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44 #include "visibility.h"
58 #include "types/membedt.h"
59 #include "types/globsig.h"
63 #include "thread_mpi/threads.h"
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)
92 ddnoSEL, ddnoINTERLEAVE, ddnoPP_PME, ddnoCARTESIAN, ddnoNR
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 */
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.)
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;
115 /* The minimum number of atoms per tMPI thread. With fewer atoms than this,
116 * the number of threads will get lowered.
118 #define MIN_ATOMS_PER_MPI_THREAD 90
119 #define MIN_ATOMS_PER_GPU 900
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,
129 t_inputrec *inputrec,
130 gmx_mtop_t *mtop,t_fcdata *fcd,
133 t_nrnb *nrnb,gmx_wallcycle_t wcycle,
136 int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
138 real cpt_period,real max_hours,
139 const char *deviceOptions,
141 gmx_runtime_t *runtime);
143 /* ROUTINES from md.c */
145 gmx_integrator_t do_md;
148 /* ROUTINES from minimize.c */
151 gmx_integrator_t do_steep;
152 /* Do steepest descents EM */
155 gmx_integrator_t do_cg;
156 /* Do conjugate gradient EM */
159 gmx_integrator_t do_lbfgs;
160 /* Do conjugate gradient L-BFGS */
163 gmx_integrator_t do_nm;
164 /* Do normal mode analysis */
166 /* ROUTINES from tpi.c */
169 gmx_integrator_t do_tpi;
170 /* Do test particle insertion */
172 void init_npt_masses(t_inputrec *ir, t_state *state, t_extmass *MassQ, gmx_bool bInit);
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);
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);
185 void get_mc_state(gmx_rng_t rng,t_state *state);
188 void set_mc_state(gmx_rng_t rng,t_state *state);
190 /* check the version */
192 void check_ir_old_tpx_versions(t_commrec *cr,FILE *fplog,
193 t_inputrec *ir,gmx_mtop_t *mtop);
195 /* Allocate and initialize node-local state entries. */
197 void set_state_entries(t_state *state,const t_inputrec *ir,int nnodes);
199 /* Broadcast the data for a simulation, and allocate node-specific settings
200 such as rng generators. */
202 void init_parallel(FILE *log, t_commrec *cr, t_inputrec *inputrec,
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 */
222 #endif /* _mdrun_h */