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58 #include "gmx_fatal.h"
61 #include "mtop_util.h"
66 static int read_g96_pos(char line[], t_symtab *symtab,
67 FILE *fp, const char *infile,
72 int nwanted, natoms, atnr, resnr = 0, oldres, newres, shift;
73 char anm[STRLEN], resnm[STRLEN];
94 oldres = -666; /* Unlikely number for the first residue! */
96 while (!bEnd && fgets2(line, STRLEN, fp))
98 bEnd = (strncmp(line, "END", 3) == 0);
99 if (!bEnd && (line[0] != '#'))
101 if (sscanf(line+shift, "%15lf%15lf%15lf", &db1, &db2, &db3) != 3)
103 gmx_fatal(FARGS, "Did not find 3 coordinates for atom %d in %s\n",
106 if ((nwanted != -1) && (natoms >= nwanted))
109 "Found more coordinates (%d) in %s than expected %d\n",
110 natoms, infile, nwanted);
115 (sscanf(line, "%5d%c%5s%c%5s%7d", &resnr, &c1, resnm, &c2, anm, &atnr)
125 strncpy(resnm, "???", sizeof(resnm)-1);
127 strncpy(anm, "???", sizeof(anm)-1);
129 atoms->atomname[natoms] = put_symtab(symtab, anm);
134 if (newres >= atoms->nr)
136 gmx_fatal(FARGS, "More residues than atoms in %s (natoms = %d)",
139 atoms->atom[natoms].resind = newres;
140 if (newres+1 > atoms->nres)
142 atoms->nres = newres+1;
144 t_atoms_set_resinfo(atoms, natoms, symtab, resnm, resnr, ' ', 0, ' ');
148 atoms->atom[natoms].resind = newres;
153 fr->x[natoms][0] = db1;
154 fr->x[natoms][1] = db2;
155 fr->x[natoms][2] = db3;
160 if ((nwanted != -1) && natoms != nwanted)
163 "Warning: found less coordinates (%d) in %s than expected %d\n",
164 natoms, infile, nwanted);
173 static int read_g96_vel(char line[], FILE *fp, const char *infile,
177 int nwanted, natoms = -1, shift;
178 double db1, db2, db3;
180 nwanted = fr->natoms;
184 if (strcmp(line, "VELOCITYRED") == 0)
194 while (!bEnd && fgets2(line, STRLEN, fp))
196 bEnd = (strncmp(line, "END", 3) == 0);
197 if (!bEnd && (line[0] != '#'))
199 if (sscanf(line+shift, "%15lf%15lf%15lf", &db1, &db2, &db3) != 3)
201 gmx_fatal(FARGS, "Did not find 3 velocities for atom %d in %s",
204 if ((nwanted != -1) && (natoms >= nwanted))
206 gmx_fatal(FARGS, "Found more velocities (%d) in %s than expected %d\n",
207 natoms, infile, nwanted);
211 fr->v[natoms][0] = db1;
212 fr->v[natoms][1] = db2;
213 fr->v[natoms][2] = db3;
218 if ((nwanted != -1) && (natoms != nwanted))
221 "Warning: found less velocities (%d) in %s than expected %d\n",
222 natoms, infile, nwanted);
229 int read_g96_conf(FILE *fp, const char *infile, t_trxframe *fr, char *line)
231 t_symtab *symtab = NULL;
232 gmx_bool bAtStart, bTime, bAtoms, bPos, bVel, bBox, bEnd, bFinished;
234 double db1, db2, db3, db4, db5, db6, db7, db8, db9;
236 bAtStart = (ftell(fp) == 0);
238 clear_trxframe(fr, FALSE);
250 while (!fr->bTitle && fgets2(line, STRLEN, fp))
252 fr->bTitle = (strcmp(line, "TITLE") == 0);
254 if (fr->title == NULL)
256 fgets2(line, STRLEN, fp);
257 fr->title = strdup(line);
260 while (!bEnd && fgets2(line, STRLEN, fp))
262 bEnd = (strcmp(line, "END") == 0);
264 fgets2(line, STRLEN, fp);
267 /* Do not get a line if we are not at the start of the file, *
268 * because without a parameter file we don't know what is in *
269 * the trajectory and we have already read the line in the *
270 * previous call (VERY DIRTY). */
274 bTime = (strcmp(line, "TIMESTEP") == 0);
275 bAtoms = (strcmp(line, "POSITION") == 0);
276 bPos = (bAtoms || (strcmp(line, "POSITIONRED") == 0));
