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46 #include "gromacs/fileio/gmxfio.h"
47 #include "gromacs/fileio/gmxfio-xdr.h"
48 #include "gromacs/fileio/xdrf.h"
49 #include "gromacs/math/functions.h"
50 #include "gromacs/math/vec.h"
51 #include "gromacs/mdtypes/inputrec.h"
52 #include "gromacs/mdtypes/md_enums.h"
53 #include "gromacs/mdtypes/state.h"
54 #include "gromacs/pbcutil/pbc.h"
55 #include "gromacs/topology/topology.h"
56 #include "gromacs/trajectory/energyframe.h"
57 #include "gromacs/utility/compare.h"
58 #include "gromacs/utility/fatalerror.h"
59 #include "gromacs/utility/futil.h"
60 #include "gromacs/utility/gmxassert.h"
61 #include "gromacs/utility/smalloc.h"
63 /* The source code in this file should be thread-safe.
64 Please keep it that way. */
66 /* This number should be increased whenever the file format changes! */
67 static const int enx_version = 5;
69 const char *enx_block_id_name[] = {
70 "Averaged orientation restraints",
71 "Instantaneous orientation restraints",
72 "Orientation restraint order tensor(s)",
73 "Distance restraints",
81 /* Stuff for reading pre 4.1 energy files */
83 gmx_bool bOldFileOpen; /* Is this an open old file? */
84 gmx_bool bReadFirstStep; /* Did we read the first step? */
85 int first_step; /* First step in the energy file */
86 int step_prev; /* Previous step */
87 int nsum_prev; /* Previous step sum length */
88 t_energy *ener_prev; /* Previous energy sums */
99 static void enxsubblock_init(t_enxsubblock *sb)
103 sb->type = xdr_datatype_double;
105 sb->type = xdr_datatype_float;
121 static void enxsubblock_free(t_enxsubblock *sb)
157 for (i = 0; i < sb->sval_alloc; i++)
170 /* allocate the appropriate amount of memory for the given type and nr */
171 static void enxsubblock_alloc(t_enxsubblock *sb)
173 /* allocate the appropriate amount of memory */
176 case xdr_datatype_float:
177 if (sb->nr > sb->fval_alloc)
179 srenew(sb->fval, sb->nr);
180 sb->fval_alloc = sb->nr;
183 case xdr_datatype_double:
184 if (sb->nr > sb->dval_alloc)
186 srenew(sb->dval, sb->nr);
187 sb->dval_alloc = sb->nr;
190 case xdr_datatype_int:
191 if (sb->nr > sb->ival_alloc)
193 srenew(sb->ival, sb->nr);
194 sb->ival_alloc = sb->nr;
197 case xdr_datatype_int64:
198 if (sb->nr > sb->lval_alloc)
200 srenew(sb->lval, sb->nr);
201 sb->lval_alloc = sb->nr;
204 case xdr_datatype_char:
205 if (sb->nr > sb->cval_alloc)
207 srenew(sb->cval, sb->nr);
208 sb->cval_alloc = sb->nr;
211 case xdr_datatype_string:
212 if (sb->nr > sb->sval_alloc)
216 srenew(sb->sval, sb->nr);
217 for (i = sb->sval_alloc; i < sb->nr; i++)
219 sb->sval[i] = nullptr;
221 sb->sval_alloc = sb->nr;
225 gmx_incons("Unknown block type: this file is corrupted or from the future");
229 static void enxblock_init(t_enxblock *eb)
237 static void enxblock_free(t_enxblock *eb)
239 if (eb->nsub_alloc > 0)
242 for (i = 0; i < eb->nsub_alloc; i++)
244 enxsubblock_free(&(eb->sub[i]));
252 void init_enxframe(t_enxframe *fr)
261 fr->nblock_alloc = 0;
266 void free_enxframe(t_enxframe *fr)
274 for (b = 0; b < fr->nblock_alloc; b++)
276 enxblock_free(&(fr->block[b]));
281 void add_blocks_enxframe(t_enxframe *fr, int n)
284 if (n > fr->nblock_alloc)
288 srenew(fr->block, n);
289 for (b = fr->nblock_alloc; b < fr->nblock; b++)
291 enxblock_init(&(fr->block[b]));
293 fr->nblock_alloc = n;
297 t_enxblock *find_block_id_enxframe(t_enxframe *ef, int id, t_enxblock *prev)
299 gmx_off_t starti = 0;
304 starti = (prev - ef->block) + 1;
306 for (i = starti; i < ef->nblock; i++)
308 if (ef->block[i].id == id)
310 return &(ef->block[i]);
316 void add_subblocks_enxblock(t_enxblock *eb, int n)
319 if (eb->nsub > eb->nsub_alloc)
