src/gromacs/mdlib/coupling.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
   7  * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
   8  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   9  * and including many others, as listed in the AUTHORS file in the
  10  * top-level source directory and at http://www.gromacs.org.
  11  *
  12  * GROMACS is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU Lesser General Public License
  14  * as published by the Free Software Foundation; either version 2.1
  15  * of the License, or (at your option) any later version.
  16  *
  17  * GROMACS is distributed in the hope that it will be useful,
  18  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  19  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  20  * Lesser General Public License for more details.
  21  *
  22  * You should have received a copy of the GNU Lesser General Public
  23  * License along with GROMACS; if not, see
  24  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  25  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  26  *
  27  * If you want to redistribute modifications to GROMACS, please
  28  * consider that scientific software is very special. Version
  29  * control is crucial - bugs must be traceable. We will be happy to
  30  * consider code for inclusion in the official distribution, but
  31  * derived work must not be called official GROMACS. Details are found
  32  * in the README & COPYING files - if they are missing, get the
  33  * official version at http://www.gromacs.org.
  34  *
  35  * To help us fund GROMACS development, we humbly ask that you cite
  36  * the research papers on the package. Check out http://www.gromacs.org.
  37  */
  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/enumerationhelpers.h"
  49 #include "gromacs/utility/real.h"
  50
  51 class gmx_ekindata_t;
  52 struct gmx_enerdata_t;
  53 struct t_commrec;
  54 struct t_extmass;
  55 struct t_grpopts;
  56 struct t_inputrec;
  57 struct t_nrnb;
  58 class t_state;
  59
  60 enum class PbcType;
  61
  62 namespace gmx
  63 {
  64 class BoxDeformation;
  65 class Constraints;
  66 class Update;
  67 template<typename>
  68 class ArrayRef;
  69 }; // namespace gmx
  70
  71 /* Update the size of per-atom arrays (e.g. after DD re-partitioning,
  72    which might increase the number of home atoms). */
  73
  74 void update_tcouple(int64_t                             step,
  75                     const t_inputrec*                   inputrec,
  76                     t_state*                            state,
  77                     gmx_ekindata_t*                     ekind,
  78                     const t_extmass*                    MassQ,
  79                     int                                 homenr,
  80                     gmx::ArrayRef<const unsigned short> cTC);
  81
  82 /* Update Parrinello-Rahman, to be called before the coordinate update */
  83 void update_pcouple_before_coordinates(FILE*             fplog,
  84                                        int64_t           step,
  85                                        const t_inputrec* inputrec,
  86                                        t_state*          state,
  87                                        matrix            parrinellorahmanMu,
  88                                        matrix            M,
  89                                        bool              bInitStep);
  90
  91 /* Update the box, to be called after the coordinate update.
  92  * For Berendsen P-coupling, also calculates the scaling factor
  93  * and scales the coordinates.
  94  * When the deform option is used, scales coordinates and box here.