277 bVel = (strncmp(line, "VELOCITY", 8) == 0);
278 bBox = (strcmp(line, "BOX") == 0);
281 if (!fr->bTime && !fr->bX)
287 bFinished = (fgets2(line, STRLEN, fp) == NULL);
289 while (!bFinished && (line[0] == '#'));
290 sscanf(line, "%15d%15lf", &(fr->step), &db1);
304 natoms = read_g96_pos(line, symtab, fp, infile, fr);
314 natoms = read_g96_vel(line, fp, infile, fr);
321 while (!bEnd && fgets2(line, STRLEN, fp))
323 bEnd = (strncmp(line, "END", 3) == 0);
324 if (!bEnd && (line[0] != '#'))
326 nbp = sscanf(line, "%15lf%15lf%15lf%15lf%15lf%15lf%15lf%15lf%15lf",
327 &db1, &db2, &db3, &db4, &db5, &db6, &db7, &db8, &db9);
330 gmx_fatal(FARGS, "Found a BOX line, but no box in %s", infile);
332 fr->box[XX][XX] = db1;
333 fr->box[YY][YY] = db2;
334 fr->box[ZZ][ZZ] = db3;
337 fr->box[XX][YY] = db4;
338 fr->box[XX][ZZ] = db5;
339 fr->box[YY][XX] = db6;
340 fr->box[YY][ZZ] = db7;
341 fr->box[ZZ][XX] = db8;
342 fr->box[ZZ][YY] = db9;
349 while (!bFinished && fgets2(line, STRLEN, fp));
358 void write_g96_conf(FILE *out, t_trxframe *fr,
359 int nindex, const atom_id *index)
377 fprintf(out, "TITLE\n%s\nEND\n", fr->title);
379 if (fr->bStep || fr->bTime)
381 /* Officially the time format is %15.9, which is not enough for 10 ns */
382 fprintf(out, "TIMESTEP\n%15d%15.6f\nEND\n", fr->step, fr->time);
388 fprintf(out, "POSITION\n");
389 for (i = 0; i < nout; i++)
399 fprintf(out, "%5d %-5s %-5s%7d%15.9f%15.9f%15.9f\n",
400 (atoms->resinfo[atoms->atom[a].resind].nr) % 100000,
401 *atoms->resinfo[atoms->atom[a].resind].name,
402 *atoms->atomname[a], (i+1) % 10000000,
403 fr->x[a][XX], fr->x[a][YY], fr->x[a][ZZ]);
408 fprintf(out, "POSITIONRED\n");
409 for (i = 0; i < nout; i++)
419 fprintf(out, "%15.9f%15.9f%15.9f\n",
420 fr->x[a][XX], fr->x[a][YY], fr->x[a][ZZ]);
423 fprintf(out, "END\n");
429 fprintf(out, "VELOCITY\n");
430 for (i = 0; i < nout; i++)
440 fprintf(out, "%5d %-5s %-5s%7d%15.9f%15.9f%15.9f\n",
441 (atoms->resinfo[atoms->atom[a].resind].nr) % 100000,
442 *atoms->resinfo[atoms->atom[a].resind].name,
443 *atoms->atomname[a], (i+1) % 10000000,
444 fr->v[a][XX], fr->v[a][YY], fr->v[a][ZZ]);
449 fprintf(out, "VELOCITYRED\n");
450 for (i = 0; i < nout; i++)
460 fprintf(out, "%15.9f%15.9f%15.9f\n",
461 fr->v[a][XX], fr->v[a][YY], fr->v[a][ZZ]);
464 fprintf(out, "END\n");
468 fprintf(out, "BOX\n");
469 fprintf(out, "%15.9f%15.9f%15.9f",
470 fr->box[XX][XX], fr->box[YY][YY], fr->box[ZZ][ZZ]);
471 if (fr->box[XX][YY] || fr->box[XX][ZZ] || fr->box[YY][XX] ||
472 fr->box[YY][ZZ] || fr->box[ZZ][XX] || fr->box[ZZ][YY])
474 fprintf(out, "%15.9f%15.9f%15.9f%15.9f%15.9f%15.9f",
475 fr->box[XX][YY], fr->box[XX][ZZ], fr->box[YY][XX],
476 fr->box[YY][ZZ], fr->box[ZZ][XX], fr->box[ZZ][YY]);
479 fprintf(out, "END\n");
483 static int get_espresso_word(FILE *fp, char word[])
495 if (i == ' ' || i == '\n' || i == '\t')
520 word[nc++] = (char)i;
524 while (i != EOF && ret == 0);
528 /* printf("'%s'\n",word); */
533 static int check_open_parenthesis(FILE *fp, int r,
534 const char *infile, const char *keyword)
546 r = get_espresso_word(fp, word);
553 gmx_fatal(FARGS, "Expected '{' after '%s' in file '%s'",
561 static int check_close_parenthesis(FILE *fp, int r,
562 const char *infile, const char *keyword)
574 r = get_espresso_word(fp, word);
581 gmx_fatal(FARGS, "Expected '}' after section '%s' in file '%s'",
