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37 #ifndef GMX_MDLIB_VSITE_H
38 #define GMX_MDLIB_VSITE_H
42 #include "gromacs/math/vectypes.h"
43 #include "gromacs/pbcutil/ishift.h"
44 #include "gromacs/topology/idef.h"
45 #include "gromacs/utility/arrayref.h"
46 #include "gromacs/utility/basedefinitions.h"
47 #include "gromacs/utility/real.h"
49 struct gmx_localtop_t;
59 /* The start and end values of for the vsite indices in the ftype enum.
60 * The validity of these values is checked in init_vsite.
61 * This is used to avoid loops over all ftypes just to get the vsite entries.
62 * (We should replace the fixed ilist array by only the used entries.)
64 static constexpr int c_ftypeVsiteStart = F_VSITE2;
65 static constexpr int c_ftypeVsiteEnd = F_VSITEN + 1;
67 /* Type for storing PBC atom information for all vsite types in the system */
68 typedef std::array<std::vector<int>, c_ftypeVsiteEnd - c_ftypeVsiteStart> VsitePbc;
70 /* Data for handling vsites, needed with OpenMP threading or with charge-groups and PBC */
77 gmx_bool bHaveChargeGroups; /* Do we have charge groups? */
78 int n_intercg_vsite; /* The number of inter charge group vsites */
79 std::vector<VsitePbc> vsite_pbc_molt; /* The pbc atoms for intercg vsites */
80 std::unique_ptr<VsitePbc> vsite_pbc_loc; /* The local pbc atoms */
81 int nthreads; /* Number of threads used for vsites */
82 std::vector < std::unique_ptr < VsiteThread>> tData; /* Thread local vsites and work structs */
83 std::vector<int> taskIndex; /* Work array */
84 bool useDomdec; /* Tells whether we use domain decomposition with more than 1 DD rank */
87 /*! \brief Create positions of vsite atoms based for the local system
89 * \param[in] vsite The vsite struct, when nullptr is passed, no MPI and no multi-threading is used
90 * \param[in,out] x The coordinates
91 * \param[in] dt The time step
92 * \param[in,out] v When != nullptr, velocities for vsites are set as displacement/dt
93 * \param[in] ip Interaction parameters
94 * \param[in] ilist The interaction list
95 * \param[in] ePBC The type of periodic boundary conditions
96 * \param[in] bMolPBC When true, molecules are broken over PBC
97 * \param[in] cr The communication record
98 * \param[in] box The box
100 void construct_vsites(const gmx_vsite_t *vsite,
103 const t_iparams ip[], const t_ilist ilist[],
104 int ePBC, gmx_bool bMolPBC,
108 /*! \brief Create positions of vsite atoms for the whole system assuming all molecules are wholex
110 * \param[in] mtop The global topology
111 * \param[in,out] x The global coordinates
113 void constructVsitesGlobal(const gmx_mtop_t &mtop,
114 gmx::ArrayRef<gmx::RVec> x);
116 void spread_vsite_f(const gmx_vsite_t *vsite,
118 rvec f[], rvec *fshift,
119 gmx_bool VirCorr, matrix vir,
120 t_nrnb *nrnb, const t_idef *idef,
121 int ePBC, gmx_bool bMolPBC, const t_graph *g, const matrix box,
122 const t_commrec *cr, gmx_wallcycle *wcycle);
123 /* Spread the force operating on the vsite atoms on the surrounding atoms.
124 * If fshift!=NULL also update the shift forces.
125 * If VirCorr=TRUE add the virial correction for non-linear vsite constructs
126 * to vir. This correction is required when the virial is not calculated
127 * afterwards from the particle position and forces, but in a different way,
128 * as for instance for the PME mesh contribution.
131 int count_intercg_vsites(const gmx_mtop_t *mtop);
132 /* Returns the number of virtual sites that cross charge groups */
134 /* Initialize the virtual site struct,
136 * \param[in] mtop The global topology
137 * \param[in] cr The communication record
138 * \returns A valid vsite struct or nullptr when there are no virtual sites
140 std::unique_ptr<gmx_vsite_t>
141 initVsite(const gmx_mtop_t &mtop,
142 const t_commrec *cr);
144 void split_vsites_over_threads(const t_ilist *ilist,
146 const t_mdatoms *mdatoms,
148 /* Divide the vsite work-load over the threads.
149 * Should be called at the end of the domain decomposition.
152 void set_vsite_top(gmx_vsite_t *vsite,
153 const gmx_localtop_t *top,
154 const t_mdatoms *md);
155 /* Set some vsite data for runs without domain decomposition.
156 * Should be called once after init_vsite, before calling other routines.