include/mdrun.h

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * Gromacs Runs On Most of All Computer Systems
  34  */
  35
  36 #ifndef _mdrun_h
  37 #define _mdrun_h
  38
  39 #include <stdio.h>
  40 #include <time.h>
  41 #include "typedefs.h"
  42 #include "network.h"
  43 #include "sim_util.h"
  44 #include "tgroup.h"
  45 #include "filenm.h"
  46 #include "mshift.h"
  47 #include "force.h"
  48 #include "edsam.h"
  49 #include "mdebin.h"
  50 #include "vcm.h"
  51 #include "vsite.h"
  52 #include "pull.h"
  53 #include "update.h"
  54 #include "types/membedt.h"
  55 #include "types/globsig.h"
  56
  57
  58 #ifdef GMX_THREAD_MPI
  59 #include "thread_mpi/threads.h"
  60 #endif
  61
  62 #ifdef __cplusplus
  63 extern "C" {
  64 #endif
  65
  66 #define MD_POLARISE       (1<<2)
  67 #define MD_IONIZE         (1<<3)
  68 #define MD_RERUN          (1<<4)
  69 #define MD_RERUN_VSITE    (1<<5)
  70 #define MD_FFSCAN         (1<<6)
  71 #define MD_SEPPOT         (1<<7)
  72 #define MD_PARTDEC        (1<<9)
  73 #define MD_DDBONDCHECK    (1<<10)
  74 #define MD_DDBONDCOMM     (1<<11)
  75 #define MD_CONFOUT        (1<<12)
  76 #define MD_REPRODUCIBLE   (1<<13)
  77 #define MD_READ_RNG       (1<<14)
  78 #define MD_APPENDFILES    (1<<15)
  79 #define MD_APPENDFILESSET (1<<21)
  80 #define MD_KEEPANDNUMCPT  (1<<16)
  81 #define MD_READ_EKIN      (1<<17)
  82 #define MD_STARTFROMCPT   (1<<18)
  83 #define MD_RESETCOUNTERSHALFWAY (1<<19)
  84 #define MD_TUNEPME        (1<<20)
  85 #define MD_TESTVERLET     (1<<22)
  86
  87 enum {
  88   ddnoSEL, ddnoINTERLEAVE, ddnoPP_PME, ddnoCARTESIAN, ddnoNR
  89 };
  90
  91 typedef struct {
  92     int      nthreads_tot;        /* Total number of threads requested (TMPI) */
  93     int      nthreads_tmpi;       /* Number of TMPI threads requested         */
  94     int      nthreads_omp;        /* Number of OpenMP threads requested       */
  95     int      nthreads_omp_pme;    /* As nthreads_omp, but for PME only nodes  */
  96     gmx_bool bThreadPinning;      /* Pin OpenMP threads to cores?             */
  97     gmx_bool bPinHyperthreading;  /* Pin pairs of threads to physical cores   */
  98     int      core_pinning_offset; /* Physical core pinning offset             */
  99     char    *gpu_id;              /* GPU id's to use, each specified as chars */
 100 } gmx_hw_opt_t;
 101
 102 /* Variables for temporary use with the deform option,
 103  * used in runner.c and md.c.
 104  * (These variables should be stored in the tpx file.)
 105  */
 106 extern gmx_large_int_t     deform_init_init_step_tpx;
 107 extern matrix              deform_init_box_tpx;
 108 #ifdef GMX_THREAD_MPI
 109 extern tMPI_Thread_mutex_t deform_init_box_mutex;
 110
 111 /* The minimum number of atoms per tMPI thread. With fewer atoms than this,
 112  * the number of threads will get lowered.