590 espID, espPOS, espTYPE, espQ, espV, espF, espMOLECULE, espNR
592 const char *esp_prop[espNR] = {
593 "id", "pos", "type", "q", "v", "f",
597 static void read_espresso_conf(const char *infile,
598 t_atoms *atoms, rvec x[], rvec *v, matrix box)
600 t_symtab *symtab = NULL;
602 char word[STRLEN], buf[STRLEN];
603 int natoms, level, npar, r, nprop, p, i, m, molnr;
606 gmx_bool bFoundParticles, bFoundProp, bFoundVariable, bMol;
616 fp = gmx_fio_fopen(infile, "r");
618 bFoundParticles = FALSE;
619 bFoundVariable = FALSE;
622 while ((r = get_espresso_word(fp, word)))
624 if (level == 1 && strcmp(word, "particles") == 0 && !bFoundParticles)
626 bFoundParticles = TRUE;
627 level += check_open_parenthesis(fp, r, infile, "particles");
629 while (level == 2 && (r = get_espresso_word(fp, word)))
632 for (p = 0; p < espNR; p++)
634 if (strcmp(word, esp_prop[p]) == 0)
638 /* printf(" prop[%d] = %s\n",nprop-1,esp_prop[prop[nprop-1]]); */
641 if (!bFoundProp && word[0] != '}')
643 gmx_fatal(FARGS, "Can not read Espresso files with particle property '%s'", word);
645 if (bFoundProp && p == espMOLECULE)
656 while (level > 0 && (r = get_espresso_word(fp, word)))
668 for (p = 0; p < nprop; p++)
673 r = get_espresso_word(fp, word);
677 for (m = 0; m < 3; m++)
679 r = get_espresso_word(fp, word);
680 sscanf(word, "%lf", &d);
685 r = get_espresso_word(fp, word);
686 atoms->atom[i].type = strtol(word, NULL, 10);
689 r = get_espresso_word(fp, word);
690 sscanf(word, "%lf", &d);
691 atoms->atom[i].q = d;
694 for (m = 0; m < 3; m++)
696 r = get_espresso_word(fp, word);
697 sscanf(word, "%lf", &d);
702 for (m = 0; m < 3; m++)
704 r = get_espresso_word(fp, word);
709 r = get_espresso_word(fp, word);
710 molnr = strtol(word, NULL, 10);
712 atoms->resinfo[atoms->atom[i-1].resind].nr != molnr)
714 atoms->atom[i].resind =
715 (i == 0 ? 0 : atoms->atom[i-1].resind+1);
716 atoms->resinfo[atoms->atom[i].resind].nr = molnr;
717 atoms->resinfo[atoms->atom[i].resind].ic = ' ';
718 atoms->resinfo[atoms->atom[i].resind].chainid = ' ';
719 atoms->resinfo[atoms->atom[i].resind].chainnum = molnr; /* Not sure if this is right? */
723 atoms->atom[i].resind = atoms->atom[i-1].resind;
728 /* Generate an atom name from the particle type */
729 sprintf(buf, "T%d", atoms->atom[i].type);
730 atoms->atomname[i] = put_symtab(symtab, buf);
733 if (i == 0 || atoms->atom[i].resind != atoms->atom[i-1].resind)
735 atoms->resinfo[atoms->atom[i].resind].name =
736 put_symtab(symtab, "MOL");
741 /* Residue number is the atom number */
742 atoms->atom[i].resind = i;
743 /* Generate an residue name from the particle type */
744 if (atoms->atom[i].type < 26)
746 sprintf(buf, "T%c", 'A'+atoms->atom[i].type);
750 sprintf(buf, "T%c%c",
751 'A'+atoms->atom[i].type/26, 'A'+atoms->atom[i].type%26);
753 t_atoms_set_resinfo(atoms, i, symtab, buf, i, ' ', 0, ' ');
763 atoms->nres = atoms->nr;
767 gmx_fatal(FARGS, "Internal inconsistency in Espresso routines, read %d atoms, expected %d atoms", i, atoms->nr);
770 else if (level == 1 && strcmp(word, "variable") == 0 && !bFoundVariable)
772 bFoundVariable = TRUE;
773 level += check_open_parenthesis(fp, r, infile, "variable");
774 while (level == 2 && (r = get_espresso_word(fp, word)))
776 if (level == 2 && strcmp(word, "box_l") == 0)
778 for (m = 0; m < 3; m++)
780 r = get_espresso_word(fp, word);
