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53 #include "types/membedt.h"
54 #include "types/globsig.h"
58 #include "thread_mpi/threads.h"
65 #define MD_POLARISE (1<<2)
66 #define MD_RERUN (1<<4)
67 #define MD_RERUN_VSITE (1<<5)
68 #define MD_SEPPOT (1<<7)
69 #define MD_PARTDEC (1<<9)
70 #define MD_DDBONDCHECK (1<<10)
71 #define MD_DDBONDCOMM (1<<11)
72 #define MD_CONFOUT (1<<12)
73 #define MD_REPRODUCIBLE (1<<13)
74 #define MD_READ_RNG (1<<14)
75 #define MD_APPENDFILES (1<<15)
76 #define MD_APPENDFILESSET (1<<21)
77 #define MD_KEEPANDNUMCPT (1<<16)
78 #define MD_READ_EKIN (1<<17)
79 #define MD_STARTFROMCPT (1<<18)
80 #define MD_RESETCOUNTERSHALFWAY (1<<19)
81 #define MD_TUNEPME (1<<20)
82 #define MD_TESTVERLET (1<<22)
84 /* The options for the domain decomposition MPI task ordering */
86 ddnoSEL, ddnoINTERLEAVE, ddnoPP_PME, ddnoCARTESIAN, ddnoNR
89 /* The options for the thread affinity setting, default: auto */
91 threadaffSEL, threadaffAUTO, threadaffON, threadaffOFF, threadaffNR
95 int nthreads_tot; /* Total number of threads requested (TMPI) */
96 int nthreads_tmpi; /* Number of TMPI threads requested */
97 int nthreads_omp; /* Number of OpenMP threads requested */
98 int nthreads_omp_pme; /* As nthreads_omp, but for PME only nodes */
99 int thread_affinity; /* Thread affinity switch, see enum above */
100 int core_pinning_stride; /* Logical core pinning stride */
101 int core_pinning_offset; /* Logical core pinning offset */
102 char *gpu_id; /* GPU id's to use, each specified as chars */
105 /* Variables for temporary use with the deform option,
106 * used in runner.c and md.c.
107 * (These variables should be stored in the tpx file.)
109 extern gmx_large_int_t deform_init_init_step_tpx;
110 extern matrix deform_init_box_tpx;
111 #ifdef GMX_THREAD_MPI
112 extern tMPI_Thread_mutex_t deform_init_box_mutex;
114 /* The minimum number of atoms per tMPI thread. With fewer atoms than this,
115 * the number of threads will get lowered.
117 #define MIN_ATOMS_PER_MPI_THREAD 90
118 #define MIN_ATOMS_PER_GPU 900
122 typedef double gmx_integrator_t (FILE *log, t_commrec *cr,
123 int nfile, const t_filenm fnm[],
124 const output_env_t oenv, gmx_bool bVerbose,
125 gmx_bool bCompact, int nstglobalcomm,
126 gmx_vsite_t *vsite, gmx_constr_t constr,
128 t_inputrec *inputrec,
129 gmx_mtop_t *mtop, t_fcdata *fcd,
132 t_nrnb *nrnb, gmx_wallcycle_t wcycle,
135 int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
137 real cpt_period, real max_hours,
138 const char *deviceOptions,
140 gmx_runtime_t *runtime);
142 /* ROUTINES from md.c */
144 gmx_integrator_t do_md;
147 /* ROUTINES from minimize.c */
149 gmx_integrator_t do_steep;
150 /* Do steepest descents EM */
152 gmx_integrator_t do_cg;
153 /* Do conjugate gradient EM */
155 gmx_integrator_t do_lbfgs;
156 /* Do conjugate gradient L-BFGS */
158 gmx_integrator_t do_nm;
159 /* Do normal mode analysis */
161 /* ROUTINES from tpi.c */
163 gmx_integrator_t do_tpi;
164 /* Do test particle insertion */
166 void init_npt_masses(t_inputrec *ir, t_state *state, t_extmass *MassQ, gmx_bool bInit);
168 void init_expanded_ensemble(gmx_bool bStateFromCP, t_inputrec *ir, gmx_rng_t *mcrng, df_history_t *dfhist);
170 int ExpandedEnsembleDynamics(FILE *log, t_inputrec *ir, gmx_enerdata_t *enerd,
171 t_state *state, t_extmass *MassQ, int fep_state, df_history_t *dfhist,
172 gmx_large_int_t step, gmx_rng_t mcrng,
173 rvec *v, t_mdatoms *mdatoms);
175 void PrintFreeEnergyInfoToFile(FILE *outfile, t_lambda *fep, t_expanded *expand, t_simtemp *simtemp, df_history_t *dfhist,
176 int fep_state, int frequency, gmx_large_int_t step);
178 void get_mc_state(gmx_rng_t rng, t_state *state);
180 void set_mc_state(gmx_rng_t rng, t_state *state);
182 /* check the version */
183 void check_ir_old_tpx_versions(t_commrec *cr, FILE *fplog,
184 t_inputrec *ir, gmx_mtop_t *mtop);
186 /* Allocate and initialize node-local state entries. */
187 void set_state_entries(t_state *state, const t_inputrec *ir, int nnodes);
189 /* Broadcast the data for a simulation, and allocate node-specific settings
190 such as rng generators. */
191 void init_parallel(t_commrec *cr, t_inputrec *inputrec,
194 int mdrunner(gmx_hw_opt_t *hw_opt,
195 FILE *fplog, t_commrec *cr, int nfile,
196 const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
197 gmx_bool bCompact, int nstglobalcomm, ivec ddxyz, int dd_node_order,
198 real rdd, real rconstr, const char *dddlb_opt, real dlb_scale,
199 const char *ddcsx, const char *ddcsy, const char *ddcsz,
200 const char *nbpu_opt,
201 gmx_large_int_t nsteps_cmdline, int nstepout, int resetstep,
202 int nmultisim, int repl_ex_nst, int repl_ex_nex,
203 int repl_ex_seed, real pforce, real cpt_period, real max_hours,
204 const char *deviceOptions, unsigned long Flags);
205 /* Driver routine, that calls the different methods */
208 do_trajectory_writing(FILE *fplog,
211 const t_filenm fnm[],
212 gmx_large_int_t step,
213 gmx_large_int_t step_rel,
217 t_state *state_global,
218 gmx_mtop_t *top_global,
223 gmx_ekindata_t *ekind,
226 gmx_wallcycle_t wcycle,
233 gmx_bool bSumEkinhOld
235 /* Wrapper routine for trajectory writing */
241 #endif /* _mdrun_h */