src/gromacs/domdec/localatomsetdata.h

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  35 /*! \file
  36  * \internal \brief
  37  * Declares gmx::internal::LocalAtomSetData.
  38  *
  39  * \author Christian Blau <cblau@gwdg.de>
  40  * \ingroup module_domdec
  41  */
  42 #ifndef GMX_DOMDEC_LOCALATOMSETDATA_H
  43 #define GMX_DOMDEC_LOCALATOMSETDATA_H
  44
  45 #include <numeric>
  46 #include <vector>
  47
  48 #include "gromacs/utility/arrayref.h"
  49 #include "gromacs/utility/basedefinitions.h"
  50
  51 class gmx_ga2la_t;
  52
  53 namespace gmx
  54 {
  55
  56 namespace internal
  57 {
  58
  59 /* \brief Internal class for storing and managing atom indices of an atom set.
  60  */
  61 class LocalAtomSetData
  62 {
  63 public:
  64     /*! \brief Store the data for an atom set with an index group.
  65      *
  66      * Prior to domain decomposition, local atom indices are global atom indices
  67      * and the collective index runs from 0..numberOfAtoms-1.
  68      * local and collective indices will be updated in setLocalAndCollectiveIndices
  69      * to match domain decompostion if domain decomposition is performed.
  70      *
  71      * \todo remove this constructor once all indices are represented
  72      *       as gmx::index instead of int.
  73      *
  74      * \note Not created if the internal int type does match gmx::index
  75      *
  76      * \param[in] globalAtomIndex Indices of the atoms to be managed
  77      */
  78     template<typename T = void, typename U = std::enable_if_t<!std::is_same_v<int, index>, T>>
  79     explicit LocalAtomSetData(ArrayRef<const int> globalAtomIndex) :
  80         globalIndex_(globalAtomIndex.begin(), globalAtomIndex.end()),
  81         localIndex_(globalAtomIndex.begin(), globalAtomIndex.end())
  82     {
  83         collectiveIndex_.resize(localIndex_.size());
  84         std::iota(collectiveIndex_.begin(), collectiveIndex_.end(), 0);
  85     }
  86
  87     /*! \brief Store the data for an atom set with an index group.
  88      *
  89      * Prior to domain decomposition, local atom indices are global atom indices
  90      * and the collective index runs from 0..numberOfAtoms-1.
  91      * local and collective indices will be updated in setLocalAndCollectiveIndices
  92      * to match domain decompostion if domain decomposition is performed.
  93      *
  94      * \param[in] globalAtomIndex Indices of the atoms to be managed
  95      */
  96     explicit LocalAtomSetData(ArrayRef<const index> globalAtomIndex);
  97
  98     /*! \brief Sets the local and collective indices from a lookup in ga2la.
  99      *
 100      * Calculate local and collective indices of home atoms, assuming a valid
 101      * global atom to local atom look-up table.
 102      *
 103      * \param[in] ga2la lookup table that reports if an atom is local.
 104      */
 105     void setLocalAndCollectiveIndices(const gmx_ga2la_t& ga2la);
 106     /*! \brief Global indices of the atoms in this set. */
 107     const std::vector<int> globalIndex_;
 108     /*! \brief Maps indices on this rank [0..num_atoms_local_) to global atom indicices,
 109      * so that localIndex[i] identifies the same atom as globalIndex[collectiveIndex[i]].
 110      *
 111      * This translation of locally dense atom data to global representation,
 112      * allows to adresses per-atom properties, e.g., scattering factors,
 113      * that are stored in a global continuous array for each atom of the atom set.
 114      */
 115     std::vector<int> collectiveIndex_;
 116     /*! \brief Local indices of the atoms.
 117      * Access the i-th local atom coordinate of this set by x[local_index_[i]].
 118      * Constructed and updated every domain-decomposition step.
 119      */
 120     std::vector<int> localIndex_;
 121 };
 122
 123 } // namespace internal
 124
 125 } // namespace gmx
 126
 127
 128 #endif