781 sscanf(word, "%lf", &d);
784 level += check_close_parenthesis(fp, r, infile, "box_l");
798 if (!bFoundParticles)
800 fprintf(stderr, "Did not find a particles section in Espresso file '%s'\n",
807 static int get_espresso_coordnum(const char *infile)
811 int natoms, level, r;
812 gmx_bool bFoundParticles;
816 fp = gmx_fio_fopen(infile, "r");
818 bFoundParticles = FALSE;
820 while ((r = get_espresso_word(fp, word)) && !bFoundParticles)
822 if (level == 1 && strcmp(word, "particles") == 0 && !bFoundParticles)
824 bFoundParticles = TRUE;
825 level += check_open_parenthesis(fp, r, infile, "particles");
826 while (level > 0 && (r = get_espresso_word(fp, word)))
851 if (!bFoundParticles)
853 fprintf(stderr, "Did not find a particles section in Espresso file '%s'\n",
862 static void write_espresso_conf_indexed(FILE *out, const char *title,
863 t_atoms *atoms, int nx, atom_id *index,
864 rvec *x, rvec *v, matrix box)
868 fprintf(out, "# %s\n", title);
871 gmx_warning("The Espresso format does not support triclinic unit-cells");
873 fprintf(out, "{variable {box_l %f %f %f}}\n", box[0][0], box[1][1], box[2][2]);
875 fprintf(out, "{particles {id pos type q%s}\n", v ? " v" : "");
876 for (i = 0; i < nx; i++)
886 fprintf(out, "\t{%d %f %f %f %d %g",
887 j, x[j][XX], x[j][YY], x[j][ZZ],
888 atoms->atom[j].type, atoms->atom[j].q);
891 fprintf(out, " %f %f %f", v[j][XX], v[j][YY], v[j][ZZ]);
898 static void get_coordnum_fp (FILE *in, char *title, int *natoms)
902 fgets2 (title, STRLEN, in);
903 fgets2 (line, STRLEN, in);
904 if (sscanf (line, "%d", natoms) != 1)
906 gmx_fatal(FARGS, "gro file does not have the number of atoms on the second line");
910 static void get_coordnum (const char *infile, int *natoms)
915 in = gmx_fio_fopen(infile, "r");
916 get_coordnum_fp(in, title, natoms);
920 static gmx_bool get_w_conf(FILE *in, const char *infile, char *title,
921 t_symtab *symtab, t_atoms *atoms, int *ndec,
922 rvec x[], rvec *v, matrix box)
925 char line[STRLEN+1], *ptr;
927 double x1, y1, z1, x2, y2, z2;
929 int natoms, i, m, resnr, newres, oldres, ddist, c;
930 gmx_bool bFirst, bVel;
934 oldres = NOTSET; /* Unlikely number for the first residue! */
937 /* Read the title and number of atoms */
938 get_coordnum_fp(in, title, &natoms);
940 if (natoms > atoms->nr)
942 gmx_fatal(FARGS, "gro file contains more atoms (%d) than expected (%d)",
945 else if (natoms < atoms->nr)
947 fprintf(stderr, "Warning: gro file contains less atoms (%d) than expected"
948 " (%d)\n", natoms, atoms->nr);
955 /* just pray the arrays are big enough */
956 for (i = 0; (i < natoms); i++)
958 if ((fgets2 (line, STRLEN, in)) == NULL)
960 unexpected_eof(infile, i+2);
962 if (strlen(line) < 39)
964 gmx_fatal(FARGS, "Invalid line in %s for atom %d:\n%s", infile, i+1, line);
967 /* determine read precision from distance between periods
972 p1 = strchr(line, '.');
975 gmx_fatal(FARGS, "A coordinate in file %s does not contain a '.'", infile);
977 p2 = strchr(&p1[1], '.');
980 gmx_fatal(FARGS, "A coordinate in file %s does not contain a '.'", infile);
985 p3 = strchr(&p2[1], '.');
988 gmx_fatal(FARGS, "A coordinate in file %s does not contain a '.'", infile);
991 if (p3 - p2 != ddist)
993 gmx_fatal(FARGS, "The spacing of the decimal points in file %s is not consistent for x, y and z", infile);
998 memcpy(name, line, 5);
