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39 #include "gromacs/commandline/filenm.h"
40 #include "gromacs/domdec/domdec.h"
41 #include "gromacs/domdec/domdec_struct.h"
42 #include "gromacs/fileio/checkpoint.h"
43 #include "gromacs/fileio/gmxfio.h"
44 #include "gromacs/fileio/tngio.h"
45 #include "gromacs/fileio/trrio.h"
46 #include "gromacs/fileio/xtcio.h"
47 #include "gromacs/fileio/xvgr.h"
48 #include "gromacs/math/vec.h"
49 #include "gromacs/mdlib/mdrun.h"
50 #include "gromacs/mdlib/trajectory_writing.h"
51 #include "gromacs/mdtypes/commrec.h"
52 #include "gromacs/mdtypes/inputrec.h"
53 #include "gromacs/mdtypes/md_enums.h"
54 #include "gromacs/timing/wallcycle.h"
55 #include "gromacs/utility/fatalerror.h"
56 #include "gromacs/utility/pleasecite.h"
57 #include "gromacs/utility/smalloc.h"
63 tng_trajectory_t tng_low_prec
;
64 int x_compression_precision
; /* only used by XTC output */
67 gmx_bool bKeepAndNumCPT
;
75 int natoms_x_compressed
;
76 gmx_groups_t
*groups
; /* for compressed position writing */
77 gmx_wallcycle_t wcycle
;
82 gmx_mdoutf_t
init_mdoutf(FILE *fplog
, int nfile
, const t_filenm fnm
[],
83 int mdrun_flags
, const t_commrec
*cr
,
84 const t_inputrec
*ir
, gmx_mtop_t
*top_global
,
85 const gmx_output_env_t
*oenv
, gmx_wallcycle_t wcycle
)
88 const char *appendMode
= "a+", *writeMode
= "w+", *filemode
;
89 gmx_bool bAppendFiles
, bCiteTng
= FALSE
;
98 of
->tng_low_prec
= NULL
;
102 of
->eIntegrator
= ir
->eI
;
103 of
->bExpanded
= ir
->bExpanded
;
104 of
->elamstats
= ir
->expandedvals
->elamstats
;
105 of
->simulation_part
= ir
->simulation_part
;
106 of
->x_compression_precision
= static_cast<int>(ir
->x_compression_precision
);
112 bAppendFiles
= (mdrun_flags
& MD_APPENDFILES
);
114 of
->bKeepAndNumCPT
= (mdrun_flags
& MD_KEEPANDNUMCPT
);
116 filemode
= bAppendFiles
? appendMode
: writeMode
;
118 if (EI_DYNAMICS(ir
->eI
) &&
119 ir
->nstxout_compressed
> 0)
121 const char *filename
;
122 filename
= ftp2fn(efCOMPRESSED
, nfile
, fnm
);
123 switch (fn2ftp(filename
))
126 of
->fp_xtc
= open_xtc(filename
, filemode
);
129 gmx_tng_open(filename
, filemode
[0], &of
->tng_low_prec
);
130 if (filemode
[0] == 'w')
132 gmx_tng_prepare_low_prec_writing(of
->tng_low_prec
, top_global
, ir
);
137 gmx_incons("Invalid reduced precision file format");
140 if ((EI_DYNAMICS(ir
->eI
) || EI_ENERGY_MINIMIZATION(ir
->eI
))
143 !(EI_DYNAMICS(ir
->eI
) &&
150 const char *filename
;
151 filename
= ftp2fn(efTRN
, nfile
, fnm
);
152 switch (fn2ftp(filename
))
156 /* If there is no uncompressed coordinate output and
157 there is compressed TNG output write forces
158 and/or velocities to the TNG file instead. */
159 if (ir
->nstxout
!= 0 || ir
->nstxout_compressed
== 0 ||
162 of
->fp_trn
= gmx_trr_open(filename
, filemode
);
