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47 #include "gromacs/fileio/gmxfio.h"
48 #include "gromacs/topology/atoms.h"
49 #include "gromacs/topology/mtop_util.h"
50 #include "gromacs/topology/symtab.h"
51 #include "gromacs/topology/topology.h"
52 #include "gromacs/trajectory/trajectoryframe.h"
53 #include "gromacs/utility/coolstuff.h"
54 #include "gromacs/utility/cstringutil.h"
55 #include "gromacs/utility/fatalerror.h"
56 #include "gromacs/utility/futil.h"
57 #include "gromacs/utility/smalloc.h"
59 static void get_coordnum_fp(FILE *in
, char *title
, int *natoms
)
63 fgets2(title
, STRLEN
, in
);
64 fgets2(line
, STRLEN
, in
);
65 if (sscanf(line
, "%d", natoms
) != 1)
67 gmx_fatal(FARGS
, "gro file does not have the number of atoms on the second line");
71 void get_coordnum(const char *infile
, int *natoms
)
76 in
= gmx_fio_fopen(infile
, "r");
77 get_coordnum_fp(in
, title
, natoms
);
81 /* Note that the .gro reading routine still support variable precision
82 * for backward compatibility with old .gro files.
83 * We have removed writing of variable precision to avoid compatibility
84 * issues with other software packages.
86 static gmx_bool
get_w_conf(FILE *in
, const char *infile
, char *title
,
87 t_symtab
*symtab
, t_atoms
*atoms
, int *ndec
,
88 rvec x
[], rvec
*v
, matrix box
)
91 char resname
[6], oldresname
[6];
92 char line
[STRLEN
+1], *ptr
;
94 double x1
, y1
, z1
, x2
, y2
, z2
;
96 int natoms
, i
, m
, resnr
, newres
, oldres
, ddist
, c
;
97 gmx_bool bFirst
, bVel
, oldResFirst
;
105 /* Read the title and number of atoms */
106 get_coordnum_fp(in
, title
, &natoms
);
108 if (natoms
> atoms
->nr
)
110 gmx_fatal(FARGS
, "gro file contains more atoms (%d) than expected (%d)",
113 else if (natoms
< atoms
->nr
)
115 fprintf(stderr
, "Warning: gro file contains less atoms (%d) than expected"
116 " (%d)\n", natoms
, atoms
->nr
);
119 atoms
->haveMass
= FALSE
;
120 atoms
->haveCharge
= FALSE
;
121 atoms
->haveType
= FALSE
;
122 atoms
->haveBState
= FALSE
;
123 atoms
->havePdbInfo
= FALSE
;
130 oldresname
[0] = '\0';
132 /* just pray the arrays are big enough */
133 for (i
= 0; (i
< natoms
); i
++)
135 if ((fgets2(line
, STRLEN
, in
)) == nullptr)
137 gmx_fatal(FARGS
, "Unexpected end of file in file %s at line %d",
140 if (strlen(line
) < 39)
142 gmx_fatal(FARGS
, "Invalid line in %s for atom %d:\n%s", infile
, i
+1, line
);
145 /* determine read precision from distance between periods
150 p1
= strchr(line
, '.');
153 gmx_fatal(FARGS
, "A coordinate in file %s does not contain a '.'", infile
);
155 p2
= strchr(&p1
[1], '.');
158 gmx_fatal(FARGS
, "A coordinate in file %s does not contain a '.'", infile
);
163 p3
= strchr(&p2
[1], '.');
166 gmx_fatal(FARGS
, "A coordinate in file %s does not contain a '.'", infile
);
169 if (p3
- p2
!= ddist
)
171 gmx_fatal(FARGS
, "The spacing of the decimal points in file %s is not consistent for x, y and z", infile
);
176 memcpy(name
, line
, 5);
178 sscanf(name
, "%d", &resnr
);
179 sscanf(line
+5, "%5s", resname
);
181 if (!oldResFirst
|| oldres
!= resnr
|| strncmp(resname
, oldresname
, sizeof(resname
)))
186 if (newres
>= natoms
)
188 gmx_fatal(FARGS
, "More residues than atoms in %s (natoms = %d)",
191 atoms
->atom
[i
].resind
= newres
;
192 t_atoms_set_resinfo(atoms
, i
, symtab
, resname
, resnr