1000 sscanf(name, "%d", &resnr);
1001 memcpy(name, line+5, 5);
1003 if (resnr != oldres)
1007 if (newres >= natoms)
1009 gmx_fatal(FARGS, "More residues than atoms in %s (natoms = %d)",
1012 atoms->atom[i].resind = newres;
1013 t_atoms_set_resinfo(atoms, i, symtab, name, resnr, ' ', 0, ' ');
1017 atoms->atom[i].resind = newres;
1021 memcpy(name, line+10, 5);
1022 atoms->atomname[i] = put_symtab(symtab, name);
1024 /* eventueel controle atomnumber met i+1 */
1026 /* coordinates (start after residue shit) */
1028 /* Read fixed format */
1029 for (m = 0; m < DIM; m++)
1031 for (c = 0; (c < ddist && ptr[0]); c++)
1037 if (sscanf (buf, "%lf %lf", &x1, &x2) != 1)
1039 gmx_fatal(FARGS, "Something is wrong in the coordinate formatting of file %s. Note that gro is fixed format (see the manual)", infile);
1047 /* velocities (start after residues and coordinates) */
1050 /* Read fixed format */
1051 for (m = 0; m < DIM; m++)
1053 for (c = 0; (c < ddist && ptr[0]); c++)
1059 if (sscanf (buf, "%lf", &x1) != 1)
1071 atoms->nres = newres + 1;
1074 fgets2 (line, STRLEN, in);
1075 if (sscanf (line, "%lf%lf%lf", &x1, &y1, &z1) != 3)
1077 gmx_warning("Bad box in file %s", infile);
1079 /* Generate a cubic box */
1080 for (m = 0; (m < DIM); m++)
1082 xmin[m] = xmax[m] = x[0][m];
1084 for (i = 1; (i < atoms->nr); i++)
1086 for (m = 0; (m < DIM); m++)
1088 xmin[m] = min(xmin[m], x[i][m]);
1089 xmax[m] = max(xmax[m], x[i][m]);
1092 for (i = 0; i < DIM; i++)
1094 for (m = 0; m < DIM; m++)
1099 for (m = 0; (m < DIM); m++)
1101 box[m][m] = (xmax[m]-xmin[m]);
1103 fprintf(stderr, "Generated a cubic box %8.3f x %8.3f x %8.3f\n",
1104 box[XX][XX], box[YY][YY], box[ZZ][ZZ]);
1108 /* We found the first three values, the diagonal elements */
1112 if (sscanf (line, "%*f%*f%*f%lf%lf%lf%lf%lf%lf",
1113 &x1, &y1, &z1, &x2, &y2, &z2) != 6)
1115 x1 = y1 = z1 = x2 = y2 = z2 = 0.0;
1128 static void read_whole_conf(const char *infile, char *title,
1129 t_atoms *atoms, rvec x[], rvec *v, matrix box)
1136 in = gmx_fio_fopen(infile, "r");
1138 open_symtab(&symtab);
1139 get_w_conf(in, infile, title, &symtab, atoms, &ndec, x, v, box);
1140 /* We can't free the symbols, as they are still used in atoms, so
1141 * the only choice is to leak them. */
1142 free_symtab(&symtab);
1147 gmx_bool gro_next_x_or_v(FILE *status, t_trxframe *fr)
1151 char title[STRLEN], *p;
1155 if (gmx_eof(status))
1160 open_symtab(&symtab);
1161 atoms.nr = fr->natoms;
1162 snew(atoms.atom, fr->natoms);
1163 atoms.nres = fr->natoms;
1164 snew(atoms.resinfo, fr->natoms);
1165 snew(atoms.atomname, fr->natoms);
1167 fr->bV = get_w_conf(status, title, title, &symtab, &atoms, &ndec, fr->x, fr->v, fr->box);
1170 /* prec = 10^ndec: */
1171 for (i = 0; i < ndec; i++)
1181 sfree(atoms.resinfo);
1182 sfree(atoms.atomname);
1183 done_symtab(&symtab);
1185 if ((p = strstr(title, "t=")) != NULL)
1188 if (sscanf(p, "%lf", &tt) == 1)
1200 if (atoms.nr != fr->natoms)
1202 gmx_fatal(FARGS, "Number of atoms in gro frame (%d) doesn't match the number in the previous frame (%d)", atoms.nr, fr->natoms);
1208 int gro_first_x_or_v(FILE *status, t_trxframe *fr)
1213 fprintf(stderr, "Reading frames from gro file");
1214 get_coordnum_fp(status, title, &fr->natoms);
1216 fprintf(stderr, " '%s', %d atoms.\n", title, fr->natoms);
1219 if (fr->natoms == 0)
