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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
49 #include "gromacs/math/vectypes.h"
50 #include "gromacs/utility/basedefinitions.h"
61 /*! \internal \brief The communication setup along a single dimension */
62 struct gmx_specatsend_t
64 std::vector<int> a; /**< The indices of atoms to send */
65 int nrecv; /**< The number of atoms to receive */
68 /*! \internal \brief Struct with setup and buffers for special atom communication */
69 struct gmx_domdec_specat_comm_t
71 /* The number of indices to receive during the setup */
72 int nreq[DIM][2][2] = { { { 0 } } }; /**< The nr. of atoms requested, per DIM, direction and direct/indirect */
73 /* The atoms to send */
74 gmx_specatsend_t spas[DIM][2]; /**< The communication setup per DIM, direction */
75 std::vector<bool> sendAtom; /**< Work buffer that tells if spec.atoms should be sent */
78 std::vector<int> ibuf; /**< Integer send buffer */
79 std::vector<gmx::RVec> vbuf; /**< rvec send buffer */
80 std::vector<gmx::RVec> vbuf2; /**< rvec send buffer */
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 */
86 /*! \brief Communicates the force for special atoms, the shift forces are reduced with \p fshift != NULL */
87 void dd_move_f_specat(gmx_domdec_t* dd, gmx_domdec_specat_comm_t* spac, rvec* f, rvec* fshift);
89 /*! \brief Communicates the coordinates for special atoms
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)
98 void dd_move_x_specat(gmx_domdec_t* dd,
99 gmx_domdec_specat_comm_t* spac,
103 gmx_bool bX1IsCoord);
105 /*! \brief Sets up the communication for special atoms
107 * \param[in] dd Domain decomposition struct
108 * \param[in,out] ireq List of requested atom indices, updated due to aggregation
109 * \param[in,out] spac Special atom communication struct
110 * \param[out] ga2la_specat Global to local special atom index
111 * \param[in] at_start Index in local state where to start storing communicated atoms
112 * \param[in] vbuf_fac Buffer factor, 1 or 2 for communicating 1 or 2 vectors
113 * \param[in] specat_type Name of the special atom, used for error message
114 * \param[in] add_err Text to add at the end of error message when atoms can't be found
116 int setup_specat_communication(gmx_domdec_t* dd,
117 std::vector<int>* ireq,
118 gmx_domdec_specat_comm_t* spac,
119 gmx::HashedMap<int>* ga2la_specat,
122 const char* specat_type,
123 const char* add_err);