Merge pull request #5175 from akva2/move_alugrid

Move AluGrid files from ebos to opm/simulators/flow
This commit is contained in:
Kai Bao
2024-03-06 00:02:12 +01:00
committed by GitHub
6 changed files with 22 additions and 35 deletions

View File

@@ -0,0 +1,274 @@
// -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
// vi: set et ts=4 sw=4 sts=4:
/*
This file is part of the Open Porous Media project (OPM).
OPM is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 2 of the License, or
(at your option) any later version.
OPM is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with OPM. If not, see <http://www.gnu.org/licenses/>.
Consult the COPYING file in the top-level source directory of this
module for the precise wording of the license and the list of
copyright holders.
*/
#ifndef OPM_ALUGRID_CARTESIAN_INDEX_MAPPER_HPP
#define OPM_ALUGRID_CARTESIAN_INDEX_MAPPER_HPP
#include <dune/alugrid/grid.hh>
#include <dune/alugrid/3d/gridview.hh>
#include <opm/grid/common/CartesianIndexMapper.hpp>
#include <dune/grid/common/datahandleif.hh>
#include <dune/grid/utility/persistentcontainer.hh>
#include <array>
#include <cassert>
#include <cstddef>
#include <memory>
#include <stdexcept>
#include <vector>
namespace Dune {
/*!
* \brief Interface class to access the logical Cartesian grid as used in industry
* standard simulator decks.
*/
//#if HAVE_MPI
template <>
class CartesianIndexMapper<Dune::ALUGrid<3, 3, Dune::cube, Dune::nonconforming>>
{
public:
#if HAVE_MPI
using Grid = Dune::ALUGrid<3, 3, Dune::cube, Dune::nonconforming, Dune::ALUGridMPIComm>;
#else
using Grid = Dune::ALUGrid<3, 3, Dune::cube, Dune::nonconforming, Dune::ALUGridNoComm>;
#endif //HAVE_MPI
// data handle for communicating global ids during load balance and communication
template <class GridView>
class GlobalIndexDataHandle : public Dune::CommDataHandleIF<GlobalIndexDataHandle<GridView>, int>
{
// global id
class GlobalCellIndex
{
public:
GlobalCellIndex()
: idx_(-1)
{}
GlobalCellIndex& operator=(const int index)
{
idx_ = index;
return *this;
}
int index() const
{ return idx_; }
private:
int idx_;
};
using GlobalIndexContainer = typename Dune::PersistentContainer<Grid, GlobalCellIndex>;
public:
// constructor copying cartesian index to persistent container
GlobalIndexDataHandle(const GridView& gridView,
std::vector<int>& cartesianIndex)
: gridView_(gridView)
, globalIndex_(gridView.grid(), 0)
, cartesianIndex_(cartesianIndex)
{
globalIndex_.resize();
initialize();
}
// constructor copying cartesian index to persistent container
GlobalIndexDataHandle(const GlobalIndexDataHandle& other) = delete ;
// destrcutor writing load balanced cartesian index back to vector
~GlobalIndexDataHandle()
{ finalize(); }
bool contains(int /* dim */, int codim) const
{ return codim == 0; }
bool fixedsize(int /* dim */, int /* codim */) const
{ return true; }
//! \brief loop over all internal data handlers and call gather for
//! given entity
template<class MessageBufferImp, class EntityType>
void gather(MessageBufferImp& buff, const EntityType& element) const
{
int globalIdx = globalIndex_[element].index();
buff.write(globalIdx);
}
//! \brief loop over all internal data handlers and call scatter for
//! given entity
template<class MessageBufferImp, class EntityType>
void scatter(MessageBufferImp& buff, const EntityType& element, std::size_t /* n */)
{
int globalIdx = -1;
buff.read(globalIdx);
if (globalIdx >= 0)
{
globalIndex_.resize();
globalIndex_[element] = globalIdx;
}
}
//! \brief loop over all internal data handlers and return sum of data
//! size of given entity
template<class EntityType>
std::size_t size(const EntityType& /* en */) const
{ return 1; }
protected:
// initialize persistent container from given vector
void initialize()
{
auto idx = cartesianIndex_.begin();
auto it = gridView_.template begin<0>();