1221 gmx_file("No coordinates in gro file");
1224 snew(fr->x, fr->natoms);
1225 snew(fr->v, fr->natoms);
1226 gro_next_x_or_v(status, fr);
1231 static void make_hconf_format(int pr, gmx_bool bVel, char format[])
1235 /* build format string for printing,
1236 something like "%8.3f" for x and "%8.4f" for v */
1249 sprintf(format, "%%%d.%df%%%d.%df%%%d.%df%%%d.%df%%%d.%df%%%d.%df\n",
1250 l, pr, l, pr, l, pr, l, vpr, l, vpr, l, vpr);
1254 sprintf(format, "%%%d.%df%%%d.%df%%%d.%df\n", l, pr, l, pr, l, pr);
1259 static void write_hconf_box(FILE *out, int pr, matrix box)
1270 if (box[XX][YY] || box[XX][ZZ] || box[YY][XX] || box[YY][ZZ] ||
1271 box[ZZ][XX] || box[ZZ][YY])
1273 sprintf(format, "%%%d.%df%%%d.%df%%%d.%df"
1274 "%%%d.%df%%%d.%df%%%d.%df%%%d.%df%%%d.%df%%%d.%df\n",
1275 l, pr, l, pr, l, pr, l, pr, l, pr, l, pr, l, pr, l, pr, l, pr);
1276 fprintf(out, format,
1277 box[XX][XX], box[YY][YY], box[ZZ][ZZ],
1278 box[XX][YY], box[XX][ZZ], box[YY][XX],
1279 box[YY][ZZ], box[ZZ][XX], box[ZZ][YY]);
1283 sprintf(format, "%%%d.%df%%%d.%df%%%d.%df\n", l, pr, l, pr, l, pr);
1284 fprintf(out, format,
1285 box[XX][XX], box[YY][YY], box[ZZ][ZZ]);
1289 void write_hconf_indexed_p(FILE *out, const char *title, t_atoms *atoms,
1290 int nx, const atom_id index[], int pr,
1291 rvec *x, rvec *v, matrix box)
1293 char resnm[6], nm[6], format[100];
1294 int ai, i, resind, resnr;
1296 bromacs(format, 99);
1297 fprintf (out, "%s\n", (title && title[0]) ? title : format);
1298 fprintf (out, "%5d\n", nx);
1300 make_hconf_format(pr, v != NULL, format);
1302 for (i = 0; (i < nx); i++)
1306 resind = atoms->atom[ai].resind;
1307 strncpy(resnm, " ??? ", sizeof(resnm)-1);
1308 if (resind < atoms->nres)
1310 strncpy(resnm, *atoms->resinfo[resind].name, sizeof(resnm)-1);
1311 resnr = atoms->resinfo[resind].nr;
1315 strncpy(resnm, " ??? ", sizeof(resnm)-1);
1321 strncpy(nm, *atoms->atomname[ai], sizeof(nm)-1);
1325 strncpy(nm, " ??? ", sizeof(nm)-1);
1328 fprintf(out, "%5d%-5.5s%5.5s%5d", resnr%100000, resnm, nm, (ai+1)%100000);
1329 /* next fprintf uses built format string */
1332 fprintf(out, format,
1333 x[ai][XX], x[ai][YY], x[ai][ZZ], v[ai][XX], v[ai][YY], v[ai][ZZ]);
1337 fprintf(out, format,
1338 x[ai][XX], x[ai][YY], x[ai][ZZ]);
1342 write_hconf_box(out, pr, box);
1347 static void write_hconf_mtop(FILE *out, const char *title, gmx_mtop_t *mtop,
1349 rvec *x, rvec *v, matrix box)
1353 gmx_mtop_atomloop_all_t aloop;
1355 char *atomname, *resname;
1357 bromacs(format, 99);
1358 fprintf (out, "%s\n", (title && title[0]) ? title : format);
1359 fprintf (out, "%5d\n", mtop->natoms);
1361 make_hconf_format(pr, v != NULL, format);
1363 aloop = gmx_mtop_atomloop_all_init(mtop);
1364 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
1366 gmx_mtop_atomloop_all_names(aloop, &atomname, &resnr, &resname);
1368 fprintf(out, "%5d%-5.5s%5.5s%5d",
1369 resnr%100000, resname, atomname, (i+1)%100000);
1370 /* next fprintf uses built format string */
1373 fprintf(out, format,
1374 x[i][XX], x[i][YY], x[i][ZZ], v[i][XX], v[i][YY], v[i][ZZ]);
1378 fprintf(out, format,
1379 x[i][XX], x[i][YY], x[i][ZZ]);
1383 write_hconf_box(out, pr, box);
1388 void write_hconf_p(FILE *out, const char *title, t_atoms *atoms, int pr,
1389 rvec *x, rvec *v, matrix box)
1394 snew(aa, atoms->nr);
1395 for (i = 0; (i < atoms->nr); i++)
