src/gromacs/domdec/domdec_specatomcomm.h

   1 /*
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   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  37 /*! \internal \file
  38  *
  39  * \brief This file declares functions for domdec to use
  40  * while managing communication of atoms required for special purposes
  41  *
  42  * \author Berk Hess <hess@kth.se>
  43  * \ingroup module_domdec
  44  */
  45
  46 #ifndef GMX_DOMDEC_DOMDEC_SPECATOMCOMM_H
  47 #define GMX_DOMDEC_DOMDEC_SPECATOMCOMM_H
  48
  49 #include <vector>
  50
  51 #include "gromacs/math/vectypes.h"
  52 #include "gromacs/utility/basedefinitions.h"
  53
  54 struct gmx_domdec_t;
  55 struct t_commrec;
  56
  57 namespace gmx
  58 {
  59 template<typename T>
  60 class HashedMap;
  61 } // namespace gmx
  62
  63 /*! \internal \brief The communication setup along a single dimension */
  64 struct gmx_specatsend_t
  65 {
  66     std::vector<int> a;     /**< The indices of atoms to send */
  67     int              nrecv; /**< The number of atoms to receive */
  68 };
  69
  70 /*! \internal \brief Struct with setup and buffers for special atom communication */
  71 struct gmx_domdec_specat_comm_t
  72 {
  73     /* The number of indices to receive during the setup */
  74     int nreq[DIM][2][2] = { { { 0 } } }; /**< The nr. of atoms requested, per DIM, direction and direct/indirect */
  75     /* The atoms to send */
  76     gmx_specatsend_t  spas[DIM][2]; /**< The communication setup per DIM, direction */
  77     std::vector<bool> sendAtom;     /**< Work buffer that tells if spec.atoms should be sent */
  78
  79     /* Send buffers */
  80     std::vector<int>       ibuf;  /**< Integer send buffer */
  81     std::vector<gmx::RVec> vbuf;  /**< rvec send buffer */
  82     std::vector<gmx::RVec> vbuf2; /**< rvec send buffer */
  83     /* The range in the local buffer(s) for received atoms */
  84     int at_start; /**< Start index of received atoms */
  85     int at_end;   /**< End index of received atoms */
  86 };
  87
  88 /*! \brief Communicates the force for special atoms, the shift forces are reduced with \p fshift != NULL */
  89 void dd_move_f_specat(const gmx_domdec_t* dd, gmx_domdec_specat_comm_t* spac, rvec* f, rvec* fshift);
  90
  91 /*! \brief Communicates the coordinates for special atoms
  92  *
  93  * \param[in]     dd         Domain decomposition struct
  94  * \param[in]     spac       Special atom communication struct
  95  * \param[in]     box        Box, used for pbc
  96  * \param[in,out] x0         Vector to communicate
  97  * \param[in,out] x1         Vector to communicate, when != NULL
  98  * \param[in]     bX1IsCoord Tells is \p x1 is a coordinate vector (needs pbc)
  99  */
 100 void dd_move_x_specat(const gmx_domdec_t*       dd,
 101                       gmx_domdec_specat_comm_t* spac,
 102                       const matrix              box,
 103                       rvec*                     x0,
 104                       rvec*                     x1,
 105                       gmx_bool                  bX1IsCoord);
 106
 107 /*! \brief Sets up the communication for special atoms
 108  *
 109  * \param[in]     dd           Domain decomposition struct
 110  * \param[in,out] ireq         List of requested atom indices, updated due to aggregation
 111  * \param[in,out] spac         Special atom communication struct
 112  * \param[out]    ga2la_specat Global to local special atom index
 113  * \param[in]     at_start     Index in local state where to start storing communicated atoms
 114  * \param[in]     vbuf_fac     Buffer factor, 1 or 2 for communicating 1 or 2 vectors
 115  * \param[in]     specat_type  Name of the special atom, used for error message
 116  * \param[in]     add_err      Text to add at the end of error message when atoms can't be found
 117  */
 118 int setup_specat_communication(gmx_domdec_t*             dd,
 119                                std::vector<int>*         ireq,
 120                                gmx_domdec_specat_comm_t* spac,
 121                                gmx::HashedMap<int>*      ga2la_specat,
 122                                int                       at_start,
 123                                int                       vbuf_fac,
 124                                const char*               specat_type,
 125                                const char*               add_err);
 126
 127 #endif