const auto& endIt = gridView_.template end<0>();
for (; it != endIt; ++it, ++idx)
globalIndex_[*it] = *idx;
}
// update vector from given persistent container
void finalize()
{
std::vector<int> newIndex ;
newIndex.reserve(gridView_.indexSet().size(0));
auto it = gridView_.template begin<0>();
const auto& endIt = gridView_.template end<0>();
for (; it != endIt; ++it)
newIndex.push_back(globalIndex_[*it].index()) ;
cartesianIndex_.swap(newIndex);
}
GridView gridView_;
GlobalIndexContainer globalIndex_;
std::vector<int>& cartesianIndex_;
};
public:
/** \brief dimension of the grid */
static constexpr int dimension = Grid::dimension ;
/** \brief constructor taking grid */
CartesianIndexMapper(const Grid& grid,
const std::array<int, dimension>& cartDims,
const std::vector<int>& cartesianIndex)
: grid_(grid)
, cartesianDimensions_(cartDims)
, cartesianIndex_(cartesianIndex)
, cartesianSize_(computeCartesianSize())
{}
/** \brief return Cartesian dimensions, i.e. number of cells in each direction */
const std::array<int, dimension>& cartesianDimensions() const
{ return cartesianDimensions_; }
/** \brief return total number of cells in the logical Cartesian grid */
int cartesianSize() const
{ return cartesianSize_; }
/** \brief return number of cells in the active grid */
int compressedSize() const
{ return cartesianIndex_.size(); }
/** \brief return number of cells in the active grid. Only for unifying calls with CpGrid and PolyhedralGrid specializations. */
int compressedLevelZeroSize() const
{ return cartesianIndex_.size(); }
/** \brief return index of the cells in the logical Cartesian grid */
int cartesianIndex(const int compressedElementIndex) const
{
assert(compressedElementIndex < compressedSize());
return cartesianIndex_[compressedElementIndex];
}
/** \brief return index of the cells in the logical Cartesian grid */
int cartesianIndex(const std::array<int, dimension>& coords) const
{
int cartIndex = coords[0];
int factor = cartesianDimensions()[0];
for (int i=1; i < dimension; ++i) {
cartIndex += coords[i] * factor;
factor *= cartesianDimensions()[i];
}
return cartIndex;
}
/** \brief return Cartesian coordinate, i.e. IJK, for a given cell */
void cartesianCoordinate(const int compressedElementIndex, std::array<int, dimension>& coords) const
{
int gc = cartesianIndex(compressedElementIndex);
if constexpr (dimension == 3) {
coords[0] = gc % cartesianDimensions()[0];
gc /= cartesianDimensions()[0];
coords[1] = gc % cartesianDimensions()[1];
coords[2] = gc / cartesianDimensions()[1];
}
else if constexpr (dimension == 2) {
coords[0] = gc % cartesianDimensions()[0];
coords[1] = gc / cartesianDimensions()[0];
}
else if constexpr (dimension == 1)
coords[0] = gc ;
else
throw std::invalid_argument("cartesianCoordinate not implemented for dimension " + std::to_string(dimension));
}
/** \brief Only for unifying calls with CartesianIndexMapper<CpGrid> where levels are relevant */
void cartesianCoordinateLevel(const int compressedElementIndex, std::array<int, dimension>& coords, int level) const
{
if (level) {
throw std::invalid_argument("Invalid level.\n");
}
cartesianCoordinate(compressedElementIndex, coords);
}
template <class GridView>
std::unique_ptr<GlobalIndexDataHandle<GridView> > dataHandle(const GridView& gridView)
{
using DataHandle = GlobalIndexDataHandle<GridView>;
assert(&grid_ == &gridView.grid());
return std::make_unique<DataHandle>(gridView, cartesianIndex_);
}
protected:
int computeCartesianSize() const
{
int size = cartesianDimensions()[0];
for (int d=1; d<dimension; ++d)
size *= cartesianDimensions()[d];
return size ;
}
const Grid& grid_;
const std::array<int, dimension> cartesianDimensions_;
std::vector<int> cartesianIndex_;
const int cartesianSize_ ;
};
} // end namespace Dune
#endif // OPM_ALUGRID_CARTESIAN_INDEX_MAPPER_HPP

