src/gromacs/mdrun/shellfc.h

   1 /*
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   7  * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
   8  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  38 #ifndef GMX_MDLIB_SHELLFC_H
  39 #define GMX_MDLIB_SHELLFC_H
  40
  41 #include <cstdio>
  42
  43 #include "gromacs/math/vectypes.h"
  44 #include "gromacs/timing/wallcycle.h"
  45 #include "gromacs/topology/atoms.h"
  46
  47 class DDBalanceRegionHandler;
  48 struct gmx_enerdata_t;
  49 struct gmx_enfrot;
  50 struct gmx_localtop_t;
  51 struct gmx_multisim_t;
  52 struct gmx_shellfc_t;
  53 struct gmx_mtop_t;
  54 class history_t;
  55 struct pull_t;
  56 struct t_forcerec;
  57 struct t_inputrec;
  58 struct t_mdatoms;
  59 struct t_nrnb;
  60 class t_state;
  61
  62 namespace gmx
  63 {
  64 template<typename>
  65 class ArrayRef;
  66 template<typename>
  67 class ArrayRefWithPadding;
  68 class Constraints;
  69 class ForceBuffersView;
  70 class ImdSession;
  71 class MdrunScheduleWorkload;
  72 class VirtualSitesHandler;
  73 } // namespace gmx
  74
  75 /*! \brief Initialization function, also predicts the initial shell positions.
  76  *
  77  * \param fplog Pointer to the log stream. Can be set to \c nullptr to disable verbose log.
  78  * \param mtop Pointer to a global system topology object.
  79  * \param nflexcon Number of flexible constraints.
  80  * \param nstcalcenergy How often are energies calculated. Must be provided for sanity check.
  81  * \param usingDomainDecomposition Whether domain decomposition is used. Must be provided for sanity check.
  82  * \param usingPmeOnGpu Set to true if GPU will be used for PME calculations. Necessary for proper buffer initialization.
  83  *
  84  * \returns a pointer to an initialized \c shellfc object.
  85  */
  86 gmx_shellfc_t* init_shell_flexcon(FILE*             fplog,
  87                                   const gmx_mtop_t* mtop,
  88                                   int               nflexcon,
  89                                   int               nstcalcenergy,
  90                                   bool              usingDomainDecomposition,
  91                                   bool              usingPmeOnGpu);
  92
  93 /* Optimize shell positions */
  94 void relax_shell_flexcon(FILE*                               log,
  95                          const t_commrec*                    cr,
  96                          const gmx_multisim_t*               ms,
  97                          gmx_bool                            bVerbose,
  98                          gmx_enfrot*                         enforcedRotation,
  99                          int64_t                             mdstep,
 100                          const t_inputrec*                   inputrec,
 101                          gmx::ImdSession*                    imdSession,
 102                          pull_t*                             pull_work,
 103                          gmx_bool                            bDoNS,
 104                          int                                 force_flags,
 105                          const gmx_localtop_t*               top,
 106                          gmx::Constraints*                   constr,
 107                          gmx_enerdata_t*                     enerd,
 108                          int                                 natoms,
 109                          gmx::ArrayRefWithPadding<gmx::RVec> x,
 110                          gmx::ArrayRefWithPadding<gmx::RVec> v,
 111                          const matrix                        box,
 112                          gmx::ArrayRef<real>                 lambda,
 113                          history_t*                          hist,
 114                          gmx::ForceBuffersView*              f,
 115                          tensor                              force_vir,
 116                          const t_mdatoms*                    md,
 117                          t_nrnb*                             nrnb,
 118                          gmx_wallcycle_t                     wcycle,
 119                          gmx_shellfc_t*                      shfc,
 120                          t_forcerec*                         fr,
 121                          gmx::MdrunScheduleWorkload*         runScheduleWork,
 122                          double                              t,
 123                          rvec                                mu_tot,
 124                          gmx::VirtualSitesHandler*           vsite,
 125                          const DDBalanceRegionHandler&       ddBalanceRegionHandler);
 126
 127 /* Print some final output and delete shellfc */
 128 void done_shellfc(FILE* fplog, gmx_shellfc_t* shellfc, int64_t numSteps);
 129
 130 /*! \brief Count the different particle types in a system
 131  *
 132  * Routine prints a warning to stderr in case an unknown particle type
 133  * is encountered.
 134  * \param[in]  fplog Print what we have found if not NULL
 135  * \param[in]  mtop  Molecular topology.
 136  * \returns Array holding the number of particles of a type
 137  */
 138 std::array<int, eptNR> countPtypes(FILE* fplog, const gmx_mtop_t* mtop);
 139
 140 #endif