src/gromacs/mdlib/coupling.h

   1 /*
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  38 #ifndef GMX_MDLIB_COUPLING_H
  39 #define GMX_MDLIB_COUPLING_H
  40
  41 #include <cstdio>
  42
  43 #include <array>
  44 #include <vector>
  45
  46 #include "gromacs/math/vectypes.h"
  47 #include "gromacs/mdtypes/md_enums.h"
  48 #include "gromacs/utility/real.h"
  49
  50 class gmx_ekindata_t;
  51 struct gmx_enerdata_t;
  52 struct t_commrec;
  53 struct t_extmass;
  54 struct t_grpopts;
  55 struct t_inputrec;
  56 struct t_nrnb;
  57 class t_state;
  58
  59 enum class PbcType;
  60
  61 namespace gmx
  62 {
  63 class BoxDeformation;
  64 class Constraints;
  65 class Update;
  66 template<typename>
  67 class ArrayRef;
  68 }; // namespace gmx
  69
  70 /* Update the size of per-atom arrays (e.g. after DD re-partitioning,
  71    which might increase the number of home atoms). */
  72
  73 void update_tcouple(int64_t                             step,
  74                     const t_inputrec*                   inputrec,
  75                     t_state*                            state,
  76                     gmx_ekindata_t*                     ekind,
  77                     const t_extmass*                    MassQ,
  78                     int                                 homenr,
  79                     gmx::ArrayRef<const unsigned short> cTC);
  80
  81 /* Update Parrinello-Rahman, to be called before the coordinate update */
  82 void update_pcouple_before_coordinates(FILE*             fplog,
  83                                        int64_t           step,
  84                                        const t_inputrec* inputrec,
  85                                        t_state*          state,
  86                                        matrix            parrinellorahmanMu,
  87                                        matrix            M,
  88                                        bool              bInitStep);
  89
  90 /* Update the box, to be called after the coordinate update.
  91  * For Berendsen P-coupling, also calculates the scaling factor
  92  * and scales the coordinates.
  93  * When the deform option is used, scales coordinates and box here.
  94  */
  95 void update_pcouple_after_coordinates(FILE*                               fplog,
  96                                       int64_t                             step,
  97                                       const t_inputrec*                   inputrec,
  98                                       int                                 homenr,
  99                                       gmx::ArrayRef<const unsigned short> cFREEZE,
 100                                       const matrix                        pressure,
 101                                       const matrix                        forceVirial,
 102                                       const matrix                        constraintVirial,
 103                                       matrix                              pressureCouplingMu,
 104                                       t_state*                            state,
 105                                       t_nrnb*                             nrnb,
 106                                       gmx::BoxDeformation*                boxDeformation,
 107                                       bool                                scaleCoordinates);
 108
 109 /* Return TRUE if OK, FALSE in case of Shake Error */
 110
 111 extern bool update_randomize_velocities(const t_inputrec*                   ir,
 112                                         int64_t                             step,
 113                                         const t_commrec*                    cr,
 114                                         int                                 homenr,
 115                                         gmx::ArrayRef<const unsigned short> cTC,
 116                                         gmx::ArrayRef<const real>           invMass,
 117                                         gmx::ArrayRef<gmx::RVec>            v,
 118                                         const gmx::Update*                  upd,
 119                                         const gmx::Constraints*             constr);
 120
 121 void berendsen_tcoupl(const t_inputrec*    ir,
 122                       gmx_ekindata_t*      ekind,
 123                       real                 dt,
 124                       std::vector<double>& therm_integral); //NOLINT(google-runtime-references)
 125
 126 void andersen_tcoupl(const t_inputrec*                   ir,
 127                      int64_t                             step,
 128                      const t_commrec*                    cr,
 129                      int                                 homenr,
 130                      gmx::ArrayRef<const unsigned short> cTC,
 131                      gmx::ArrayRef<const real>           invMass,
 132                      gmx::ArrayRef<gmx::RVec>            v,
 133                      real                                rate,
 134                      const std::vector<bool>&            randomize,
 135                      gmx::ArrayRef<const real>           boltzfac);
 136
 137 void nosehoover_tcoupl(const t_grpopts*      opts,
 138                        const gmx_ekindata_t* ekind,
 139                        real                  dt,
 140                        gmx::ArrayRef<double> xi,
 141                        gmx::ArrayRef<double> vxi,
 142                        const t_extmass*      MassQ);
 143
 144 void trotter_update(const t_inputrec*                   ir,
 145                     int64_t                             step,
 146                     gmx_ekindata_t*                     ekind,
 147                     const gmx_enerdata_t*               enerd,
 148                     t_state*                            state,
 149                     const tensor                        vir,
 150                     int                                 homenr,
 151                     gmx::ArrayRef<const unsigned short> cTC,
 152                     gmx::ArrayRef<const real>           invMass,
 153                     const t_extmass*                    MassQ,
 154                     gmx::ArrayRef<std::vector<int>>     trotter_seqlist,
 155                     int                                 trotter_seqno);
 156
 157 std::array<std::vector<int>, ettTSEQMAX>
 158 init_npt_vars(const t_inputrec* ir, t_state* state, t_extmass* Mass, bool bTrotter);
 159
 160 real NPT_energy(const t_inputrec* ir, const t_state* state, const t_extmass* MassQ);
 161 /* computes all the pressure/tempertature control energy terms to get a conserved energy */
 162
 163 void vrescale_tcoupl(const t_inputrec*     ir,
 164                      int64_t               step,
 165                      gmx_ekindata_t*       ekind,
 166                      real                  dt,
 167                      gmx::ArrayRef<double> therm_integral);
 168 /* Compute temperature scaling. For V-rescale it is done in update. */
 169
 170 void rescale_velocities(const gmx_ekindata_t*               ekind,
 171                         gmx::ArrayRef<const unsigned short> cTC,
 172                         int                                 start,
 173                         int                                 end,
 174                         gmx::ArrayRef<gmx::RVec>            v);
 175 /* Rescale the velocities with the scaling factor in ekind */
 176
 177 //! Check whether we do simulated annealing.