  95  */
  96 void update_pcouple_after_coordinates(FILE*                               fplog,
  97                                       int64_t                             step,
  98                                       const t_inputrec*                   inputrec,
  99                                       int                                 homenr,
 100                                       gmx::ArrayRef<const unsigned short> cFREEZE,
 101                                       const matrix                        pressure,
 102                                       const matrix                        forceVirial,
 103                                       const matrix                        constraintVirial,
 104                                       matrix                              pressureCouplingMu,
 105                                       t_state*                            state,
 106                                       t_nrnb*                             nrnb,
 107                                       gmx::BoxDeformation*                boxDeformation,
 108                                       bool                                scaleCoordinates);
 109
 110 /* Return TRUE if OK, FALSE in case of Shake Error */
 111
 112 extern bool update_randomize_velocities(const t_inputrec*                   ir,
 113                                         int64_t                             step,
 114                                         const t_commrec*                    cr,
 115                                         int                                 homenr,
 116                                         gmx::ArrayRef<const unsigned short> cTC,
 117                                         gmx::ArrayRef<const real>           invMass,
 118                                         gmx::ArrayRef<gmx::RVec>            v,
 119                                         const gmx::Update*                  upd,
 120                                         const gmx::Constraints*             constr);
 121
 122 void berendsen_tcoupl(const t_inputrec*    ir,
 123                       gmx_ekindata_t*      ekind,
 124                       real                 dt,
 125                       std::vector<double>& therm_integral); //NOLINT(google-runtime-references)
 126
 127 void andersen_tcoupl(const t_inputrec*                   ir,
 128                      int64_t                             step,
 129                      const t_commrec*                    cr,
 130                      int                                 homenr,
 131                      gmx::ArrayRef<const unsigned short> cTC,
 132                      gmx::ArrayRef<const real>           invMass,
 133                      gmx::ArrayRef<gmx::RVec>            v,
 134                      real                                rate,
 135                      const std::vector<bool>&            randomize,
 136                      gmx::ArrayRef<const real>           boltzfac);
 137
 138 void nosehoover_tcoupl(const t_grpopts*      opts,
 139                        const gmx_ekindata_t* ekind,
 140                        real                  dt,
 141                        gmx::ArrayRef<double> xi,
 142                        gmx::ArrayRef<double> vxi,
 143                        const t_extmass*      MassQ);
 144
 145 void trotter_update(const t_inputrec*                   ir,
 146                     int64_t                             step,
 147                     gmx_ekindata_t*                     ekind,
 148                     const gmx_enerdata_t*               enerd,
 149                     t_state*                            state,
 150                     const tensor                        vir,
 151                     int                                 homenr,
 152                     gmx::ArrayRef<const unsigned short> cTC,
 153                     gmx::ArrayRef<const real>           invMass,
 154                     const t_extmass*                    MassQ,
 155                     gmx::ArrayRef<std::vector<int>>     trotter_seqlist,
 156                     TrotterSequence                     trotter_seqno);
 157
 158 gmx::EnumerationArray<TrotterSequence, std::vector<int>>
 159 init_npt_vars(const t_inputrec* ir, t_state* state, t_extmass* Mass, bool bTrotter);
 160
 161 real NPT_energy(const t_inputrec* ir, const t_state* state, const t_extmass* MassQ);
 162 /* computes all the pressure/tempertature control energy terms to get a conserved energy */
 163
 164 void vrescale_tcoupl(const t_inputrec*     ir,
 165                      int64_t               step,
 166                      gmx_ekindata_t*       ekind,
 167                      real                  dt,
 168                      gmx::ArrayRef<double> therm_integral);
 169 /* Compute temperature scaling. For V-rescale it is done in update. */
 170
 171 void rescale_velocities(const gmx_ekindata_t*               ekind,
 172                         gmx::ArrayRef<const unsigned short> cTC,
 173                         int                                 start,
 174                         int                                 end,
 175                         gmx::ArrayRef<gmx::RVec>            v);
 176 /* Rescale the velocities with the scaling factor in ekind */
 177
 178 /*!
 179  * \brief Compute the new annealing temperature for a temperature group
 180  *
 181  * \param inputrec          The input record
 182  * \param temperatureGroup  The temperature group
 183  * \param time              The current time
 184  * \return  The new reference temperature for the group
 185  */
 186 real computeAnnealingTargetTemperature(const t_inputrec& inputrec, int temperatureGroup, real time);
 187
 188 //! Check whether we do simulated annealing.
 189 bool doSimulatedAnnealing(const t_inputrec* ir);
 190
 191 //! Initialize simulated annealing.
