*/
class GridSet
{
- public:
- /*! \internal
- * \brief Description of the domain setup: PBC and the connections between domains
- */
- struct DomainSetup
- {
- //! Constructor, without DD \p numDDCells and \p ddZones should be nullptr
- DomainSetup(int ePBC,
- bool doTestParticleInsertion,
- const ivec *numDDCells,
- const gmx_domdec_zones_t *ddZones);
-
- //! The type of PBC
- int ePBC;
- //! Tells whether we are doing test-particle insertion
- bool doTestParticleInsertion;
- //! Are there multiple domains?
- bool haveMultipleDomains;
- //! Are there multiple domains along each dimension?
- std::array<bool, DIM> haveMultipleDomainsPerDim;
- //! The domain decomposition zone setup
- const gmx_domdec_zones_t *zones;
- };
-
- //! Constructs a grid set for 1 or multiple DD zones, when numDDCells!=nullptr
- GridSet(int ePBC,
- bool doTestParticleInsertion,
- const ivec *numDDCells,
- const gmx_domdec_zones_t *ddZones,
- PairlistType pairlistType,
- bool haveFep,
- int numThreads,
- gmx::PinningPolicy pinningPolicy);
-
- //! Puts the atoms on the grid with index \p gridIndex and copies the coordinates to \p nbat
- void putOnGrid(const matrix box,
- int gridIndex,
- const rvec lowerCorner,
- const rvec upperCorner,
- const gmx::UpdateGroupsCog *updateGroupsCog,
- gmx::Range<int> atomRange,
- real atomDensity,
- gmx::ArrayRef<const int> atomInfo,
- gmx::ArrayRef<const gmx::RVec> x,
- int numAtomsMoved,
- const int *move,
- nbnxn_atomdata_t *nbat);
-
- //! Returns the domain setup
- DomainSetup domainSetup() const
- {
- return domainSetup_;
- }
-
- //! Returns the total number of atoms in the grid set, including padding
- int numGridAtomsTotal() const
- {
- return grids_.back().atomIndexEnd();
- }
-
- //! Returns the number of local real atoms, i.e. without padded atoms
- int numRealAtomsLocal() const
- {
- return numRealAtomsLocal_;
- }
-
- //! Returns the number of total real atoms, i.e. without padded atoms
- int numRealAtomsTotal() const
- {
- return numRealAtomsTotal_;
- }
-
- //! Returns the atom order on the grid for the local atoms
- gmx::ArrayRef<const int> getLocalAtomorder() const
- {
- /* Return the atom order for the home cell (index 0) */
- const int numIndices = grids_[0].atomIndexEnd() - grids_[0].firstAtomInColumn(0);
-
- return gmx::constArrayRefFromArray(atomIndices().data(), numIndices);
- }
-
- //! Sets the order of the local atoms to the order grid atom ordering
- void setLocalAtomOrder();
-
- //! Returns the list of grids
- gmx::ArrayRef<const Grid> grids() const
- {
- return grids_;
- }
-
- //! Returns the grid atom indices covering all grids
- gmx::ArrayRef<const int> cells() const
- {
- return gridSetData_.cells;
- }
-
- //! Returns the grid atom indices covering all grids
- gmx::ArrayRef<const int> atomIndices() const
- {
- return gridSetData_.atomIndices;
- }
-
- //! Returns whether we have perturbed non-bonded interactions
- bool haveFep() const
- {
- return haveFep_;
- }
-
- //! Returns the unit cell in \p box
- void getBox(matrix box) const
- {
- copy_mat(box_, box);
- }
-
- //! Returns the maximum number of columns across all grids
- int numColumnsMax() const
- {
- return numColumnsMax_;
- }
-
- //! Sets the maximum number of columns across all grids
- void setNumColumnsMax(int numColumnsMax)
- {
- numColumnsMax_ = numColumnsMax;
- }
-
- private:
- /* Data members */
- //! The domain setup
- DomainSetup domainSetup_;
- //! The search grids
- std::vector<Grid> grids_;
- //! The cell and atom index data which runs over all grids
- GridSetData gridSetData_;
- //! Tells whether we have perturbed non-bonded interactions
- bool haveFep_;
- //! The periodic unit-cell
- matrix box_;
- //! The number of local real atoms, i.e. without padded atoms, local atoms: 0 to numAtomsLocal_
- int numRealAtomsLocal_;
- //! The total number of real atoms, i.e. without padded atoms
- int numRealAtomsTotal_;
- //! Working data for constructing a single grid, one entry per thread
- std::vector<GridWork> gridWork_;
- //! Maximum number of columns across all grids
- int numColumnsMax_;
-
+public:
+ /*! \internal
+ * \brief Description of the domain setup: PBC and the connections between domains
+ */
+ struct DomainSetup
+ {
+ //! Constructor, without DD \p numDDCells and \p ddZones should be nullptr
+ DomainSetup(int ePBC,
+ bool doTestParticleInsertion,
+ const ivec* numDDCells,
+ const gmx_domdec_zones_t* ddZones);
+
+ //! The type of PBC
+ int ePBC;
+ //! Tells whether we are doing test-particle insertion
+ bool doTestParticleInsertion;
+ //! Are there multiple domains?
