src/gromacs/mdlib/vsite.h

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  37 #ifndef GMX_MDLIB_VSITE_H
  38 #define GMX_MDLIB_VSITE_H
  39
  40 #include "gromacs/math/vectypes.h"
  41 #include "gromacs/pbcutil/ishift.h"
  42 #include "gromacs/topology/idef.h"
  43 #include "gromacs/utility/basedefinitions.h"
  44 #include "gromacs/utility/real.h"
  45
  46 struct gmx_localtop_t;
  47 struct gmx_mtop_t;
  48 struct t_commrec;
  49 struct t_graph;
  50 struct t_ilist;
  51 struct t_mdatoms;
  52 struct t_nrnb;
  53
  54 typedef struct gmx_vsite_t {
  55     gmx_bool             bHaveChargeGroups;    /* Do we have charge groups?               */
  56     int                  n_intercg_vsite;      /* The number of inter charge group vsites */
  57     int                  nvsite_pbc_molt;      /* The array size of vsite_pbc_molt        */
  58     int               ***vsite_pbc_molt;       /* The pbc atoms for intercg vsites        */
  59     int                **vsite_pbc_loc;        /* The local pbc atoms                     */
  60     int                 *vsite_pbc_loc_nalloc; /* Sizes of vsite_pbc_loc                  */
  61     int                  nthreads;             /* Number of threads used for vsites       */
  62     struct VsiteThread **tData;                /* Thread local vsites and work structs    */
  63     int                 *taskIndex;            /* Work array                              */
  64     int                  taskIndexNalloc;      /* Size of taskIndex                       */
  65 } gmx_vsite_t;
  66
  67 void construct_vsites(const gmx_vsite_t *vsite,
  68                       rvec x[],
  69                       real dt, rvec v[],
  70                       const t_iparams ip[], const t_ilist ilist[],
  71                       int ePBC, gmx_bool bMolPBC,
  72                       t_commrec *cr, matrix box);
  73 /* Create positions of vsite atoms based on surrounding atoms
  74  * for the local system.
  75  * If v is passed, the velocities of the vsites will be calculated
  76  * as the new positions minus the old positions divided by dt,
  77  * thus v should only be passed when the coordinates have been
  78  * updated with a full time step.
  79  * Note that velocitis of vsites are completely irrelevant
  80  * for the integration, they are only useful for analysis.
  81  */
  82
  83 void construct_vsites_mtop(gmx_vsite_t *vsite,
  84                            gmx_mtop_t *mtop, rvec x[]);
  85 /* Create positions of vsite atoms based on surrounding atoms
  86  * for the whole system.
  87  * This function assumes that all molecules are whole.
  88  */
  89
  90 void spread_vsite_f(const gmx_vsite_t *vsite,
  91                     const rvec x[],
  92                     rvec f[], rvec *fshift,
  93                     gmx_bool VirCorr, matrix vir,
  94                     t_nrnb *nrnb, const t_idef *idef,
  95                     int ePBC, gmx_bool bMolPBC, const t_graph *g, const matrix box,
  96                     t_commrec *cr);
  97 /* Spread the force operating on the vsite atoms on the surrounding atoms.
  98  * If fshift!=NULL also update the shift forces.
  99  * If VirCorr=TRUE add the virial correction for non-linear vsite constructs
 100  * to vir. This correction is required when the virial is not calculated
 101  * afterwards from the particle position and forces, but in a different way,
 102  * as for instance for the PME mesh contribution.
 103  */
 104
 105 int count_intercg_vsites(const gmx_mtop_t *mtop);
 106 /* Returns the number of virtual sites that cross charge groups */
 107
 108 gmx_vsite_t *init_vsite(const gmx_mtop_t *mtop, t_commrec *cr,
 109                         gmx_bool bSerial_NoPBC);
 110 /* Initialize the virtual site struct,
 111  * returns NULL when there are no virtual sites.
 112  * bSerial_NoPBC is to generate a simple vsite setup to be
 113  * used only serial (no MPI or thread parallelization) and without pbc;
 114  * this is useful for correction vsites of the initial configuration.
 115  */
 116
 117 void split_vsites_over_threads(const t_ilist   *ilist,
 118                                const t_iparams *ip,
 119                                const t_mdatoms *mdatoms,
 120                                gmx_bool         bLimitRange,
 121                                gmx_vsite_t     *vsite);
 122 /* Divide the vsite work-load over the threads.
 123  * Should be called at the end of the domain decomposition.
 124  */
 125
 126 void set_vsite_top(gmx_vsite_t *vsite, gmx_localtop_t *top, t_mdatoms *md,
 127                    t_commrec *cr);
 128 /* Set some vsite data for runs without domain decomposition.
 129  * Should be called once after init_vsite, before calling other routines.
 130  */
 131
 132 #endif