166 gmx_tng_open(filename
, filemode
[0], &of
->tng
);
167 if (filemode
[0] == 'w')
169 gmx_tng_prepare_md_writing(of
->tng
, top_global
, ir
);
174 gmx_incons("Invalid full precision file format");
177 if (EI_DYNAMICS(ir
->eI
) || EI_ENERGY_MINIMIZATION(ir
->eI
))
179 of
->fp_ene
= open_enx(ftp2fn(efEDR
, nfile
, fnm
), filemode
);
181 of
->fn_cpt
= opt2fn("-cpo", nfile
, fnm
);
183 if ((ir
->efep
!= efepNO
|| ir
->bSimTemp
) && ir
->fepvals
->nstdhdl
> 0 &&
184 (ir
->fepvals
->separate_dhdl_file
== esepdhdlfileYES
) &&
189 of
->fp_dhdl
= gmx_fio_fopen(opt2fn("-dhdl", nfile
, fnm
), filemode
);
193 of
->fp_dhdl
= open_dhdl(opt2fn("-dhdl", nfile
, fnm
), ir
, oenv
);
197 if (opt2bSet("-field", nfile
, fnm
) &&
198 (ir
->ex
[XX
].n
|| ir
->ex
[YY
].n
|| ir
->ex
[ZZ
].n
))
202 of
->fp_field
= gmx_fio_fopen(opt2fn("-field", nfile
, fnm
),
207 of
->fp_field
= xvgropen(opt2fn("-field", nfile
, fnm
),
208 "Applied electric field", "Time (ps)",
213 /* Set up atom counts so they can be passed to actual
214 trajectory-writing routines later. Also, XTC writing needs
215 to know what (and how many) atoms might be in the XTC
216 groups, and how to look up later which ones they are. */
217 of
->natoms_global
= top_global
->natoms
;
218 of
->groups
= &top_global
->groups
;
219 of
->natoms_x_compressed
= 0;
220 for (i
= 0; (i
< top_global
->natoms
); i
++)
222 if (ggrpnr(of
->groups
, egcCompressedX
, i
) == 0)
224 of
->natoms_x_compressed
++;
228 if (ir
->nstfout
&& DOMAINDECOMP(cr
))
230 snew(of
->f_global
, top_global
->natoms
);
236 please_cite(fplog
, "Lundborg2014");
242 FILE *mdoutf_get_fp_field(gmx_mdoutf_t of
)
247 ener_file_t
mdoutf_get_fp_ene(gmx_mdoutf_t of
)
252 FILE *mdoutf_get_fp_dhdl(gmx_mdoutf_t of
)
257 gmx_wallcycle_t
mdoutf_get_wcycle(gmx_mdoutf_t of
)
262 void mdoutf_write_to_trajectory_files(FILE *fplog
, t_commrec
*cr
,
265 gmx_mtop_t
*top_global
,
266 gmx_int64_t step
, double t
,
267 t_state
*state_local
, t_state
*state_global
,
274 /* MRS -- defining these variables is to manage the difference
275 * between half step and full step velocities, but there must be a better way . . . */
277 local_v
= state_local
->v
;
278 global_v
= state_global
->v
;
280 if (DOMAINDECOMP(cr
))
282 if (mdof_flags
& MDOF_CPT
)
284 dd_collect_state(cr
->dd
, state_local
, state_global
);
288 if (mdof_flags
& (MDOF_X
| MDOF_X_COMPRESSED
))
290 dd_collect_vec(cr
->dd
, state_local
, state_local
->x
,
293 if (mdof_flags
& MDOF_V
)
295 dd_collect_vec(cr
->dd
, state_local
, local_v
,
299 f_global
= of
->f_global
;
300 if (mdof_flags
& MDOF_F
)
302 dd_collect_vec(cr
->dd
, state_local
, f_local
, f_global
);
307 if (mdof_flags
& MDOF_CPT
)
309 /* All pointers in state_local are equal to state_global,
310 * but we need to copy the non-pointer entries.