+ bool haveMultipleDomains;
+ //! Are there multiple domains along each dimension?
+ std::array<bool, DIM> haveMultipleDomainsPerDim;
+ //! The domain decomposition zone setup
+ const gmx_domdec_zones_t* zones;
+ };
+
+ //! Constructs a grid set for 1 or multiple DD zones, when numDDCells!=nullptr
+ GridSet(int ePBC,
+ bool doTestParticleInsertion,
+ const ivec* numDDCells,
+ const gmx_domdec_zones_t* ddZones,
+ PairlistType pairlistType,
+ bool haveFep,
+ int numThreads,
+ gmx::PinningPolicy pinningPolicy);
+
+ //! Puts the atoms on the grid with index \p gridIndex and copies the coordinates to \p nbat
+ void putOnGrid(const matrix box,
+ int gridIndex,
+ const rvec lowerCorner,
+ const rvec upperCorner,
+ const gmx::UpdateGroupsCog* updateGroupsCog,
+ gmx::Range<int> atomRange,
+ real atomDensity,
+ gmx::ArrayRef<const int> atomInfo,
+ gmx::ArrayRef<const gmx::RVec> x,
+ int numAtomsMoved,
+ const int* move,
+ nbnxn_atomdata_t* nbat);
+
+ //! Returns the domain setup
+ DomainSetup domainSetup() const { return domainSetup_; }
+
+ //! Returns the total number of atoms in the grid set, including padding
+ int numGridAtomsTotal() const { return grids_.back().atomIndexEnd(); }
+
+ //! Returns the number of local real atoms, i.e. without padded atoms
+ int numRealAtomsLocal() const { return numRealAtomsLocal_; }
+
+ //! Returns the number of total real atoms, i.e. without padded atoms
+ int numRealAtomsTotal() const { return numRealAtomsTotal_; }
+
+ //! Returns the atom order on the grid for the local atoms
+ gmx::ArrayRef<const int> getLocalAtomorder() const
+ {
+ /* Return the atom order for the home cell (index 0) */
+ const int numIndices = grids_[0].atomIndexEnd() - grids_[0].firstAtomInColumn(0);
+
+ return gmx::constArrayRefFromArray(atomIndices().data(), numIndices);
+ }
+
+ //! Sets the order of the local atoms to the order grid atom ordering
+ void setLocalAtomOrder();
+
+ //! Returns the list of grids
+ gmx::ArrayRef<const Grid> grids() const { return grids_; }
+
+ //! Returns the grid atom indices covering all grids
+ gmx::ArrayRef<const int> cells() const { return gridSetData_.cells; }
+
+ //! Returns the grid atom indices covering all grids
+ gmx::ArrayRef<const int> atomIndices() const { return gridSetData_.atomIndices; }
+
+ //! Returns whether we have perturbed non-bonded interactions
+ bool haveFep() const { return haveFep_; }
+
+ //! Returns the unit cell in \p box
+ void getBox(matrix box) const { copy_mat(box_, box); }
+
+ //! Returns the maximum number of columns across all grids
+ int numColumnsMax() const { return numColumnsMax_; }
+
+ //! Sets the maximum number of columns across all grids
+ void setNumColumnsMax(int numColumnsMax) { numColumnsMax_ = numColumnsMax; }
+
+private:
+ /* Data members */
+ //! The domain setup
+ DomainSetup domainSetup_;
+ //! The search grids
+ std::vector<Grid> grids_;
+ //! The cell and atom index data which runs over all grids
+ GridSetData gridSetData_;
+ //! Tells whether we have perturbed non-bonded interactions
+ bool haveFep_;
+ //! The periodic unit-cell
+ matrix box_;
+ //! The number of local real atoms, i.e. without padded atoms, local atoms: 0 to numAtomsLocal_
+ int numRealAtomsLocal_;
+ //! The total number of real atoms, i.e. without padded atoms
+ int numRealAtomsTotal_;
+ //! Working data for constructing a single grid, one entry per thread
+ std::vector<GridWork> gridWork_;
+ //! Maximum number of columns across all grids
+ int numColumnsMax_;
};
} // namespace Nbnxm
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff