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37 #include "gromacs/legacyheaders/xvgr.h"
38 #include "gromacs/legacyheaders/mdrun.h"
39 #include "gromacs/legacyheaders/smalloc.h"
40 #include "gromacs/legacyheaders/mvdata.h"
41 #include "gromacs/legacyheaders/domdec.h"
45 #include "trajectory_writing.h"
46 #include "checkpoint.h"
53 tng_trajectory_t tng_low_prec;
54 int x_compression_precision; /* only used by XTC output */
57 gmx_bool bKeepAndNumCPT;
65 int natoms_x_compressed;
66 gmx_groups_t *groups; /* for compressed position writing */
70 gmx_mdoutf_t init_mdoutf(FILE *fplog, int nfile, const t_filenm fnm[],
71 int mdrun_flags, const t_commrec *cr,
72 const t_inputrec *ir, gmx_mtop_t *top_global,
73 const output_env_t oenv)
77 gmx_bool bAppendFiles, bCiteTng = FALSE;
86 of->tng_low_prec = NULL;
90 of->eIntegrator = ir->eI;
91 of->bExpanded = ir->bExpanded;
92 of->elamstats = ir->expandedvals->elamstats;
93 of->simulation_part = ir->simulation_part;
94 of->x_compression_precision = ir->x_compression_precision;
98 bAppendFiles = (mdrun_flags & MD_APPENDFILES);
100 of->bKeepAndNumCPT = (mdrun_flags & MD_KEEPANDNUMCPT);
102 sprintf(filemode, bAppendFiles ? "a+" : "w+");
104 if ((EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI))
107 !(EI_DYNAMICS(ir->eI) &&
114 const char *filename;
115 filename = ftp2fn(efTRN, nfile, fnm);
116 switch (fn2ftp(filename))
120 of->fp_trn = open_trn(filename, filemode);
123 gmx_tng_open(filename, filemode[0], &of->tng);
124 if (filemode[0] == 'w')
126 gmx_tng_prepare_md_writing(of->tng, top_global, ir);
131 gmx_incons("Invalid full precision file format");
134 if (EI_DYNAMICS(ir->eI) &&
135 ir->nstxout_compressed > 0)
137 const char *filename;
138 filename = ftp2fn(efCOMPRESSED, nfile, fnm);
139 switch (fn2ftp(filename))
142 of->fp_xtc = open_xtc(filename, filemode);
145 gmx_tng_open(filename, filemode[0], &of->tng_low_prec);
146 if (filemode[0] == 'w')
148 gmx_tng_prepare_low_prec_writing(of->tng_low_prec, top_global, ir);
153 gmx_incons("Invalid reduced precision file format");
156 if (EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI))
158 of->fp_ene = open_enx(ftp2fn(efEDR, nfile, fnm), filemode);
160 of->fn_cpt = opt2fn("-cpo", nfile, fnm);
162 if ((ir->efep != efepNO || ir->bSimTemp) && ir->fepvals->nstdhdl > 0 &&
163 (ir->fepvals->separate_dhdl_file == esepdhdlfileYES ) &&
168 of->fp_dhdl = gmx_fio_fopen(opt2fn("-dhdl", nfile, fnm), filemode);
172 of->fp_dhdl = open_dhdl(opt2fn("-dhdl", nfile, fnm), ir, oenv);
176 if (opt2bSet("-field", nfile, fnm) &&
177 (ir->ex[XX].n || ir->ex[YY].n || ir->ex[ZZ].n))
181 of->fp_dhdl = gmx_fio_fopen(opt2fn("-field", nfile, fnm),
186 of->fp_field = xvgropen(opt2fn("-field", nfile, fnm),
187 "Applied electric field", "Time (ps)",
192 /* Set up atom counts so they can be passed to actual
193 trajectory-writing routines later. Also, XTC writing needs
194 to know what (and how many) atoms might be in the XTC
195 groups, and how to look up later which ones they are. */
196 of->natoms_global = top_global->natoms;
197 of->groups = &top_global->groups;
198 of->natoms_x_compressed = 0;
199 for (i = 0; (i < top_global->natoms); i++)
201 if (ggrpnr(of->groups, egcCompressedX, i) == 0)
203 of->natoms_x_compressed++;
210 please_cite(fplog, "Lundborg2014");
216 FILE *mdoutf_get_fp_field(gmx_mdoutf_t of)
221 ener_file_t mdoutf_get_fp_ene(gmx_mdoutf_t of)
226 FILE *mdoutf_get_fp_dhdl(gmx_mdoutf_t of)
231 void mdoutf_write_to_trajectory_files(FILE *fplog, t_commrec *cr,
234 gmx_mtop_t *top_global,
235 gmx_int64_t step, double t,
236 t_state *state_local, t_state *state_global,
237 rvec *f_local, rvec *f_global)
242 /* MRS -- defining these variables is to manage the difference
243 * between half step and full step velocities, but there must be a better way . . . */
245 local_v = state_local->v;
246 global_v = state_global->v;
248 if (DOMAINDECOMP(cr))
250 if (mdof_flags & MDOF_CPT)
252 dd_collect_state(cr->dd, state_local, state_global);
256 if (mdof_flags & (MDOF_X | MDOF_X_COMPRESSED))
258 dd_collect_vec(cr->dd, state_local, state_local->x,
261 if (mdof_flags & MDOF_V)
263 dd_collect_vec(cr->dd, state_local, local_v,
267 if (mdof_flags & MDOF_F)
269 dd_collect_vec(cr->dd, state_local, f_local, f_global);
274 if (mdof_flags & MDOF_CPT)
276 /* All pointers in state_local are equal to state_global,
277 * but we need to copy the non-pointer entries.
