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43 #include "gromacs/utility/smalloc.h"
46 #include "gromacs/utility/cstringutil.h"
48 #include "gromacs/math/vec.h"
50 #include "gromacs/utility/futil.h"
56 #include "gromacs/utility/fatalerror.h"
58 #include "gromacs/pbcutil/pbc.h"
59 #include "mtop_util.h"
64 static int read_g96_pos(char line[], t_symtab *symtab,
65 FILE *fp, const char *infile,
70 int nwanted, natoms, atnr, resnr = 0, oldres, newres, shift;
71 char anm[STRLEN], resnm[STRLEN];
92 oldres = -666; /* Unlikely number for the first residue! */
94 while (!bEnd && fgets2(line, STRLEN, fp))
96 bEnd = (strncmp(line, "END", 3) == 0);
97 if (!bEnd && (line[0] != '#'))
99 if (sscanf(line+shift, "%15lf%15lf%15lf", &db1, &db2, &db3) != 3)
101 gmx_fatal(FARGS, "Did not find 3 coordinates for atom %d in %s\n",
104 if ((nwanted != -1) && (natoms >= nwanted))
107 "Found more coordinates (%d) in %s than expected %d\n",
108 natoms, infile, nwanted);
113 (sscanf(line, "%5d%c%5s%c%5s%7d", &resnr, &c1, resnm, &c2, anm, &atnr)
123 strncpy(resnm, "???", sizeof(resnm)-1);
125 strncpy(anm, "???", sizeof(anm)-1);
127 atoms->atomname[natoms] = put_symtab(symtab, anm);
132 if (newres >= atoms->nr)
134 gmx_fatal(FARGS, "More residues than atoms in %s (natoms = %d)",
137 atoms->atom[natoms].resind = newres;
138 if (newres+1 > atoms->nres)
140 atoms->nres = newres+1;
142 t_atoms_set_resinfo(atoms, natoms, symtab, resnm, resnr, ' ', 0, ' ');
146 atoms->atom[natoms].resind = newres;
151 fr->x[natoms][0] = db1;
152 fr->x[natoms][1] = db2;
153 fr->x[natoms][2] = db3;
158 if ((nwanted != -1) && natoms != nwanted)
161 "Warning: found less coordinates (%d) in %s than expected %d\n",
162 natoms, infile, nwanted);
171 static int read_g96_vel(char line[], FILE *fp, const char *infile,
175 int nwanted, natoms = -1, shift;
176 double db1, db2, db3;
178 nwanted = fr->natoms;
182 if (strcmp(line, "VELOCITYRED") == 0)
192 while (!bEnd && fgets2(line, STRLEN, fp))
194 bEnd = (strncmp(line, "END", 3) == 0);
195 if (!bEnd && (line[0] != '#'))
197 if (sscanf(line+shift, "%15lf%15lf%15lf", &db1, &db2, &db3) != 3)
199 gmx_fatal(FARGS, "Did not find 3 velocities for atom %d in %s",
202 if ((nwanted != -1) && (natoms >= nwanted))
204 gmx_fatal(FARGS, "Found more velocities (%d) in %s than expected %d\n",
205 natoms, infile, nwanted);
209 fr->v[natoms][0] = db1;
210 fr->v[natoms][1] = db2;
211 fr->v[natoms][2] = db3;
216 if ((nwanted != -1) && (natoms != nwanted))
219 "Warning: found less velocities (%d) in %s than expected %d\n",
220 natoms, infile, nwanted);
227 int read_g96_conf(FILE *fp, const char *infile, t_trxframe *fr, char *line)
229 t_symtab *symtab = NULL;
230 gmx_bool bAtStart, bTime, bAtoms, bPos, bVel, bBox, bEnd, bFinished;
232 double db1, db2, db3, db4, db5, db6, db7, db8, db9;
234 bAtStart = (ftell(fp) == 0);
236 clear_trxframe(fr, FALSE);
248 while (!fr->bTitle && fgets2(line, STRLEN, fp))
250 fr->bTitle = (strcmp(line, "TITLE") == 0);
252 if (fr->title == NULL)
254 fgets2(line, STRLEN, fp);
255 fr->title = strdup(line);
258 while (!bEnd && fgets2(line, STRLEN, fp))
260 bEnd = (strcmp(line, "END") == 0);
