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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_IONIZE (1<<3)
67 #define MD_RERUN (1<<4)
68 #define MD_RERUN_VSITE (1<<5)
69 #define MD_SEPPOT (1<<7)
70 #define MD_PARTDEC (1<<9)
71 #define MD_DDBONDCHECK (1<<10)
72 #define MD_DDBONDCOMM (1<<11)
73 #define MD_CONFOUT (1<<12)
74 #define MD_REPRODUCIBLE (1<<13)
75 #define MD_READ_RNG (1<<14)
76 #define MD_APPENDFILES (1<<15)
77 #define MD_APPENDFILESSET (1<<21)
78 #define MD_KEEPANDNUMCPT (1<<16)
79 #define MD_READ_EKIN (1<<17)
80 #define MD_STARTFROMCPT (1<<18)
81 #define MD_RESETCOUNTERSHALFWAY (1<<19)
82 #define MD_TUNEPME (1<<20)
83 #define MD_TESTVERLET (1<<22)
85 /* The options for the domain decomposition MPI task ordering */
87 ddnoSEL, ddnoINTERLEAVE, ddnoPP_PME, ddnoCARTESIAN, ddnoNR
90 /* The options for the thread affinity setting, default: auto */
92 threadaffSEL, threadaffAUTO, threadaffON, threadaffOFF, threadaffNR
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 int thread_affinity; /* Thread affinity switch, see enum above */
101 int core_pinning_stride; /* Logical core pinning stride */
102 int core_pinning_offset; /* Logical 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 */
150 gmx_integrator_t do_steep;
151 /* Do steepest descents EM */
153 gmx_integrator_t do_cg;
154 /* Do conjugate gradient EM */
156 gmx_integrator_t do_lbfgs;
157 /* Do conjugate gradient L-BFGS */
159 gmx_integrator_t do_nm;
160 /* Do normal mode analysis */
162 /* ROUTINES from tpi.c */
164 gmx_integrator_t do_tpi;
165 /* Do test particle insertion */
167 void init_npt_masses(t_inputrec *ir, t_state *state, t_extmass *MassQ, gmx_bool bInit);
169 int ExpandedEnsembleDynamics(FILE *log, t_inputrec *ir, gmx_enerdata_t *enerd,
170 t_state *state, t_extmass *MassQ, df_history_t *dfhist,
171 gmx_large_int_t step, gmx_rng_t mcrng,
172 rvec *v, t_mdatoms *mdatoms);
174 void PrintFreeEnergyInfoToFile(FILE *outfile, t_lambda *fep, t_expanded *expand, t_simtemp *simtemp, df_history_t *dfhist,
175 int nlam, int frequency, gmx_large_int_t step);
177 void get_mc_state(gmx_rng_t rng, t_state *state);
179 void set_mc_state(gmx_rng_t rng, t_state *state);
181 /* check the version */
182 void check_ir_old_tpx_versions(t_commrec *cr, FILE *fplog,
183 t_inputrec *ir, gmx_mtop_t *mtop);
185 /* Allocate and initialize node-local state entries. */
186 void set_state_entries(t_state *state, const t_inputrec *ir, int nnodes);
188 /* Broadcast the data for a simulation, and allocate node-specific settings
189 such as rng generators. */
190 void init_parallel(t_commrec *cr, t_inputrec *inputrec,
193 int mdrunner(gmx_hw_opt_t *hw_opt,
194 FILE *fplog, t_commrec *cr, int nfile,
195 const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
196 gmx_bool bCompact, int nstglobalcomm, ivec ddxyz, int dd_node_order,
197 real rdd, real rconstr, const char *dddlb_opt, real dlb_scale,
198 const char *ddcsx, const char *ddcsy, const char *ddcsz,
199 const char *nbpu_opt,
200 gmx_large_int_t nsteps_cmdline, int nstepout, int resetstep,
201 int nmultisim, int repl_ex_nst, int repl_ex_nex,
202 int repl_ex_seed, real pforce, real cpt_period, real max_hours,
203 const char *deviceOptions, unsigned long Flags);
204 /* Driver routine, that calls the different methods */
210 #endif /* _mdrun_h */