X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=blobdiff_plain;f=src%2Fgromacs%2Ffileio%2Fconfio.cpp;h=14093492279b5a84534198799be21ea7e873b7e3;hb=86d17b51f8c88e4c25e4ee89885545056cd150a6;hp=b9844ba9671bec3b1fd5a29134099ae3db9e189b;hpb=6d710a72324939e6e1be178868cf79fb2f6a9203;p=alexxy%2Fgromacs.git diff --git a/src/gromacs/fileio/confio.cpp b/src/gromacs/fileio/confio.cpp index b9844ba967..1409349227 100644 --- a/src/gromacs/fileio/confio.cpp +++ b/src/gromacs/fileio/confio.cpp @@ -49,11 +49,11 @@ #include "gromacs/fileio/filenm.h" #include "gromacs/fileio/g96io.h" #include "gromacs/fileio/gmxfio.h" +#include "gromacs/fileio/groio.h" #include "gromacs/fileio/pdbio.h" #include "gromacs/fileio/tpxio.h" #include "gromacs/fileio/trx.h" #include "gromacs/fileio/trxio.h" -#include "gromacs/legacyheaders/copyrite.h" #include "gromacs/math/vec.h" #include "gromacs/pbcutil/pbc.h" #include "gromacs/topology/atomprop.h" @@ -483,549 +483,6 @@ static void write_espresso_conf_indexed(FILE *out, const char *title, fprintf(out, "}\n"); } -static void get_coordnum_fp (FILE *in, char *title, int *natoms) -{ - char line[STRLEN+1]; - - fgets2 (title, STRLEN, in); - fgets2 (line, STRLEN, in); - if (sscanf (line, "%d", natoms) != 1) - { - gmx_fatal(FARGS, "gro file does not have the number of atoms on the second line"); - } -} - -static void get_coordnum (const char *infile, int *natoms) -{ - FILE *in; - char title[STRLEN]; - - in = gmx_fio_fopen(infile, "r"); - get_coordnum_fp(in, title, natoms); - gmx_fio_fclose (in); -} - -static gmx_bool get_w_conf(FILE *in, const char *infile, char *title, - t_symtab *symtab, t_atoms *atoms, int *ndec, - rvec x[], rvec *v, matrix box) -{ - char name[6]; - char resname[6], oldresname[6]; - char line[STRLEN+1], *ptr; - char buf[256]; - double x1, y1, z1, x2, y2, z2; - rvec xmin, xmax; - int natoms, i, m, resnr, newres, oldres, ddist, c; - gmx_bool bFirst, bVel; - char *p1, *p2, *p3; - - newres = -1; - oldres = -12345; /* Unlikely number for the first residue! */ - ddist = 0; - - /* Read the title and number of atoms */ - get_coordnum_fp(in, title, &natoms); - - if (natoms > atoms->nr) - { - gmx_fatal(FARGS, "gro file contains more atoms (%d) than expected (%d)", - natoms, atoms->nr); - } - else if (natoms < atoms->nr) - { - fprintf(stderr, "Warning: gro file contains less atoms (%d) than expected" - " (%d)\n", natoms, atoms->nr); - } - - bFirst = TRUE; - - bVel = FALSE; - - resname[0] = '\0'; - oldresname[0] = '\0'; - - /* just pray the arrays are big enough */ - for (i = 0; (i < natoms); i++) - { - if ((fgets2 (line, STRLEN, in)) == NULL) - { - gmx_fatal(FARGS, "Unexpected end of file in file %s at line %d", - infile, i+2); - } - if (strlen(line) < 39) - { - gmx_fatal(FARGS, "Invalid line in %s for atom %d:\n%s", infile, i+1, line); - } - - /* determine read precision from distance between periods - (decimal points) */ - if (bFirst) - { - bFirst = FALSE; - p1 = strchr(line, '.'); - if (p1 == NULL) - { - gmx_fatal(FARGS, "A coordinate in file %s does not contain a '.'", infile); - } - p2 = strchr(&p1[1], '.'); - if (p2 == NULL) - { - gmx_fatal(FARGS, "A coordinate in file %s does not contain a '.'", infile); - } - ddist = p2 - p1; - *ndec = ddist - 5; - - p3 = strchr(&p2[1], '.'); - if (p3 == NULL) - { - gmx_fatal(FARGS, "A coordinate in file %s does not contain a '.'", infile); - } - - if (p3 - p2 != ddist) - { - gmx_fatal(FARGS, "The spacing of the decimal points in file %s is not consistent for x, y and z", infile); - } - } - - /* residue number*/ - memcpy(name, line, 5); - name[5] = '\0'; - sscanf(name, "%d", &resnr); - sscanf(line+5, "%5s", resname); - - if (resnr != oldres || strncmp(resname, oldresname, sizeof(resname))) - { - oldres = resnr; - newres++; - if (newres >= natoms) - { - gmx_fatal(FARGS, "More residues than atoms in %s (natoms = %d)", - infile, natoms); - } - atoms->atom[i].resind = newres; - t_atoms_set_resinfo(atoms, i, symtab, resname, resnr, ' ', 0, ' '); - } - else - { - atoms->atom[i].resind = newres; - } - - /* atomname */ - std::memcpy(name, line+10, 5); - atoms->atomname[i] = put_symtab(symtab, name); - - /* Copy resname to oldresname after we are done with the sanity check above */ - std::strncpy(oldresname, resname, sizeof(oldresname)); - - /* eventueel controle atomnumber met i+1 */ - - /* coordinates (start after residue data) */ - ptr = line + 20; - /* Read fixed format */ - for (m = 0; m < DIM; m++) - { - for (c = 0; (c < ddist && ptr[0]); c++) - { - buf[c] = ptr[0]; - ptr++; - } - buf[c] = '\0'; - if (sscanf (buf, "%lf %lf", &x1, &x2) != 1) - { - gmx_fatal(FARGS, "Something is wrong in the coordinate formatting of file %s. Note that gro is fixed format (see the manual)", infile); - } - else - { - x[i][m] = x1; - } - } - - /* velocities (start after residues and coordinates) */ - if (v) - { - /* Read fixed format */ - for (m = 0; m < DIM; m++) - { - for (c = 0; (c < ddist && ptr[0]); c++) - { - buf[c] = ptr[0]; - ptr++; - } - buf[c] = '\0'; - if (sscanf (buf, "%lf", &x1) != 1) - { - v[i][m] = 0; - } - else - { - v[i][m] = x1; - bVel = TRUE; - } - } - } - } - atoms->nres = newres + 1; - - /* box */ - fgets2 (line, STRLEN, in); - if (sscanf (line, "%lf%lf%lf", &x1, &y1, &z1) != 3) - { - gmx_warning("Bad box in file %s", infile); - - /* Generate a cubic box */ - for (m = 0; (m < DIM); m++) - { - xmin[m] = xmax[m] = x[0][m]; - } - for (i = 1; (i < atoms->nr); i++) - { - for (m = 0; (m < DIM); m++) - { - xmin[m] = std::min(xmin[m], x[i][m]); - xmax[m] = std::max(xmax[m], x[i][m]); - } - } - for (i = 0; i < DIM; i++) - { - for (m = 0; m < DIM; m++) - { - box[i][m] = 0.0; - } - } - for (m = 0; (m < DIM); m++) - { - box[m][m] = (xmax[m]-xmin[m]); - } - fprintf(stderr, "Generated a cubic box %8.3f x %8.3f x %8.3f\n", - box[XX][XX], box[YY][YY], box[ZZ][ZZ]); - } - else - { - /* We found the first three values, the diagonal elements */ - box[XX][XX] = x1; - box[YY][YY] = y1; - box[ZZ][ZZ] = z1; - if (sscanf (line, "%*f%*f%*f%lf%lf%lf%lf%lf%lf", - &x1, &y1, &z1, &x2, &y2, &z2) != 6) - { - x1 = y1 = z1 = x2 = y2 = z2 = 0.0; - } - box[XX][YY] = x1; - box[XX][ZZ] = y1; - box[YY][XX] = z1; - box[YY][ZZ] = x2; - box[ZZ][XX] = y2; - box[ZZ][YY] = z2; - } - - return bVel; -} - -static void read_whole_conf(const char *infile, char *title, - t_atoms *atoms, rvec x[], rvec *v, matrix box) -{ - FILE *in; - int ndec; - t_symtab symtab; - - /* open file */ - in = gmx_fio_fopen(infile, "r"); - - open_symtab(&symtab); - get_w_conf(in, infile, title, &symtab, atoms, &ndec, x, v, box); - /* We can't