262 fgets2(line, STRLEN, fp);
265 /* Do not get a line if we are not at the start of the file, *
266 * because without a parameter file we don't know what is in *
267 * the trajectory and we have already read the line in the *
268 * previous call (VERY DIRTY). */
272 bTime = (strcmp(line, "TIMESTEP") == 0);
273 bAtoms = (strcmp(line, "POSITION") == 0);
274 bPos = (bAtoms || (strcmp(line, "POSITIONRED") == 0));
275 bVel = (strncmp(line, "VELOCITY", 8) == 0);
276 bBox = (strcmp(line, "BOX") == 0);
279 if (!fr->bTime && !fr->bX)
285 bFinished = (fgets2(line, STRLEN, fp) == NULL);
287 while (!bFinished && (line[0] == '#'));
288 sscanf(line, "%15d%15lf", &(fr->step), &db1);
302 natoms = read_g96_pos(line, symtab, fp, infile, fr);
312 natoms = read_g96_vel(line, fp, infile, fr);
319 while (!bEnd && fgets2(line, STRLEN, fp))
321 bEnd = (strncmp(line, "END", 3) == 0);
322 if (!bEnd && (line[0] != '#'))
324 nbp = sscanf(line, "%15lf%15lf%15lf%15lf%15lf%15lf%15lf%15lf%15lf",
325 &db1, &db2, &db3, &db4, &db5, &db6, &db7, &db8, &db9);
328 gmx_fatal(FARGS, "Found a BOX line, but no box in %s", infile);
330 fr->box[XX][XX] = db1;
331 fr->box[YY][YY] = db2;
332 fr->box[ZZ][ZZ] = db3;
335 fr->box[XX][YY] = db4;
336 fr->box[XX][ZZ] = db5;
337 fr->box[YY][XX] = db6;
338 fr->box[YY][ZZ] = db7;
339 fr->box[ZZ][XX] = db8;
340 fr->box[ZZ][YY] = db9;
347 while (!bFinished && fgets2(line, STRLEN, fp));
356 void write_g96_conf(FILE *out, t_trxframe *fr,
357 int nindex, const atom_id *index)
375 fprintf(out, "TITLE\n%s\nEND\n", fr->title);
377 if (fr->bStep || fr->bTime)
379 /* Officially the time format is %15.9, which is not enough for 10 ns */
380 fprintf(out, "TIMESTEP\n%15d%15.6f\nEND\n", fr->step, fr->time);
386 fprintf(out, "POSITION\n");
387 for (i = 0; i < nout; i++)
397 fprintf(out, "%5d %-5s %-5s%7d%15.9f%15.9f%15.9f\n",
398 (atoms->resinfo[atoms->atom[a].resind].nr) % 100000,
399 *atoms->resinfo[atoms->atom[a].resind].name,
400 *atoms->atomname[a], (i+1) % 10000000,
401 fr->x[a][XX], fr->x[a][YY], fr->x[a][ZZ]);
406 fprintf(out, "POSITIONRED\n");
407 for (i = 0; i < nout; i++)
417 fprintf(out, "%15.9f%15.9f%15.9f\n",
418 fr->x[a][XX], fr->x[a][YY], fr->x[a][ZZ]);
421 fprintf(out, "END\n");
427 fprintf(out, "VELOCITY\n");
428 for (i = 0; i < nout; i++)
438 fprintf(out, "%5d %-5s %-5s%7d%15.9f%15.9f%15.9f\n",
439 (atoms->resinfo[atoms->atom[a].resind].nr) % 100000,
440 *atoms->resinfo[atoms->atom[a].resind].name,
441 *atoms->atomname[a], (i+1) % 10000000,
442 fr->v[a][XX], fr->v[a][YY], fr->v[a][ZZ]);
447 fprintf(out, "VELOCITYRED\n");
448 for (i = 0; i < nout; i++)
458 fprintf(out, "%15.9f%15.9f%15.9f\n",
459 fr->v[a][XX], fr->v[a][YY], fr->v[a][ZZ]);
462 fprintf(out, "END\n");
466 fprintf(out, "BOX\n");
467 fprintf(out, "%15.9f%15.9f%15.9f",
468 fr->box[XX][XX], fr->box[YY][YY], fr->box[ZZ][ZZ]);
469 if (fr->box[XX][YY] || fr->box[XX][ZZ] || fr->box[YY][XX] ||
470 fr->box[YY][ZZ] || fr->box[ZZ][XX] || fr->box[ZZ][YY])
472 fprintf(out, "%15.9f%15.9f%15.9f%15.9f%15.9f%15.9f",
473 fr->box[XX][YY], fr->box[XX][ZZ], fr->box[YY][XX],
474 fr->box[YY][ZZ], fr->box[ZZ][XX], fr->box[ZZ][YY]);