324 for (b = eb->nsub_alloc; b < n; b++)
326 enxsubblock_init(&(eb->sub[b]));
332 static void enx_warning(const char *msg)
334 if (getenv("GMX_ENX_NO_FATAL") != nullptr)
336 gmx_warning("%s", msg);
340 gmx_fatal(FARGS, "%s\n%s",
342 "If you want to use the correct frames before the corrupted frame and avoid this fatal error set the env.var. GMX_ENX_NO_FATAL");
346 static void edr_strings(XDR *xdr, gmx_bool bRead, int file_version,
347 int n, gmx_enxnm_t **nms)
356 for (i = 0; i < n; i++)
372 if (!xdr_string(xdr, &(nm->name), STRLEN))
374 gmx_file("Cannot write energy names to file; maybe you are out of disk space?");
376 if (file_version >= 2)
378 if (!xdr_string(xdr, &(nm->unit), STRLEN))
380 gmx_file("Cannot write energy names to file; maybe you are out of disk space?");
385 nm->unit = gmx_strdup("kJ/mol");
390 void do_enxnms(ener_file_t ef, int *nre, gmx_enxnm_t **nms)
394 gmx_bool bRead = gmx_fio_getread(ef->fio);
397 xdr = gmx_fio_getxdr(ef->fio);
399 if (!xdr_int(xdr, &magic))
403 gmx_file("Cannot write energy names to file; maybe you are out of disk space?");
410 /* Assume this is an old edr format */
413 ef->eo.bOldFileOpen = TRUE;
414 ef->eo.bReadFirstStep = FALSE;
415 srenew(ef->eo.ener_prev, *nre);
419 ef->eo.bOldFileOpen = FALSE;
423 gmx_fatal(FARGS, "Energy names magic number mismatch, this is not a GROMACS edr file");
425 file_version = enx_version;
426 xdr_int(xdr, &file_version);
427 if (file_version > enx_version)
429 gmx_fatal(FARGS, "reading tpx file (%s) version %d with version %d program", gmx_fio_getname(ef->fio), file_version, enx_version);
433 if (file_version != enx_version)
435 fprintf(stderr, "Note: enx file_version %d, software version %d\n",
436 file_version, enx_version);
439 edr_strings(xdr, bRead, file_version, *nre, nms);
442 static gmx_bool do_eheader(ener_file_t ef, int *file_version, t_enxframe *fr,
443 int nre_test, gmx_bool *bWrongPrecision, gmx_bool *bOK)
445 int magic = -7777777;
446 real first_real_to_check;
447 int b, zero = 0, dum = 0;
448 gmx_bool bRead = gmx_fio_getread(ef->fio);
452 xdr_datatype dtreal = xdr_datatype_float;
454 xdr_datatype dtreal = xdr_datatype_double;
459 *bWrongPrecision = FALSE;
463 /* The original energy frame started with a real,
464 * so we have to use a real for compatibility.
465 * This is VERY DIRTY code, since do_eheader can be called
466 * with the wrong precision set and then we could read r > -1e10,
467 * while actually the intention was r < -1e10.
468 * When nre_test >= 0, do_eheader should therefore terminate
469 * before the number of i/o calls starts depending on what has been read
470 * (which is the case for for instance the block sizes for variable
471 * number of blocks, where this number is read before).
473 first_real_to_check = -2e10;
474 if (!gmx_fio_do_real(ef->fio, first_real_to_check))
478 if (first_real_to_check > -1e10)
480 /* Assume we are reading an old format */
482 fr->t = first_real_to_check;
483 if (!gmx_fio_do_int(ef->fio, dum))
491 if (!gmx_fio_do_int(ef->fio, magic))
495 if (magic != -7777777)
497 enx_warning("Energy header magic number mismatch, this is not a GROMACS edr file");
501 *file_version = enx_version;
502 // cppcheck-suppress redundantPointerOp
503 if (!gmx_fio_do_int(ef->fio, *file_version))
507 if (*bOK && *file_version > enx_version)
509 gmx_fatal(FARGS, "reading tpx file (%s) version %d with version %d program", gmx_fio_getname(ef->fio), file_version, enx_version);
511 if (!gmx_fio_do_double(ef->fio, fr->t))
515 if (!gmx_fio_do_int64(ef->fio, fr->step))
519 if (!bRead && fr->nsum == 1)
521 /* Do not store sums of length 1,
522 * since this does not add information.
524 if (!gmx_fio_do_int(ef->fio, zero))
531 if (!gmx_fio_do_int(ef->fio, fr->nsum))
536 if (*file_version >= 3)
538 if (!gmx_fio_do_int64(ef->fio, fr->nsteps))
545 fr->nsteps = std::max(1, fr->nsum);
547 if (*file_version >= 5)
549 if (!gmx_fio_do_double(ef->fio, fr->dt))
559 if (!gmx_fio_do_int(ef->fio, fr->nre))
563 if (*file_version < 4)
565 if (!gmx_fio_do_int(ef->fio, ndisre))
572 /* now reserved for possible future use */
573 if (!gmx_fio_do_int(ef->fio, dum))
579 if (!gmx_fio_do_int(ef->fio, fr->nblock))
590 if (*file_version >= 4)
592 enx_warning("Distance restraint blocks in old style in new style file");
600 /* Frames could have nre=0, so we can not rely only on the fr->nre check */
601 if (bRead && nre_test >= 0 &&
602 ((fr->nre > 0 && fr->nre != nre_test) ||
603 fr->nre < 0 || ndisre < 0 || fr->nblock < 0))
607 *bWrongPrecision = TRUE;
612 /* we now know what these should be, or we've already bailed out because
613 of wrong precision */
614 if (*file_version == 1 && (fr->t < 0 || fr->t > 1e20 || fr->step < 0 ) )
616 enx_warning("edr file with negative step number or unreasonable time (and without version number).");
624 add_blocks_enxframe(fr, fr->nblock);
630 /* sub[0] is the instantaneous data, sub[1] is time averaged */
631 add_subblocks_enxblock(&(fr->block[0]), 2);
632 fr->block[0].id = enxDISRE;
633 fr->block[0].sub[0].nr = ndisre;
634 fr->block[0].sub[1].nr = ndisre;
635 fr->block[0].sub[0].type = dtreal;
636 fr->block[0].sub[1].type = dtreal;
640 /* read block header info */
641 for (b = startb; b < fr->nblock; b++)
643 if (*file_version < 4)
645 /* blocks in old version files always have 1 subblock that
646 consists of reals. */
651 add_subblocks_enxblock(&(fr->block[b]), 1);
655 if (fr->block[b].nsub != 1)
657 gmx_incons("Writing an old version .edr file with too many subblocks");
659 if (fr->block[b].sub[0].type != dtreal)
661 gmx_incons("Writing an old version .edr file the wrong subblock type");
664 nrint = fr->block[b].sub[0].nr;
666 if (!gmx_fio_do_int(ef->fio, nrint))
670 fr->block[b].id = b - startb;
671 fr->block[b].sub[0].nr = nrint;
672 fr->block[b].sub[0].type = dtreal;
677 /* in the new version files, the block header only contains
678 the ID and the number of subblocks */
679 int nsub = fr->block[b].nsub;
680 *bOK = *bOK && gmx_fio_do_int(ef->fio, fr->block[b].id);
681 *bOK = *bOK && gmx_fio_do_int(ef->fio, nsub);
683 fr->block[b].nsub = nsub;
686 add_subblocks_enxblock(&(fr->block[b]), nsub);
689 /* read/write type & size for each subblock */
690 for (i = 0; i < nsub; i++)
692 t_enxsubblock *sub = &(fr->block[b].sub[i]); /* shortcut */
693 int typenr = sub->type;
695 *bOK = *bOK && gmx_fio_do_int(ef->fio, typenr);
696 *bOK = *bOK && gmx_fio_do_int(ef->fio, sub->nr);
698 sub->type = (xdr_datatype)typenr;
702 if (!gmx_fio_do_int(ef->fio, fr->e_size))
707 /* now reserved for possible future use */
708 if (!gmx_fio_do_int(ef->fio, dum))
713 /* Do a dummy int to keep the format compatible with the old code */
714 if (!gmx_fio_do_int(ef->fio, dum))
719 if (*bOK && *file_version == 1 && nre_test < 0)
721 if (!ef->eo.bReadFirstStep)
723 ef->eo.bReadFirstStep = TRUE;
724 ef->eo.first_step = fr->step;
725 ef->eo.step_prev = fr->step;
726 ef->eo.nsum_prev = 0;
729 fr->nsum = fr->step - ef->eo.first_step + 1;
730 fr->nsteps = fr->step - ef->eo.step_prev;
737 void free_enxnms(int n, gmx_enxnm_t *nms)
741 for (i = 0; i < n; i++)
750 void close_enx(ener_file_t ef)
757 if (gmx_fio_close(ef->fio) != 0)
759 gmx_file("Cannot close energy file; it might be corrupt, or maybe you are out of disk space?");
763 void done_ener_file(ener_file_t ef)
765 // Free the contents, then the pointer itself
770 /*!\brief Return TRUE if a file exists but is empty, otherwise FALSE.
