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 gmx_multisim_t;
  51 struct t_extmass;
  52 struct t_fcdata;
  53 struct t_graph;
  54 struct t_grpopts;
  55 struct t_idef;
  56 struct t_inputrec;
  57 struct t_mdatoms;
  58 struct t_nrnb;
  59 class t_state;
  60
  61 /* Abstract type for update */
  62 struct gmx_update_t;
  63
  64 namespace gmx
  65 {
  66 class Constraints;
  67 }
  68
  69 /* Initialize the stochastic dynamics struct */
  70 gmx_update_t *init_update(const t_inputrec *ir);
  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                               gmx_int64_t step, matrix box);
  87
  88 void update_tcouple(gmx_int64_t       step,
  89                     t_inputrec       *inputrec,
  90                     t_state          *state,
  91                     gmx_ekindata_t   *ekind,
  92                     t_extmass        *MassQ,
  93                     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                                        gmx_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                                       gmx_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(gmx_int64_t                    step,
 123                    t_inputrec                    *inputrec, /* input record and box stuff       */
 124                    t_mdatoms                     *md,
 125                    t_state                       *state,
 126                    gmx::PaddedArrayRef<gmx::RVec> f, /* forces on home particles */
 127                    t_fcdata                      *fcd,
 128                    gmx_ekindata_t                *ekind,
 129                    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                    gmx::Constraints              *constr);
 134
 135 /* Return TRUE if OK, FALSE in case of Shake Error */
 136
 137 extern gmx_bool update_randomize_velocities(t_inputrec *ir, gmx_int64_t step, const t_commrec *cr, t_mdatoms *md, t_state *state, gmx_update_t *upd, gmx::Constraints *constr);
 138
 139 void constrain_velocities(gmx_int64_t                    step,
 140                           real                          *dvdlambda, /* the contribution to be added to the bonded interactions */
 141                           const t_inputrec              *inputrec,  /* input record and box stuff */
 142                           t_mdatoms                     *md,
 143                           t_state                       *state,
 144                           gmx_bool                       bMolPBC,
 145                           t_idef                        *idef,
 146                           tensor                         vir_part,
 147                           const t_commrec               *cr,
 148                           const gmx_multisim_t          *ms,
 149                           t_nrnb                        *nrnb,
 150                           gmx_wallcycle_t                wcycle,
 151                           gmx::Constraints              *constr,
 152                           gmx_bool                       bCalcVir,
 153                           bool                           do_log,
 154                           bool                           do_ene);
 155
 156 void constrain_coordinates(gmx_int64_t                    step,
 157                            real                          *dvdlambda, /* the contribution to be added to the bonded interactions */
 158                            const t_inputrec              *inputrec,  /* input record and box stuff */
 159                            t_mdatoms                     *md,
 160                            t_state                       *state,
 161                            gmx_bool                       bMolPBC,
 162                            t_idef                        *idef,
 163                            tensor                         vir_part,
 164                            const t_commrec               *cr,
 165                            const gmx_multisim_t          *ms,
 166                            t_nrnb                        *nrnb,
 167                            gmx_wallcycle_t                wcycle,
 168                            gmx_update_t                  *upd,
 169                            gmx::Constraints              *constr,
 170                            gmx_bool                       bCalcVir,
 171                            bool                           do_log,
 172                            bool                           do_ene);
 173
 174 void update_sd_second_half(gmx_int64_t                    step,
 175                            real                          *dvdlambda, /* the contribution to be added to the bonded interactions */
 176                            const t_inputrec              *inputrec,  /* input record and box stuff */
 177                            t_mdatoms                     *md,
 178                            t_state                       *state,
 179                            gmx_bool                       bMolPBC,
 180                            gmx::PaddedArrayRef<gmx::RVec> force,  /* forces on home particles */
 181                            t_idef                        *idef,
 182                            const t_commrec               *cr,
 183                            const gmx_multisim_t          *ms,
 184                            t_nrnb                        *nrnb,
 185                            gmx_wallcycle_t                wcycle,
 186                            gmx_update_t                  *upd,
 187                            gmx::Constraints              *constr,
 188                            bool                           do_log,
 189                            bool                           do_ene);
 190
 191 void finish_update(const t_inputrec              *inputrec,
 192                    t_mdatoms                     *md,
 193                    t_state                       *state,
 194                    t_graph                       *graph,
 195                    t_nrnb                        *nrnb,
 196                    gmx_wallcycle_t                wcycle,
 197                    gmx_update_t                  *upd,
 198                    gmx::Constraints              *constr);
 199
 200 /* Return TRUE if OK, FALSE in case of Shake Error */
 201
 202 void calc_ke_part(t_state *state, t_grpopts *opts, t_mdatoms *md,
 203                   gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel);
 204 /*
 205  * Compute the partial kinetic energy for home particles;
 206  * will be accumulated in the calling routine.
