zone) + : m_zone(std::static_pointer_cast(zone)) +{ +} + +void ALERotate::v_UpdateGridVel( + NekDouble time, Array &fields, + Array> &gridVelocity) +{ + boost::ignore_unused(time, fields, gridVelocity); + + auto angVel = m_zone->GetAngularVel(time); + auto axis = m_zone->GetAxis(); + auto origin = m_zone->GetOrigin(); + + auto exp = fields[0]->GetExp(); + + auto elements = m_zone->GetElements(); + for (auto &el : elements) + { + int indx = fields[0]->GetElmtToExpId(el->GetGlobalID()); + int offset = fields[0]->GetPhys_Offset(indx); + auto expansion = (*exp)[indx]; + + int nq = expansion->GetTotPoints(); + + Array xc(nq, 0.0), yc(nq, 0.0), zc(nq, 0.0); + expansion->GetCoords(xc, yc, zc); + for (int i = 0; i < nq; ++i) + { + // Vector from origin to point + DNekVec pointMinOrigin = {xc[i] - origin(0), yc[i] - origin(1), + zc[i] - origin(2)}; + + // Vector orthogonal to plane formed by axis and point + DNekVec norm = pointMinOrigin.Cross(axis); + // We negate here as by convention a positive angular velocity is + // counter-clockwise + norm = norm * -angVel; + + for (int j = 0; j < gridVelocity.size(); ++j) + { + gridVelocity[j][offset + i] = norm[j]; + } + } + } +} + +ALEPrescribe::ALEPrescribe(SpatialDomains::ZoneBaseShPtr zone) + : m_zone(std::static_pointer_cast(zone)) +{ + auto elements = zone->GetElements(); + for (auto &el : zone->GetElements()) + { + for (int j = 0; j < 4; ++j) + { + Array coords(3); + el->GetVertex(j)->GetCoords(coords); + m_coords[el->GetGlobalID()][j] = coords; + } + } +} + +void ALEPrescribe::v_UpdateGridVel( + NekDouble time, Array &fields, + Array> &gridVelocity) +{ + boost::ignore_unused(time, fields, gridVelocity); + + auto exp = fields[0]->GetExp(); + auto elements = m_zone->GetElements(); + for (auto &el : elements) + { + int indx = fields[0]->GetElmtToExpId(el->GetGlobalID()); + int offset = fields[0]->GetPhys_Offset(indx); + auto expansion = (*exp)[indx]; + + LibUtilities::BasisKey bkeyx(expansion->GetBasis(0)->GetBasisType(), 2, + expansion->GetBasis(0)->GetPointsKey()); + LibUtilities::BasisKey bkeyy(expansion->GetBasis(1)->GetBasisType(), 2, + expansion->GetBasis(1)->GetPointsKey()); + StdRegions::StdQuadExp stdexp(bkeyx, bkeyy); + + // Grid velocity of each quadrilateral vertex. + Array tmpx(4), tmpy(4); + for (int j = 0; j < 4; ++j) + { + auto vert = expansion->GetGeom()->GetVertex(j); + Array coords = m_coords[el->GetGlobalID()][j]; + // x/y velocity for each vertex + /*tmpx[j] = 0.5 * 2 * M_PI / 7.07106781187 * + cos(2 * M_PI * time / 7.07106781187) * + sin(2 * M_PI * coords[0] / 20) * + sin(2 * M_PI * coords[1] / 20); + tmpy[j] = 0.5 * 2 * M_PI / 7.07106781187 * + cos(2 * M_PI * time / 7.07106781187) * + sin(2 * M_PI * coords[0] / 20) * + sin(2 * M_PI * coords[1] / 20);*/ + + tmpx[j] = 0.5 * 2 * M_PI / sqrt(50) * cos(2 * M_PI * time / sqrt(50)) * + sin(2 * M_PI * vert->x() / 20) * + sin(2 * M_PI * vert->y() / 20); + tmpy[j] = 0.5 * 2 * M_PI / sqrt(50) * cos(2 * M_PI * time / sqrt(50)) * + sin(2 * M_PI * vert->x() / 20) * + sin(2 * M_PI * vert->y() / 20); + } + + // swap to match tensor product order of coefficients + // vs. anti-clockwise order of vertices. + std::swap(tmpx[2], tmpx[3]); + std::swap(tmpy[2], tmpy[3]); + + // Evaluate at all points in the deformed (time t) high-order + // element. + Array tmp; + stdexp.BwdTrans(tmpx, tmp = gridVelocity[0] + offset); + stdexp.BwdTrans(tmpy, tmp = gridVelocity[1] + offset); + } +} + +} // namespace SolverUtils +} // namespace Nektar \ No newline at end of file diff --git a/library/SolverUtils/ALEHelper.h b/library/SolverUtils/ALEHelper.h new file mode 100644 index 0000000000000000000000000000000000000000..895555a295b5f2fa0876dbbfe410603a0889a7da --- /dev/null +++ b/library/SolverUtils/ALEHelper.h @@ -0,0 +1,133 @@ +#ifndef NEKTAR_ALEHELPER_H +#define NEKTAR_ALEHELPER_H + +#include + +namespace Nektar +{ + +namespace SolverUtils +{ + +struct ALEBase; +typedef std::shared_ptr ALEBaseShPtr; + +class ALEHelper +{ +public: + void InitObject(int spaceDim, + Array &fields); + + void UpdateGridVelocity(const NekDouble &time); + + void ALEPreMultiplyMass(Array> &fields); + + void ALEDoElmtInvMass(Array> &traceNormals, + Array> &fields, + NekDouble time); + + void ALEDoElmtInvMassBwdTrans( + const Array> &inarray, + Array> &outarray); + + void MoveMesh(const NekDouble &time, + Array> &traceNormals); + + inline const Array> &GetGridVelocity() + { + return m_gridVelocity; + } + + const Array> &GetGridVelocityTrace(); + +protected: + Array m_fieldsALE; + Array> m_gridVelocity; + Array> m_gridVelocityTrace; + std::vector m_ALEs; + bool m_ALESolver = false; + NekDouble m_prevStageTime = 0.0; + int m_spaceDim; +}; + +struct ALEBase +{ + virtual ~ALEBase() = default; + + inline void UpdateGridVel( + const NekDouble time, + Array &fields, + Array> &gridVelocity) + { + v_UpdateGridVel(time, fields, gridVelocity); + } + +private: + virtual void v_UpdateGridVel( + const NekDouble time, + Array &fields, + Array> &gridVelocity) = 0; +}; + +struct ALEFixed final : public ALEBase +{ + ALEFixed(SpatialDomains::ZoneBaseShPtr zone); + + virtual void v_UpdateGridVel( + const NekDouble time, + Array &fields, + Array> &gridVelocity) final; + +private: + SpatialDomains::ZoneFixedShPtr m_zone; +}; + +struct ALETranslate final : public ALEBase +{ + ALETranslate(SpatialDomains::ZoneBaseShPtr zone); + + virtual void v_UpdateGridVel( + const NekDouble time, + Array &fields, + Array> &gridVelocity) final; + +private: + SpatialDomains::ZoneTranslateShPtr m_zone; +}; + +struct ALERotate final : public ALEBase +{ + ALERotate(SpatialDomains::ZoneBaseShPtr zone); + + virtual void v_UpdateGridVel( + const NekDouble time, + Array &fields, + Array> &gridVelocity) final; + +private: + SpatialDomains::ZoneRotateShPtr m_zone; +}; + +struct ALEPrescribe final : public ALEBase +{ + ALEPrescribe(SpatialDomains::ZoneBaseShPtr zone); + + virtual void v_UpdateGridVel( + const NekDouble time, + Array &fields, + Array> &gridVelocity) final; + +private: + SpatialDomains::ZonePrescribeShPtr m_zone; + std::map>> m_coords; +}; + +typedef std::shared_ptr ALEFixedShPtr; +typedef std::shared_ptr ALETranslateShPtr; +typedef std::shared_ptr ALERotateShPtr; +typedef std::shared_ptr ALEPrescribeShPtr; + +} // namespace SolverUtils + +} // namespace Nektar +#endif // NEKTAR_ALEHELPER_H diff --git a/library/SolverUtils/Advection/AdvectionWeakDG.cpp b/library/SolverUtils/Advection/AdvectionWeakDG.cpp index e12200ebe7af00652861cd6fa4ebf7bc7760baa1..a5856b2ca23633cd68e61de51175f223c0ea0672 100644 --- a/library/SolverUtils/Advection/AdvectionWeakDG.cpp +++ b/library/SolverUtils/Advection/AdvectionWeakDG.cpp @@ -104,16 +104,26 @@ void AdvectionWeakDG::v_Advect( timer.Stop(); timer.AccumulateRegion("AdvWeakDG:v_AdvectCoeffs", 2); + // Multiply by inverse mass matrix + LibUtilities::Timer timer2; + for (int i = 0; i < nConvectiveFields; ++i) + { + timer2.Start(); + fields[i]->MultiplyByElmtInvMass(tmp[i], tmp[i]); + timer2.Stop(); + timer2.AccumulateRegion("AdvWeakDG:_MultiplyByElmtInvMass", 1); + } + // why was this broken in many loops over convective fields? // this is terrible for locality - - timer.Start(); + LibUtilities::Timer timer3; + timer3.Start(); for (int i = 0; i < nConvectiveFields; ++i) { fields[i]->BwdTrans(tmp[i], outarray[i]); } - timer.Stop(); - timer.AccumulateRegion("AdvWeakDG:_BwdTrans", 10); + timer3.Stop(); + timer3.AccumulateRegion("AdvWeakDG:_BwdTrans", 1); timer1.Stop(); timer1.AccumulateRegion("AdvWeakDG:All", 10); } @@ -127,6 +137,9 @@ void AdvectionWeakDG::v_AdvectCoeffs( const Array> &pFwd, const Array> &pBwd) { + LibUtilities::Timer timer1; + timer1.Start(); + size_t nPointsTot = fields[0]->GetTotPoints(); size_t nCoeffs = fields[0]->GetNcoeffs(); size_t nTracePointsTot = fields[0]->GetTrace()->GetTotPoints(); @@ -178,13 +191,11 @@ void AdvectionWeakDG::v_AdvectCoeffs( timer.Start(); fields[i]->AddTraceIntegral(numflux[i], outarray[i]); timer.Stop(); - timer.AccumulateRegion("AdvWeakDG:_AddTraceIntegral", 10); - - timer.Start(); - fields[i]->MultiplyByElmtInvMass(outarray[i], outarray[i]); - timer.Stop(); - timer.AccumulateRegion("AdvWeakDG:_MultiplyByElmtInvMass", 10); + timer.AccumulateRegion("AdvWeakDG:_AddTraceIntegral", 1); } + + timer1.Stop(); + timer1.AccumulateRegion("AdvWeakDG: Coeff All"); } void AdvectionWeakDG::v_AdvectTraceFlux( diff --git a/library/SolverUtils/CMakeLists.txt b/library/SolverUtils/CMakeLists.txt index 63d1b03b222c79a3246bb54026ba5a5bd612112b..543904366fabc451112b15ee1529151578a258e9 100644 --- a/library/SolverUtils/CMakeLists.txt +++ b/library/SolverUtils/CMakeLists.txt @@ -4,6 +4,7 @@ SET(SOLVER_UTILS_SOURCES Core/Misc.cpp Core/SessionFunction.cpp AdvectionSystem.cpp + ALEHelper.cpp Advection/Advection.cpp Advection/Advection3DHomogeneous1D.cpp Advection/AdvectionFR.cpp @@ -31,6 +32,7 @@ SET(SOLVER_UTILS_SOURCES Filters/FilterEnergy.cpp Filters/FilterError.cpp Filters/FilterHistoryPoints.cpp + Filters/FilterIntegral.cpp Filters/FilterMean.cpp Filters/FilterModalEnergy.cpp Filters/FilterMovingAverage.cpp @@ -56,6 +58,7 @@ SET(SOLVER_UTILS_HEADERS Core/Misc.h Core/SessionFunction.h AdvectionSystem.h + ALEHelper.h Advection/Advection.h Advection/AdvectionFR.h Advection/Advection3DHomogeneous1D.h @@ -84,6 +87,7 @@ SET(SOLVER_UTILS_HEADERS Filters/FilterError.h Filters/FilterHistoryPoints.h Filters/FilterInterfaces.hpp + Filters/FilterIntegral.h Filters/FilterMean.h Filters/FilterModalEnergy.h Filters/FilterMovingAverage.h diff --git a/library/SolverUtils/Diffusion/Diffusion.h b/library/SolverUtils/Diffusion/Diffusion.h index 10267c4c1199c41249b5ab3fb4ecc6351ff9a0b5..605c1cb00d7a164b0577535f92646a4dae9c5f40 100644 --- a/library/SolverUtils/Diffusion/Diffusion.h +++ b/library/SolverUtils/Diffusion/Diffusion.h @@ -372,6 +372,12 @@ public: std::placeholders::_5, std::placeholders::_6); } + inline void SetGridVelocityTrace( + Array> &gridVelocityTrace) + { + m_gridVelocityTrace = gridVelocityTrace; + } + inline void SetHomoDerivs(Array> &deriv) { v_SetHomoDerivs(deriv); @@ -408,7 +414,7 @@ protected: DiffusionFluxCons m_FunctorDiffusionfluxConsTrace; SpecialBndTreat m_SpecialBndTreat; DiffusionSymmFluxCons m_FunctorSymmetricfluxCons; - + Array> m_gridVelocityTrace; NekDouble m_time = 0.0; SOLVER_UTILS_EXPORT virtual void v_InitObject( diff --git a/library/SolverUtils/Diffusion/DiffusionLDG.cpp b/library/SolverUtils/Diffusion/DiffusionLDG.cpp index b09b96cd3e6fe82418032587c1b13665cfe54f72..371d87e5c11a4127ad7925652208f98e6fa117d6 100644 --- a/library/SolverUtils/Diffusion/DiffusionLDG.cpp +++ b/library/SolverUtils/Diffusion/DiffusionLDG.cpp @@ -92,6 +92,17 @@ void DiffusionLDG::v_Diffuse( DiffusionLDG::v_DiffuseCoeffs(nConvectiveFields, fields, inarray, tmp, pFwd, pBwd); + // Multiply by inverse mass matrix // @TODO: We don't want + // MultiplyByElmtInvMassfor ALE so we moved out of the diffusecoeffs method + LibUtilities::Timer timer; + for (int i = 0; i < nConvectiveFields; ++i) + { + timer.Start(); + fields[i]->MultiplyByElmtInvMass(tmp[i], tmp[i]); + timer.Stop(); + timer.AccumulateRegion("MultiplyByElmtInvMass"); + } + for (std::size_t i = 0; i < nConvectiveFields; ++i) { fields[i]->BwdTrans(tmp[i], outarray[i]); @@ -106,13 +117,17 @@ void DiffusionLDG::v_DiffuseCoeffs( const Array> &pFwd, const Array> &pBwd) { + if (fields[0]->GetGraph()->GetMovement()->GetMoveFlag()) // i.e. if + // m_ALESolver + { + fields[0]->GetTrace()->GetNormals(m_traceNormals); + } + std::size_t nDim = fields[0]->GetCoordim(0); std::size_t nPts = fields[0]->GetTotPoints(); std::size_t nCoeffs = fields[0]->GetNcoeffs(); std::size_t nTracePts = fields[0]->GetTrace()->GetTotPoints(); - Array tmp{nCoeffs}; - TensorOfArray3D qfield{nDim}; for (std::size_t j = 0; j < nDim; ++j) { @@ -146,19 +161,17 @@ void DiffusionLDG::v_DiffuseCoeffs( pBwd); Array> qdbase{nDim}; - for (std::size_t i = 0; i < nConvectiveFields; ++i) { for (std::size_t j = 0; j < nDim; ++j) { qdbase[j] = viscTensor[j][i]; } - fields[i]->IProductWRTDerivBase(qdbase, tmp); + fields[i]->IProductWRTDerivBase(qdbase, outarray[i]); - Vmath::Neg(nCoeffs, tmp, 1); - fields[i]->AddTraceIntegral(traceflux[i], tmp); + Vmath::Neg(nCoeffs, outarray[i], 1); + fields[i]->AddTraceIntegral(traceflux[i], outarray[i]); fields[i]->SetPhysState(false); - fields[i]->MultiplyByElmtInvMass(tmp, outarray[i]); } } @@ -321,7 +334,10 @@ void DiffusionLDG::ApplyScalarBCs( "WallViscous") || boost::iequals( fields[var]->GetBndConditions()[i]->GetUserDefined(), - "WallAdiabatic")) + "WallAdiabatic") || + boost::iequals( + fields[var]->GetBndConditions()[i]->GetUserDefined(), + "WallRotational")) { Vmath::Vcopy(nBndEdgePts, &Fwd[id2], 1, &penaltyflux[id2], 1); } @@ -461,7 +477,10 @@ void DiffusionLDG::ApplyVectorBCs( "WallViscous") || boost::iequals( fields[var]->GetBndConditions()[i]->GetUserDefined(), - "WallAdiabatic")) + "WallAdiabatic") || + boost::iequals( + fields[var]->GetBndConditions()[i]->GetUserDefined(), + "WallRotational")) { Vmath::Zero(nBndEdgePts, &penaltyflux[id2], 1); } diff --git a/library/SolverUtils/DriverStandard.cpp b/library/SolverUtils/DriverStandard.cpp index 618789767c29dc4f6debf6388ff8cc0121e7879e..bdee3ca3c5661a0c74fcb6fc28b1e90865adbebd 100644 --- a/library/SolverUtils/DriverStandard.cpp +++ b/library/SolverUtils/DriverStandard.cpp @@ -75,23 +75,23 @@ void DriverStandard::v_InitObject(ostream &out) void DriverStandard::v_Execute(ostream &out) { - time_t starttime, endtime; + clock_t starttime, endtime; NekDouble CPUtime; m_equ[0]->PrintSummary(out); - time(&starttime); + starttime = clock(); m_equ[0]->DoInitialise(); m_equ[0]->DoSolve(); - time(&endtime); + endtime = clock(); m_equ[0]->Output(); if (m_comm->GetRank() == 0) { - CPUtime = difftime(endtime, starttime); + CPUtime = (endtime - starttime) / NekDouble(CLOCKS_PER_SEC); cout << "-------------------------------------------" << endl; cout << "Total Computation Time = " << CPUtime << "s" << endl; cout << "-------------------------------------------" << endl; diff --git a/library/SolverUtils/EquationSystem.cpp b/library/SolverUtils/EquationSystem.cpp index 307423a65c74adf8da68109d00c15b6a0370c56b..9635c163298708061d9880b6e18ecfe2f18f7b96 100644 --- a/library/SolverUtils/EquationSystem.cpp +++ b/library/SolverUtils/EquationSystem.cpp @@ -594,13 +594,32 @@ void EquationSystem::v_InitObject(bool DeclareFields) } else { - for (i = 0; i < m_fields.size(); i++) + i = 0; + MultiRegions::DisContFieldSharedPtr firstfield; + firstfield = MemoryManager:: + AllocateSharedPtr(m_session, m_graph, + m_session->GetVariable(i)); + m_fields[0] = firstfield; + for (i = 1; i < m_fields.size(); i++) { - m_fields[i] = - MemoryManager:: - AllocateSharedPtr( - m_session, m_graph, - m_session->GetVariable(i)); + if (m_graph->SameExpansionInfo( + m_session->GetVariable(0), + m_session->GetVariable(i))) + { + m_fields[i] = + MemoryManager:: + AllocateSharedPtr( + *firstfield, m_graph, + m_session->GetVariable(i)); + } + else + { + m_fields[i] = + MemoryManager:: + AllocateSharedPtr( + m_session, m_graph, + m_session->GetVariable(i)); + } } } @@ -616,13 +635,32 @@ void EquationSystem::v_InitObject(bool DeclareFields) } else { - for (i = 0; i < m_fields.size(); i++) + i = 0; + MultiRegions::DisContFieldSharedPtr firstfield = + MemoryManager:: + AllocateSharedPtr(m_session, m_graph, + m_session->GetVariable(i)); + m_fields[0] = firstfield; + for (i = 1; i < m_fields.size(); i++) { - m_fields[i] = - MemoryManager:: - AllocateSharedPtr( - m_session, m_graph, - m_session->GetVariable(i)); + if (m_graph->SameExpansionInfo( + m_session->GetVariable(0), + m_session->GetVariable(i))) + { + m_fields[i] = + MemoryManager:: + AllocateSharedPtr( + *firstfield, m_graph, + m_session->GetVariable(i)); + } + else + { + m_fields[i] = + MemoryManager:: + AllocateSharedPtr( + m_session, m_graph, + m_session->GetVariable(i)); + } } } break; @@ -1454,6 +1492,24 @@ void EquationSystem::SessionSummary(SummaryList &s) "Mixed Continuous Galerkin and Discontinuous"); } + if (m_session->DefinesSolverInfo("DiffusionType")) + { + std::string DiffusionType; + DiffusionType = m_session->GetSolverInfo("DiffusionType"); + AddSummaryItem( + s, "Diffusion Type", + GetDiffusionFactory().GetClassDescription(DiffusionType)); + } + else if (m_projectionType == MultiRegions::eDiscontinuous) + { + AddSummaryItem(s, "Projection Type", "Discontinuous Galerkin"); + } + else if (m_projectionType == MultiRegions::eMixed_CG_Discontinuous) + { + AddSummaryItem(s, "Projection Type", + "Mixed Continuous Galerkin and Discontinuous"); + } + if (m_session->DefinesSolverInfo("DiffusionType")) { std::string DiffusionType; diff --git a/library/SolverUtils/Filters/FilterError.cpp b/library/SolverUtils/Filters/FilterError.cpp index bd5ffca8478690f76579fa5b2a1199806ce13fb3..2c084d0e274ca502dbd3ddee657d165d4a06e32c 100644 --- a/library/SolverUtils/Filters/FilterError.cpp +++ b/library/SolverUtils/Filters/FilterError.cpp @@ -99,6 +99,20 @@ FilterError::FilterError(const LibUtilities::SessionReaderSharedPtr &pSession, LibUtilities::Equation equ(m_session->GetInterpreter(), it->second); m_outputFrequency = round(equ.Evaluate()); } + + // ConsoleOutput + it = pParams.find("ConsoleOutput"); + if (it == pParams.end()) + { + m_consoleOutput = false; + } + else + { + ASSERTL0(it->second.length() > 0, "Empty parameter 'ConsoleOutput'."); + ASSERTL0(it->second == "0" || it->second == "1", + "Parameter 'ConsoleOutput' can only be '0' or '1'."); + m_consoleOutput = boost::lexical_cast(it->second); + } } void FilterError::v_Initialise( @@ -142,6 +156,16 @@ void FilterError::v_Update( if (m_comm->GetRank() == 0) { m_outFile << " " << vL2Error << " " << vLinfError; + + if (m_consoleOutput) + { + std::cout << "L 2 error (variable " + << equationSys->GetVariable(i) << ") : " << vL2Error + << std::endl; + std::cout << "L inf error (variable " + << equationSys->GetVariable(i) << ") : " << vLinfError + << std::endl; + } } } diff --git a/library/SolverUtils/Filters/FilterError.h b/library/SolverUtils/Filters/FilterError.h index 496716d5a1c488f4c18ee9514471750438b122bd..53933bf4615b7052aa391fc410b6efa2f098642d 100644 --- a/library/SolverUtils/Filters/FilterError.h +++ b/library/SolverUtils/Filters/FilterError.h @@ -81,6 +81,7 @@ protected: private: size_t m_index = 0; size_t m_outputFrequency; + bool m_consoleOutput; size_t m_numVariables; std::ofstream m_outFile; LibUtilities::CommSharedPtr m_comm; diff --git a/library/SolverUtils/Filters/FilterIntegral.cpp b/library/SolverUtils/Filters/FilterIntegral.cpp new file mode 100644 index 0000000000000000000000000000000000000000..0cf87adb642542691a1937d402cd358628dc2874 --- /dev/null +++ b/library/SolverUtils/Filters/FilterIntegral.cpp @@ -0,0 +1,396 @@ +/////////////////////////////////////////////////////////////////////////////// +// +// File FilterIntegral.cpp +// +// For more information, please see: http://www.nektar.info +// +// The MIT License +// +// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA), +// Department of Aeronautics, Imperial College London (UK), and Scientific +// Computing and Imaging Institute, University of Utah (USA). +// +// Permission is hereby granted, free of charge, to any person obtaining a +// copy of this software and associated documentation files (the "Software"), +// to deal in the Software without restriction, including without limitation +// the rights to use, copy, modify, merge, publish, distribute, sublicense, +// and/or sell copies of the Software, and to permit persons to whom the +// Software is furnished to do so, subject to the following conditions: +// +// The above copyright notice and this permission notice shall be included +// in all copies or substantial portions of the Software. +// +// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +// DEALINGS IN THE SOFTWARE. +// +// Description: Outputs integrals of fields during time-stepping. +// +/////////////////////////////////////////////////////////////////////////////// + +#include +#include +#include +#include +#include + +#include +#include + +namespace Nektar +{ +namespace SolverUtils +{ +std::string FilterIntegral::className = + GetFilterFactory().RegisterCreatorFunction("Integral", + FilterIntegral::create); + +FilterIntegral::FilterIntegral( + const LibUtilities::SessionReaderSharedPtr &pSession, + const std::weak_ptr &pEquation, const ParamMap &pParams) + : Filter(pSession, pEquation) +{ + std::string outName; + + // OutputFile + auto it = pParams.find("OutputFile"); + if (it == pParams.end()) + { + outName = m_session->GetSessionName(); + } + else + { + ASSERTL0(it->second.length() > 0, "Empty parameter 'OutputFile'."); + outName = it->second; + } + outName += ".int"; + + // Composites (to calculate integrals on) + it = pParams.find("Composites"); + ASSERTL0(it != pParams.end(), "Missing parameter 'Composites'."); + ASSERTL0(it->second.length() > 0, "Empty parameter 'Composites'."); + + std::vector splitComposite; + boost::split(m_splitCompString, it->second, boost::is_any_of(","), + boost::token_compress_on); + + for (auto &comp : m_splitCompString) + { + boost::trim(comp); + size_t first = comp.find_first_of('[') + 1; + size_t last = comp.find_last_of(']') - 1; + auto tmpString = comp.substr(first, last - first + 1); + + std::vector tmpVec; + bool parseGood = ParseUtils::GenerateSeqVector(tmpString, tmpVec); + + ASSERTL0(parseGood && !tmpVec.empty(), + "Unable to read composite regions index range for " + "FilterIntegral: " + + comp); + + m_compVector.emplace_back(tmpVec); + } + + // OutputPrecision + size_t precision; + it = pParams.find("OutputPrecision"); + if (it == pParams.end()) + { + precision = 7; + } + else + { + ASSERTL0(it->second.length() > 0, "Empty parameter 'OutputPrecision'."); + precision = std::stoi(it->second); + } + + // Lock equation system pointer + auto equationSys = m_equ.lock(); + ASSERTL0(equationSys, "Weak pointer expired"); + + m_numVariables = equationSys->GetNvariables(); + + m_comm = pSession->GetComm(); + if (m_comm->GetRank() == 0) + { + m_outFile.open(outName); + ASSERTL0(m_outFile.good(), "Unable to open: '" + outName + "'"); + m_outFile.setf(std::ios::scientific, std::ios::floatfield); + m_outFile.precision(precision); + m_outFile << "#Time"; + + for (auto &compName : m_splitCompString) + { + for (size_t j = 0; j < m_numVariables; ++j) + { + std::string varName = equationSys->GetVariable(j); + m_outFile << " " + compName + "_" + varName + "_integral"; + } + } + m_outFile << std::endl; + } + + // OutputFrequency + it = pParams.find("OutputFrequency"); + if (it == pParams.end()) + { + m_outputFrequency = 1; + } + else + { + ASSERTL0(it->second.length() > 0, "Empty parameter 'OutputFrequency'."); + LibUtilities::Equation equ(m_session->GetInterpreter(), it->second); + m_outputFrequency = round(equ.Evaluate()); + } +} + +void FilterIntegral::v_Initialise( + const Array &pFields, + const NekDouble &time) +{ + + // Create map from element ID -> expansion list ID + auto expList = pFields[0]->GetExp(); + auto meshGraph = pFields[0]->GetGraph(); + + for (size_t i = 0; i < expList->size(); ++i) + { + auto exp = (*expList)[i]; + m_geomElmtIdToExpId[exp->GetGeom()->GetGlobalID()] = i; + } + + // Create a map from geom ID -> trace expansion list ID + std::map geomIdToTraceId; + auto trace = pFields[0]->GetTrace()->GetExp(); + for (size_t i = 0; i < trace->size(); ++i) + { + auto exp = (*trace)[i]; + geomIdToTraceId[exp->GetGeom()->GetGlobalID()] = i; + } + + // Get comp list dimension from first composite & element + auto composites = pFields[0]->GetGraph()->GetComposites(); + size_t meshDim = pFields[0]->GetGraph()->GetMeshDimension(); + + for (int i = 0; i < m_compVector.size(); ++i) + { + // Check composite is present in the rank + if (composites.find(m_compVector[i][0]) == composites.end()) + { + continue; + } + + std::vector> geomVec = + composites[m_compVector[i][0]]->m_geomVec; + size_t dim = + composites[m_compVector[i][0]]->m_geomVec[0]->GetShapeDim(); + + // Vector of all geometry IDs contained within the composite list + std::vector compGeomIds; + for (auto compNum : m_compVector[i]) + { + ASSERTL0(composites.find(compNum) != composites.end(), + "In FilterIntegral defined composite C[" + + std::to_string(compNum) + + "] does not exist in the mesh.") + + auto compGeom = composites[compNum]->m_geomVec; + + for (auto &geom : compGeom) + { + compGeomIds.emplace_back(geom->GetGlobalID()); + } + + // Only check first element in each comp for dimension + ASSERTL0( + dim == compGeom[0]->GetShapeDim(), + "Differing geometry dimensions specified in FilterIntegral '" + + m_splitCompString[i] + "'."); + } + + std::vector> + tmpCompExp(compGeomIds.size()); + + // If dimension of composite == dimension of mesh then we only need the + // expansion of the element + if (dim == pFields[0]->GetShapeDimension()) + { + for (size_t j = 0; j < compGeomIds.size(); ++j) + { + tmpCompExp[j] = std::make_pair( + (*expList)[m_geomElmtIdToExpId[compGeomIds[j]]], -1); + } + } + // however if the dimension is less we need the expansion of the element + // containing the global composite geometry and the face/edge local ID + // within that. 3D mesh -> 2D, 2D -> 1D. + // @TODO: Restructure with the new dimension independent functions + // and check all is correct with this filter. + else if (meshDim == 3 && dim == 2) + { + for (size_t j = 0; j < compGeomIds.size(); ++j) + { + LocalRegions::ExpansionSharedPtr exp = + (*trace)[geomIdToTraceId[compGeomIds[j]]]; + LocalRegions::Expansion2DSharedPtr exp2D = + std::dynamic_pointer_cast(exp); + + LocalRegions::ExpansionSharedPtr leftAdjElmtExp = + std::dynamic_pointer_cast( + exp2D->GetLeftAdjacentElementExp()); + int leftAdjElmtFace = exp2D->GetLeftAdjacentElementTrace(); + + tmpCompExp[j] = std::make_pair(leftAdjElmtExp, leftAdjElmtFace); + } + } + else if (meshDim == 2 && dim == 1) + { + for (size_t j = 0; j < compGeomIds.size(); ++j) + { + LocalRegions::ExpansionSharedPtr exp = + (*trace)[geomIdToTraceId[compGeomIds[j]]]; + LocalRegions::Expansion1DSharedPtr exp1D = + std::dynamic_pointer_cast(exp); + + LocalRegions::ExpansionSharedPtr leftAdjElmtExp = + std::dynamic_pointer_cast( + exp1D->GetLeftAdjacentElementExp()); + int leftAdjElmtEdge = exp1D->GetLeftAdjacentElementTrace(); + + tmpCompExp[j] = std::make_pair(leftAdjElmtExp, leftAdjElmtEdge); + } + } + else + { + ASSERTL0(false, + "FilterIntegral: Only composite dimensions equal to or " + "one lower than the mesh dimension are supported.") + } + + m_compExpMap[i] = tmpCompExp; + } + + v_Update(pFields, time); +} + +void FilterIntegral::v_Update( + const Array &pFields, + const NekDouble &time) +{ + if (m_index++ % m_outputFrequency > 0) + { + return; + } + + if (m_comm->GetRank() == 0) + { + m_outFile << time; + } + + for (size_t j = 0; j < m_compVector.size(); ++j) + { + for (size_t i = 0; i < m_numVariables; ++i) + { + Array phys; + phys = pFields[i]->GetPhys(); + + NekDouble sum = 0.0; + NekDouble c = 0.0; + + // Check if composite is on the rank + if (m_compExpMap.find(j) != m_compExpMap.end()) + { + auto compExp = m_compExpMap[j]; + size_t dim = compExp[0].first->GetGeom()->GetShapeDim(); + size_t meshDim = pFields[i]->GetGraph()->GetMeshDimension(); + + // Evaluate integral using improved Kahan–Babuška summation + // algorithm to reduce numerical error from adding floating + // points + for (auto &expPair : compExp) + { + NekDouble input = 0; + auto exp = expPair.first; + + if (meshDim == dim) + { + size_t offset = pFields[i]->GetPhys_Offset( + m_geomElmtIdToExpId[exp->GetGeom()->GetGlobalID()]); + input = exp->Integral(phys + offset); + } + else if (meshDim == 3 && dim == 2) + { + Array facePhys; + exp->GetTracePhysVals(expPair.second, exp, phys, + facePhys); + input = + pFields[i] + ->GetTrace() + ->GetExp(exp->GetGeom()->GetTid(expPair.second)) + ->Integral(facePhys); + } + else if (meshDim == 2 && dim == 1) + { + Array edgePhys; + exp->GetTracePhysVals(expPair.second, exp, phys, + edgePhys); + input = + pFields[i] + ->GetTrace() + ->GetExp(exp->GetGeom()->GetTid(expPair.second)) + ->Integral(edgePhys); + } + else + { + ASSERTL0(false, + "FilterIntegral: Only composite dimensions " + "equal to or one lower than the mesh " + "dimension are supported.") + } + + NekDouble t = sum + input; + c += fabs(sum) >= fabs(input) ? (sum - t) + input + : (input - t) + sum; + sum = t; + } + } + + // Sum integral values from all ranks + Array sumArray(1, sum + c); + m_comm->AllReduce(sumArray, LibUtilities::ReduceSum); + if (m_comm->GetRank() == 0) + { + m_outFile << " " << sumArray[0]; + } + } + } + + if (m_comm->GetRank() == 0) + { + m_outFile << std::endl; + } +} + +void FilterIntegral::v_Finalise( + const Array &pFields, + const NekDouble &time) +{ + boost::ignore_unused(pFields, time); + + if (m_comm->GetRank() == 0) + { + m_outFile.close(); + } +} + +bool FilterIntegral::v_IsTimeDependent() +{ + return true; +} +} // namespace SolverUtils +} // namespace Nektar diff --git a/library/SolverUtils/Filters/FilterIntegral.h b/library/SolverUtils/Filters/FilterIntegral.h new file mode 100644 index 0000000000000000000000000000000000000000..3f56aa148b27aef13bfd1bd96b1ffd7203781aa9 --- /dev/null +++ b/library/SolverUtils/Filters/FilterIntegral.h @@ -0,0 +1,131 @@ +/////////////////////////////////////////////////////////////////////////////// +// +// File FilterIntegral.h +// +// For more information, please see: http://www.nektar.info +// +// The MIT License +// +// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA), +// Department of Aeronautics, Imperial College London (UK), and Scientific +// Computing and Imaging Institute, University of Utah (USA). +// +// Permission is hereby granted, free of charge, to any person obtaining a +// copy of this software and associated documentation files (the "Software"), +// to deal in the Software without restriction, including without limitation +// the rights to use, copy, modify, merge, publish, distribute, sublicense, +// and/or sell copies of the Software, and to permit persons to whom the +// Software is furnished to do so, subject to the following conditions: +// +// The above copyright notice and this permission notice shall be included +// in all copies or substantial portions of the Software. +// +// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +// DEALINGS IN THE SOFTWARE. +// +// Description: Outputs integrals of fields during time-stepping. +// +/////////////////////////////////////////////////////////////////////////////// + +#ifndef NEKTAR_SOLVERUTILS_FILTERS_FILTERINTEGRAL_H +#define NEKTAR_SOLVERUTILS_FILTERS_FILTERINTEGRAL_H + +#include + +namespace Nektar +{ +namespace SolverUtils +{ +class FilterIntegral : public Filter +{ +public: + friend class MemoryManager; + + /// Creates an instance of this class + static FilterSharedPtr create( + const LibUtilities::SessionReaderSharedPtr &pSession, + const std::weak_ptr &pEquation, + const std::map &pParams) + { + FilterSharedPtr p = MemoryManager::AllocateSharedPtr( + pSession, pEquation, pParams); + return p; + } + + /// Name of the class + static std::string className; + + /// Constructs the integral filter and parses filter options, opens file + SOLVER_UTILS_EXPORT FilterIntegral( + const LibUtilities::SessionReaderSharedPtr &pSession, + const std::weak_ptr &pEquation, + const ParamMap &pParams); + + /// Default destructor + SOLVER_UTILS_EXPORT virtual ~FilterIntegral() = default; + +protected: + /** + * Initialises the integral filter and stores the composite expansions in + * #m_compExpMap for all composites specified in the XML file + * + * @param pFields Field data + * @param time Current time + */ + virtual void v_Initialise( + const Array &pFields, + const NekDouble &time) final; + + /** + * Performs the integration on the stored composite expansions and outputs + * in to the output data file + * + * @param pFields Field data + * @param time Current time + */ + virtual void v_Update( + const Array &pFields, + const NekDouble &time) final; + + /** + * Closes the output data file + * + * @param pFields Field data + * @param time Current time + */ + virtual void v_Finalise( + const Array &pFields, + const NekDouble &time) final; + + /// Returns true as filter depends on time + virtual bool v_IsTimeDependent() final; + +private: + size_t m_index = 0; + /// Frequency to write to output data file in timesteps + size_t m_outputFrequency; + /// Number of fields to perform integral on + size_t m_numVariables; + /// Out file + std::ofstream m_outFile; + /// Global communicator + LibUtilities::CommSharedPtr m_comm; + /// Vector of composite IDs as a single string + std::vector m_splitCompString; + /// Vector of vector of composites IDs as integers + std::vector> m_compVector; + /// Mapping from geometry ID to expansion ID + std::map m_geomElmtIdToExpId; + /// Map of composite ID to vector of expansions an face/edge local ID + std::map>> + m_compExpMap; +}; +} // namespace SolverUtils +} // namespace Nektar + +#endif /* NEKTAR_SOLVERUTILS_FILTERS_FILTERIntegral_H */ diff --git a/library/SolverUtils/RiemannSolvers/RiemannSolver.cpp b/library/SolverUtils/RiemannSolvers/RiemannSolver.cpp index f2c32a28ab7d971425a49c02215072f326e9b4b5..cedd4d5f8109dd3574f207f30100d2e91e67190f 100644 --- a/library/SolverUtils/RiemannSolvers/RiemannSolver.cpp +++ b/library/SolverUtils/RiemannSolvers/RiemannSolver.cpp @@ -134,10 +134,48 @@ void RiemannSolver::Solve(const int nDim, } } + // auto vgt = m_vectors["vgt"](); + // Array> rot1(nFields); + // Array> veclocs(1); + // veclocs[0] = Array(2); + // veclocs[0][0] = 0.0; + // veclocs[0][1] = 1.0; + // for (int i =0; i < nFields; ++i) + //{ + // rot1[i] = Array(nPts); + //} + // rotateToNormal(vgt, normals, veclocs, rot1); + rotateToNormal(Fwd, normals, vecLocs, m_rotStorage[0]); rotateToNormal(Bwd, normals, vecLocs, m_rotStorage[1]); + + // for (int i = 0; i < 2; ++i) + //{ + // std::cout << "nfields = " << nFields << std::endl; + // for (int j = 0; j < m_rotStorage[0][0].size(); ++j) + // { + // m_rotStorage[0][i+1][j] -= rot1[i][j] * m_rotStorage[0][0][j]; + // m_rotStorage[1][i+1][j] -= rot1[i][j] * m_rotStorage[0][0][j]; + // } + //} + v_Solve(nDim, m_rotStorage[0], m_rotStorage[1], m_rotStorage[2]); rotateFromNormal(m_rotStorage[2], normals, vecLocs, flux); + + // Attempt to subtract (\vec{U}\vec{vg})\dot n for ALE + if (m_ALESolver) + { + auto vgt = m_vectors["vgt"](); + auto N = m_vectors["N"](); + for (int i = 0; i < flux.size(); ++i) + { + for (int j = 0; j < flux[i].size(); ++j) + { + flux[i][j] -= 0.5 * (Fwd[i][j] + Bwd[i][j]) * + (N[0][j] * vgt[0][j] + N[1][j] * vgt[1][j]); + } + } + } } else { diff --git a/library/SolverUtils/RiemannSolvers/RiemannSolver.h b/library/SolverUtils/RiemannSolvers/RiemannSolver.h index 6b19825baf40ac6fd13180b49c08baffbb520c1b..0a3860956e2e305b81d6d6a59118ff6486fa8c39 100644 --- a/library/SolverUtils/RiemannSolvers/RiemannSolver.h +++ b/library/SolverUtils/RiemannSolvers/RiemannSolver.h @@ -90,6 +90,11 @@ public: m_params[name] = std::bind(func, obj); } + void SetALEFlag(bool &ALE) + { + m_ALESolver = ALE; + } + void SetParam(std::string name, RSParamFuncType fp) { m_params[name] = fp; @@ -152,6 +157,8 @@ protected: Array> m_rotMat; /// Rotation storage Array>> m_rotStorage; + /// Flag if using the ALE formulation + bool m_ALESolver = false; SOLVER_UTILS_EXPORT RiemannSolver(); SOLVER_UTILS_EXPORT RiemannSolver( diff --git a/library/SolverUtils/UnsteadySystem.cpp b/library/SolverUtils/UnsteadySystem.cpp index 184035a9dee15b17691d9f8707acd460b5a86d35..ef055eddea788a4fd5fe8ecfcb9cd52681b76b89 100644 --- a/library/SolverUtils/UnsteadySystem.cpp +++ b/library/SolverUtils/UnsteadySystem.cpp @@ -68,7 +68,8 @@ namespace SolverUtils UnsteadySystem::UnsteadySystem( const LibUtilities::SessionReaderSharedPtr &pSession, const SpatialDomains::MeshGraphSharedPtr &pGraph) - : EquationSystem(pSession, pGraph), m_infosteps(10) + : EquationSystem(pSession, pGraph), SolverUtils::ALEHelper(), + m_infosteps(10) { } @@ -79,6 +80,7 @@ UnsteadySystem::UnsteadySystem( void UnsteadySystem::v_InitObject(bool DeclareField) { EquationSystem::v_InitObject(DeclareField); + ALEHelper::InitObject(m_spacedim, m_fields); m_initialStep = 0; @@ -226,12 +228,23 @@ void UnsteadySystem::v_DoSolve() Array> fields(nvariables); // Order storage to list time-integrated fields first. + // @TODO: Refactor to take coeffs (FwdTrans) if boolean flag (in constructor + // function) says to. for (i = 0; i < nvariables; ++i) { fields[i] = m_fields[m_intVariables[i]]->GetPhys(); m_fields[m_intVariables[i]]->SetPhysState(false); } + // @TODO: Virtual function that allows to transform the field space, embed + // the MultiplyMassMatrix in here. + // @TODO: Specify what the fields variables are physical or coefficient, + // boolean in UnsteadySystem class... + if (m_ALESolver) + { + ALEHelper::ALEPreMultiplyMass(fields); + } + // Initialise time integration scheme m_intScheme->InitializeScheme(m_timestep, fields, m_time, m_ode); @@ -321,7 +334,9 @@ void UnsteadySystem::v_DoSolve() // Perform any solver-specific pre-integration steps timer.Start(); - if (v_PreIntegrate(step)) + if (v_PreIntegrate( + step)) // Could be possible to put a preintegrate step in the + // ALEHelper class, put in the Unsteady Advection class { break; } @@ -365,19 +380,30 @@ void UnsteadySystem::v_DoSolve() } } - // Transform data into coefficient space - for (i = 0; i < nvariables; ++i) + // @TODO: Another virtual function with this in it based on if ALE or + // not. + if (m_ALESolver) // Change to advect coeffs, change flag to physical vs + // coefficent space + { + SetBoundaryConditions(m_time); + ALEHelper::ALEDoElmtInvMass(m_traceNormals, fields, m_time); + } + else { - // copy fields into ExpList::m_phys and assign the new - // array to fields - m_fields[m_intVariables[i]]->SetPhys(fields[i]); - fields[i] = m_fields[m_intVariables[i]]->UpdatePhys(); - if (v_RequireFwdTrans()) + // Transform data into coefficient space + for (i = 0; i < nvariables; ++i) { - m_fields[m_intVariables[i]]->FwdTransLocalElmt( - fields[i], m_fields[m_intVariables[i]]->UpdateCoeffs()); + // copy fields into ExpList::m_phys and assign the new + // array to fields + m_fields[m_intVariables[i]]->SetPhys(fields[i]); + fields[i] = m_fields[m_intVariables[i]]->UpdatePhys(); + if (v_RequireFwdTrans()) + { + m_fields[m_intVariables[i]]->FwdTransLocalElmt( + fields[i], m_fields[m_intVariables[i]]->UpdateCoeffs()); + } + m_fields[m_intVariables[i]]->SetPhysState(false); } - m_fields[m_intVariables[i]]->SetPhysState(false); } // Perform any solver-specific post-integration steps @@ -470,7 +496,7 @@ void UnsteadySystem::v_DoSolve() // Write out checkpoint files if ((m_checksteps && !