772 * If the file exists but has length larger than zero, if it does not exist, or
773 * if there is a file system error, FALSE will be returned instead.
775 * \param fn File name to test
777 * \return TRUE if file could be open but is empty, otherwise FALSE.
780 empty_file(const char *fn)
787 fp = gmx_fio_fopen(fn, "r");
788 ret = fread(&dum, sizeof(dum), 1, fp);
792 // bEmpty==TRUE but ret!=0 would likely be some strange I/O error, but at
793 // least it's not a normal empty file, so we return FALSE in that case.
794 return (bEmpty && ret == 0);
798 ener_file_t open_enx(const char *fn, const char *mode)
801 gmx_enxnm_t *nms = nullptr;
802 int file_version = -1;
804 gmx_bool bWrongPrecision, bOK = TRUE;
805 struct ener_file *ef;
811 ef->fio = gmx_fio_open(fn, mode);
812 gmx_fio_setprecision(ef->fio, FALSE);
813 do_enxnms(ef, &nre, &nms);
815 do_eheader(ef, &file_version, fr, nre, &bWrongPrecision, &bOK);
818 gmx_file("Cannot read energy file header. Corrupt file?");
821 /* Now check whether this file is in single precision */
822 if (!bWrongPrecision &&
823 ((fr->e_size && (fr->nre == nre) &&
824 (nre*4*(long int)sizeof(float) == fr->e_size)) ) )
826 fprintf(stderr, "Opened %s as single precision energy file\n", fn);
827 free_enxnms(nre, nms);
831 gmx_fio_rewind(ef->fio);
832 gmx_fio_setprecision(ef->fio, TRUE);
833 do_enxnms(ef, &nre, &nms);
834 do_eheader(ef, &file_version, fr, nre, &bWrongPrecision, &bOK);
837 gmx_file("Cannot write energy file header; maybe you are out of disk space?");
840 if (((fr->e_size && (fr->nre == nre) &&
841 (nre*4*(long int)sizeof(double) == fr->e_size)) ))
843 fprintf(stderr, "Opened %s as double precision energy file\n",
850 gmx_fatal(FARGS, "File %s is empty", fn);
854 gmx_fatal(FARGS, "Energy file %s not recognized, maybe different CPU?",
858 free_enxnms(nre, nms);
862 gmx_fio_rewind(ef->fio);
866 ef->fio = gmx_fio_open(fn, mode);
874 t_fileio *enx_file_pointer(const ener_file* ef)
879 static void convert_full_sums(ener_old_t *ener_old, t_enxframe *fr)
883 double esum_all, eav_all;
889 for (i = 0; i < fr->nre; i++)
891 if (fr->ener[i].e != 0)
895 if (fr->ener[i].esum != 0)
900 if (ne > 0 && ns == 0)
902 /* We do not have all energy sums */
907 /* Convert old full simulation sums to sums between energy frames */
908 nstep_all = fr->step - ener_old->first_step + 1;
909 if (fr->nsum > 1 && fr->nsum == nstep_all && ener_old->nsum_prev > 0)
911 /* Set the new sum length: the frame step difference */
912 fr->nsum = fr->step - ener_old->step_prev;
913 for (i = 0; i < fr->nre; i++)
915 esum_all = fr->ener[i].esum;
916 eav_all = fr->ener[i].eav;
917 fr->ener[i].esum = esum_all - ener_old->ener_prev[i].esum;
918 fr->ener[i].eav = eav_all - ener_old->ener_prev[i].eav
919 - gmx::square(ener_old->ener_prev[i].esum/(nstep_all - fr->nsum)
920 - esum_all/nstep_all)*
921 (nstep_all - fr->nsum)*nstep_all/(double)fr->nsum;
922 ener_old->ener_prev[i].esum = esum_all;
923 ener_old->ener_prev[i].eav = eav_all;
925 ener_old->nsum_prev = nstep_all;
927 else if (fr->nsum > 0)
929 if (fr->nsum != nstep_all)
931 fprintf(stderr, "\nWARNING: something is wrong with the energy sums, will not use exact averages\n");
932 ener_old->nsum_prev = 0;
936 ener_old->nsum_prev = nstep_all;
938 /* Copy all sums to ener_prev */