 192 bool initSimulatedAnnealing(t_inputrec* ir, gmx::Update* upd);
 193
 194 // TODO: This is the only function in update.h altering the inputrec
 195 void update_annealing_target_temp(t_inputrec* ir, real t, gmx::Update* upd);
 196 /* Set reference temp for simulated annealing at time t*/
 197
 198 real calc_temp(real ekin, real nrdf);
 199 /* Calculate the temperature */
 200
 201 real calc_pres(PbcType pbcType, int nwall, const matrix box, const tensor ekin, const tensor vir, tensor pres);
 202 /* Calculate the pressure tensor, returns the scalar pressure.
 203  * The unit of pressure is bar.
 204  */
 205
 206 void parrinellorahman_pcoupl(FILE*             fplog,
 207                              int64_t           step,
 208                              const t_inputrec* ir,
 209                              real              dt,
 210                              const tensor      pres,
 211                              const tensor      box,
 212                              tensor            box_rel,
 213                              tensor            boxv,
 214                              tensor            M,
 215                              matrix            mu,
 216                              bool              bFirstStep);
 217
 218 /*! \brief Calculate the pressure coupling scaling matrix
 219  *
 220  * Used by Berendsen and C-Rescale pressure coupling, this function
 221  * computes the current value of the scaling matrix. The template
 222  * parameter determines the pressure coupling algorithm.
 223  */
 224 template<PressureCoupling pressureCouplingType>
 225 void pressureCouplingCalculateScalingMatrix(FILE*             fplog,
 226                                             int64_t           step,
 227                                             const t_inputrec* ir,
 228                                             real              dt,
 229                                             const tensor      pres,
 230                                             const matrix      box,
 231                                             const matrix      force_vir,
 232                                             const matrix      constraint_vir,
 233                                             matrix            mu,
 234                                             double*           baros_integral);
 235
 236 /*! \brief Scale the box and coordinates
 237  *
 238  * Used by Berendsen and C-Rescale pressure coupling, this function scales
 239  * the box, the positions, and the velocities (C-Rescale only) according to
 240  * the scaling matrix mu. The template parameter determines the pressure
 241  * coupling algorithm.
 242  */
 243 template<PressureCoupling pressureCouplingType>
 244 void pressureCouplingScaleBoxAndCoordinates(const t_inputrec*                   ir,
 245                                             const matrix                        mu,
 246                                             matrix                              box,
 247                                             matrix                              box_rel,
 248                                             int                                 start,
 249                                             int                                 nr_atoms,
 250                                             gmx::ArrayRef<gmx::RVec>            x,
 251                                             gmx::ArrayRef<gmx::RVec>            v,
 252                                             gmx::ArrayRef<const unsigned short> cFREEZE,
 253                                             t_nrnb*                             nrnb,
 254                                             bool                                scaleCoordinates);
 255
 256 void pleaseCiteCouplingAlgorithms(FILE* fplog, const t_inputrec& ir);
 257
 258 /*! \brief Generate a new kinetic energy for the v-rescale thermostat
 259  *
 260  * Generates a new value for the kinetic energy, according to
 261  * Bussi et al JCP (2007), Eq. (A7)
 262  *
 263  * This is used by update_tcoupl(), and by the VRescaleThermostat of the modular
 264  * simulator.
 265  * \todo Move this to the VRescaleThermostat once the modular simulator becomes
 266  *       the default code path.
 267  *
 268  * \param[in] kk     present value of the kinetic energy of the atoms to be thermalized (in
 269  * arbitrary units) \param[in] sigma  target average value of the kinetic energy (ndeg k_b T/2)  (in
 270  * the same units as kk) \param[in] ndeg   number of degrees of freedom of the atoms to be
 271  * thermalized \param[in] taut   relaxation time of the thermostat, in units of 'how often this
 272  * routine is called' \param[in] step   the time step this routine is called on \param[in] seed the
 273  * random number generator seed \return  the new kinetic energy
 274  */
 275 real vrescale_resamplekin(real kk, real sigma, real ndeg, real taut, int64_t step, int64_t seed);
 276
 277 #endif // GMX_MDLIB_COUPLING_H