((step + 1) % m_checksteps)) || doCheckTime) { - if (m_HomogeneousType != eNotHomogeneous) + if (m_HomogeneousType != eNotHomogeneous && !m_ALESolver) { vector transformed(nfields, false); for (i = 0; i < nfields; i++) @@ -535,28 +561,30 @@ void UnsteadySystem::v_DoSolve() } // If homogeneous, transform back into physical space if necessary. - if (m_HomogeneousType != eNotHomogeneous) + if (!m_ALESolver) { - for (i = 0; i < nfields; i++) + if (m_HomogeneousType != eNotHomogeneous) { - if (m_fields[i]->GetWaveSpace()) + for (i = 0; i < nfields; i++) { - m_fields[i]->SetWaveSpace(false); - m_fields[i]->BwdTrans(m_fields[i]->GetCoeffs(), - m_fields[i]->UpdatePhys()); - m_fields[i]->SetPhysState(true); + if (m_fields[i]->GetWaveSpace()) + { + m_fields[i]->SetWaveSpace(false); + m_fields[i]->BwdTrans(m_fields[i]->GetCoeffs(), + m_fields[i]->UpdatePhys()); + m_fields[i]->SetPhysState(true); + } } } - } - else - { - for (i = 0; i < nvariables; ++i) + else { - m_fields[m_intVariables[i]]->SetPhys(fields[i]); - m_fields[m_intVariables[i]]->SetPhysState(true); + for (i = 0; i < nvariables; ++i) + { + m_fields[m_intVariables[i]]->SetPhys(fields[i]); + m_fields[m_intVariables[i]]->SetPhysState(true); + } } } - // Finalise filters for (auto &x : m_filters) { @@ -578,6 +606,12 @@ void UnsteadySystem::v_DoInitialise() CheckForRestartTime(m_time, m_nchk); SetBoundaryConditions(m_time); SetInitialConditions(m_time); + + if (m_ALESolver) + { + UpdateGridVelocity(m_time); + } + InitializeSteadyState(); } diff --git a/library/SolverUtils/UnsteadySystem.h b/library/SolverUtils/UnsteadySystem.h index b72d27973b9a02b672b6b16d35ee35936c9f8dde..dc8ec834ea0cc73a1fd7d210506e8e48cc89b8cf 100644 --- a/library/SolverUtils/UnsteadySystem.h +++ b/library/SolverUtils/UnsteadySystem.h @@ -37,6 +37,7 @@ #include #include +#include #include #include @@ -45,7 +46,7 @@ namespace Nektar namespace SolverUtils { /// Base class for unsteady solvers. -class UnsteadySystem : public EquationSystem +class UnsteadySystem : public EquationSystem, public SolverUtils::ALEHelper { public: /// Destructor diff --git a/library/SpatialDomains/CMakeLists.txt b/library/SpatialDomains/CMakeLists.txt index d544d76a815b222a8e209d2b2978baf0f3f914aa..ab27d6000257fad4578a00d557ef75a1eda91279 100644 --- a/library/SpatialDomains/CMakeLists.txt +++ b/library/SpatialDomains/CMakeLists.txt @@ -18,6 +18,8 @@ SegGeom.cpp PointGeom.cpp TetGeom.cpp TriGeom.cpp +Movement/Zones.cpp +Movement/Movement.cpp ) SET(SPATIAL_DOMAINS_HEADERS @@ -44,6 +46,9 @@ SpatialDomainsDeclspec.h TetGeom.h TriGeom.h SpatialDomains.hpp +Movement/Zones.h + Movement/InterfaceInterpolation.h +Movement/Movement.h ) IF(NEKTAR_USE_HDF5) diff --git a/library/SpatialDomains/Geometry.cpp b/library/SpatialDomains/Geometry.cpp index 85550990b23345e9d21fe1fa913d8ae90231615f..a1ca0be50f447b456f492ad4f28639e56ec9a064 100644 --- a/library/SpatialDomains/Geometry.cpp +++ b/library/SpatialDomains/Geometry.cpp @@ -273,6 +273,15 @@ bool Geometry::v_ContainsPoint(const Array &gloCoord, } } +NekDouble Geometry::v_FindDistance(const Array &xs, + Array &xi) +{ + boost::ignore_unused(xs, xi); + NEKERROR(ErrorUtil::efatal, + "This function has not been defined for this geometry"); + return false; +} + /** * @copydoc Geometry::GetVertexEdgeMap() */ @@ -447,8 +456,8 @@ std::array Geometry::GetBoundingBox() for (int j = 0; j < 3; ++j) { const NekDouble len = max[j] - min[j]; - min[j] -= (0.1 + NekConstants::kGeomFactorsTol) * len; - max[j] += (0.1 + NekConstants::kGeomFactorsTol) * len; + min[j] -= (0.1 * len + NekConstants::kGeomFactorsTol); + max[j] += (0.1 * len + NekConstants::kGeomFactorsTol); } // save bounding box @@ -462,6 +471,11 @@ std::array Geometry::GetBoundingBox() return {{min[0], min[1], min[2], max[0], max[1], max[2]}}; } +void Geometry::ClearBoundingBox() +{ + m_boundingBox = {}; +} + /** * @brief Check if given global coord is within the BoundingBox * of the element. diff --git a/library/SpatialDomains/Geometry.h b/library/SpatialDomains/Geometry.h index 2fbeba412cf76758741271c640d59ae087cde5fb..01777296d6889707a1998e166fb26693f3505be8 100644 --- a/library/SpatialDomains/Geometry.h +++ b/library/SpatialDomains/Geometry.h @@ -137,6 +137,7 @@ public: // Point lookups //--------------------------------------- SPATIAL_DOMAINS_EXPORT std::array GetBoundingBox(); + SPATIAL_DOMAINS_EXPORT void ClearBoundingBox(); SPATIAL_DOMAINS_EXPORT inline bool ContainsPoint( const Array &gloCoord, NekDouble tol = 0.0); @@ -153,8 +154,11 @@ public: const int i, const Array &Lcoord); SPATIAL_DOMAINS_EXPORT bool MinMaxCheck( const Array &gloCoord); - SPATIAL_DOMAINS_EXPORT bool ClampLocCoords(Array &locCoord, - NekDouble tol); + SPATIAL_DOMAINS_EXPORT bool ClampLocCoords( + Array &locCoord, + NekDouble tol = std::numeric_limits::epsilon()); + SPATIAL_DOMAINS_EXPORT inline NekDouble FindDistance( + const Array &xs, Array &xi); //--------------------------------------- // Misc. helper functions @@ -169,8 +173,14 @@ public: SPATIAL_DOMAINS_EXPORT inline void Reset(CurveMap &curvedEdges, CurveMap &curvedFaces); + SPATIAL_DOMAINS_EXPORT inline void ResetNonRecursive(CurveMap &curvedEdges, + CurveMap &curvedFaces); + SPATIAL_DOMAINS_EXPORT inline void Setup(); + /// Handles generation of geometry factors. + void GenGeomFactors(); + protected: SPATIAL_DOMAINS_EXPORT static GeomFactorsSharedPtr ValidateRegGeomFactor( GeomFactorsSharedPtr geomFactor); @@ -199,9 +209,6 @@ protected: /// Array containing bounding box Array m_boundingBox; - /// Handles generation of geometry factors. - void GenGeomFactors(); - //--------------------------------------- // Helper functions //--------------------------------------- @@ -226,6 +233,8 @@ protected: const Array &Lcoord); virtual NekDouble v_GetLocCoords(const Array &coords, Array &Lcoords); + virtual NekDouble v_FindDistance(const Array &xs, + Array &xi); virtual int v_GetVertexEdgeMap(int i, int j) const; virtual int v_GetVertexFaceMap(int i, int j) const; @@ -545,6 +554,12 @@ inline NekDouble Geometry::GetCoord(const int i, return v_GetCoord(i, Lcoord); } +inline NekDouble Geometry::FindDistance(const Array &xs, + Array &xi) +{ + return v_FindDistance(xs, xi); +} + /** * @brief Returns the standard element edge IDs that are connected to a given * vertex. @@ -649,6 +664,17 @@ inline void Geometry::Reset(CurveMap &curvedEdges, CurveMap &curvedFaces) { v_Reset(curvedEdges, curvedFaces); } + +/** + * @brief Reset this geometry object non-recursively: unset the current state, + * zero Geometry::m_coeffs and remove allocated GeomFactors. + */ +inline void Geometry::ResetNonRecursive(CurveMap &curvedEdges, + CurveMap &curvedFaces) +{ + Geometry::v_Reset(curvedEdges, curvedFaces); +} + inline void Geometry::Setup() { v_Setup(); diff --git a/library/SpatialDomains/Geometry2D.cpp b/library/SpatialDomains/Geometry2D.cpp index 0ac1bec46a8fbc63fc562e7963b8648da29acfdd..07c8a721a84db5703954c8afdaa3d0f755663f03 100644 --- a/library/SpatialDomains/Geometry2D.cpp +++ b/library/SpatialDomains/Geometry2D.cpp @@ -69,7 +69,7 @@ void Geometry2D::NewtonIterationForLocCoord( NekDouble &dist) { // Maximum iterations for convergence - const int MaxIterations = 51; + const int MaxIterations = NekConstants::kNewtonIterations; // |x-xp|^2 < EPSILON error tolerance const NekDouble Tol = 1.e-8; // |r,s| > LcoordDIV stop the search @@ -351,5 +351,231 @@ int Geometry2D::v_GetShapeDim() const return 2; } +NekDouble Geometry2D::v_FindDistance(const Array &xs, + Array &xiOut) +{ + if (m_geomFactors->GetGtype() == eRegular) + { + xiOut = Array(2, 0.0); + + GetLocCoords(xs, xiOut); + ClampLocCoords(xiOut); + + Array gloCoord(3); + gloCoord[0] = GetCoord(0, xiOut); + gloCoord[1] = GetCoord(1, xiOut); + gloCoord[2] = GetCoord(2, xiOut); + + return sqrt((xs[0] - gloCoord[0]) * (xs[0] - gloCoord[0]) + + (xs[1] - gloCoord[1]) * (xs[1] - gloCoord[1]) + + (xs[2] - gloCoord[2]) * (xs[2] - gloCoord[2])); + } + // If deformed edge then the inverse mapping is non-linear so need to + // numerically solve for the local coordinate + else if (m_geomFactors->GetGtype() == eDeformed) + { + // Choose starting based on closest quad + Array xi(2, 0.0), eta(2, 0.0); + m_xmap->LocCollapsedToLocCoord(eta, xi); + + // Armijo constants: + // https://en.wikipedia.org/wiki/Backtracking_line_search + const NekDouble c1 = 1e-4, c2 = 0.9; + + int nq = m_xmap->GetTotPoints(); + + Array x(nq), y(nq), z(nq); + m_xmap->BwdTrans(m_coeffs[0], x); + m_xmap->BwdTrans(m_coeffs[1], y); + m_xmap->BwdTrans(m_coeffs[2], z); + + Array xderxi1(nq, 0.0), yderxi1(nq, 0.0), + zderxi1(nq, 0.0), xderxi2(nq, 0.0), yderxi2(nq, 0.0), + zderxi2(nq, 0.0), xderxi1xi1(nq, 0.0), yderxi1xi1(nq, 0.0), + zderxi1xi1(nq, 0.0), xderxi1xi2(nq, 0.0), yderxi1xi2(nq, 0.0), + zderxi1xi2(nq, 0.0), xderxi2xi1(nq, 0.0), yderxi2xi1(nq, 0.0), + zderxi2xi1(nq, 0.0), xderxi2xi2(nq, 0.0), yderxi2xi2(nq, 0.0), + zderxi2xi2(nq, 0.0); + + // Get first & second derivatives & partial derivatives of x,y,z values + std::array xc_derxi, yc_derxi, zc_derxi; + + m_xmap->PhysDeriv(x, xderxi1, xderxi2); + m_xmap->PhysDeriv(y, yderxi1, yderxi2); + m_xmap->PhysDeriv(z, zderxi1, zderxi2); + + m_xmap->PhysDeriv(xderxi1, xderxi1xi1, xderxi1xi2); + m_xmap->PhysDeriv(yderxi1, yderxi1xi1, yderxi1xi2); + m_xmap->PhysDeriv(zderxi1, zderxi1xi1, zderxi1xi2); + + m_xmap->PhysDeriv(yderxi2, yderxi2xi1, yderxi2xi2); + m_xmap->PhysDeriv(xderxi2, xderxi2xi1, xderxi2xi2); + m_xmap->PhysDeriv(zderxi2, zderxi2xi1, zderxi2xi2); + + // Minimisation loop (Quasi-newton method) + NekDouble fx_prev = std::numeric_limits::max(); + for (int i = 0; i < NekConstants::kNewtonIterations; ++i) + { + // Compute the objective function, f(x_k) and its derivatives + NekDouble xc = m_xmap->PhysEvaluate(xi, x, xc_derxi); + NekDouble yc = m_xmap->PhysEvaluate(xi, y, yc_derxi); + NekDouble zc = m_xmap->PhysEvaluate(xi, z, zc_derxi); + + NekDouble xc_derxi1xi1 = m_xmap->PhysEvaluate(xi, xderxi1xi1); + NekDouble yc_derxi1xi1 = m_xmap->PhysEvaluate(xi, yderxi1xi1); + NekDouble zc_derxi1xi1 = m_xmap->PhysEvaluate(xi, zderxi1xi1); + + NekDouble xc_derxi1xi2 = m_xmap->PhysEvaluate(xi, xderxi1xi2); + NekDouble yc_derxi1xi2 = m_xmap->PhysEvaluate(xi, yderxi1xi2); + NekDouble zc_derxi1xi2 = m_xmap->PhysEvaluate(xi, zderxi1xi2); + + NekDouble xc_derxi2xi2 = m_xmap->PhysEvaluate(xi, xderxi2xi2); + NekDouble yc_derxi2xi2 = m_xmap->PhysEvaluate(xi, yderxi2xi2); + NekDouble zc_derxi2xi2 = m_xmap->PhysEvaluate(xi, zderxi2xi2); + + // Objective function is the distance to the search point + NekDouble xdiff = xc - xs[0]; + NekDouble ydiff = yc - xs[1]; + NekDouble zdiff = zc - xs[2]; + + NekDouble fx = xdiff * xdiff + ydiff * ydiff + zdiff * zdiff; + + NekDouble fx_derxi1 = 2.0 * xdiff * xc_derxi[0] + + 2.0 * ydiff * yc_derxi[0] + + 2.0 * zdiff * zc_derxi[0]; + + NekDouble fx_derxi2 = 2.0 * xdiff * xc_derxi[1] + + 2.0 * ydiff * yc_derxi[1] + + 2.0 * zdiff * zc_derxi[1]; + + NekDouble fx_derxi1xi1 = + 2.0 * xdiff * xc_derxi1xi1 + 2.0 * xc_derxi[0] * xc_derxi[0] + + 2.0 * ydiff * yc_derxi1xi1 + 2.0 * yc_derxi[0] * yc_derxi[0] + + 2.0 * zdiff * zc_derxi1xi1 + 2.0 * zc_derxi[0] * zc_derxi[0]; + + NekDouble fx_derxi1xi2 = + 2.0 * xdiff * xc_derxi1xi2 + 2.0 * xc_derxi[1] * xc_derxi[0] + + 2.0 * ydiff * yc_derxi1xi2 + 2.0 * yc_derxi[1] * yc_derxi[0] + + 2.0 * zdiff * zc_derxi1xi2 + 2.0 * zc_derxi[1] * zc_derxi[0]; + + NekDouble fx_derxi2xi2 = + 2.0 * xdiff * xc_derxi2xi2 + 2.0 * xc_derxi[1] * xc_derxi[1] + + 2.0 * ydiff * yc_derxi2xi2 + 2.0 * yc_derxi[1] * yc_derxi[1] + + 2.0 * zdiff * zc_derxi2xi2 + 2.0 * zc_derxi[1] * zc_derxi[1]; + + // Jacobian + NekDouble jac[2]; + jac[0] = fx_derxi1; + jac[1] = fx_derxi2; + + // Inverse of 2x2 hessian + NekDouble hessInv[2][2]; + + NekDouble det = + 1 / (fx_derxi1xi1 * fx_derxi2xi2 - fx_derxi1xi2 * fx_derxi1xi2); + hessInv[0][0] = det * fx_derxi2xi2; + hessInv[0][1] = det * -fx_derxi1xi2; + hessInv[1][0] = det * -fx_derxi1xi2; + hessInv[1][1] = det * fx_derxi1xi1; + + // Check for convergence + if (abs(fx - fx_prev) < 1e-12) + { + fx_prev = fx; + break; + } + else + { + fx_prev = fx; + } + + NekDouble gamma = 1.0; + bool conv = false; + + // Search direction: Newton's method + NekDouble pk[2]; + pk[0] = -(hessInv[0][0] * jac[0] + hessInv[1][0] * jac[1]); + pk[1] = -(hessInv[0][1] * jac[0] + hessInv[1][1] * jac[1]); + + // Backtracking line search + while (gamma > 1e-10) + { + Array xi_pk(2); + xi_pk[0] = xi[0] + pk[0] * gamma; + xi_pk[1] = xi[1] + pk[1] * gamma; + + Array eta_pk(2, 0.0); + m_xmap->LocCoordToLocCollapsed(xi_pk, eta_pk); + + if (eta_pk[0] < + (-1 - std::numeric_limits::epsilon()) || + eta_pk[0] > + (1 + std::numeric_limits::epsilon()) || + eta_pk[1] < + (-1 - std::numeric_limits::epsilon()) || + eta_pk[1] > (1 + std::numeric_limits::epsilon())) + { + gamma /= 2.0; + continue; + } + + std::array xc_pk_derxi, yc_pk_derxi, zc_pk_derxi; + + NekDouble xc_pk = m_xmap->PhysEvaluate(xi_pk, x, xc_pk_derxi); + NekDouble yc_pk = m_xmap->PhysEvaluate(xi_pk, y, yc_pk_derxi); + NekDouble zc_pk = m_xmap->PhysEvaluate(xi_pk, z, zc_pk_derxi); + + NekDouble xc_pk_diff = xc_pk - xs[0]; + NekDouble yc_pk_diff = yc_pk - xs[1]; + NekDouble zc_pk_diff = zc_pk - xs[2]; + + NekDouble fx_pk = xc_pk_diff * xc_pk_diff + + yc_pk_diff * yc_pk_diff + + zc_pk_diff * zc_pk_diff; + + NekDouble fx_pk_derxi1 = 2.0 * xc_pk_diff * xc_pk_derxi[0] + + 2.0 * yc_pk_diff * yc_pk_derxi[0] + + 2.0 * zc_pk_diff * zc_pk_derxi[0]; + + NekDouble fx_pk_derxi2 = 2.0 * xc_pk_diff * xc_pk_derxi[1] + + 2.0 * yc_pk_diff * yc_pk_derxi[1] + + 2.0 * zc_pk_diff * zc_pk_derxi[1]; + + // Check Wolfe conditions using Armijo constants + // https://en.wikipedia.org/wiki/Wolfe_conditions + NekDouble tmp = pk[0] * fx_derxi1 + pk[1] * fx_derxi2; + NekDouble tmp2 = pk[0] * fx_pk_derxi1 + pk[1] * fx_pk_derxi2; + if ((fx_pk - (fx + c1 * gamma * tmp)) < + std::numeric_limits::epsilon() && + (-tmp2 - (-c2 * tmp)) < + std::numeric_limits::epsilon()) + { + conv = true; + break; + } + + gamma /= 2.0; + } + + if (!conv) + { + break; + } + + xi[0] += gamma * pk[0]; + xi[1] += gamma * pk[1]; + } + + xiOut = xi; + return sqrt(fx_prev); + } + else + { + ASSERTL0(false, "Geometry type unknown") + } + + return -1.0; +} + } // namespace SpatialDomains } // namespace Nektar diff --git a/library/SpatialDomains/Geometry2D.h b/library/SpatialDomains/Geometry2D.h index b8600324735cd815db78bffba18f02e296143149..59ed58c674f929a7a371bde45d8364cf069edb00 100644 --- a/library/SpatialDomains/Geometry2D.h +++ b/library/SpatialDomains/Geometry2D.h @@ -73,6 +73,10 @@ public: SPATIAL_DOMAINS_EXPORT virtual ~Geometry2D(); SPATIAL_DOMAINS_EXPORT static const int kDim = 2; + SPATIAL_DOMAINS_EXPORT CurveSharedPtr GetCurve() + { + return m_curve; + } protected: PointGeomVector m_verts; @@ -100,6 +104,9 @@ private: virtual int v_GetNumVerts() const; virtual int v_GetNumEdges() const; virtual StdRegions::Orientation v_GetEorient(const int i) const; + + virtual NekDouble v_FindDistance(const Array &xs, + Array &xi) final; }; } // namespace SpatialDomains diff --git a/library/SpatialDomains/Geometry3D.cpp b/library/SpatialDomains/Geometry3D.cpp index 06d484d26eafb1c484c78110a948edef566c0b4f..578a34be5101ba8c2c599656c466dd97935df0e9 100644 --- a/library/SpatialDomains/Geometry3D.cpp +++ b/library/SpatialDomains/Geometry3D.cpp @@ -77,7 +77,7 @@ void Geometry3D::NewtonIterationForLocCoord( NekDouble &dist) { // maximum iterations for convergence - const int MaxIterations = 51; + const int MaxIterations = NekConstants::kNewtonIterations; // |x-xp|^2 < EPSILON error tolerance const NekDouble Tol = 1.e-8; // |r,s| > LcoordDIV stop the search diff --git a/library/SpatialDomains/MeshGraph.cpp b/library/SpatialDomains/MeshGraph.cpp index c33dd70c5d510a71e17899039209af8090c68188..4c3e3a786f75cbda2dffd741b593a49dc3c06053 100644 --- a/library/SpatialDomains/MeshGraph.cpp +++ b/library/SpatialDomains/MeshGraph.cpp @@ -47,6 +47,7 @@ #include #include +#include // These are required for the Write(...) and Import(...) functions. #include @@ -199,13 +200,17 @@ void MeshGraph::FillGraph() break; case 1: { - for (auto x : m_segGeoms) + for (auto &x : m_segGeoms) { x.second->Setup(); } } break; } + + // Populate the movement object + m_movement = MemoryManager::AllocateSharedPtr( + m_session, this); } void MeshGraph::FillBoundingBoxTree() @@ -588,7 +593,7 @@ void MeshGraph::GetCompositeList(const std::string &compositeStr, addedVector.push_back(*iter); ASSERTL0(m_meshComposites.find(*iter) != m_meshComposites.end(), - "Composite not found."); + "Composite C[" + std::to_string(*iter) + "] not found."); CompositeSharedPtr composite = m_meshComposites.find(*iter)->second; if (composite) @@ -598,7 +603,7 @@ void MeshGraph::GetCompositeList(const std::string &compositeStr, else { char str[64]; - ::sprintf(str, "%d", *iter); + ::snprintf(str, 64, "%d", *iter); NEKERROR(ErrorUtil::ewarning, (std::string("Undefined composite: ") + str).c_str()); } @@ -2544,36 +2549,31 @@ ExpansionInfoMapShPtr MeshGraph::SetUpExpansionInfoMap(void) for (auto &d : m_domain) { - for (auto compIter = d.second.begin(); compIter != d.second.end(); - ++compIter) + for (auto &compIter : d.second) { // regular elements first - for (auto x = compIter->second->m_geomVec.begin(); - x != compIter->second->m_geomVec.end(); ++x) + for (auto &x : compIter.second->m_geomVec) { - if ((*x)->GetGeomFactors()->GetGtype() != + if (x->GetGeomFactors()->GetGtype() != SpatialDomains::eDeformed) { LibUtilities::BasisKeyVector def; ExpansionInfoShPtr expansionElementShPtr = - MemoryManager::AllocateSharedPtr(*x, - def); - int id = (*x)->GetGlobalID(); + MemoryManager::AllocateSharedPtr(x, def); + int id = x->GetGlobalID(); (*returnval)[id] = expansionElementShPtr; } } // deformed elements - for (auto x = compIter->second->m_geomVec.begin(); - x != compIter->second->m_geomVec.end(); ++x) + for (auto &x : compIter.second->m_geomVec) { - if ((*x)->GetGeomFactors()->GetGtype() == + if (x->GetGeomFactors()->GetGtype() == SpatialDomains::eDeformed) { LibUtilities::BasisKeyVector def; ExpansionInfoShPtr expansionElementShPtr = - MemoryManager::AllocateSharedPtr(*x, - def); - int id = (*x)->GetGlobalID(); + MemoryManager::AllocateSharedPtr(x, def); + int id = x->GetGlobalID(); (*returnval)[id] = expansionElementShPtr; } } @@ -2977,8 +2977,11 @@ void MeshGraph::ReadExpansionInfo() { auto x = expansionMap->find((*geomVecIter)->GetGlobalID()); - ASSERTL0(x != expansionMap->end(), - "Expansion not found!!"); + ASSERTL0( + x != expansionMap->end(), + "Expansion " + + std::to_string((*geomVecIter)->GetGlobalID()) + + " not found!!"); if (useExpansionType) { (x->second)->m_basisKeyVector = @@ -3536,10 +3539,9 @@ GeometryLinkSharedPtr MeshGraph::GetElementsFromEdge(Geometry1DSharedPtr edge) for (auto &d : m_domain) { - for (auto compIter = d.second.begin(); compIter != d.second.end(); - ++compIter) + for (auto &compIter : d.second) { - for (auto &geomIter : compIter->second->m_geomVec) + for (auto &geomIter : compIter.second->m_geomVec) { triGeomShPtr = std::dynamic_pointer_cast(geomIter); quadGeomShPtr = std::dynamic_pointer_cast(geomIter); diff --git a/library/SpatialDomains/MeshGraph.h b/library/SpatialDomains/MeshGraph.h index 8c64dd8eb31c670b39169a932a61842abdd2f7cf..84992f322a8b14013b459e68604b0bfd612800e2 100644 --- a/library/SpatialDomains/MeshGraph.h +++ b/library/SpatialDomains/MeshGraph.h @@ -172,6 +172,9 @@ typedef std::map MeshMetaDataMap; class MeshGraph; typedef std::shared_ptr MeshGraphSharedPtr; +class Movement; +typedef std::shared_ptr MovementSharedPtr; + /// Base class for a spectral/hp element mesh. class MeshGraph { @@ -436,6 +439,11 @@ public: SPATIAL_DOMAINS_EXPORT std::map CreateMeshEntities(); SPATIAL_DOMAINS_EXPORT CompositeDescriptor CreateCompositeDescriptor(); + SPATIAL_DOMAINS_EXPORT inline MovementSharedPtr &GetMovement() + { + return m_movement; + } + protected: void PopulateFaceToElMap(Geometry3DSharedPtr element, int kNfaces); ExpansionInfoMapShPtr SetUpExpansionInfoMap(); @@ -479,6 +487,7 @@ protected: struct GeomRTree; std::unique_ptr m_boundingBoxTree; + MovementSharedPtr m_movement = nullptr; }; typedef std::shared_ptr MeshGraphSharedPtr; typedef LibUtilities::NekFactory MeshGraphFactory; diff --git a/library/SpatialDomains/MeshGraphHDF5.cpp b/library/SpatialDomains/MeshGraphHDF5.cpp index 278a76d1ad1861cc45ed1f59159db67c13438fd2..bc137e385a0324b632ed4dfbb378e49ad2caa69d 100644 --- a/library/SpatialDomains/MeshGraphHDF5.cpp +++ b/library/SpatialDomains/MeshGraphHDF5.cpp @@ -46,7 +46,7 @@ #define TIME_RESULT(verb, msg, timer) \ if (verb) \ { \ - std::cout << " - " << msg << ": " << timer.TimePerTest(1) \ + std::cout << " - " << msg << ": " << timer.TimePerTest(1) << "\n" \ << std::endl; \ } @@ -60,7 +60,7 @@ namespace SpatialDomains /// Version of the Nektar++ HDF5 geometry format, which is embedded into the /// main NEKTAR/GEOMETRY group as an attribute. -const unsigned int MeshGraphHDF5::FORMAT_VERSION = 1; +const unsigned int MeshGraphHDF5::FORMAT_VERSION = 2; std::string MeshGraphHDF5::className = GetMeshGraphFactory().RegisterCreatorFunction("HDF5", MeshGraphHDF5::create, @@ -251,7 +251,6 @@ void MeshGraphHDF5::PartitionMesh(LibUtilities::SessionReaderSharedPtr session) ASSERTL0(root2, "Cannot find NEKTAR/GEOMETRY group in HDF5 file."); // Check format version - unsigned int formatVersion; H5::Group::AttrIterator attrIt = root2->attr_begin(); H5::Group::AttrIterator attrEnd = root2->attr_end(); for (; attrIt != attrEnd; ++attrIt) @@ -263,9 +262,9 @@ void MeshGraphHDF5::PartitionMesh(LibUtilities::SessionReaderSharedPtr session) } ASSERTL0(attrIt != attrEnd, "Unable to determine Nektar++ geometry HDF5 file version."); - root2->GetAttribute("FORMAT_VERSION", formatVersion); + root2->GetAttribute("FORMAT_VERSION", m_inFormatVersion); - ASSERTL0(formatVersion <= FORMAT_VERSION, + ASSERTL0(m_inFormatVersion <= FORMAT_VERSION, "File format in " + m_hdf5Name + " is higher than supported in " "this version of Nektar++"); @@ -1063,14 +1062,42 @@ void MeshGraphHDF5::ReadCurveMap(CurveMap &curveMap, std::string dsName, void MeshGraphHDF5::ReadDomain() { - map fullDomain; + if (m_inFormatVersion == 1) + { + map fullDomain; + H5::DataSetSharedPtr dst = m_mesh->OpenDataSet("DOMAIN"); + H5::DataSpaceSharedPtr space = dst->GetSpace(); + + vector data; + dst->ReadVectorString(data, space, m_readPL); + GetCompositeList(data[0], fullDomain); + m_domain[0] = fullDomain; + + return; + } + + std::vector fullDomain; H5::DataSetSharedPtr dst = m_mesh->OpenDataSet("DOMAIN"); H5::DataSpaceSharedPtr space = dst->GetSpace(); vector data; dst->ReadVectorString(data, space, m_readPL); - GetCompositeList(data[0], fullDomain); - m_domain[0] = fullDomain; + for (auto &dIt : data) + { + fullDomain.push_back(CompositeMap()); + GetCompositeList(dIt, fullDomain.back()); + } + + H5::DataSetSharedPtr mdata = m_maps->OpenDataSet("DOMAIN"); + H5::DataSpaceSharedPtr mspace = mdata->GetSpace(); + + vector ids; + mdata->Read(ids, mspace); + + for (int i = 0; i < ids.size(); ++i) + { + m_domain[ids[i]] = fullDomain[i]; + } } void MeshGraphHDF5::ReadComposites() @@ -1476,21 +1503,43 @@ void MeshGraphHDF5::WriteComposites(CompositeMap &composites) dst->Write(c_map, ds); } -void MeshGraphHDF5::WriteDomain(map &domain) +void MeshGraphHDF5::WriteDomain(std::map &domain) { - vector idxList; - for (auto cIt = domain[0].begin(); cIt != domain[0].end(); ++cIt) + // dont need location map only a id map + // will filter the composites per parition on read, its easier + // composites do not need to be written in paralell. + vector d_map; + std::vector> idxList; + + int cnt = 0; + for (auto &dIt : domain) { - idxList.push_back(cIt->first); + idxList.push_back(std::vector()); + for (auto cIt = dIt.second.begin(); cIt != dIt.second.end(); ++cIt) + { + idxList[cnt].push_back(cIt->first); + } + + ++cnt; + d_map.push_back(dIt.first); } + stringstream domString; vector doms; - doms.push_back(ParseUtils::GenerateSeqString(idxList)); + for (auto &cIt : idxList) + { + doms.push_back(ParseUtils::GenerateSeqString(cIt)); + } H5::DataTypeSharedPtr tp = H5::DataType::String(); H5::DataSpaceSharedPtr ds = H5::DataSpace::OneD(doms.size()); H5::DataSetSharedPtr dst = m_mesh->CreateDataSet("DOMAIN", tp, ds); dst->WriteVectorString(doms, ds, tp); + + tp = H5::DataType::OfObject(d_map[0]); + ds = H5::DataSpace::OneD(d_map.size()); + dst = m_maps->CreateDataSet("DOMAIN", tp, ds); + dst->Write(d_map, ds); } void MeshGraphHDF5::WriteGeometry( diff --git a/library/SpatialDomains/MeshGraphHDF5.h b/library/SpatialDomains/MeshGraphHDF5.h index 0eaaf1d0c09fa4bced28b99b8be5e86c54b2e4ed..18e222791248cf7517e2162572fd4321f4bc33b6 100644 --- a/library/SpatialDomains/MeshGraphHDF5.h +++ b/library/SpatialDomains/MeshGraphHDF5.h @@ -113,6 +113,7 @@ private: LibUtilities::H5::PListSharedPtr m_readPL; LibUtilities::H5::GroupSharedPtr m_mesh; LibUtilities::H5::GroupSharedPtr m_maps; + unsigned int m_inFormatVersion; static const unsigned int FORMAT_VERSION; }; diff --git a/library/SpatialDomains/MeshGraphXml.cpp b/library/SpatialDomains/MeshGraphXml.cpp index 1bfc699a3cbea73ee90c4dd7f72badcd8fabfccf..9012f3b098bb8c90abe615fca8f100705be8bad5 100644 --- a/library/SpatialDomains/MeshGraphXml.cpp +++ b/library/SpatialDomains/MeshGraphXml.cpp @@ -2024,7 +2024,7 @@ void MeshGraphXml::ResolveGeomRef1D(const std::string &prevToken, if (m_vertSet.find(*iter) == m_vertSet.end()) { char errStr[16] = ""; - ::sprintf(errStr, "%d", *iter); + ::snprintf(errStr, 16, "%d", *iter); NEKERROR( ErrorUtil::ewarning, (std::string("Unknown vertex index: ") + errStr) @@ -2044,7 +2044,7 @@ void MeshGraphXml::ResolveGeomRef1D(const std::string &prevToken, if (m_segGeoms.find(*iter) == m_segGeoms.end()) { char errStr[16] = ""; - ::sprintf(errStr, "%d", *iter); + ::snprintf(errStr, 16, "%d", *iter); NEKERROR( ErrorUtil::ewarning, (std::string("Unknown segment index: ") + errStr) @@ -2128,7 +2128,7 @@ void MeshGraphXml::ResolveGeomRef2D(const std::string &prevToken, if (m_segGeoms.find(*seqIter) == m_segGeoms.end()) { char errStr[16] = ""; - ::sprintf(errStr, "%d", *seqIter); + ::snprintf(errStr, 16, "%d", *seqIter); NEKERROR(ErrorUtil::ewarning, (std::string("Unknown edge index: ") + errStr) .c_str()); @@ -2148,7 +2148,7 @@ void MeshGraphXml::ResolveGeomRef2D(const std::string &prevToken, if (m_triGeoms.count(*seqIter) == 0) { char errStr[16] = ""; - ::sprintf(errStr, "%d", *seqIter); + ::snprintf(errStr, 16, "%d", *seqIter); NEKERROR( ErrorUtil::ewarning, (std::string("Unknown triangle index: ") + errStr) @@ -2174,7 +2174,7 @@ void MeshGraphXml::ResolveGeomRef2D(const std::string &prevToken, if (m_quadGeoms.count(*seqIter) == 0) { char errStr[16] = ""; - ::sprintf(errStr, "%d", *seqIter); + ::snprintf(errStr, 16, "%d", *seqIter); NEKERROR(ErrorUtil::ewarning, (std::string("Unknown quad index: ") + errStr + std::string(" in Composite section")) @@ -2199,7 +2199,7 @@ void MeshGraphXml::ResolveGeomRef2D(const std::string &prevToken, if (*seqIter >= m_vertSet.size()) { char errStr[16] = ""; - ::sprintf(errStr, "%d", *seqIter); + ::snprintf(errStr, 16, "%d", *seqIter); NEKERROR( ErrorUtil::ewarning, (std::string("Unknown vertex index: ") + errStr) @@ -2292,7 +2292,7 @@ void MeshGraphXml::ResolveGeomRef3D(const std::string &prevToken, if (m_vertSet.find(*seqIter) == m_vertSet.end()) { char errStr[16] = ""; - ::sprintf(errStr, "%d", *seqIter); + ::snprintf(errStr, 16, "%d", *seqIter); NEKERROR( ErrorUtil::ewarning, (std::string("Unknown vertex index: ") + errStr) @@ -2312,7 +2312,7 @@ void MeshGraphXml::ResolveGeomRef3D(const std::string &prevToken, if (m_segGeoms.find(*seqIter) == m_segGeoms.end()) { char errStr[16] = ""; - ::sprintf(errStr, "%d", *seqIter); + ::snprintf(errStr, 16, "%d", *seqIter); NEKERROR(ErrorUtil::ewarning, (std::string("Unknown edge index: ") + errStr) .c_str()); @@ -2332,7 +2332,7 @@ void MeshGraphXml::ResolveGeomRef3D(const std::string &prevToken, if (face == Geometry2DSharedPtr()) { char errStr[16] = ""; - ::sprintf(errStr, "%d", *seqIter); + ::snprintf(errStr, 16, "%d", *seqIter); NEKERROR(ErrorUtil::ewarning, (std::string("Unknown face index: ") + errStr) .c_str()); @@ -2354,7 +2354,7 @@ void MeshGraphXml::ResolveGeomRef3D(const std::string &prevToken, if (m_triGeoms.find(*seqIter) == m_triGeoms.end()) { char errStr[16] = ""; - ::sprintf(errStr, "%d", *seqIter); + ::snprintf(errStr, 16, "%d", *seqIter); NEKERROR( ErrorUtil::ewarning, (std::string("Unknown triangle index: ") + errStr) @@ -2378,7 +2378,7 @@ void MeshGraphXml::ResolveGeomRef3D(const std::string &prevToken, if (m_quadGeoms.find(*seqIter) == m_quadGeoms.end()) { char errStr[16] = ""; - ::sprintf(errStr, "%d", *seqIter); + ::snprintf(errStr, 16, "%d", *seqIter); NEKERROR(ErrorUtil::ewarning, (std::string("Unknown quad index: ") + errStr) .c_str()); @@ -2402,7 +2402,7 @@ void MeshGraphXml::ResolveGeomRef3D(const std::string &prevToken, if (m_tetGeoms.find(*seqIter) == m_tetGeoms.end()) { char errStr[16] = ""; - ::sprintf(errStr, "%d", *seqIter); + ::snprintf(errStr, 16, "%d", *seqIter); NEKERROR(ErrorUtil::ewarning, (std::string("Unknown tet index: ") + errStr) .c_str()); @@ -2426,7 +2426,7 @@ void MeshGraphXml::ResolveGeomRef3D(const std::string &prevToken, if (m_pyrGeoms.find(*seqIter) == m_pyrGeoms.end()) { char errStr[16] = ""; - ::sprintf(errStr, "%d", *seqIter); + ::snprintf(errStr, 16, "%d", *seqIter); NEKERROR( ErrorUtil::ewarning, (std::string("Unknown pyramid index: ") + errStr) @@ -2451,7 +2451,7 @@ void MeshGraphXml::ResolveGeomRef3D(const std::string &prevToken, if (m_prismGeoms.find(*seqIter) == m_prismGeoms.end()) { char errStr[16] = ""; - ::sprintf(errStr, "%d", *seqIter); + ::snprintf(errStr, 16, "%d", *seqIter); NEKERROR(ErrorUtil::ewarning, (std::string("Unknown prism index: ") + errStr) .c_str()); @@ -2475,7 +2475,7 @@ void MeshGraphXml::ResolveGeomRef3D(const std::string &prevToken, if (m_hexGeoms.find(*seqIter) == m_hexGeoms.end()) { char errStr[16] = ""; - ::sprintf(errStr, "%d", *seqIter); + ::snprintf(errStr, 16, "%d", *seqIter); NEKERROR(ErrorUtil::ewarning, (std::string("Unknown hex index: ") + errStr) .c_str()); @@ -2728,29 +2728,29 @@ void MeshGraphXml::WriteComposites(TiXmlElement *geomTag, CompositeMap &comps, } void MeshGraphXml::WriteDomain(TiXmlElement *geomTag, - map &domain) + std::map &domainMap) { TiXmlElement *domTag = new TiXmlElement("DOMAIN"); - for (auto &d : domain) + vector idxList; + for (auto &domain : domainMap) { - stringstream domString; - if (d.second.size()) - { - domString.clear(); - TiXmlElement *dtag = new TiXmlElement("D"); - dtag->SetAttribute("ID", d.first); + TiXmlElement *c = new TiXmlElement("D"); + idxList.clear(); + stringstream s; + s << " " + << "C" + << "["; - vector idxList; - for (auto cIt = d.second.begin(); cIt != d.second.end(); ++cIt) - { - idxList.push_back(cIt->first); - } - domString << " C[" << ParseUtils::GenerateSeqString(idxList) - << "] "; - dtag->LinkEndChild(new TiXmlText(domString.str())); - domTag->LinkEndChild(dtag); + for (const auto &elem : domain.second) + { + idxList.push_back(elem.first); } + + s << ParseUtils::GenerateSeqString(idxList) << "] "; + c->SetAttribute("ID", domain.first); + c->LinkEndChild(new TiXmlText(s.str())); + domTag->LinkEndChild(c); } geomTag->LinkEndChild(domTag); @@ -2804,6 +2804,11 @@ void MeshGraphXml::WriteGeometry(std::string &outfilename, bool defaultExp, geomTag->SetAttribute("DIM", m_meshDimension); geomTag->SetAttribute("SPACE", m_spaceDimension); + if (m_session != nullptr && !m_session->GetComm()->IsSerial()) + { + geomTag->SetAttribute("PARTITION", m_session->GetComm()->GetRank()); + } + // Clear existing elements. geomTag->Clear(); @@ -3140,17 +3145,19 @@ void MeshGraphXml::WriteXMLGeometry(std::string outname, WriteComposites(geomTag, localComp, localCompLabels); map domain; - for (auto &d : m_domain) + for (auto &j : localComp) { - CompositeMap domMap; - for (auto &j : localComp) + for (auto &dom : m_domain) { - if (d.second.count(j.first)) + for (auto &dIt : dom.second) { - domMap[j.first] = j.second; + if (j.first == dIt.first) + { + domain[dom.first][j.first] = j.second; + break; + } } } - domain[d.first] = domMap; } WriteDomain(geomTag, domain); diff --git a/library/SpatialDomains/Movement/InterfaceInterpolation.h b/library/SpatialDomains/Movement/InterfaceInterpolation.h new file mode 100644 index 0000000000000000000000000000000000000000..4f23d2ef4d2429182282964c0aa1a386cacb0ea8 --- /dev/null +++ b/library/SpatialDomains/Movement/InterfaceInterpolation.h @@ -0,0 +1,163 @@ +//////////////////////////////////////////////////////////////////////////////// +// +// File: InterfaceInterpolation.hpp +// +// For more information, please see: http://www.nektar.info/ +// +// The MIT License +// +// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA), +// Department of Aeronautics, Imperial College London (UK), and Scientific +// Computing and Imaging Institute, University of Utah (USA). +// +// License for the specific language governing rights and limitations under +// Permission is hereby granted, free of charge, to any person obtaining a +// copy of this software and associated documentation files (the "Software"), +// to deal in the Software without restriction, including without limitation +// the rights to use, copy, modify, merge, publish, distribute, sublicense, +// and/or sell copies of the Software, and to permit persons to whom the +// Software is furnished to do so, subject to the following s: +// +// The above copyright notice and this permission notice shall be included +// in all copies or substantial portions of the Software. +// +// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +// DEALINGS IN THE SOFTWARE. +// +// Description: Interface handling for zones using the interpolation method +// +// +//////////////////////////////////////////////////////////////////////////////// +#ifndef NEKTAR_SPATIALDOMAINS_INTERFACEINTERPOLATION_H +#define NEKTAR_SPATIALDOMAINS_INTERFACEINTERPOLATION_H + +#include + +namespace Nektar +{ + +namespace SpatialDomains +{ + +// Fwd def to allow for inclusion in meshgraph +struct Composite; +typedef std::shared_ptr CompositeSharedPtr; +typedef std::map CompositeMap; + +/// A interface which is a single edge on a zone for handling non-conformality +struct Interface +{ + /// Constructor + Interface(int indx, const CompositeMap &edge, bool skipCoordCheck) + : m_id(indx), m_skipCoordCheck(skipCoordCheck) + { + // Fill element Ids + for (auto &comp : edge) + { + for (auto &geom : comp.second->m_geomVec) + { + m_edge[geom->GetGlobalID()] = geom; + } + } + } + + /// Default destructor + virtual ~Interface() = default; + + /// Returns map of global ID to geometry of the interface edge + inline std::map const &GetEdge() const + { + return m_edge; + } + + /// Returns geometry of the interface edge with global ID @param id + inline GeometrySharedPtr const &GetEdge(int id) + { + return m_edge[id]; + } + + /// Checks if the interface edge is empty (used for parallelisation) + inline bool IsEmpty() const + { + return m_edge.empty(); + } + + /// Returns the matching opposite interface from the interface pair + inline std::shared_ptr &GetOppInterface() + { + return m_oppInterface; + } + + /// Returns the interface ID + inline int &GetId() + { + return m_id; + } + + /// Return the skip check flag for coordinate exchange in InterfaceMapDG + inline bool GetSkipCoordCheck() const + { + return m_skipCoordCheck; + } + +protected: + /// Matching opposite interface of the interface pair + std::shared_ptr m_oppInterface; + /// Interface ID + int m_id; + /// Map