939 for (i = 0; i < fr->nre; i++)
941 ener_old->ener_prev[i].esum = fr->ener[i].esum;
942 ener_old->ener_prev[i].eav = fr->ener[i].eav;
946 ener_old->step_prev = fr->step;
949 gmx_bool do_enx(ener_file_t ef, t_enxframe *fr)
951 int file_version = -1;
953 gmx_bool bRead, bOK, bOK1, bSane;
954 real tmp1, tmp2, rdum;
958 bRead = gmx_fio_getread(ef->fio);
961 fr->e_size = fr->nre*sizeof(fr->ener[0].e)*4;
962 /*d_size = fr->ndisre*(sizeof(real)*2);*/
965 if (!do_eheader(ef, &file_version, fr, -1, nullptr, &bOK))
969 fprintf(stderr, "\rLast energy frame read %d time %8.3f ",
970 ef->framenr-1, ef->frametime);
976 "\nWARNING: Incomplete energy frame: nr %d time %8.3f\n",
982 gmx_file("Cannot write energy file header; maybe you are out of disk space?");
988 if ((ef->framenr < 20 || ef->framenr % 10 == 0) &&
989 (ef->framenr < 200 || ef->framenr % 100 == 0) &&
990 (ef->framenr < 2000 || ef->framenr % 1000 == 0))
992 fprintf(stderr, "\rReading energy frame %6d time %8.3f ",
996 ef->frametime = fr->t;
998 /* Check sanity of this header */
1000 for (b = 0; b < fr->nblock; b++)
1002 bSane = bSane || (fr->block[b].nsub > 0);
1004 if (!((fr->step >= 0) && bSane) && bRead)
1006 fprintf(stderr, "\nWARNING: there may be something wrong with energy file %s\n",
1007 gmx_fio_getname(ef->fio));
1008 fprintf(stderr, "Found: step=%" GMX_PRId64 ", nre=%d, nblock=%d, time=%g.\n",
1009 fr->step, fr->nre, fr->nblock, fr->t);
1011 if (bRead && fr->nre > fr->e_alloc)
1013 srenew(fr->ener, fr->nre);
1014 for (i = fr->e_alloc; (i < fr->nre); i++)
1017 fr->ener[i].eav = 0;
1018 fr->ener[i].esum = 0;
1020 fr->e_alloc = fr->nre;
1023 for (i = 0; i < fr->nre; i++)
1025 bOK = bOK && gmx_fio_do_real(ef->fio, fr->ener[i].e);
1027 /* Do not store sums of length 1,
1028 * since this does not add information.
1030 if (file_version == 1 ||
1031 (bRead && fr->nsum > 0) || fr->nsum > 1)
1033 tmp1 = fr->ener[i].eav;
1034 bOK = bOK && gmx_fio_do_real(ef->fio, tmp1);
1037 fr->ener[i].eav = tmp1;
1040 /* This is to save only in single precision (unless compiled in DP) */
1041 tmp2 = fr->ener[i].esum;
1042 bOK = bOK && gmx_fio_do_real(ef->fio, tmp2);
1045 fr->ener[i].esum = tmp2;
1048 if (file_version == 1)
1050 /* Old, unused real */
1052 bOK = bOK && gmx_fio_do_real(ef->fio, rdum);
1057 /* Here we can not check for file_version==1, since one could have
1058 * continued an old format simulation with a new one with mdrun -append.
1060 if (bRead && ef->eo.bOldFileOpen)
1062 /* Convert old full simulation sums to sums between energy frames */
1063 convert_full_sums(&(ef->eo), fr);
1065 /* read the blocks */
1066 for (b = 0; b < fr->nblock; b++)
1068 /* now read the subblocks. */
1069 int nsub = fr->block[b].nsub; /* shortcut */
1072 for (i = 0; i < nsub; i++)
1074 t_enxsubblock *sub = &(fr->block[b].sub[i]); /* shortcut */
1078 enxsubblock_alloc(sub);
1081 /* read/write data */
1084 case xdr_datatype_float:
1085 bOK1 = gmx_fio_ndo_float(ef->fio, sub->fval, sub->nr);
1087 case xdr_datatype_double:
1088 bOK1 = gmx_fio_ndo_double(ef->fio, sub->dval, sub->nr);
1090 case xdr_datatype_int:
1091 bOK1 = gmx_fio_ndo_int(ef->fio, sub->ival, sub->nr);
1093 case xdr_datatype_int64:
1094 bOK1 = gmx_fio_ndo_int64(ef->fio, sub->lval, sub->nr);
1096 case xdr_datatype_char:
1097 bOK1 = gmx_fio_ndo_uchar(ef->fio, sub->cval, sub->nr);
