src/gromacs/mdlib/update.h

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  38 #ifndef GMX_MDLIB_UPDATE_H
  39 #define GMX_MDLIB_UPDATE_H
  40
  41 #include "gromacs/math/paddedvector.h"
  42 #include "gromacs/math/vectypes.h"
  43 #include "gromacs/mdtypes/md_enums.h"
  44 #include "gromacs/timing/wallcycle.h"
  45 #include "gromacs/utility/arrayref.h"
  46 #include "gromacs/utility/basedefinitions.h"
  47 #include "gromacs/utility/classhelpers.h"
  48 #include "gromacs/utility/real.h"
  49
  50 class ekinstate_t;
  51 struct gmx_ekindata_t;
  52 struct gmx_enerdata_t;
  53 enum class PbcType;
  54 struct t_extmass;
  55 struct t_fcdata;
  56 struct t_graph;
  57 struct t_grpopts;
  58 struct t_inputrec;
  59 struct t_mdatoms;
  60 struct t_nrnb;
  61 class t_state;
  62
  63 /* Abstract type for update */
  64 struct gmx_stochd_t;
  65
  66 namespace gmx
  67 {
  68 class BoxDeformation;
  69 class Constraints;
  70
  71
  72 /*! \libinternal
  73  * \brief Contains data for update phase */
  74 class Update
  75 {
  76 public:
  77     //! Constructor
  78     Update(const t_inputrec* ir, BoxDeformation* boxDeformation);
  79     ~Update();
  80     // TODO Get rid of getters when more free functions are incorporated as member methods
  81     //! Returns handle to stochd_t struct
  82     gmx_stochd_t* sd() const;
  83     //! Returns pointer to PaddedVector xp
  84     PaddedVector<gmx::RVec>* xp();
  85     //! Returns handle to box deformation class
  86     BoxDeformation* deform() const;
  87     //! Resizes xp
  88     void setNumAtoms(int nAtoms);
  89
  90 private:
  91     //! Implementation type.
  92     class Impl;
  93     //! Implementation object.
  94     PrivateImplPointer<Impl> impl_;
  95 };
  96
  97 }; // namespace gmx
  98
  99 /* Update pre-computed constants that depend on the reference
 100  * temperature for coupling.
 101  *
 102  * This could change e.g. in simulated annealing. */
 103 void update_temperature_constants(gmx_stochd_t* sd, const t_inputrec* ir);
 104
 105 /* Update the size of per-atom arrays (e.g. after DD re-partitioning,
 106    which might increase the number of home atoms). */
 107
 108 void update_tcouple(int64_t           step,
 109                     const t_inputrec* inputrec,
 110                     t_state*          state,
 111                     gmx_ekindata_t*   ekind,
 112                     const t_extmass*  MassQ,
 113                     const t_mdatoms*  md);
 114
 115 /* Update Parrinello-Rahman, to be called before the coordinate update */
 116 void update_pcouple_before_coordinates(FILE*             fplog,
 117                                        int64_t           step,
 118                                        const t_inputrec* inputrec,
 119                                        t_state*          state,
 120                                        matrix            parrinellorahmanMu,
 121                                        matrix            M,
 122                                        gmx_bool          bInitStep);
 123
 124 /* Update the box, to be called after the coordinate update.
 125  * For Berendsen P-coupling, also calculates the scaling factor
 126  * and scales the coordinates.
 127  * When the deform option is used, scales coordinates and box here.