477 fprintf(out, "END\n");
481 static int get_espresso_word(FILE *fp, char word[])
493 if (i == ' ' || i == '\n' || i == '\t')
518 word[nc++] = (char)i;
522 while (i != EOF && ret == 0);
526 /* printf("'%s'\n",word); */
531 static int check_open_parenthesis(FILE *fp, int r,
532 const char *infile, const char *keyword)
544 r = get_espresso_word(fp, word);
551 gmx_fatal(FARGS, "Expected '{' after '%s' in file '%s'",
559 static int check_close_parenthesis(FILE *fp, int r,
560 const char *infile, const char *keyword)
572 r = get_espresso_word(fp, word);
579 gmx_fatal(FARGS, "Expected '}' after section '%s' in file '%s'",
588 espID, espPOS, espTYPE, espQ, espV, espF, espMOLECULE, espNR
590 const char *esp_prop[espNR] = {
591 "id", "pos", "type", "q", "v", "f",
595 static void read_espresso_conf(const char *infile,
596 t_atoms *atoms, rvec x[], rvec *v, matrix box)
598 t_symtab *symtab = NULL;
600 char word[STRLEN], buf[STRLEN];
601 int natoms, level, npar, r, nprop, p, i, m, molnr;
604 gmx_bool bFoundParticles, bFoundProp, bFoundVariable, bMol;
614 fp = gmx_fio_fopen(infile, "r");
616 bFoundParticles = FALSE;
617 bFoundVariable = FALSE;
620 while ((r = get_espresso_word(fp, word)))
622 if (level == 1 && strcmp(word, "particles") == 0 && !bFoundParticles)
624 bFoundParticles = TRUE;
625 level += check_open_parenthesis(fp, r, infile, "particles");
627 while (level == 2 && (r = get_espresso_word(fp, word)))
630 for (p = 0; p < espNR; p++)
632 if (strcmp(word, esp_prop[p]) == 0)
636 /* printf(" prop[%d] = %s\n",nprop-1,esp_prop[prop[nprop-1]]); */
639 if (!bFoundProp && word[0] != '}')
641 gmx_fatal(FARGS, "Can not read Espresso files with particle property '%s'", word);
643 if (bFoundProp && p == espMOLECULE)
654 while (level > 0 && (r = get_espresso_word(fp, word)))
666 for (p = 0; p < nprop; p++)
671 r = get_espresso_word(fp, word);
675 for (m = 0; m < 3; m++)
677 r = get_espresso_word(fp, word);
678 sscanf(word, "%lf", &d);
683 r = get_espresso_word(fp, word);
684 atoms->atom[i].type = strtol(word, NULL, 10);
687 r = get_espresso_word(fp, word);
688 sscanf(word, "%lf", &d);
689 atoms->atom[i].q = d;
692 for (m = 0; m < 3; m++)
694 r = get_espresso_word(fp, word);
695 sscanf(word, "%lf", &d);
700 for (m = 0; m < 3; m++)
702 r = get_espresso_word(fp, word);
707 r = get_espresso_word(fp, word);
708 molnr = strtol(word, NULL, 10);
710 atoms->resinfo[atoms->atom[i-1].resind].nr != molnr)
712 atoms->atom[i].resind =
713 (i == 0 ? 0 : atoms->atom[i-1].resind+1);
714 atoms->resinfo[atoms->atom[i].resind].nr = molnr;
715 atoms->resinfo[atoms->atom[i].resind].ic = ' ';
716 atoms->resinfo[atoms->atom[i].resind].chainid = ' ';
717 atoms->resinfo[atoms->atom[i].resind].chainnum = molnr; /* Not sure if this is right? */
721 atoms->atom[i].resind = atoms->atom[i-1].resind;
726 /* Generate an atom name from the particle type */
727 sprintf(buf, "T%d", atoms->atom[i].type);
728 atoms->atomname[i] = put_symtab(symtab, buf);
731 if (i == 0 || atoms->atom[i].resind != atoms->atom[i-1].resind)
733 atoms->resinfo[atoms->atom[i].resind].name =
734 put_symtab(symtab, "MOL");
739 /* Residue number is the atom number */
