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 <vector>
  46
  47 #include "gromacs/utility/arrayref.h"
  48
  49 class gmx_ga2la_t;
  50
  51 namespace gmx
  52 {
  53
  54 namespace internal
  55 {
  56
  57 /* \brief Internal class for storing and managing atom indices of an atom set.
  58  */
  59 class LocalAtomSetData
  60 {
  61     public:
  62         /*! \brief Store the data for an atom set with an index group.
  63          *
  64          * Prior to domain decomposition, local atom indices are global atom indices
  65          * and the collective index runs from 0..numberOfAtoms-1.
  66          * local and collective indices will be updated in setLocalAndCollectiveIndices
  67          * to match domain decompostion if domain decomposition is performed.
  68          *
  69          * \param[in] globalAtomIndex Indices of the atoms to be managed
  70          */
  71         explicit LocalAtomSetData(ArrayRef<const int> globalAtomIndex);
  72         /*! \brief Sets the local and collective indices from a lookup in ga2la.
  73          *
  74          * Calculate local and collective indices of home atoms, assuming a valid
  75          * global atom to local atom look-up table.
  76          *
  77          * \param[in] ga2la lookup table that reports if an atom is local.
  78          */
  79         void setLocalAndCollectiveIndices(const gmx_ga2la_t &ga2la);
  80         /*! \brief Global indices of the atoms in this set. */
  81         const std::vector<int> globalIndex_;
  82         /*! \brief Maps indices on this rank [0..num_atoms_local_) to global atom indicices,
  83          * so that localIndex[i] = globalIndex[collectiveIndex[i]].
  84          *
  85          * This translation of locally dense atom data to global representation,
  86          * allows to adresses per-atom properties, e.g., scattering factors,
  87          * that are stored in a global continuous array for each atom of the atom set.
  88          */
  89         std::vector<int> collectiveIndex_;
  90         /*! \brief Local indices of the atoms.
  91          * Access the i-th local atom coordinate of this set by x[local_index_[i]].
  92          * Constructed and updated every domain-decomposition step.
  93          */
  94         std::vector<int> localIndex_;
  95 };
  96
  97 } // namespace internal
  98
  99 } // namespace gmx
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 104 #endif