 207  * The tensor is
 208  *
 209  * Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
 210  *
 211  *     use v[i] = v[i] - u[i] when calculating temperature
 212  *
 213  * u must be accumulated already.
 214  *
 215  * Now also computes the contribution of the kinetic energy to the
 216  * free energy
 217  *
 218  */
 219
 220
 221 void
 222 init_ekinstate(ekinstate_t *ekinstate, const t_inputrec *ir);
 223
 224 void
 225 update_ekinstate(ekinstate_t *ekinstate, gmx_ekindata_t *ekind);
 226
 227 /*! \brief Restores data from \p ekinstate to \p ekind, then broadcasts it
 228    to the rest of the simulation */
 229 void
 230 restore_ekinstate_from_state(const t_commrec *cr,
 231                              gmx_ekindata_t *ekind, const ekinstate_t *ekinstate);
 232
 233 void berendsen_tcoupl(const t_inputrec *ir, const gmx_ekindata_t *ekind, real dt,
 234                       std::vector<double> &therm_integral);
 235
 236 void andersen_tcoupl(t_inputrec *ir, gmx_int64_t step,
 237                      const t_commrec *cr, const t_mdatoms *md, t_state *state, real rate, const gmx_bool *randomize, const real *boltzfac);
 238
 239 void nosehoover_tcoupl(t_grpopts *opts, gmx_ekindata_t *ekind, real dt,
 240                        double xi[], double vxi[], t_extmass *MassQ);
 241
 242 void trotter_update(t_inputrec *ir, gmx_int64_t step, gmx_ekindata_t *ekind,
 243                     gmx_enerdata_t *enerd, t_state *state, tensor vir, t_mdatoms *md,
 244                     t_extmass *MassQ, int **trotter_seqlist, int trotter_seqno);
 245
 246 int **init_npt_vars(t_inputrec *ir, t_state *state, t_extmass *Mass, gmx_bool bTrotter);
 247
 248 real NPT_energy(const t_inputrec *ir, const t_state *state, const t_extmass *MassQ);
 249 /* computes all the pressure/tempertature control energy terms to get a conserved energy */
 250
 251 void NBaroT_trotter(t_grpopts *opts, real dt,
 252                     double xi[], double vxi[], real *veta, t_extmass *MassQ);
 253
 254 void vrescale_tcoupl(t_inputrec *ir, gmx_int64_t step,
 255                      gmx_ekindata_t *ekind, real dt,
 256                      double therm_integral[]);
 257 /* Compute temperature scaling. For V-rescale it is done in update. */
 258
 259 void rescale_velocities(gmx_ekindata_t *ekind, t_mdatoms *mdatoms,
 260                         int start, int end, rvec v[]);
 261 /* Rescale the velocities with the scaling factor in ekind */
 262
 263 void update_annealing_target_temp(t_inputrec *ir, real t, gmx_update_t *upd);
 264 /* Set reference temp for simulated annealing at time t*/
 265
 266 real calc_temp(real ekin, real nrdf);
 267 /* Calculate the temperature */
 268
 269 real calc_pres(int ePBC, int nwall, matrix box, tensor ekin, tensor vir,
 270                tensor pres);
 271 /* Calculate the pressure tensor, returns the scalar pressure.
 272  * The unit of pressure is bar.
 273  */
 274
 275 void parrinellorahman_pcoupl(FILE *fplog, gmx_int64_t step,
 276                              const t_inputrec *ir, real dt, const tensor pres,
 277                              tensor box, tensor box_rel, tensor boxv,
 278                              tensor M, matrix mu,
 279                              gmx_bool bFirstStep);
 280
 281 void berendsen_pcoupl(FILE *fplog, gmx_int64_t step,
 282                       const t_inputrec *ir, real dt,
 283                       const tensor pres, const matrix box,
 284                       const matrix force_vir, const matrix constraint_vir,
 285                       matrix mu, double *baros_integral);
 286
 287 void berendsen_pscale(const t_inputrec *ir, const matrix mu,
 288                       matrix box, matrix box_rel,
 289                       int start, int nr_atoms,
 290                       rvec x[], const unsigned short cFREEZE[],
 291                       t_nrnb *nrnb);
 292
 293 void correct_ekin(FILE *log, int start, int end, rvec v[],
 294                   rvec vcm, real mass[], real tmass, tensor ekin);
 295 /* Correct ekin for vcm */
 296
 297 #endif