include/mdrun.h

   1 /*
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   5  * Copyright (c) 2001-2004, The GROMACS development team,
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  38
  39 #ifndef _mdrun_h
  40 #define _mdrun_h
  41
  42 #include <stdio.h>
  43 #include <time.h>
  44 #include "visibility.h"
  45 #include "typedefs.h"
  46 #include "network.h"
  47 #include "sim_util.h"
  48 #include "tgroup.h"
  49 #include "filenm.h"
  50 #include "mshift.h"
  51 #include "force.h"
  52 #include "edsam.h"
  53 #include "mdebin.h"
  54 #include "vcm.h"
  55 #include "vsite.h"
  56 #include "pull.h"
  57 #include "update.h"
  58 #include "types/membedt.h"
  59 #include "types/globsig.h"
  60
  61
  62 #ifdef GMX_THREAD_MPI
  63 #include "thread_mpi/threads.h"
  64 #endif
  65
  66 #ifdef __cplusplus
  67 extern "C" {
  68 #endif
  69
  70 #define MD_POLARISE       (1<<2)
  71 #define MD_IONIZE         (1<<3)
  72 #define MD_RERUN          (1<<4)
  73 #define MD_RERUN_VSITE    (1<<5)
  74 #define MD_FFSCAN         (1<<6)
  75 #define MD_SEPPOT         (1<<7)
  76 #define MD_PARTDEC        (1<<9)
  77 #define MD_DDBONDCHECK    (1<<10)
  78 #define MD_DDBONDCOMM     (1<<11)
  79 #define MD_CONFOUT        (1<<12)
  80 #define MD_REPRODUCIBLE   (1<<13)
  81 #define MD_READ_RNG       (1<<14)
  82 #define MD_APPENDFILES    (1<<15)
  83 #define MD_APPENDFILESSET (1<<21)
  84 #define MD_KEEPANDNUMCPT  (1<<16)
  85 #define MD_READ_EKIN      (1<<17)
  86 #define MD_STARTFROMCPT   (1<<18)
  87 #define MD_RESETCOUNTERSHALFWAY (1<<19)
  88 #define MD_TUNEPME        (1<<20)
  89 #define MD_TESTVERLET     (1<<22)
  90
  91 enum {
  92   ddnoSEL, ddnoINTERLEAVE, ddnoPP_PME, ddnoCARTESIAN, ddnoNR
  93 };
  94
  95 typedef struct {
  96     int      nthreads_tot;        /* Total number of threads requested (TMPI) */
  97     int      nthreads_tmpi;       /* Number of TMPI threads requested         */
  98     int      nthreads_omp;        /* Number of OpenMP threads requested       */
  99     int      nthreads_omp_pme;    /* As nthreads_omp, but for PME only nodes  */
 100     gmx_bool bThreadPinning;      /* Pin OpenMP threads to cores?             */
 101     gmx_bool bPinHyperthreading;  /* Pin pairs of threads to physical cores   */
 102     int      core_pinning_offset; /* Physical core pinning offset             */
 103     char    *gpu_id;              /* GPU id's to use, each specified as chars */
 104 } gmx_hw_opt_t;
 105
 106 /* Variables for temporary use with the deform option,
 107  * used in runner.c and md.c.
 108  * (These variables should be stored in the tpx file.)
 109  */
 110 extern gmx_large_int_t     deform_init_init_step_tpx;
 111 extern matrix              deform_init_box_tpx;
 112 #ifdef GMX_THREAD_MPI
 113 extern tMPI_Thread_mutex_t deform_init_box_mutex;
 114
 115 /* The minimum number of atoms per tMPI thread. With fewer atoms than this,
 116  * the number of threads will get lowered.