312 state_global
->lambda
= state_local
->lambda
;
313 state_global
->veta
= state_local
->veta
;
314 state_global
->vol0
= state_local
->vol0
;
315 copy_mat(state_local
->box
, state_global
->box
);
316 copy_mat(state_local
->boxv
, state_global
->boxv
);
317 copy_mat(state_local
->svir_prev
, state_global
->svir_prev
);
318 copy_mat(state_local
->fvir_prev
, state_global
->fvir_prev
);
319 copy_mat(state_local
->pres_prev
, state_global
->pres_prev
);
326 if (mdof_flags
& MDOF_CPT
)
329 fflush_tng(of
->tng_low_prec
);
330 ivec one_ivec
= { 1, 1, 1 };
331 write_checkpoint(of
->fn_cpt
, of
->bKeepAndNumCPT
,
333 DOMAINDECOMP(cr
) ? cr
->dd
->nc
: one_ivec
,
334 DOMAINDECOMP(cr
) ? cr
->dd
->nnodes
: cr
->nnodes
,
335 of
->eIntegrator
, of
->simulation_part
,
336 of
->bExpanded
, of
->elamstats
, step
, t
, state_global
);
339 if (mdof_flags
& (MDOF_X
| MDOF_V
| MDOF_F
))
343 gmx_trr_write_frame(of
->fp_trn
, step
, t
, state_local
->lambda
[efptFEP
],
344 state_local
->box
, top_global
->natoms
,
345 (mdof_flags
& MDOF_X
) ? state_global
->x
: NULL
,
346 (mdof_flags
& MDOF_V
) ? global_v
: NULL
,
347 (mdof_flags
& MDOF_F
) ? f_global
: NULL
);
348 if (gmx_fio_flush(of
->fp_trn
) != 0)
350 gmx_file("Cannot write trajectory; maybe you are out of disk space?");
354 /* If a TNG file is open for uncompressed coordinate output also write
355 velocities and forces to it. */
358 gmx_fwrite_tng(of
->tng
, FALSE
, step
, t
, state_local
->lambda
[efptFEP
],
361 (mdof_flags
& MDOF_X
) ? state_global
->x
: NULL
,
362 (mdof_flags
& MDOF_V
) ? global_v
: NULL
,
363 (mdof_flags
& MDOF_F
) ? f_global
: NULL
);
365 /* If only a TNG file is open for compressed coordinate output (no uncompressed
366 coordinate output) also write forces and velocities to it. */
367 else if (of
->tng_low_prec
)
369 gmx_fwrite_tng(of
->tng_low_prec
, FALSE
, step
, t
, state_local
->lambda
[efptFEP
],
372 (mdof_flags
& MDOF_X
) ? state_global
->x
: NULL
,
373 (mdof_flags
& MDOF_V
) ? global_v
: NULL
,
374 (mdof_flags
& MDOF_F
) ? f_global
: NULL
);
377 if (mdof_flags
& MDOF_X_COMPRESSED
)
381 if (of
->natoms_x_compressed
== of
->natoms_global
)
383 /* We are writing the positions of all of the atoms to
384 the compressed output */
385 xxtc
= state_global
->x
;
389 /* We are writing the positions of only a subset of
390 the atoms to the compressed output, so we have to
391 make a copy of the subset of coordinates. */
394 snew(xxtc
, of
->natoms_x_compressed
);
395 for (i
= 0, j
= 0; (i
< of
->natoms_global
); i
++)
397 if (ggrpnr(of
->groups
, egcCompressedX
, i
) == 0)
399 copy_rvec(state_global
->x
[i
], xxtc
[j
++]);
403 if (write_xtc(of
->fp_xtc
, of
->natoms_x_compressed
, step
, t
,
404 state_local
->box
, xxtc
, of
->x_compression_precision
) == 0)
406 gmx_fatal(FARGS
, "XTC error - maybe you are out of disk space?");
408 gmx_fwrite_tng(of
->tng_low_prec
,
412 state_local
->lambda
[efptFEP
],
414 of
->natoms_x_compressed
,
418 if (of
->natoms_x_compressed
!= of
->natoms_global
)
426 void mdoutf_tng_close(gmx_mdoutf_t of
)
428 if (of
->tng
|| of
->tng_low_prec
)
430 wallcycle_start(of
->wcycle
, ewcTRAJ
);
431 gmx_tng_close(&of
->tng
);
432 gmx_tng_close(&of
->tng_low_prec
);
433 wallcycle_stop(of
->wcycle
, ewcTRAJ
);
437 void done_mdoutf(gmx_mdoutf_t of
)
439 if (of
->fp_ene
!= NULL
)
441 close_enx(of
->fp_ene
);
445 close_xtc(of
->fp_xtc
);
449 gmx_trr_close(of
->fp_trn
);
451 if (of
->fp_dhdl
!= NULL
)
453 gmx_fio_fclose(of
->fp_dhdl
);
455 if (of
->fp_field
!= NULL
)
457 /* This is opened sometimes with xvgropen, sometimes with
458 * gmx_fio_fopen, so we use the least common denominator for closing.
460 gmx_fio_fclose(of
->fp_field
);
462 if (of
->f_global
!= NULL
)
467 gmx_tng_close(&of
->tng
);
468 gmx_tng_close(&of
->tng_low_prec
);