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46 #include "gromacs/commandline/pargs.h"
47 #include "gromacs/fileio/confio.h"
48 #include "gromacs/fileio/enxio.h"
49 #include "gromacs/fileio/gmxfio.h"
50 #include "gromacs/fileio/tpxio.h"
51 #include "gromacs/fileio/trxio.h"
52 #include "gromacs/fileio/xtcio.h"
53 #include "gromacs/math/functions.h"
54 #include "gromacs/math/units.h"
55 #include "gromacs/math/vec.h"
56 #include "gromacs/mdrun/mdmodules.h"
57 #include "gromacs/mdtypes/inputrec.h"
58 #include "gromacs/mdtypes/md_enums.h"
59 #include "gromacs/mdtypes/state.h"
60 #include "gromacs/pbcutil/pbc.h"
61 #include "gromacs/topology/atomprop.h"
62 #include "gromacs/topology/block.h"
63 #include "gromacs/topology/ifunc.h"
64 #include "gromacs/topology/index.h"
65 #include "gromacs/topology/mtop_util.h"
66 #include "gromacs/topology/topology.h"
67 #include "gromacs/trajectory/energyframe.h"
68 #include "gromacs/trajectory/trajectoryframe.h"
69 #include "gromacs/utility/arraysize.h"
70 #include "gromacs/utility/fatalerror.h"
71 #include "gromacs/utility/futil.h"
72 #include "gromacs/utility/smalloc.h"
96 static void comp_tpx(const char* fn1
, const char* fn2
, gmx_bool bRMSD
, real ftol
, real abstol
)
106 for (i
= 0; i
< (fn2
? 2 : 1); i
++)
108 ir
[i
] = new t_inputrec();
109 read_tpx_state(ff
[i
], ir
[i
], &state
[i
], &(mtop
[i
]));
110 gmx::MDModules().adjustInputrecBasedOnModules(ir
[i
]);
114 cmp_inputrec(stdout
, ir
[0], ir
[1], ftol
, abstol
);
115 compareMtop(stdout
, mtop
[0], mtop
[1], ftol
, abstol
);
116 comp_state(&state
[0], &state
[1], bRMSD
, ftol
, abstol
);
120 if (ir
[0]->efep
== efepNO
)
122 fprintf(stdout
, "inputrec->efep = %s\n", efep_names
[ir
[0]->efep
]);
128 comp_pull_AB(stdout
, ir
[0]->pull
, ftol
, abstol
);
130 compareMtopAB(stdout
, mtop
[0], ftol
, abstol
);
135 static void comp_trx(const gmx_output_env_t
* oenv
, const char* fn1
, const char* fn2
, gmx_bool bRMSD
, real ftol
, real abstol
)
140 t_trxstatus
* status
[2];
145 fprintf(stderr
, "Comparing trajectory files %s and %s\n", fn1
, fn2
);
146 for (i
= 0; i
< 2; i
++)
148 b
[i
] = read_first_frame(oenv
, &status
[i
], fn
[i
], &fr
[i
], TRX_READ_X
| TRX_READ_V
| TRX_READ_F
);
155 comp_frame(stdout
, &(fr
[0]), &(fr
[1]), bRMSD
, ftol
, abstol
);
157 for (i
= 0; i
< 2; i
++)
159 b
[i
] = read_next_frame(oenv
, status
[i
], &fr
[i
]);
161 } while (b
[0] && b
[1]);
163 for (i
= 0; i
< 2; i
++)
165 if (b
[i
] && !b
[1 - i
])
167 fprintf(stdout
, "\nEnd of file on %s but not on %s\n", fn
[1 - i
], fn
[i
]);
169 close_trx(status
[i
]);
174 fprintf(stdout
, "\nBoth files read correctly\n");
178 static void chk_coords(int frame
, int natoms
, rvec
* x
