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
44 #include "gromacs/timing/walltime_accounting.h"
56 gmx_bool bKeepAndNumCPT;
65 typedef struct gmx_global_stat *gmx_global_stat_t;
67 void do_pbc_first(FILE *log, matrix box, t_forcerec *fr,
68 t_graph *graph, rvec x[]);
70 void do_pbc_first_mtop(FILE *fplog, int ePBC, matrix box,
71 gmx_mtop_t *mtop, rvec x[]);
73 void do_pbc_mtop(FILE *fplog, int ePBC, matrix box,
74 gmx_mtop_t *mtop, rvec x[]);
78 /* ROUTINES from stat.c */
79 gmx_global_stat_t global_stat_init(t_inputrec *ir);
81 void global_stat_destroy(gmx_global_stat_t gs);
83 void global_stat(FILE *log, gmx_global_stat_t gs,
84 t_commrec *cr, gmx_enerdata_t *enerd,
85 tensor fvir, tensor svir, rvec mu_tot,
87 gmx_ekindata_t *ekind,
88 gmx_constr_t constr, t_vcm *vcm,
90 gmx_mtop_t *top_global, t_state *state_local,
91 gmx_bool bSumEkinhOld, int flags);
92 /* Communicate statistics over cr->mpi_comm_mysim */
94 gmx_mdoutf_t *init_mdoutf(int nfile, const t_filenm fnm[],
96 const t_commrec *cr, const t_inputrec *ir,
97 const output_env_t oenv);
98 /* Returns a pointer to a data structure with all output file pointers
99 * and names required by mdrun.
102 void done_mdoutf(gmx_mdoutf_t *of);
103 /* Close all open output files and free the of pointer */
105 #define MDOF_X (1<<0)
106 #define MDOF_V (1<<1)
107 #define MDOF_F (1<<2)
108 #define MDOF_XTC (1<<3)
109 #define MDOF_CPT (1<<4)
111 void write_traj(FILE *fplog, t_commrec *cr,
114 gmx_mtop_t *top_global,
115 gmx_large_int_t step, double t,
116 t_state *state_local, t_state *state_global,
117 rvec *f_local, rvec *f_global,
118 int *n_xtc, rvec **x_xtc);
119 /* Routine that writes frames to trn, xtc and/or checkpoint.
120 * What is written is determined by the mdof_flags defined above.
121 * Data is collected to the master node only when necessary.
124 int do_per_step(gmx_large_int_t step, gmx_large_int_t nstep);
125 /* Return TRUE if io should be done */
127 /* ROUTINES from sim_util.c */
129 void print_time(FILE *out, gmx_walltime_accounting_t walltime_accounting,
130 gmx_large_int_t step, t_inputrec *ir, t_commrec *cr);
132 void print_date_and_time(FILE *log, int pid, const char *title,
133 const gmx_walltime_accounting_t walltime_accounting);
135 void finish_run(FILE *log, t_commrec *cr,
136 t_inputrec *inputrec,
137 t_nrnb nrnb[], gmx_wallcycle_t wcycle,
138 gmx_walltime_accounting_t walltime_accounting,
139 wallclock_gpu_t *gputimes,
140 gmx_bool bWriteStat);
142 void calc_enervirdiff(FILE *fplog, int eDispCorr, t_forcerec *fr);
144 void calc_dispcorr(FILE *fplog, t_inputrec *ir, t_forcerec *fr,
145 gmx_large_int_t step, int natoms,
146 matrix box, real lambda, tensor pres, tensor virial,
147 real *prescorr, real *enercorr, real *dvdlcorr);
149 void initialize_lambdas(FILE *fplog, t_inputrec *ir, int *fep_state, real *lambda, double *lam0);
151 void do_constrain_first(FILE *log, gmx_constr_t constr,
152 t_inputrec *inputrec, t_mdatoms *md,
153 t_state *state, t_commrec *cr, t_nrnb *nrnb,
154 t_forcerec *fr, gmx_localtop_t *top);
156 void init_md(FILE *fplog,
157 t_commrec *cr, t_inputrec *ir, const output_env_t oenv,
158 double *t, double *t0,
159 real *lambda, int *fep_state, double *lam0,
160 t_nrnb *nrnb, gmx_mtop_t *mtop,
162 int nfile, const t_filenm fnm[],
163 gmx_mdoutf_t **outf, t_mdebin **mdebin,
164 tensor force_vir, tensor shake_vir,
166 gmx_bool *bSimAnn, t_vcm **vcm, unsigned long Flags);
167 /* Routine in sim_util.c */
173 #endif /* _sim_util_h */