1399 write_hconf_indexed_p(out, title, atoms, atoms->nr, aa, pr, x, v, box);
1403 void write_conf_p(const char *outfile, const char *title,
1404 t_atoms *atoms, int pr,
1405 rvec *x, rvec *v, matrix box)
1409 out = gmx_fio_fopen(outfile, "w");
1410 write_hconf_p(out, title, atoms, pr, x, v, box);
1412 gmx_fio_fclose (out);
1415 static void write_conf(const char *outfile, const char *title, t_atoms *atoms,
1416 rvec *x, rvec *v, matrix box)
1418 write_conf_p(outfile, title, atoms, 3, x, v, box);
1421 void write_sto_conf_indexed(const char *outfile, const char *title,
1423 rvec x[], rvec *v, int ePBC, matrix box,
1424 atom_id nindex, atom_id index[])
1430 ftp = fn2ftp(outfile);
1434 out = gmx_fio_fopen(outfile, "w");
1435 write_hconf_indexed_p(out, title, atoms, nindex, index, 3, x, v, box);
1436 gmx_fio_fclose(out);
1439 clear_trxframe(&fr, TRUE);
1442 fr.natoms = atoms->nr;
1453 copy_mat(box, fr.box);
1454 out = gmx_fio_fopen(outfile, "w");
1455 write_g96_conf(out, &fr, nindex, index);
1456 gmx_fio_fclose(out);
1462 out = gmx_fio_fopen(outfile, "w");
1463 write_pdbfile_indexed(out, title, atoms, x, ePBC, box, ' ', -1, nindex, index, NULL, TRUE);
1464 gmx_fio_fclose(out);
1467 out = gmx_fio_fopen(outfile, "w");
1468 write_espresso_conf_indexed(out, title, atoms, nindex, index, x, v, box);
1469 gmx_fio_fclose(out);
1474 gmx_fatal(FARGS, "Sorry, can not write a topology to %s", outfile);
1477 gmx_incons("Not supported in write_sto_conf_indexed");
1481 static void write_xyz_conf(const char *outfile, const char *title,
1482 t_atoms *atoms, rvec *x)
1488 gmx_atomprop_t aps = gmx_atomprop_init();
1490 fp = gmx_fio_fopen(outfile, "w");
1491 fprintf(fp, "%3d\n", atoms->nr);
1492 fprintf(fp, "%s\n", title);
1493 for (i = 0; (i < atoms->nr); i++)
1495 anr = atoms->atom[i].atomnumber;
1496 name = *atoms->atomname[i];
1499 if (gmx_atomprop_query(aps, epropElement, "???", name, &value))
1501 anr = gmx_nint(value);
1504 if ((ptr = gmx_atomprop_element(aps, anr)) == NULL)
1508 fprintf(fp, "%3s%10.5f%10.5f%10.5f\n", ptr,
1509 10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ]);
1512 gmx_atomprop_destroy(aps);
1515 void write_sto_conf(const char *outfile, const char *title, t_atoms *atoms,
1516 rvec x[], rvec *v, int ePBC, matrix box)
1522 ftp = fn2ftp(outfile);
1526 write_conf(outfile, title, atoms, x, v, box);
1529 clear_trxframe(&fr, TRUE);
1532 fr.natoms = atoms->nr;
1543 copy_mat(box, fr.box);
1544 out = gmx_fio_fopen(outfile, "w");
1545 write_g96_conf(out, &fr, -1, NULL);
1546 gmx_fio_fclose(out);
1549 write_xyz_conf(outfile, (strlen(title) > 0) ? title : outfile, atoms, x);
1554 out = gmx_fio_fopen(outfile, "w");
1555 write_pdbfile(out, title, atoms, x, ePBC, box, ' ', -1, NULL, TRUE);
1556 gmx_fio_fclose(out);
1559 out = gmx_fio_fopen(outfile, "w");
1560 write_espresso_conf_indexed(out, title, atoms, atoms->nr, NULL, x, v, box);
1561 gmx_fio_fclose(out);
1566 gmx_fatal(FARGS, "Sorry, can not write a topology to %s", outfile);
1569 gmx_incons("Not supported in write_sto_conf");
1573 void write_sto_conf_mtop(const char *outfile, const char *title,
1575 rvec x[], rvec *v, int ePBC, matrix box)
1581 ftp = fn2ftp(outfile);
1585 out = gmx_fio_fopen(outfile, "w");
1586 write_hconf_mtop(out, title, mtop, 3, x, v, box);
1587 gmx_fio_fclose(out);
1590 /* This is a brute force approach which requires a lot of memory.