 113  */
 114 #define MIN_ATOMS_PER_MPI_THREAD    90
 115 #define MIN_ATOMS_PER_GPU           900
 116 #endif
 117
 118
 119 typedef double gmx_integrator_t(FILE *log,t_commrec *cr,
 120                                 int nfile,const t_filenm fnm[],
 121                                 const output_env_t oenv, gmx_bool bVerbose,
 122                                 gmx_bool bCompact, int nstglobalcomm,
 123                                 gmx_vsite_t *vsite,gmx_constr_t constr,
 124                                 int stepout,
 125                                 t_inputrec *inputrec,
 126                                 gmx_mtop_t *mtop,t_fcdata *fcd,
 127                                 t_state *state,
 128                                 t_mdatoms *mdatoms,
 129                                 t_nrnb *nrnb,gmx_wallcycle_t wcycle,
 130                                 gmx_edsam_t ed,
 131                                 t_forcerec *fr,
 132                                 int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
 133                                 gmx_membed_t membed,
 134                                 real cpt_period,real max_hours,
 135                                 const char *deviceOptions,
 136                                 unsigned long Flags,
 137                                 gmx_runtime_t *runtime);
 138
 139 /* ROUTINES from md.c */
 140
 141 gmx_integrator_t do_md;
 142
 143 gmx_integrator_t do_md_openmm;
 144
 145
 146
 147 /* ROUTINES from minimize.c */
 148
 149 gmx_integrator_t do_steep;
 150 /* Do steepest descents EM */
 151
 152 gmx_integrator_t do_cg;
 153 /* Do conjugate gradient EM */
 154
 155 gmx_integrator_t do_lbfgs;
 156 /* Do conjugate gradient L-BFGS */
 157
 158 gmx_integrator_t do_nm;
 159 /* Do normal mode analysis */
 160
 161 /* ROUTINES from tpi.c */
 162
 163 gmx_integrator_t do_tpi;
 164 /* Do test particle insertion */
 165
 166 void init_npt_masses(t_inputrec *ir, t_state *state, t_extmass *MassQ, gmx_bool bInit);
 167
 168 int ExpandedEnsembleDynamics(FILE *log,t_inputrec *ir, gmx_enerdata_t *enerd,
 169                              t_state *state, t_extmass *MassQ, df_history_t *dfhist,
 170                              gmx_large_int_t step, gmx_rng_t mcrng,
 171                              rvec *v, t_mdatoms *mdatoms);
 172
 173 void PrintFreeEnergyInfoToFile(FILE *outfile, t_lambda *fep, t_expanded *expand, t_simtemp *simtemp, df_history_t *dfhist,
 174                                int nlam, int frequency, gmx_large_int_t step);
 175
 176 void get_mc_state(gmx_rng_t rng,t_state *state);
 177
 178 void set_mc_state(gmx_rng_t rng,t_state *state);
 179
 180 /* check the version */
 181 void check_ir_old_tpx_versions(t_commrec *cr,FILE *fplog,
 182                                t_inputrec *ir,gmx_mtop_t *mtop);
 183
 184 /* Allocate and initialize node-local state entries. */
 185 void set_state_entries(t_state *state,const t_inputrec *ir,int nnodes);
 186
 187 /* Broadcast the data for a simulation, and allocate node-specific settings
 188    such as rng generators. */
 189 void init_parallel(FILE *log, t_commrec *cr, t_inputrec *inputrec,
 190                           gmx_mtop_t *mtop);
 191
 192 int mdrunner(gmx_hw_opt_t *hw_opt,
 193              FILE *fplog,t_commrec *cr,int nfile,
 194              const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
 195              gmx_bool bCompact, int nstglobalcomm, ivec ddxyz,int dd_node_order,
 196              real rdd, real rconstr, const char *dddlb_opt,real dlb_scale,
 197              const char *ddcsx,const char *ddcsy,const char *ddcsz,
 198              const char *nbpu_opt,
 199              int nsteps_cmdline, int nstepout, int resetstep,
 200              int nmultisim, int repl_ex_nst, int repl_ex_nex,
 201              int repl_ex_seed, real pforce,real cpt_period,real max_hours,
 202              const char *deviceOptions, unsigned long Flags);
 203 /* Driver routine, that calls the different methods */
 204
 205 #ifdef __cplusplus
 206 }
 207 #endif
 208
 209 #endif  /* _mdrun_h */