View File

@@ -0,0 +1,366 @@
// -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
// vi: set et ts=4 sw=4 sts=4:
/*
This file is part of the Open Porous Media project (OPM).
OPM is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 2 of the License, or
(at your option) any later version.
OPM is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with OPM. If not, see <http://www.gnu.org/licenses/>.
Consult the COPYING file in the top-level source directory of this
module for the precise wording of the license and the list of
copyright holders.
*/
/*!
* \file
* \copydoc Opm::AluGridVanguard
*/
#ifndef OPM_ALUGRID_VANGUARD_HPP
#define OPM_ALUGRID_VANGUARD_HPP
#include <dune/alugrid/common/fromtogridfactory.hh>
#include <dune/alugrid/dgf.hh>
#include <dune/alugrid/grid.hh>
#include <ebos/eclbasevanguard.hh>
#include <ebos/ecltransmissibility.hh>
#include <opm/common/OpmLog/OpmLog.hpp>
#include <opm/grid/CpGrid.hpp>
#include <opm/models/common/multiphasebaseproperties.hh>
#include <opm/simulators/flow/AluGridCartesianIndexMapper.hpp>
#include <opm/simulators/utils/ParallelEclipseState.hpp>
#include <array>
#include <cstddef>
#include <memory>
#include <tuple>
#include <vector>
namespace Opm {
template <class TypeTag>
class FlowAluGridVanguard;
} // namespace Opm
namespace Opm::Properties {
namespace TTag {
struct AluGridVanguard {
using InheritsFrom = std::tuple<EclBaseVanguard>;
};
}
// declare the properties
template<class TypeTag>
struct Vanguard<TypeTag, TTag::AluGridVanguard> {
using type = Opm::FlowAluGridVanguard<TypeTag>;
};
template<class TypeTag>
struct Grid<TypeTag, TTag::AluGridVanguard> {
#if HAVE_MPI
using type = Dune::ALUGrid<3, 3, Dune::cube, Dune::nonconforming, Dune::ALUGridMPIComm>;
#else
using type = Dune::ALUGrid<3, 3, Dune::cube, Dune::nonconforming, Dune::ALUGridNoComm>;
#endif //HAVE_MPI
};
template<class TypeTag>
struct EquilGrid<TypeTag, TTag::AluGridVanguard> {
using type = Dune::CpGrid;
};
} // namespace Opm::Properties
namespace Opm {
/*!
* \ingroup EclBlackOilSimulator
*
* \brief Helper class for grid instantiation of ECL file-format using problems.
*
* This class uses Dune::ALUGrid as the simulation grid.
*/
template <class TypeTag>
class AluGridVanguard : public EclBaseVanguard<TypeTag>
{
friend class EclBaseVanguard<TypeTag>;
using ParentType = EclBaseVanguard<TypeTag>;
using ElementMapper = GetPropType<TypeTag, Properties::ElementMapper>;
using Scalar = GetPropType<TypeTag, Properties::Scalar>;
using Simulator = GetPropType<TypeTag, Properties::Simulator>;
public:
using Grid = GetPropType<TypeTag, Properties::Grid>;
using EquilGrid = GetPropType<TypeTag, Properties::EquilGrid>;
using GridView = GetPropType<TypeTag, Properties::GridView>;
using CartesianIndexMapper = Dune::CartesianIndexMapper<Grid>;
using EquilCartesianIndexMapper = Dune::CartesianIndexMapper<EquilGrid>;
using TransmissibilityType = EclTransmissibility<Grid, GridView, ElementMapper, CartesianIndexMapper, Scalar>;
using Factory = Dune::FromToGridFactory<Grid>;
static constexpr int dimension = Grid::dimension;
static constexpr int dimensionworld = Grid::dimensionworld;
AluGridVanguard(Simulator& simulator)
: EclBaseVanguard<TypeTag>(simulator)
{
this->mpiRank = EclGenericVanguard::comm().rank();
this->callImplementationInit();
}
/*!
* \brief Return a reference to the simulation grid.
*/
Grid& grid()
{ return *grid_; }
/*!
* \brief Return a reference to the simulation grid.
*/
const Grid& grid() const
{ return *grid_; }
