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Make Serial Mesh files work without APF
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,12 @@ | ||
| #ifndef PUMGEN_AUX_DISTRIBUTOR_H_ | ||
| #define PUMGEN_AUX_DISTRIBUTOR_H_ | ||
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| #include <cstdlib> | ||
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| // no namespace for now | ||
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| constexpr std::size_t getChunksize(std::size_t total, int rank, int size) { | ||
| return (total / size) + (total % size > rank); | ||
| } | ||
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| #endif // PUMGEN_AUX_DISTRIBUTOR_H_ |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,151 @@ | ||
| /** | ||
| * @file | ||
| * This file is part of PUMGen | ||
| * | ||
| * For conditions of distribution and use, please see the copyright | ||
| * notice in the file 'COPYING' at the root directory of this package | ||
| * and the copyright notice at https://github.com/SeisSol/PUMGen | ||
| * | ||
| * @copyright 2017 Technical University of Munich | ||
| * @author Sebastian Rettenberger <sebastian.rettenberger@tum.de> | ||
| */ | ||
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| #ifndef SERIAL_MESH_FILE_H | ||
| #define SERIAL_MESH_FILE_H | ||
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| #ifdef PARALLEL | ||
| #include <mpi.h> | ||
| #endif // PARALLEL | ||
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| #include "ApfConvertWrapper.h" | ||
| #include "aux/Distributor.h" | ||
| #include <PCU.h> | ||
| #include <apfMDS.h> | ||
| #include <apfMesh2.h> | ||
| #include <gmi_null.h> | ||
| #include <vector> | ||
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| #include "MeshInput.h" | ||
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| /** | ||
| * Read a mesh from a serial file | ||
| */ | ||
| template <typename T> class SerialMeshFile : public MeshInput { | ||
| private: | ||
| #ifdef PARALLEL | ||
| MPI_Comm m_comm; | ||
| #endif // PARALLEL | ||
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| int m_rank; | ||
| int m_nProcs; | ||
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| T m_meshReader; | ||
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| public: | ||
| #ifdef PARALLEL | ||
| SerialMeshFile(const char* meshFile, MPI_Comm comm = MPI_COMM_WORLD) | ||
| : m_comm(comm), m_meshReader(comm) { | ||
| init(); | ||
| open(meshFile); | ||
| } | ||
| #else // PARALLEL | ||
| SerialMeshFile(const char* meshFile) { | ||
| init(); | ||
| open(meshFile); | ||
| } | ||
| #endif // PARALLEL | ||
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| private: | ||
| /** | ||
| * Sets some parameters (called from the constructor) | ||
| */ | ||
| void init() { | ||
| #ifdef PARALLEL | ||
| MPI_Comm_rank(m_comm, &m_rank); | ||
| MPI_Comm_size(m_comm, &m_nProcs); | ||
| #else // PARALLLEL | ||
| m_rank = 0; | ||
| m_nProcs = 1; | ||
| #endif // PARALLEL | ||
| } | ||
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| void open(const char* meshFile) { | ||
| m_meshReader.open(meshFile); | ||
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| const std::size_t nVertices = m_meshReader.nVertices(); | ||
| const std::size_t nElements = m_meshReader.nElements(); | ||
| const std::size_t nLocalVertices = getChunksize(nVertices, m_rank, m_nProcs); | ||
| const std::size_t nLocalElements = getChunksize(nElements, m_rank, m_nProcs); | ||
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| gmi_register_null(); | ||
| gmi_model* model = gmi_load(".null"); | ||
| m_mesh = apf::makeEmptyMdsMesh(model, 3, false); | ||
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| // Create elements | ||
| logInfo(m_rank) << "Handle cell connectivity"; | ||
| apf::GlobalToVert vertMap; | ||
| { | ||
| std::vector<ElementID> elements; | ||
| { | ||
| std::vector<std::size_t> elementsInt(nLocalElements * 4); | ||
| m_meshReader.readElements(elementsInt.data()); | ||
| elements = std::vector<ElementID>(elementsInt.begin(), elementsInt.end()); | ||
| } | ||
| logInfo(m_rank) << "Create APF connectivity"; | ||
| apf::construct(m_mesh, elements.data(), nLocalElements, apf::Mesh::TET, vertMap); | ||
| } | ||
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| apf::alignMdsRemotes(m_mesh); | ||
| apf::deriveMdsModel(m_mesh); | ||
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| // Set vertices | ||
| logInfo(m_rank) << "Handle vertex coordinates"; | ||
| { | ||
| std::vector<double> vertices(nLocalVertices * 3); | ||
| m_meshReader.readVertices(vertices.data()); | ||
| apf::setCoords(m_mesh, vertices.data(), nLocalVertices, vertMap); | ||
| } | ||
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| // Set boundaries | ||
| logInfo(m_rank) << "Handle boundary conditions"; | ||
| apf::MeshTag* boundaryTag = m_mesh->createIntTag("boundary condition", 1); | ||
| { | ||
| std::vector<int> boundaries(nLocalElements * 4); | ||
| m_meshReader.readBoundaries(boundaries.data()); | ||
| apf::MeshIterator* it = m_mesh->begin(3); | ||
| std::size_t i = 0; | ||
| while (apf::MeshEntity* element = m_mesh->iterate(it)) { | ||
| apf::Adjacent adjacent; | ||
| m_mesh->getAdjacent(element, 2, adjacent); | ||
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| for (int j = 0; j < 4; j++) { | ||
| if (!boundaries[i * 4 + j]) { | ||
| continue; | ||
| } | ||
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| m_mesh->setIntTag(adjacent[j], boundaryTag, &boundaries[i * 4 + j]); | ||
| } | ||
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| i++; | ||
| } | ||
| m_mesh->end(it); | ||
| } | ||
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| // Set groups | ||
| logInfo(m_rank) << "Handle cell groups"; | ||
| apf::MeshTag* groupTag = m_mesh->createIntTag("group", 1); | ||
| { | ||
| std::vector<int> groups(nLocalElements); | ||
| m_meshReader.readGroups(groups.data()); | ||
| apf::MeshIterator* it = m_mesh->begin(3); | ||
| std::size_t i = 0; | ||
| while (apf::MeshEntity* element = m_mesh->iterate(it)) { | ||
| m_mesh->setIntTag(element, groupTag, &groups[i]); | ||
| i++; | ||
| } | ||
| m_mesh->end(it); | ||
| } | ||
| } | ||
| }; | ||
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| #endif // SERIAL_MESH_FILE_H |
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