279 state_global->lambda = state_local->lambda;
280 state_global->veta = state_local->veta;
281 state_global->vol0 = state_local->vol0;
282 copy_mat(state_local->box, state_global->box);
283 copy_mat(state_local->boxv, state_global->boxv);
284 copy_mat(state_local->svir_prev, state_global->svir_prev);
285 copy_mat(state_local->fvir_prev, state_global->fvir_prev);
286 copy_mat(state_local->pres_prev, state_global->pres_prev);
292 if (mdof_flags & MDOF_CPT)
295 fflush_tng(of->tng_low_prec);
296 write_checkpoint(of->fn_cpt, of->bKeepAndNumCPT,
297 fplog, cr, of->eIntegrator, of->simulation_part,
298 of->bExpanded, of->elamstats, step, t, state_global);
301 if (mdof_flags & (MDOF_X | MDOF_V | MDOF_F))
305 fwrite_trn(of->fp_trn, step, t, state_local->lambda[efptFEP],
306 state_local->box, top_global->natoms,
307 (mdof_flags & MDOF_X) ? state_global->x : NULL,
308 (mdof_flags & MDOF_V) ? global_v : NULL,
309 (mdof_flags & MDOF_F) ? f_global : NULL);
310 if (gmx_fio_flush(of->fp_trn) != 0)
312 gmx_file("Cannot write trajectory; maybe you are out of disk space?");
316 gmx_fwrite_tng(of->tng, FALSE, step, t, state_local->lambda[efptFEP],
317 (const rvec *) state_local->box,
319 (mdof_flags & MDOF_X) ? (const rvec *) state_global->x : NULL,
320 (mdof_flags & MDOF_V) ? (const rvec *) global_v : NULL,
321 (mdof_flags & MDOF_F) ? (const rvec *) f_global : NULL);
323 if (mdof_flags & MDOF_X_COMPRESSED)
327 if (of->natoms_x_compressed == of->natoms_global)
329 /* We are writing the positions of all of the atoms to
330 the compressed output */
331 xxtc = state_global->x;
335 /* We are writing the positions of only a subset of
336 the atoms to the compressed output, so we have to
337 make a copy of the subset of coordinates. */
340 snew(xxtc, of->natoms_x_compressed);
341 for (i = 0, j = 0; (i < of->natoms_x_compressed); i++)
343 if (ggrpnr(of->groups, egcCompressedX, i) == 0)
345 copy_rvec(state_global->x[i], xxtc[j++]);
349 if (write_xtc(of->fp_xtc, of->natoms_x_compressed, step, t,
350 state_local->box, xxtc, of->x_compression_precision) == 0)
352 gmx_fatal(FARGS, "XTC error - maybe you are out of disk space?");
354 gmx_fwrite_tng(of->tng_low_prec,
358 state_local->lambda[efptFEP],
359 (const rvec *) state_local->box,
360 of->natoms_x_compressed,
364 if (of->natoms_x_compressed != of->natoms_global)
372 void done_mdoutf(gmx_mdoutf_t of)
374 if (of->fp_ene != NULL)
376 close_enx(of->fp_ene);
380 close_xtc(of->fp_xtc);
384 close_trn(of->fp_trn);
386 if (of->fp_dhdl != NULL)
388 gmx_fio_fclose(of->fp_dhdl);
390 if (of->fp_field != NULL)
392 gmx_fio_fclose(of->fp_field);
394 gmx_tng_close(&of->tng);
395 gmx_tng_close(&of->tng_low_prec);