of global ID to geometry of the interface edge + std::map m_edge; + /// Skip the coord found check in InterfaceMapDG + bool m_skipCoordCheck; +}; + +typedef std::shared_ptr InterfaceShPtr; + +/** + * Interface pair consisting of a 'left' and 'right' interface. The allocation + * of 'left' and 'right' is arbitrary for any interface as long as it stays + * consistent. Every full interface will consist of exactly one 'left' and one + * 'right' interface, the nomenclature helps keep code understandable. + */ +struct InterfacePair +{ + /// Constructor + InterfacePair(const InterfaceShPtr &leftInterface, + const InterfaceShPtr &rightInterface) + : m_leftInterface(leftInterface), m_rightInterface(rightInterface) + { + // Sets the opposite interfaces + leftInterface->GetOppInterface() = rightInterface; + rightInterface->GetOppInterface() = leftInterface; + } + + /// 'Left' interface of the interface pair + InterfaceShPtr m_leftInterface; + /// 'Right' interface of the interface pair + InterfaceShPtr m_rightInterface; + +public: + /// Return the 'left' interface from the interface pair + inline const InterfaceShPtr &GetLeftInterface() const + { + return m_leftInterface; + } + + /// Return the 'right' interface from the interface pair + inline const InterfaceShPtr &GetRightInterface() const + { + return m_rightInterface; + } +}; + +typedef std::shared_ptr InterfacePairShPtr; + +} // namespace SpatialDomains +} // namespace Nektar + +#endif // NEKTAR_SPATIALDOMAINS_INTERFACEINTERPOLATION_H diff --git a/library/SpatialDomains/Movement/Movement.cpp b/library/SpatialDomains/Movement/Movement.cpp new file mode 100644 index 0000000000000000000000000000000000000000..ac8045d6c0ca87ce035cc0ddeb0f9be8df3a8470 --- /dev/null +++ b/library/SpatialDomains/Movement/Movement.cpp @@ -0,0 +1,471 @@ +//////////////////////////////////////////////////////////////////////////////// +// +// File: Movement.cpp +// +// For more information, please see: http://www.nektar.info/ +// +// The MIT License +// +// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA), +// Department of Aeronautics, Imperial College London (UK), and Scientific +// Computing and Imaging Institute, University of Utah (USA). +// +// License for the specific language governing rights and limitations under +// Permission is hereby granted, free of charge, to any person obtaining a +// copy of this software and associated documentation files (the "Software"), +// to deal in the Software without restriction, including without limitation +// the rights to use, copy, modify, merge, publish, distribute, sublicense, +// and/or sell copies of the Software, and to permit persons to whom the +// Software is furnished to do so, subject to the following conditions: +// +// The above copyright notice and this permission notice shall be included +// in all copies or substantial portions of the Software. +// +// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +// DEALINGS IN THE SOFTWARE. +// +// Description: This file contains the base class for implementing +// non-conformal geometry using the Movement object +// +//////////////////////////////////////////////////////////////////////////////// + +#include +#include +#include +#include + +namespace Nektar +{ +namespace SpatialDomains +{ + +std::string static inline ReadTag(std::string &tagStr) +{ + std::string::size_type indxBeg = tagStr.find_first_of('[') + 1; + std::string::size_type indxEnd = tagStr.find_last_of(']') - 1; + + ASSERTL0( + indxBeg <= indxEnd, + (std::string("Error reading interface region definition:") + tagStr) + .c_str()); + + std::string indxStr = tagStr.substr(indxBeg, indxEnd - indxBeg + 1); + + return indxStr; +} + +Movement::Movement(const LibUtilities::SessionReaderSharedPtr &pSession, + MeshGraph *meshGraph) +{ + TiXmlNode *nektar = pSession->GetElement("NEKTAR"); + if (nektar == nullptr) + { + return; + } + + TiXmlNode *movement = nektar->FirstChild("MOVEMENT"); + if (movement != nullptr) + { + bool zones = movement->FirstChild("ZONES") != nullptr; + if (zones) + { + ReadZones(pSession->GetElement("NEKTAR/MOVEMENT/ZONES"), meshGraph, + pSession); + } + + bool interfaces = movement->FirstChild("INTERFACES") != nullptr; + if (interfaces) + { + ReadInterfaces(pSession->GetElement("NEKTAR/MOVEMENT/INTERFACES"), + meshGraph); + } + + ASSERTL0(zones == interfaces, + "Only one of ZONES or INTERFACES present in the MOVEMENT " + "block.") + + // Don't support interior penalty yet + if (pSession->DefinesSolverInfo("DiffusionType")) + { + ASSERTL0(pSession->GetSolverInfo("DiffusionType") == "LDGNS", + "Only LDGNS is supported as the DiffusionType in " + "SOLVERINFO when a MOVEMENT block is defined.") + } + } + + // DEBUG COMMENTS + if (movement != nullptr && pSession->DefinesCmdLineArgument("verbose")) + { + auto comm = pSession->GetComm(); + if (comm->TreatAsRankZero()) + { + std::cout << "Movement Info:\n"; + std::cout << "\tNum zones: " << m_zones.size() << "\n"; + } + + for (auto &zone : m_zones) + { + auto numEl = zone.second->GetElements().size(); + comm->AllReduce(numEl, LibUtilities::ReduceSum); + + // Find shape type if not on this proc + int shapeType = + !zone.second->GetElements().empty() + ? zone.second->GetElements().front()->GetShapeType() + : -1; + comm->AllReduce(shapeType, LibUtilities::ReduceMax); + + if (comm->TreatAsRankZero()) + { + std::cout << "\t- " << zone.first << " " + << MovementTypeStr[static_cast( + zone.second->GetMovementType())] + << ": " << numEl << " " + << LibUtilities::ShapeTypeMap[shapeType] << "s\n"; + } + } + + if (comm->TreatAsRankZero()) + { + std::cout << "\tNum interfaces: " << m_interfaces.size() << "\n"; + } + + for (auto &interface : m_interfaces) + { + auto numLeft = + interface.second->GetLeftInterface()->GetEdge().size(); + auto numRight = + interface.second->GetRightInterface()->GetEdge().size(); + comm->AllReduce(numLeft, LibUtilities::ReduceSum); + comm->AllReduce(numRight, LibUtilities::ReduceSum); + + // Find shape type if not on this proc + int shapeTypeLeft = + !interface.second->GetLeftInterface()->GetEdge().empty() + ? interface.second->GetLeftInterface() + ->GetEdge() + .begin() + ->second->GetShapeType() + : -1; + comm->AllReduce(shapeTypeLeft, LibUtilities::ReduceMax); + int shapeTypeRight = + !interface.second->GetRightInterface()->GetEdge().empty() + ? interface.second->GetRightInterface() + ->GetEdge() + .begin() + ->second->GetShapeType() + : -1; + comm->AllReduce(shapeTypeRight, LibUtilities::ReduceMax); + + if (comm->TreatAsRankZero()) + { + std::cout << "\t- \"" << interface.first.second << "\": " + << interface.second->GetLeftInterface()->GetId() + << " (" << numLeft << " " + << LibUtilities::ShapeTypeMap[shapeTypeLeft] + << "s) <-> " + << interface.second->GetRightInterface()->GetId() + << " (" << numRight << " " + << LibUtilities::ShapeTypeMap[shapeTypeRight] + << "s)\n"; + } + } + + comm->Block(); + if (comm->TreatAsRankZero()) + { + std::cout << std::endl; + } + } +} + +void Movement::ReadZones(TiXmlElement *zonesTag, MeshGraph *meshGraph, + const LibUtilities::SessionReaderSharedPtr &pSession) +{ + int coordDim = meshGraph->GetSpaceDimension(); + + ASSERTL0(zonesTag, "Unable to find ZONES tag in file."); + TiXmlElement *zonesElement = zonesTag->FirstChildElement(); + while (zonesElement) + { + std::string zoneType = zonesElement->Value(); + + int err; + int indx; + + err = zonesElement->QueryIntAttribute("ID", &indx); + ASSERTL0(err == TIXML_SUCCESS, "Unable to read zone ID."); + + std::string interfaceDomainStr; + err = zonesElement->QueryStringAttribute("DOMAIN", &interfaceDomainStr); + ASSERTL0(err == TIXML_SUCCESS, "Unable to read zone domain."); + + auto &domains = meshGraph->GetDomain(); + auto domFind = stoi(ReadTag(interfaceDomainStr)); + std::map domain; + if (domains.find(domFind) != domains.end()) + { + domain = domains.at(domFind); + } + + ZoneBaseShPtr zone; + if (zoneType == "F" || zoneType == "FIXED") + { + zone = ZoneFixedShPtr(MemoryManager::AllocateSharedPtr( + indx, domain, coordDim)); + } + else if (zoneType == "R" || zoneType == "ROTATE" || + zoneType == "ROTATING") + { + std::string originStr; + err = zonesElement->QueryStringAttribute("ORIGIN", &originStr); + ASSERTL0(err == TIXML_SUCCESS, "Unable to read origin."); + std::vector originVec; + ParseUtils::GenerateVector(originStr, originVec); + NekPoint origin = + NekPoint(originVec[0], originVec[1], originVec[2]); + + std::string axisStr; + err = zonesElement->QueryStringAttribute("AXIS", &axisStr); + ASSERTL0(err == TIXML_SUCCESS, "Unable to read axis."); + DNekVec axis(axisStr); + axis.Normalize(); + + std::string angularVelStr; + err = zonesElement->QueryStringAttribute("ANGVEL", &angularVelStr); + ASSERTL0(err == TIXML_SUCCESS, "Unable to read angular velocity."); + + pSession->SubstituteExpressions(angularVelStr); + LibUtilities::EquationSharedPtr angularVelEqn = + MemoryManager::AllocateSharedPtr( + pSession->GetInterpreter(), angularVelStr); + + zone = ZoneRotateShPtr(MemoryManager::AllocateSharedPtr( + indx, domain, coordDim, origin, axis, angularVelEqn)); + + m_moveFlag = true; + } + else if (zoneType == "T" || zoneType == "TRANSLATE" || + zoneType == "TRANSLATING") + { + // Read velocity information + std::string velocityStr; + err = zonesElement->QueryStringAttribute("VELOCITY", &velocityStr); + ASSERTL0(err == TIXML_SUCCESS, + "Unable to read VELOCITY for translating zone " + + std::to_string(indx)); + + std::vector velocityStrSplit; + ParseUtils::GenerateVector(velocityStr, velocityStrSplit); + + ASSERTL0(velocityStrSplit.size() >= coordDim, + "VELOCITY dimensions must be greater than or equal to the " + "coordinate dimension for translating zone " + + std::to_string(indx)); + + Array velocityEqns(coordDim); + for (int i = 0; i < coordDim; ++i) + { + pSession->SubstituteExpressions(velocityStrSplit[i]); + + velocityEqns[i] = + MemoryManager::AllocateSharedPtr( + pSession->GetInterpreter(), velocityStrSplit[i]); + } + + // Read displacement information + std::string displacementStr; + err = zonesElement->QueryStringAttribute("DISPLACEMENT", + &displacementStr); + ASSERTL0(err == TIXML_SUCCESS, + "Unable to read DISPLACEMENT for translating zone " + + std::to_string(indx)); + + std::vector displacementStrSplit; + ParseUtils::GenerateVector(displacementStr, displacementStrSplit); + + ASSERTL0( + displacementStrSplit.size() >= coordDim, + "DISPLACEMENT dimensions must be greater than or equal to the " + "coordinate dimension for translating zone " + + std::to_string(indx)); + + Array displacementEqns( + coordDim); + for (int i = 0; i < coordDim; ++i) + { + pSession->SubstituteExpressions(displacementStrSplit[i]); + + displacementEqns[i] = + MemoryManager::AllocateSharedPtr( + pSession->GetInterpreter(), displacementStrSplit[i]); + } + + zone = ZoneTranslateShPtr( + MemoryManager::AllocateSharedPtr( + indx, domain, coordDim, velocityEqns, displacementEqns)); + + m_moveFlag = true; + } + else if (zoneType == "P" || zoneType == "PRESCRIBED") + { + std::string xDeformStr; + err = zonesElement->QueryStringAttribute("XDEFORM", &xDeformStr); + ASSERTL0(err == TIXML_SUCCESS, "Unable to read x deform equation."); + LibUtilities::EquationSharedPtr xDeformEqn = + std::make_shared( + pSession->GetInterpreter(), xDeformStr); + + std::string yDeformStr; + err = zonesElement->QueryStringAttribute("YDEFORM", &yDeformStr); + ASSERTL0(err == TIXML_SUCCESS, "Unable to read y deform equation."); + LibUtilities::EquationSharedPtr yDeformEqn = + std::make_shared( + pSession->GetInterpreter(), yDeformStr); + + std::string zDeformStr; + err = zonesElement->QueryStringAttribute("ZDEFORM", &zDeformStr); + ASSERTL0(err == TIXML_SUCCESS, "Unable to read z deform equation."); + LibUtilities::EquationSharedPtr zDeformEqn = + std::make_shared( + pSession->GetInterpreter(), zDeformStr); + + zone = ZonePrescribeShPtr( + MemoryManager::AllocateSharedPtr( + indx, domain, coordDim, xDeformEqn, yDeformEqn, + zDeformEqn)); + + m_moveFlag = true; + } + else + { + WARNINGL0(false, "Zone type '" + zoneType + + "' is unsupported. Valid types are: 'Fixed', " + "'Rotate', 'Translate', or 'Prescribe'.") + } + + m_zones[indx] = zone; + zonesElement = zonesElement->NextSiblingElement(); + } +} + +void Movement::ReadInterfaces(TiXmlElement *interfacesTag, MeshGraph *meshGraph) +{ + ASSERTL0(interfacesTag, "Unable to find INTERFACES tag in file."); + TiXmlElement *interfaceElement = interfacesTag->FirstChildElement(); + + while (interfaceElement) + { + ASSERTL0( + "INTERFACE" == (std::string)interfaceElement->Value(), + "Only INTERFACE tags may be present inside the INTERFACES block.") + + int err; + + std::string name; + err = interfaceElement->QueryStringAttribute("NAME", &name); + ASSERTL0(err == TIXML_SUCCESS, "Unable to read interface name."); + TiXmlElement *sideElement = interfaceElement->FirstChildElement(); + + Array interfaces(2); + std::vector cnt; + while (sideElement) + { + ASSERTL0( + cnt.size() < 2, + "In INTERFACE NAME " + name + + ", only two sides may be present in each INTERFACE block.") + + // Read ID + int indx; + err = sideElement->QueryIntAttribute("ID", &indx); + ASSERTL0(err == TIXML_SUCCESS, "Unable to read interface ID."); + + // Read boundary + std::string boundaryStr; + err = sideElement->QueryStringAttribute("BOUNDARY", &boundaryStr); + ASSERTL0(err == TIXML_SUCCESS, + "Unable to read BOUNDARY in interface " + + std::to_string(indx)); + + CompositeMap boundaryEdge; + std::string indxStr = ReadTag(boundaryStr); + meshGraph->GetCompositeList(indxStr, boundaryEdge); + + // Read SKIPCHECK flag + bool skipCheck = false; + err = sideElement->QueryBoolAttribute("SKIPCHECK", &skipCheck); + + // Sets location in interface pair to 0 for left, and 1 for right + auto sideElVal = sideElement->ValueStr(); + if (sideElVal == "LEFT" || sideElVal == "L") + { + cnt.emplace_back(0); + } + else if (sideElVal == "RIGHT" || sideElVal == "R") + { + cnt.emplace_back(1); + } + else + { + NEKERROR(ErrorUtil::efatal, + sideElement->ValueStr() + + " is not a valid interface side for interface " + "NAME " + + name + ". Please only use LEFT or RIGHT.") + } + + interfaces[cnt[cnt.size() - 1]] = + InterfaceShPtr(MemoryManager::AllocateSharedPtr( + indx, boundaryEdge, skipCheck)); + + sideElement = sideElement->NextSiblingElement(); + } + + ASSERTL0(std::accumulate(cnt.begin(), cnt.end(), 0) == 1, + "You must have only one LEFT and one RIGHT side" + " present in interface NAME " + + name) + + m_interfaces[std::make_pair(m_interfaces.size(), name)] = + InterfacePairShPtr(MemoryManager::AllocateSharedPtr( + interfaces[0], interfaces[1])); + interfaceElement = interfaceElement->NextSiblingElement(); + } +} + +// Acts as a placeholder for when ALE function and moving geometry capability +// is added. Currently unused. +void Movement::PerformMovement(NekDouble timeStep) +{ + std::set movedZoneIds; + for (auto &zone : m_zones) + { + if (zone.second->Move(timeStep)) + { + movedZoneIds.insert(zone.first); + } + } + + // If zone has moved, set all interfaces on that zone to moved. + for (auto &interPair : m_interfaces) + { + int leftId = interPair.second->GetLeftInterface()->GetId(); + int rightId = interPair.second->GetRightInterface()->GetId(); + + if (movedZoneIds.find(leftId) != movedZoneIds.end() || + movedZoneIds.find(rightId) != movedZoneIds.end()) + { + m_zones[leftId]->GetMoved() = true; + m_zones[rightId]->GetMoved() = true; + } + } +} + +} // namespace SpatialDomains +} // namespace Nektar diff --git a/library/SpatialDomains/Movement/Movement.h b/library/SpatialDomains/Movement/Movement.h new file mode 100644 index 0000000000000000000000000000000000000000..8b6af59fc549fded3f11eea887611af561da9d3d --- /dev/null +++ b/library/SpatialDomains/Movement/Movement.h @@ -0,0 +1,104 @@ +//////////////////////////////////////////////////////////////////////////////// +// +// File: Movement.h +// +// For more information, please see: http://www.nektar.info/ +// +// The MIT License +// +// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA), +// Department of Aeronautics, Imperial College London (UK), and Scientific +// Computing and Imaging Institute, University of Utah (USA). +// +// License for the specific language governing rights and limitations under +// Permission is hereby granted, free of charge, to any person obtaining a +// copy of this software and associated documentation files (the "Software"), +// to deal in the Software without restriction, including without limitation +// the rights to use, copy, modify, merge, publish, distribute, sublicense, +// and/or sell copies of the Software, and to permit persons to whom the +// Software is furnished to do so, subject to the following s: +// +// The above copyright notice and this permission notice shall be included +// in all copies or substantial portions of the Software. +// +// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +// DEALINGS IN THE SOFTWARE. +// +// Description: This file contains the base class for implementing +// non-conformal geometry using the Movement object +// +//////////////////////////////////////////////////////////////////////////////// +#ifndef NEKTAR_SPATIALDOMAINS_MOVEMENT_H +#define NEKTAR_SPATIALDOMAINS_MOVEMENT_H + +#include +#include + +namespace Nektar +{ + +namespace SpatialDomains +{ + +typedef std::map, InterfacePairShPtr> + InterfaceCollection; + +class Movement +{ +public: + /// Constructor + SPATIAL_DOMAINS_EXPORT Movement( + const LibUtilities::SessionReaderSharedPtr &pSession, + MeshGraph *meshGraph); + + /// Default destructor + SPATIAL_DOMAINS_EXPORT ~Movement() = default; + + inline const InterfaceCollection &GetInterfaces() const + { + return m_interfaces; + } + + inline const std::map &GetZones() const + { + return m_zones; + } + + void PerformMovement(NekDouble timeStep); + + inline const bool &GetMoveFlag() const + { + return m_moveFlag; + } + + inline bool &GetCoordExchangeFlag() + { + return m_coordExchangeFlag; + } + +protected: + InterfaceCollection m_interfaces; + std::map m_zones; + bool m_moveFlag = false; // Flags presence of moving zones + bool m_coordExchangeFlag = + true; // Flags if missing coordinates need to be calculated + +private: + /// Read zones given TiXmlDocument + void ReadZones(TiXmlElement *zonesTag, MeshGraph *meshGraph, + const LibUtilities::SessionReaderSharedPtr &pSession); + /// Read interfaces given TiXmlDocument + void ReadInterfaces(TiXmlElement *interfacesTag, MeshGraph *meshGraph); +}; + +typedef std::shared_ptr MovementSharedPtr; + +} // namespace SpatialDomains +} // namespace Nektar + +#endif // NEKTAR_SPATIALDOMAINS_MOVEMENT_H \ No newline at end of file diff --git a/library/SpatialDomains/Movement/Zones.cpp b/library/SpatialDomains/Movement/Zones.cpp new file mode 100644 index 0000000000000000000000000000000000000000..af78e51bbf07716b62cc8aee9b1b63e5a90ecb13 --- /dev/null +++ b/library/SpatialDomains/Movement/Zones.cpp @@ -0,0 +1,377 @@ +//////////////////////////////////////////////////////////////////////////////// +// +// File: Zones.cpp +// +// For more information, please see: http://www.nektar.info/ +// +// The MIT License +// +// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA), +// Department of Aeronautics, Imperial College London (UK), and Scientific +// Computing and Imaging Institute, University of Utah (USA). +// +// License for the specific language governing rights and limitations under +// Permission is hereby granted, free of charge, to any person obtaining a +// copy of this software and associated documentation files (the "Software"), +// to deal in the Software without restriction, including without limitation +// the rights to use, copy, modify, merge, publish, distribute, sublicense, +// and/or sell copies of the Software, and to permit persons to whom the +// Software is furnished to do so, subject to the following conditions: +// +// The above copyright notice and this permission notice shall be included +// in all copies or substantial portions of the Software. +// +// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +// DEALINGS IN THE SOFTWARE. +// +// Description: Zones used in the non-conformal interfaces +// and ALE implementations +// +//////////////////////////////////////////////////////////////////////////////// + +#include +#include +#include +#include + +namespace Nektar +{ +namespace SpatialDomains +{ + +ZoneBase::ZoneBase(MovementType type, int indx, CompositeMap domain, + int coordDim) + : m_type(type), m_id(indx), m_domain(domain), m_coordDim(coordDim) +{ + for (auto &comp : domain) + { + for (auto &geom : comp.second->m_geomVec) + { + m_elements.emplace_back(geom); + + // Fill constituent elements (i.e. faces and edges) + switch (geom->GetShapeDim()) + { + case 3: + for (int i = 0; i < geom->GetNumFaces(); ++i) + { + m_constituentElements[2].insert(geom->GetFace(i)); + } + /* fall through */ + case 2: + for (int i = 0; i < geom->GetNumEdges(); ++i) + { + m_constituentElements[1].insert(geom->GetEdge(i)); + } + /* fall through */ + case 1: + m_constituentElements[0].insert(geom); + /* fall through */ + default: + break; + } + } + } + + // The seenVerts/Edges/Faces keeps track of geometry so duplicates aren't + // emplaced in to the storage vector + std::unordered_set seenVerts, seenEdges, seenFaces; + + // Fill verts/edges/faces vector storage that are to be moved each timestep + for (auto &comp : m_domain) + { + for (auto &geom : comp.second->m_geomVec) + { + for (int i = 0; i < geom->GetNumVerts(); ++i) + { + PointGeomSharedPtr vert = geom->GetVertex(i); + + if (seenVerts.find(vert->GetGlobalID()) != seenVerts.end()) + { + continue; + } + + seenVerts.insert(vert->GetGlobalID()); + m_verts.emplace_back(vert); + } + + for (int i = 0; i < geom->GetNumEdges(); ++i) + { + SegGeomSharedPtr edge = + std::static_pointer_cast(geom->GetEdge(i)); + + if (seenEdges.find(edge->GetGlobalID()) != seenEdges.end()) + { + continue; + } + + seenEdges.insert(edge->GetGlobalID()); + + CurveSharedPtr curve = edge->GetCurve(); + if (!curve) + { + continue; + } + + m_curves.emplace_back(curve); + } + + for (int i = 0; i < geom->GetNumFaces(); ++i) + { + Geometry2DSharedPtr face = + std::static_pointer_cast(geom->GetFace(i)); + + if (seenFaces.find(face->GetGlobalID()) != seenFaces.end()) + { + continue; + } + + seenFaces.insert(face->GetGlobalID()); + + CurveSharedPtr curve = face->GetCurve(); + if (!curve) + { + continue; + } + + m_curves.emplace_back(curve); + } + } + } + + // Copy points so we know original positions. + for (auto &pt : m_verts) + { + m_origVerts.emplace_back(*pt); + } + + for (auto &curve : m_curves) + { + for (auto &pt : curve->m_points) + { + m_origVerts.emplace_back(*pt); + } + } +} + +ZoneRotate::ZoneRotate(int id, const CompositeMap &domain, const int coordDim, + const NekPoint &origin, const DNekVec &axis, + const LibUtilities::EquationSharedPtr &angularVelEqn) + : ZoneBase(MovementType::eRotate, id, domain, coordDim), m_origin(origin), + m_axis(axis), m_angularVelEqn(angularVelEqn) +{ + // Construct rotation matrix + m_W(0, 1) = -m_axis[2]; + m_W(0, 2) = m_axis[1]; + m_W(1, 0) = m_axis[2]; + m_W(1, 2) = -m_axis[0]; + m_W(2, 0) = -m_axis[1]; + m_W(2, 1) = m_axis[0]; + + m_W2 = m_W * m_W; +} + +void ZoneBase::ClearBoundingBoxes() +{ + // Clear bboxes (these will be regenerated next time GetBoundingBox is + // called) + for (auto &el : m_elements) + { + el->ClearBoundingBox(); + + int nfaces = el->GetNumFaces(); + for (int i = 0; i < nfaces; ++i) + { + el->GetFace(i)->ClearBoundingBox(); + } + + int nedges = el->GetNumEdges(); + for (int i = 0; i < nedges; ++i) + { + el->GetEdge(i)->ClearBoundingBox(); + } + } +} + +NekDouble ZoneRotate::GetAngularVel(NekDouble &time) const +{ + NekDouble rampTime = 1; + if (time < rampTime) + { + return m_angularVelEqn->Evaluate(0, 0, 0, time) * time/rampTime; + } + else + { + return m_angularVelEqn->Evaluate(0, 0, 0, time); + } +} + +// Calculate new location of points using Rodrigues formula +bool ZoneRotate::v_Move(NekDouble time) +{ + // This works for a linear ramp + NekDouble rampTime = 1; + NekDouble angle; + if (time < rampTime) + { + angle = GetAngularVel(time) * (time/rampTime) / 2; + } + else + { + angle = GetAngularVel(rampTime) * rampTime / 2 + GetAngularVel(time) * (time - rampTime); + } + + // TODO: I want to integrate m_angularVelEqn up to current time + + // Identity matrix + DNekMat rot(3, 3, 0.0); + rot(0, 0) = 1.0; + rot(1, 1) = 1.0; + rot(2, 2) = 1.0; + + // Rodrigues' rotation formula in matrix form + rot = rot + sin(angle) * m_W + (1 - cos(angle)) * m_W2; + + int cnt = 0; + for (auto &vert : m_verts) + { + NekPoint pnt = m_origVerts[cnt] - m_origin; + DNekVec pntVec = {pnt[0], pnt[1], pnt[2]}; + + DNekVec newLoc = rot * pntVec; + + vert->UpdatePosition(newLoc(0) + m_origin[0], newLoc(1) + m_origin[1], + newLoc(2) + m_origin[2]); + cnt++; + } + + for (auto &curve : m_curves) + { + for (auto &vert : curve->m_points) + { + NekPoint pnt = m_origVerts[cnt] - m_origin; + DNekVec pntVec = {pnt[0], pnt[1], pnt[2]}; + + DNekVec newLoc = rot * pntVec; + + vert->UpdatePosition(newLoc(0) + m_origin[0], + newLoc(1) + m_origin[1], + newLoc(2) + m_origin[2]); + cnt++; + } + } + + ClearBoundingBoxes(); + + return true; +} + +std::vector ZoneTranslate::GetVel(NekDouble &time) const +{ + std::vector vel(m_coordDim); + for (int i = 0; i < m_coordDim; ++i) + { + vel[i] = m_velocityEqns[i]->Evaluate(0, 0, 0, time); + } + + return vel; +} + +std::vector ZoneTranslate::GetDisp(NekDouble &time) const +{ + std::vector disp(m_coordDim); + for (int i = 0; i < m_coordDim; ++i) + { + disp[i] = m_displacementEqns[i]->Evaluate(0, 0, 0, time); + } + + return disp; +} + +bool ZoneTranslate::v_Move(NekDouble time) +{ + auto disp = GetDisp(time); + + int cnt = 0; + for (auto &vert : m_verts) + { + Array newLoc(3, 0.0); + auto pnt = m_origVerts[cnt]; + + for (int i = 0; i < m_coordDim; ++i) + { + newLoc[i] = pnt(i) + disp[i]; + } + + vert->UpdatePosition(newLoc[0], newLoc[1], newLoc[2]); + cnt++; + } + + for (auto &curve : m_curves) + { + for (auto &vert : curve->m_points) + { + Array newLoc(3, 0.0); + auto pnt = m_origVerts[cnt]; + + for (int i = 0; i < m_coordDim; ++i) + { + newLoc[i] = pnt(i) + disp[i]; + } + + vert->UpdatePosition(newLoc[0], newLoc[1], newLoc[2]); + cnt++; + } + } + + ClearBoundingBoxes(); + + return true; +} + +bool ZoneFixed::v_Move(NekDouble time) +{ + boost::ignore_unused(time); + return false; +} + +bool ZonePrescribe::v_Move(NekDouble time) +{ + int cnt = 0; + for (auto &vert : m_verts) + { + auto pnt = m_origVerts[cnt++]; + + Array coords(3, 0.0); + vert->GetCoords(coords); + + Array newLoc(3, 0.0); + /*newLoc[0] = + m_xDeform->Evaluate(coords[0], coords[1], coords[2], time) + pnt(0); + newLoc[1] = + m_yDeform->Evaluate(coords[0], coords[1], coords[2], time) + pnt(1); + newLoc[2] = + m_zDeform->Evaluate(coords[0], coords[1], coords[2], time) + pnt(2);*/ + + newLoc[0] = pnt(0) + 0.5 * sin(2 * M_PI * time / sqrt(50)) * + sin(2 * M_PI * coords[0] / 20) * + sin(2 * M_PI * coords[1] / 20); + newLoc[1] = pnt(1) + 0.5 * sin(2 * M_PI * time / sqrt(50)) * + sin(2 * M_PI * coords[0] / 20) * + sin(2 * M_PI * coords[1] / 20); + newLoc[2] = 0.0; + vert->UpdatePosition(newLoc[0], newLoc[1], newLoc[2]); + } + + ClearBoundingBoxes(); + + return true; +} + +} // namespace SpatialDomains +} // namespace Nektar diff --git a/library/SpatialDomains/Movement/Zones.h b/library/SpatialDomains/Movement/Zones.h new file mode 100644 index 0000000000000000000000000000000000000000..453422e2e4a2b6d12099a2478178abd87bf4366c --- /dev/null +++ b/library/SpatialDomains/Movement/Zones.h @@ -0,0 +1,339 @@ +//////////////////////////////////////////////////////////////////////////////// +// +// File: Zones.h +// +// For more information, please see: http://www.nektar.info/ +// +// The MIT License +// +// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA), +// Department of Aeronautics, Imperial College London (UK), and Scientific +// Computing and Imaging Institute, University of Utah (USA). +// +// License for the specific language governing rights and limitations under +// Permission is hereby granted, free of charge, to any person obtaining a +// copy of this software and associated documentation files (the "Software"), +// to deal in the Software without restriction, including without limitation +// the rights to use, copy, modify, merge, publish, distribute, sublicense, +// and/or sell copies of the Software, and to permit persons to whom the +// Software is furnished to do so, subject to the following s: +// +// The above copyright notice and this permission notice shall be included +// in all copies or substantial portions of the Software. +// +// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +// DEALINGS IN THE SOFTWARE. +// +// Description: Zones used in the non-conformal interfaces +// and ALE implementations +// +//////////////////////////////////////////////////////////////////////////////// +#ifndef NEKTAR_SPATIALDOMAINS_ZONES_H +#define NEKTAR_SPATIALDOMAINS_ZONES_H + +#include + +namespace Nektar +{ + +namespace SpatialDomains +{ + +/// Enum of zone movement type +enum class MovementType +{ + eNone, + eFixed, + eRotate, + eTranslate, + ePrescribe +}; + +/// Map of zone movement type to movement type string +const std::string MovementTypeStr[] = {"None", "Fixed", "Rotated", "Translated", + "Prescribed"}; + +/// Zone base: Contains the shared functions and variables +struct ZoneBase +{ + /// Constructor + ZoneBase(MovementType type, int indx, CompositeMap domain, int coordDim); + + /// Default destructor + virtual ~ZoneBase() = default; + + /// Returns the type of movement + inline MovementType GetMovementType() const + { + return m_type; + } + + /// Returns the domain the zone is on + inline CompositeMap GetDomain() const + { + return m_domain; + } + + /// Returns the zone ID + inline int &GetId() + { + return m_id; + } + + /// Virtual function for movement of the zone at @param time + inline virtual bool v_Move(NekDouble time) + { + boost::ignore_unused(time); + return false; + } + + /// Performs the movement of the zone at @param time + inline bool Move(NekDouble time) + { + return v_Move(time); + } + + /// Returns all highest dimension elements in the zone + inline std::vector const &GetElements() const + { + return m_elements; + } + + /// Returns the flag which states if the zone has moved in this timestep + inline bool &GetMoved() + { + return m_moved; + } + + /// Clears all bounding boxes associated with the zones elements + void ClearBoundingBoxes(); + + /// Returns constituent elements, i.e. faces + edges + inline std::array, 3> &GetConstituentElements() + { + return m_constituentElements; + } + +protected: + /// Type of zone movement + MovementType m_type = MovementType::eNone; + /// Zone ID + int m_id; + /// Zone domain + CompositeMap m_domain; + /// Vector of highest dimension zone elements + std::vector m_elements; + /// Array of all dimension elements i.e. faces = [2], edges = [1], geom = + /// [0] + std::array, 3> m_constituentElements; + /// Moved flag + bool m_moved = true; + /// Coordinate dimension + int m_coordDim; + /// Vector of all points in the zone + std::vector m_verts; + /// Vector of all curves in the zone + std::vector m_curves; + /// Vector of all points in the zone at initialisation + std::vector m_origVerts; +}; + +typedef std::shared_ptr ZoneBaseShPtr; + +/// Rotating zone: Motion of every point around a given axis on an origin +struct ZoneRotate final : public ZoneBase +{ + /** + * Constructor for rotating zones + * + * @param id Zone ID + * @param domain Domain that the zone consists of + * @param coordDim Coordinate dimension + * @param origin Origin that the zone rotates about + * @param axis Axis that the zone rotates about + * @param angularVelEqn Equation for the angular velocity of rotation + */ + ZoneRotate(int id, const CompositeMap &domain, const int coordDim, + const NekPoint &origin, const DNekVec &axis, + const LibUtilities::EquationSharedPtr &angularVelEqn); + + /// Default destructor + virtual ~ZoneRotate() = default; + + /// Return the angular velocity of the zone at @param time + NekDouble GetAngularVel(NekDouble &time) const; + + /// Virtual function for movement of the zone at @param time + virtual bool v_Move(NekDouble time) final; + + inline NekPoint GetOrigin() const + { + return m_origin; + } + + inline DNekVec GetAxis() const + { + return m_axis; + } + +protected: + /// Origin point rotation is performed around + NekPoint m_origin; + /// Axis rotation is performed around + DNekVec m_axis; + /// Equation defining angular velocity as a function of time + LibUtilities::EquationSharedPtr m_angularVelEqn; + /// W matrix Rodrigues' rotation formula, cross product of axis + DNekMat m_W = DNekMat(3, 3, 0.0); + /// W^2 matrix Rodrigues' rotation formula, cross product of axis squared + DNekMat m_W2 = DNekMat(3, 3, 0.0); +}; + +/// Translating zone: addition of a constant vector to every point +struct ZoneTranslate final : public ZoneBase +{ + /** + * Constructor for translating zone + * + * @param id Zone ID + * @param domain Domain that the zone consists of + * @param coordDim Coordinate dimension + * @param velocity Vector of translation velocity in x,y,z direction + */ + ZoneTranslate(int id, const CompositeMap &domain, const int coordDim, + const Array &velocityEqns, + const Array &displacementEqns) + : ZoneBase(MovementType::eTranslate, id, domain, coordDim), + m_velocityEqns(velocityEqns), m_displacementEqns(displacementEqns) + { + } + + /// Default destructor + virtual ~ZoneTranslate() = default; + + /// Returns the velocity of the zone + std::vector GetVel(NekDouble &time) const; + + /// Returns the displacement of the zone + std::vector GetDisp(NekDouble &time) const; + + /// Virtual function for movement of the zone at @param time + virtual bool v_Move(NekDouble time) final; + +protected: + Array m_velocityEqns; + Array m_displacementEqns; +}; + +/// Prescribed zone: applies equation to every point +struct ZonePrescribe final : public ZoneBase +{ + /** + * Constructor for prescribed zone + * + * @param id Zone ID + * @param domain Domain that the zone consists of + * @param coordDim Coordinate dimension + * @param xDeform Equation for prescribed motion of x-coordinate + * @param yDeform Equation for prescribed motion of y-coordinate + * @param zDeform Equation for prescribed motion of z-coordinate + */ + ZonePrescribe(int id, const CompositeMap &domain, const int coordDim, + LibUtilities::EquationSharedPtr xDeform, + LibUtilities::EquationSharedPtr yDeform, + LibUtilities::EquationSharedPtr zDeform) + : ZoneBase(MovementType::ePrescribe, id, domain, coordDim), + m_xDeform(xDeform), m_yDeform(yDeform), m_zDeform(zDeform) + { + } + + /// Default destructor + virtual ~ZonePrescribe() = default; + + /** + * Returns point @param x @param y @param z deformation in the x direction + * at time @param t + * @param x x-coordinate + * @param y y-coordinate + * @param z z-coordinate + * @param t time + * @return deformation in x direction + */ + inline NekDouble GetXDeform(NekDouble x, NekDouble y, NekDouble z, + NekDouble t) const + { + return m_xDeform->Evaluate(x, y, z, t); + } + + /** + * Returns point @param x @param y @param z deformation in the y direction + * at time @param t + * @param x x-coordinate + * @param y y-coordinate + * @param z z-coordinate + * @param t time + * @return deformation in y direction + */ + inline NekDouble GetYDeform(NekDouble x, NekDouble y, NekDouble z, + NekDouble t) const + { + return m_yDeform->Evaluate(x, y, z, t); + } + + /** + * Returns point @param x @param y @param z deformation in the z direction + * at time @param t + * @param x x-coordinate + * @param y y-coordinate + * @param z z-coordinate + * @param t time + * @return deformation in z direction + */ + inline NekDouble GetZDeform(NekDouble x, NekDouble y, NekDouble z, + NekDouble t) const + { + return m_zDeform->Evaluate(x, y, z, t); + } + + /// Virtual function for movement of the zone at @param time + virtual bool v_Move(NekDouble time) final; + +protected: + /// Equation specifying prescribed motion in x-direction + LibUtilities::EquationSharedPtr m_xDeform; + /// Equation specifying prescribed motion in y-direction + LibUtilities::EquationSharedPtr m_yDeform; + /// Equation specifying prescribed motion in z-direction + LibUtilities::EquationSharedPtr m_zDeform; +}; + +/// Fixed zone: does not move +struct ZoneFixed final : public ZoneBase +{ + /// Constructor + ZoneFixed(int id, const CompositeMap &domain, const int coordDim) + : ZoneBase(MovementType::eFixed, id, domain, coordDim) + { + } + + /// Default destructor + virtual ~ZoneFixed() = default; + + /// Virtual function for movement of the zone at @param time + virtual bool v_Move(NekDouble time) final; +}; + +typedef std::shared_ptr ZoneRotateShPtr; +typedef std::shared_ptr ZoneTranslateShPtr; +typedef std::shared_ptr ZonePrescribeShPtr; +typedef std::shared_ptr ZoneFixedShPtr; + +} // namespace SpatialDomains +} // namespace Nektar + +#endif // NEKTAR_SPATIALDOMAINS_ZONES_H diff --git