740 atoms->atom[i].resind = i;
741 /* Generate an residue name from the particle type */
742 if (atoms->atom[i].type < 26)
744 sprintf(buf, "T%c", 'A'+atoms->atom[i].type);
748 sprintf(buf, "T%c%c",
749 'A'+atoms->atom[i].type/26, 'A'+atoms->atom[i].type%26);
751 t_atoms_set_resinfo(atoms, i, symtab, buf, i, ' ', 0, ' ');
761 atoms->nres = atoms->nr;
765 gmx_fatal(FARGS, "Internal inconsistency in Espresso routines, read %d atoms, expected %d atoms", i, atoms->nr);
768 else if (level == 1 && strcmp(word, "variable") == 0 && !bFoundVariable)
770 bFoundVariable = TRUE;
771 level += check_open_parenthesis(fp, r, infile, "variable");
772 while (level == 2 && (r = get_espresso_word(fp, word)))
774 if (level == 2 && strcmp(word, "box_l") == 0)
776 for (m = 0; m < 3; m++)
778 r = get_espresso_word(fp, word);
779 sscanf(word, "%lf", &d);
782 level += check_close_parenthesis(fp, r, infile, "box_l");
796 if (!bFoundParticles)
798 fprintf(stderr, "Did not find a particles section in Espresso file '%s'\n",
805 static int get_espresso_coordnum(const char *infile)
809 int natoms, level, r;
810 gmx_bool bFoundParticles;
814 fp = gmx_fio_fopen(infile, "r");
816 bFoundParticles = FALSE;
818 while ((r = get_espresso_word(fp, word)) && !bFoundParticles)
820 if (level == 1 && strcmp(word, "particles") == 0 && !bFoundParticles)
822 bFoundParticles = TRUE;
823 level += check_open_parenthesis(fp, r, infile, "particles");
824 while (level > 0 && (r = get_espresso_word(fp, word)))
849 if (!bFoundParticles)
851 fprintf(stderr, "Did not find a particles section in Espresso file '%s'\n",
860 static void write_espresso_conf_indexed(FILE *out, const char *title,
861 t_atoms *atoms, int nx, atom_id *index,
862 rvec *x, rvec *v, matrix box)
866 fprintf(out, "# %s\n", title);
869 gmx_warning("The Espresso format does not support triclinic unit-cells");
871 fprintf(out, "{variable {box_l %f %f %f}}\n", box[0][0], box[1][1], box[2][2]);
873 fprintf(out, "{particles {id pos type q%s}\n", v ? " v" : "");
874 for (i = 0; i < nx; i++)
884 fprintf(out, "\t{%d %f %f %f %d %g",
885 j, x[j][XX], x[j][YY], x[j][ZZ],
886 atoms->atom[j].type, atoms->atom[j].q);
889 fprintf(out, " %f %f %f", v[j][XX], v[j][YY], v[j][ZZ]);
896 static void get_coordnum_fp (FILE *in, char *title, int *natoms)
900 fgets2 (title, STRLEN, in);
901 fgets2 (line, STRLEN, in);
902 if (sscanf (line, "%d", natoms) != 1)
904 gmx_fatal(FARGS, "gro file does not have the number of atoms on the second line");
908 static void get_coordnum (const char *infile, int *natoms)
913 in = gmx_fio_fopen(infile, "r");
914 get_coordnum_fp(in, title, natoms);
918 static gmx_bool get_w_conf(FILE *in, const char *infile, char *title,
919 t_symtab *symtab, t_atoms *atoms, int *ndec,
920 rvec x[], rvec *v, matrix box)
923 char line[STRLEN+1], *ptr;
925 double x1, y1, z1, x2, y2, z2;
927 int natoms, i, m, resnr, newres, oldres, ddist, c;
928 gmx_bool bFirst, bVel;
932 oldres = NOTSET; /* Unlikely number for the first residue! */
935 /* Read the title and number of atoms */
936 get_coordnum_fp(in, title, &natoms);
938 if (natoms > atoms->nr)