, matrix box
, real fac
, real tol
)
184 for (i
= 0; (i
< natoms
); i
++)
186 for (j
= 0; (j
< DIM
); j
++)
188 if ((vol
> 0) && (fabs(x
[i
][j
]) > fac
* box
[j
][j
]))
190 printf("Warning at frame %d: coordinates for atom %d are large (%g)\n", frame
, i
, x
[i
][j
]);
193 if ((fabs(x
[i
][XX
]) < tol
) && (fabs(x
[i
][YY
]) < tol
) && (fabs(x
[i
][ZZ
]) < tol
))
200 printf("Warning at frame %d: there are %d particles with all coordinates zero\n", frame
, nNul
);
204 static void chk_vels(int frame
, int natoms
, rvec
* v
)
208 for (i
= 0; (i
< natoms
); i
++)
210 for (j
= 0; (j
< DIM
); j
++)
212 if (fabs(v
[i
][j
]) > 500)
214 printf("Warning at frame %d. Velocities for atom %d are large (%g)\n", frame
, i
, v
[i
][j
]);
220 static void chk_forces(int frame
, int natoms
, rvec
* f
)
224 for (i
= 0; (i
< natoms
); i
++)
226 for (j
= 0; (j
< DIM
); j
++)
228 if (fabs(f
[i
][j
]) > 10000)
230 printf("Warning at frame %d. Forces for atom %d are large (%g)\n", frame
, i
, f
[i
][j
]);
236 static void chk_bonds(t_idef
* idef
, int ePBC
, rvec
* x
, matrix box
, real tol
)
238 int ftype
, k
, ai
, aj
, type
;
239 real b0
, blen
, deviation
;
243 set_pbc(&pbc
, ePBC
, box
);
244 for (ftype
= 0; (ftype
< F_NRE
); ftype
++)
246 if ((interaction_function
[ftype
].flags
& IF_CHEMBOND
) == IF_CHEMBOND
)
248 for (k
= 0; (k
< idef
->il
[ftype
].nr
);)
250 type
= idef
->il
[ftype
].iatoms
[k
++];
251 ai
= idef
->il
[ftype
].iatoms
[k
++];
252 aj
= idef
->il
[ftype
].iatoms
[k
++];
256 case F_BONDS
: b0
= idef
->iparams
[type
].harmonic
.rA
; break;
257 case F_G96BONDS
: b0
= std::sqrt(idef
->iparams
[type
].harmonic
.rA
); break;
258 case F_MORSE
: b0
= idef
->iparams
[type
].morse
.b0A
; break;
259 case F_CUBICBONDS
: b0
= idef
->iparams
[type
].cubic
.b0
; break;
260 case F_CONSTR
: b0
= idef
->iparams
[type
].constr
.dA
; break;
265 pbc_dx(&pbc
, x
[ai
], x
[aj
], dx
);
267 deviation
= gmx::square(blen
- b0
);
268 if (std::sqrt(deviation
/ gmx::square(b0
)) > tol
)
270 fprintf(stderr
, "Distance between atoms %d and %d is %.3f, should be %.3f\n",
271 ai
+ 1, aj
+ 1, blen
, b0
);
279 static void chk_trj(const gmx_output_env_t
* oenv
, const char* fn
, const char* tpr
, real tol
)
283 t_fr_time first
, last
;
284 int j
= -1, new_natoms
, natoms
;
286 gmx_bool bShowTimestep
= TRUE
, newline
= FALSE
;
295 read_tpx_state(tpr
, &ir
, &state
, &mtop
);
296 gmx_mtop_generate_local_top(mtop
, &top
, ir
.efep
!= efepNO
);
301 printf("Checking file %s\n", fn
);
331 read_first_frame(oenv
, &status
, fn
, &fr
, TRX_READ_X
| TRX_READ_V
| TRX_READ_F
);
337 fprintf(stderr
, "\n# Atoms %d\n", fr
.natoms
);
340 fprintf(stderr
, "Precision %g (nm)\n", 1 / fr
.prec
);
344 if ((natoms
