src/gromacs/mdlib/update_vv.h

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  38 #ifndef GMX_MDLIB_UPDATE_VV_H
  39 #define GMX_MDLIB_UPDATE_VV_H
  40
  41 #include <vector>
  42
  43 #include "gromacs/math/vectypes.h"
  44 #include "gromacs/mdrunutility/handlerestart.h"
  45 #include "gromacs/mdtypes/md_enums.h"
  46
  47 struct gmx_ekindata_t;
  48 struct gmx_enerdata_t;
  49 struct gmx_global_stat;
  50 struct gmx_localtop_t;
  51 struct gmx_mtop_t;
  52 struct gmx_wallcycle;
  53 struct pull_t;
  54 struct t_commrec;
  55 struct t_extmass;
  56 struct t_fcdata;
  57 struct t_forcerec;
  58 struct t_inputrec;
  59 struct t_mdatoms;
  60 struct t_nrnb;
  61 class t_state;
  62 struct t_vcm;
  63
  64 namespace gmx
  65 {
  66 class Constraints;
  67 class ForceBuffers;
  68 class MDLogger;
  69 class SimulationSignaller;
  70 class Update;
  71 } // namespace gmx
  72
  73 /*! \brief Make the first step of Velocity Verlet integration
  74  *
  75  * \param[in]  step              Current timestep.
  76  * \param[in]  bFirstStep        Is it a first step.
  77  * \param[in]  bInitStep         Is it an initialization step.
  78  * \param[in]  startingBehavior  Describes whether this is a restart appending to output files.
  79  * \param[in]  nstglobalcomm     Will globals be computed on this step.
  80  * \param[in]  ir                Input record.
  81  * \param[in]  fr                Force record.
  82  * \param[in]  cr                Comunication record.
  83  * \param[in]  state             Simulation state.
  84  * \param[in]  mdatoms           MD atoms data.
  85  * \param[in]  fcdata            Force calculation data.
  86  * \param[in]  MassQ             Mass/pressure data.
  87  * \param[in]  vcm               Center of mass motion removal.
  88  * \param[in]  top_global        Global topology.
  89  * \param[in]  top               Local topology.
  90  * \param[in]  enerd             Energy data.
  91  * \param[in]  ekind             Kinetic energy data.
  92  * \param[in]  gstat             Storage of thermodynamic parameters data.
  93  * \param[out] last_ekin         Kinetic energies of the last step.
  94  * \param[in]  bCalcVir          If the virial is computed on this step.
  95  * \param[in]  total_vir         Total virial tensor.
  96  * \param[in]  shake_vir         Constraints virial.
  97  * \param[in]  force_vir         Force virial.
  98  * \param[in]  pres              Pressure tensor.
  99  * \param[in]  M                 Parrinello-Rahman velocity scaling matrix.
 100  * \param[in]  do_log            Do logging on this step.
 101  * \param[in]  do_ene            Print energies on this step.
 102  * \param[in]  bCalcEner         Compute energies on this step.
 103  * \param[in]  bGStat            Collect globals this step.
 104  * \param[in]  bStopCM           Stop the center of mass motion on this step.
 105  * \param[in]  bTrotter          Do trotter routines this step.
 106  * \param[in]  bExchanged        If this is a replica exchange step.
 107  * \param[out] bSumEkinhOld      Old kinetic energies will need to be summed up.
 108  * \param[out] shouldCheckNumberOfBondedInteractions  If checks for missing bonded
 109  *                                                    interactions will be needed.
 110  * \param[out] saved_conserved_quantity  Place to store the conserved energy.
 111  * \param[in]  f                 Force buffers.
 112  * \param[in]  upd               Update object.
 113  * \param[in]  constr            Constraints object.
 114  * \param[in]  nullSignaller     Simulation signaller.
 115  * \param[in]  trotter_seq       NPT variables.
 116  * \param[in]  nrnb              Cycle counters.
 117  * \param[in]  mdlog             Logger.
 118  * \param[in]  fplog             Another logger.
 119  * \param[in]  wcycle            Wall-clock cycle counter.