940 gmx_fatal(FARGS, "gro file contains more atoms (%d) than expected (%d)",
943 else if (natoms < atoms->nr)
945 fprintf(stderr, "Warning: gro file contains less atoms (%d) than expected"
946 " (%d)\n", natoms, atoms->nr);
953 /* just pray the arrays are big enough */
954 for (i = 0; (i < natoms); i++)
956 if ((fgets2 (line, STRLEN, in)) == NULL)
958 gmx_fatal(FARGS, "Unexpected end of file in file %s at line %d",
961 if (strlen(line) < 39)
963 gmx_fatal(FARGS, "Invalid line in %s for atom %d:\n%s", infile, i+1, line);
966 /* determine read precision from distance between periods
971 p1 = strchr(line, '.');
974 gmx_fatal(FARGS, "A coordinate in file %s does not contain a '.'", infile);
976 p2 = strchr(&p1[1], '.');
979 gmx_fatal(FARGS, "A coordinate in file %s does not contain a '.'", infile);
984 p3 = strchr(&p2[1], '.');
987 gmx_fatal(FARGS, "A coordinate in file %s does not contain a '.'", infile);
990 if (p3 - p2 != ddist)
992 gmx_fatal(FARGS, "The spacing of the decimal points in file %s is not consistent for x, y and z", infile);
997 memcpy(name, line, 5);
999 sscanf(name, "%d", &resnr);
1000 memcpy(name, line+5, 5);
1002 if (resnr != oldres)
1006 if (newres >= natoms)
1008 gmx_fatal(FARGS, "More residues than atoms in %s (natoms = %d)",
1011 atoms->atom[i].resind = newres;
1012 t_atoms_set_resinfo(atoms, i, symtab, name, resnr, ' ', 0, ' ');
1016 atoms->atom[i].resind = newres;
1020 memcpy(name, line+10, 5);
1021 atoms->atomname[i] = put_symtab(symtab, name);
1023 /* eventueel controle atomnumber met i+1 */
1025 /* coordinates (start after residue data) */
1027 /* Read fixed format */
1028 for (m = 0; m < DIM; m++)
1030 for (c = 0; (c < ddist && ptr[0]); c++)
1036 if (sscanf (buf, "%lf %lf", &x1, &x2) != 1)
1038 gmx_fatal(FARGS, "Something is wrong in the coordinate formatting of file %s. Note that gro is fixed format (see the manual)", infile);
1046 /* velocities (start after residues and coordinates) */
1049 /* Read fixed format */
1050 for (m = 0; m < DIM; m++)
1052 for (c = 0; (c < ddist && ptr[0]); c++)
1058 if (sscanf (buf, "%lf", &x1) != 1)
1070 atoms->nres = newres + 1;
1073 fgets2 (line, STRLEN, in);
1074 if (sscanf (line, "%lf%lf%lf", &x1, &y1, &z1) != 3)
1076 gmx_warning("Bad box in file %s", infile);
1078 /* Generate a cubic box */
1079 for (m = 0; (m < DIM); m++)
1081 xmin[m] = xmax[m] = x[0][m];
1083 for (i = 1; (i < atoms->nr); i++)
1085 for (m = 0; (m < DIM); m++)
1087 xmin[m] = min(xmin[m], x[i][m]);
1088 xmax[m] = max(xmax[m], x[i][m]);
1091 for (i = 0; i < DIM; i++)
1093 for (m = 0; m < DIM; m++)
1098 for (m = 0; (m < DIM); m++)
1100 box[m][m] = (xmax[m]-xmin[m]);
1102 fprintf(stderr, "Generated a cubic box %8.3f x %8.3f x %8.3f\n",
1103 box[XX][XX], box[YY][YY], box[ZZ][ZZ]);
1107 /* We found the first three values, the diagonal elements */
1111 if (sscanf (line, "%*f%*f%*f%lf%lf%lf%lf%lf%lf",
1112 &x1, &y1, &z1, &x2, &y2, &z2) != 6)
1114 x1 = y1 = z1 = x2 = y2 = z2 = 0.0;
1127 static void read_whole_conf(const char *infile, char *title,
1128 t_atoms *atoms, rvec x[], rvec *v, matrix box)
1135 in = gmx_fio_fopen(infile, "r");
1137 open_symtab(&symtab);