, ' ', 0, ' ');
196 atoms
->atom
[i
].resind
= newres
;
200 std::memcpy(name
, line
+10, 5);
201 atoms
->atomname
[i
] = put_symtab(symtab
, name
);
203 /* Copy resname to oldresname after we are done with the sanity check above */
204 std::strncpy(oldresname
, resname
, sizeof(oldresname
));
206 /* eventueel controle atomnumber met i+1 */
208 /* coordinates (start after residue data) */
210 /* Read fixed format */
211 for (m
= 0; m
< DIM
; m
++)
213 for (c
= 0; (c
< ddist
&& ptr
[0]); c
++)
219 if (sscanf(buf
, "%lf %lf", &x1
, &x2
) != 1)
221 gmx_fatal(FARGS
, "Something is wrong in the coordinate formatting of file %s. Note that gro is fixed format (see the manual)", infile
);
229 /* velocities (start after residues and coordinates) */
232 /* Read fixed format */
233 for (m
= 0; m
< DIM
; m
++)
235 for (c
= 0; (c
< ddist
&& ptr
[0]); c
++)
241 if (sscanf(buf
, "%lf", &x1
) != 1)
253 atoms
->nres
= newres
+ 1;
256 fgets2(line
, STRLEN
, in
);
257 if (sscanf(line
, "%lf%lf%lf", &x1
, &y1
, &z1
) != 3)
259 gmx_warning("Bad box in file %s", infile
);
261 /* Generate a cubic box */
262 for (m
= 0; (m
< DIM
); m
++)
264 xmin
[m
] = xmax
[m
] = x
[0][m
];
266 for (i
= 1; (i
< atoms
->nr
); i
++)
268 for (m
= 0; (m
< DIM
); m
++)
270 xmin
[m
] = std::min(xmin
[m
], x
[i
][m
]);
271 xmax
[m
] = std::max(xmax
[m
], x
[i
][m
]);
274 for (i
= 0; i
< DIM
; i
++)
276 for (m
= 0; m
< DIM
; m
++)
281 for (m
= 0; (m
< DIM
); m
++)
283 box
[m
][m
] = (xmax
[m
]-xmin
[m
]);
285 fprintf(stderr
, "Generated a cubic box %8.3f x %8.3f x %8.3f\n",
286 box
[XX
][XX
], box
[YY
][YY
], box
[ZZ
][ZZ
]);
290 /* We found the first three values, the diagonal elements */
294 if (sscanf (line
, "%*f%*f%*f%lf%lf%lf%lf%lf%lf",
295 &x1
, &y1
, &z1
, &x2
, &y2
, &z2
) != 6)
297 x1
= y1
= z1
= x2
= y2
= z2
= 0.0;
310 void gmx_gro_read_conf(const char *infile
,
311 t_symtab
*symtab
, char **name
, t_atoms
*atoms
,
312 rvec x
[], rvec
*v
, matrix box
)
314 FILE *in
= gmx_fio_fopen(infile
, "r");
317 get_w_conf(in
, infile
, title
, symtab
, atoms
, &ndec
, x
, v
, box
);
320 *name
= gmx_strdup(title
);
325 static gmx_bool
gmx_one_before_eof(FILE *fp
)
330 if ((beof
= fread(data
, 1, 1, fp
)) == 1)
332 gmx_fseek(fp
, -1, SEEK_CUR
);
337 gmx_bool
gro_next_x_or_v(FILE *status
, t_trxframe
*fr
)
341 char title
[STRLEN
], *p
;
345 if (gmx_one_before_eof(status
))
350 open_symtab(&symtab
);
351 atoms
.nr
= fr
->natoms
;
352 snew(atoms
.atom
, fr
->natoms
);
353 atoms
.nres
= fr
->natoms
;
354 snew(atoms
.resinfo
, fr
->natoms
);
355 snew(atoms
.atomname
, fr
->natoms
);
357 fr
->bV
= get_w_conf(status
, title
, title
, &symtab
, &atoms
, &ndec
, fr
->x
, fr
->v
, fr
->box
);
360 /* prec = 10^ndec: */
361 for (i
= 0; i
< ndec
; i
++)
369 sfree(atoms
.resinfo
);
370 sfree(atoms
.atomname
);
371 done_symtab(&symtab
);
373 if ((p
= strstr(title
, "t=")) != nullptr)
376 if (sscanf(p
, "%lf", &tt
) == 1)
388 if (atoms
.nr
!= fr
->natoms
)
390 gmx_fatal(FARGS
, "Number of atoms in gro frame (%d) doesn't match the number in the previous frame (%d)", atoms
.nr
, fr
->natoms
);
396 int gro_first_x_or_v(FILE *status
, t_trxframe
*fr
)
401 fprintf(stderr
, "Reading frames from gro file");
402 get_coordnum_fp(status
, title
, &fr
->natoms
);
404 fprintf(stderr
, " '%s', %d atoms.\n", title
, fr
->natoms
);