/*!
* \brief Returns a refefence to the grid which should be used by the EQUIL
* initialization code.
*
* The EQUIL keyword is used to specify the initial condition of the reservoir in
* hydrostatic equilibrium. Since the code which does this is not accepting arbitrary
* DUNE grids (the code is part of the opm-core module), this is not necessarily the
* same as the grid which is used for the actual simulation.
*/
const EquilGrid& equilGrid() const
{ return *equilGrid_; }
/*!
* \brief Indicates that the initial condition has been computed and the memory used
* by the EQUIL grid can be released.
*
* Depending on the implementation, subsequent accesses to the EQUIL grid lead to
* crashes.
*/
void releaseEquilGrid()
{
delete equilCartesianIndexMapper_;
equilCartesianIndexMapper_ = nullptr;
delete equilGrid_;
equilGrid_ = nullptr;
}
/*!
* \brief Distribute the simulation grid over multiple processes
*
* (For parallel simulation runs.)
*/
void loadBalance()
{
auto gridView = grid().leafGridView();
auto dataHandle = cartesianIndexMapper_->dataHandle(gridView);
grid().loadBalance(*dataHandle);
// communicate non-interior cells values
grid().communicate(*dataHandle,
Dune::InteriorBorder_All_Interface,
Dune::ForwardCommunication );
if (grid().size(0))
{
globalTrans_ = std::make_unique<TransmissibilityType>(this->eclState(),
this->gridView(),
this->cartesianIndexMapper(),
this->grid(),
this->cellCentroids(),
getPropValue<TypeTag,
Properties::EnableEnergy>(),
getPropValue<TypeTag,
Properties::EnableDiffusion>(),
getPropValue<TypeTag,
Properties::EnableDispersion>());
// Re-ordering for ALUGrid
globalTrans_->update(false, [&](unsigned int i) { return gridEquilIdxToGridIdx(i);});
}
}
template<class DataHandle>
void scatterData(DataHandle& /*handle*/) const
{
// not existing for this type of grid yet
}
template<class DataHandle>
void gatherData(DataHandle& /*handle*/) const
{
// not existing for this type of grid yet
}
template<class DataHandle, class InterfaceType, class CommunicationDirection>
void communicate (DataHandle& /*data*/, InterfaceType /*iftype*/,
CommunicationDirection /*dir*/) const
{
// not existing for this type of grid yet
}
/*!
* \brief Free the memory occupied by the global transmissibility object.
*
* After writing the initial solution, this array should not be necessary anymore.
*/
void releaseGlobalTransmissibilities()
{
globalTrans_.reset();
}
/*!
* \brief Returns the object which maps a global element index of the simulation grid
* to the corresponding element index of the logically Cartesian index.
*/
const CartesianIndexMapper& cartesianIndexMapper() const
{ return *cartesianIndexMapper_; }
/*!
* \brief Returns mapper from compressed to cartesian indices for the EQUIL grid
*/
const EquilCartesianIndexMapper& equilCartesianIndexMapper() const
{ return *equilCartesianIndexMapper_; }
/*!
* \brief Get function to query cell centroids for a distributed grid.
*
* Currently this only non-empty for a loadbalanced CpGrid.
* It is a function return the centroid for the given element
* index.
*/
std::function<std::array<double,dimensionworld>(int)>
cellCentroids() const
{
return this->cellCentroids_(this->cartesianIndexMapper(), false);
}
const TransmissibilityType& globalTransmissibility() const
{
assert( globalTrans_ != nullptr );
return *globalTrans_;
}
void releaseGlobalTransmissibility()
{
globalTrans_.reset();
}
const std::vector<int>& globalCell()
{
return cartesianCellId_;
}
std::vector<int> cellPartition() const