1138 get_w_conf(in, infile, title, &symtab, atoms, &ndec, x, v, box);
1139 /* We can't free the symbols, as they are still used in atoms, so
1140 * the only choice is to leak them. */
1141 free_symtab(&symtab);
1146 static gmx_bool gmx_one_before_eof(FILE *fp)
1151 if ((beof = fread(data, 1, 1, fp)) == 1)
1153 gmx_fseek(fp, -1, SEEK_CUR);
1158 gmx_bool gro_next_x_or_v(FILE *status, t_trxframe *fr)
1162 char title[STRLEN], *p;
1166 if (gmx_one_before_eof(status))
1171 open_symtab(&symtab);
1172 atoms.nr = fr->natoms;
1173 snew(atoms.atom, fr->natoms);
1174 atoms.nres = fr->natoms;
1175 snew(atoms.resinfo, fr->natoms);
1176 snew(atoms.atomname, fr->natoms);
1178 fr->bV = get_w_conf(status, title, title, &symtab, &atoms, &ndec, fr->x, fr->v, fr->box);
1181 /* prec = 10^ndec: */
1182 for (i = 0; i < ndec; i++)
1192 sfree(atoms.resinfo);
1193 sfree(atoms.atomname);
1194 done_symtab(&symtab);
1196 if ((p = strstr(title, "t=")) != NULL)
1199 if (sscanf(p, "%lf", &tt) == 1)
1211 if (atoms.nr != fr->natoms)
1213 gmx_fatal(FARGS, "Number of atoms in gro frame (%d) doesn't match the number in the previous frame (%d)", atoms.nr, fr->natoms);
1219 int gro_first_x_or_v(FILE *status, t_trxframe *fr)
1224 fprintf(stderr, "Reading frames from gro file");
1225 get_coordnum_fp(status, title, &fr->natoms);
1227 fprintf(stderr, " '%s', %d atoms.\n", title, fr->natoms);
1230 if (fr->natoms == 0)
1232 gmx_file("No coordinates in gro file");
1235 snew(fr->x, fr->natoms);
1236 snew(fr->v, fr->natoms);
1237 gro_next_x_or_v(status, fr);
1242 static void make_hconf_format(int pr, gmx_bool bVel, char format[])
1246 /* build format string for printing,
1247 something like "%8.3f" for x and "%8.4f" for v */
1260 sprintf(format, "%%%d.%df%%%d.%df%%%d.%df%%%d.%df%%%d.%df%%%d.%df\n",
1261 l, pr, l, pr, l, pr, l, vpr, l, vpr, l, vpr);
1265 sprintf(format, "%%%d.%df%%%d.%df%%%d.%df\n", l, pr, l, pr, l, pr);
1270 static void write_hconf_box(FILE *out, int pr, matrix box)
1281 if (box[XX][YY] || box[XX][ZZ] || box[YY][XX] || box[YY][ZZ] ||
1282 box[ZZ][XX] || box[ZZ][YY])
1284 sprintf(format, "%%%d.%df%%%d.%df%%%d.%df"
1285 "%%%d.%df%%%d.%df%%%d.%df%%%d.%df%%%d.%df%%%d.%df\n",
1286 l, pr, l, pr, l, pr, l, pr, l, pr, l, pr, l, pr, l, pr, l, pr);
1287 fprintf(out, format,
1288 box[XX][XX], box[YY][YY], box[ZZ][ZZ],
1289 box[XX][YY], box[XX][ZZ], box[YY][XX],
1290 box[YY][ZZ], box[ZZ][XX], box[ZZ][YY]);
1294 sprintf(format, "%%%d.%df%%%d.%df%%%d.%df\n", l, pr, l, pr, l, pr);
1295 fprintf(out, format,
1296 box[XX][XX], box[YY][YY], box[ZZ][ZZ]);
1300 void write_hconf_indexed_p(FILE *out, const char *title, t_atoms *atoms,
1301 int nx, const atom_id index[], int pr,
1302 rvec *x, rvec *v, matrix box)
1304 char resnm[6], nm[6], format[100];
1305 int ai, i, resind, resnr;
1307 bromacs(format, 99);
1308 fprintf (out, "%s\n", (title && title[0]) ? title : format);
1309 fprintf (out, "%5d\n", nx);
1311 make_hconf_format(pr, v != NULL, format);
1313 for (i = 0; (i < nx); i++)
1317 resind = atoms->atom[ai].resind;
1318 strncpy(resnm, " ??? ", sizeof(resnm)-1);
1319 if (resind < atoms->nres)
1321 strncpy(resnm, *atoms->resinfo[resind].name, sizeof(resnm)-1);