 128  */
 129 void update_pcouple_after_coordinates(FILE*             fplog,
 130                                       int64_t           step,
 131                                       const t_inputrec* inputrec,
 132                                       const t_mdatoms*  md,
 133                                       const matrix      pressure,
 134                                       const matrix      forceVirial,
 135                                       const matrix      constraintVirial,
 136                                       matrix            pressureCouplingMu,
 137                                       t_state*          state,
 138                                       t_nrnb*           nrnb,
 139                                       gmx::Update*      upd,
 140                                       bool              scaleCoordinates);
 141
 142 void update_coords(int64_t           step,
 143                    const t_inputrec* inputrec, /* input record and box stuff    */
 144                    const t_mdatoms*  md,
 145                    t_state*          state,
 146                    gmx::ArrayRefWithPadding<const gmx::RVec> f, /* forces on home particles */
 147                    const t_fcdata*                           fcd,
 148                    const gmx_ekindata_t*                     ekind,
 149                    const matrix                              M,
 150                    gmx::Update*                              upd,
 151                    int                                       bUpdatePart,
 152                    const t_commrec* cr, /* these shouldn't be here -- need to think about it */
 153                    const gmx::Constraints* constr);
 154
 155 /* Return TRUE if OK, FALSE in case of Shake Error */
 156
 157 extern gmx_bool update_randomize_velocities(const t_inputrec*        ir,
 158                                             int64_t                  step,
 159                                             const t_commrec*         cr,
 160                                             const t_mdatoms*         md,
 161                                             gmx::ArrayRef<gmx::RVec> v,
 162                                             const gmx::Update*       upd,
 163                                             const gmx::Constraints*  constr);
 164
 165 void constrain_velocities(int64_t step,
 166                           real* dvdlambda, /* the contribution to be added to the bonded interactions */
 167                           t_state*          state,
 168                           tensor            vir_part,
 169                           gmx::Constraints* constr,
 170                           gmx_bool          bCalcVir,
 171                           bool              do_log,
 172                           bool              do_ene);
 173
 174 void constrain_coordinates(int64_t step,
 175                            real* dvdlambda, /* the contribution to be added to the bonded interactions */
 176                            t_state*          state,
 177                            tensor            vir_part,
 178                            gmx::Update*      upd,
 179                            gmx::Constraints* constr,
 180                            gmx_bool          bCalcVir,
 181                            bool              do_log,
 182                            bool              do_ene);
 183
 184 void update_sd_second_half(int64_t step,
 185                            real* dvdlambda, /* the contribution to be added to the bonded interactions */
 186                            const t_inputrec* inputrec, /* input record and box stuff */
 187                            const t_mdatoms*  md,
 188                            t_state*          state,
 189                            const t_commrec*  cr,
 190                            t_nrnb*           nrnb,
 191                            gmx_wallcycle_t   wcycle,
 192                            gmx::Update*      upd,
 193                            gmx::Constraints* constr,
 194                            bool              do_log,
 195                            bool              do_ene);
 196
 197 void finish_update(const t_inputrec*       inputrec,
 198                    const t_mdatoms*        md,
 199                    t_state*                state,
 200                    const t_graph*          graph,
 201                    t_nrnb*                 nrnb,
 202                    gmx_wallcycle_t         wcycle,
 203                    gmx::Update*            upd,
 204                    const gmx::Constraints* constr);
 205
 206 /* Return TRUE if OK, FALSE in case of Shake Error */
 207
 208 void calc_ke_part(const rvec*      x,
 209                   const rvec*      v,
 210                   const matrix     box,
 211                   const t_grpopts* opts,
 212                   const t_mdatoms* md,
 213                   gmx_ekindata_t*  ekind,
 214                   t_nrnb*          nrnb,
 215                   gmx_bool         bEkinAveVel);
 216 /*
 217  * Compute the partial kinetic energy for home particles;
 218  * will be accumulated in the calling routine.
 219  * The tensor is
 220  *
 221  * Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
 222  *
 223  *     use v[i] = v[i] - u[i] when calculating temperature
 224  *
 225  * u must be accumulated already.
 226  *
 227  * Now also computes the contribution of the kinetic energy to the
 228  * free energy
 229  *
 230  */
 231
 232
 233 void init_ekinstate(ekinstate_t* ekinstate, const t_inputrec* ir);
 234
 235 void update_ekinstate(ekinstate_t* ekinstate, const gmx_ekindata_t* ekind);
 236
 237 /*! \brief Restores data from \p ekinstate to \p ekind, then broadcasts it
 238    to the rest of the simulation */
 239 void restore_ekinstate_from_state(const t_commrec* cr, gmx_ekindata_t* ekind, const ekinstate_t* ekinstate);
 240
 241 void berendsen_tcoupl(const t_inputrec*    ir,
 242                       gmx_ekindata_t*      ekind,
 243                       real                 dt,
 244                       std::vector<double>& therm_integral); //NOLINT(google-runtime-references)
 245
 246 void andersen_tcoupl(const t_inputrec*         ir,
 247                      int64_t                   step,
 248                      const t_commrec*          cr,
 249                      const t_mdatoms*          md,
 250                      gmx::ArrayRef<gmx::RVec>  v,
 251                      real                      rate,
 252                      const std::vector<bool>&  randomize,
 253                      gmx::ArrayRef<const real> boltzfac);
 254
 255 void nosehoover_tcoupl(const t_grpopts*      opts,
 256                        const gmx_ekindata_t* ekind,
 257                        real                  dt,
 258                        double                xi[],
 259                        double                vxi[],
 260                        const t_extmass*      MassQ);
 261
 262 void trotter_update(const t_inputrec*               ir,
 263                     int64_t                         step,
 264                     gmx_ekindata_t*                 ekind,
 265                     const gmx_enerdata_t*           enerd,
 266                     t_state*                        state,
 267                     const tensor                    vir,
 268                     const t_mdatoms*                md,
 269                     const t_extmass*                MassQ,
 270                     gmx::ArrayRef<std::vector<int>> trotter_seqlist,
 271                     int                             trotter_seqno);
 272
 273 std::array<std::vector<int>, ettTSEQMAX>
 274 init_npt_vars(const t_inputrec* ir, t_state* state, t_extmass* Mass, gmx_bool bTrotter);
 275
 276 real NPT_energy(const t_inputrec* ir, const t_state* state, const t_extmass* MassQ);
 277 /* computes all the pressure/tempertature control energy terms to get a conserved energy */
 278
 279 void vrescale_tcoupl(const t_inputrec* ir, int64_t step, gmx_ekindata_t* ekind, real dt, double therm_integral[]);
 280 /* Compute temperature scaling. For V-rescale it is done in update. */
 281
 282 void rescale_velocities(const gmx_ekindata_t* ekind, const t_mdatoms* mdatoms, int start, int end, rvec v[]);
 283 /* Rescale the velocities with the scaling factor in ekind */
 284
 285 //! Check whether we do simulated annealing.