1591 * We should implement mtop versions of all writing routines.
1593 atoms = gmx_mtop_global_atoms(mtop);
1595 write_sto_conf(outfile, title, &atoms, x, v, ePBC, box);
1602 static int get_xyz_coordnum(const char *infile)
1607 fp = gmx_fio_fopen(infile, "r");
1608 if (fscanf(fp, "%d", &n) != 1)
1610 gmx_fatal(FARGS, "Can not read number of atoms from %s", infile);
1617 static void read_xyz_conf(const char *infile, char *title,
1618 t_atoms *atoms, rvec *x)
1624 char atomnm[32], buf[STRLEN];
1627 fp = gmx_fio_fopen(infile, "r");
1628 fgets2(buf, STRLEN-1, fp);
1629 if (sscanf(buf, "%d", &n) != 1)
1631 gmx_fatal(FARGS, "Can not read number of atoms from %s", infile);
1633 fgets2(buf, STRLEN-1, fp);
1635 for (i = 0; (i < n); i++)
1637 fgets2(buf, STRLEN-1, fp);
1638 if (sscanf(buf, "%s%lf%lf%lf", atomnm, &xx, &yy, &zz) != 4)
1640 gmx_fatal(FARGS, "Can not read coordinates from %s", infile);
1642 atoms->atomname[i] = put_symtab(tab, atomnm);
1650 void get_stx_coordnum(const char *infile, int *natoms)
1653 int ftp, tpxver, tpxgen;
1655 char g96_line[STRLEN+1];
1657 ftp = fn2ftp(infile);
1658 range_check(ftp, 0, efNR);
1662 get_coordnum(infile, natoms);
1665 in = gmx_fio_fopen(infile, "r");
1672 *natoms = read_g96_conf(in, infile, &fr, g96_line);
1676 *natoms = get_xyz_coordnum(infile);
1681 in = gmx_fio_fopen(infile, "r");
1682 get_pdb_coordnum(in, natoms);
1686 *natoms = get_espresso_coordnum(infile);
1694 read_tpxheader(infile, &tpx, TRUE, &tpxver, &tpxgen);
1695 *natoms = tpx.natoms;
1699 gmx_fatal(FARGS, "File type %s not supported in get_stx_coordnum",
1704 void read_stx_conf(const char *infile, char *title, t_atoms *atoms,
1705 rvec x[], rvec *v, int *ePBC, matrix box)
1714 char g96_line[STRLEN+1];
1718 fprintf(stderr, "Warning: Number of atoms in %s is 0\n", infile);
1720 else if (atoms->atom == NULL)
1722 gmx_mem("Uninitialized array atom");
1730 ftp = fn2ftp(infile);
1734 read_whole_conf(infile, title, atoms, x, v, box);
1737 read_xyz_conf(infile, title, atoms, x);
1741 fr.natoms = atoms->nr;
1746 in = gmx_fio_fopen(infile, "r");
1747 read_g96_conf(in, infile, &fr, g96_line);
1749 copy_mat(fr.box, box);
1750 strncpy(title, fr.title, STRLEN);
1755 read_pdb_conf(infile, title, atoms, x, ePBC, box, TRUE, NULL);
1758 read_espresso_conf(infile, atoms, x, v, box);
1764 i = read_tpx(infile, NULL, box, &natoms, x, v, NULL, mtop);
1770 strcpy(title, *(mtop->name));
1772 /* Free possibly allocated memory */
1775 *atoms = gmx_mtop_global_atoms(mtop);
1776 top = gmx_mtop_t_to_t_topology(mtop);
1777 tpx_make_chain_identifiers(atoms, &top.mols);
1780 /* The strings in the symtab are still in use in the returned t_atoms
1781 * structure, so we should not free them. But there is no place to put the
1782 * symbols; the only choice is to leak the memory...
1783 * So we clear the symbol table before freeing the topology structure. */
1784 free_symtab(&top.symtab);
1789 gmx_incons("Not supported in read_stx_conf");