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