 286 bool doSimulatedAnnealing(const t_inputrec* ir);
 287
 288 //! Initialize simulated annealing.
 289 bool initSimulatedAnnealing(t_inputrec* ir, gmx::Update* upd);
 290
 291 // TODO: This is the only function in update.h altering the inputrec
 292 void update_annealing_target_temp(t_inputrec* ir, real t, gmx::Update* upd);
 293 /* Set reference temp for simulated annealing at time t*/
 294
 295 real calc_temp(real ekin, real nrdf);
 296 /* Calculate the temperature */
 297
 298 real calc_pres(PbcType pbcType, int nwall, const matrix box, const tensor ekin, const tensor vir, tensor pres);
 299 /* Calculate the pressure tensor, returns the scalar pressure.
 300  * The unit of pressure is bar.
 301  */
 302
 303 void parrinellorahman_pcoupl(FILE*             fplog,
 304                              int64_t           step,
 305                              const t_inputrec* ir,
 306                              real              dt,
 307                              const tensor      pres,
 308                              const tensor      box,
 309                              tensor            box_rel,
 310                              tensor            boxv,
 311                              tensor            M,
 312                              matrix            mu,
 313                              gmx_bool          bFirstStep);
 314
 315 void berendsen_pcoupl(FILE*             fplog,
 316                       int64_t           step,
 317                       const t_inputrec* ir,
 318                       real              dt,
 319                       const tensor      pres,
 320                       const matrix      box,
 321                       const matrix      force_vir,
 322                       const matrix      constraint_vir,
 323                       matrix            mu,
 324                       double*           baros_integral);
 325
 326 void berendsen_pscale(const t_inputrec*    ir,
 327                       const matrix         mu,
 328                       matrix               box,
 329                       matrix               box_rel,
 330                       int                  start,
 331                       int                  nr_atoms,
 332                       rvec                 x[],
 333                       const unsigned short cFREEZE[],
 334                       t_nrnb*              nrnb,
 335                       bool                 scaleCoordinates);
 336
 337 void pleaseCiteCouplingAlgorithms(FILE* fplog, const t_inputrec& ir);
 338
 339 /*! \brief Computes the atom range for a thread to operate on, ensuring SIMD aligned ranges
 340  *
 341  * \param[in]  numThreads   The number of threads to divide atoms over
 342  * \param[in]  threadIndex  The thread to get the range for
 343  * \param[in]  numAtoms     The total number of atoms (on this rank)
 344  * \param[out] startAtom    The start of the atom range
 345  * \param[out] endAtom      The end of the atom range, note that this is in general not a multiple of the SIMD width
 346  */
 347 void getThreadAtomRange(int numThreads, int threadIndex, int numAtoms, int* startAtom, int* endAtom);
 348
 349 /*! \brief Generate a new kinetic energy for the v-rescale thermostat
 350  *
 351  * Generates a new value for the kinetic energy, according to
 352  * Bussi et al JCP (2007), Eq. (A7)
 353  *
 354  * This is used by update_tcoupl(), and by the VRescaleThermostat of the modular
 355  * simulator.
 356  * TODO: Move this to the VRescaleThermostat once the modular simulator becomes
 357  *       the default code path.
 358  *
 359  * @param kk     present value of the kinetic energy of the atoms to be thermalized (in arbitrary units)
 360  * @param sigma  target average value of the kinetic energy (ndeg k_b T/2)  (in the same units as kk)
 361  * @param ndeg   number of degrees of freedom of the atoms to be thermalized
 362  * @param taut   relaxation time of the thermostat, in units of 'how often this routine is called'
 363  * @param step   the time step this routine is called on
 364  * @param seed   the random number generator seed
 365  * @return  the new kinetic energy
 366  */
 367 real vrescale_resamplekin(real kk, real sigma, real ndeg, real taut, int64_t step, int64_t seed);
 368
 369 #endif