 178 bool doSimulatedAnnealing(const t_inputrec* ir);
 179
 180 //! Initialize simulated annealing.
 181 bool initSimulatedAnnealing(t_inputrec* ir, gmx::Update* upd);
 182
 183 // TODO: This is the only function in update.h altering the inputrec
 184 void update_annealing_target_temp(t_inputrec* ir, real t, gmx::Update* upd);
 185 /* Set reference temp for simulated annealing at time t*/
 186
 187 real calc_temp(real ekin, real nrdf);
 188 /* Calculate the temperature */
 189
 190 real calc_pres(PbcType pbcType, int nwall, const matrix box, const tensor ekin, const tensor vir, tensor pres);
 191 /* Calculate the pressure tensor, returns the scalar pressure.
 192  * The unit of pressure is bar.
 193  */
 194
 195 void parrinellorahman_pcoupl(FILE*             fplog,
 196                              int64_t           step,
 197                              const t_inputrec* ir,
 198                              real              dt,
 199                              const tensor      pres,
 200                              const tensor      box,
 201                              tensor            box_rel,
 202                              tensor            boxv,
 203                              tensor            M,
 204                              matrix            mu,
 205                              bool              bFirstStep);
 206
 207 /*! \brief Calculate the pressure coupling scaling matrix
 208  *
 209  * Used by Berendsen and C-Rescale pressure coupling, this function
 210  * computes the current value of the scaling matrix. The template
 211  * parameter determines the pressure coupling algorithm.
 212  */
 213 template<PressureCoupling pressureCouplingType>
 214 void pressureCouplingCalculateScalingMatrix(FILE*             fplog,
 215                                             int64_t           step,
 216                                             const t_inputrec* ir,
 217                                             real              dt,
 218                                             const tensor      pres,
 219                                             const matrix      box,
 220                                             const matrix      force_vir,
 221                                             const matrix      constraint_vir,
 222                                             matrix            mu,
 223                                             double*           baros_integral);
 224
 225 /*! \brief Scale the box and coordinates
 226  *
 227  * Used by Berendsen and C-Rescale pressure coupling, this function scales
 228  * the box, the positions, and the velocities (C-Rescale only) according to
 229  * the scaling matrix mu. The template parameter determines the pressure
 230  * coupling algorithm.
 231  */
 232 template<PressureCoupling pressureCouplingType>
 233 void pressureCouplingScaleBoxAndCoordinates(const t_inputrec*                   ir,
 234                                             const matrix                        mu,
 235                                             matrix                              box,
 236                                             matrix                              box_rel,
 237                                             int                                 start,
 238                                             int                                 nr_atoms,
 239                                             gmx::ArrayRef<gmx::RVec>            x,
 240                                             gmx::ArrayRef<gmx::RVec>            v,
 241                                             gmx::ArrayRef<const unsigned short> cFREEZE,
 242                                             t_nrnb*                             nrnb,
 243                                             bool                                scaleCoordinates);
 244
 245 void pleaseCiteCouplingAlgorithms(FILE* fplog, const t_inputrec& ir);
 246
 247 /*! \brief Generate a new kinetic energy for the v-rescale thermostat
 248  *
 249  * Generates a new value for the kinetic energy, according to
 250  * Bussi et al JCP (2007), Eq. (A7)
 251  *
 252  * This is used by update_tcoupl(), and by the VRescaleThermostat of the modular
 253  * simulator.
 254  * \todo Move this to the VRescaleThermostat once the modular simulator becomes
 255  *       the default code path.
 256  *
 257  * \param[in] kk     present value of the kinetic energy of the atoms to be thermalized (in
 258  * arbitrary units) \param[in] sigma  target average value of the kinetic energy (ndeg k_b T/2)  (in
 259  * the same units as kk) \param[in] ndeg   number of degrees of freedom of the atoms to be
 260  * thermalized \param[in] taut   relaxation time of the thermostat, in units of 'how often this
 261  * routine is called' \param[in] step   the time step this routine is called on \param[in] seed the
 262  * random number generator seed \return  the new kinetic energy
 263  */
 264 real vrescale_resamplekin(real kk, real sigma, real ndeg, real taut, int64_t step, int64_t seed);
 265
 266 #endif // GMX_MDLIB_COUPLING_H