3 * This source code is part of
7 * GROningen MAchine for Chemical Simulations
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.
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.
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.
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.
30 * For more info, check our website at http://www.gromacs.org
33 * Gromacs Runs On Most of All Computer Systems
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,
162 t_inputrec *inputrec,
163 t_nrnb nrnb[], gmx_wallcycle_t wcycle,
164 gmx_runtime_t *runtime,
165 wallclock_gpu_t *gputimes,
166 gmx_bool bWriteStat);
168 void calc_enervirdiff(FILE *fplog, int eDispCorr, t_forcerec *fr);
170 void calc_dispcorr(FILE *fplog, t_inputrec *ir, t_forcerec *fr,
171 gmx_large_int_t step, int natoms,
172 matrix box, real lambda, tensor pres, tensor virial,
173 real *prescorr, real *enercorr, real *dvdlcorr);
175 void initialize_lambdas(FILE *fplog, t_inputrec *ir, int *fep_state, real *lambda, double *lam0);
177 void do_constrain_first(FILE *log, gmx_constr_t constr,
178 t_inputrec *inputrec, t_mdatoms *md,
179 t_state *state, t_commrec *cr, t_nrnb *nrnb,
180 t_forcerec *fr, gmx_localtop_t *top);
182 void init_md(FILE *fplog,
183 t_commrec *cr, t_inputrec *ir, const output_env_t oenv,
184 double *t, double *t0,
185 real *lambda, int *fep_state, double *lam0,
186 t_nrnb *nrnb, gmx_mtop_t *mtop,
188 int nfile, const t_filenm fnm[],
189 gmx_mdoutf_t **outf, t_mdebin **mdebin,
190 tensor force_vir, tensor shake_vir,
192 gmx_bool *bSimAnn, t_vcm **vcm, unsigned long Flags);
193 /* Routine in sim_util.c */
199 #endif /* _sim_util_h */