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