1322 resnr = atoms->resinfo[resind].nr;
1326 strncpy(resnm, " ??? ", sizeof(resnm)-1);
1332 strncpy(nm, *atoms->atomname[ai], sizeof(nm)-1);
1336 strncpy(nm, " ??? ", sizeof(nm)-1);
1339 fprintf(out, "%5d%-5.5s%5.5s%5d", resnr%100000, resnm, nm, (ai+1)%100000);
1340 /* next fprintf uses built format string */
1343 fprintf(out, format,
1344 x[ai][XX], x[ai][YY], x[ai][ZZ], v[ai][XX], v[ai][YY], v[ai][ZZ]);
1348 fprintf(out, format,
1349 x[ai][XX], x[ai][YY], x[ai][ZZ]);
1353 write_hconf_box(out, pr, box);
1358 static void write_hconf_mtop(FILE *out, const char *title, gmx_mtop_t *mtop,
1360 rvec *x, rvec *v, matrix box)
1364 gmx_mtop_atomloop_all_t aloop;
1366 char *atomname, *resname;
1368 bromacs(format, 99);
1369 fprintf (out, "%s\n", (title && title[0]) ? title : format);
1370 fprintf (out, "%5d\n", mtop->natoms);
1372 make_hconf_format(pr, v != NULL, format);
1374 aloop = gmx_mtop_atomloop_all_init(mtop);
1375 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
1377 gmx_mtop_atomloop_all_names(aloop, &atomname, &resnr, &resname);
1379 fprintf(out, "%5d%-5.5s%5.5s%5d",
1380 resnr%100000, resname, atomname, (i+1)%100000);
1381 /* next fprintf uses built format string */
1384 fprintf(out, format,
1385 x[i][XX], x[i][YY], x[i][ZZ], v[i][XX], v[i][YY], v[i][ZZ]);
1389 fprintf(out, format,
1390 x[i][XX], x[i][YY], x[i][ZZ]);
1394 write_hconf_box(out, pr, box);
1399 void write_hconf_p(FILE *out, const char *title, t_atoms *atoms, int pr,
1400 rvec *x, rvec *v, matrix box)
1405 snew(aa, atoms->nr);
1406 for (i = 0; (i < atoms->nr); i++)
1410 write_hconf_indexed_p(out, title, atoms, atoms->nr, aa, pr, x, v, box);
1414 void write_conf_p(const char *outfile, const char *title,
1415 t_atoms *atoms, int pr,
1416 rvec *x, rvec *v, matrix box)
1420 out = gmx_fio_fopen(outfile, "w");
1421 write_hconf_p(out, title, atoms, pr, x, v, box);
1423 gmx_fio_fclose (out);
1426 static void write_conf(const char *outfile, const char *title, t_atoms *atoms,
1427 rvec *x, rvec *v, matrix box)
1429 write_conf_p(outfile, title, atoms, 3, x, v, box);
1432 void write_sto_conf_indexed(const char *outfile, const char *title,
1434 rvec x[], rvec *v, int ePBC, matrix box,
1435 atom_id nindex, atom_id index[])
1441 ftp = fn2ftp(outfile);
1445 out = gmx_fio_fopen(outfile, "w");
1446 write_hconf_indexed_p(out, title, atoms, nindex, index, 3, x, v, box);
1447 gmx_fio_fclose(out);
1450 clear_trxframe(&fr, TRUE);
1453 fr.natoms = atoms->nr;
1464 copy_mat(box, fr.box);
1465 out = gmx_fio_fopen(outfile, "w");
1466 write_g96_conf(out, &fr, nindex, index);
1467 gmx_fio_fclose(out);
1473 out = gmx_fio_fopen(outfile, "w");
1474 write_pdbfile_indexed(out, title, atoms, x, ePBC, box, ' ', -1, nindex, index, NULL, TRUE);
1475 gmx_fio_fclose(out);
1478 out = gmx_fio_fopen(outfile, "w");
1479 write_espresso_conf_indexed(out, title, atoms, nindex, index, x, v, box);
1480 gmx_fio_fclose(out);
1485 gmx_fatal(FARGS, "Sorry, can not write a topology to %s", outfile);
1488 gmx_incons("Not supported in write_sto_conf_indexed");
1492 void write_sto_conf(const char *outfile, const char *title, t_atoms *atoms,