 117  */
 118 #define MIN_ATOMS_PER_MPI_THREAD    90
 119 #define MIN_ATOMS_PER_GPU           900
 120 #endif
 121
 122
 123 typedef double gmx_integrator_t(FILE *log,t_commrec *cr,
 124                                 int nfile,const t_filenm fnm[],
 125                                 const output_env_t oenv, gmx_bool bVerbose,
 126                                 gmx_bool bCompact, int nstglobalcomm,
 127                                 gmx_vsite_t *vsite,gmx_constr_t constr,
 128                                 int stepout,
 129                                 t_inputrec *inputrec,
 130                                 gmx_mtop_t *mtop,t_fcdata *fcd,
 131                                 t_state *state,
 132                                 t_mdatoms *mdatoms,
 133                                 t_nrnb *nrnb,gmx_wallcycle_t wcycle,
 134                                 gmx_edsam_t ed,
 135                                 t_forcerec *fr,
 136                                 int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
 137                                 gmx_membed_t membed,
 138                                 real cpt_period,real max_hours,
 139                                 const char *deviceOptions,
 140                                 unsigned long Flags,
 141                                 gmx_runtime_t *runtime);
 142
 143 /* ROUTINES from md.c */
 144
 145 gmx_integrator_t do_md;
 146
 147
 148 /* ROUTINES from minimize.c */
 149
 150 GMX_LIBMD_EXPORT
 151 gmx_integrator_t do_steep;
 152 /* Do steepest descents EM */
 153
 154 GMX_LIBMD_EXPORT
 155 gmx_integrator_t do_cg;
 156 /* Do conjugate gradient EM */
 157
 158 GMX_LIBMD_EXPORT
 159 gmx_integrator_t do_lbfgs;
 160 /* Do conjugate gradient L-BFGS */
 161
 162 GMX_LIBMD_EXPORT
 163 gmx_integrator_t do_nm;
 164 /* Do normal mode analysis */
 165
 166 /* ROUTINES from tpi.c */
 167
 168 GMX_LIBMD_EXPORT
 169 gmx_integrator_t do_tpi;
 170 /* Do test particle insertion */
 171
 172 void init_npt_masses(t_inputrec *ir, t_state *state, t_extmass *MassQ, gmx_bool bInit);
 173
 174 GMX_LIBMD_EXPORT
 175 int ExpandedEnsembleDynamics(FILE *log,t_inputrec *ir, gmx_enerdata_t *enerd,
 176                              t_state *state, t_extmass *MassQ, df_history_t *dfhist,
 177                              gmx_large_int_t step, gmx_rng_t mcrng,
 178                              rvec *v, t_mdatoms *mdatoms);
 179
 180 GMX_LIBMD_EXPORT
 181 void PrintFreeEnergyInfoToFile(FILE *outfile, t_lambda *fep, t_expanded *expand, t_simtemp *simtemp, df_history_t *dfhist,
 182                                int nlam, int frequency, gmx_large_int_t step);
 183
 184 GMX_LIBMD_EXPORT
 185 void get_mc_state(gmx_rng_t rng,t_state *state);
 186
 187 GMX_LIBMD_EXPORT
 188 void set_mc_state(gmx_rng_t rng,t_state *state);
 189
 190 /* check the version */
 191 GMX_LIBMD_EXPORT
 192 void check_ir_old_tpx_versions(t_commrec *cr,FILE *fplog,
 193                                t_inputrec *ir,gmx_mtop_t *mtop);
 194
 195 /* Allocate and initialize node-local state entries. */
 196 GMX_LIBMD_EXPORT
 197 void set_state_entries(t_state *state,const t_inputrec *ir,int nnodes);
 198
 199 /* Broadcast the data for a simulation, and allocate node-specific settings
 200    such as rng generators. */
 201 GMX_LIBMD_EXPORT
 202 void init_parallel(FILE *log, t_commrec *cr, t_inputrec *inputrec,
 203                           gmx_mtop_t *mtop);
 204
 205 int mdrunner(gmx_hw_opt_t *hw_opt,
 206              FILE *fplog,t_commrec *cr,int nfile,
 207              const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
 208              gmx_bool bCompact, int nstglobalcomm, ivec ddxyz,int dd_node_order,
 209              real rdd, real rconstr, const char *dddlb_opt,real dlb_scale,
 210              const char *ddcsx,const char *ddcsy,const char *ddcsz,
 211              const char *nbpu_opt,
 212              int nsteps_cmdline, int nstepout, int resetstep,
 213              int nmultisim, int repl_ex_nst, int repl_ex_nex,
 214              int repl_ex_seed, real pforce,real cpt_period,real max_hours,
 215              const char *deviceOptions, unsigned long Flags);
 216 /* Driver routine, that calls the different methods */
 217
 218 #ifdef __cplusplus
 219 }
 220 #endif
 221
 222 #endif  /* _mdrun_h */