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_constr;
  49 struct gmx_localtop_t;
  50 struct gmx_output_env_t;
  51 struct gmx_update_t;
  52 struct MdrunOptions;
  53 struct nonbonded_verlet_t;
  54 struct t_mdatoms;
  55 struct t_nrnb;
  56
  57 namespace gmx
  58 {
  59 class IMDOutputProvider;
  60 class MDLogger;
  61 }
  62
  63 typedef struct gmx_global_stat *gmx_global_stat_t;
  64
  65 void do_pbc_first_mtop(FILE *fplog, int ePBC, const matrix box,
  66                        const gmx_mtop_t *mtop, rvec x[]);
  67
  68 void do_pbc_mtop(FILE *fplog, int ePBC, const matrix box,
  69                  const gmx_mtop_t *mtop, rvec x[]);
  70
  71 /*! \brief Parallellizes put_atoms_in_box()
  72  *
  73  * This wrapper function around put_atoms_in_box() with the ugly manual
  74  * workload splitting is needed to avoid silently introducing multithreading
  75  * in tools.
  76  * \param[in]    ePBC   The pbc type
  77  * \param[in]    box    The simulation box
  78  * \param[in]    natoms The number of atoms
  79  * \param[inout] x      The coordinates of the atoms
  80  */
  81 void put_atoms_in_box_omp(int ePBC, const matrix box, int natoms, rvec x[]);
  82
  83
  84
  85 /* ROUTINES from stat.c */
  86 gmx_global_stat_t global_stat_init(t_inputrec *ir);
  87
  88 void global_stat_destroy(gmx_global_stat_t gs);
  89
  90 void global_stat(gmx_global_stat_t gs,
  91                  t_commrec *cr, gmx_enerdata_t *enerd,
  92                  tensor fvir, tensor svir, rvec mu_tot,
  93                  t_inputrec *inputrec,
  94                  gmx_ekindata_t *ekind,
  95                  gmx_constr *constr, t_vcm *vcm,
  96                  int nsig, real *sig,
  97                  int *totalNumberOfBondedInteractions,
  98                  gmx_bool bSumEkinhOld, int flags);
  99 /* All-reduce energy-like quantities over cr->mpi_comm_mysim */
 100
 101 int do_per_step(gmx_int64_t step, gmx_int64_t nstep);
 102 /* Return TRUE if io should be done */
 103
 104 /* ROUTINES from sim_util.c */
 105
 106 void print_time(FILE *out, gmx_walltime_accounting_t walltime_accounting,
 107                 gmx_int64_t step, t_inputrec *ir, t_commrec *cr);
 108
 109 /*! \brief Print date, time, MPI rank and a description of this point
 110  * in time.
 111  *
 112  * \param[in] log       logfile, or NULL to suppress output
 113  * \param[in] rank      MPI rank to include in the output
 114  * \param[in] title     Description to include in the output
 115  * \param[in] the_time  Seconds since the epoch, e.g. as reported by gmx_gettime
 116  */
 117 void print_date_and_time(FILE *log, int rank, const char *title,
 118                          double the_time);
 119
 120 void print_start(FILE *fplog, t_commrec *cr,
 121                  gmx_walltime_accounting_t walltime_accounting,
 122                  const char *name);
 123
 124 void finish_run(FILE *log, const gmx::MDLogger &mdlog, t_commrec *cr,
 125                 const t_inputrec *inputrec,
 126                 t_nrnb nrnb[], gmx_wallcycle_t wcycle,
 127                 gmx_walltime_accounting_t walltime_accounting,
 128                 nonbonded_verlet_t *nbv,
 129                 gmx_pme_t *pme,
 130                 gmx_bool bWriteStat);
 131
 132 void calc_enervirdiff(FILE *fplog, int eDispCorr, t_forcerec *fr);
 133
 134 void calc_dispcorr(t_inputrec *ir, t_forcerec *fr,
 135                    matrix box, real lambda, tensor pres, tensor virial,
 136                    real *prescorr, real *enercorr, real *dvdlcorr);
 137
 138 void initialize_lambdas(FILE *fplog, t_inputrec *ir, int *fep_state, gmx::ArrayRef<real> lambda, double *lam0);
 139
 140 void do_constrain_first(FILE *log, gmx_constr *constr,
 141                         t_inputrec *inputrec, t_mdatoms *md,
 142                         t_state *state, t_commrec *cr, t_nrnb *nrnb,
 143                         t_forcerec *fr, gmx_localtop_t *top);
 144
 145 void init_md(FILE *fplog,
 146              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              int nfile, const t_filenm fnm[],
 154              gmx_mdoutf_t *outf, t_mdebin **mdebin,
 155              tensor force_vir, tensor shake_vir,
 156              rvec mu_tot,
 157              gmx_bool *bSimAnn, t_vcm **vcm,
 158              gmx_wallcycle_t wcycle);
 159 /* Routine in sim_util.c */
 160
 161 gmx_bool use_GPU(const nonbonded_verlet_t *nbv);
 162
 163 #endif