1099 case xdr_datatype_string:
1100 bOK1 = gmx_fio_ndo_string(ef->fio, sub->sval, sub->nr);
1103 gmx_incons("Reading unknown block data type: this file is corrupted or from the future");
1111 if (gmx_fio_flush(ef->fio) != 0)
1113 gmx_file("Cannot write energy file; maybe you are out of disk space?");
1121 fprintf(stderr, "\nLast energy frame read %d",
1123 fprintf(stderr, "\nWARNING: Incomplete energy frame: nr %d time %8.3f\n",
1124 ef->framenr, fr->t);
1128 gmx_fatal(FARGS, "could not write energies");
1136 static real find_energy(const char *name, int nre, gmx_enxnm_t *enm,
1141 for (i = 0; i < nre; i++)
1143 if (std::strcmp(enm[i].name, name) == 0)
1145 return fr->ener[i].e;
1149 gmx_fatal(FARGS, "Could not find energy term named '%s'. Either the energy file is from a different run or this state variable is not stored in the energy file. In the latter case (and if you did not modify the T/P-coupling setup), you can read the state in mdrun instead, by passing in a checkpoint file.", name);
1153 void get_enx_state(const char *fn, real t, const gmx_groups_t *groups, t_inputrec *ir,
1156 /* Should match the names in mdebin.c */
1157 static const char *boxvel_nm[] = {
1158 "Box-Vel-XX", "Box-Vel-YY", "Box-Vel-ZZ",
1159 "Box-Vel-YX", "Box-Vel-ZX", "Box-Vel-ZY"
1162 static const char *baro_nm[] = {
1167 int ind0[] = { XX, YY, ZZ, YY, ZZ, ZZ };
1168 int ind1[] = { XX, YY, ZZ, XX, XX, YY };
1169 int nre, nfr, i, j, ni, npcoupl;
1172 gmx_enxnm_t *enm = nullptr;
1176 in = open_enx(fn, "r");
1177 do_enxnms(in, &nre, &enm);
1180 while ((nfr == 0 || fr->t != t) && do_enx(in, fr))
1185 fprintf(stderr, "\n");
1187 if (nfr == 0 || fr->t != t)
1189 gmx_fatal(FARGS, "Could not find frame with time %f in '%s'", t, fn);
1192 npcoupl = TRICLINIC(ir->compress) ? 6 : 3;
1193 if (ir->epc == epcPARRINELLORAHMAN)
1195 clear_mat(state->boxv);
1196 for (i = 0; i < npcoupl; i++)
1198 state->boxv[ind0[i]][ind1[i]] =
1199 find_energy(boxvel_nm[i], nre, enm, fr);
1201 fprintf(stderr, "\nREAD %d BOX VELOCITIES FROM %s\n\n", npcoupl, fn);
1204 if (ir->etc == etcNOSEHOOVER)
1210 for (i = 0; i < state->ngtc; i++)
1212 ni = groups->grps[egcTC].nm_ind[i];
1213 bufi = *(groups->grpname[ni]);
1214 for (j = 0; (j < state->nhchainlength); j++)
1216 if (inputrecNvtTrotter(ir))
1218 sprintf(cns, "-%d", j);
1220 sprintf(buf, "Xi%s-%s", cns, bufi);
1221 state->nosehoover_xi[i] = find_energy(buf, nre, enm, fr);
1222 sprintf(buf, "vXi%s-%s", cns, bufi);
1223 state->nosehoover_vxi[i] = find_energy(buf, nre, enm, fr);
1227 fprintf(stderr, "\nREAD %d NOSE-HOOVER Xi chains FROM %s\n\n", state->ngtc, fn);
1229 if (inputrecNptTrotter(ir) || inputrecNphTrotter(ir))
1231 for (i = 0; i < state->nnhpres; i++)
1233 bufi = baro_nm[0]; /* All barostat DOF's together for now */
1234 for (j = 0; (j < state->nhchainlength); j++)
1236 sprintf(buf, "Xi-%d-%s", j, bufi);
1237 state->nhpres_xi[i] = find_energy(buf, nre, enm, fr);
1238 sprintf(buf, "vXi-%d-%s", j, bufi);
1239 state->nhpres_vxi[i] = find_energy(buf, nre, enm, fr);
1242 fprintf(stderr, "\nREAD %d NOSE-HOOVER BAROSTAT Xi chains FROM %s\n\n", state->nnhpres, fn);
1246 free_enxnms(nre, enm);
1251 static real ener_tensor_diag(int n, const int *ind1, const int *ind2,
1253 const int *tensi, int i,
1254 t_energy e1[], t_energy e2[])
