src/gromacs/domdec/domdec_specatomcomm.h

   1 /*
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  35 /*! \internal \file
  36  *
  37  * \brief This file declares functions for domdec to use
  38  * while managing communication of atoms required for special purposes
  39  *
  40  * \author Berk Hess <hess@kth.se>
  41  * \ingroup module_domdec
  42  */
  43
  44 #ifndef GMX_DOMDEC_DOMDEC_SPECATOMCOMM_H
  45 #define GMX_DOMDEC_DOMDEC_SPECATOMCOMM_H
  46
  47 #include <vector>
  48
  49 #include "gromacs/math/vectypes.h"
  50 #include "gromacs/utility/basedefinitions.h"
  51
  52 struct gmx_domdec_t;
  53 struct t_commrec;
  54
  55 namespace gmx
  56 {
  57 template <typename T> class HashedMap;
  58 } // namespace
  59
  60 /*! \internal \brief The communication setup along a single dimension */
  61 struct gmx_specatsend_t
  62 {
  63     std::vector<int> a;     /**< The indices of atoms to send */
  64     int              nrecv; /**< The number of atoms to receive */
  65 };
  66
  67 /*! \internal \brief Struct with setup and buffers for special atom communication */
  68 struct gmx_domdec_specat_comm_t
  69 {
  70     /* The number of indices to receive during the setup */
  71     int               nreq[DIM][2][2] = {{{0}}}; /**< The nr. of atoms requested, per DIM, direction and direct/indirect */
  72     /* The atoms to send */
  73     gmx_specatsend_t  spas[DIM][2];              /**< The communication setup per DIM, direction */
  74     std::vector<bool> sendAtom;                  /**< Work buffer that tells if spec.atoms should be sent */
  75
  76     /* Send buffers */
  77     std::vector<int>       ibuf;       /**< Integer send buffer */
  78     std::vector<gmx::RVec> vbuf;       /**< rvec send buffer */
  79     std::vector<gmx::RVec> vbuf2;      /**< rvec send buffer */
  80     /* The range in the local buffer(s) for received atoms */
  81     int                    at_start;   /**< Start index of received atoms */
  82     int                    at_end;     /**< End index of received atoms */
  83 };
  84
  85 /*! \brief Communicates the force for special atoms, the shift forces are reduced with \p fshift != NULL */
  86 void dd_move_f_specat(gmx_domdec_t *dd, gmx_domdec_specat_comm_t *spac,
  87                       rvec *f, rvec *fshift);
  88
  89 /*! \brief Communicates the coordinates for special atoms
  90  *
  91  * \param[in]     dd         Domain decomposition struct
  92  * \param[in]     spac       Special atom communication struct
  93  * \param[in]     box        Box, used for pbc
  94  * \param[in,out] x0         Vector to communicate
  95  * \param[in,out] x1         Vector to communicate, when != NULL
  96  * \param[in]     bX1IsCoord Tells is \p x1 is a coordinate vector (needs pbc)
  97  */
  98 void dd_move_x_specat(gmx_domdec_t *dd, gmx_domdec_specat_comm_t *spac,
  99                       const matrix box,
 100                       rvec *x0,
 101                       rvec *x1, gmx_bool bX1IsCoord);
 102
 103 /*! \brief Sets up the communication for special atoms
 104  *
 105  * \param[in]     dd           Domain decomposition struct
 106  * \param[in,out] ireq         List of requested atom indices, updated due to aggregation
 107  * \param[in,out] spac         Special atom communication struct
 108  * \param[out]    ga2la_specat Global to local special atom index
 109  * \param[in]     at_start     Index in local state where to start storing communicated atoms
 110  * \param[in]     vbuf_fac     Buffer factor, 1 or 2 for communicating 1 or 2 vectors
 111  * \param[in]     specat_type  Name of the special atom, used for error message
 112  * \param[in]     add_err      Text to add at the end of error message when atoms can't be found
 113  */
 114 int setup_specat_communication(gmx_domdec_t               *dd,
 115                                std::vector<int>           *ireq,
 116                                gmx_domdec_specat_comm_t   *spac,
 117                                gmx::HashedMap<int>        *ga2la_specat,
 118                                int                         at_start,
 119                                int                         vbuf_fac,
 120                                const char                 *specat_type,
 121                                const char                 *add_err);
 122
 123 #endif