src/gromacs/mdlib/update.h

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  37 #ifndef GMX_MDLIB_UPDATE_H
  38 #define GMX_MDLIB_UPDATE_H
  39
  40 #include "gromacs/math/paddedvector.h"
  41 #include "gromacs/math/vectypes.h"
  42 #include "gromacs/timing/wallcycle.h"
  43 #include "gromacs/utility/arrayref.h"
  44 #include "gromacs/utility/basedefinitions.h"
  45 #include "gromacs/utility/real.h"
  46
  47 class ekinstate_t;
  48 struct gmx_ekindata_t;
  49 struct gmx_enerdata_t;
  50 struct t_extmass;
  51 struct t_fcdata;
  52 struct t_graph;
  53 struct t_grpopts;
  54 struct t_inputrec;
  55 struct t_mdatoms;
  56 struct t_nrnb;
  57 class t_state;
  58
  59 /* Abstract type for update */
  60 struct gmx_update_t;
  61
  62 namespace gmx
  63 {
  64 class BoxDeformation;
  65 class Constraints;
  66 }
  67
  68 /* Initialize the stochastic dynamics struct */
  69 gmx_update_t *init_update(const t_inputrec    *ir,
  70                           gmx::BoxDeformation *deform);
  71
  72 /* Update pre-computed constants that depend on the reference
  73  * temperature for coupling.
  74  *
  75  * This could change e.g. in simulated annealing. */
  76 void update_temperature_constants(gmx_update_t *upd, const t_inputrec *ir);
  77
  78 /* Update the size of per-atom arrays (e.g. after DD re-partitioning,
  79    which might increase the number of home atoms). */
  80 void update_realloc(gmx_update_t *upd, int natoms);
  81
  82 /* Store the box at step step
  83  * as a reference state for simulations with box deformation.
  84  */
  85 void set_deform_reference_box(gmx_update_t *upd,
  86                               int64_t step, matrix box);
  87
  88 void update_tcouple(int64_t           step,
  89                     const t_inputrec *inputrec,
  90                     t_state          *state,
  91                     gmx_ekindata_t   *ekind,
  92                     const t_extmass  *MassQ,
  93                     const t_mdatoms  *md
  94                     );
  95
  96 /* Update Parrinello-Rahman, to be called before the coordinate update */
  97 void update_pcouple_before_coordinates(FILE             *fplog,
  98                                        int64_t           step,
  99                                        const t_inputrec *inputrec,
 100                                        t_state          *state,
 101                                        matrix            parrinellorahmanMu,
 102                                        matrix            M,
 103                                        gmx_bool          bInitStep);
 104
 105 /* Update the box, to be called after the coordinate update.
 106  * For Berendsen P-coupling, also calculates the scaling factor
 107  * and scales the coordinates.
 108  * When the deform option is used, scales coordinates and box here.
 109  */
 110 void update_pcouple_after_coordinates(FILE             *fplog,
 111                                       int64_t           step,
 112                                       const t_inputrec *inputrec,
 113                                       const t_mdatoms  *md,
 114                                       const matrix      pressure,
 115                                       const matrix      forceVirial,
 116                                       const matrix      constraintVirial,
 117                                       const matrix      parrinellorahmanMu,
 118                                       t_state          *state,
 119                                       t_nrnb           *nrnb,
 120                                       gmx_update_t     *upd);
 121
 122 void update_coords(int64_t                              step,
 123                    const t_inputrec                    *inputrec, /* input record and box stuff */
 124                    const t_mdatoms                     *md,
 125                    t_state                             *state,
 126                    gmx::PaddedArrayRef<gmx::RVec>       f, /* forces on home particles */
 127                    const t_fcdata                      *fcd,
 128                    const gmx_ekindata_t                *ekind,
 129                    const matrix                         M,
 130                    gmx_update_t                        *upd,
 131                    int                                  bUpdatePart,
 132                    const t_commrec                     *cr, /* these shouldn't be here -- need to think about it */
 133                    const gmx::Constraints              *constr);
 134
 135 /* Return TRUE if OK, FALSE in case of Shake Error */
 136
 137 extern gmx_bool update_randomize_velocities(const t_inputrec *ir, int64_t step, const t_commrec *cr,
 138                                             const t_mdatoms *md, t_state *state, const gmx_update_t *upd,
 139                                             const gmx::Constraints *constr);
 140
 141 void constrain_velocities(int64_t                        step,
 142                           real                          *dvdlambda, /* the contribution to be added to the bonded interactions */
 143                           t_state                       *state,
 144                           tensor                         vir_part,
 145                           gmx_wallcycle_t                wcycle,
 146                           gmx::Constraints              *constr,
 147                           gmx_bool                       bCalcVir,
 148                           bool                           do_log,
 149                           bool                           do_ene);
 150
 151 void constrain_coordinates(int64_t                        step,
 152                            real                          *dvdlambda, /* the contribution to be added to the bonded interactions */
 153                            t_state                       *state,
 154                            tensor                         vir_part,
 155                            gmx_wallcycle_t                wcycle,
 156                            gmx_update_t                  *upd,
 157                            gmx::Constraints              *constr,
 158                            gmx_bool                       bCalcVir,
 159                            bool                           do_log,
 160                            bool                           do_ene);
 161
 162 void update_sd_second_half(int64_t                        step,
 163                            real                          *dvdlambda, /* the contribution to be added to the bonded interactions */
 164                            const t_inputrec              *inputrec,  /* input record and box stuff */
 165                            const t_mdatoms               *md,
 166                            t_state                       *state,
 167                            const t_commrec               *cr,
 168                            t_nrnb                        *nrnb,
 169                            gmx_wallcycle_t                wcycle,
 170                            gmx_update_t                  *upd,
 171                            gmx::Constraints              *constr,
 172                            bool                           do_log,
 173                            bool                           do_ene);
 174
 175 void finish_update(const t_inputrec              *inputrec,
 176                    const t_mdatoms               *md,
 177                    t_state                       *state,
 178                    const t_graph                 *graph,
 179                    t_nrnb                        *nrnb,
 180                    gmx_wallcycle_t                wcycle,
 181                    gmx_update_t                  *upd,
 182                    const gmx::Constraints        *constr);
 183
 184 /* Return TRUE if OK, FALSE in case of Shake Error */
 185
 186 void calc_ke_part(const t_state *state, const t_grpopts *opts, const t_mdatoms *md,
 187                   gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel);
 188 /*
 189  * Compute the partial kinetic energy for home particles;
 190  * will be accumulated in the calling routine.
