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37 * \brief This file declares functions for domdec to use
38 * while managing communication of atoms required for special purposes
40 * \author Berk Hess <hess@kth.se>
41 * \ingroup module_domdec
44 #ifndef GMX_DOMDEC_DOMDEC_SPECATOMCOMM_H
45 #define GMX_DOMDEC_DOMDEC_SPECATOMCOMM_H
47 #include "gromacs/math/vectypes.h"
48 #include "gromacs/utility/basedefinitions.h"
67 /*! \internal \brief Struct with setup and buffers for special atom communication */
68 struct gmx_domdec_specat_comm_t
{
69 /* The number of indices to receive during the setup */
70 int nreq
[DIM
][2][2]; /**< The nr. of atoms requested, per DIM, direction and direct/indirect */
71 /* The atoms to send */
72 gmx_specatsend_t spas
[DIM
][2]; /**< The communication setup per DIM, direction */
73 gmx_bool
*bSendAtom
; /**< Work buffer that tells if spec.atoms should be sent */
74 int bSendAtom_nalloc
; /**< Allocation size of \p bSendAtom */
76 int *ibuf
; /**< Integer send buffer */
77 int ibuf_nalloc
; /**< Allocation size of \p ibuf */
78 rvec
*vbuf
; /**< rvec send buffer */
79 int vbuf_nalloc
; /**< Allocation size of \p vbuf */
80 rvec
*vbuf2
; /**< rvec send buffer */
81 int vbuf2_nalloc
; /**< Allocation size of \p vbuf2 */
82 /* The range in the local buffer(s) for received atoms */
83 int at_start
; /**< Start index of received atoms */
84 int at_end
; /**< End index of received atoms */
86 /* The atom indices we need from the surrounding cells.
87 * We can gather the indices over nthread threads.
89 int nthread
; /**< Number of threads used for spec.atom communication */
90 ind_req_t
*ireq
; /**< Index request buffer per thread, allocation size \p nthread */
93 /*! \brief Communicates the force for special atoms, the shift forces are reduced with \p fshift != NULL */
94 void dd_move_f_specat(gmx_domdec_t
*dd
, gmx_domdec_specat_comm_t
*spac
,
95 rvec
*f
, rvec
*fshift
);
97 /*! \brief Communicates the coordinates for special atoms
99 * \param[in] dd Domain decomposition struct
100 * \param[in] spac Special atom communication struct
101 * \param[in] box Box, used for pbc
102 * \param[in,out] x0 Vector to communicate
103 * \param[in,out] x1 Vector to communicate, when != NULL
104 * \param[in] bX1IsCoord Tells is \p x1 is a coordinate vector (needs pbc)
106 void dd_move_x_specat(gmx_domdec_t
*dd
, gmx_domdec_specat_comm_t
*spac
,
109 rvec
*x1
, gmx_bool bX1IsCoord
);
111 /*! \brief Sets up the communication for special atoms
113 * \param[in] dd Domain decomposition struct
114 * \param[in] ireq List of requested atom indices
115 * \param[in,out] spac Special atom communication struct
116 * \param[out] ga2la_specat Global to local special atom index
117 * \param[in] at_start Index in local state where to start storing communicated atoms
118 * \param[in] vbuf_fac Buffer factor, 1 or 2 for communicating 1 or 2 vectors
119 * \param[in] specat_type Name of the special atom, used for error message
120 * \param[in] add_err Text to add at the end of error message when atoms can't be found
122 int setup_specat_communication(gmx_domdec_t
*dd
,
124 gmx_domdec_specat_comm_t
*spac
,
125 gmx_hash_t
*ga2la_specat
,
128 const char *specat_type
,
129 const char *add_err
);
131 /*! \brief Initialize a special communication struct */
132 gmx_domdec_specat_comm_t
*specat_comm_init(int nthread
);