include/mdrun.h

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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 /* The options for the domain decomposition MPI task ordering */
  92 enum {
  93     ddnoSEL, ddnoINTERLEAVE, ddnoPP_PME, ddnoCARTESIAN, ddnoNR
  94 };
  95
  96 /* The options for the thread affinity setting, default: auto */
  97 enum {
  98     threadaffSEL, threadaffAUTO, threadaffON, threadaffOFF, threadaffNR
  99 };
 100
 101 typedef struct {
 102     int      nthreads_tot;        /* Total number of threads requested (TMPI) */
 103     int      nthreads_tmpi;       /* Number of TMPI threads requested         */
 104     int      nthreads_omp;        /* Number of OpenMP threads requested       */
 105     int      nthreads_omp_pme;    /* As nthreads_omp, but for PME only nodes  */
 106     int      thread_affinity;     /* Thread affinity switch, see enum above   */
 107     int      core_pinning_stride; /* Logical core pinning stride              */
 108     int      core_pinning_offset; /* Logical core pinning offset              */
 109     char    *gpu_id;              /* GPU id's to use, each specified as chars */
 110 } gmx_hw_opt_t;
 111
 112 /* Variables for temporary use with the deform option,
 113  * used in runner.c and md.c.
 114  * (These variables should be stored in the tpx file.)
 115  */
 116 extern gmx_large_int_t     deform_init_init_step_tpx;
 117 extern matrix              deform_init_box_tpx;
 118 #ifdef GMX_THREAD_MPI
 119 extern tMPI_Thread_mutex_t deform_init_box_mutex;
 120
 121 /* The minimum number of atoms per tMPI thread. With fewer atoms than this,
 122  * the number of threads will get lowered.
 123  */
 124 #define MIN_ATOMS_PER_MPI_THREAD    90
 125 #define MIN_ATOMS_PER_GPU           900
 126 #endif
 127
 128
 129 typedef double gmx_integrator_t (FILE *log, t_commrec *cr,
 130                                  int nfile, const t_filenm fnm[],
 131                                  const output_env_t oenv, gmx_bool bVerbose,
 132                                  gmx_bool bCompact, int nstglobalcomm,
 133                                  gmx_vsite_t *vsite, gmx_constr_t constr,
 134                                  int stepout,
 135                                  t_inputrec *inputrec,
 136                                  gmx_mtop_t *mtop, t_fcdata *fcd,
 137                                  t_state *state,
 138                                  t_mdatoms *mdatoms,
 139                                  t_nrnb *nrnb, gmx_wallcycle_t wcycle,
 140                                  gmx_edsam_t ed,
 141                                  t_forcerec *fr,
 142                                  int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
 143                                  gmx_membed_t membed,
 144                                  real cpt_period, real max_hours,
 145                                  const char *deviceOptions,
 146                                  unsigned long Flags,
 147                                  gmx_runtime_t *runtime);
 148
 149 /* ROUTINES from md.c */
 150
 151 gmx_integrator_t do_md;
 152
 153
 154 /* ROUTINES from minimize.c */
 155
 156 GMX_LIBMD_EXPORT
 157 gmx_integrator_t do_steep;
 158 /* Do steepest descents EM */
 159
 160 GMX_LIBMD_EXPORT
 161 gmx_integrator_t do_cg;
 162 /* Do conjugate gradient EM */
 163
 164 GMX_LIBMD_EXPORT
 165 gmx_integrator_t do_lbfgs;
 166 /* Do conjugate gradient L-BFGS */
 167
 168 GMX_LIBMD_EXPORT
 169 gmx_integrator_t do_nm;
 170 /* Do normal mode analysis */
 171
 172 /* ROUTINES from tpi.c */
 173
 174 GMX_LIBMD_EXPORT
 175 gmx_integrator_t do_tpi;
 176 /* Do test particle insertion */
 177
 178 void init_npt_masses(t_inputrec *ir, t_state *state, t_extmass *MassQ, gmx_bool bInit);
 179
 180 GMX_LIBMD_EXPORT
 181 int ExpandedEnsembleDynamics(FILE *log, t_inputrec *ir, gmx_enerdata_t *enerd,
 182                              t_state *state, t_extmass *MassQ, df_history_t *dfhist,
 183                              gmx_large_int_t step, gmx_rng_t mcrng,
 184                              rvec *v, t_mdatoms *mdatoms);
 185
 186 GMX_LIBMD_EXPORT
 187 void PrintFreeEnergyInfoToFile(FILE *outfile, t_lambda *fep, t_expanded *expand, t_simtemp *simtemp, df_history_t *dfhist,
 188                                int nlam, int frequency, gmx_large_int_t step);
 189
 190 GMX_LIBMD_EXPORT
 191 void get_mc_state(gmx_rng_t rng, t_state *state);
 192
 193 GMX_LIBMD_EXPORT
 194 void set_mc_state(gmx_rng_t rng, t_state *state);
 195
 196 /* check the version */
 197 GMX_LIBMD_EXPORT
 198 void check_ir_old_tpx_versions(t_commrec *cr, FILE *fplog,
 199                                t_inputrec *ir, gmx_mtop_t *mtop);
 200
 201 /* Allocate and initialize node-local state entries. */
 202 GMX_LIBMD_EXPORT
 203 void set_state_entries(t_state *state, const t_inputrec *ir, int nnodes);
 204
 205 /* Broadcast the data for a simulation, and allocate node-specific settings
 206    such as rng generators. */
 207 GMX_LIBMD_EXPORT
 208 void init_parallel(FILE *log, t_commrec *cr, t_inputrec *inputrec,
 209                    gmx_mtop_t *mtop);
 210
 211 int mdrunner(gmx_hw_opt_t *hw_opt,
 212              FILE *fplog, t_commrec *cr, int nfile,
 213              const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
 214              gmx_bool bCompact, int nstglobalcomm, ivec ddxyz, int dd_node_order,
 215              real rdd, real rconstr, const char *dddlb_opt, real dlb_scale,
 216              const char *ddcsx, const char *ddcsy, const char *ddcsz,
 217              const char *nbpu_opt,
 218              gmx_large_int_t nsteps_cmdline, int nstepout, int resetstep,
 219              int nmultisim, int repl_ex_nst, int repl_ex_nex,
 220              int repl_ex_seed, real pforce, real cpt_period, real max_hours,
 221              const char *deviceOptions, unsigned long Flags);
 222 /* Driver routine, that calls the different methods */
 223
 224 #ifdef __cplusplus
 225 }
 226 #endif
 227
 228 #endif  /* _mdrun_h */