 191  * The tensor is
 192  *
 193  * Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
 194  *
 195  *     use v[i] = v[i] - u[i] when calculating temperature
 196  *
 197  * u must be accumulated already.
 198  *
 199  * Now also computes the contribution of the kinetic energy to the
 200  * free energy
 201  *
 202  */
 203
 204
 205 void
 206 init_ekinstate(ekinstate_t *ekinstate, const t_inputrec *ir);
 207
 208 void
 209 update_ekinstate(ekinstate_t *ekinstate, const gmx_ekindata_t *ekind);
 210
 211 /*! \brief Restores data from \p ekinstate to \p ekind, then broadcasts it
 212    to the rest of the simulation */
 213 void
 214 restore_ekinstate_from_state(const t_commrec *cr,
 215                              gmx_ekindata_t *ekind, const ekinstate_t *ekinstate);
 216
 217 void berendsen_tcoupl(const t_inputrec *ir, const gmx_ekindata_t *ekind, real dt,
 218                       std::vector<double> &therm_integral); //NOLINT(google-runtime-references)
 219
 220 void andersen_tcoupl(const t_inputrec *ir, int64_t step,
 221                      const t_commrec *cr, const t_mdatoms *md, t_state *state, real rate, const gmx_bool *randomize, const real *boltzfac);
 222
 223 void nosehoover_tcoupl(const t_grpopts *opts, const gmx_ekindata_t *ekind, real dt,
 224                        double xi[], double vxi[], const t_extmass *MassQ);
 225
 226 void trotter_update(const t_inputrec *ir, int64_t step, gmx_ekindata_t *ekind,
 227                     const gmx_enerdata_t *enerd, t_state *state, const tensor vir, const t_mdatoms *md,
 228                     const t_extmass *MassQ, const int * const *trotter_seqlist, int trotter_seqno);
 229
 230 int **init_npt_vars(const t_inputrec *ir, t_state *state, t_extmass *Mass, gmx_bool bTrotter);
 231
 232 real NPT_energy(const t_inputrec *ir, const t_state *state, const t_extmass *MassQ);
 233 /* computes all the pressure/tempertature control energy terms to get a conserved energy */
 234
 235 // TODO: This doesn't seem to be used or implemented anywhere
 236 void NBaroT_trotter(t_grpopts *opts, real dt,
 237                     double xi[], double vxi[], real *veta, t_extmass *MassQ);
 238
 239 void vrescale_tcoupl(const t_inputrec *ir, int64_t step,
 240                      gmx_ekindata_t *ekind, real dt,
 241                      double therm_integral[]);
 242 /* Compute temperature scaling. For V-rescale it is done in update. */
 243
 244 void rescale_velocities(const gmx_ekindata_t *ekind, const t_mdatoms *mdatoms,
 245                         int start, int end, rvec v[]);
 246 /* Rescale the velocities with the scaling factor in ekind */
 247
 248 // TODO: This is the only function in update.h altering the inputrec
 249 void update_annealing_target_temp(t_inputrec *ir, real t, gmx_update_t *upd);
 250 /* Set reference temp for simulated annealing at time t*/
 251
 252 real calc_temp(real ekin, real nrdf);
 253 /* Calculate the temperature */
 254
 255 real calc_pres(int ePBC, int nwall, const matrix box, const tensor ekin, const tensor vir,
 256                tensor pres);
 257 /* Calculate the pressure tensor, returns the scalar pressure.
 258  * The unit of pressure is bar.
 259  */
 260
 261 void parrinellorahman_pcoupl(FILE *fplog, int64_t step,
 262                              const t_inputrec *ir, real dt, const tensor pres,
 263                              const tensor box, tensor box_rel, tensor boxv,
 264                              tensor M, matrix mu,
 265                              gmx_bool bFirstStep);
 266
 267 void berendsen_pcoupl(FILE *fplog, int64_t step,
 268                       const t_inputrec *ir, real dt,
 269                       const tensor pres, const matrix box,
 270                       const matrix force_vir, const matrix constraint_vir,
 271                       matrix mu, double *baros_integral);
 272
 273 void berendsen_pscale(const t_inputrec *ir, const matrix mu,
 274                       matrix box, matrix box_rel,
 275                       int start, int nr_atoms,
 276                       rvec x[], const unsigned short cFREEZE[],
 277                       t_nrnb *nrnb);
 278
 279 // TODO: This doesn't seem to be used or implemented anywhere
 280 void correct_ekin(FILE *log, int start, int end, rvec v[],
 281                   rvec vcm, real mass[], real tmass, tensor ekin);
 282 /* Correct ekin for vcm */
 283
 284 #endif