a/library/SpatialDomains/QuadGeom.cpp b/library/SpatialDomains/QuadGeom.cpp index 7905dd0a4544ddc40c09125d1908c0012becc288..0bed61dc5d1b73cd6474d4174a47995f6d19dc0c 100644 --- a/library/SpatialDomains/QuadGeom.cpp +++ b/library/SpatialDomains/QuadGeom.cpp @@ -317,7 +317,7 @@ void QuadGeom::v_GenGeomFactors() { if (fabs((*m_verts[0])(i) - (*m_verts[1])(i) + (*m_verts[2])(i) - (*m_verts[3])(i)) > - NekConstants::kNekZeroTol) + NekConstants::kGeomFactorsTol) { Gtype = eDeformed; break; diff --git a/library/SpatialDomains/SegGeom.cpp b/library/SpatialDomains/SegGeom.cpp index 521ef8f08f339cda59c2d287b5271b2bd6fd9369..9761bc359aae6ac7cc90d43064fbb1ae8f8c9f0d 100644 --- a/library/SpatialDomains/SegGeom.cpp +++ b/library/SpatialDomains/SegGeom.cpp @@ -349,5 +349,149 @@ int SegGeom::v_GetNumVerts() const return kNverts; } +NekDouble SegGeom::v_FindDistance(const Array &xs, + Array &xiOut) +{ + if (m_geomFactors->GetGtype() == eRegular) + { + xiOut = Array(1, 0.0); + + GetLocCoords(xs, xiOut); + ClampLocCoords(xiOut); + + Array gloCoord(m_coordim); + NekDouble tmp = 0; + for (int i = 0; i < m_coordim; ++i) + { + gloCoord[i] = GetCoord(i, xiOut); + tmp += (xs[i] - gloCoord[i]) * (xs[i] - gloCoord[i]); + } + + return sqrt(tmp); + } + // If deformed edge then the inverse mapping is non-linear so need to + // numerically solve for the local coordinate + else if (m_geomFactors->GetGtype() == eDeformed) + { + Array xi(1, 0.0); + + // Armijo constants: + // https://en.wikipedia.org/wiki/Backtracking_line_search + const NekDouble c1 = 1e-4, c2 = 0.9; + + int dim = GetCoordim(); + int nq = m_xmap->GetTotPoints(); + + Array> x(dim), xder(dim), xder2(dim); + // Get x,y,z phys values from coefficients + for (int i = 0; i < dim; ++i) + { + x[i] = Array(nq); + xder[i] = Array(nq); + xder2[i] = Array(nq); + + m_xmap->BwdTrans(m_coeffs[i], x[i]); + } + + NekDouble fx_prev = std::numeric_limits::max(); + + // Minimisation loop (Quasi-newton method) + for (int i = 0; i < NekConstants::kNewtonIterations; ++i) + { + // Compute the objective function, f(x_k) and its derivatives + Array xc(dim); + Array> xc_der(dim); + Array> xc_der2(dim); + NekDouble fx = 0, fxp = 0, fxp2 = 0, xcDiff = 0; + for (int j = 0; j < dim; ++j) + { + xc[j] = m_xmap->PhysEvaluate(xi, x[j], xc_der[j], xc_der2[j]); + + xcDiff = xc[j] - xs[j]; + // Objective function is the distance to the search point + fx += xcDiff * xcDiff; + fxp += xc_der[j][0] * xcDiff; + fxp2 += xc_der2[j][0] * xcDiff + xc_der[j][0] * xc_der[j][0]; + } + + fxp *= 2; + fxp2 *= 2; + + // Check for convergence + if (std::abs(fx - fx_prev) < 1e-12) + { + fx_prev = fx; + break; + } + else + { + fx_prev = fx; + } + + NekDouble gamma = 1.0; + bool conv = false; + + // Search direction: Newton's method + NekDouble pk = -fxp / fxp2; + + // Perform backtracking line search + while (gamma > 1e-10) + { + Array xi_pk(1); + xi_pk[0] = xi[0] + pk * gamma; + + if (xi_pk[0] < -1.0 || xi_pk[0] > 1.0) + { + gamma /= 2.0; + continue; + } + + Array xc_pk(dim); + Array> xc_der_pk(dim); + NekDouble fx_pk = 0, fxp_pk = 0, xc_pkDiff = 0; + for (int j = 0; j < dim; ++j) + { + xc_pk[j] = m_xmap->PhysEvaluate(xi_pk, x[j], xc_der_pk[j]); + + xc_pkDiff = xc_pk[j] - xs[j]; + fx_pk += xc_pkDiff * xc_pkDiff; + fxp_pk += xc_der_pk[j][0] * xc_pkDiff; + } + + fxp_pk *= 2; + + // Check Wolfe conditions using Armijo constants + // https://en.wikipedia.org/wiki/Wolfe_conditions + if ((fx_pk - (fx + c1 * gamma * pk * fxp)) < + std::numeric_limits::epsilon() && + (-pk * fxp_pk + c2 * pk * fxp) < + std::numeric_limits::epsilon()) + { + conv = true; + break; + } + + gamma /= 2.0; + } + + if (!conv) + { + break; + } + + xi[0] += gamma * pk; + } + + xiOut = xi; + return sqrt(fx_prev); + } + else + { + ASSERTL0(false, "Geometry type unknown") + } + + return -1.0; +} + } // namespace SpatialDomains } // namespace Nektar diff --git a/library/SpatialDomains/SegGeom.h b/library/SpatialDomains/SegGeom.h index 29348642d7324cce352b40dcd8f64ad7352b289e..5b93fd3e95f7e8419a273accd077bff62ba6c8ba 100644 --- a/library/SpatialDomains/SegGeom.h +++ b/library/SpatialDomains/SegGeom.h @@ -89,6 +89,8 @@ protected: virtual NekDouble v_GetCoord(const int i, const Array &Lcoord); virtual int v_GetNumVerts() const; + virtual NekDouble v_FindDistance(const Array &xs, + Array &xi); private: /// Boolean indicating whether object owns the data diff --git a/library/StdRegions/StdExpansion.cpp b/library/StdRegions/StdExpansion.cpp index 1032082d5a80089ac282391e06e42b4d43e668ce..a856b4794b963a9427e3b8f244ef4df8b3c7eb70 100644 --- a/library/StdRegions/StdExpansion.cpp +++ b/library/StdRegions/StdExpansion.cpp @@ -42,10 +42,6 @@ namespace Nektar { namespace StdRegions { -StdExpansion::StdExpansion(void) : m_elmt_id(0), m_ncoeffs(0) -{ -} - StdExpansion::StdExpansion(const int numcoeffs, const int numbases, const LibUtilities::BasisKey &Ba, const LibUtilities::BasisKey &Bb, @@ -91,10 +87,6 @@ StdExpansion::StdExpansion(const StdExpansion &T) { } -StdExpansion::~StdExpansion() -{ -} - NekDouble StdExpansion::Linf(const Array &phys, const Array &sol) { @@ -1303,6 +1295,35 @@ NekDouble StdExpansion::v_PhysEvaluateBasis( return 0; } +NekDouble StdExpansion::v_PhysEvaluate( + const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) +{ + boost::ignore_unused(coord, inarray, firstOrderDerivs); + NEKERROR(ErrorUtil::efatal, + "PhysEvaluate first order derivative method does not exist" + " for this shape type: " + + static_cast( + LibUtilities::ShapeTypeMap[DetShapeType()])); + return 0; +} + +NekDouble StdExpansion::v_PhysEvaluate( + const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs, + std::array &secondOrderDerivs) +{ + boost::ignore_unused(coord, inarray, firstOrderDerivs, secondOrderDerivs); + NEKERROR(ErrorUtil::efatal, + "PhysEvaluate second order derivative method does not exist" + " for this shape type: " + + static_cast( + LibUtilities::ShapeTypeMap[DetShapeType()])); + return 0; +} + void StdExpansion::v_FillMode(const int mode, Array &outarray) { boost::ignore_unused(mode, outarray); diff --git a/library/StdRegions/StdExpansion.h b/library/StdRegions/StdExpansion.h index 635bd406e46b3f3aa7d68e71cb4dd4e9252f2b51..ce7319938253b5cf1caf0d8bba7ebbedb6593b74 100644 --- a/library/StdRegions/StdExpansion.h +++ b/library/StdRegions/StdExpansion.h @@ -71,7 +71,7 @@ class StdExpansion : public std::enable_shared_from_this { public: /** \brief Default Constructor */ - STD_REGIONS_EXPORT StdExpansion(); + STD_REGIONS_EXPORT StdExpansion() = default; /** \brief Constructor */ STD_REGIONS_EXPORT StdExpansion( @@ -84,7 +84,7 @@ public: STD_REGIONS_EXPORT StdExpansion(const StdExpansion &T); /** \brief Destructor */ - STD_REGIONS_EXPORT virtual ~StdExpansion(); + STD_REGIONS_EXPORT virtual ~StdExpansion() = default; // Standard Expansion Routines Applicable Regardless of Region @@ -923,6 +923,35 @@ public: return v_PhysEvaluate(coords, physvals); } + /** \brief This function evaluates the first derivative of the expansion + * at a single (arbitrary) point of the domain + * + * This function is a wrapper around the virtual function + * \a v_PhysEvaluate() + + * Based on the value of the expansion at the quadrature + * points provided in \a physvals, this function + * calculates the value of the expansion at a set of points + * given in \a coords + */ + inline NekDouble PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) + + { + return v_PhysEvaluate(coord, inarray, firstOrderDerivs); + } + + inline NekDouble PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs, + std::array &secondOrderDerivs) + + { + return v_PhysEvaluate(coord, inarray, firstOrderDerivs, + secondOrderDerivs); + } + /** \brief This function evaluates the expansion at a single * (arbitrary) point of the domain * @@ -1290,6 +1319,9 @@ protected: * @brief This function performs the barycentric interpolation of * the polynomial stored in @p coord at a point @p physvals using * barycentric interpolation weights in direction @tparam DIR. + * It can also perform the barycentric interpolation of the + * derivative of the polynomial if @tparam DERIV is set to true, + * which outputs in to @param deriv. * * This method is intended to be used a helper function for * StdExpansion::PhysEvaluate and its elemental instances, so that @@ -1299,15 +1331,20 @@ protected: * * @param coord The coordinate of the single point. * @param physvals The polynomial stored at each quadrature point. + * @param deriv The value of the derivative. + * @param deriv The value of the 2nd derivative. * @tparam DIR The direction of evaluation. + * @tparam DERIV Bool to find derivative. * * @return The value of @p physvals at @p coord in direction @p dir. */ - template + template inline NekDouble BaryEvaluate(const NekDouble &coord, - const NekDouble *physvals) + const NekDouble *physvals, NekDouble &deriv, + NekDouble &deriv2) { - NekDouble numer = 0.0, denom = 0.0; + NekDouble numer1 = 0.0, numer2 = 0.0, numer3 = 0.0, numer4 = 0.0, + numer5 = 0.0, denom = 0.0; ASSERTL2(DIR < m_base.size(), "Direction should be less than shape dimension."); @@ -1316,7 +1353,6 @@ protected: const Array &bw = m_base[DIR]->GetBaryWeights(); const auto nquad = z.size(); - for (int i = 0; i < nquad; ++i) { NekDouble xdiff = z[i] - coord; @@ -1329,17 +1365,74 @@ protected: * the paper here: *https://people.maths.ox.ac.uk/trefethen/barycentric.pdf */ - if (xdiff == 0.0) + if ((!DERIV && xdiff == 0.0) || + ((DERIV || DERIV2) && std::abs(xdiff) < 1e-15)) { + + if (DERIV2) + { + DNekMatSharedPtr D0 = m_base[DIR]->GetD(); + + // take ith row of z and multiply with physvals + Array tmp(nquad); + for (int kk = 0; kk < nquad; kk++) + { + tmp[kk] = Vmath::Dot(nquad, &(D0->GetPtr())[kk], nquad, + &physvals[0], 1); + } + + deriv2 = Vmath::Dot(nquad, &(D0->GetPtr())[i], nquad, + &tmp[0], 1); + deriv = tmp[i]; + } + else if (DERIV) + { + DNekMatSharedPtr D0 = m_base[DIR]->GetD(); + + // take ith row of z and multiply with physvals + deriv = Vmath::Dot(z.size(), &(D0->GetPtr())[i], z.size(), + &physvals[0], 1); + } + return pval; } NekDouble tmp = bw[i] / xdiff; - numer += tmp * pval; + numer1 += tmp * pval; denom += tmp; + + if (DERIV || DERIV2) + { + NekDouble tmp2 = tmp / xdiff; + numer2 += tmp2 * pval; + numer3 += tmp2; + + if (DERIV2) + { + NekDouble tmp3 = tmp2 / xdiff; + numer4 += tmp3 * pval; + numer5 += tmp3; + } + } } - return numer / denom; + if (DERIV || DERIV2) + { + NekDouble denomdenom = denom * denom; + NekDouble numer1numer3 = numer1 * numer3; + + deriv = (numer2 * denom - numer1numer3) / (denomdenom); + + if (DERIV2) + { + deriv2 = (2.0 * numer4 / denom) - + (2.0 * numer5 * numer1) / (denomdenom) - + (2.0 * numer2 * numer3) / (denomdenom) + + (2.0 * numer3 * numer1numer3) / (denomdenom * denom); + } + } + + return numer1 / denom; } /** @@ -1361,6 +1454,35 @@ protected: &(m_base[DIR]->GetBdata())[0] + nquad * mode); } + /** + * @brief Helper function to pass an unused value by reference into + * BaryEvaluate. + * + * @param coord The coordinate of the single point. + * @param physvals The polynomial stored at each quadrature point. + * @tparam DIR The direction of evaluation. + * @tparam DERIV Bool to find derivative. + * + * @return The value of @p physvals at @p coord in direction @p dir. + */ + template + inline NekDouble BaryEvaluate(const NekDouble &coord, + const NekDouble *physvals) + { + NekDouble unusedValue = 0.0; + return BaryEvaluate(coord, physvals, unusedValue, + unusedValue); + } + + template + inline NekDouble BaryEvaluate(const NekDouble &coord, + const NekDouble *physvals, NekDouble &deriv) + { + NekDouble unusedValue = 0.0; + return BaryEvaluate(coord, physvals, deriv, + unusedValue); + } + private: // Virtual functions STD_REGIONS_EXPORT virtual int v_GetNverts() const = 0; @@ -1483,6 +1605,17 @@ private: const Array &I, const Array &physvals); + STD_REGIONS_EXPORT virtual NekDouble v_PhysEvaluate( + const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs); + + STD_REGIONS_EXPORT virtual NekDouble v_PhysEvaluate( + const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs, + std::array &secondOrderDerivs); + STD_REGIONS_EXPORT virtual NekDouble v_PhysEvaluateBasis( const Array &coords, int mode); diff --git a/library/StdRegions/StdExpansion0D.cpp b/library/StdRegions/StdExpansion0D.cpp index 6d5af1c971d8cff5a5c063ee95747800494cc8a5..36ffc8e3d3fd0ba2e56bd8281b0f910bd8b90d76 100644 --- a/library/StdRegions/StdExpansion0D.cpp +++ b/library/StdRegions/StdExpansion0D.cpp @@ -40,11 +40,6 @@ namespace Nektar { namespace StdRegions { - -StdExpansion0D::StdExpansion0D() -{ -} - StdExpansion0D::StdExpansion0D(int numcoeffs, const LibUtilities::BasisKey &Ba) : StdExpansion(numcoeffs, 1, Ba) { @@ -54,10 +49,6 @@ StdExpansion0D::StdExpansion0D(const StdExpansion0D &T) : StdExpansion(T) { } -StdExpansion0D::~StdExpansion0D() -{ -} - //---------------------------- // Differentiation Methods //----------------------------- @@ -87,14 +78,20 @@ NekDouble StdExpansion0D::v_PhysEvaluate( const Array &Lcoord, const Array &physvals) { - int nquad = GetTotPoints(); - NekDouble val; - DNekMatSharedPtr I = m_base[0]->GetI(Lcoord); + ASSERTL2(Lcoord[0] >= -1 - NekConstants::kNekZeroTol, "Lcoord[0] < -1"); + ASSERTL2(Lcoord[0] <= 1 + NekConstants::kNekZeroTol, "Lcoord[0] > 1"); + + return StdExpansion::BaryEvaluate<0>(Lcoord[0], &physvals[0]); +} - ASSERTL2(Lcoord[0] >= -1, "Lcoord[0] < -1"); - ASSERTL2(Lcoord[0] <= 1, "Lcoord[0] > 1"); +NekDouble StdExpansion0D::v_PhysEvaluate( + const Array &I, + const Array &physvals) +{ + NekDouble val; + int nquad = GetTotPoints(); - val = Blas::Ddot(nquad, I->GetPtr(), 1, physvals, 1); + val = Blas::Ddot(nquad, I[0]->GetPtr(), 1, physvals, 1); return val; } diff --git a/library/StdRegions/StdExpansion0D.h b/library/StdRegions/StdExpansion0D.h index 514e909007b1f668d8c06c3f7635e0cdea0014b4..7ce01ed506a72e081aa3b0ee1a09dd3dc40355b6 100644 --- a/library/StdRegions/StdExpansion0D.h +++ b/library/StdRegions/StdExpansion0D.h @@ -49,35 +49,41 @@ class StdExpansion0D : virtual public StdExpansion { public: - STD_REGIONS_EXPORT StdExpansion0D(); + STD_REGIONS_EXPORT StdExpansion0D() : StdExpansion() + { + } + STD_REGIONS_EXPORT StdExpansion0D(int numcoeffs, const LibUtilities::BasisKey &Ba); STD_REGIONS_EXPORT StdExpansion0D(const StdExpansion0D &T); - STD_REGIONS_EXPORT virtual ~StdExpansion0D(); + STD_REGIONS_EXPORT ~StdExpansion0D() override = default; STD_REGIONS_EXPORT void PhysTensorDeriv( const Array &inarray, Array &outarray); + // Virtual Functions ---------------------------------------- protected: STD_REGIONS_EXPORT virtual NekDouble v_PhysEvaluate( const Array &coords, - const Array &physvals); + const Array &physvals) final; -private: - // Virtual Functions ---------------------------------------- + STD_REGIONS_EXPORT virtual NekDouble v_PhysEvaluate( + const Array &I, + const Array &physvals) override; - virtual int v_GetCoordim(void) +private: + virtual int v_GetCoordim(void) final { return 1; } - virtual int v_GetShapeDimension() const + virtual int v_GetShapeDimension() const final { return 1; } - virtual int v_GetNtraces() const + virtual int v_GetNtraces() const override { return 0; } diff --git a/library/StdRegions/StdExpansion1D.cpp b/library/StdRegions/StdExpansion1D.cpp index 3cf213473081ff0912f58c76467576faaf4071e6..708d96b7135fd0cd0173dda170be31adedcd8a31 100644 --- a/library/StdRegions/StdExpansion1D.cpp +++ b/library/StdRegions/StdExpansion1D.cpp @@ -40,11 +40,6 @@ namespace Nektar { namespace StdRegions { - -StdExpansion1D::StdExpansion1D() -{ -} - StdExpansion1D::StdExpansion1D(int numcoeffs, const LibUtilities::BasisKey &Ba) : StdExpansion(numcoeffs, 1, Ba) { @@ -54,10 +49,6 @@ StdExpansion1D::StdExpansion1D(const StdExpansion1D &T) : StdExpansion(T) { } -StdExpansion1D::~StdExpansion1D() -{ -} - //---------------------------- // Differentiation Methods //----------------------------- @@ -93,5 +84,24 @@ NekDouble StdExpansion1D::v_PhysEvaluate( return StdExpansion::BaryEvaluate<0>(Lcoord[0], &physvals[0]); } +NekDouble StdExpansion1D::v_PhysEvaluate( + const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) +{ + boost::ignore_unused(coord, inarray, firstOrderDerivs); + return 0; +} + +NekDouble StdExpansion1D::v_PhysEvaluate( + const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs, + std::array &secondOrderDerivs) +{ + boost::ignore_unused(coord, inarray, firstOrderDerivs, secondOrderDerivs); + return 0; +} + } // namespace StdRegions } // namespace Nektar diff --git a/library/StdRegions/StdExpansion1D.h b/library/StdRegions/StdExpansion1D.h index 959ed6141bde8115b1e87b42447b96b09658f2ec..e0cd9366d593319c40934a79e28c3eda26ad7114 100644 --- a/library/StdRegions/StdExpansion1D.h +++ b/library/StdRegions/StdExpansion1D.h @@ -49,11 +49,11 @@ class StdExpansion1D : virtual public StdExpansion { public: - STD_REGIONS_EXPORT StdExpansion1D(); + STD_REGIONS_EXPORT StdExpansion1D() = default; STD_REGIONS_EXPORT StdExpansion1D(int numcoeffs, const LibUtilities::BasisKey &Ba); STD_REGIONS_EXPORT StdExpansion1D(const StdExpansion1D &T); - STD_REGIONS_EXPORT virtual ~StdExpansion1D(); + STD_REGIONS_EXPORT ~StdExpansion1D() override = default; /** \brief Evaluate the derivative \f$ d/d{\xi_1} \f$ at the * physical quadrature points given by \a inarray and return in @@ -69,20 +69,52 @@ public: const Array &inarray, Array &outarray); + // find derivative of u (inarray) at all coords points + STD_REGIONS_EXPORT inline NekDouble BaryTensorDeriv( + const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) + { + return StdExpansion::BaryEvaluate<0, true>(coord[0], &inarray[0], + firstOrderDerivs[0]); + } + + // find derivative/2nd Derivative of u (inarray) at all coords points + STD_REGIONS_EXPORT inline NekDouble BaryTensorDeriv( + const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs, + std::array &secondOrderDerivs) + { + return StdExpansion::BaryEvaluate<0, true, true>( + coord[0], &inarray[0], firstOrderDerivs[0], secondOrderDerivs[0]); + } + protected: STD_REGIONS_EXPORT virtual NekDouble v_PhysEvaluate( const Array &coords, const Array &physvals) override; + STD_REGIONS_EXPORT virtual NekDouble v_PhysEvaluate( + const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) override; + + STD_REGIONS_EXPORT virtual NekDouble v_PhysEvaluate( + const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs, + std::array &secondOrderDerivs) override; + private: // Virtual Functions ---------------------------------------- - virtual int v_GetCoordim(void) override + int v_GetCoordim(void) override { return 1; } - virtual int v_GetShapeDimension() const final + int v_GetShapeDimension() const final { return 1; } diff --git a/library/StdRegions/StdExpansion2D.cpp b/library/StdRegions/StdExpansion2D.cpp index 71f18bf13e1d4793596b80d7a7e90b6593e19d8e..7924ab54c74fcb88094d572eecd731b815e6c81e 100644 --- a/library/StdRegions/StdExpansion2D.cpp +++ b/library/StdRegions/StdExpansion2D.cpp @@ -44,11 +44,6 @@ namespace Nektar { namespace StdRegions { - -StdExpansion2D::StdExpansion2D() -{ -} - StdExpansion2D::StdExpansion2D(int numcoeffs, const LibUtilities::BasisKey &Ba, const LibUtilities::BasisKey &Bb) : StdExpansion(numcoeffs, 2, Ba, Bb) @@ -59,10 +54,6 @@ StdExpansion2D::StdExpansion2D(const StdExpansion2D &T) : StdExpansion(T) { } -StdExpansion2D::~StdExpansion2D() -{ -} - //---------------------------- // Differentiation Methods //---------------------------- @@ -159,6 +150,15 @@ NekDouble StdExpansion2D::v_PhysEvaluate( return val; } +NekDouble StdExpansion2D::v_PhysEvaluate( + const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) +{ + boost::ignore_unused(coord, inarray, firstOrderDerivs); + return 0; +} + ////////////////////////////// // Integration Methods ////////////////////////////// diff --git a/library/StdRegions/StdExpansion2D.h b/library/StdRegions/StdExpansion2D.h index a510059bf0b008f1bbd77febe40930008906e1be..8d451f2271afd33d323e588cfbfd0f3f6c5ca983 100644 --- a/library/StdRegions/StdExpansion2D.h +++ b/library/StdRegions/StdExpansion2D.h @@ -48,12 +48,12 @@ namespace StdRegions class StdExpansion2D : virtual public StdExpansion { public: - STD_REGIONS_EXPORT StdExpansion2D(); + STD_REGIONS_EXPORT StdExpansion2D() = default; STD_REGIONS_EXPORT StdExpansion2D(int numcoeffs, const LibUtilities::BasisKey &Ba, const LibUtilities::BasisKey &Bb); STD_REGIONS_EXPORT StdExpansion2D(const StdExpansion2D &T); - STD_REGIONS_EXPORT virtual ~StdExpansion2D(); + STD_REGIONS_EXPORT virtual ~StdExpansion2D() override = default; // Generic operations in different element @@ -99,6 +99,31 @@ public: const Array &w0, const Array &w1); + // find derivative of u (inarray) at all coords points + STD_REGIONS_EXPORT inline NekDouble BaryTensorDeriv( + const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) + { + const int nq0 = m_base[0]->GetNumPoints(); + const int nq1 = m_base[1]->GetNumPoints(); + + const NekDouble *ptr = &inarray[0]; + Array deriv0(nq1, 0.0); + Array phys0(nq1, 0.0); + + for (int j = 0; j < nq1; ++j, ptr += nq0) + { + phys0[j] = + StdExpansion::BaryEvaluate<0, true>(coord[0], ptr, deriv0[j]); + } + firstOrderDerivs[0] = + StdExpansion::BaryEvaluate<1, false>(coord[1], &deriv0[0]); + + return StdExpansion::BaryEvaluate<1, true>(coord[1], &phys0[0], + firstOrderDerivs[1]); + } + STD_REGIONS_EXPORT void BwdTrans_SumFacKernel( const Array &base0, const Array &base1, @@ -138,11 +163,16 @@ protected: */ STD_REGIONS_EXPORT virtual NekDouble v_PhysEvaluate( const Array &coords, - const Array &physvals); + const Array &physvals) override; STD_REGIONS_EXPORT virtual NekDouble v_PhysEvaluate( const Array &I, - const Array &physvals); + const Array &physvals) override; + + STD_REGIONS_EXPORT virtual NekDouble v_PhysEvaluate( + const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) override; STD_REGIONS_EXPORT virtual void v_BwdTrans_SumFacKernel( const Array &base0, @@ -160,34 +190,38 @@ protected: STD_REGIONS_EXPORT virtual void v_LaplacianMatrixOp_MatFree( const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); + Array &outarray, + const StdRegions::StdMatrixKey &mkey) override; STD_REGIONS_EXPORT virtual void v_HelmholtzMatrixOp_MatFree( const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); + Array &outarray, + const StdRegions::StdMatrixKey &mkey) override; STD_REGIONS_EXPORT virtual void v_GetTraceCoeffMap( - const unsigned int traceid, Array &maparray); + const unsigned int traceid, + Array &maparray) override; STD_REGIONS_EXPORT virtual void v_GetElmtTraceToTraceMap( const unsigned int eid, Array &maparray, - Array &signarray, Orientation edgeOrient, int P, int Q); + Array &signarray, Orientation edgeOrient, int P, + int Q) override; STD_REGIONS_EXPORT virtual void v_GetTraceToElementMap( const int eid, Array &maparray, Array &signarray, Orientation edgeOrient = eForwards, - int P = -1, int Q = -1); + int P = -1, int Q = -1) override; - STD_REGIONS_EXPORT virtual void v_GenStdMatBwdDeriv(const int dir, - DNekMatSharedPtr &mat); + STD_REGIONS_EXPORT virtual void v_GenStdMatBwdDeriv( + const int dir, DNekMatSharedPtr &mat) override; private: // Virtual Functions ---------------------------------------- - virtual int v_GetShapeDimension() const + virtual int v_GetShapeDimension() const final { return 2; } - virtual int v_GetCoordim(void) + virtual int v_GetCoordim(void) override { return 2; } diff --git a/library/StdRegions/StdExpansion3D.cpp b/library/StdRegions/StdExpansion3D.cpp index ca8b7b766e6639f939f904c55819f394b0fa5b3c..42fbf7697c0ee515e7f4f7a338fa7b64967c0fba 100644 --- a/library/StdRegions/StdExpansion3D.cpp +++ b/library/StdRegions/StdExpansion3D.cpp @@ -46,10 +46,6 @@ namespace Nektar { namespace StdRegions { -StdExpansion3D::StdExpansion3D() -{ -} - StdExpansion3D::StdExpansion3D(int numcoeffs, const LibUtilities::BasisKey &Ba, const LibUtilities::BasisKey &Bb, const LibUtilities::BasisKey &Bc) @@ -61,9 +57,6 @@ StdExpansion3D::StdExpansion3D(const StdExpansion3D &T) : StdExpansion(T) { } -StdExpansion3D::~StdExpansion3D() -{ -} void StdExpansion3D::PhysTensorDeriv( const Array &inarray, Array &out_dx, Array &out_dy, Array &out_dz) @@ -278,6 +271,15 @@ NekDouble StdExpansion3D::v_PhysEvaluate( return value; } +NekDouble StdExpansion3D::v_PhysEvaluate( + const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) +{ + boost::ignore_unused(coord, inarray, firstOrderDerivs); + return 0; +} + /** * @param inarray Input coefficients. * @param output Output coefficients. diff --git a/library/StdRegions/StdExpansion3D.h b/library/StdRegions/StdExpansion3D.h index 0c7ca062271adc2d9c72796d56d748792453c84c..0df665512b1af2214118414ec46e9820dd63d6a7 100644 --- a/library/StdRegions/StdExpansion3D.h +++ b/library/StdRegions/StdExpansion3D.h @@ -52,13 +52,13 @@ class StdExpansion3D : virtual public StdExpansion { public: - STD_REGIONS_EXPORT StdExpansion3D(); + STD_REGIONS_EXPORT StdExpansion3D() = default; STD_REGIONS_EXPORT StdExpansion3D(int numcoeffs, const LibUtilities::BasisKey &Ba, const LibUtilities::BasisKey &Bb, const LibUtilities::BasisKey &Bc); STD_REGIONS_EXPORT StdExpansion3D(const StdExpansion3D &T); - STD_REGIONS_EXPORT virtual ~StdExpansion3D(); + STD_REGIONS_EXPORT virtual ~StdExpansion3D() override = default; // Differentiation @@ -173,11 +173,16 @@ protected: */ STD_REGIONS_EXPORT virtual NekDouble v_PhysEvaluate( const Array &coords, - const Array &physvals); + const Array &physvals) override; STD_REGIONS_EXPORT virtual NekDouble v_PhysEvaluate( const Array &I, - const Array &physvals); + const Array &physvals) override; + + STD_REGIONS_EXPORT virtual NekDouble v_PhysEvaluate( + const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) override; STD_REGIONS_EXPORT virtual void v_BwdTrans_SumFacKernel( const Array &base0, @@ -197,36 +202,94 @@ protected: STD_REGIONS_EXPORT virtual void v_LaplacianMatrixOp_MatFree( const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); + Array &outarray, + const StdRegions::StdMatrixKey &mkey) override; STD_REGIONS_EXPORT virtual void v_HelmholtzMatrixOp_MatFree( const Array &inarray, - Array &outarray, const StdRegions::StdMatrixKey &mkey); + Array &outarray, + const StdRegions::StdMatrixKey &mkey) override; STD_REGIONS_EXPORT virtual NekDouble v_Integral( - const Array &inarray); + const Array &inarray) override; STD_REGIONS_EXPORT virtual int v_GetNedges(void) const; STD_REGIONS_EXPORT virtual int v_GetEdgeNcoeffs(const int i) const; + /** + * Performs tensor product evaluation in 3D to evaluate the physical + * and derivative values in each direction at input coordinate + * @param coord using input physical values at quadrature points + * @param inarray. Returns via reference the derivatives. + + * @param coord Global coordinate + * @param inarray Phys values + * @param out_d0 Return by reference parameter for 0th derivative + * @param out_d1 Return by reference parameter for 1st derivative + * @param out_d2 Return by reference parameter for 2nd derivative + * @return Physical value at @param coord + */ + STD_REGIONS_EXPORT inline NekDouble BaryTensorDeriv( + const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) + { + const int nq0 = m_base[0]->GetNumPoints(); + const int nq1 = m_base[1]->GetNumPoints(); + const int nq2 = m_base[2]->GetNumPoints(); + + const NekDouble *ptr = &inarray[0]; + Array deriv0(nq1 * nq2, 0.0); + Array phys0(nq1 * nq2, 0.0); + Array deriv0phys1(nq1, 0.0); + Array phys0deriv1(nq1, 0.0); + Array phys0phys1(nq1, 0.0); + + for (int j = 0; j < nq1 * nq2; ++j, ptr += nq0) + { + phys0[j] = + StdExpansion::BaryEvaluate<0, true>(coord[0], ptr, deriv0[j]); + } + + for (int j = 0; j < nq2; ++j) + { + deriv0phys1[j] = StdExpansion::BaryEvaluate<1, false>( + coord[1], &deriv0[j * nq1]); + } + firstOrderDerivs[0] = + StdExpansion::BaryEvaluate<2, false>(coord[2], &deriv0phys1[0]); + + for (int j = 0; j < nq2; ++j) + { + phys0phys1[j] = StdExpansion::BaryEvaluate<1, true>( + coord[1], &phys0[j * nq1], phys0deriv1[j]); + } + firstOrderDerivs[1] = + StdExpansion::BaryEvaluate<2, false>(coord[2], &phys0deriv1[0]); + + return StdExpansion::BaryEvaluate<2, true>(coord[2], &phys0phys1[0], + firstOrderDerivs[2]); + } + STD_REGIONS_EXPORT virtual void v_GetEdgeInteriorToElementMap( const int tid, Array &maparray, Array &signarray, Orientation traceOrient = eForwards); STD_REGIONS_EXPORT virtual void v_GetTraceToElementMap( const int tid, Array &maparray, - Array &signarray, Orientation traceOrient, int P, int Q); + Array &signarray, Orientation traceOrient, int P, + int Q) override; - STD_REGIONS_EXPORT virtual void v_GenStdMatBwdDeriv(const int dir, - DNekMatSharedPtr &mat); + STD_REGIONS_EXPORT virtual void v_GenStdMatBwdDeriv( + const int dir, DNekMatSharedPtr &mat) override; private: - virtual int v_GetShapeDimension() const + virtual int v_GetShapeDimension() const final { return 3; } - virtual int v_GetCoordim(void) + virtual int v_GetCoordim(void) override { return 3; } diff --git a/library/StdRegions/StdHexExp.cpp b/library/StdRegions/StdHexExp.cpp index a41e59b09e49a0dcb6873c8237256cd500e5ffa5..a692a38787d5700a8ed578fbd8a759d3cacf79cf 100644 --- a/library/StdRegions/StdHexExp.cpp +++ b/library/StdRegions/StdHexExp.cpp @@ -44,11 +44,6 @@ namespace Nektar { namespace StdRegions { - -StdHexExp::StdHexExp() -{ -} - StdHexExp::StdHexExp(const LibUtilities::BasisKey &Ba, const LibUtilities::BasisKey &Bb, const LibUtilities::BasisKey &Bc) @@ -63,10 +58,6 @@ StdHexExp::StdHexExp(const StdHexExp &T) : StdExpansion(T), StdExpansion3D(T) { } -StdHexExp::~StdHexExp() -{ -} - bool StdHexExp::v_IsBoundaryInteriorExpansion() { return (m_base[0]->GetBasisType() == LibUtilities::eModified_A && @@ -1177,6 +1168,13 @@ void StdHexExp::v_GetBoundaryMap(Array &outarray) sort(outarray.get(), outarray.get() + nBndCoeffs); } +NekDouble StdHexExp::v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) +{ + return BaryTensorDeriv(coord, inarray, firstOrderDerivs); +} + /** * Only for basis type Modified_A or GLL_LAGRANGE in all directions. */ diff --git a/library/StdRegions/StdHexExp.h b/library/StdRegions/StdHexExp.h index e505939ca2704c55f9afaef63f4dd5bd316e307d..e378c773b8d1129e6117b47be563bc76d829adb3 100644 --- a/library/StdRegions/StdHexExp.h +++ b/library/StdRegions/StdHexExp.h @@ -48,207 +48,216 @@ class StdHexExp : virtual public StdExpansion3D { public: - STD_REGIONS_EXPORT StdHexExp(); + STD_REGIONS_EXPORT StdHexExp() = default; STD_REGIONS_EXPORT StdHexExp(const LibUtilities::BasisKey &Ba, const LibUtilities::BasisKey &Bb, const LibUtilities::BasisKey &Bc); STD_REGIONS_EXPORT StdHexExp(const StdHexExp &T); - STD_REGIONS_EXPORT ~StdHexExp(); + STD_REGIONS_EXPORT ~StdHexExp() override = default; protected: //---------------------------- // Differentiation Methods //---------------------------- - STD_REGIONS_EXPORT virtual void v_PhysDeriv( + STD_REGIONS_EXPORT void v_PhysDeriv( const Array &inarray, Array &out_d0, Array &out_d1, - Array &out_d2); - STD_REGIONS_EXPORT virtual void v_PhysDeriv( + Array &out_d2) override; + STD_REGIONS_EXPORT void v_PhysDeriv( const int dir, const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_StdPhysDeriv( + Array &outarray) override; + STD_REGIONS_EXPORT void v_StdPhysDeriv( const Array &inarray, Array &out_d0, Array &out_d1, - Array &out_d2); - STD_REGIONS_EXPORT virtual void v_StdPhysDeriv( + Array &out_d2) override; + STD_REGIONS_EXPORT void v_StdPhysDeriv( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Transforms //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_BwdTrans( + STD_REGIONS_EXPORT void v_BwdTrans( const Array &inarray, - Array &outarray); + Array &outarray) override; - STD_REGIONS_EXPORT virtual void v_BwdTrans_SumFac( + STD_REGIONS_EXPORT void v_BwdTrans_SumFac( const Array &inarray, - Array &outarray); + Array &outarray) override; - STD_REGIONS_EXPORT virtual void v_BwdTrans_SumFacKernel( + STD_REGIONS_EXPORT void v_BwdTrans_SumFacKernel( const Array &base0, const Array &base1, const Array &base2, const Array &inarray, Array &outarray, Array &wsp, - bool doCheckCollDir0, bool doCheckCollDir1, bool doCheckCollDir2); + bool doCheckCollDir0, bool doCheckCollDir1, + bool doCheckCollDir2) override; - STD_REGIONS_EXPORT virtual void v_FwdTrans( + STD_REGIONS_EXPORT void v_FwdTrans( const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Inner product functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_IProductWRTBase( + STD_REGIONS_EXPORT void v_IProductWRTBase( const Array &inarray, - Array &outarray); + Array &outarray) override; STD_REGIONS_EXPORT virtual void v_IProductWRTBase_MatOp( const Array &inarray, Array &outarray); - STD_REGIONS_EXPORT virtual void v_IProductWRTBase_SumFac( + STD_REGIONS_EXPORT void v_IProductWRTBase_SumFac( const Array &inarray, - Array &outarray, bool multbyweights = true); + Array &outarray, bool multbyweights = true) override; - STD_REGIONS_EXPORT virtual void v_IProductWRTBase_SumFacKernel( + STD_REGIONS_EXPORT void v_IProductWRTBase_SumFacKernel( const Array &base0, const Array &base1, const Array &base2, const Array &inarray, Array &outarray, Array &wsp, - bool doCheckCollDir0, bool doCheckCollDir1, bool doCheckCollDir2); + bool doCheckCollDir0, bool doCheckCollDir1, + bool doCheckCollDir2) override; - STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase( + STD_REGIONS_EXPORT void v_IProductWRTDerivBase( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase_MatOp( const int dir, const Array &inarray, Array &outarray); - STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase_SumFac( + STD_REGIONS_EXPORT void v_IProductWRTDerivBase_SumFac( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Evaluation functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_LocCoordToLocCollapsed( - const Array &xi, Array &eta); - STD_REGIONS_EXPORT virtual void v_LocCollapsedToLocCoord( - const Array &eta, Array &xi); - STD_REGIONS_EXPORT virtual void v_FillMode( - const int mode, Array &outarray); + STD_REGIONS_EXPORT void v_LocCoordToLocCollapsed( + const Array &xi, + Array &eta) override; + STD_REGIONS_EXPORT void v_LocCollapsedToLocCoord( + const Array &eta, + Array &xi) override; + STD_REGIONS_EXPORT void v_FillMode( + const int mode, Array &outarray) override; STD_REGIONS_EXPORT NekDouble v_PhysEvaluateBasis( const Array &coords, int mode) final; + STD_REGIONS_EXPORT NekDouble + v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) override; //--------------------------- // Helper functions //--------------------------- - STD_REGIONS_EXPORT virtual int v_GetNverts() const; - STD_REGIONS_EXPORT virtual int v_GetNedges() const; - STD_REGIONS_EXPORT virtual int v_GetNtraces() const; - STD_REGIONS_EXPORT virtual LibUtilities::ShapeType v_DetShapeType() const; - STD_REGIONS_EXPORT virtual int v_NumBndryCoeffs() const; - STD_REGIONS_EXPORT virtual int v_NumDGBndryCoeffs() const; - STD_REGIONS_EXPORT virtual int v_GetTraceNcoeffs(const int i) const; - STD_REGIONS_EXPORT virtual int v_GetTotalTraceIntNcoeffs() const; - STD_REGIONS_EXPORT virtual int v_GetTraceIntNcoeffs(const int i) const; - STD_REGIONS_EXPORT virtual int v_GetTraceNumPoints(const int i) const; - - STD_REGIONS_EXPORT virtual LibUtilities::PointsKey v_GetTracePointsKey( - const int i, const int j) const; - STD_REGIONS_EXPORT virtual int v_CalcNumberOfCoefficients( - const std::vector &nummodes, int &modes_offset); - STD_REGIONS_EXPORT virtual const LibUtilities::BasisKey v_GetTraceBasisKey( - const int i, const int k) const; - STD_REGIONS_EXPORT virtual bool v_IsBoundaryInteriorExpansion(); - STD_REGIONS_EXPORT virtual void v_GetCoords( + STD_REGIONS_EXPORT int v_GetNverts() const override; + STD_REGIONS_EXPORT int v_GetNedges() const override; + STD_REGIONS_EXPORT int v_GetNtraces() const override; + STD_REGIONS_EXPORT LibUtilities::ShapeType v_DetShapeType() const override; + STD_REGIONS_EXPORT int v_NumBndryCoeffs() const override; + STD_REGIONS_EXPORT int v_NumDGBndryCoeffs() const override; + STD_REGIONS_EXPORT int v_GetTraceNcoeffs(const int i) const override; + STD_REGIONS_EXPORT int v_GetTotalTraceIntNcoeffs() const override; + STD_REGIONS_EXPORT int v_GetTraceIntNcoeffs(const int i) const override; + STD_REGIONS_EXPORT int v_GetTraceNumPoints(const int i) const override; + + STD_REGIONS_EXPORT LibUtilities::PointsKey v_GetTracePointsKey( + const int i, const int j) const override; + STD_REGIONS_EXPORT int v_CalcNumberOfCoefficients( + const std::vector &nummodes, int &modes_offset) override; + STD_REGIONS_EXPORT const LibUtilities::BasisKey v_GetTraceBasisKey( + const int i, const int k) const override; + STD_REGIONS_EXPORT bool v_IsBoundaryInteriorExpansion() override; + STD_REGIONS_EXPORT void v_GetCoords( Array &coords_x, Array &coords_y, - Array &coords_z); - STD_REGIONS_EXPORT virtual void v_GetTraceNumModes( + Array &coords_z) override; + STD_REGIONS_EXPORT void v_GetTraceNumModes( const int fid, int &numModes0, int &numModes1, - Orientation faceOrient = eDir1FwdDir1_Dir2FwdDir2); + Orientation faceOrient = eDir1FwdDir1_Dir2FwdDir2) override; - STD_REGIONS_EXPORT virtual int v_GetEdgeNcoeffs(const int i) const; + STD_REGIONS_EXPORT int v_GetEdgeNcoeffs(const