 120  */
 121 void integrateVVFirstStep(int64_t                   step,
 122                           bool                      bFirstStep,
 123                           bool                      bInitStep,
 124                           gmx::StartingBehavior     startingBehavior,
 125                           int                       nstglobalcomm,
 126                           const t_inputrec*         ir,
 127                           t_forcerec*               fr,
 128                           t_commrec*                cr,
 129                           t_state*                  state,
 130                           t_mdatoms*                mdatoms,
 131                           const t_fcdata&           fcdata,
 132                           t_extmass*                MassQ,
 133                           t_vcm*                    vcm,
 134                           const gmx_mtop_t*         top_global,
 135                           const gmx_localtop_t&     top,
 136                           gmx_enerdata_t*           enerd,
 137                           gmx_ekindata_t*           ekind,
 138                           gmx_global_stat*          gstat,
 139                           real*                     last_ekin,
 140                           bool                      bCalcVir,
 141                           tensor                    total_vir,
 142                           tensor                    shake_vir,
 143                           tensor                    force_vir,
 144                           tensor                    pres,
 145                           matrix                    M,
 146                           bool                      do_log,
 147                           bool                      do_ene,
 148                           bool                      bCalcEner,
 149                           bool                      bGStat,
 150                           bool                      bStopCM,
 151                           bool                      bTrotter,
 152                           bool                      bExchanged,
 153                           bool*                     bSumEkinhOld,
 154                           bool*                     shouldCheckNumberOfBondedInteractions,
 155                           real*                     saved_conserved_quantity,
 156                           gmx::ForceBuffers*        f,
 157                           gmx::Update*              upd,
 158                           gmx::Constraints*         constr,
 159                           gmx::SimulationSignaller* nullSignaller,
 160                           std::array<std::vector<int>, ettTSEQMAX> trotter_seq,
 161                           t_nrnb*                                  nrnb,
 162                           const gmx::MDLogger&                     mdlog,
 163                           FILE*                                    fplog,
 164                           gmx_wallcycle*                           wcycle);
 165
 166
 167 /*! \brief Make the second step of Velocity Verlet integration
 168  *
 169  * \param[in]  step              Current timestep.
 170  * \param[in]  ir                Input record.
 171  * \param[in]  fr                Force record.
 172  * \param[in]  cr                Comunication record.
 173  * \param[in]  state             Simulation state.
 174  * \param[in]  mdatoms           MD atoms data.
 175  * \param[in]  fcdata            Force calculation data.
 176  * \param[in]  MassQ             Mass/pressure data.
 177  * \param[in]  vcm               Center of mass motion removal.
 178  * \param[in]  pull_work         Pulling data.
 179  * \param[in]  enerd             Energy data.
 180  * \param[in]  ekind             Kinetic energy data.
 181  * \param[in]  gstat             Storage of thermodynamic parameters data.
 182  * \param[out] dvdl_constr       FEP data for constraints.
 183  * \param[in]  bCalcVir          If the virial is computed on this step.
 184  * \param[in]  total_vir         Total virial tensor.
 185  * \param[in]  shake_vir         Constraints virial.
 186  * \param[in]  force_vir         Force virial.
 187  * \param[in]  pres              Pressure tensor.
 188  * \param[in]  M                 Parrinello-Rahman velocity scaling matrix.
 189  * \param[in]  lastbox           Last recorded PBC box.
 190  * \param[in]  do_log            Do logging on this step.
 191  * \param[in]  do_ene            Print energies on this step.
 192  * \param[in]  bGStat            Collect globals this step.
 193  * \param[out] bSumEkinhOld      Old kinetic energies need to be summed up.
 194  * \param[in]  f                 Force buffers.
 195  * \param[in]  cbuf              Buffer to store intermediate coordinates
 196  * \param[in]  upd               Update object.
 197  * \param[in]  constr            Constraints object.
 198  * \param[in]  nullSignaller     Simulation signaller.
 199  * \param[in]  trotter_seq       NPT variables.
 200  * \param[in]  nrnb              Cycle counters.
 201  * \param[in]  wcycle            Wall-clock cycle counter.
 202  */
 203 void integrateVVSecondStep(int64_t                                  step,
 204                            const t_inputrec*                        ir,
 205                            t_forcerec*                              fr,
 206                            t_commrec*                               cr,
 207                            t_state*                                 state,
 208                            t_mdatoms*                               mdatoms,
 209                            const t_fcdata&                          fcdata,
 210                            t_extmass*                               MassQ,
 211                            t_vcm*                                   vcm,
 212                            pull_t*                                  pull_work,
 213                            gmx_enerdata_t*                          enerd,
 214                            gmx_ekindata_t*                          ekind,
 215                            gmx_global_stat*                         gstat,
 216                            real*                                    dvdl_constr,
 217                            bool                                     bCalcVir,
 218                            tensor                                   total_vir,
 219                            tensor                                   shake_vir,
 220                            tensor                                   force_vir,
 221                            tensor                                   pres,
 222                            matrix                                   M,
 223                            matrix                                   lastbox,
 224                            bool                                     do_log,
 225                            bool                                     do_ene,
 226                            bool                                     bGStat,
 227                            bool*                                    bSumEkinhOld,
 228                            gmx::ForceBuffers*                       f,
 229                            std::vector<gmx::RVec>*                  cbuf,
 230                            gmx::Update*                             upd,
 231                            gmx::Constraints*                        constr,
 232                            gmx::SimulationSignaller*                nullSignaller,
 233                            std::array<std::vector<int>, ettTSEQMAX> trotter_seq,
 234                            t_nrnb*                                  nrnb,
 235                            gmx_wallcycle*                           wcycle);
 236
 237
 238 #endif // GMX_MDLIB_UPDATE_VV_H