1493 rvec x[], rvec *v, int ePBC, matrix box)
1499 ftp = fn2ftp(outfile);
1503 write_conf(outfile, title, atoms, x, v, box);
1506 clear_trxframe(&fr, TRUE);
1509 fr.natoms = atoms->nr;
1520 copy_mat(box, fr.box);
1521 out = gmx_fio_fopen(outfile, "w");
1522 write_g96_conf(out, &fr, -1, NULL);
1523 gmx_fio_fclose(out);
1528 out = gmx_fio_fopen(outfile, "w");
1529 write_pdbfile(out, title, atoms, x, ePBC, box, ' ', -1, NULL, TRUE);
1530 gmx_fio_fclose(out);
1533 out = gmx_fio_fopen(outfile, "w");
1534 write_espresso_conf_indexed(out, title, atoms, atoms->nr, NULL, x, v, box);
1535 gmx_fio_fclose(out);
1540 gmx_fatal(FARGS, "Sorry, can not write a topology to %s", outfile);
1543 gmx_incons("Not supported in write_sto_conf");
1547 void write_sto_conf_mtop(const char *outfile, const char *title,
1549 rvec x[], rvec *v, int ePBC, matrix box)
1555 ftp = fn2ftp(outfile);
1559 out = gmx_fio_fopen(outfile, "w");
1560 write_hconf_mtop(out, title, mtop, 3, x, v, box);
1561 gmx_fio_fclose(out);
1564 /* This is a brute force approach which requires a lot of memory.
1565 * We should implement mtop versions of all writing routines.
1567 atoms = gmx_mtop_global_atoms(mtop);
1569 write_sto_conf(outfile, title, &atoms, x, v, ePBC, box);
1576 void get_stx_coordnum(const char *infile, int *natoms)
1579 int ftp, tpxver, tpxgen;
1581 char g96_line[STRLEN+1];
1583 ftp = fn2ftp(infile);
1584 range_check(ftp, 0, efNR);
1588 get_coordnum(infile, natoms);
1591 in = gmx_fio_fopen(infile, "r");
1598 *natoms = read_g96_conf(in, infile, &fr, g96_line);
1604 in = gmx_fio_fopen(infile, "r");
1605 get_pdb_coordnum(in, natoms);
1609 *natoms = get_espresso_coordnum(infile);
1617 read_tpxheader(infile, &tpx, TRUE, &tpxver, &tpxgen);
1618 *natoms = tpx.natoms;
1622 gmx_fatal(FARGS, "File type %s not supported in get_stx_coordnum",
1627 void read_stx_conf(const char *infile, char *title, t_atoms *atoms,
1628 rvec x[], rvec *v, int *ePBC, matrix box)
1637 char g96_line[STRLEN+1];
1641 fprintf(stderr, "Warning: Number of atoms in %s is 0\n", infile);
1643 else if (atoms->atom == NULL)
1645 gmx_mem("Uninitialized array atom");
1653 ftp = fn2ftp(infile);
1657 read_whole_conf(infile, title, atoms, x, v, box);
1661 fr.natoms = atoms->nr;
1666 in = gmx_fio_fopen(infile, "r");
1667 read_g96_conf(in, infile, &fr, g96_line);
1669 copy_mat(fr.box, box);
1670 strncpy(title, fr.title, STRLEN);
1675 read_pdb_conf(infile, title, atoms, x, ePBC, box, TRUE, NULL);
1678 read_espresso_conf(infile, atoms, x, v, box);
1684 i = read_tpx(infile, NULL, box, &natoms, x, v, NULL, mtop);
1690 strcpy(title, *(mtop->name));
1692 /* Free possibly allocated memory */
1695 *atoms = gmx_mtop_global_atoms(mtop);
1696 top = gmx_mtop_t_to_t_topology(mtop);
1697 tpx_make_chain_identifiers(atoms, &top.mols);
1700 /* The strings in the symtab are still in use in the returned t_atoms
1701 * structure, so we should not free them. But there is no place to put the
1702 * symbols; the only choice is to leak the memory...
1703 * So we clear the symbol table before freeing the topology structure. */
1704 free_symtab(&top.symtab);
1709 gmx_incons("Not supported in read_stx_conf");