free the symbols, as they are still used in atoms, so - * the only choice is to leak them. */ - free_symtab(&symtab); - - gmx_fio_fclose(in); -} - -static gmx_bool gmx_one_before_eof(FILE *fp) -{ - char data[4]; - gmx_bool beof; - - if ((beof = fread(data, 1, 1, fp)) == 1) - { - gmx_fseek(fp, -1, SEEK_CUR); - } - return !beof; -} - -gmx_bool gro_next_x_or_v(FILE *status, t_trxframe *fr) -{ - t_atoms atoms; - t_symtab symtab; - char title[STRLEN], *p; - double tt; - int ndec = 0, i; - - if (gmx_one_before_eof(status)) - { - return FALSE; - } - - open_symtab(&symtab); - atoms.nr = fr->natoms; - snew(atoms.atom, fr->natoms); - atoms.nres = fr->natoms; - snew(atoms.resinfo, fr->natoms); - snew(atoms.atomname, fr->natoms); - - fr->bV = get_w_conf(status, title, title, &symtab, &atoms, &ndec, fr->x, fr->v, fr->box); - fr->bPrec = TRUE; - fr->prec = 1; - /* prec = 10^ndec: */ - for (i = 0; i < ndec; i++) - { - fr->prec *= 10; - } - fr->title = title; - fr->bTitle = TRUE; - fr->bX = TRUE; - fr->bBox = TRUE; - - sfree(atoms.atom); - sfree(atoms.resinfo); - sfree(atoms.atomname); - done_symtab(&symtab); - - if ((p = strstr(title, "t=")) != NULL) - { - p += 2; - if (sscanf(p, "%lf", &tt) == 1) - { - fr->time = tt; - fr->bTime = TRUE; - } - else - { - fr->time = 0; - fr->bTime = FALSE; - } - } - - if (atoms.nr != fr->natoms) - { - gmx_fatal(FARGS, "Number of atoms in gro frame (%d) doesn't match the number in the previous frame (%d)", atoms.nr, fr->natoms); - } - - return TRUE; -} - -int gro_first_x_or_v(FILE *status, t_trxframe *fr) -{ - char title[STRLEN]; - - frewind(status); - fprintf(stderr, "Reading frames from gro file"); - get_coordnum_fp(status, title, &fr->natoms); - frewind(status); - fprintf(stderr, " '%s', %d atoms.\n", title, fr->natoms); - fr->bTitle = TRUE; - fr->title = title; - if (fr->natoms == 0) - { - gmx_file("No coordinates in gro file"); - } - - snew(fr->x, fr->natoms); - snew(fr->v, fr->natoms); - gro_next_x_or_v(status, fr); - - return fr->natoms; -} - -static void make_hconf_format(int pr, gmx_bool bVel, char format[]) -{ - int l, vpr; - - /* build format string for printing, - something like "%8.3f" for x and "%8.4f" for v */ - if (pr < 0) - { - pr = 0; - } - if (pr > 30) - { - pr = 30; - } - l = pr+5; - vpr = pr+1; - if (bVel) - { - sprintf(format, "%%%d.%df%%%d.%df%%%d.%df%%%d.%df%%%d.%df%%%d.%df\n", - l, pr, l, pr, l, pr, l, vpr, l, vpr, l, vpr); - } - else - { - sprintf(format, "%%%d.%df%%%d.%df%%%d.%df\n", l, pr, l, pr, l, pr); - } - -} - -static void write_hconf_box(FILE *out, int pr, matrix box) -{ - char format[100]; - int l; - - if (pr < 5) - { - pr = 5; - } - l = pr+5; - - if (box[XX][YY] || box[XX][ZZ] || box[YY][XX] || box[YY][ZZ] || - box[ZZ][XX] || box[ZZ][YY]) - { - sprintf(format, "%%%d.%df%%%d.%df%%%d.%df" - "%%%d.%df%%%d.%df%%%d.%df%%%d.%df%%%d.%df%%%d.%df\n", - l, pr, l, pr, l, pr, l, pr, l, pr, l, pr, l, pr, l, pr, l, pr); - fprintf(out, format, - box[XX][XX], box[YY][YY], box[ZZ][ZZ], - box[XX][YY], box[XX][ZZ], box[YY][XX], - box[YY][ZZ], box[ZZ][XX], box[ZZ][YY]); - } - else - { - sprintf(format, "%%%d.%df%%%d.%df%%%d.