{
// not required for this type of grid yet
return {};
}
unsigned int gridEquilIdxToGridIdx(unsigned int elemIndex) const {
return equilGridToGrid_[elemIndex];
}
unsigned int gridIdxToEquilGridIdx(unsigned int elemIndex) const {
return ordering_[elemIndex];
}
protected:
void createGrids_()
{
// we use separate grid objects: one for the calculation of the initial condition
// via EQUIL and one for the actual simulation. The reason is that the EQUIL code
// cannot cope with arbitrary Dune grids and is also allergic to distributed
// grids.
/////
// create the EQUIL grid
/////
const EclipseGrid* input_grid = nullptr;
std::vector<double> global_porv;
// At this stage the ParallelEclipseState instance is still in global
// view; on rank 0 we have undistributed data for the entire grid, on
// the other ranks the EclipseState is empty.
if (mpiRank == 0) {
// Processing grid
input_grid = &this->eclState().getInputGrid();
global_porv = this->eclState().fieldProps().porv(true);
OpmLog::info("\nProcessing grid");
}
#if HAVE_MPI
this->equilGrid_ = std::make_unique<Dune::CpGrid>(EclGenericVanguard::comm());
#else
this->equilGrid_ = std::make_unique<Dune::CpGrid>();
#endif
// Note: removed_cells is guaranteed to be empty on ranks other than 0.
auto removed_cells =
this->equilGrid_->processEclipseFormat(input_grid,
&this->eclState(),
/*isPeriodic=*/false,
/*flipNormals=*/false,
/*clipZ=*/false);
cartesianCellId_ = this->equilGrid_->globalCell();
for (unsigned i = 0; i < dimension; ++i)
cartesianDimension_[i] = this->equilGrid_->logicalCartesianSize()[i];
equilCartesianIndexMapper_ = std::make_unique<EquilCartesianIndexMapper>(*equilGrid_);
/////
// create the simulation grid
/////
factory_ = std::make_unique<Factory>();
grid_ = factory_->convert(*equilGrid_, cartesianCellId_, ordering_);
OpmLog::warning("Space Filling Curve Ordering is not yet supported: DISABLE_ALUGRID_SFC_ORDERING is enabled");
equilGridToGrid_.resize(ordering_.size());
for (std::size_t index = 0; index < ordering_.size(); ++index) {
equilGridToGrid_[ordering_[index]] = index;
}
cartesianIndexMapper_ = std::make_unique<CartesianIndexMapper>(*grid_, cartesianDimension_, cartesianCellId_);
this->updateGridView_();
this->updateCartesianToCompressedMapping_();
this->updateCellDepths_();
this->updateCellThickness_();
}
void filterConnections_()
{
// not handling the removal of completions for this type of grid yet.
}
std::unique_ptr<Grid> grid_;
std::unique_ptr<EquilGrid> equilGrid_;
std::vector<int> cartesianCellId_;
std::vector<unsigned int> ordering_;
std::vector<unsigned int> equilGridToGrid_;
std::array<int,dimension> cartesianDimension_;
std::unique_ptr<CartesianIndexMapper> cartesianIndexMapper_;
std::unique_ptr<EquilCartesianIndexMapper> equilCartesianIndexMapper_;
std::unique_ptr<Factory> factory_;
std::unique_ptr<TransmissibilityType> globalTrans_;
int mpiRank;
};
} // namespace Opm
#endif // OPM_ALUGRID_VANGUARD_HPP

View File

@@ -38,13 +38,6 @@
#include <opm/simulators/linalg/bda/WellContributions.hpp>
#endif
#if HAVE_DUNE_ALUGRID
#include <dune/alugrid/grid.hh>
#include <ebos/alucartesianindexmapper.hh>
#endif // HAVE_DUNE_ALUGRID
#include <opm/grid/polyhedralgrid.hh>
namespace Opm {
namespace detail {

View File

@@ -38,7 +38,7 @@
#if HAVE_DUNE_ALUGRID
#include <dune/alugrid/grid.hh>
#include <ebos/alucartesianindexmapper.hh>
#include <opm/simulators/flow/AluGridCartesianIndexMapper.hpp>
#endif // HAVE_DUNE_ALUGRID
#include <opm/grid/polyhedralgrid.hh>