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56 gmx_bool bKeepAndNumCPT
;
65 typedef struct gmx_global_stat
*gmx_global_stat_t
;
78 gmx_large_int_t nsteps_done
;
82 void do_pbc_first(FILE *log
,matrix box
,t_forcerec
*fr
,
83 t_graph
*graph
,rvec x
[]);
85 void do_pbc_first_mtop(FILE *fplog
,int ePBC
,matrix box
,
86 gmx_mtop_t
*mtop
,rvec x
[]);
88 void do_pbc_mtop(FILE *fplog
,int ePBC
,matrix box
,
89 gmx_mtop_t
*mtop
,rvec x
[]);
93 /* ROUTINES from stat.c */
94 gmx_global_stat_t
global_stat_init(t_inputrec
*ir
);
96 void global_stat_destroy(gmx_global_stat_t gs
);
98 void global_stat(FILE *log
,gmx_global_stat_t gs
,
99 t_commrec
*cr
,gmx_enerdata_t
*enerd
,
100 tensor fvir
,tensor svir
,rvec mu_tot
,
101 t_inputrec
*inputrec
,
102 gmx_ekindata_t
*ekind
,
103 gmx_constr_t constr
,t_vcm
*vcm
,
105 gmx_mtop_t
*top_global
, t_state
*state_local
,
106 gmx_bool bSumEkinhOld
, int flags
);
107 /* Communicate statistics over cr->mpi_comm_mysim */
109 gmx_mdoutf_t
*init_mdoutf(int nfile
,const t_filenm fnm
[],
111 const t_commrec
*cr
,const t_inputrec
*ir
,
112 const output_env_t oenv
);
113 /* Returns a pointer to a data structure with all output file pointers
114 * and names required by mdrun.
117 void done_mdoutf(gmx_mdoutf_t
*of
);
118 /* Close all open output files and free the of pointer */
120 #define MDOF_X (1<<0)
121 #define MDOF_V (1<<1)
122 #define MDOF_F (1<<2)
123 #define MDOF_XTC (1<<3)
124 #define MDOF_CPT (1<<4)
126 void write_traj(FILE *fplog
,t_commrec
*cr
,
129 gmx_mtop_t
*top_global
,
130 gmx_large_int_t step
,double t
,
131 t_state
*state_local
,t_state
*state_global
,
132 rvec
*f_local
,rvec
*f_global
,
133 int *n_xtc
,rvec
**x_xtc
);
134 /* Routine that writes frames to trn, xtc and/or checkpoint.
135 * What is written is determined by the mdof_flags defined above.
136 * Data is collected to the master node only when necessary.
139 int do_per_step(gmx_large_int_t step
,gmx_large_int_t nstep
);
140 /* Return TRUE if io should be done */
142 /* ROUTINES from sim_util.c */
144 double gmx_gettime();
146 void print_time(FILE *out
, gmx_runtime_t
*runtime
,
147 gmx_large_int_t step
,t_inputrec
*ir
, t_commrec
*cr
);
149 void runtime_start(gmx_runtime_t
*runtime
);
151 void runtime_end(gmx_runtime_t
*runtime
);
153 void runtime_upd_proc(gmx_runtime_t
*runtime
);
154 /* The processor time should be updated every once in a while,
155 * since on 32-bit manchines it loops after 72 minutes.
158 void print_date_and_time(FILE *log
,int pid
,const char *title
,
159 const gmx_runtime_t
*runtime
);
161 void finish_run(FILE *log
,t_commrec
*cr
,const char *confout
,
162 t_inputrec
*inputrec
,
163 t_nrnb nrnb
[],gmx_wallcycle_t wcycle
,
164 gmx_runtime_t
*runtime
,
165 wallclock_gpu_t
*gputimes
,
167 gmx_bool bWriteStat
);
169 void calc_enervirdiff(FILE *fplog
,int eDispCorr
,t_forcerec
*fr
);
171 void calc_dispcorr(FILE *fplog
,t_inputrec
*ir
,t_forcerec
*fr
,
172 gmx_large_int_t step
, int natoms
,
173 matrix box
,real lambda
,tensor pres
,tensor virial
,
174 real
*prescorr
, real
*enercorr
, real
*dvdlcorr
);
176 void initialize_lambdas(FILE *fplog
,t_inputrec
*ir
,int *fep_state
,real
*lambda
,double *lam0
);
178 void do_constrain_first(FILE *log
,gmx_constr_t constr
,
179 t_inputrec
*inputrec
,t_mdatoms
*md
,
180 t_state
*state
,rvec
*f
,
181 t_graph
*graph
,t_commrec
*cr
,t_nrnb
*nrnb
,
182 t_forcerec
*fr
, gmx_localtop_t
*top
, tensor shake_vir
);
184 void init_md(FILE *fplog
,
185 t_commrec
*cr
,t_inputrec
*ir
, const output_env_t oenv
,
186 double *t
,double *t0
,
187 real
*lambda
,int *fep_state
, double *lam0
,
188 t_nrnb
*nrnb
,gmx_mtop_t
*mtop
,
190 int nfile
,const t_filenm fnm
[],
191 gmx_mdoutf_t
**outf
,t_mdebin
**mdebin
,
192 tensor force_vir
,tensor shake_vir
,
194 gmx_bool
*bSimAnn
,t_vcm
**vcm
,
195 t_state
*state
, unsigned long Flags
);
196 /* Routine in sim_util.c */
202 #endif /* _sim_util_h */