int i) const override; //-------------------------- // Mappings //-------------------------- - STD_REGIONS_EXPORT virtual int v_GetVertexMap(int localVertexId, - bool useCoeffPacking = false); - STD_REGIONS_EXPORT virtual void v_GetInteriorMap( - Array &outarray); - STD_REGIONS_EXPORT virtual void v_GetBoundaryMap( - Array &outarray); - STD_REGIONS_EXPORT virtual void v_GetTraceCoeffMap( - const unsigned int fid, Array &maparray); - STD_REGIONS_EXPORT virtual void v_GetElmtTraceToTraceMap( + STD_REGIONS_EXPORT int v_GetVertexMap( + int localVertexId, bool useCoeffPacking = false) override; + STD_REGIONS_EXPORT void v_GetInteriorMap( + Array &outarray) override; + STD_REGIONS_EXPORT void v_GetBoundaryMap( + Array &outarray) override; + STD_REGIONS_EXPORT void v_GetTraceCoeffMap( + const unsigned int fid, Array &maparray) override; + STD_REGIONS_EXPORT void v_GetElmtTraceToTraceMap( const unsigned int fid, Array &maparray, - Array &signarray, Orientation faceOrient, int P, int Q); - STD_REGIONS_EXPORT virtual void v_GetEdgeInteriorToElementMap( + Array &signarray, Orientation faceOrient, int P, + int Q) override; + STD_REGIONS_EXPORT void v_GetEdgeInteriorToElementMap( const int tid, Array &maparray, Array &signarray, - const Orientation traceOrient = eDir1FwdDir1_Dir2FwdDir2); + const Orientation traceOrient = eDir1FwdDir1_Dir2FwdDir2) override; - STD_REGIONS_EXPORT virtual void v_GetTraceInteriorToElementMap( + STD_REGIONS_EXPORT void v_GetTraceInteriorToElementMap( const int tid, Array &maparray, Array &signarray, - const Orientation traceOrient = eDir1FwdDir1_Dir2FwdDir2); + const Orientation traceOrient = eDir1FwdDir1_Dir2FwdDir2) override; //--------------------------------------- // Wrapper functions //--------------------------------------- - STD_REGIONS_EXPORT virtual DNekMatSharedPtr v_GenMatrix( - const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual DNekMatSharedPtr v_CreateStdMatrix( - const StdMatrixKey &mkey); + STD_REGIONS_EXPORT DNekMatSharedPtr + v_GenMatrix(const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT DNekMatSharedPtr + v_CreateStdMatrix(const StdMatrixKey &mkey) override; //--------------------------------------- // Output interpolation functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_GetSimplexEquiSpacedConnectivity( - Array &conn, bool standard = true); + STD_REGIONS_EXPORT void v_GetSimplexEquiSpacedConnectivity( + Array &conn, bool standard = true) override; //--------------------------------------- // Operator evaluation functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_MassMatrixOp( + STD_REGIONS_EXPORT void v_MassMatrixOp( const Array &inarray, - Array &outarray, const StdMatrixKey &mkey); + Array &outarray, const StdMatrixKey &mkey) override; - STD_REGIONS_EXPORT virtual void v_LaplacianMatrixOp( + STD_REGIONS_EXPORT void v_LaplacianMatrixOp( const Array &inarray, - Array &outarray, const StdMatrixKey &mkey); + Array &outarray, const StdMatrixKey &mkey) override; - STD_REGIONS_EXPORT virtual void v_LaplacianMatrixOp( + STD_REGIONS_EXPORT void v_LaplacianMatrixOp( const int k1, const int k2, const Array &inarray, - Array &outarray, const StdMatrixKey &mkey); + Array &outarray, const StdMatrixKey &mkey) override; - STD_REGIONS_EXPORT virtual void v_WeakDerivMatrixOp( + STD_REGIONS_EXPORT void v_WeakDerivMatrixOp( const int i, const Array &inarray, - Array &outarray, const StdMatrixKey &mkey); + Array &outarray, const StdMatrixKey &mkey) override; - STD_REGIONS_EXPORT virtual void v_HelmholtzMatrixOp( + STD_REGIONS_EXPORT void v_HelmholtzMatrixOp( const Array &inarray, - Array &outarray, const StdMatrixKey &mkey); + Array &outarray, const StdMatrixKey &mkey) override; STD_REGIONS_EXPORT virtual void v_GeneralMatrixOp_MatOp( const Array &inarray, Array &outarray, const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual void v_MultiplyByStdQuadratureMetric( + STD_REGIONS_EXPORT void v_MultiplyByStdQuadratureMetric( const Array &inarray, - Array &outarray); + Array &outarray) override; - STD_REGIONS_EXPORT virtual void v_SVVLaplacianFilter( - Array &array, const StdMatrixKey &mkey); + STD_REGIONS_EXPORT void v_SVVLaplacianFilter( + Array &array, const StdMatrixKey &mkey) override; - STD_REGIONS_EXPORT virtual void v_ExponentialFilter( + STD_REGIONS_EXPORT void v_ExponentialFilter( Array &array, const NekDouble alpha, - const NekDouble exponent, const NekDouble cutoff); + const NekDouble exponent, const NekDouble cutoff) override; }; typedef std::shared_ptr StdHexExpSharedPtr; diff --git a/library/StdRegions/StdNodalPrismExp.cpp b/library/StdRegions/StdNodalPrismExp.cpp index 1cd31186a17b3409a8dadda7ef2610c262428dfa..c4c8323d2489fdf16696e0d186f84e0f2b2523de 100644 --- a/library/StdRegions/StdNodalPrismExp.cpp +++ b/library/StdRegions/StdNodalPrismExp.cpp @@ -64,10 +64,6 @@ StdNodalPrismExp::StdNodalPrismExp(const StdNodalPrismExp &T) { } -StdNodalPrismExp::~StdNodalPrismExp() -{ -} - bool StdNodalPrismExp::v_IsNodalNonTensorialExp() { return true; @@ -152,7 +148,7 @@ DNekMatSharedPtr StdNodalPrismExp::GenNBasisTransMatrix() c[0] = r[j]; c[1] = s[j]; c[2] = t[j]; - (*Mat)(j, i) = StdPrismExp::v_PhysEvaluate(c, tmp_phys); + (*Mat)(j, i) = StdExpansion3D::v_PhysEvaluate(c, tmp_phys); } } diff --git a/library/StdRegions/StdNodalPrismExp.h b/library/StdRegions/StdNodalPrismExp.h index d8300047fcbc36747e1e2ce93bcdeca8782e279a..6c6c2086b344e139768e3c67e5d11fd63e2a50a8 100644 --- a/library/StdRegions/StdNodalPrismExp.h +++ b/library/StdRegions/StdNodalPrismExp.h @@ -42,16 +42,16 @@ namespace Nektar { namespace StdRegions { -class StdNodalPrismExp : public StdPrismExp +class StdNodalPrismExp final : public StdPrismExp { public: - STD_REGIONS_EXPORT StdNodalPrismExp(); + STD_REGIONS_EXPORT StdNodalPrismExp() = default; STD_REGIONS_EXPORT StdNodalPrismExp(const LibUtilities::BasisKey &Ba, const LibUtilities::BasisKey &Bb, const LibUtilities::BasisKey &Bc, const LibUtilities::PointsType Ntype); STD_REGIONS_EXPORT StdNodalPrismExp(const StdNodalPrismExp &T); - STD_REGIONS_EXPORT ~StdNodalPrismExp(); + STD_REGIONS_EXPORT ~StdNodalPrismExp() override = default; //------------------------------- // Nodal basis specific routines @@ -73,66 +73,66 @@ public: protected: LibUtilities::PointsKey m_nodalPointsKey; - STD_REGIONS_EXPORT virtual const LibUtilities::PointsKey v_GetNodalPointsKey() - const + STD_REGIONS_EXPORT const LibUtilities::PointsKey v_GetNodalPointsKey() + const override { return m_nodalPointsKey; }; - STD_REGIONS_EXPORT virtual bool v_IsNodalNonTensorialExp(); + STD_REGIONS_EXPORT bool v_IsNodalNonTensorialExp() override; //--------------------------------------- // Transforms //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_BwdTrans( + STD_REGIONS_EXPORT void v_BwdTrans( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_BwdTrans_SumFac( + Array &outarray) override; + STD_REGIONS_EXPORT void v_BwdTrans_SumFac( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_FwdTrans( + Array &outarray) override; + STD_REGIONS_EXPORT void v_FwdTrans( const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Inner product functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_IProductWRTBase( + STD_REGIONS_EXPORT void v_IProductWRTBase( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_IProductWRTBase_SumFac( + Array &outarray) override; + STD_REGIONS_EXPORT void v_IProductWRTBase_SumFac( const Array &inarray, - Array &outarray, bool mult = true); - STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase( + Array &outarray, bool mult = true) override; + STD_REGIONS_EXPORT void v_IProductWRTDerivBase( const int dir, const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase_SumFac( + Array &outarray) override; + STD_REGIONS_EXPORT void v_IProductWRTDerivBase_SumFac( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Evaluation functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_FillMode( - const int mode, Array &outarray); + STD_REGIONS_EXPORT void v_FillMode( + const int mode, Array &outarray) override; //--------------------------------------- // Mapping functions //--------------------------------------- - STD_REGIONS_EXPORT virtual int v_GetVertexMap(const int localVertexId, - bool useCoeffPacking = false); - STD_REGIONS_EXPORT virtual void v_GetBoundaryMap( - Array &outarray); - STD_REGIONS_EXPORT virtual void v_GetInteriorMap( - Array &outarray); + STD_REGIONS_EXPORT int v_GetVertexMap( + const int localVertexId, bool useCoeffPacking = false) override; + STD_REGIONS_EXPORT void v_GetBoundaryMap( + Array &outarray) override; + STD_REGIONS_EXPORT void v_GetInteriorMap( + Array &outarray) override; //--------------------------------------- // Wrapper functions //--------------------------------------- - STD_REGIONS_EXPORT virtual DNekMatSharedPtr v_GenMatrix( - const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual DNekMatSharedPtr v_CreateStdMatrix( - const StdMatrixKey &mkey); + STD_REGIONS_EXPORT DNekMatSharedPtr + v_GenMatrix(const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT DNekMatSharedPtr + v_CreateStdMatrix(const StdMatrixKey &mkey) override; }; typedef std::shared_ptr StdNodalPrismExpSharedPtr; diff --git a/library/StdRegions/StdNodalTetExp.cpp b/library/StdRegions/StdNodalTetExp.cpp index f7b4633c5d3119228d90da6025dab68a8146c6ff..f513c1c013216638bcd37a15aebeeb3a7d2fb446 100644 --- a/library/StdRegions/StdNodalTetExp.cpp +++ b/library/StdRegions/StdNodalTetExp.cpp @@ -70,10 +70,6 @@ StdNodalTetExp::StdNodalTetExp(const StdNodalTetExp &T) { } -StdNodalTetExp::~StdNodalTetExp() -{ -} - bool StdNodalTetExp::v_IsNodalNonTensorialExp() { return true; @@ -157,7 +153,7 @@ DNekMatSharedPtr StdNodalTetExp::GenNBasisTransMatrix() c[0] = r[j]; c[1] = s[j]; c[2] = t[j]; - (*Mat)(j, i) = StdTetExp::v_PhysEvaluate(c, tmp_phys); + (*Mat)(j, i) = StdExpansion3D::v_PhysEvaluate(c, tmp_phys); } } diff --git a/library/StdRegions/StdNodalTetExp.h b/library/StdRegions/StdNodalTetExp.h index fc4c17c790e5f253ddc874cbbe143b3bec9404c3..34844b1385dc71a9264a264a7cec49fd66730c62 100644 --- a/library/StdRegions/StdNodalTetExp.h +++ b/library/StdRegions/StdNodalTetExp.h @@ -42,16 +42,16 @@ namespace Nektar { namespace StdRegions { -class StdNodalTetExp : public StdTetExp +class StdNodalTetExp : virtual public StdTetExp { public: - STD_REGIONS_EXPORT StdNodalTetExp(); + STD_REGIONS_EXPORT StdNodalTetExp() = default; STD_REGIONS_EXPORT StdNodalTetExp(const LibUtilities::BasisKey &Ba, const LibUtilities::BasisKey &Bb, const LibUtilities::BasisKey &Bc, const LibUtilities::PointsType Ntype); STD_REGIONS_EXPORT StdNodalTetExp(const StdNodalTetExp &T); - STD_REGIONS_EXPORT ~StdNodalTetExp(); + STD_REGIONS_EXPORT ~StdNodalTetExp() override = default; //------------------------------- // Nodal basis specific routines @@ -73,66 +73,66 @@ public: protected: LibUtilities::PointsKey m_nodalPointsKey; - STD_REGIONS_EXPORT virtual const LibUtilities::PointsKey v_GetNodalPointsKey() - const + STD_REGIONS_EXPORT const LibUtilities::PointsKey v_GetNodalPointsKey() + const override { return m_nodalPointsKey; }; - STD_REGIONS_EXPORT virtual bool v_IsNodalNonTensorialExp(); + STD_REGIONS_EXPORT bool v_IsNodalNonTensorialExp() override; //--------------------------------------- // Transforms //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_BwdTrans( + STD_REGIONS_EXPORT void v_BwdTrans( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_BwdTrans_SumFac( + Array &outarray) override; + STD_REGIONS_EXPORT void v_BwdTrans_SumFac( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_FwdTrans( + Array &outarray) override; + STD_REGIONS_EXPORT void v_FwdTrans( const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Inner product functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_IProductWRTBase( + STD_REGIONS_EXPORT void v_IProductWRTBase( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_IProductWRTBase_SumFac( + Array &outarray) override; + STD_REGIONS_EXPORT void v_IProductWRTBase_SumFac( const Array &inarray, - Array &outarray, bool mult = true); - STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase( + Array &outarray, bool mult = true) override; + STD_REGIONS_EXPORT void v_IProductWRTDerivBase( const int dir, const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase_SumFac( + Array &outarray) override; + STD_REGIONS_EXPORT void v_IProductWRTDerivBase_SumFac( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Evaluation functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_FillMode( - const int mode, Array &outarray); + STD_REGIONS_EXPORT void v_FillMode( + const int mode, Array &outarray) override; //--------------------------------------- // Mapping functions //--------------------------------------- - STD_REGIONS_EXPORT virtual int v_GetVertexMap(const int localVertexId, - bool useCoeffPacking = false); - STD_REGIONS_EXPORT virtual void v_GetBoundaryMap( - Array &outarray); - STD_REGIONS_EXPORT virtual void v_GetInteriorMap( - Array &outarray); + STD_REGIONS_EXPORT int v_GetVertexMap( + const int localVertexId, bool useCoeffPacking = false) override; + STD_REGIONS_EXPORT void v_GetBoundaryMap( + Array &outarray) override; + STD_REGIONS_EXPORT void v_GetInteriorMap( + Array &outarray) override; //--------------------------------------- // Wrapper functions //--------------------------------------- - STD_REGIONS_EXPORT virtual DNekMatSharedPtr v_GenMatrix( - const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual DNekMatSharedPtr v_CreateStdMatrix( - const StdMatrixKey &mkey); + STD_REGIONS_EXPORT DNekMatSharedPtr + v_GenMatrix(const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT DNekMatSharedPtr + v_CreateStdMatrix(const StdMatrixKey &mkey) override; }; typedef std::shared_ptr StdNodalTetExpSharedPtr; diff --git a/library/StdRegions/StdNodalTriExp.cpp b/library/StdRegions/StdNodalTriExp.cpp index 8d2d8bd510965d0e5d8027fa8dbbbef3e7d6b4e8..72ab2e140b37a54c2833f32b8f12fa580865de74 100644 --- a/library/StdRegions/StdNodalTriExp.cpp +++ b/library/StdRegions/StdNodalTriExp.cpp @@ -43,10 +43,6 @@ namespace Nektar { namespace StdRegions { -StdNodalTriExp::StdNodalTriExp() : StdTriExp(), m_nodalPointsKey() -{ -} - StdNodalTriExp::StdNodalTriExp(const LibUtilities::BasisKey &Ba, const LibUtilities::BasisKey &Bb, LibUtilities::PointsType Ntype) @@ -69,10 +65,6 @@ StdNodalTriExp::StdNodalTriExp(const StdNodalTriExp &T) { } -StdNodalTriExp::~StdNodalTriExp() -{ -} - bool StdNodalTriExp::v_IsNodalNonTensorialExp() { return true; @@ -154,7 +146,7 @@ DNekMatSharedPtr StdNodalTriExp::GenNBasisTransMatrix() { c[0] = r[j]; c[1] = s[j]; - (*Mat)(j, i) = StdTriExp::v_PhysEvaluate(c, phys); + (*Mat)(j, i) = StdExpansion2D::v_PhysEvaluate(c, phys); } } return Mat; diff --git a/library/StdRegions/StdNodalTriExp.h b/library/StdRegions/StdNodalTriExp.h index 2977a58845e0c7982bae646f46e48ac16350cf5a..1a457ea6b996beb34d4de205b540caccfab4cf82 100644 --- a/library/StdRegions/StdNodalTriExp.h +++ b/library/StdRegions/StdNodalTriExp.h @@ -44,15 +44,15 @@ namespace Nektar { namespace StdRegions { -class StdNodalTriExp : public StdTriExp +class StdNodalTriExp : virtual public StdTriExp { public: - STD_REGIONS_EXPORT StdNodalTriExp(); + STD_REGIONS_EXPORT StdNodalTriExp() = default; STD_REGIONS_EXPORT StdNodalTriExp(const LibUtilities::BasisKey &Ba, const LibUtilities::BasisKey &Bb, const LibUtilities::PointsType Ntype); STD_REGIONS_EXPORT StdNodalTriExp(const StdNodalTriExp &T); - STD_REGIONS_EXPORT ~StdNodalTriExp(); + STD_REGIONS_EXPORT ~StdNodalTriExp() override = default; //------------------------------- // Nodal basis specific routines @@ -73,100 +73,102 @@ public: protected: LibUtilities::PointsKey m_nodalPointsKey; - STD_REGIONS_EXPORT virtual const LibUtilities::PointsKey v_GetNodalPointsKey() - const + STD_REGIONS_EXPORT const LibUtilities::PointsKey v_GetNodalPointsKey() + const override { return m_nodalPointsKey; }; - STD_REGIONS_EXPORT virtual bool v_IsNodalNonTensorialExp(); + STD_REGIONS_EXPORT bool v_IsNodalNonTensorialExp() override; //--------------------------------------- // Transforms //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_BwdTrans( + STD_REGIONS_EXPORT void v_BwdTrans( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_BwdTrans_SumFac( + Array &outarray) override; + STD_REGIONS_EXPORT void v_BwdTrans_SumFac( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_FwdTrans( + Array &outarray) override; + STD_REGIONS_EXPORT void v_FwdTrans( const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Inner product functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_IProductWRTBase( + STD_REGIONS_EXPORT void v_IProductWRTBase( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_IProductWRTBase_SumFac( + Array &outarray) override; + STD_REGIONS_EXPORT void v_IProductWRTBase_SumFac( const Array &inarray, - Array &outarray, bool multiplybyweights = true); - STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase( + Array &outarray, + bool multiplybyweights = true) override; + STD_REGIONS_EXPORT void v_IProductWRTDerivBase( const int dir, const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase_SumFac( + Array &outarray) override; + STD_REGIONS_EXPORT void v_IProductWRTDerivBase_SumFac( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Evaluation functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_FillMode( - const int mode, Array &outarray); + STD_REGIONS_EXPORT void v_FillMode( + const int mode, Array &outarray) override; //--------------------------- // Helper functions //--------------------------- - STD_REGIONS_EXPORT virtual int v_NumBndryCoeffs() const; + STD_REGIONS_EXPORT int v_NumBndryCoeffs() const override; //-------------------------- // Mappings //-------------------------- - STD_REGIONS_EXPORT virtual int v_GetVertexMap(int localVertexId, - bool useCoeffPacking = false); + STD_REGIONS_EXPORT int v_GetVertexMap( + int localVertexId, bool useCoeffPacking = false) override; - STD_REGIONS_EXPORT virtual void v_GetTraceToElementMap( + STD_REGIONS_EXPORT void v_GetTraceToElementMap( const int eid, Array &maparray, Array &signarray, Orientation edgeOrient = eForwards, - int P = -1, int Q = -1); + int P = -1, int Q = -1) override; - STD_REGIONS_EXPORT virtual void v_GetTraceInteriorToElementMap( + STD_REGIONS_EXPORT void v_GetTraceInteriorToElementMap( const int eid, Array &maparray, - Array &signarray, const Orientation edgeOrient = eForwards); + Array &signarray, + const Orientation edgeOrient = eForwards) override; - STD_REGIONS_EXPORT virtual void v_GetInteriorMap( - Array &outarray); - STD_REGIONS_EXPORT virtual void v_GetBoundaryMap( - Array &outarray); + STD_REGIONS_EXPORT void v_GetInteriorMap( + Array &outarray) override; + STD_REGIONS_EXPORT void v_GetBoundaryMap( + Array &outarray) override; //--------------------------------------- // Operator evaluation functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_MassMatrixOp( + STD_REGIONS_EXPORT void v_MassMatrixOp( const Array &inarray, - Array &outarray, const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual void v_LaplacianMatrixOp( + Array &outarray, const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT void v_LaplacianMatrixOp( const Array &inarray, - Array &outarray, const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual void v_LaplacianMatrixOp( + Array &outarray, const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT void v_LaplacianMatrixOp( const int k1, const int k2, const Array &inarray, - Array &outarray, const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual void v_WeakDerivMatrixOp( + Array &outarray, const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT void v_WeakDerivMatrixOp( const int i, const Array &inarray, - Array &outarray, const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual void v_HelmholtzMatrixOp( + Array &outarray, const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT void v_HelmholtzMatrixOp( const Array &inarray, - Array &outarray, const StdMatrixKey &mkey); + Array &outarray, const StdMatrixKey &mkey) override; //--------------------------------------- // Wrapper functions //--------------------------------------- - STD_REGIONS_EXPORT virtual DNekMatSharedPtr v_GenMatrix( - const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual DNekMatSharedPtr v_CreateStdMatrix( - const StdMatrixKey &mkey); + STD_REGIONS_EXPORT DNekMatSharedPtr + v_GenMatrix(const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT DNekMatSharedPtr + v_CreateStdMatrix(const StdMatrixKey &mkey) override; }; typedef std::shared_ptr StdNodalTriExpSharedPtr; diff --git a/library/StdRegions/StdPrismExp.cpp b/library/StdRegions/StdPrismExp.cpp index 9df6d34c282b6668cbd4a259a1a0c9ba9b432642..7c53f26cd5a927baca2216777a251f4907aebc17 100644 --- a/library/StdRegions/StdPrismExp.cpp +++ b/library/StdRegions/StdPrismExp.cpp @@ -43,12 +43,6 @@ namespace Nektar { namespace StdRegions { - -StdPrismExp::StdPrismExp() // Deafult construct of standard expansion directly - // called. -{ -} - StdPrismExp::StdPrismExp(const LibUtilities::BasisKey &Ba, const LibUtilities::BasisKey &Bb, const LibUtilities::BasisKey &Bc) @@ -68,11 +62,6 @@ StdPrismExp::StdPrismExp(const StdPrismExp &T) { } -// Destructor -StdPrismExp::~StdPrismExp() -{ -} - //--------------------------------------- // Differentiation Methods //--------------------------------------- @@ -600,7 +589,6 @@ void StdPrismExp::v_IProductWRTDerivBase_SumFac( m_base[2]->GetBdata(), tmp0, outarray, wsp, true, true, true); break; } - case 1: { MultiplyByQuadratureMetric(inarray, tmp0); @@ -696,6 +684,54 @@ void StdPrismExp::v_GetCoords(Array &xi_x, } } +NekDouble StdPrismExp::v_PhysEvaluate( + const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) +{ + // Collapse coordinates + Array coll(3, 0.0); + LocCoordToLocCollapsed(coord, coll); + + // If near singularity do the old interpolation matrix method + // @TODO: Dave thinks there might be a way in the Barycentric to + // mathematically remove this singularity? + if ((1 - coll[2]) < 1e-5) + { + int totPoints = GetTotPoints(); + Array EphysDeriv0(totPoints), EphysDeriv1(totPoints), + EphysDeriv2(totPoints); + PhysDeriv(inarray, EphysDeriv0, EphysDeriv1, EphysDeriv2); + + Array I(3); + I[0] = GetBase()[0]->GetI(coll); + I[1] = GetBase()[1]->GetI(coll + 1); + I[2] = GetBase()[2]->GetI(coll + 2); + + firstOrderDerivs[0] = PhysEvaluate(I, EphysDeriv0); + firstOrderDerivs[1] = PhysEvaluate(I, EphysDeriv1); + firstOrderDerivs[2] = PhysEvaluate(I, EphysDeriv2); + return PhysEvaluate(I, inarray); + } + + NekDouble val = BaryTensorDeriv(coll, inarray, firstOrderDerivs); + + NekDouble dEta_bar1 = firstOrderDerivs[0]; + + NekDouble fac = 2.0 / (1.0 - coll[2]); + firstOrderDerivs[0] = fac * dEta_bar1; + + // divide dEta_Bar1 by (1-eta_z) + fac = 1.0 / (1.0 - coll[2]); + dEta_bar1 = fac * dEta_bar1; + + // Multiply dEta_Bar1 by (1+eta_x) and add ot out_dxi3 + fac = 1.0 + coll[0]; + firstOrderDerivs[2] += fac * dEta_bar1; + + return val; +} + void StdPrismExp::v_FillMode(const int mode, Array &outarray) { Array tmp(m_ncoeffs, 0.0); diff --git a/library/StdRegions/StdPrismExp.h b/library/StdRegions/StdPrismExp.h index 8235809052d58bfb57ebf6307d61b123dff2c10d..34258619ccd7b07eab1a0da848a2bfaead7b93e0 100644 --- a/library/StdRegions/StdPrismExp.h +++ b/library/StdRegions/StdPrismExp.h @@ -49,7 +49,7 @@ class StdPrismExp : virtual public StdExpansion3D { public: - STD_REGIONS_EXPORT StdPrismExp(); + STD_REGIONS_EXPORT StdPrismExp() = default; STD_REGIONS_EXPORT StdPrismExp(const LibUtilities::BasisKey &Ba, const LibUtilities::BasisKey &Bb, @@ -62,164 +62,174 @@ public: STD_REGIONS_EXPORT StdPrismExp(const StdPrismExp &T); - STD_REGIONS_EXPORT ~StdPrismExp(); + STD_REGIONS_EXPORT ~StdPrismExp() override = default; protected: //--------------------------------------- // Differentiation Methods //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_PhysDeriv( + STD_REGIONS_EXPORT void v_PhysDeriv( const Array &inarray, Array &out_d0, Array &out_d1, - Array &out_d2); - STD_REGIONS_EXPORT virtual void v_PhysDeriv( + Array &out_d2) override; + STD_REGIONS_EXPORT void v_PhysDeriv( const int dir, const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_StdPhysDeriv( + Array &outarray) override; + STD_REGIONS_EXPORT void v_StdPhysDeriv( const Array &inarray, Array &out_d0, Array &out_d1, - Array &out_d2); - STD_REGIONS_EXPORT virtual void v_StdPhysDeriv( + Array &out_d2) override; + STD_REGIONS_EXPORT void v_StdPhysDeriv( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Transforms //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_BwdTrans( + STD_REGIONS_EXPORT void v_BwdTrans( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_BwdTrans_SumFac( + Array &outarray) override; + STD_REGIONS_EXPORT void v_BwdTrans_SumFac( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_BwdTrans_SumFacKernel( + Array &outarray) override; + STD_REGIONS_EXPORT void v_BwdTrans_SumFacKernel( const Array &base0, const Array &base1, const Array &base2, const Array &inarray, Array &outarray, Array &wsp, - bool doCheckCollDir0, bool doCheckCollDir1, bool doCheckCollDir2); - STD_REGIONS_EXPORT virtual void v_FwdTrans( + bool doCheckCollDir0, bool doCheckCollDir1, + bool doCheckCollDir2) override; + STD_REGIONS_EXPORT void v_FwdTrans( const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Inner product functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_IProductWRTBase( + STD_REGIONS_EXPORT void v_IProductWRTBase( const Array &inarray, - Array &outarray); + Array &outarray) override; STD_REGIONS_EXPORT virtual void v_IProductWRTBase_MatOp( const Array &inarray, Array &outarray); - STD_REGIONS_EXPORT virtual void v_IProductWRTBase_SumFac( + STD_REGIONS_EXPORT void v_IProductWRTBase_SumFac( const Array &inarray, - Array &outarray, bool multiplybyweights = true); - STD_REGIONS_EXPORT virtual void v_IProductWRTBase_SumFacKernel( + Array &outarray, + bool multiplybyweights = true) override; + STD_REGIONS_EXPORT void v_IProductWRTBase_SumFacKernel( const Array &base0, const Array &base1, const Array &base2, const Array &inarray, Array &outarray, Array &wsp, - bool doCheckCollDir0, bool doCheckCollDir1, bool doCheckCollDir2); - STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase( + bool doCheckCollDir0, bool doCheckCollDir1, + bool doCheckCollDir2) override; + STD_REGIONS_EXPORT void v_IProductWRTDerivBase( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase_MatOp( const int dir, const Array &inarray, Array &outarray); - STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase_SumFac( + STD_REGIONS_EXPORT void v_IProductWRTDerivBase_SumFac( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Evaluation functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_LocCoordToLocCollapsed( - const Array &xi, Array &eta); - STD_REGIONS_EXPORT virtual void v_LocCollapsedToLocCoord( - const Array &eta, Array &xi); - STD_REGIONS_EXPORT virtual void v_GetCoords(Array &xi_x, - Array &xi_y, - Array &xi_z); - STD_REGIONS_EXPORT virtual void v_FillMode( - const int mode, Array &outarray); + STD_REGIONS_EXPORT void v_LocCoordToLocCollapsed( + const Array &xi, + Array &eta) override; + STD_REGIONS_EXPORT void v_LocCollapsedToLocCoord( + const Array &eta, + Array &xi) override; + STD_REGIONS_EXPORT void v_GetCoords(Array &xi_x, + Array &xi_y, + Array &xi_z) override; + STD_REGIONS_EXPORT void v_FillMode( + const int mode, Array &outarray) override; STD_REGIONS_EXPORT NekDouble v_PhysEvaluateBasis( const Array &coords, int mode) final; - STD_REGIONS_EXPORT virtual void v_GetTraceNumModes( + STD_REGIONS_EXPORT NekDouble + v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) override; + STD_REGIONS_EXPORT void v_GetTraceNumModes( const int fid, int &numModes0, int &numModes1, - Orientation faceOrient = eDir1FwdDir1_Dir2FwdDir2); + Orientation faceOrient = eDir1FwdDir1_Dir2FwdDir2) override; //--------------------------------------- // Helper functions //--------------------------------------- - STD_REGIONS_EXPORT virtual int v_GetNverts() const; - STD_REGIONS_EXPORT virtual int v_GetNedges() const; - STD_REGIONS_EXPORT virtual int v_GetNtraces() const; - STD_REGIONS_EXPORT virtual LibUtilities::ShapeType v_DetShapeType() const; - STD_REGIONS_EXPORT virtual int v_NumBndryCoeffs() const; - STD_REGIONS_EXPORT virtual int v_NumDGBndryCoeffs() const; - STD_REGIONS_EXPORT virtual int v_GetTraceNcoeffs(const int i) const; - STD_REGIONS_EXPORT virtual int v_GetTotalTraceIntNcoeffs() const; - STD_REGIONS_EXPORT virtual int v_GetTraceIntNcoeffs(const int i) const; - STD_REGIONS_EXPORT virtual int v_GetTraceNumPoints(const int i) const; + STD_REGIONS_EXPORT int v_GetNverts() const override; + STD_REGIONS_EXPORT int v_GetNedges() const override; + STD_REGIONS_EXPORT int v_GetNtraces() const override; + STD_REGIONS_EXPORT LibUtilities::ShapeType v_DetShapeType() const override; + STD_REGIONS_EXPORT int v_NumBndryCoeffs() const override; + STD_REGIONS_EXPORT int v_NumDGBndryCoeffs() const override; + STD_REGIONS_EXPORT int v_GetTraceNcoeffs(const int i) const override; + STD_REGIONS_EXPORT int v_GetTotalTraceIntNcoeffs() const override; + STD_REGIONS_EXPORT int v_GetTraceIntNcoeffs(const int i) const override; + STD_REGIONS_EXPORT int v_GetTraceNumPoints(const int i) const override; - STD_REGIONS_EXPORT virtual int v_GetEdgeNcoeffs(const int i) const; + STD_REGIONS_EXPORT int v_GetEdgeNcoeffs(const int i) const override; - STD_REGIONS_EXPORT virtual const LibUtilities::BasisKey v_GetTraceBasisKey( - const int i, const int k) const; - STD_REGIONS_EXPORT virtual LibUtilities::PointsKey v_GetTracePointsKey( - const int i, const int j) const; + STD_REGIONS_EXPORT const LibUtilities::BasisKey v_GetTraceBasisKey( + const int i, const int k) const override; + STD_REGIONS_EXPORT LibUtilities::PointsKey v_GetTracePointsKey( + const int i, const int j) const override; - STD_REGIONS_EXPORT virtual int v_CalcNumberOfCoefficients( - const std::vector &nummodes, int &modes_offset); - STD_REGIONS_EXPORT virtual bool v_IsBoundaryInteriorExpansion(); + STD_REGIONS_EXPORT int v_CalcNumberOfCoefficients( + const std::vector &nummodes, int &modes_offset) override; + STD_REGIONS_EXPORT bool v_IsBoundaryInteriorExpansion() override; //--------------------------------------- // Mappings //--------------------------------------- - STD_REGIONS_EXPORT virtual int v_GetVertexMap(int localVertexId, - bool useCoeffPacking = false); - STD_REGIONS_EXPORT virtual void v_GetInteriorMap( - Array &outarray); - STD_REGIONS_EXPORT virtual void v_GetBoundaryMap( - Array &outarray); - STD_REGIONS_EXPORT virtual void v_GetTraceCoeffMap( - const unsigned int fid, Array &maparray); - STD_REGIONS_EXPORT virtual void v_GetElmtTraceToTraceMap( + STD_REGIONS_EXPORT int v_GetVertexMap( + int localVertexId, bool useCoeffPacking = false) override; + STD_REGIONS_EXPORT void v_GetInteriorMap( + Array &outarray) override; + STD_REGIONS_EXPORT void v_GetBoundaryMap( + Array &outarray) override; + STD_REGIONS_EXPORT void v_GetTraceCoeffMap( + const unsigned int fid, Array &maparray) override; + STD_REGIONS_EXPORT void v_GetElmtTraceToTraceMap( const unsigned int fid, Array &maparray, - Array &signarray, Orientation faceOrient, int P, int Q); - STD_REGIONS_EXPORT virtual void v_GetEdgeInteriorToElementMap( + Array &signarray, Orientation faceOrient, int P, + int Q) override; + STD_REGIONS_EXPORT void v_GetEdgeInteriorToElementMap( const int tid, Array &maparray, Array &signarray, - const Orientation traceOrient = eDir1FwdDir1_Dir2FwdDir2); + const Orientation traceOrient = eDir1FwdDir1_Dir2FwdDir2) override; - STD_REGIONS_EXPORT virtual void v_GetTraceInteriorToElementMap( + STD_REGIONS_EXPORT void v_GetTraceInteriorToElementMap( const int tid, Array &maparray, Array &signarray, - const Orientation traceOrient = eDir1FwdDir1_Dir2FwdDir2); + const Orientation traceOrient = eDir1FwdDir1_Dir2FwdDir2) override; //--------------------------------------- // Wrapper functions //--------------------------------------- - STD_REGIONS_EXPORT virtual DNekMatSharedPtr v_GenMatrix( - const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual DNekMatSharedPtr v_CreateStdMatrix( - const StdMatrixKey &mkey); + STD_REGIONS_EXPORT DNekMatSharedPtr + v_GenMatrix(const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT DNekMatSharedPtr + v_CreateStdMatrix(const StdMatrixKey &mkey) override; - STD_REGIONS_EXPORT virtual void v_MultiplyByStdQuadratureMetric( + STD_REGIONS_EXPORT void v_MultiplyByStdQuadratureMetric( const Array &inarray, - Array &outarray); + Array &outarray) override; - STD_REGIONS_EXPORT void v_SVVLaplacianFilter(Array &array, - const StdMatrixKey &mkey); + STD_REGIONS_EXPORT void v_SVVLaplacianFilter( + Array &array, const StdMatrixKey &mkey) override; //--------------------------------------- // Method for applying sensors //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_ReduceOrderCoeffs( + STD_REGIONS_EXPORT void v_ReduceOrderCoeffs( int numMin, const Array &inarray, - Array &outarray); + Array &outarray) override; private: //--------------------------------------- diff --git a/library/StdRegions/StdPyrExp.cpp b/library/StdRegions/StdPyrExp.cpp index 2320c07dd30475091d0433097a4c81393746c939..47651f42621327de1a875887d3149ee28bb563b7 100644 --- a/library/StdRegions/StdPyrExp.cpp +++ b/library/StdRegions/StdPyrExp.cpp @@ -44,11 +44,6 @@ namespace Nektar { namespace StdRegions { -StdPyrExp::StdPyrExp() // Deafult construct of standard expansion directly - // called. -{ -} - StdPyrExp::StdPyrExp(const LibUtilities::BasisKey &Ba, const LibUtilities::BasisKey &Bb, const LibUtilities::BasisKey &Bc) @@ -76,11 +71,6 @@ StdPyrExp::StdPyrExp(const StdPyrExp &T) : StdExpansion(T), StdExpansion3D(T) { } -// Destructor -StdPyrExp::~StdPyrExp() -{ -} - //--------------------------------------- // Differentiation/integration Methods //--------------------------------------- @@ -726,6 +716,47 @@ void StdPyrExp::v_GetCoords(Array &xi_x, } } +NekDouble StdPyrExp::v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) +{ + // Collapse coordinates + Array coll(3, 0.0); + LocCoordToLocCollapsed(coord, coll); + + // If near singularity do the old interpolation matrix method + if ((1 - coll[2]) < 1e-5) + { + int totPoints = GetTotPoints(); + Array EphysDeriv0(totPoints), EphysDeriv1(totPoints), + EphysDeriv2(totPoints); + PhysDeriv(inarray, EphysDeriv0, EphysDeriv1, EphysDeriv2); + + Array I(3); + I[0] = GetBase()[0]->GetI(coll); + I[1] = GetBase()[1]->GetI(coll + 1); + I[2] = GetBase()[2]->GetI(coll + 2); + + firstOrderDerivs[0] = PhysEvaluate(I, EphysDeriv0); + firstOrderDerivs[1] = PhysEvaluate(I, EphysDeriv1); + firstOrderDerivs[2] = PhysEvaluate(I, EphysDeriv2); + return PhysEvaluate(I, inarray); + } + + std::array interDeriv; + NekDouble val = StdExpansion3D::BaryTensorDeriv(coll, inarray, interDeriv); + + NekDouble fac = 2.0 / (1.0 - coll[2]); + + firstOrderDerivs[0] = fac * interDeriv[0]; + firstOrderDerivs[1] = fac * interDeriv[1]; + firstOrderDerivs[2] = ((1.0 + coll[0]) / (1.0 - coll[2])) * interDeriv[0] + + ((1.0 + coll[1]) / (1.0 - coll[2])) * interDeriv[1] + + interDeriv[2]; + + return val; +} + void StdPyrExp::v_FillMode(const int mode, Array &outarray) { Array tmp(m_ncoeffs, 0.0); diff --git a/library/StdRegions/StdPyrExp.h b/library/StdRegions/StdPyrExp.h index bb24e4f8d214237434d234265968e64c4a54d42b..ef3f9d3151673d77812ec2e60ddc0a74fcd202ed 100644 --- a/library/StdRegions/StdPyrExp.h +++ b/library/StdRegions/StdPyrExp.h @@ -80,7 +80,7 @@ struct cmpop class StdPyrExp : virtual public StdExpansion3D { public: - STD_REGIONS_EXPORT StdPyrExp(); + STD_REGIONS_EXPORT StdPyrExp() = default; STD_REGIONS_EXPORT StdPyrExp(const LibUtilities::BasisKey &Ba, const LibUtilities::BasisKey &Bb, @@ -93,151 +93,161 @@ public: STD_REGIONS_EXPORT StdPyrExp(const StdPyrExp &T); - STD_REGIONS_EXPORT ~StdPyrExp(); + STD_REGIONS_EXPORT ~StdPyrExp() override = default; protected: //--------------------------------------- // Differentiation/integration Methods //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_PhysDeriv( + STD_REGIONS_EXPORT void v_PhysDeriv( const Array &inarray, Array &out_d0, Array &out_d1, - Array &out_d2); - STD_REGIONS_EXPORT virtual void v_PhysDeriv( + Array &out_d2) override; + STD_REGIONS_EXPORT void v_PhysDeriv( const int dir, const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_StdPhysDeriv( + Array &outarray) override; + STD_REGIONS_EXPORT void v_StdPhysDeriv( const Array &inarray, Array &out_d0, Array &out_d1, - Array &out_d2); - STD_REGIONS_EXPORT virtual void v_StdPhysDeriv( + Array &out_d2) override; + STD_REGIONS_EXPORT void v_StdPhysDeriv( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; STD_REGIONS_EXPORT void v_MultiplyByStdQuadratureMetric( const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Transforms //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_BwdTrans( + STD_REGIONS_EXPORT void v_BwdTrans( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_BwdTrans_SumFac( + Array &outarray) override; + STD_REGIONS_EXPORT void