src/gromacs/domdec/domdec_specatomcomm.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2005,2006,2007,2008,2009,2010,2012,2013,2014,2015, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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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 "gromacs/math/vectypes.h"
  48 #include "gromacs/mdtypes/commrec.h"
  49 #include "gromacs/utility/basedefinitions.h"
  50
  51 struct gmx_hash_t;
  52
  53 typedef struct {
  54     int  nsend;
  55     int *a;
  56     int  a_nalloc;
  57     int  nrecv;
  58 } gmx_specatsend_t;
  59
  60 typedef struct {
  61     int *ind;
  62     int  nalloc;
  63     int  n;
  64 } ind_req_t;
  65
  66 /*! \internal \brief Struct with setup and buffers for special atom communication */
  67 struct gmx_domdec_specat_comm_t {
  68     /* The number of indices to receive during the setup */
  69     int              nreq[DIM][2][2];  /**< The nr. of atoms requested, per DIM, direction and direct/indirect */
  70     /* The atoms to send */
  71     gmx_specatsend_t spas[DIM][2];     /**< The communication setup per DIM, direction */
  72     gmx_bool        *bSendAtom;        /**< Work buffer that tells if spec.atoms should be sent */
  73     int              bSendAtom_nalloc; /**< Allocation size of \p bSendAtom */
  74     /* Send buffers */
  75     int             *ibuf;             /**< Integer send buffer */
  76     int              ibuf_nalloc;      /**< Allocation size of \p ibuf */
  77     rvec            *vbuf;             /**< rvec send buffer */
  78     int              vbuf_nalloc;      /**< Allocation size of \p vbuf */
  79     rvec            *vbuf2;            /**< rvec send buffer */
  80     int              vbuf2_nalloc;     /**< Allocation size of \p vbuf2 */
  81     /* The range in the local buffer(s) for received atoms */
  82     int              at_start;         /**< Start index of received atoms */
  83     int              at_end;           /**< End index of received atoms */
  84
  85     /* The atom indices we need from the surrounding cells.
  86      * We can gather the indices over nthread threads.
  87      */
  88     int        nthread;                /**< Number of threads used for spec.atom communication */
  89     ind_req_t *ireq;                   /**< Index request buffer per thread, allocation size \p nthread */
  90 };
  91
  92 /*! \brief Communicates the force for special atoms, the shift forces are reduced with \p fshift != NULL */
  93 void dd_move_f_specat(gmx_domdec_t *dd, gmx_domdec_specat_comm_t *spac,
  94                       rvec *f, rvec *fshift);
  95
  96 /*! \brief Communicates the coordinates for special atoms
  97  *
  98  * \param[in]     dd         Domain decomposition struct
  99  * \param[in]     spac       Special atom communication struct
 100  * \param[in]     box        Box, used for pbc
 101  * \param[in,out] x0         Vector to communicate
 102  * \param[in,out] x1         Vector to communicate, when != NULL
 103  * \param[in]     bX1IsCoord Tells is \p x1 is a coordinate vector (needs pbc)
 104  */
 105 void dd_move_x_specat(gmx_domdec_t *dd, gmx_domdec_specat_comm_t *spac,
 106                       matrix box,
 107                       rvec *x0,
 108                       rvec *x1, gmx_bool bX1IsCoord);
 109
 110 /*! \brief Sets up the communication for special atoms
 111  *
 112  * \param[in]     dd         Domain decomposition struct
 113  * \param[in]     ireq List of requested atom indices
 114  * \param[in,out] spac   Special atom communication struct
 115  * \param[out]    ga2la_specat Global to local special atom index
 116  * \param[in]     at_start     Index in local state where to start storing communicated atoms
 117  * \param[in]     vbuf_fac     Buffer factor, 1 or 2 for communicating 1 or 2 vectors
 118  * \param[in]     specat_type  Name of the special atom, used for error message
 119  * \param[in]     add_err      Text to add at the end of error message when atoms can't be found
 120  */
 121 int setup_specat_communication(gmx_domdec_t               *dd,
 122                                ind_req_t                  *ireq,
 123                                gmx_domdec_specat_comm_t   *spac,
 124                                gmx_hash_t                 *ga2la_specat,
 125                                int                         at_start,
 126                                int                         vbuf_fac,
 127                                const char                 *specat_type,
 128                                const char                 *add_err);
 129
 130 /*! \brief Initialize a special communication struct */
 131 gmx_domdec_specat_comm_t *specat_comm_init(int nthread);
 132
 133 #endif