1263 d2 = tensi[i] - d1*DIM;
1265 /* Find the diagonal elements d1 and d2 */
1266 len = std::strlen(enm1[ind1[i]].name);
1270 for (j = 0; j < n; j++)
1272 if (tensi[j] >= 0 &&
1273 std::strlen(enm1[ind1[j]].name) == len &&
1274 std::strncmp(enm1[ind1[i]].name, enm1[ind1[j]].name, len-2) == 0 &&
1275 (tensi[j] == d1*DIM+d1 || tensi[j] == d2*DIM+d2))
1277 prod1 *= fabs(e1[ind1[j]].e);
1278 prod2 *= fabs(e2[ind2[j]].e);
1285 return 0.5*(std::sqrt(prod1) + std::sqrt(prod2));
1293 static gmx_bool enernm_equal(const char *nm1, const char *nm2)
1297 len1 = std::strlen(nm1);
1298 len2 = std::strlen(nm2);
1300 /* Remove " (bar)" at the end of a name */
1301 if (len1 > 6 && std::strcmp(nm1+len1-6, " (bar)") == 0)
1305 if (len2 > 6 && std::strcmp(nm2+len2-6, " (bar)") == 0)
1310 return (len1 == len2 && gmx_strncasecmp(nm1, nm2, len1) == 0);
1313 static void cmp_energies(FILE *fp, int step1, int step2,
1314 t_energy e1[], t_energy e2[],
1316 real ftol, real abstol,
1317 int nre, int *ind1, int *ind2, int maxener)
1320 int *tensi, len, d1, d2;
1321 real ftol_i, abstol_i;
1323 snew(tensi, maxener);
1324 /* Check for tensor elements ending on "-XX", "-XY", ... , "-ZZ" */
1325 for (i = 0; (i < maxener); i++)
1329 len = std::strlen(enm1[ii].name);
1330 if (len > 3 && enm1[ii].name[len-3] == '-')
1332 d1 = enm1[ii].name[len-2] - 'X';
1333 d2 = enm1[ii].name[len-1] - 'X';
1334 if (d1 >= 0 && d1 < DIM &&
1335 d2 >= 0 && d2 < DIM)
1337 tensi[i] = d1*DIM + d2;
1342 for (i = 0; (i < maxener); i++)
1344 /* Check if this is an off-diagonal tensor element */
1345 if (tensi[i] >= 0 && tensi[i] != 0 && tensi[i] != 4 && tensi[i] != 8)
1347 /* Turn on the relative tolerance check (4 is maximum relative diff.) */
1349 /* Do the relative tolerance through an absolute tolerance times
1350 * the size of diagonal components of the tensor.
1352 abstol_i = ftol*ener_tensor_diag(nre, ind1, ind2, enm1, tensi, i, e1, e2);
1355 fprintf(debug, "tensor '%s' val %f diag %f\n",
1356 enm1[i].name, e1[i].e, abstol_i/ftol);
1360 /* We found a diagonal, we need to check with the minimum tolerance */
1361 abstol_i = std::min(abstol_i, abstol);
1365 /* We did not find a diagonal, ignore the relative tolerance check */
1374 if (!equal_real(e1[ind1[i]].e, e2[ind2[i]].e, ftol_i, abstol_i))
1376 fprintf(fp, "%-15s step %3d: %12g, step %3d: %12g\n",
1378 step1, e1[ind1[i]].e,
1379 step2, e2[ind2[i]].e);
1387 static void cmp_disres(t_enxframe *fr1, t_enxframe *fr2, real ftol, real abstol)
1390 char bav[64], bt[64], bs[22];
1392 cmp_int(stdout, "ndisre", -1, fr1->ndisre, fr2->ndisre);
1393 if ((fr1->ndisre == fr2->ndisre) && (fr1->ndisre > 0))
1395 sprintf(bav, "step %s: disre rav", gmx_step_str(fr1->step, bs));
1396 sprintf(bt, "step %s: disre rt", gmx_step_str(fr1->step, bs));
1397 for (i = 0; (i < fr1->ndisre); i++)
1399 cmp_real(stdout, bav, i, fr1->disre_rm3tav[i], fr2->disre_rm3tav[i], ftol, abstol);
1400 cmp_real(stdout, bt, i, fr1->disre_rt[i], fr2->disre_rt[i], ftol, abstol);
1406 static void cmp_eblocks(t_enxframe *fr1, t_enxframe *fr2, real ftol, real abstol)
1409 char buf[64], bs[22];
1411 cmp_int(stdout, "nblock", -1, fr1->nblock, fr2->nblock);
1412 if ((fr1->nblock == fr2->nblock) && (fr1->nblock > 0))
1414 for (j = 0; (j < fr1->nblock); j++)
1416 t_enxblock *b1, *b2; /* convenience vars */