v_BwdTrans_SumFac( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_BwdTrans_SumFacKernel( + Array &outarray) override; + STD_REGIONS_EXPORT void v_BwdTrans_SumFacKernel( const Array &base0, const Array &base1, const Array &base2, const Array &inarray, Array &outarray, Array &wsp, - bool doCheckCollDir0, bool doCheckCollDir1, bool doCheckCollDir2); - STD_REGIONS_EXPORT virtual void v_FwdTrans( + bool doCheckCollDir0, bool doCheckCollDir1, + bool doCheckCollDir2) override; + STD_REGIONS_EXPORT void v_FwdTrans( const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Inner product functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_IProductWRTBase( + STD_REGIONS_EXPORT void v_IProductWRTBase( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_IProductWRTBase_SumFac( + Array &outarray) override; + STD_REGIONS_EXPORT void v_IProductWRTBase_SumFac( const Array &inarray, - Array &outarray, bool multiplybyweights = true); - STD_REGIONS_EXPORT virtual void v_IProductWRTBase_SumFacKernel( + Array &outarray, + bool multiplybyweights = true) override; + STD_REGIONS_EXPORT void v_IProductWRTBase_SumFacKernel( const Array &base0, const Array &base1, const Array &base2, const Array &inarray, Array &outarray, Array &wsp, - bool doCheckCollDir0, bool doCheckCollDir1, bool doCheckCollDir2); - STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase( + bool doCheckCollDir0, bool doCheckCollDir1, + bool doCheckCollDir2) override; + STD_REGIONS_EXPORT void v_IProductWRTDerivBase( const int dir, const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase_SumFac( + Array &outarray) override; + STD_REGIONS_EXPORT void v_IProductWRTDerivBase_SumFac( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Evaluation functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_LocCoordToLocCollapsed( - const Array &xi, Array &eta); - STD_REGIONS_EXPORT virtual void v_LocCollapsedToLocCoord( - const Array &eta, Array &xi); - STD_REGIONS_EXPORT virtual void v_GetCoords(Array &xi_x, - Array &xi_y, - Array &xi_z); - STD_REGIONS_EXPORT virtual void v_FillMode( - const int mode, Array &outarray); - STD_REGIONS_EXPORT virtual void v_GetTraceNumModes( + STD_REGIONS_EXPORT void v_LocCoordToLocCollapsed( + const Array &xi, + Array &eta) override; + STD_REGIONS_EXPORT void v_LocCollapsedToLocCoord( + const Array &eta, + Array &xi) override; + STD_REGIONS_EXPORT void v_GetCoords(Array &xi_x, + Array &xi_y, + Array &xi_z) override; + STD_REGIONS_EXPORT void v_FillMode( + const int mode, Array &outarray) override; + STD_REGIONS_EXPORT void v_GetTraceNumModes( const int fid, int &numModes0, int &numModes1, - Orientation faceOrient = eDir1FwdDir1_Dir2FwdDir2); + Orientation faceOrient = eDir1FwdDir1_Dir2FwdDir2) override; STD_REGIONS_EXPORT NekDouble v_PhysEvaluateBasis( const Array &coords, int mode) final; + STD_REGIONS_EXPORT NekDouble + v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) override; //--------------------------------------- // Helper functions //--------------------------------------- - STD_REGIONS_EXPORT virtual int v_GetNverts() const; - STD_REGIONS_EXPORT virtual int v_GetNedges() const; - STD_REGIONS_EXPORT virtual int v_GetNtraces() const; - STD_REGIONS_EXPORT virtual LibUtilities::ShapeType v_DetShapeType() const; - STD_REGIONS_EXPORT virtual int v_NumBndryCoeffs() const; - STD_REGIONS_EXPORT virtual int v_NumDGBndryCoeffs() const; - STD_REGIONS_EXPORT virtual int v_GetTraceNcoeffs(const int i) const; - STD_REGIONS_EXPORT virtual int v_GetTraceIntNcoeffs(const int i) const; - STD_REGIONS_EXPORT virtual int v_GetTraceNumPoints(const int i) const; + STD_REGIONS_EXPORT int v_GetNverts() const override; + STD_REGIONS_EXPORT int v_GetNedges() const override; + STD_REGIONS_EXPORT int v_GetNtraces() const override; + STD_REGIONS_EXPORT LibUtilities::ShapeType v_DetShapeType() const override; + STD_REGIONS_EXPORT int v_NumBndryCoeffs() const override; + STD_REGIONS_EXPORT int v_NumDGBndryCoeffs() const override; + STD_REGIONS_EXPORT int v_GetTraceNcoeffs(const int i) const override; + STD_REGIONS_EXPORT int v_GetTraceIntNcoeffs(const int i) const override; + STD_REGIONS_EXPORT int v_GetTraceNumPoints(const int i) const override; - STD_REGIONS_EXPORT virtual int v_GetEdgeNcoeffs(const int i) const; - STD_REGIONS_EXPORT virtual int v_CalcNumberOfCoefficients( - const std::vector &nummodes, int &modes_offset); - STD_REGIONS_EXPORT virtual const LibUtilities::BasisKey v_GetTraceBasisKey( - const int i, const int k) const; + STD_REGIONS_EXPORT int v_GetEdgeNcoeffs(const int i) const override; + STD_REGIONS_EXPORT int v_CalcNumberOfCoefficients( + const std::vector &nummodes, int &modes_offset) override; + STD_REGIONS_EXPORT const LibUtilities::BasisKey v_GetTraceBasisKey( + const int i, const int k) const override; //--------------------------------------- // Mappings //--------------------------------------- - STD_REGIONS_EXPORT virtual int v_GetVertexMap(int localVertexId, - bool useCoeffPacking = false); - STD_REGIONS_EXPORT virtual void v_GetInteriorMap( - Array &outarray); - STD_REGIONS_EXPORT virtual void v_GetBoundaryMap( - Array &outarray); - STD_REGIONS_EXPORT virtual void v_GetTraceCoeffMap( - const unsigned int fid, Array &maparray); - STD_REGIONS_EXPORT virtual void v_GetElmtTraceToTraceMap( + STD_REGIONS_EXPORT int v_GetVertexMap( + int localVertexId, bool useCoeffPacking = false) override; + STD_REGIONS_EXPORT void v_GetInteriorMap( + Array &outarray) override; + STD_REGIONS_EXPORT void v_GetBoundaryMap( + Array &outarray) override; + STD_REGIONS_EXPORT void v_GetTraceCoeffMap( + const unsigned int fid, Array &maparray) override; + STD_REGIONS_EXPORT void v_GetElmtTraceToTraceMap( const unsigned int fid, Array &maparray, - Array &signarray, Orientation faceOrient, int P, int Q); - STD_REGIONS_EXPORT virtual void v_GetEdgeInteriorToElementMap( + Array &signarray, Orientation faceOrient, int P, + int Q) override; + STD_REGIONS_EXPORT void v_GetEdgeInteriorToElementMap( const int tid, Array &maparray, Array &signarray, - const Orientation traceOrient = eDir1FwdDir1_Dir2FwdDir2); - STD_REGIONS_EXPORT virtual void v_GetTraceInteriorToElementMap( + const Orientation traceOrient = eDir1FwdDir1_Dir2FwdDir2) override; + STD_REGIONS_EXPORT void v_GetTraceInteriorToElementMap( const int tid, Array &maparray, Array &signarray, - const Orientation traceOrient = eDir1FwdDir1_Dir2FwdDir2); + const Orientation traceOrient = eDir1FwdDir1_Dir2FwdDir2) override; //--------------------------------------- // Wrapper functions //--------------------------------------- - STD_REGIONS_EXPORT virtual DNekMatSharedPtr v_GenMatrix( - const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual DNekMatSharedPtr v_CreateStdMatrix( - const StdMatrixKey &mkey); + STD_REGIONS_EXPORT DNekMatSharedPtr + v_GenMatrix(const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT DNekMatSharedPtr + v_CreateStdMatrix(const StdMatrixKey &mkey) override; - STD_REGIONS_EXPORT virtual void v_SVVLaplacianFilter( - Array &array, const StdMatrixKey &mkey); + STD_REGIONS_EXPORT void v_SVVLaplacianFilter( + Array &array, const StdMatrixKey &mkey) override; //--------------------------------------- // Method for applying sensors //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_ReduceOrderCoeffs( + STD_REGIONS_EXPORT void v_ReduceOrderCoeffs( int numMin, const Array &inarray, - Array &outarray); + Array &outarray) override; private: //--------------------------------------- diff --git a/library/StdRegions/StdQuadExp.cpp b/library/StdRegions/StdQuadExp.cpp index 43429e33d202e79142d56fe28eb72f09e95362dc..ccd42179ff71b18f50a371e4a4f7408ddd1e4289 100644 --- a/library/StdRegions/StdQuadExp.cpp +++ b/library/StdRegions/StdQuadExp.cpp @@ -45,11 +45,6 @@ namespace Nektar { namespace StdRegions { - -StdQuadExp::StdQuadExp() -{ -} - /** \brief Constructor using BasisKey class for quadrature * points and order definition */ @@ -65,11 +60,6 @@ StdQuadExp::StdQuadExp(const StdQuadExp &T) : StdExpansion(T), StdExpansion2D(T) { } -/** \brief Destructor */ -StdQuadExp::~StdQuadExp() -{ -} - ///////////////////////// // Integration Methods // ///////////////////////// diff --git a/library/StdRegions/StdQuadExp.h b/library/StdRegions/StdQuadExp.h index b1791ef431aecee60e0ee3104e213db2cf99fedd..cb04c171258776db9a8bf9ffa470f6f1ed2acd8f 100644 --- a/library/StdRegions/StdQuadExp.h +++ b/library/StdRegions/StdQuadExp.h @@ -53,83 +53,84 @@ class StdQuadExp : virtual public StdExpansion2D typedef std::shared_ptr StdExpansion1DSharedPtr; public: - STD_REGIONS_EXPORT StdQuadExp(); + STD_REGIONS_EXPORT StdQuadExp() = default; STD_REGIONS_EXPORT StdQuadExp(const LibUtilities::BasisKey &Ba, const LibUtilities::BasisKey &Bb); STD_REGIONS_EXPORT StdQuadExp(const StdQuadExp &T); - STD_REGIONS_EXPORT ~StdQuadExp(); + STD_REGIONS_EXPORT ~StdQuadExp() override = default; protected: //------------------------------- // Integration Methods //------------------------------- STD_REGIONS_EXPORT NekDouble - v_Integral(const Array &inarray); + v_Integral(const Array &inarray) override; //------------------------------- // Differentiation Methods //------------------------------- - STD_REGIONS_EXPORT virtual void v_PhysDeriv( + STD_REGIONS_EXPORT void v_PhysDeriv( const Array &inarray, Array &out_d0, Array &out_d1, - Array &out_d2 = NullNekDouble1DArray); - STD_REGIONS_EXPORT virtual void v_PhysDeriv( + Array &out_d2 = NullNekDouble1DArray) override; + STD_REGIONS_EXPORT void v_PhysDeriv( const int dir, const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_StdPhysDeriv( + Array &outarray) override; + STD_REGIONS_EXPORT void v_StdPhysDeriv( const Array &inarray, Array &out_d0, Array &out_d1, - Array &out_d2 = NullNekDouble1DArray); - STD_REGIONS_EXPORT virtual void v_StdPhysDeriv( + Array &out_d2 = NullNekDouble1DArray) override; + STD_REGIONS_EXPORT void v_StdPhysDeriv( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Transforms //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_BwdTrans( + STD_REGIONS_EXPORT void v_BwdTrans( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_FwdTransBndConstrained( + Array &outarray) override; + STD_REGIONS_EXPORT void v_FwdTransBndConstrained( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_BwdTrans_SumFac( + Array &outarray) override; + STD_REGIONS_EXPORT void v_BwdTrans_SumFac( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_BwdTrans_SumFacKernel( + Array &outarray) override; + STD_REGIONS_EXPORT void v_BwdTrans_SumFacKernel( const Array &base0, const Array &base1, const Array &inarray, Array &outarray, Array &wsp, - bool doCheckCollDir0, bool doCheckCollDir1); - STD_REGIONS_EXPORT virtual void v_FwdTrans( + bool doCheckCollDir0, bool doCheckCollDir1) override; + STD_REGIONS_EXPORT void v_FwdTrans( const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Inner product functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_IProductWRTBase( + STD_REGIONS_EXPORT void v_IProductWRTBase( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_IProductWRTBase_SumFac( + Array &outarray) override; + STD_REGIONS_EXPORT void v_IProductWRTBase_SumFac( const Array &inarray, - Array &outarray, bool multiplybyweights = true); + Array &outarray, + bool multiplybyweights = true) override; STD_REGIONS_EXPORT virtual void v_IProductWRTBase_MatOp( const Array &inarray, Array &outarray); - STD_REGIONS_EXPORT virtual void v_IProductWRTBase_SumFacKernel( + STD_REGIONS_EXPORT void v_IProductWRTBase_SumFacKernel( const Array &base0, const Array &base1, const Array &inarray, Array &outarray, Array &wsp, - bool doCheckCollDir0, bool doCheckCollDir1); - STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase( + bool doCheckCollDir0, bool doCheckCollDir1) override; + STD_REGIONS_EXPORT void v_IProductWRTDerivBase( const int dir, const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase_SumFac( + Array &outarray) override; + STD_REGIONS_EXPORT void v_IProductWRTDerivBase_SumFac( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase_MatOp( const int dir, const Array &inarray, Array &outarray); @@ -138,98 +139,109 @@ protected: // Evaluation functions //--------------------------------------- STD_REGIONS_EXPORT virtual void v_LocCoordToLocCollapsed( - const Array &xi, Array &eta); + const Array &xi, + Array &eta) override; STD_REGIONS_EXPORT virtual void v_LocCollapsedToLocCoord( - const Array &eta, Array &xi); + const Array &eta, + Array &xi) override; - STD_REGIONS_EXPORT virtual void v_FillMode(const int mode, - Array &array); + STD_REGIONS_EXPORT virtual void v_FillMode( + const int mode, Array &array) override; //--------------------------- // Helper functions //--------------------------- - STD_REGIONS_EXPORT virtual int v_GetNverts() const; - STD_REGIONS_EXPORT virtual int v_GetNtraces() const; - STD_REGIONS_EXPORT virtual int v_GetTraceNcoeffs(const int i) const; - STD_REGIONS_EXPORT virtual int v_GetTraceNumPoints(const int i) const; - STD_REGIONS_EXPORT virtual int v_NumBndryCoeffs() const; - STD_REGIONS_EXPORT virtual int v_NumDGBndryCoeffs() const; - - STD_REGIONS_EXPORT virtual int v_CalcNumberOfCoefficients( - const std::vector &nummodes, int &modes_offset); - STD_REGIONS_EXPORT virtual const LibUtilities::BasisKey v_GetTraceBasisKey( - const int i, const int j) const; - STD_REGIONS_EXPORT virtual LibUtilities::ShapeType v_DetShapeType() const; - STD_REGIONS_EXPORT virtual bool v_IsBoundaryInteriorExpansion(); - STD_REGIONS_EXPORT virtual void v_GetCoords( + STD_REGIONS_EXPORT int v_GetNverts() const override; + STD_REGIONS_EXPORT int v_GetNtraces() const override; + STD_REGIONS_EXPORT int v_GetTraceNcoeffs(const int i) const override; + STD_REGIONS_EXPORT int v_GetTraceNumPoints(const int i) const override; + STD_REGIONS_EXPORT int v_NumBndryCoeffs() const override; + STD_REGIONS_EXPORT int v_NumDGBndryCoeffs() const override; + + STD_REGIONS_EXPORT int v_CalcNumberOfCoefficients( + const std::vector &nummodes, int &modes_offset) override; + STD_REGIONS_EXPORT const LibUtilities::BasisKey v_GetTraceBasisKey( + const int i, const int j) const override; + STD_REGIONS_EXPORT LibUtilities::ShapeType v_DetShapeType() const override; + STD_REGIONS_EXPORT bool v_IsBoundaryInteriorExpansion() override; + STD_REGIONS_EXPORT void v_GetCoords( Array &coords_0, Array &coords_1, - Array &coords_2); - STD_REGIONS_EXPORT virtual NekDouble v_PhysEvaluateBasis( - const Array &coords, int mode); + Array &coords_2) override; + STD_REGIONS_EXPORT NekDouble v_PhysEvaluateBasis( + const Array &coords, int mode) override; + STD_REGIONS_EXPORT inline NekDouble v_PhysEvaluate( + const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) override + { + return BaryTensorDeriv(coord, inarray, firstOrderDerivs); + } //-------------------------- // Mappings //-------------------------- - STD_REGIONS_EXPORT virtual void v_GetBoundaryMap( - Array &outarray); - STD_REGIONS_EXPORT virtual void v_GetInteriorMap( - Array &outarray); - STD_REGIONS_EXPORT virtual int v_GetVertexMap(int localVertexId, - bool useCoeffPacking = false); - - STD_REGIONS_EXPORT virtual void v_GetTraceCoeffMap( - const unsigned int traceid, Array &maparray); - - STD_REGIONS_EXPORT virtual void v_GetTraceInteriorToElementMap( + STD_REGIONS_EXPORT void v_GetBoundaryMap( + Array &outarray) override; + STD_REGIONS_EXPORT void v_GetInteriorMap( + Array &outarray) override; + STD_REGIONS_EXPORT int v_GetVertexMap( + int localVertexId, bool useCoeffPacking = false) override; + + STD_REGIONS_EXPORT void v_GetTraceCoeffMap( + const unsigned int traceid, + Array &maparray) override; + + STD_REGIONS_EXPORT void v_GetTraceInteriorToElementMap( const int eid, Array &maparray, - Array &signarray, const Orientation edgeOrient = eForwards); + Array &signarray, + const Orientation edgeOrient = eForwards) override; //--------------------------------------- // Wrapper functions //--------------------------------------- - STD_REGIONS_EXPORT virtual DNekMatSharedPtr v_GenMatrix( - const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual DNekMatSharedPtr v_CreateStdMatrix( - const StdMatrixKey &mkey); + STD_REGIONS_EXPORT DNekMatSharedPtr + v_GenMatrix(const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT DNekMatSharedPtr + v_CreateStdMatrix(const StdMatrixKey &mkey) override; //--------------------------------------- // Operator evaluation functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_MassMatrixOp( + STD_REGIONS_EXPORT void v_MassMatrixOp( const Array &inarray, - Array &outarray, const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual void v_LaplacianMatrixOp( + Array &outarray, const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT void v_LaplacianMatrixOp( const Array &inarray, - Array &outarray, const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual void v_LaplacianMatrixOp( + Array &outarray, const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT void v_LaplacianMatrixOp( const int k1, const int k2, const Array &inarray, - Array &outarray, const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual void v_WeakDerivMatrixOp( + Array &outarray, const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT void v_WeakDerivMatrixOp( const int i, const Array &inarray, - Array &outarray, const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual void v_HelmholtzMatrixOp( + Array &outarray, const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT void v_HelmholtzMatrixOp( const Array &inarray, - Array &outarray, const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual void v_SVVLaplacianFilter( - Array &array, const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual void v_ExponentialFilter( + Array &outarray, const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT void v_SVVLaplacianFilter( + Array &array, const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT void v_ExponentialFilter( Array &array, const NekDouble alpha, - const NekDouble exponent, const NekDouble cutoff); - STD_REGIONS_EXPORT virtual void v_ReduceOrderCoeffs( + const NekDouble exponent, const NekDouble cutoff) override; + STD_REGIONS_EXPORT void v_ReduceOrderCoeffs( int numMin, const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT void v_GeneralMatrixOp_MatOp( + Array &outarray) override; + STD_REGIONS_EXPORT virtual void v_GeneralMatrixOp_MatOp( const Array &inarray, Array &outarray, const StdMatrixKey &mkey); STD_REGIONS_EXPORT void v_MultiplyByStdQuadratureMetric( const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Output interpolation functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_GetSimplexEquiSpacedConnectivity( - Array &conn, bool standard = true); + STD_REGIONS_EXPORT void v_GetSimplexEquiSpacedConnectivity( + Array &conn, bool standard = true) override; }; typedef std::shared_ptr StdQuadExpSharedPtr; diff --git a/library/StdRegions/StdSegExp.cpp b/library/StdRegions/StdSegExp.cpp index ab0dcc90e1f63456a417acb8019048735b6d8b01..d6f65b8e8337b27c987c1279818ec1bb431a7ce3 100644 --- a/library/StdRegions/StdSegExp.cpp +++ b/library/StdRegions/StdSegExp.cpp @@ -43,20 +43,12 @@ namespace Nektar { namespace StdRegions { - -/** \brief Default constructor */ - -StdSegExp::StdSegExp() -{ -} - /** \brief Constructor using BasisKey class for quadrature points and * order definition * * \param Ba BasisKey class definition containing order and quadrature * points. */ - StdSegExp::StdSegExp(const LibUtilities::BasisKey &Ba) : StdExpansion(Ba.GetNumModes(), 1, Ba), StdExpansion1D(Ba.GetNumModes(), Ba) @@ -64,15 +56,10 @@ StdSegExp::StdSegExp(const LibUtilities::BasisKey &Ba) } /** \brief Copy Constructor */ - StdSegExp::StdSegExp(const StdSegExp &T) : StdExpansion(T), StdExpansion1D(T) { } -StdSegExp::~StdSegExp() -{ -} - /** \brief Return Shape of region, using ShapeType enum list. * i.e. Segment */ diff --git a/library/StdRegions/StdSegExp.h b/library/StdRegions/StdSegExp.h index d70f81f64b89df0a26c179ab5d1164166db05805..9bd84bd8e8ea07f02bcb5a89f4cf69522052172e 100644 --- a/library/StdRegions/StdSegExp.h +++ b/library/StdRegions/StdSegExp.h @@ -42,203 +42,223 @@ namespace Nektar { namespace StdRegions { - -class StdSegExp; -typedef std::shared_ptr StdSegExpSharedPtr; - /// Class representing a segment element in reference space - /// All interface of this class sits in StdExpansion class - class StdSegExp : virtual public StdExpansion1D { public: - STD_REGIONS_EXPORT StdSegExp(); + STD_REGIONS_EXPORT StdSegExp() = default; STD_REGIONS_EXPORT StdSegExp(const LibUtilities::BasisKey &Ba); STD_REGIONS_EXPORT StdSegExp(const StdSegExp &T); - STD_REGIONS_EXPORT ~StdSegExp(); + STD_REGIONS_EXPORT ~StdSegExp() override = default; protected: //---------------------------- // Integration Methods //---------------------------- - STD_REGIONS_EXPORT virtual NekDouble v_Integral( - const Array &inarray); + STD_REGIONS_EXPORT NekDouble + v_Integral(const Array &inarray) override; //----------------------------- // Differentiation Methods //----------------------------- - STD_REGIONS_EXPORT virtual void v_PhysDeriv( + STD_REGIONS_EXPORT void v_PhysDeriv( const Array &inarray, Array &out_d0, Array &out_d1 = NullNekDouble1DArray, - Array &out_d2 = NullNekDouble1DArray); + Array &out_d2 = NullNekDouble1DArray) override; - STD_REGIONS_EXPORT virtual void v_PhysDeriv( + STD_REGIONS_EXPORT void v_PhysDeriv( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; - STD_REGIONS_EXPORT virtual void v_StdPhysDeriv( + STD_REGIONS_EXPORT void v_StdPhysDeriv( const Array &inarray, Array &out_d0, Array &out_d1 = NullNekDouble1DArray, - Array &out_d2 = NullNekDouble1DArray); + Array &out_d2 = NullNekDouble1DArray) override; - STD_REGIONS_EXPORT virtual void v_StdPhysDeriv( + STD_REGIONS_EXPORT void v_StdPhysDeriv( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; //----------------------------- // Transforms //----------------------------- - STD_REGIONS_EXPORT virtual void v_BwdTrans( + STD_REGIONS_EXPORT void v_BwdTrans( const Array &inarray, - Array &outarray); + Array &outarray) override; - STD_REGIONS_EXPORT virtual void v_FwdTrans( + STD_REGIONS_EXPORT void v_FwdTrans( const Array &inarray, - Array &outarray); + Array &outarray) override; - STD_REGIONS_EXPORT virtual void v_BwdTrans_SumFac( + STD_REGIONS_EXPORT void v_BwdTrans_SumFac( const Array &inarray, - Array &outarray); + Array &outarray) override; - STD_REGIONS_EXPORT virtual void v_FwdTransBndConstrained( + STD_REGIONS_EXPORT void v_FwdTransBndConstrained( const Array &inarray, - Array &outarray); + Array &outarray) override; //---------------------------- // Inner product functions //---------------------------- - STD_REGIONS_EXPORT virtual void v_IProductWRTBase( + STD_REGIONS_EXPORT void v_IProductWRTBase( const Array &inarray, - Array &outarray); + Array &outarray) override; - STD_REGIONS_EXPORT virtual void v_IProductWRTBase( + STD_REGIONS_EXPORT void v_IProductWRTBase( const Array &base, const Array &inarray, - Array &outarray, int coll_check); + Array &outarray, int coll_check) override; - STD_REGIONS_EXPORT virtual void v_IProductWRTBase_SumFac( + STD_REGIONS_EXPORT void v_IProductWRTBase_SumFac( const Array &inarray, - Array &outarray, bool multiplybyweights = true); + Array &outarray, + bool multiplybyweights = true) override; - STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase( + STD_REGIONS_EXPORT void v_IProductWRTDerivBase( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; - STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase_SumFac( + STD_REGIONS_EXPORT void v_IProductWRTDerivBase_SumFac( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; //---------------------------- // Evaluations Methods //--------------------------- - STD_REGIONS_EXPORT virtual void v_LocCoordToLocCollapsed( - const Array &xi, Array &eta); + STD_REGIONS_EXPORT void v_LocCoordToLocCollapsed( + const Array &xi, + Array &eta) override; - STD_REGIONS_EXPORT virtual void v_LocCollapsedToLocCoord( - const Array &eta, Array &xi); + STD_REGIONS_EXPORT void v_LocCollapsedToLocCoord( + const Array &eta, + Array &xi) override; STD_REGIONS_EXPORT NekDouble v_PhysEvaluateBasis( const Array &coords, int mode) final; - STD_REGIONS_EXPORT virtual void v_LaplacianMatrixOp( + STD_REGIONS_EXPORT inline NekDouble v_PhysEvaluate( + const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) override + { + return StdExpansion1D::BaryTensorDeriv(coord, inarray, + firstOrderDerivs); + } + + STD_REGIONS_EXPORT inline NekDouble v_PhysEvaluate( + const Array &coord, const Array &inarray, - Array &outarray, const StdMatrixKey &mkey); + std::array &firstOrderDerivs, + std::array &secondOrderDerivs) override + { + return StdExpansion1D::BaryTensorDeriv(coord, inarray, firstOrderDerivs, + secondOrderDerivs); + } + + STD_REGIONS_EXPORT void v_LaplacianMatrixOp( + const Array &inarray, + Array &outarray, const StdMatrixKey &mkey) override; - STD_REGIONS_EXPORT virtual void v_HelmholtzMatrixOp( + STD_REGIONS_EXPORT void v_HelmholtzMatrixOp( const Array &inarray, - Array &outarray, const StdMatrixKey &mkey); + Array &outarray, const StdMatrixKey &mkey) override; - STD_REGIONS_EXPORT virtual void v_SVVLaplacianFilter( - Array &array, const StdMatrixKey &mkey); + STD_REGIONS_EXPORT void v_SVVLaplacianFilter( + Array &array, const StdMatrixKey &mkey) override; - STD_REGIONS_EXPORT virtual void v_ExponentialFilter( + STD_REGIONS_EXPORT void v_ExponentialFilter( Array &array, const NekDouble alpha, - const NekDouble exponent, const NekDouble cutoff); + const NekDouble exponent, const NekDouble cutoff) override; - STD_REGIONS_EXPORT virtual void v_MultiplyByStdQuadratureMetric( + STD_REGIONS_EXPORT void v_MultiplyByStdQuadratureMetric( const Array &inarray, - Array &outarray); + Array &outarray) override; - STD_REGIONS_EXPORT virtual void v_FillMode( - const int mode, Array &outarray); + STD_REGIONS_EXPORT void v_FillMode( + const int mode, Array &outarray) override; - STD_REGIONS_EXPORT virtual void v_GetCoords( + STD_REGIONS_EXPORT void v_GetCoords( Array &coords_0, Array &coords_1, - Array &coords_2); + Array &coords_2) override; //---------------------------- // Public Mappings //--------------------------- - STD_REGIONS_EXPORT virtual void v_GetBoundaryMap( - Array &outarray); + STD_REGIONS_EXPORT void v_GetBoundaryMap( + Array &outarray) override; - STD_REGIONS_EXPORT virtual void v_GetInteriorMap( - Array &outarray); + STD_REGIONS_EXPORT void v_GetInteriorMap( + Array &outarray) override; - STD_REGIONS_EXPORT virtual int v_GetVertexMap(int localVertexId, - bool useCoeffPacking = false); + STD_REGIONS_EXPORT int v_GetVertexMap( + int localVertexId, bool useCoeffPacking = false) override; //---------------------------- // Helper functions //--------------------------- - STD_REGIONS_EXPORT virtual int v_GetNverts() const; - STD_REGIONS_EXPORT virtual int v_GetNtraces() const; - STD_REGIONS_EXPORT virtual int v_GetTraceNcoeffs(const int i) const; - STD_REGIONS_EXPORT virtual int v_GetTraceNumPoints(const int i) const; - STD_REGIONS_EXPORT virtual int v_NumBndryCoeffs() const; - STD_REGIONS_EXPORT virtual int v_NumDGBndryCoeffs() const; - STD_REGIONS_EXPORT virtual bool v_IsBoundaryInteriorExpansion(); - STD_REGIONS_EXPORT virtual int v_CalcNumberOfCoefficients( - const std::vector &nummodes, int &modes_offset); - STD_REGIONS_EXPORT virtual LibUtilities::ShapeType v_DetShapeType() const; + STD_REGIONS_EXPORT int v_GetNverts() const override; + STD_REGIONS_EXPORT int v_GetNtraces() const override; + STD_REGIONS_EXPORT int v_GetTraceNcoeffs(const int i) const override; + STD_REGIONS_EXPORT int v_GetTraceNumPoints(const int i) const override; + STD_REGIONS_EXPORT int v_NumBndryCoeffs() const override; + STD_REGIONS_EXPORT int v_NumDGBndryCoeffs() const override; + STD_REGIONS_EXPORT bool v_IsBoundaryInteriorExpansion() override; + STD_REGIONS_EXPORT int v_CalcNumberOfCoefficients( + const std::vector &nummodes, int &modes_offset) override; + STD_REGIONS_EXPORT LibUtilities::ShapeType v_DetShapeType() const override; //---------------------------- // Wrapper functions //--------------------------- - STD_REGIONS_EXPORT virtual DNekMatSharedPtr v_GenMatrix( - const StdMatrixKey &mkey); + STD_REGIONS_EXPORT DNekMatSharedPtr + v_GenMatrix(const StdMatrixKey &mkey) override; - STD_REGIONS_EXPORT virtual DNekMatSharedPtr v_CreateStdMatrix( - const StdMatrixKey &mkey); + STD_REGIONS_EXPORT DNekMatSharedPtr + v_CreateStdMatrix(const StdMatrixKey &mkey) override; //--------------------------------------- // Output interpolation functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_GetSimplexEquiSpacedConnectivity( - Array &conn, bool standard = true); + STD_REGIONS_EXPORT void v_GetSimplexEquiSpacedConnectivity( + Array &conn, bool standard = true) override; // Operator evaluation functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_ReduceOrderCoeffs( + STD_REGIONS_EXPORT void v_ReduceOrderCoeffs( int numMin, const Array &inarray, - Array &outarray); + Array &outarray) override; - STD_REGIONS_EXPORT virtual void v_GetTraceCoeffMap( - const unsigned int traceid, Array &maparray); + STD_REGIONS_EXPORT void v_GetTraceCoeffMap( + const unsigned int traceid, + Array &maparray) override; - STD_REGIONS_EXPORT virtual void v_GetElmtTraceToTraceMap( + STD_REGIONS_EXPORT void v_GetElmtTraceToTraceMap( const unsigned int eid, Array &maparray, - Array &signarray, Orientation edgeOrient, int P, int Q); + Array &signarray, Orientation edgeOrient, int P, + int Q) override; - STD_REGIONS_EXPORT virtual void v_GetTraceToElementMap( + STD_REGIONS_EXPORT void v_GetTraceToElementMap( const int tid, Array &maparray, - Array &signarray, Orientation edgeOrient, int P, int Q); + Array &signarray, Orientation edgeOrient, int P, + int Q) override; private: }; +typedef std::shared_ptr StdSegExpSharedPtr; } // namespace StdRegions } // namespace Nektar diff --git a/library/StdRegions/StdTetExp.cpp b/library/StdRegions/StdTetExp.cpp index 8372ab48a528e7282618c0f23dbdb1a9c18fbee1..0bc9ef754b6ab41c6414601f23ca7da1414b011a 100644 --- a/library/StdRegions/StdTetExp.cpp +++ b/library/StdRegions/StdTetExp.cpp @@ -43,10 +43,6 @@ namespace Nektar { namespace StdRegions { -StdTetExp::StdTetExp() -{ -} - StdTetExp::StdTetExp(const LibUtilities::BasisKey &Ba, const LibUtilities::BasisKey &Bb, const LibUtilities::BasisKey &Bc) @@ -72,10 +68,6 @@ StdTetExp::StdTetExp(const StdTetExp &T) : StdExpansion(T), StdExpansion3D(T) { } -StdTetExp::~StdTetExp() -{ -} - //---------------------------- // Differentiation Methods //---------------------------- @@ -912,6 +904,70 @@ NekDouble StdTetExp::v_PhysEvaluateBasis( StdExpansion::BaryEvaluateBasis<2>(coll[2], mode2); } +NekDouble StdTetExp::v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) +{ + // Collapse coordinates + Array coll(3, 0.0); + LocCoordToLocCollapsed(coord, coll); + + // If near singularity do the old interpolation matrix method + if ((1 - coll[1]) < 1e-5 || (1 - coll[2]) < 1e-5) + { + int totPoints = GetTotPoints(); + Array EphysDeriv0(totPoints), EphysDeriv1(totPoints), + EphysDeriv2(totPoints); + PhysDeriv(inarray, EphysDeriv0, EphysDeriv1, EphysDeriv2); + + Array I(3); + I[0] = GetBase()[0]->GetI(coll); + I[1] = GetBase()[1]->GetI(coll + 1); + I[2] = GetBase()[2]->GetI(coll + 2); + + firstOrderDerivs[0] = PhysEvaluate(I, EphysDeriv0); + firstOrderDerivs[1] = PhysEvaluate(I, EphysDeriv1); + firstOrderDerivs[2] = PhysEvaluate(I, EphysDeriv2); + return PhysEvaluate(I, inarray); + } + + std::array interDeriv; + NekDouble val = BaryTensorDeriv(coll, inarray, interDeriv); + + // calculate 2.0/((1-eta_1)(1-eta_2)) * Out_dEta0 + NekDouble temp = 2.0 / ((1 - coll[1]) * (1 - coll[2])); + interDeriv[0] *= temp; + + // out_dxi0 = 4.0/((1-eta_1)(1-eta_2)) * Out_dEta0 + firstOrderDerivs[0] = 2 * interDeriv[0]; + + // fac0 = 1 + eta_0 + NekDouble fac0; + fac0 = 1 + coll[0]; + + // calculate 2.0*(1+eta_0)/((1-eta_1)(1-eta_2)) * Out_dEta0 + interDeriv[0] *= fac0; + + // calculate 2/(1.0-eta_2) * out_dEta1 + fac0 = 2 / (1 - coll[2]); + interDeriv[1] *= fac0; + + // calculate out_dxi1 = 2.0(1+eta_0)/((1-eta_1)(1-eta_2)) + // * Out_dEta0 + 2/(1.0-eta_2) out_dEta1 + firstOrderDerivs[1] = interDeriv[0] + interDeriv[1]; + + // calculate (1 + eta_1)/(1 -eta_2)*out_dEta1 + fac0 = (1 + coll[1]) / 2; + interDeriv[1] *= fac0; + + // calculate out_dxi2 = + // 2.0(1+eta_0)/((1-eta_1)(1-eta_2)) Out_dEta0 + + // (1 + eta_1)/(1 -eta_2)*out_dEta1 + out_dEta2 + firstOrderDerivs[2] = interDeriv[0] + interDeriv[1] + interDeriv[2]; + + return val; +} + void StdTetExp::v_GetTraceNumModes(const int fid, int &numModes0, int &numModes1, diff --git a/library/StdRegions/StdTetExp.h b/library/StdRegions/StdTetExp.h index 1a69922ae14282d1784b7fdfb79d250c74ea2ec3..0c64e78e452c12bf8a944ed396e396014bac817c 100644 --- a/library/StdRegions/StdTetExp.h +++ b/library/StdRegions/StdTetExp.h @@ -50,7 +50,7 @@ class StdTetExp : virtual public StdExpansion3D { public: - STD_REGIONS_EXPORT StdTetExp(); + STD_REGIONS_EXPORT StdTetExp() = default; STD_REGIONS_EXPORT StdTetExp(const LibUtilities::BasisKey &Ba, const LibUtilities::BasisKey &Bb, const LibUtilities::BasisKey &Bc); @@ -59,7 +59,7 @@ public: const LibUtilities::BasisKey &Bc, NekDouble *coeffs, NekDouble *phys); STD_REGIONS_EXPORT StdTetExp(const StdTetExp &T); - STD_REGIONS_EXPORT ~StdTetExp(); + STD_REGIONS_EXPORT ~StdTetExp() override = default; LibUtilities::ShapeType DetShapeType() const { @@ -75,167 +75,177 @@ protected: //---------------------------- // Differentiation Methods //---------------------------- - STD_REGIONS_EXPORT virtual void v_PhysDeriv( + STD_REGIONS_EXPORT void v_PhysDeriv( const Array &inarray, Array &out_dx, Array &out_dy, - Array &out_dz); - STD_REGIONS_EXPORT virtual void v_PhysDeriv( + Array &out_dz) override; + STD_REGIONS_EXPORT void v_PhysDeriv( const int dir, const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_StdPhysDeriv( + Array &outarray) override; + STD_REGIONS_EXPORT void v_StdPhysDeriv( const Array &inarray, Array &out_d0, Array &out_d1, - Array &out_d2); - STD_REGIONS_EXPORT virtual void v_StdPhysDeriv( + Array &out_d2) override; + STD_REGIONS_EXPORT void v_StdPhysDeriv( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Transforms //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_BwdTrans( + STD_REGIONS_EXPORT void v_BwdTrans( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_BwdTrans_SumFac( + Array &outarray) override; + STD_REGIONS_EXPORT void v_BwdTrans_SumFac( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_BwdTrans_SumFacKernel( + Array &outarray) override; + STD_REGIONS_EXPORT void v_BwdTrans_SumFacKernel( const Array &base0, const Array &base1, const Array &base2, const Array &inarray, Array &outarray, Array &wsp, - bool doCheckCollDir0, bool doCheckCollDir1, bool doCheckCollDir2); - STD_REGIONS_EXPORT virtual void v_FwdTrans( + bool doCheckCollDir0, bool doCheckCollDir1, + bool doCheckCollDir2) override; + STD_REGIONS_EXPORT void v_FwdTrans( const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Inner product functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_IProductWRTBase( + STD_REGIONS_EXPORT void v_IProductWRTBase( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_IProductWRTBase_MatOp( + Array &outarray) override; + STD_REGIONS_EXPORT void v_IProductWRTBase_MatOp( const Array &inarray, Array &outarray); - STD_REGIONS_EXPORT virtual void v_IProductWRTBase_SumFac( + STD_REGIONS_EXPORT void v_IProductWRTBase_SumFac( const Array &inarray, - Array &outarray, bool multiplybyweights = true); - STD_REGIONS_EXPORT virtual void v_IProductWRTBase_SumFacKernel( + Array &outarray, + bool multiplybyweights = true) override; + STD_REGIONS_EXPORT void v_IProductWRTBase_SumFacKernel( const Array &base0, const Array &base1, const Array &base2, const Array &inarray, Array &outarray, Array &wsp, - bool doCheckCollDir0, bool doCheckCollDir1, bool doCheckCollDir2); - STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase( + bool doCheckCollDir0, bool doCheckCollDir1, + bool doCheckCollDir2) override; + STD_REGIONS_EXPORT void v_IProductWRTDerivBase( const int dir, const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase_MatOp( + Array &outarray) override; + STD_REGIONS_EXPORT void v_IProductWRTDerivBase_MatOp( const int dir, const Array &inarray, Array &outarray); - STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase_SumFac( + STD_REGIONS_EXPORT void v_IProductWRTDerivBase_SumFac( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Evaluation functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_LocCoordToLocCollapsed( - const Array &xi, Array &eta); - STD_REGIONS_EXPORT virtual void v_LocCollapsedToLocCoord( - const Array &eta, Array &xi); - STD_REGIONS_EXPORT virtual void v_GetCoords( + STD_REGIONS_EXPORT void v_LocCoordToLocCollapsed( + const Array &xi, + Array &eta) override; + STD_REGIONS_EXPORT void v_LocCollapsedToLocCoord( + const Array &eta, + Array &xi) override; + STD_REGIONS_EXPORT void v_GetCoords( Array &coords_x, Array &coords_y, - Array &coords_z); - STD_REGIONS_EXPORT virtual void v_FillMode( - const int mode, Array &outarray); + Array &coords_z) override; + STD_REGIONS_EXPORT