> 0) && (new_natoms
!= natoms
))
346 fprintf(stderr
, "\nNumber of atoms at t=%g don't match (%d, %d)\n", old_t1
, natoms
, new_natoms
);
351 if (std::fabs((fr
.time
- old_t1
) - (old_t1
- old_t2
))
352 > 0.1 * (std::fabs(fr
.time
- old_t1
) + std::fabs(old_t1
- old_t2
)))
354 bShowTimestep
= FALSE
;
355 fprintf(stderr
, "%sTimesteps at t=%g don't match (%g, %g)\n", newline
? "\n" : "",
356 old_t1
, old_t1
- old_t2
, fr
.time
- old_t1
);
362 chk_bonds(&top
.idef
, ir
.ePBC
, fr
.x
, fr
.box
, tol
);
366 chk_coords(j
, natoms
, fr
.x
, fr
.box
, 1e5
, tol
);
370 chk_vels(j
, natoms
, fr
.v
);
374 chk_forces(j
, natoms
, fr
.f
);
380 new_natoms
= fr
.natoms
;
381 #define INC(s, n, f, l, item) \
386 first.item = fr.time; \
388 last.item = fr.time; \
391 INC(fr
, count
, first
, last
, bStep
)
392 INC(fr
, count
, first
, last
, bTime
)
393 INC(fr
, count
, first
, last
, bLambda
)
394 INC(fr
, count
, first
, last
, bX
)
395 INC(fr
, count
, first
, last
, bV
)
396 INC(fr
, count
, first
, last
, bF
)
397 INC(fr
, count
, first
, last
, bBox
)
399 } while (read_next_frame(oenv
, status
, &fr
));
401 fprintf(stderr
, "\n");
405 fprintf(stderr
, "\nItem #frames");
408 fprintf(stderr
, " Timestep (ps)");
410 fprintf(stderr
, "\n");
411 #define PRINTITEM(label, item) \
412 fprintf(stderr, "%-10s %6d", label, count.item); \
413 if ((bShowTimestep) && (count.item > 1)) \
415 fprintf(stderr, " %g\n", (last.item - first.item) / (count.item - 1)); \
418 fprintf(stderr, "\n")
419 PRINTITEM("Step", bStep
);
420 PRINTITEM("Time", bTime
);
421 PRINTITEM("Lambda", bLambda
);
422 PRINTITEM("Coords", bX
);
423 PRINTITEM("Velocities", bV
);
424 PRINTITEM("Forces", bF
);
425 PRINTITEM("Box", bBox
);
428 static void chk_tps(const char* fn
, real vdw_fac
, real bon_lo
, real bon_hi
)
438 gmx_bool bV
, bX
, bB
, bFirst
, bOut
;
439 real r2
, ekin
, temp1
, temp2
, dist2
, vdwfac2
, bonlo2
, bonhi2
;
442 fprintf(stderr
, "Checking coordinate file %s\n", fn
);
443 read_tps_conf(fn
, &top
, &ePBC
, &x
, &v
, box
, TRUE
);
446 fprintf(stderr
, "%d atoms in file\n", atoms
->nr
);
448 /* check coordinates and box */
451 for (i
= 0; (i
< natom
) && !(bV
&& bX
); i
++)
453 for (j
= 0; (j
< DIM
) && !(bV
&& bX
); j
++)
455 bV
= bV
|| (v
[i
][j
] != 0);
456 bX
= bX
|| (x
[i
][j
] != 0);
460 for (i
= 0; (i
< DIM
) && !bB
; i
++)
462 for (j
= 0; (j
< DIM
) && !bB
; j
++)
464 bB
= bB
|| (box
[i
][j
] != 0);
468 fprintf(stderr
, "coordinates %s\n", bX
? "found" : "absent");
469 fprintf(stderr
, "box %s\n", bB
? "found" : "absent");
470 fprintf(stderr
, "velocities %s\n", bV
? "found" : "absent");
471 fprintf(stderr
, "\n");
473 /* check velocities */
477 for (i
= 0; (i
< natom