1418 b1 = &(fr1->block[j]);
1419 b2 = &(fr2->block[j]);
1421 sprintf(buf, "step %s: block[%d]", gmx_step_str(fr1->step, bs), j);
1422 cmp_int(stdout, buf, -1, b1->nsub, b2->nsub);
1423 cmp_int(stdout, buf, -1, b1->id, b2->id);
1425 if ( (b1->nsub == b2->nsub) && (b1->id == b2->id) )
1427 for (i = 0; i < b1->nsub; i++)
1429 t_enxsubblock *s1, *s2;
1434 cmp_int(stdout, buf, -1, (int)s1->type, (int)s2->type);
1435 cmp_int64(stdout, buf, s1->nr, s2->nr);
1437 if ((s1->type == s2->type) && (s1->nr == s2->nr))
1441 case xdr_datatype_float:
1442 for (k = 0; k < s1->nr; k++)
1444 cmp_float(stdout, buf, i,
1445 s1->fval[k], s2->fval[k],
1449 case xdr_datatype_double:
1450 for (k = 0; k < s1->nr; k++)
1452 cmp_double(stdout, buf, i,
1453 s1->dval[k], s2->dval[k],
1457 case xdr_datatype_int:
1458 for (k = 0; k < s1->nr; k++)
1460 cmp_int(stdout, buf, i,
1461 s1->ival[k], s2->ival[k]);
1464 case xdr_datatype_int64:
1465 for (k = 0; k < s1->nr; k++)
1467 cmp_int64(stdout, buf,
1468 s1->lval[k], s2->lval[k]);
1471 case xdr_datatype_char:
1472 for (k = 0; k < s1->nr; k++)
1474 cmp_uc(stdout, buf, i,
1475 s1->cval[k], s2->cval[k]);
1478 case xdr_datatype_string:
1479 for (k = 0; k < s1->nr; k++)
1481 cmp_str(stdout, buf, i,
1482 s1->sval[k], s2->sval[k]);
1486 gmx_incons("Unknown data type!!");
1495 void comp_enx(const char *fn1, const char *fn2, real ftol, real abstol, const char *lastener)
1497 int nre, nre1, nre2;
1498 ener_file_t in1, in2;
1499 int i, j, maxener, *ind1, *ind2, *have;
1500 gmx_enxnm_t *enm1 = nullptr, *enm2 = nullptr;
1501 t_enxframe *fr1, *fr2;
1504 fprintf(stdout, "comparing energy file %s and %s\n\n", fn1, fn2);
1506 in1 = open_enx(fn1, "r");
1507 in2 = open_enx(fn2, "r");
1508 do_enxnms(in1, &nre1, &enm1);
1509 do_enxnms(in2, &nre2, &enm2);
1512 fprintf(stdout, "There are %d and %d terms in the energy files\n\n",
1517 fprintf(stdout, "There are %d terms in the energy files\n\n", nre1);
1524 for (i = 0; i < nre1; i++)
1526 for (j = 0; j < nre2; j++)
1528 if (enernm_equal(enm1[i].name, enm2[j].name))
1537 if (nre == 0 || ind1[nre-1] != i)
1539 cmp_str(stdout, "enm", i, enm1[i].name, "-");
1542 for (i = 0; i < nre2; i++)
1546 cmp_str(stdout, "enm", i, "-", enm2[i].name);
1551 for (i = 0; i < nre; i++)
1553 if ((lastener != nullptr) && (std::strstr(enm1[i].name, lastener) != nullptr))
1560 fprintf(stdout, "There are %d terms to compare in the energy files\n\n",
1563 for (i = 0; i < maxener; i++)
1565 cmp_str(stdout, "unit", i, enm1[ind1[i]].unit, enm2[ind2[i]].unit);
1572 b1 = do_enx(in1, fr1);
1573 b2 = do_enx(in2, fr2);
1576 fprintf(stdout, "\nEnd of file on %s but not on %s\n", fn2, fn1);
1580 fprintf(stdout, "\nEnd of file on %s but not on %s\n", fn1, fn2);
1582 else if (!b1 && !b2)
1584 fprintf(stdout, "\nFiles read successfully\n");
1588 cmp_real(stdout, "t", -1, fr1->t, fr2->t, ftol, abstol);
1589 cmp_int(stdout, "step", -1, fr1->step, fr2->step);
1590 /* We don't want to print the nre mismatch for every frame */
1591 /* cmp_int(stdout,"nre",-1,fr1->nre,fr2->nre); */
1592 if ((fr1->nre >= nre) && (fr2->nre >= nre))
1594 cmp_energies(stdout, fr1->step, fr1->step, fr1->ener, fr2->ener,
1595 enm1, ftol, abstol, nre, ind1, ind2, maxener);
1597 /*cmp_disres(fr1,fr2,ftol,abstol);*/
1598 cmp_eblocks(fr1, fr2, ftol, abstol);