%df\n", l, pr, l, pr, l, pr); - fprintf(out, format, - box[XX][XX], box[YY][YY], box[ZZ][ZZ]); - } -} - -void write_hconf_indexed_p(FILE *out, const char *title, t_atoms *atoms, - int nx, const atom_id index[], int pr, - rvec *x, rvec *v, matrix box) -{ - char resnm[6], nm[6], format[100]; - int ai, i, resind, resnr; - - bromacs(format, 99); - fprintf (out, "%s\n", (title && title[0]) ? title : format); - fprintf (out, "%5d\n", nx); - - make_hconf_format(pr, v != NULL, format); - - for (i = 0; (i < nx); i++) - { - ai = index[i]; - - resind = atoms->atom[ai].resind; - std::strncpy(resnm, " ??? ", sizeof(resnm)-1); - if (resind < atoms->nres) - { - std::strncpy(resnm, *atoms->resinfo[resind].name, sizeof(resnm)-1); - resnr = atoms->resinfo[resind].nr; - } - else - { - std::strncpy(resnm, " ??? ", sizeof(resnm)-1); - resnr = resind + 1; - } - - if (atoms->atom) - { - std::strncpy(nm, *atoms->atomname[ai], sizeof(nm)-1); - } - else - { - std::strncpy(nm, " ??? ", sizeof(nm)-1); - } - - fprintf(out, "%5d%-5.5s%5.5s%5d", resnr%100000, resnm, nm, (ai+1)%100000); - /* next fprintf uses built format string */ - if (v) - { - fprintf(out, format, - x[ai][XX], x[ai][YY], x[ai][ZZ], v[ai][XX], v[ai][YY], v[ai][ZZ]); - } - else - { - fprintf(out, format, - x[ai][XX], x[ai][YY], x[ai][ZZ]); - } - } - - write_hconf_box(out, pr, box); - - fflush(out); -} - -static void write_hconf_mtop(FILE *out, const char *title, gmx_mtop_t *mtop, - int pr, - rvec *x, rvec *v, matrix box) -{ - char format[100]; - int i, resnr; - gmx_mtop_atomloop_all_t aloop; - t_atom *atom; - char *atomname, *resname; - - bromacs(format, 99); - fprintf (out, "%s\n", (title && title[0]) ? title : format); - fprintf (out, "%5d\n", mtop->natoms); - - make_hconf_format(pr, v != NULL, format); - - aloop = gmx_mtop_atomloop_all_init(mtop); - while (gmx_mtop_atomloop_all_next(aloop, &i, &atom)) - { - gmx_mtop_atomloop_all_names(aloop, &atomname, &resnr, &resname); - - fprintf(out, "%5d%-5.5s%5.5s%5d", - resnr%100000, resname, atomname, (i+1)%100000); - /* next fprintf uses built format string */ - if (v) - { - fprintf(out, format, - x[i][XX], x[i][YY], x[i][ZZ], v[i][XX], v[i][YY], v[i][ZZ]); - } - else - { - fprintf(out, format, - x[i][XX], x[i][YY], x[i][ZZ]); - } - } - - write_hconf_box(out, pr, box); - - fflush(out); -} - -void write_hconf_p(FILE *out, const char *title, t_atoms *atoms, int pr, - rvec *x, rvec *v, matrix box) -{ - atom_id *aa; - int i; - - snew(aa, atoms->nr); - for (i = 0; (i < atoms->nr); i++) - { - aa[i] = i; - } - write_hconf_indexed_p(out, title, atoms, atoms->nr, aa, pr, x, v, box); - sfree(aa); -} - -void write_conf_p(const char *outfile, const char *title, - t_atoms *atoms, int pr, - rvec *x, rvec *v, matrix box) -{ - FILE *out; - - out = gmx_fio_fopen(outfile, "w"); - write_hconf_p(out, title, atoms, pr, x, v, box); - - gmx_fio_fclose (out); -} - -static void write_conf(const char *outfile, const char *title, t_atoms *atoms, - rvec *x, rvec *v, matrix box) -{ - write_conf_p(outfile, title, atoms, 3, x, v, box); -} - void write_sto_conf_indexed(const char *outfile, const char *title, t_atoms *atoms, rvec x[], rvec *v, int ePBC, matrix box, @@ -1095,7 +552,7 @@ void write_sto_conf(const char *outfile, const char *title, t_atoms *atoms, switch (ftp) { case efGRO: - write_conf(outfile, title, atoms, x, v, box); + write_conf_p(outfile, title, atoms, 3, x, v, box); break; case efG96: clear_trxframe(&fr, TRUE);