src/gromacs/mdlib/sim_util.h

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  37 #ifndef GMX_MDLIB_SIM_UTIL_H
  38 #define GMX_MDLIB_SIM_UTIL_H
  39
  40 #include "gromacs/fileio/enxio.h"
  41 #include "gromacs/mdlib/mdebin.h"
  42 #include "gromacs/mdlib/mdoutf.h"
  43 #include "gromacs/mdlib/vcm.h"
  44 #include "gromacs/timing/wallcycle.h"
  45 #include "gromacs/timing/walltime_accounting.h"
  46 #include "gromacs/utility/arrayref.h"
  47
  48 struct gmx_output_env_t;
  49 struct gmx_pme_t;
  50 struct gmx_update_t;
  51 struct MdrunOptions;
  52 struct nonbonded_verlet_t;
  53 struct t_forcerec;
  54 struct t_mdatoms;
  55 struct t_nrnb;
  56
  57 namespace gmx
  58 {
  59 class BoxDeformation;
  60 class Constraints;
  61 class IMDOutputProvider;
  62 class MDLogger;
  63 }
  64
  65 typedef struct gmx_global_stat *gmx_global_stat_t;
  66
  67 void do_pbc_first_mtop(FILE *fplog, int ePBC, const matrix box,
  68                        const gmx_mtop_t *mtop, rvec x[]);
  69
  70 void do_pbc_mtop(FILE *fplog, int ePBC, const matrix box,
  71                  const gmx_mtop_t *mtop, rvec x[]);
  72
  73 /*! \brief Parallellizes put_atoms_in_box()
  74  *
  75  * This wrapper function around put_atoms_in_box() with the ugly manual
  76  * workload splitting is needed to avoid silently introducing multithreading
  77  * in tools.
  78  * \param[in]    ePBC   The pbc type
  79  * \param[in]    box    The simulation box
  80  * \param[inout] x      The coordinates of the atoms
  81  */
  82 void put_atoms_in_box_omp(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x);
  83
  84
  85
  86 /* ROUTINES from stat.c */
  87 gmx_global_stat_t global_stat_init(const t_inputrec *ir);
  88
  89 void global_stat_destroy(gmx_global_stat_t gs);
  90
  91 void global_stat(const gmx_global_stat *gs,
  92                  const t_commrec *cr, gmx_enerdata_t *enerd,
  93                  tensor fvir, tensor svir, rvec mu_tot,
  94                  const t_inputrec *inputrec,
  95                  gmx_ekindata_t *ekind,
  96                  const gmx::Constraints *constr, t_vcm *vcm,
  97                  int nsig, real *sig,
  98                  int *totalNumberOfBondedInteractions,
  99                  gmx_bool bSumEkinhOld, int flags);
 100 /* All-reduce energy-like quantities over cr->mpi_comm_mysim */
 101
 102 bool do_per_step(int64_t step, int64_t nstep);
 103 /* Return TRUE if io should be done */
 104
 105 /* ROUTINES from sim_util.c */
 106
 107 void print_time(FILE *out, gmx_walltime_accounting_t walltime_accounting,
 108                 int64_t step, const t_inputrec *ir, const t_commrec *cr);
 109
 110 /*! \brief Print date, time, MPI rank and a description of this point
 111  * in time.
 112  *
 113  * \param[in] log       logfile, or NULL to suppress output
 114  * \param[in] rank      MPI rank to include in the output
 115  * \param[in] title     Description to include in the output
 116  * \param[in] the_time  Seconds since the epoch, e.g. as reported by gmx_gettime
 117  */
 118 void print_date_and_time(FILE *log, int rank, const char *title,
 119                          double the_time);
 120
 121 void print_start(FILE *fplog, const t_commrec *cr,
 122                  gmx_walltime_accounting_t walltime_accounting,
 123                  const char *name);
 124
 125 void finish_run(FILE *log, const gmx::MDLogger &mdlog, const t_commrec *cr,
 126                 const t_inputrec *inputrec,
 127                 t_nrnb nrnb[], gmx_wallcycle_t wcycle,
 128                 gmx_walltime_accounting_t walltime_accounting,
 129                 nonbonded_verlet_t *nbv,
 130                 const gmx_pme_t *pme,
 131                 gmx_bool bWriteStat);
 132
 133 void calc_enervirdiff(FILE *fplog, int eDispCorr, t_forcerec *fr);
 134
 135 void calc_dispcorr(const t_inputrec *ir, const t_forcerec *fr,
 136                    const matrix box, real lambda, tensor pres, tensor virial,
 137                    real *prescorr, real *enercorr, real *dvdlcorr);
 138
 139 void initialize_lambdas(FILE *fplog, t_inputrec *ir, int *fep_state, gmx::ArrayRef<real> lambda, double *lam0);
 140
 141 void do_constrain_first(FILE *log, gmx::Constraints *constr,
 142                         const t_inputrec *inputrec, const t_mdatoms *md,
 143                         t_state *state);
 144
 145 void init_md(FILE *fplog,
 146              const t_commrec *cr, gmx::IMDOutputProvider *outputProvider,
 147              t_inputrec *ir, const gmx_output_env_t *oenv,
 148              const MdrunOptions &mdrunOptions,
 149              double *t, double *t0,
 150              t_state *globalState, double *lam0,
 151              t_nrnb *nrnb, gmx_mtop_t *mtop,
 152              gmx_update_t **upd,
 153              gmx::BoxDeformation *deform,
 154              int nfile, const t_filenm fnm[],
 155              gmx_mdoutf_t *outf, t_mdebin **mdebin,
 156              tensor force_vir, tensor shake_vir,
 157              tensor total_vir, tensor pres,
 158              rvec mu_tot,
 159              gmx_bool *bSimAnn, t_vcm **vcm,
 160              gmx_wallcycle_t wcycle);
 161
 162 void init_rerun(FILE *fplog,
 163                 const t_commrec *cr, gmx::IMDOutputProvider *outputProvider,
 164                 t_inputrec *ir, const gmx_output_env_t *oenv,
 165                 const MdrunOptions &mdrunOptions,
 166                 t_state *globalState, double *lam0,
 167                 t_nrnb *nrnb, gmx_mtop_t *mtop,
 168                 int nfile, const t_filenm fnm[],
 169                 gmx_mdoutf_t *outf, t_mdebin **mdebin,
 170                 gmx_wallcycle_t wcycle);
 171
 172 /* Routine in sim_util.c */
 173
 174 gmx_bool use_GPU(const nonbonded_verlet_t *nbv);
 175
 176 #endif