void v_FillMode( + const int mode, Array &outarray) override; STD_REGIONS_EXPORT NekDouble v_PhysEvaluateBasis( const Array &coords, int mode) final; - STD_REGIONS_EXPORT virtual void v_GetTraceNumModes( + STD_REGIONS_EXPORT NekDouble + v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) override; + + STD_REGIONS_EXPORT void v_GetTraceNumModes( const int fid, int &numModes0, int &numModes1, - Orientation traceOrient = eDir1FwdDir1_Dir2FwdDir2); + Orientation traceOrient = eDir1FwdDir1_Dir2FwdDir2) override; //--------------------------- // Helper functions //--------------------------- - STD_REGIONS_EXPORT virtual int v_GetNverts() const; - STD_REGIONS_EXPORT virtual int v_GetNedges() const; - STD_REGIONS_EXPORT virtual int v_GetNtraces() const; - STD_REGIONS_EXPORT virtual LibUtilities::ShapeType v_DetShapeType() const; - STD_REGIONS_EXPORT virtual int v_NumBndryCoeffs() const; - STD_REGIONS_EXPORT virtual int v_NumDGBndryCoeffs() const; - STD_REGIONS_EXPORT virtual int v_GetTraceNcoeffs(const int i) const; - STD_REGIONS_EXPORT virtual int v_GetTotalTraceIntNcoeffs() const; - STD_REGIONS_EXPORT virtual int v_GetTraceIntNcoeffs(const int i) const; - STD_REGIONS_EXPORT virtual int v_GetTraceNumPoints(const int i) const; - STD_REGIONS_EXPORT virtual int v_GetEdgeNcoeffs(const int i) const; - STD_REGIONS_EXPORT virtual LibUtilities::PointsKey v_GetTracePointsKey( - const int i, const int j) const; - STD_REGIONS_EXPORT virtual int v_CalcNumberOfCoefficients( - const std::vector &nummodes, int &modes_offset); - STD_REGIONS_EXPORT virtual const LibUtilities::BasisKey v_GetTraceBasisKey( - const int i, const int k) const; - STD_REGIONS_EXPORT virtual bool v_IsBoundaryInteriorExpansion(); + STD_REGIONS_EXPORT int v_GetNverts() const override; + STD_REGIONS_EXPORT int v_GetNedges() const override; + STD_REGIONS_EXPORT int v_GetNtraces() const override; + STD_REGIONS_EXPORT LibUtilities::ShapeType v_DetShapeType() const override; + STD_REGIONS_EXPORT int v_NumBndryCoeffs() const override; + STD_REGIONS_EXPORT int v_NumDGBndryCoeffs() const override; + STD_REGIONS_EXPORT int v_GetTraceNcoeffs(const int i) const override; + STD_REGIONS_EXPORT int v_GetTotalTraceIntNcoeffs() const override; + STD_REGIONS_EXPORT int v_GetTraceIntNcoeffs(const int i) const override; + STD_REGIONS_EXPORT int v_GetTraceNumPoints(const int i) const override; + STD_REGIONS_EXPORT int v_GetEdgeNcoeffs(const int i) const override; + STD_REGIONS_EXPORT LibUtilities::PointsKey v_GetTracePointsKey( + const int i, const int j) const override; + STD_REGIONS_EXPORT int v_CalcNumberOfCoefficients( + const std::vector &nummodes, int &modes_offset) override; + STD_REGIONS_EXPORT const LibUtilities::BasisKey v_GetTraceBasisKey( + const int i, const int k) const override; + STD_REGIONS_EXPORT bool v_IsBoundaryInteriorExpansion() override; //-------------------------- // Mappings //-------------------------- - STD_REGIONS_EXPORT virtual int v_GetVertexMap(int localVertexId, - bool useCoeffPacking = false); - STD_REGIONS_EXPORT virtual void v_GetInteriorMap( - Array &outarray); - STD_REGIONS_EXPORT virtual void v_GetBoundaryMap( - Array &outarray); - STD_REGIONS_EXPORT virtual void v_GetTraceCoeffMap( - const unsigned int fid, Array &maparray); - - STD_REGIONS_EXPORT virtual void v_GetElmtTraceToTraceMap( + STD_REGIONS_EXPORT int v_GetVertexMap( + int localVertexId, bool useCoeffPacking = false) override; + STD_REGIONS_EXPORT void v_GetInteriorMap( + Array &outarray) override; + STD_REGIONS_EXPORT void v_GetBoundaryMap( + Array &outarray) override; + STD_REGIONS_EXPORT void v_GetTraceCoeffMap( + const unsigned int fid, Array &maparray) override; + + STD_REGIONS_EXPORT void v_GetElmtTraceToTraceMap( const unsigned int tid, Array &maparray, Array &signarray, Orientation traceOrient = eForwards, - int P = -1, int Q = -1); + int P = -1, int Q = -1) override; - STD_REGIONS_EXPORT virtual void v_GetEdgeInteriorToElementMap( + STD_REGIONS_EXPORT void v_GetEdgeInteriorToElementMap( const int tid, Array &maparray, Array &signarray, - const Orientation traceOrient = eDir1FwdDir1_Dir2FwdDir2); + const Orientation traceOrient = eDir1FwdDir1_Dir2FwdDir2) override; - STD_REGIONS_EXPORT virtual void v_GetTraceInteriorToElementMap( + STD_REGIONS_EXPORT void v_GetTraceInteriorToElementMap( const int tid, Array &maparray, Array &signarray, - const Orientation traceOrient = eDir1FwdDir1_Dir2FwdDir2); + const Orientation traceOrient = eDir1FwdDir1_Dir2FwdDir2) override; //--------------------------------------- // Wrapper functions //--------------------------------------- - STD_REGIONS_EXPORT virtual DNekMatSharedPtr v_GenMatrix( - const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual DNekMatSharedPtr v_CreateStdMatrix( - const StdMatrixKey &mkey); + STD_REGIONS_EXPORT DNekMatSharedPtr + v_GenMatrix(const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT DNekMatSharedPtr + v_CreateStdMatrix(const StdMatrixKey &mkey) override; - STD_REGIONS_EXPORT virtual void v_MultiplyByStdQuadratureMetric( + STD_REGIONS_EXPORT void v_MultiplyByStdQuadratureMetric( const Array &inarray, - Array &outarray); + Array &outarray) override; - STD_REGIONS_EXPORT virtual void v_SVVLaplacianFilter( - Array &array, const StdMatrixKey &mkey); + STD_REGIONS_EXPORT void v_SVVLaplacianFilter( + Array &array, const StdMatrixKey &mkey) override; //--------------------------------------- // Method for applying sensors //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_ReduceOrderCoeffs( + STD_REGIONS_EXPORT void v_ReduceOrderCoeffs( int numMin, const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Output interpolation functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_GetSimplexEquiSpacedConnectivity( - Array &conn, bool standard = true); + STD_REGIONS_EXPORT void v_GetSimplexEquiSpacedConnectivity( + Array &conn, bool standard = true) override; private: //--------------------------------------- diff --git a/library/StdRegions/StdTriExp.cpp b/library/StdRegions/StdTriExp.cpp index 7d6274a86583ed616314840741a16ba1e5707f5d..866cc370ca97f98ed654e5a6b109aebeb91417ae 100644 --- a/library/StdRegions/StdTriExp.cpp +++ b/library/StdRegions/StdTriExp.cpp @@ -45,11 +45,6 @@ namespace Nektar { namespace StdRegions { - -StdTriExp::StdTriExp() -{ -} - StdTriExp::StdTriExp(const LibUtilities::BasisKey &Ba, const LibUtilities::BasisKey &Bb) : StdExpansion(LibUtilities::StdTriData::getNumberOfCoefficients( @@ -68,10 +63,6 @@ StdTriExp::StdTriExp(const StdTriExp &T) : StdExpansion(T), StdExpansion2D(T) { } -StdTriExp::~StdTriExp() -{ -} - //------------------------------- // Integration Methods //------------------------------- @@ -739,6 +730,51 @@ NekDouble StdTriExp::v_PhysEvaluateBasis( } } +NekDouble StdTriExp::v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) +{ + // Collapse coordinates + Array coll(2, 0.0); + LocCoordToLocCollapsed(coord, coll); + + // If near singularity do the old interpolation matrix method + if ((1 - coll[1]) < 1e-5) + { + int totPoints = GetTotPoints(); + Array EphysDeriv0(totPoints), EphysDeriv1(totPoints); + PhysDeriv(inarray, EphysDeriv0, EphysDeriv1); + + Array I(2); + I[0] = GetBase()[0]->GetI(coll); + I[1] = GetBase()[1]->GetI(coll + 1); + + firstOrderDerivs[0] = PhysEvaluate(I, EphysDeriv0); + firstOrderDerivs[1] = PhysEvaluate(I, EphysDeriv1); + return PhysEvaluate(I, inarray); + } + + // set up geometric factor: 2.0/(1.0-z1) + NekDouble fac0 = 2 / (1 - coll[1]); + + NekDouble val = BaryTensorDeriv(coll, inarray, firstOrderDerivs); + + // Copy d0 into temp for d1 + NekDouble temp; + temp = firstOrderDerivs[0]; + + // Multiply by geometric factor + firstOrderDerivs[0] = firstOrderDerivs[0] * fac0; + + // set up geometric factor: (1+z0)/(1-z1) + NekDouble fac1 = fac0 * (coll[0] + 1) / 2; + + // Multiply out_d0 by geometric factor and add to out_d1 + firstOrderDerivs[1] += fac1 * temp; + + return val; +} + int StdTriExp::v_GetNverts() const { return 3; diff --git a/library/StdRegions/StdTriExp.h b/library/StdRegions/StdTriExp.h index 1b810b1f06c72a877e851317c24adbbde9d152e5..62b45b0fafd0a11f57e79f952f1abd5274f9d6e9 100644 --- a/library/StdRegions/StdTriExp.h +++ b/library/StdRegions/StdTriExp.h @@ -48,131 +48,140 @@ class StdMatrixKey; class StdTriExp : virtual public StdExpansion2D { public: - STD_REGIONS_EXPORT StdTriExp(); + STD_REGIONS_EXPORT StdTriExp() = default; STD_REGIONS_EXPORT StdTriExp(const LibUtilities::BasisKey &Ba, const LibUtilities::BasisKey &Bb); STD_REGIONS_EXPORT StdTriExp(const StdTriExp &T); - STD_REGIONS_EXPORT ~StdTriExp(); + STD_REGIONS_EXPORT ~StdTriExp() override = default; protected: //------------------------------- // Integration Methods //------------------------------- - STD_REGIONS_EXPORT virtual NekDouble v_Integral( - const Array &inarray); + STD_REGIONS_EXPORT NekDouble + v_Integral(const Array &inarray) override; //---------------------------- // Differentiation Methods //---------------------------- - STD_REGIONS_EXPORT virtual void v_PhysDeriv( + STD_REGIONS_EXPORT void v_PhysDeriv( const Array &inarray, Array &out_d0, Array &out_d1, - Array &out_d2 = NullNekDouble1DArray); - STD_REGIONS_EXPORT virtual void v_PhysDeriv( + Array &out_d2 = NullNekDouble1DArray) override; + STD_REGIONS_EXPORT void v_PhysDeriv( const int dir, const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_StdPhysDeriv( + Array &outarray) override; + STD_REGIONS_EXPORT void v_StdPhysDeriv( const Array &inarray, Array &out_d0, Array &out_d1, - Array &out_d2 = NullNekDouble1DArray); - STD_REGIONS_EXPORT virtual void v_StdPhysDeriv( + Array &out_d2 = NullNekDouble1DArray) override; + STD_REGIONS_EXPORT void v_StdPhysDeriv( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Transforms //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_BwdTrans( + STD_REGIONS_EXPORT void v_BwdTrans( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_BwdTrans_SumFac( + Array &outarray) override; + STD_REGIONS_EXPORT void v_BwdTrans_SumFac( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_BwdTrans_SumFacKernel( + Array &outarray) override; + STD_REGIONS_EXPORT void v_BwdTrans_SumFacKernel( const Array &base0, const Array &base1, const Array &inarray, Array &outarray, Array &wsp, - bool doCheckCollDir0, bool doCheckCollDir1); - STD_REGIONS_EXPORT virtual void v_FwdTrans( + bool doCheckCollDir0, bool doCheckCollDir1) override; + STD_REGIONS_EXPORT void v_FwdTrans( const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_FwdTransBndConstrained( + Array &outarray) override; + STD_REGIONS_EXPORT void v_FwdTransBndConstrained( const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Inner product functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_IProductWRTBase( + STD_REGIONS_EXPORT void v_IProductWRTBase( const Array &inarray, - Array &outarray); + Array &outarray) override; STD_REGIONS_EXPORT virtual void v_IProductWRTBase_MatOp( const Array &inarray, Array &outarray); - STD_REGIONS_EXPORT virtual void v_IProductWRTBase_SumFac( + STD_REGIONS_EXPORT void v_IProductWRTBase_SumFac( const Array &inarray, - Array &outarray, bool multiplybyweights = true); - STD_REGIONS_EXPORT virtual void v_IProductWRTBase_SumFacKernel( + Array &outarray, + bool multiplybyweights = true) override; + STD_REGIONS_EXPORT void v_IProductWRTBase_SumFacKernel( const Array &base0, const Array &base1, const Array &inarray, Array &outarray, Array &wsp, - bool doCheckCollDir0, bool doCheckCollDir1); - STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase( + bool doCheckCollDir0, bool doCheckCollDir1) override; + STD_REGIONS_EXPORT void v_IProductWRTDerivBase( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase_MatOp( const int dir, const Array &inarray, Array &outarray); - STD_REGIONS_EXPORT virtual void v_IProductWRTDerivBase_SumFac( + STD_REGIONS_EXPORT void v_IProductWRTDerivBase_SumFac( const int dir, const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Evaluation functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_LocCoordToLocCollapsed( - const Array &xi, Array &eta); - STD_REGIONS_EXPORT virtual void v_LocCollapsedToLocCoord( - const Array &eta, Array &xi); - STD_REGIONS_EXPORT virtual void v_FillMode( - const int mode, Array &outarray); + STD_REGIONS_EXPORT void v_LocCoordToLocCollapsed( + const Array &xi, + Array &eta) override; + STD_REGIONS_EXPORT void v_LocCollapsedToLocCoord( + const Array &eta, + Array &xi) override; + STD_REGIONS_EXPORT void v_FillMode( + const int mode, Array &outarray) override; STD_REGIONS_EXPORT NekDouble v_PhysEvaluateBasis( const Array &coords, int mode) final; + STD_REGIONS_EXPORT NekDouble + v_PhysEvaluate(const Array &coord, + const Array &inarray, + std::array &firstOrderDerivs) override; + //--------------------------- // Helper functions //--------------------------- - STD_REGIONS_EXPORT virtual int v_GetNverts() const; - STD_REGIONS_EXPORT virtual int v_GetNtraces() const; - STD_REGIONS_EXPORT virtual LibUtilities::ShapeType v_DetShapeType() const; - STD_REGIONS_EXPORT virtual int v_NumBndryCoeffs() const; - STD_REGIONS_EXPORT virtual int v_NumDGBndryCoeffs() const; - STD_REGIONS_EXPORT virtual int v_GetTraceNcoeffs(const int i) const; - STD_REGIONS_EXPORT virtual int v_GetTraceNumPoints(const int i) const; - STD_REGIONS_EXPORT virtual int v_CalcNumberOfCoefficients( - const std::vector &nummodes, int &modes_offset); - STD_REGIONS_EXPORT virtual void v_GetCoords( + STD_REGIONS_EXPORT int v_GetNverts() const override; + STD_REGIONS_EXPORT int v_GetNtraces() const override; + STD_REGIONS_EXPORT LibUtilities::ShapeType v_DetShapeType() const override; + STD_REGIONS_EXPORT int v_NumBndryCoeffs() const override; + STD_REGIONS_EXPORT int v_NumDGBndryCoeffs() const override; + STD_REGIONS_EXPORT int v_GetTraceNcoeffs(const int i) const override; + STD_REGIONS_EXPORT int v_GetTraceNumPoints(const int i) const override; + STD_REGIONS_EXPORT int v_CalcNumberOfCoefficients( + const std::vector &nummodes, int &modes_offset) override; + STD_REGIONS_EXPORT void v_GetCoords( Array &coords_x, Array &coords_y, - Array &coords_z); - STD_REGIONS_EXPORT virtual bool v_IsBoundaryInteriorExpansion(); - STD_REGIONS_EXPORT virtual const LibUtilities::BasisKey v_GetTraceBasisKey( - const int i, const int j) const; + Array &coords_z) override; + STD_REGIONS_EXPORT bool v_IsBoundaryInteriorExpansion() override; + STD_REGIONS_EXPORT const LibUtilities::BasisKey v_GetTraceBasisKey( + const int i, const int j) const override; //-------------------------- // Mappings //-------------------------- - STD_REGIONS_EXPORT virtual int v_GetVertexMap(int localVertexId, - bool useCoeffPacking = false); - STD_REGIONS_EXPORT virtual void v_GetInteriorMap( - Array &outarray); + STD_REGIONS_EXPORT int v_GetVertexMap( + int localVertexId, bool useCoeffPacking = false) override; + STD_REGIONS_EXPORT void v_GetInteriorMap( + Array &outarray) override; - STD_REGIONS_EXPORT virtual void v_GetBoundaryMap( - Array &outarray); + STD_REGIONS_EXPORT void v_GetBoundaryMap( + Array &outarray) override; - STD_REGIONS_EXPORT virtual void v_GetTraceCoeffMap( - const unsigned int traceid, Array &maparray); + STD_REGIONS_EXPORT void v_GetTraceCoeffMap( + const unsigned int traceid, + Array &maparray) override; #if 0 STD_REGIONS_EXPORT virtual void v_GetTraceToElementMap( const int eid, @@ -183,54 +192,55 @@ protected: int Q = -1); #endif - STD_REGIONS_EXPORT virtual void v_GetTraceInteriorToElementMap( + STD_REGIONS_EXPORT void v_GetTraceInteriorToElementMap( const int eid, Array &maparray, - Array &signarray, const Orientation edgeOrient = eForwards); + Array &signarray, + const Orientation edgeOrient = eForwards) override; //--------------------------------------- // Wrapper functions //--------------------------------------- - STD_REGIONS_EXPORT virtual DNekMatSharedPtr v_GenMatrix( - const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual DNekMatSharedPtr v_CreateStdMatrix( - const StdMatrixKey &mkey); + STD_REGIONS_EXPORT DNekMatSharedPtr + v_GenMatrix(const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT DNekMatSharedPtr + v_CreateStdMatrix(const StdMatrixKey &mkey) override; //--------------------------------------- // Operator evaluation functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_MassMatrixOp( + STD_REGIONS_EXPORT void v_MassMatrixOp( const Array &inarray, - Array &outarray, const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual void v_LaplacianMatrixOp( + Array &outarray, const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT void v_LaplacianMatrixOp( const Array &inarray, - Array &outarray, const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual void v_SVVLaplacianFilter( - Array &array, const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual void v_ReduceOrderCoeffs( + Array &outarray, const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT void v_SVVLaplacianFilter( + Array &array, const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT void v_ReduceOrderCoeffs( int numMin, const Array &inarray, - Array &outarray); - STD_REGIONS_EXPORT virtual void v_LaplacianMatrixOp( + Array &outarray) override; + STD_REGIONS_EXPORT void v_LaplacianMatrixOp( const int k1, const int k2, const Array &inarray, - Array &outarray, const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual void v_WeakDerivMatrixOp( + Array &outarray, const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT void v_WeakDerivMatrixOp( const int i, const Array &inarray, - Array &outarray, const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual void v_HelmholtzMatrixOp( + Array &outarray, const StdMatrixKey &mkey) override; + STD_REGIONS_EXPORT void v_HelmholtzMatrixOp( const Array &inarray, - Array &outarray, const StdMatrixKey &mkey); + Array &outarray, const StdMatrixKey &mkey) override; STD_REGIONS_EXPORT virtual void v_GeneralMatrixOp_MatOp( const Array &inarray, Array &outarray, const StdMatrixKey &mkey); - STD_REGIONS_EXPORT virtual void v_MultiplyByStdQuadratureMetric( + STD_REGIONS_EXPORT void v_MultiplyByStdQuadratureMetric( const Array &inarray, - Array &outarray); + Array &outarray) override; //--------------------------------------- // Output interpolation functions //--------------------------------------- - STD_REGIONS_EXPORT virtual void v_GetSimplexEquiSpacedConnectivity( - Array &conn, bool standard = true); + STD_REGIONS_EXPORT void v_GetSimplexEquiSpacedConnectivity( + Array &conn, bool standard = true) override; }; typedef std::shared_ptr StdTriExpSharedPtr; } // namespace StdRegions diff --git a/solvers/ADRSolver/ADRSolver.cpp b/solvers/ADRSolver/ADRSolver.cpp index 06cf83d9ba6858040fd9cccfccc82cae4d4ff76c..d76db275f4ee53741cb44a0ad356eb47cd6f81b7 100644 --- a/solvers/ADRSolver/ADRSolver.cpp +++ b/solvers/ADRSolver/ADRSolver.cpp @@ -77,7 +77,10 @@ int main(int argc, char *argv[]) // Print out timings if verbose if (session->DefinesCmdLineArgument("verbose")) { - LibUtilities::Timer::PrintElapsedRegions(session->GetComm()); + int iolevel; + session->LoadParameter("IO_Timer_Level", iolevel, 1); + LibUtilities::Timer::PrintElapsedRegions(session->GetComm(), + std::cout, iolevel); } LIKWID_MARKER_CLOSE; diff --git a/solvers/ADRSolver/CMakeLists.txt b/solvers/ADRSolver/CMakeLists.txt index a4cbab98016815f541297e1e5d2c142f91670c82..4934ab8028e48e6d9fc62ebb3ca506ce82060f5b 100644 --- a/solvers/ADRSolver/CMakeLists.txt +++ b/solvers/ADRSolver/CMakeLists.txt @@ -221,6 +221,15 @@ IF( NEKTAR_SOLVER_ADR ) ADD_NEKTAR_TEST(SVV_Prism) ADD_NEKTAR_TEST(SVV_Tet) + # Movement tests + ADD_NEKTAR_TEST(Movement_fixed_interfaces232_dirichlet) + ADD_NEKTAR_TEST(Movement_fixed_interfaces232_periodic) + ADD_NEKTAR_TEST(Movement_fixed_3D_Hex41) + ADD_NEKTAR_TEST(Movement_fixed_2D_curved_quads) + ADD_NEKTAR_TEST(Movement_fixed_2D_varied) + ADD_NEKTAR_TEST(Movement_fixed_3D_stacked_cylinders_curved) + ADD_NEKTAR_TEST(Movement_translate_interfaces232_dirichlet) + IF (NEKTAR_USE_FFTW) ADD_NEKTAR_TEST(Helmholtz_3DHomo1D_FFT) ADD_NEKTAR_TEST(Helmholtz_3DHomo2D_FFT) @@ -258,8 +267,17 @@ IF( NEKTAR_SOLVER_ADR ) ADD_NEKTAR_TEST(Advection2D_m12_DG_quad_VarP_par) ADD_NEKTAR_TEST(Advection2D_m12_DG_tri_VarP_par) ADD_NEKTAR_TEST(Advection2D_dirichlet_regular_GAUSS_LAGRANGE_10x10_MF_par) + ADD_NEKTAR_TEST(Movement_fixed_interfaces232_periodic_par) + ADD_NEKTAR_TEST(Movement_fixed_3D_Hex41_par) + ADD_NEKTAR_TEST(Movement_fixed_3D_Hex_3zones_Periodic_par) + ADD_NEKTAR_TEST(Movement_fixed_2D_varied_par) + ADD_NEKTAR_TEST(Movement_fixed_3D_stacked_cylinders_curved_par) + ADD_NEKTAR_TEST(Movement_rotate_3D_stacked_cylinders_curved_par) + ADD_NEKTAR_TEST(Movement_translate_interfaces232_dirichlet_par) IF (NEKTAR_USE_HDF5) ADD_NEKTAR_TEST(Advection3D_m10_DG_prism_VarP_hdf) + ADD_NEKTAR_TEST(Movement_fixed_3D_stacked_cylinders_curved_hdf5) + ADD_NEKTAR_TEST(Movement_fixed_3D_stacked_cylinders_curved_hdf5_par) ENDIF() ADD_NEKTAR_TEST(RotPerBcs3D_Annulus LENGTHY) ADD_NEKTAR_TEST(UnsteadyAdvection_WDG_3DHomo1D_MVM_NPZ) diff --git a/solvers/ADRSolver/EquationSystems/UnsteadyAdvection.cpp b/solvers/ADRSolver/EquationSystems/UnsteadyAdvection.cpp index adbd3a8b9a5dd61e8eff63c4115fb6e921fff776..6c3e535d67f315de38a52def0a02ac5971c7a151 100644 --- a/solvers/ADRSolver/EquationSystems/UnsteadyAdvection.cpp +++ b/solvers/ADRSolver/EquationSystems/UnsteadyAdvection.cpp @@ -49,9 +49,9 @@ string UnsteadyAdvection::className = UnsteadyAdvection::UnsteadyAdvection( const LibUtilities::SessionReaderSharedPtr &pSession, const SpatialDomains::MeshGraphSharedPtr &pGraph) - : UnsteadySystem(pSession, pGraph), AdvectionSystem(pSession, pGraph) + : UnsteadySystem(pSession, pGraph), AdvectionSystem(pSession, pGraph), + m_planeNumber(0) { - m_planeNumber = 0; } /** @@ -76,9 +76,9 @@ void UnsteadyAdvection::v_InitObject(bool DeclareFields) m_session->LoadParameter("GJPJumpScale", m_GJPJumpScale, 1.0); std::vector vel; - vel.push_back("Vx"); - vel.push_back("Vy"); - vel.push_back("Vz"); + vel.emplace_back("Vx"); + vel.emplace_back("Vy"); + vel.emplace_back("Vz"); // Resize the advection velocities vector to dimension of the problem vel.resize(m_spacedim); @@ -144,7 +144,6 @@ void UnsteadyAdvection::v_InitObject(bool DeclareFields) riemName, m_session); m_riemannSolver->SetScalar( "Vn", &UnsteadyAdvection::GetNormalVelocity, this); - m_advObject->SetRiemannSolver(m_riemannSolver); m_advObject->InitObject(m_session, m_fields); break; @@ -173,13 +172,6 @@ void UnsteadyAdvection::v_InitObject(bool DeclareFields) } } -/** - * @brief Unsteady linear advection equation destructor. - */ -UnsteadyAdvection::~UnsteadyAdvection() -{ -} - /** * @brief Get the normal velocity for the linear advection equation. */ @@ -188,18 +180,22 @@ Array &UnsteadyAdvection::GetNormalVelocity() // Number of trace (interface) points int i; int nTracePts = GetTraceNpoints(); + int nPts = m_velocity[0].size(); // Auxiliary variable to compute the normal velocity - Array tmp(nTracePts); + Array tmp(nPts), tmp2(nTracePts); // Reset the normal velocity Vmath::Zero(nTracePts, m_traceVn, 1); for (i = 0; i < m_velocity.size(); ++i) { - m_fields[0]->ExtractTracePhys(m_velocity[i], tmp); + // velocity - grid velocity for ALE before getting trace velocity + Vmath::Vsub(nPts, m_velocity[i], 1, m_gridVelocity[i], 1, tmp, 1); + + m_fields[0]->ExtractTracePhys(tmp, tmp2); - Vmath::Vvtvp(nTracePts, m_traceNormals[i], 1, tmp, 1, m_traceVn, 1, + Vmath::Vvtvp(nTracePts, m_traceNormals[i], 1, tmp2, 1, m_traceVn, 1, m_traceVn, 1); } @@ -217,28 +213,35 @@ void UnsteadyAdvection::DoOdeRhs( const Array> &inarray, Array> &outarray, const NekDouble time) { - // Counter variable - int i; - // Number of fields (variables of the problem) int nVariables = inarray.size(); - // Number of solution points - int nSolutionPts = GetNpoints(); - LibUtilities::Timer timer; - timer.Start(); - // RHS computation using the new advection base class - m_advObject->Advect(nVariables, m_fields, m_velocity, inarray, outarray, - time); - timer.Stop(); + if (m_ALESolver) + { + timer.Start(); + Array> tmpIn(nVariables); + // If ALE we must take Mu coefficient space to u physical space + ALEHelper::ALEDoElmtInvMassBwdTrans(inarray, tmpIn); + m_advObject->AdvectCoeffs(nVariables, m_fields, m_velocity, tmpIn, + outarray, time); + timer.Stop(); + } + else + { + timer.Start(); + m_advObject->Advect(nVariables, m_fields, m_velocity, inarray, outarray, + time); + timer.Stop(); + } + // Elapsed time timer.AccumulateRegion("Advect"); // Negate the RHS - for (i = 0; i < nVariables; ++i) + for (int i = 0; i < nVariables; ++i) { - Vmath::Neg(nSolutionPts, outarray[i], 1); + Vmath::Neg(outarray[i].size(), outarray[i], 1); } for (auto &x : m_forcing) @@ -265,6 +268,12 @@ void UnsteadyAdvection::DoOdeProjection( // Number of fields (variables of the problem) int nVariables = inarray.size(); + // Perform ALE movement + if (m_ALESolver) + { + MoveMesh(time, m_traceNormals); + } + // Set the boundary conditions SetBoundaryConditions(time); @@ -274,13 +283,10 @@ void UnsteadyAdvection::DoOdeProjection( // Discontinuous projection case MultiRegions::eDiscontinuous: { - // Number of quadrature points - int nQuadraturePts = GetNpoints(); - // Just copy over array for (i = 0; i < nVariables; ++i) { - Vmath::Vcopy(nQuadraturePts, inarray[i], 1, outarray[i], 1); + Vmath::Vcopy(inarray[i].size(), inarray[i], 1, outarray[i], 1); } break; } @@ -374,7 +380,12 @@ void UnsteadyAdvection::GetFluxVector( { for (j = 0; j < flux[0].size(); ++j) { - Vmath::Vmul(nq, physfield[i], 1, m_velocity[j], 1, flux[i][j], 1); + for (int k = 0; k < nq; ++k) + { + // If ALE we need to take off the grid velocity + flux[i][j][k] = + physfield[i][k] * (m_velocity[j][k] - m_gridVelocity[j][k]); + } } } } @@ -466,4 +477,33 @@ void UnsteadyAdvection::v_GenerateSummary(SolverUtils::SummaryList &s) SolverUtils::AddSummaryItem(s, "GJP Stab. JumpScale", m_GJPJumpScale); } } + +bool UnsteadyAdvection::v_PreIntegrate(int step) +{ + boost::ignore_unused(step); + return false; +} + +void UnsteadyAdvection::v_ExtraFldOutput( + std::vector> &fieldcoeffs, + std::vector &variables) +{ + bool extraFields; + m_session->MatchSolverInfo("OutputExtraFields", "True", extraFields, true); + + if (extraFields && m_ALESolver) + { + int nCoeffs = m_fields[0]->GetNcoeffs(); + + // Adds extra output variables for grid velocity + std::string gridVarName[3] = {"gridVx", "gridVy", "gridVz"}; + for (int i = 0; i < m_spacedim; ++i) + { + Array gridVel(nCoeffs, 0.0); + m_fields[0]->FwdTransLocalElmt(m_gridVelocity[i], gridVel); + fieldcoeffs.emplace_back(gridVel); + variables.emplace_back(gridVarName[i]); + } + } +} } // namespace Nektar diff --git a/solvers/ADRSolver/EquationSystems/UnsteadyAdvection.h b/solvers/ADRSolver/EquationSystems/UnsteadyAdvection.h index 62b5a33ee9aba3d0d08269ac56500b8490ad8693..570a2c5e68c6cce649b333e7c31b5fabda028e2b 100644 --- a/solvers/ADRSolver/EquationSystems/UnsteadyAdvection.h +++ b/solvers/ADRSolver/EquationSystems/UnsteadyAdvection.h @@ -62,7 +62,7 @@ public: static std::string className; /// Destructor - virtual ~UnsteadyAdvection(); + ~UnsteadyAdvection() final = default; protected: bool m_useGJPStabilisation; @@ -113,6 +113,12 @@ protected: /// Print Summary virtual void v_GenerateSummary(SolverUtils::SummaryList &s); + bool v_PreIntegrate(int step) final; + + virtual void v_ExtraFldOutput( + std::vector> &fieldcoeffs, + std::vector &variables); + private: NekDouble m_waveFreq; }; diff --git a/solvers/ADRSolver/EquationSystems/UnsteadyAdvectionDiffusion.cpp b/solvers/ADRSolver/EquationSystems/UnsteadyAdvectionDiffusion.cpp index bbc97dd4a44a5976e43b8153b9d8842fd693e1d5..15702a1f6414c8680d595f7a31aedac7b6ec5a76 100644 --- a/solvers/ADRSolver/EquationSystems/UnsteadyAdvectionDiffusion.cpp +++ b/solvers/ADRSolver/EquationSystems/UnsteadyAdvectionDiffusion.cpp @@ -45,7 +45,8 @@ using namespace LibUtilities; std::string UnsteadyAdvectionDiffusion::className = SolverUtils::GetEquationSystemFactory().RegisterCreatorFunction( - "UnsteadyAdvectionDiffusion", UnsteadyAdvectionDiffusion::create); + "UnsteadyAdvectionDiffusion", UnsteadyAdvectionDiffusion::create, + "Unsteady Advection-Diffusion equation."); UnsteadyAdvectionDiffusion::UnsteadyAdvectionDiffusion( const LibUtilities::SessionReaderSharedPtr &pSession, @@ -64,7 +65,7 @@ void UnsteadyAdvectionDiffusion::v_InitObject(bool DeclareFields) AdvectionSystem::v_InitObject(DeclareFields); m_session->LoadParameter("wavefreq", m_waveFreq, 0.0); - m_session->LoadParameter("epsilon", m_epsilon, 1.0); + m_session->LoadParameter("epsilon", m_epsilon, 1.0); // Diffusion // turn on substepping m_session->MatchSolverInfo("Extrapolation", "SubStepping", @@ -108,6 +109,12 @@ void UnsteadyAdvectionDiffusion::v_InitObject(bool DeclareFields) // Do not forwards transform initial condition m_homoInitialFwd = false; + // Define the normal velocity fields + if (m_fields[0]->GetTrace()) + { + m_traceVn = Array(GetTraceNpoints()); + } + // Advection term std::string advName; std::string riemName; @@ -200,13 +207,6 @@ void UnsteadyAdvectionDiffusion::v_InitObject(bool DeclareFields) } } -/** - * @brief Unsteady linear advection diffusion equation destructor. - */ -UnsteadyAdvectionDiffusion::~UnsteadyAdvectionDiffusion() -{ -} - /** * @brief Get the normal velocity for the unsteady linear advection * diffusion equation. @@ -222,19 +222,23 @@ Array &UnsteadyAdvectionDiffusion::GetNormalVel( // Number of trace (interface) points int i; int nTracePts = GetTraceNpoints(); + int nPts = velfield[0].size(); // Auxiliary variable to compute the normal velocity - Array tmp(nTracePts); - m_traceVn = Array(nTracePts, 0.0); + Array tmp(nPts), tmp2(nTracePts); // Reset the normal velocity Vmath::Zero(nTracePts, m_traceVn, 1); for (i = 0; i < velfield.size(); ++i) { - m_fields[0]->ExtractTracePhys(velfield[i], tmp); + // Subtract grid velocity here from velocity + // velocity - grid velocity + Vmath::Vsub(nPts, velfield[i], 1, m_gridVelocity[i], 1, tmp, 1); - Vmath::Vvtvp(nTracePts, m_traceNormals[i], 1, tmp, 1, m_traceVn, 1, + m_fields[0]->ExtractTracePhys(tmp, tmp2); + + Vmath::Vvtvp(nTracePts, m_traceNormals[i], 1, tmp2, 1, m_traceVn, 1, m_traceVn, 1); } @@ -256,17 +260,25 @@ void UnsteadyAdvectionDiffusion::DoOdeRhs( // Number of fields (variables of the problem) int nVariables = inarray.size(); - // Number of solution points - int nSolutionPts = GetNpoints(); - - // RHS computation using the new advection base class - m_advObject->Advect(nVariables, m_fields, m_velocity, inarray, outarray, - time); + Array> tmpIn(nVariables); + if (m_ALESolver) + { + ALEHelper::ALEDoElmtInvMassBwdTrans(inarray, tmpIn); + m_advObject->AdvectCoeffs(nVariables, m_fields, m_velocity, tmpIn, + outarray, time); + } + else + { + tmpIn = inarray; // If not ALE then we pass through inarray + // RHS computation using the new advection base class + m_advObject->Advect(nVariables, m_fields, m_velocity, inarray, outarray, + time); + } // Negate the RHS for (int i = 0; i < nVariables; ++i) { - Vmath::Neg(nSolutionPts, outarray[i], 1); + Vmath::Neg(outarray[i].size(), outarray[i], 1); } if (m_explicitDiffusion) @@ -274,15 +286,23 @@ void UnsteadyAdvectionDiffusion::DoOdeRhs( Array> outarrayDiff(nVariables); for (int i = 0; i < nVariables; ++i) { - outarrayDiff[i] = Array(nSolutionPts, 0.0); + outarrayDiff[i] = Array(outarray[i].size(), 0.0); } - m_diffusion->Diffuse(nVariables, m_fields, inarray, outarrayDiff); + if (m_ALESolver) + { + m_diffusion->DiffuseCoeffs(nVariables, m_fields, tmpIn, + outarrayDiff); // Using tmpIn from above + } + else + { + m_diffusion->Diffuse(nVariables, m_fields, inarray, outarrayDiff); + } for (int i = 0; i < nVariables; ++i) { - Vmath::Vadd(nSolutionPts, &outarrayDiff[i][0], 1, &outarray[i][0], - 1, &outarray[i][0], 1); + Vmath::Vadd(outarray[i].size(), &outarrayDiff[i][0], 1, + &outarray[i][0], 1, &outarray[i][0], 1); } } @@ -306,19 +326,23 @@ void UnsteadyAdvectionDiffusion::DoOdeProjection( const Array> &inarray, Array> &outarray, const NekDouble time) { - int i; int nvariables = inarray.size(); + + // Perform ALE movement + if (m_ALESolver) + { + MoveMesh(time, m_traceNormals); + } + SetBoundaryConditions(time); + switch (m_projectionType) { case MultiRegions::eDiscontinuous: { - // Just copy over array - int npoints = GetNpoints(); - - for (i = 0; i < nvariables; ++i) + for (int i = 0; i < nvariables; ++i) { - Vmath::Vcopy(npoints, inarray[i], 1, outarray[i], 1); + Vmath::Vcopy(inarray[i].size(), inarray[i], 1, outarray[i], 1); } break; } @@ -327,7 +351,7 @@ void UnsteadyAdvectionDiffusion::DoOdeProjection( { Array coeffs(m_fields[0]->GetNcoeffs()); - for (i = 0; i < nvariables; ++i) + for (int i = 0; i < nvariables; ++i) { m_fields[i]->FwdTrans(inarray[i], coeffs); m_fields[i]->BwdTrans(coeffs, outarray[i]); @@ -424,7 +448,13 @@ void UnsteadyAdvectionDiffusion::GetFluxVectorAdv( { for (int j = 0; j < flux[0].size(); ++j) { - Vmath::Vmul(nq, physfield[i], 1, m_velocity[j], 1, flux[i][j], 1); + + for (int k = 0; k < nq; ++k) + { + // If ALE we need to take off the grid velocity + flux[i][j][k] = + physfield[i][k] * (m_velocity[j][k] - m_gridVelocity[j][k]); + } } } } @@ -470,6 +500,29 @@ void UnsteadyAdvectionDiffusion::v_GenerateSummary(SolverUtils::SummaryList &s) } } +void UnsteadyAdvectionDiffusion::v_ExtraFldOutput( + std::vector> &fieldcoeffs, + std::vector &variables) +{ + bool extraFields; + m_session->MatchSolverInfo("OutputExtraFields", "True", extraFields, true); + + if (extraFields && m_ALESolver) + { + int nCoeffs = m_fields[0]->GetNcoeffs(); + + // Adds extra output variables for grid velocity + std::string gridVarName[3] = {"gridVx", "gridVy", "gridVz"}; + for (int i = 0; i < m_spacedim; ++i) + { + Array gridVel(nCoeffs, 0.0); + m_fields[0]->FwdTransLocalElmt(m_gridVelocity[i], gridVel); + fieldcoeffs.emplace_back(gridVel); + variables.emplace_back(gridVarName[i]); + } + } +} + /** * Perform the extrapolation. */ diff --git a/solvers/ADRSolver/EquationSystems/UnsteadyAdvectionDiffusion.h b/solvers/ADRSolver/EquationSystems/UnsteadyAdvectionDiffusion.h index 8d45f713543107493bad8ff405b9b45f7969c277..81f31856fa46c35b762b797b6a056af57f3fe4ed 100644 --- a/solvers/ADRSolver/EquationSystems/UnsteadyAdvectionDiffusion.h +++ b/solvers/ADRSolver/EquationSystems/UnsteadyAdvectionDiffusion.h @@ -63,7 +63,7 @@ public: static std::string className; /// Destructor - virtual ~UnsteadyAdvectionDiffusion(); + ~UnsteadyAdvectionDiffusion() final = default; protected: bool m_subSteppingScheme; @@ -134,6 +134,10 @@ protected: /// PreIntegration step for substepping. virtual bool v_PreIntegrate(int step); + virtual void v_ExtraFldOutput( + std::vector> &fieldcoeffs, + std::vector &variables); + // SubsStepping methods -> Probably could be set up in separate class void SubStepAdvance(int nstep, NekDouble time); NekDouble GetSubstepTimeStep(); diff --git a/solvers/ADRSolver/Tests/Movement_fixed_2D_curved_quads.tst b/solvers/ADRSolver/Tests/Movement_fixed_2D_curved_quads.tst new file mode 100644 index 0000000000000000000000000000000000000000..36387dd6c914833448f7cf6ac5bf3e7444fc36d5 --- /dev/null +++ b/solvers/ADRSolver/Tests/Movement_fixed_2D_curved_quads.tst @@ -0,0 +1,19 @@ + + + 2D advection with 2 zones and 1 non-conformal curved interfaces with dirichlet BCs on quads + ADRSolver + Movement_fixed_2D_curved_quads.xml + + Movement_fixed_2D_curved_quads.xml + + + + 1.31573e-05 + + + 9.84901e-05 + + + + + diff --git a/solvers/ADRSolver/Tests/Movement_fixed_2D_curved_quads.xml b/solvers/ADRSolver/Tests/Movement_fixed_2D_curved_quads.xml new file mode 100644 index 0000000000000000000000000000000000000000..ad4a1e12fe1350b301b96c858b41a96735f8aab5 --- /dev/null +++ b/solvers/ADRSolver/Tests/Movement_fixed_2D_curved_quads.xml @@ -0,0 +1,390 @@ + + + + + 0.00000000e+00 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7.78819778e-01 4.95899644e-01 0.00000000e+00 8.09719909e-01 6.63992824e-01 0.00000000e+00 8.08773827e-01 6.36065428e-01 0.00000000e+00 8.07827745e-01 6.08138032e-01 0.00000000e+00 8.06881663e-01 5.80210636e-01 0.00000000e+00 8.05935581e-01 5.52283240e-01 0.00000000e+00 8.04989499e-01 5.24355843e-01 0.00000000e+00 8.04043417e-01 4.96428447e-01 0.00000000e+00 8.33970380e-01 6.64361160e-01 0.00000000e+00 8.33186492e-01 6.36460508e-01 0.00000000e+00 8.32402605e-01 6.08559857e-01 0.00000000e+00 8.31618717e-01 5.80659205e-01 0.00000000e+00 8.30834830e-01 5.52758553e-01 0.00000000e+00 8.30050943e-01 5.24857902e-01 0.00000000e+00 8.29267055e-01 4.96957250e-01 0.00000000e+00 8.58220850e-01 6.64729496e-01 0.00000000e+00 8.57599157e-01 6.36855589e-01 0.00000000e+00 8.56977465e-01 6.08981682e-01 0.00000000e+00 8.56355772e-01 5.81107774e-01 0.00000000e+00 8.55734079e-01 5.53233867e-01 0.00000000e+00 8.55112387e-01 5.25359960e-01 0.00000000e+00 8.54490694e-01 4.97486053e-01 0.00000000e+00 + + + E[8-11] + E[6-7,22-25] + E[0-1,12-15,32] + E[2-5] + E[26-31] + E[16-21] + Q[0-7] + Q[8-31] + + + C[409] + C[410] + + + + + + 12e49d1fdba69f4059fb63283125517d696b13c2 + Edwards-MacBook-Pro.local + 5.0.0 + 18-Jan-2021 11:52:31 + + basic.msh basic.xml:xml:uncompress + + + + + + + + + + + + + + + + + + + + + +