407 gmx_file("No coordinates in gro file");
410 snew(fr
->x
, fr
->natoms
);
411 snew(fr
->v
, fr
->natoms
);
412 gro_next_x_or_v(status
, fr
);
417 static const char *get_hconf_format(bool haveVelocities
)
421 return "%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f\n";
425 return "%8.3f%8.3f%8.3f\n";
430 static void write_hconf_box(FILE *out
, const matrix box
)
432 if (box
[XX
][YY
] || box
[XX
][ZZ
] || box
[YY
][XX
] || box
[YY
][ZZ
] ||
433 box
[ZZ
][XX
] || box
[ZZ
][YY
])
435 fprintf(out
, "%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f\n",
436 box
[XX
][XX
], box
[YY
][YY
], box
[ZZ
][ZZ
],
437 box
[XX
][YY
], box
[XX
][ZZ
], box
[YY
][XX
],
438 box
[YY
][ZZ
], box
[ZZ
][XX
], box
[ZZ
][YY
]);
442 fprintf(out
, "%10.5f%10.5f%10.5f\n",
443 box
[XX
][XX
], box
[YY
][YY
], box
[ZZ
][ZZ
]);
447 void write_hconf_indexed_p(FILE *out
, const char *title
, const t_atoms
*atoms
,
448 int nx
, const int index
[],
449 const rvec
*x
, const rvec
*v
, const matrix box
)
451 char resnm
[6], nm
[6];
452 int ai
, i
, resind
, resnr
;
454 fprintf(out
, "%s\n", (title
&& title
[0]) ? title
: gmx::bromacs().c_str());
455 fprintf(out
, "%5d\n", nx
);
457 const char *format
= get_hconf_format(v
!= nullptr);
459 for (i
= 0; (i
< nx
); i
++)
463 resind
= atoms
->atom
[ai
].resind
;
464 std::strncpy(resnm
, " ??? ", sizeof(resnm
)-1);
465 if (resind
< atoms
->nres
)
467 std::strncpy(resnm
, *atoms
->resinfo
[resind
].name
, sizeof(resnm
)-1);
468 resnr
= atoms
->resinfo
[resind
].nr
;
472 std::strncpy(resnm
, " ??? ", sizeof(resnm
)-1);
478 std::strncpy(nm
, *atoms
->atomname
[ai
], sizeof(nm
)-1);
482 std::strncpy(nm
, " ??? ", sizeof(nm
)-1);
485 fprintf(out
, "%5d%-5.5s%5.5s%5d", resnr
%100000, resnm
, nm
, (ai
+1)%100000);
486 /* next fprintf uses built format string */
490 x
[ai
][XX
], x
[ai
][YY
], x
[ai
][ZZ
], v
[ai
][XX
], v
[ai
][YY
], v
[ai
][ZZ
]);
495 x
[ai
][XX
], x
[ai
][YY
], x
[ai
][ZZ
]);
499 write_hconf_box(out
, box
);
504 void write_hconf_mtop(FILE *out
, const char *title
, gmx_mtop_t
*mtop
,
505 const rvec
*x
, const rvec
*v
, const matrix box
)
508 gmx_mtop_atomloop_all_t aloop
;
510 char *atomname
, *resname
;
512 fprintf(out
, "%s\n", (title
&& title
[0]) ? title
: gmx::bromacs().c_str());
513 fprintf(out
, "%5d\n", mtop
->natoms
);
515 const char *format
= get_hconf_format(v
!= nullptr);
517 aloop
= gmx_mtop_atomloop_all_init(mtop
);
518 while (gmx_mtop_atomloop_all_next(aloop
, &i
, &atom
))
520 gmx_mtop_atomloop_all_names(aloop
, &atomname
, &resnr
, &resname
);
522 fprintf(out
, "%5d%-5.5s%5.5s%5d",
523 resnr
%100000, resname
, atomname
, (i
+1)%100000);
524 /* next fprintf uses built format string */
528 x
[i
][XX
], x
[i
][YY
], x
[i
][ZZ
], v
[i
][XX
], v
[i
][YY
], v
[i
][ZZ
]);
533 x
[i
][XX
], x
[i
][YY
], x
[i
][ZZ
]);
537 write_hconf_box(out
, box
);
542 void write_hconf_p(FILE *out
, const char *title
, const t_atoms
*atoms
,
543 const rvec
*x
, const rvec
*v
, const matrix box
)
549 for (i
= 0; (i
< atoms
->nr
); i
++)
553 write_hconf_indexed_p(out
, title
, atoms
, atoms
->nr
, aa
, x
, v
, box
);
557 void write_conf_p(const char *outfile
, const char *title
,
558 const t_atoms
*atoms
,
559 const rvec
*x
, const rvec
*v
, const matrix box
)
563 out
= gmx_fio_fopen(outfile
, "w");
564 write_hconf_p(out
, title
, atoms
, x
, v
, box
);