FinTime = 1

+

TimeStep = 0.001

+

NumSteps = FinTime/TimeStep

+

IO_CheckSteps = 9999

+

IO_InfoSteps = 100

+

advx = 1

+

advy = 0

+

k = 2*PI

+ + + + + + + + + + + + + u + + + + C[401] + C[407] + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/solvers/ADRSolver/Tests/Movement_fixed_2D_varied.tst b/solvers/ADRSolver/Tests/Movement_fixed_2D_varied.tst new file mode 100644 index 0000000000000000000000000000000000000000..fc0ea9bc7ed1ad752166b1a3fab287179dac89bf --- /dev/null +++ b/solvers/ADRSolver/Tests/Movement_fixed_2D_varied.tst @@ -0,0 +1,21 @@ + + + 2D advection with 3 zones and 2 non-conformal interfaces (one curved) with 2 fields + ADRSolver + Movement_fixed_2D_varied.xml + + Movement_fixed_2D_varied.xml + + + + 3.98672e-06 + 2.70806e-06 + + + 6.90779e-05 + 1.78188e-05 + + + + + diff --git a/solvers/ADRSolver/Tests/Movement_fixed_2D_varied.xml b/solvers/ADRSolver/Tests/Movement_fixed_2D_varied.xml new file mode 100644 index 0000000000000000000000000000000000000000..92ac096d9dadb8530585178b1e3506f9ff22743d --- /dev/null +++ b/solvers/ADRSolver/Tests/Movement_fixed_2D_varied.xml @@ -0,0 +1,415 @@ + + + + + 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0.00000000e+00 7.52443301e-01 8.31384039e-01 0.00000000e+00 7.75099526e-01 8.31568703e-01 0.00000000e+00 7.97755750e-01 8.31753367e-01 0.00000000e+00 8.20411975e-01 8.31938031e-01 0.00000000e+00 8.43068200e-01 8.32122695e-01 0.00000000e+00 8.65724424e-01 8.32307359e-01 0.00000000e+00 + 8.65724424e-01 8.32307359e-01 0.00000000e+00 8.88103687e-01 8.32478355e-01 0.00000000e+00 9.10482949e-01 8.32649350e-01 0.00000000e+00 9.32862212e-01 8.32820346e-01 0.00000000e+00 9.55241475e-01 8.32991342e-01 0.00000000e+00 9.77620737e-01 8.33162338e-01 0.00000000e+00 1.00000000e+00 8.33333333e-01 0.00000000e+00 + 1.00000000e+00 8.33333333e-01 0.00000000e+00 1.00000000e+00 8.61111111e-01 0.00000000e+00 1.00000000e+00 8.88888889e-01 0.00000000e+00 1.00000000e+00 9.16666667e-01 0.00000000e+00 1.00000000e+00 9.44444444e-01 0.00000000e+00 1.00000000e+00 9.72222222e-01 0.00000000e+00 1.00000000e+00 1.00000000e+00 0.00000000e+00 + 7.12718028e-01 6.62519481e-01 0.00000000e+00 7.36968498e-01 6.62887817e-01 0.00000000e+00 7.61218968e-01 6.63256153e-01 0.00000000e+00 7.85469439e-01 6.63624489e-01 0.00000000e+00 8.09719909e-01 6.63992824e-01 0.00000000e+00 8.33970380e-01 6.64361160e-01 0.00000000e+00 8.58220850e-01 6.64729496e-01 0.00000000e+00 + 8.58220850e-01 6.64729496e-01 0.00000000e+00 8.59471446e-01 6.92659140e-01 0.00000000e+00 8.60722041e-01 7.20588784e-01 0.00000000e+00 8.61972637e-01 7.48518427e-01 0.00000000e+00 8.63223233e-01 7.76448071e-01 0.00000000e+00 8.64473828e-01 8.04377715e-01 0.00000000e+00 8.65724424e-01 8.32307359e-01 0.00000000e+00 + 1.00000000e+00 6.66666667e-01 0.00000000e+00 1.00000000e+00 6.94444444e-01 0.00000000e+00 1.00000000e+00 7.22222222e-01 0.00000000e+00 1.00000000e+00 7.50000000e-01 0.00000000e+00 1.00000000e+00 7.77777778e-01 0.00000000e+00 1.00000000e+00 8.05555556e-01 0.00000000e+00 1.00000000e+00 8.33333333e-01 0.00000000e+00 + 8.58220850e-01 6.64729496e-01 0.00000000e+00 8.81850708e-01 6.65052358e-01 0.00000000e+00 9.05480567e-01 6.65375219e-01 0.00000000e+00 9.29110425e-01 6.65698081e-01 0.00000000e+00 9.52740283e-01 6.66020943e-01 0.00000000e+00 9.76370142e-01 6.66343805e-01 0.00000000e+00 1.00000000e+00 6.66666667e-01 0.00000000e+00 + 1.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00 2.77777778e-02 0.00000000e+00 1.00000000e+00 5.55555556e-02 0.00000000e+00 1.00000000e+00 8.33333333e-02 0.00000000e+00 1.00000000e+00 1.11111111e-01 0.00000000e+00 1.00000000e+00 1.38888889e-01 0.00000000e+00 1.00000000e+00 1.66666667e-01 0.00000000e+00 + 1.00000000e+00 1.66666667e-01 0.00000000e+00 9.77291152e-01 1.66411458e-01 0.00000000e+00 9.54582303e-01 1.66156250e-01 0.00000000e+00 9.31873455e-01 1.65901041e-01 0.00000000e+00 9.09164607e-01 1.65645833e-01 0.00000000e+00 8.86455758e-01 1.65390624e-01 0.00000000e+00 8.63746910e-01 1.65135416e-01 0.00000000e+00 + 7.23228643e-01 1.62816229e-01 0.00000000e+00 7.46648354e-01 1.63202760e-01 0.00000000e+00 7.70068065e-01 1.63589291e-01 0.00000000e+00 7.93487776e-01 1.63975822e-01 0.00000000e+00 8.16907487e-01 1.64362353e-01 0.00000000e+00 8.40327199e-01 1.64748885e-01 0.00000000e+00 8.63746910e-01 1.65135416e-01 0.00000000e+00 + 8.63746910e-01 1.65135416e-01 0.00000000e+00 8.65622425e-01 1.37612846e-01 0.00000000e+00 8.67497940e-01 1.10090277e-01 0.00000000e+00 8.69373455e-01 8.25677079e-02 0.00000000e+00 8.71248970e-01 5.50451386e-02 0.00000000e+00 8.73124485e-01 2.75225693e-02 0.00000000e+00 8.75000000e-01 0.00000000e+00 0.00000000e+00 + 8.75000000e-01 0.00000000e+00 0.00000000e+00 8.95833333e-01 0.00000000e+00 0.00000000e+00 9.16666667e-01 0.00000000e+00 0.00000000e+00 9.37500000e-01 0.00000000e+00 0.00000000e+00 9.58333333e-01 0.00000000e+00 0.00000000e+00 9.79166667e-01 0.00000000e+00 0.00000000e+00 1.00000000e+00 0.00000000e+00 0.00000000e+00 + 7.50000000e-01 0.00000000e+00 0.00000000e+00 7.70833333e-01 0.00000000e+00 0.00000000e+00 7.91666667e-01 0.00000000e+00 0.00000000e+00 8.12500000e-01 0.00000000e+00 0.00000000e+00 8.33333333e-01 0.00000000e+00 0.00000000e+00 8.54166667e-01 0.00000000e+00 0.00000000e+00 8.75000000e-01 0.00000000e+00 0.00000000e+00 + 8.56214575e-01 3.30889246e-01 0.00000000e+00 8.57469965e-01 3.03263607e-01 0.00000000e+00 8.58725354e-01 2.75637969e-01 0.00000000e+00 8.59980743e-01 2.48012331e-01 0.00000000e+00 8.61236132e-01 2.20386692e-01 0.00000000e+00 8.62491521e-01 1.92761054e-01 0.00000000e+00 8.63746910e-01 1.65135416e-01 0.00000000e+00 + 8.56214575e-01 3.30889246e-01 0.00000000e+00 8.31162290e-01 3.30315135e-01 0.00000000e+00 8.06110004e-01 3.29741024e-01 0.00000000e+00 7.81057718e-01 3.29166914e-01 0.00000000e+00 7.56005432e-01 3.28592803e-01 0.00000000e+00 7.30953146e-01 3.28018692e-01 0.00000000e+00 7.05900860e-01 3.27444582e-01 0.00000000e+00 + 1.00000000e+00 1.66666667e-01 0.00000000e+00 1.00000000e+00 1.94444444e-01 0.00000000e+00 1.00000000e+00 2.22222222e-01 0.00000000e+00 1.00000000e+00 2.50000000e-01 0.00000000e+00 1.00000000e+00 2.77777778e-01 0.00000000e+00 1.00000000e+00 3.05555556e-01 0.00000000e+00 1.00000000e+00 3.33333333e-01 0.00000000e+00 + 8.56214575e-01 3.30889246e-01 0.00000000e+00 8.55927262e-01 3.58655380e-01 0.00000000e+00 8.55639948e-01 3.86421515e-01 0.00000000e+00 8.55352635e-01 4.14187649e-01 0.00000000e+00 8.55065321e-01 4.41953784e-01 0.00000000e+00 8.54778008e-01 4.69719918e-01 0.00000000e+00 8.54490694e-01 4.97486053e-01 0.00000000e+00 + 8.54490694e-01 4.97486053e-01 0.00000000e+00 8.29267055e-01 4.96957250e-01 0.00000000e+00 8.04043417e-01 4.96428447e-01 0.00000000e+00 7.78819778e-01 4.95899644e-01 0.00000000e+00 7.53596139e-01 4.95370842e-01 0.00000000e+00 7.28372501e-01 4.94842039e-01 0.00000000e+00 7.03148862e-01 4.94313236e-01 0.00000000e+00 + 8.58220850e-01 6.64729496e-01 0.00000000e+00 8.57599157e-01 6.36855589e-01 0.00000000e+00 8.56977465e-01 6.08981682e-01 0.00000000e+00 8.56355772e-01 5.81107774e-01 0.00000000e+00 8.55734079e-01 5.53233867e-01 0.00000000e+00 8.55112387e-01 5.25359960e-01 0.00000000e+00 8.54490694e-01 4.97486053e-01 0.00000000e+00 + 1.00000000e+00 3.33333333e-01 0.00000000e+00 1.00000000e+00 3.61111111e-01 0.00000000e+00 1.00000000e+00 3.88888889e-01 0.00000000e+00 1.00000000e+00 4.16666667e-01 0.00000000e+00 1.00000000e+00 4.44444444e-01 0.00000000e+00 1.00000000e+00 4.72222222e-01 0.00000000e+00 1.00000000e+00 5.00000000e-01 0.00000000e+00 + 1.00000000e+00 5.00000000e-01 0.00000000e+00 9.75748449e-01 4.99581009e-01 0.00000000e+00 9.51496898e-01 4.99162018e-01 0.00000000e+00 9.27245347e-01 4.98743026e-01 0.00000000e+00 9.02993796e-01 4.98324035e-01 0.00000000e+00 8.78742245e-01 4.97905044e-01 0.00000000e+00 8.54490694e-01 4.97486053e-01 0.00000000e+00 + 1.00000000e+00 5.00000000e-01 0.00000000e+00 1.00000000e+00 5.27777778e-01 0.00000000e+00 1.00000000e+00 5.55555556e-01 0.00000000e+00 1.00000000e+00 5.83333333e-01 0.00000000e+00 1.00000000e+00 6.11111111e-01 0.00000000e+00 1.00000000e+00 6.38888889e-01 0.00000000e+00 1.00000000e+00 6.66666667e-01 0.00000000e+00 + 1.00000000e+00 0.00000000e+00 0.00000000e+00 1.04166667e+00 0.00000000e+00 0.00000000e+00 1.08333333e+00 0.00000000e+00 0.00000000e+00 1.12500000e+00 0.00000000e+00 0.00000000e+00 1.16666667e+00 0.00000000e+00 0.00000000e+00 1.20833333e+00 0.00000000e+00 0.00000000e+00 1.25000000e+00 0.00000000e+00 0.00000000e+00 + 1.25000000e+00 0.00000000e+00 0.00000000e+00 1.25000000e+00 8.33333333e-02 0.00000000e+00 1.25000000e+00 1.66666667e-01 0.00000000e+00 1.25000000e+00 2.50000000e-01 0.00000000e+00 1.25000000e+00 3.33333333e-01 0.00000000e+00 1.25000000e+00 4.16666667e-01 0.00000000e+00 1.25000000e+00 5.00000000e-01 0.00000000e+00 + 1.25000000e+00 5.00000000e-01 0.00000000e+00 1.20833333e+00 5.00000000e-01 0.00000000e+00 1.16666667e+00 5.00000000e-01 0.00000000e+00 1.12500000e+00 5.00000000e-01 0.00000000e+00 1.08333333e+00 5.00000000e-01 0.00000000e+00 1.04166667e+00 5.00000000e-01 0.00000000e+00 1.00000000e+00 5.00000000e-01 0.00000000e+00 + 1.00000000e+00 5.00000000e-01 0.00000000e+00 1.00000000e+00 4.16666667e-01 0.00000000e+00 1.00000000e+00 3.33333333e-01 0.00000000e+00 1.00000000e+00 2.50000000e-01 0.00000000e+00 1.00000000e+00 1.66666667e-01 0.00000000e+00 1.00000000e+00 8.33333333e-02 0.00000000e+00 1.00000000e+00 0.00000000e+00 0.00000000e+00 + 1.00000000e+00 1.00000000e+00 0.00000000e+00 1.00000000e+00 9.16666667e-01 0.00000000e+00 1.00000000e+00 8.33333333e-01 0.00000000e+00 1.00000000e+00 7.50000000e-01 0.00000000e+00 1.00000000e+00 6.66666667e-01 0.00000000e+00 1.00000000e+00 5.83333333e-01 0.00000000e+00 1.00000000e+00 5.00000000e-01 0.00000000e+00 + 1.50000000e+00 0.00000000e+00 0.00000000e+00 1.50000000e+00 8.33333333e-02 0.00000000e+00 1.50000000e+00 1.66666667e-01 0.00000000e+00 1.50000000e+00 2.50000000e-01 0.00000000e+00 1.50000000e+00 3.33333333e-01 0.00000000e+00 1.50000000e+00 4.16666667e-01 0.00000000e+00 1.50000000e+00 5.00000000e-01 0.00000000e+00 + 1.50000000e+00 5.00000000e-01 0.00000000e+00 1.45833333e+00 5.00000000e-01 0.00000000e+00 1.41666667e+00 5.00000000e-01 0.00000000e+00 1.37500000e+00 5.00000000e-01 0.00000000e+00 1.33333333e+00 5.00000000e-01 0.00000000e+00 1.29166667e+00 5.00000000e-01 0.00000000e+00 1.25000000e+00 5.00000000e-01 0.00000000e+00 + 1.50000000e+00 1.00000000e+00 0.00000000e+00 1.45833333e+00 1.00000000e+00 0.00000000e+00 1.41666667e+00 1.00000000e+00 0.00000000e+00 1.37500000e+00 1.00000000e+00 0.00000000e+00 1.33333333e+00 1.00000000e+00 0.00000000e+00 1.29166667e+00 1.00000000e+00 0.00000000e+00 1.25000000e+00 1.00000000e+00 0.00000000e+00 + 1.25000000e+00 1.00000000e+00 0.00000000e+00 1.25000000e+00 9.16666667e-01 0.00000000e+00 1.25000000e+00 8.33333333e-01 0.00000000e+00 1.25000000e+00 7.50000000e-01 0.00000000e+00 1.25000000e+00 6.66666667e-01 0.00000000e+00 1.25000000e+00 5.83333333e-01 0.00000000e+00 1.25000000e+00 5.00000000e-01 0.00000000e+00 + 1.25000000e+00 0.00000000e+00 0.00000000e+00 1.29166667e+00 0.00000000e+00 0.00000000e+00 1.33333333e+00 0.00000000e+00 0.00000000e+00 1.37500000e+00 0.00000000e+00 0.00000000e+00 1.41666667e+00 0.00000000e+00 0.00000000e+00 1.45833333e+00 0.00000000e+00 0.00000000e+00 1.50000000e+00 0.00000000e+00 0.00000000e+00 + 1.00000000e+00 3.33333333e-01 0.00000000e+00 9.76035763e-01 3.32925985e-01 0.00000000e+00 9.52071525e-01 3.32518637e-01 0.00000000e+00 9.28107288e-01 3.32111289e-01 0.00000000e+00 9.04143050e-01 3.31703942e-01 0.00000000e+00 8.80178813e-01 3.31296594e-01 0.00000000e+00 8.56214575e-01 3.30889246e-01 0.00000000e+00 + 1.25000000e+00 1.00000000e+00 0.00000000e+00 1.20833333e+00 1.00000000e+00 0.00000000e+00 1.16666667e+00 1.00000000e+00 0.00000000e+00 1.12500000e+00 1.00000000e+00 0.00000000e+00 1.08333333e+00 1.00000000e+00 0.00000000e+00 1.04166667e+00 1.00000000e+00 0.00000000e+00 1.00000000e+00 1.00000000e+00 0.00000000e+00 + 1.50000000e+00 5.00000000e-01 0.00000000e+00 1.50000000e+00 5.83333333e-01 0.00000000e+00 1.50000000e+00 6.66666667e-01 0.00000000e+00 1.50000000e+00 7.50000000e-01 0.00000000e+00 1.50000000e+00 8.33333333e-01 0.00000000e+00 1.50000000e+00 9.16666667e-01 0.00000000e+00 1.50000000e+00 1.00000000e+00 0.00000000e+00 + + + E[10,3,12,17] + E[84,89] + E[7,11,54,59,22,28,87,91] + E[15,20,52,47,73,67,80,86] + E[18,21,4,9] + E[26,31,37,41,50,53] + E[64,70,76,79,62,57] + E[90,83] + Q[0-7] + Q[8-31] + Q[32-35] + + + C[409] + C[410] + C[411] + + + + + refs/heads/feature/Moving-geometry + cfa86575403703d9a2872df9aeea74e407963066 + Edwards-MacBook-Pro.local + 4.5.0 + 05-Jun-2019 15:22:16 + + basic.msh basic.xml:xml:uncompress + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

FinTime = 1

+

TimeStep = 0.001

+

NumSteps = FinTime/TimeStep

+

IO_CheckSteps = 9999

+

IO_InfoSteps = 100

+

advx = 1

+

advy = 1

+

k = PI

+ + + + + + + + + + + + + u + v + + + + C[401] + C[402] + C[403] + C[404] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/solvers/ADRSolver/Tests/Movement_fixed_2D_varied_par.tst b/solvers/ADRSolver/Tests/Movement_fixed_2D_varied_par.tst new file mode 100644 index 0000000000000000000000000000000000000000..868992abdd857d11c52a400930892399645d40d5 --- /dev/null +++ b/solvers/ADRSolver/Tests/Movement_fixed_2D_varied_par.tst @@ -0,0 +1,22 @@ + + + 2D advection with 3 zones and 2 non-conformal interfaces (one curved) with 2 fields + ADRSolver + Movement_fixed_2D_varied.xml + 4 + + Movement_fixed_2D_varied.xml + + + + 3.98672e-06 + 2.70806e-06 + + + 6.90779e-05 + 1.78188e-05 + + + + + diff --git a/solvers/ADRSolver/Tests/Movement_fixed_3D_Hex41.tst b/solvers/ADRSolver/Tests/Movement_fixed_3D_Hex41.tst new file mode 100644 index 0000000000000000000000000000000000000000..7bc74ba1b0f5a33156801eff55b0e2f0c1c0ccf9 --- /dev/null +++ b/solvers/ADRSolver/Tests/Movement_fixed_3D_Hex41.tst @@ -0,0 +1,19 @@ + + + 3D advection with 2 zones and 1 non-conformal interfaces with dirichlet BCs on hexes + ADRSolver + Movement_fixed_3D_Hex41.xml + + Movement_fixed_3D_Hex41.xml + + + + 5.4459e-06 + + + 3.65216e-05 + + + + + diff --git a/solvers/ADRSolver/Tests/Movement_fixed_3D_Hex41.xml b/solvers/ADRSolver/Tests/Movement_fixed_3D_Hex41.xml new file mode 100644 index 0000000000000000000000000000000000000000..f612f7d2f4cbea3345bad510d88429a26b267c83 --- /dev/null +++ b/solvers/ADRSolver/Tests/Movement_fixed_3D_Hex41.xml @@ -0,0 +1,214 @@ + + + + + 0.00000000e+00 0.00000000e+00 5.00000000e-01 + 5.00000000e-01 0.00000000e+00 5.00000000e-01 + 5.00000000e-01 0.00000000e+00 0.00000000e+00 + 0.00000000e+00 0.00000000e+00 0.00000000e+00 + 0.00000000e+00 5.00000000e-01 5.00000000e-01 + 5.00000000e-01 5.00000000e-01 5.00000000e-01 + 5.00000000e-01 5.00000000e-01 0.00000000e+00 + 0.00000000e+00 5.00000000e-01 0.00000000e+00 + 0.00000000e+00 1.00000000e+00 5.00000000e-01 + 5.00000000e-01 1.00000000e+00 5.00000000e-01 + 5.00000000e-01 1.00000000e+00 0.00000000e+00 + 0.00000000e+00 1.00000000e+00 0.00000000e+00 + 0.00000000e+00 0.00000000e+00 1.00000000e+00 + 5.00000000e-01 0.00000000e+00 1.00000000e+00 + 0.00000000e+00 5.00000000e-01 1.00000000e+00 + 5.00000000e-01 5.00000000e-01 1.00000000e+00 + 0.00000000e+00 1.00000000e+00 1.00000000e+00 + 5.00000000e-01 1.00000000e+00 1.00000000e+00 + + 5.00000000e-01 0.00000000e+00 1.00000000e+00 + 1.00000000e+00 0.00000000e+00 1.00000000e+00 + 1.00000000e+00 0.00000000e+00 0.00000000e+00 + 5.00000000e-01 0.00000000e+00 0.00000000e+00 + 5.00000000e-01 1.00000000e+00 1.00000000e+00 + 1.00000000e+00 1.00000000e+00 1.00000000e+00 + 1.00000000e+00 1.00000000e+00 0.00000000e+00 + 5.00000000e-01 1.00000000e+00 0.00000000e+00 + + + 0 1 + 1 2 + 2 3 + 3 0 + 0 4 + 1 5 + 2 6 + 3 7 + 4 5 + 5 6 + 6 7 + 7 4 + 4 8 + 5 9 + 6 10 + 7 11 + 8 9 + 9 10 + 10 11 + 11 8 + 12 13 + 13 1 + 0 12 + 12 14 + 13 15 + 14 15 + 15 5 + 4 14 + 14 16 + 15 17 + 16 17 + 17 9 + 8 16 + + 18 19 + 19 20 + 20 21 + 21 18 + 18 22 + 19 23 + 20 24 + 21 25 + 22 23 + 23 24 + 24 25 + 25 22 + + + 0 1 2 3 + 0 5 8 4 + 1 6 9 5 + 2 6 10 7 + 3 7 11 4 + 8 9 10 11 + 8 13 16 12 + 9 14 17 13 + 10 14 18 15 + 11 15 19 12 + 16 17 18 19 + 20 21 0 22 + 20 24 25 23 + 21 5 26 24 + 22 4 27 23 + 25 26 8 27 + 25 29 30 28 + 26 13 31 29 + 27 12 32 28 + 30 31 16 32 + + 33 34 35 36 + 33 38 41 37 + 34 39 42 38 + 35 39 43 40 + 36 40 44 37 + 41 42 43 44 + + + 0 1 2 3 4 5 + 5 6 7 8 9 10 + 11 12 13 1 14 15 + 15 16 17 6 18 19 + + 20 21 22 23 24 25 + + + + F[0,3-4,8-12,14-16,18-19] + F[20-23,25] + + F[2,7,13,17] + F[24] + + H[0-3] + H[4] + + + + C[10] + C[11] + + + + + refs/heads/feature/Moving-geometry + 4010859a4dd7218c178588a6f7de92227c605093 + Edwards-MacBook-Pro.local + 5.0.0 + 24-Jul-2020 12:01:28 + + cube.msh cube.xml:xml:uncompress + + + + + + + + + + + + + + + + + + + + + +

FinTime = 0.2

+

TimeStep = 0.001

+

NumSteps = FinTime/TimeStep

+

IO_CheckSteps = 9999

+

IO_InfoSteps = 100

+

advx = 1

+

advy = 1

+

advz = 1

+

k = 2*PI

+ + + + + + + + + + + + + u + + + + C[1,2] + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/solvers/ADRSolver/Tests/Movement_fixed_3D_Hex41_par.tst b/solvers/ADRSolver/Tests/Movement_fixed_3D_Hex41_par.tst new file mode 100644 index 0000000000000000000000000000000000000000..1f8b2cd6792832ef7fbce73e9572c6ce234c24bc --- /dev/null +++ b/solvers/ADRSolver/Tests/Movement_fixed_3D_Hex41_par.tst @@ -0,0 +1,20 @@ + + + 3D advection with 2 zones and 1 non-conformal interfaces with dirichlet BCs on hexes on 4 processes + ADRSolver + Movement_fixed_3D_Hex41.xml + 4 + + Movement_fixed_3D_Hex41.xml + + + + 5.43568e-06 + + + 3.57418e-05 + + + + + diff --git a/solvers/ADRSolver/Tests/Movement_fixed_3D_Hex_3zones_Periodic_par.tst b/solvers/ADRSolver/Tests/Movement_fixed_3D_Hex_3zones_Periodic_par.tst new file mode 100644 index 0000000000000000000000000000000000000000..d2c3adf483092650daecd610589e34208f9c986a --- /dev/null +++ b/solvers/ADRSolver/Tests/Movement_fixed_3D_Hex_3zones_Periodic_par.tst @@ -0,0 +1,20 @@ + + + 3D advection with 3 zones and 2 non-conformal interfaces with periodic BCs on hexes on 4 processes + ADRSolver + Movement_fixed_3D_Hex_3zones_Periodic_par.xml + 4 + + Movement_fixed_3D_Hex_3zones_Periodic_par.xml + + + + 1.58599e-06 + + + 3.03816e-05 + + + + + diff --git a/solvers/ADRSolver/Tests/Movement_fixed_3D_Hex_3zones_Periodic_par.xml b/solvers/ADRSolver/Tests/Movement_fixed_3D_Hex_3zones_Periodic_par.xml new file mode 100644 index 0000000000000000000000000000000000000000..91a323d2725c4c643cdd864337aeae6db883b729 --- /dev/null +++ b/solvers/ADRSolver/Tests/Movement_fixed_3D_Hex_3zones_Periodic_par.xml @@ -0,0 +1,5990 @@ + + + + + 0.00000000e+00 0.00000000e+00 0.00000000e+00 + 1.25000000e-01 0.00000000e+00 0.00000000e+00 + 1.25000000e-01 1.25000000e-01 0.00000000e+00 + 0.00000000e+00 1.25000000e-01 0.00000000e+00 + 0.00000000e+00 0.00000000e+00 1.25000000e-01 + 1.25000000e-01 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