); i
++)
479 for (j
= 0; (j
< DIM
); j
++)
481 ekin
+= 0.5 * atoms
->atom
[i
].m
* v
[i
][j
] * v
[i
][j
];
484 temp1
= (2.0 * ekin
) / (natom
* DIM
* BOLTZ
);
485 temp2
= (2.0 * ekin
) / (natom
* (DIM
- 1) * BOLTZ
);
486 fprintf(stderr
, "Kinetic energy: %g (kJ/mol)\n", ekin
);
488 "Assuming the number of degrees of freedom to be "
489 "Natoms * %d or Natoms * %d,\n"
490 "the velocities correspond to a temperature of the system\n"
491 "of %g K or %g K respectively.\n\n",
492 DIM
, DIM
- 1, temp1
, temp2
);
495 /* check coordinates */
498 vdwfac2
= gmx::square(vdw_fac
);
499 bonlo2
= gmx::square(bon_lo
);
500 bonhi2
= gmx::square(bon_hi
);
503 "Checking for atoms closer than %g and not between %g and %g,\n"
504 "relative to sum of Van der Waals distance:\n",
505 vdw_fac
, bon_lo
, bon_hi
);
506 snew(atom_vdw
, natom
);
508 for (i
= 0; (i
< natom
); i
++)
510 aps
.setAtomProperty(epropVDW
, *(atoms
->resinfo
[atoms
->atom
[i
].resind
].name
),
511 *(atoms
->atomname
[i
]), &(atom_vdw
[i
]));
514 fprintf(debug
, "%5d %4s %4s %7g\n", i
+ 1, *(atoms
->resinfo
[atoms
->atom
[i
].resind
].name
),
515 *(atoms
->atomname
[i
]), atom_vdw
[i
]);
520 set_pbc(&pbc
, ePBC
, box
);
524 for (i
= 0; (i
< natom
); i
++)
526 if (((i
+ 1) % 10) == 0)
528 fprintf(stderr
, "\r%5d", i
+ 1);
531 for (j
= i
+ 1; (j
< natom
); j
++)
535 pbc_dx(&pbc
, x
[i
], x
[j
], dx
);
539 rvec_sub(x
[i
], x
[j
], dx
);
542 dist2
= gmx::square(atom_vdw
[i
] + atom_vdw
[j
]);
543 if ((r2
<= dist2
* bonlo2
) || ((r2
>= dist2
* bonhi2
) && (r2
<= dist2
* vdwfac2
)))
547 fprintf(stderr
, "\r%5s %4s %8s %5s %5s %4s %8s %5s %6s\n", "atom#", "name",
548 "residue", "r_vdw", "atom#", "name", "residue", "r_vdw", "distance");
551 fprintf(stderr
, "\r%5d %4s %4s%4d %-5.3g %5d %4s %4s%4d %-5.3g %-6.4g\n", i
+ 1,
552 *(atoms
->atomname
[i
]), *(atoms
->resinfo
[atoms
->atom
[i
].resind
].name
),
553 atoms
->resinfo
[atoms
->atom
[i
].resind
].nr
, atom_vdw
[i
], j
+ 1,
554 *(atoms
->atomname
[j
]), *(atoms
->resinfo
[atoms
->atom
[j
].resind
].name
),
555 atoms
->resinfo
[atoms
->atom
[j
].resind
].nr
, atom_vdw
[j
], std::sqrt(r2
));
561 fprintf(stderr
, "\rno close atoms found\n");
563 fprintf(stderr
, "\r \n");
570 for (i
= 0; (i
< natom
) && (k
< 10); i
++)
573 for (j
= 0; (j
< DIM
) && !bOut
; j
++)
575 bOut
= bOut
|| (x
[i
][j
] < 0) || (x
[i
][j
] > box
[j
][j
]);
582 fprintf(stderr
, "Atoms outside box ( ");
583 for (j
= 0; (j
< DIM
); j
++)
585 fprintf(stderr
, "%g ", box
[j
][j
]);
589 "(These may occur often and are normally not a problem)\n"
590 "%5s %4s %8s %5s %s\n",
591 "atom#", "name", "residue", "r_vdw", "coordinate");
594 fprintf(stderr
, "%5d %4s %4s%4d %-5.3g", i
, *(atoms
->atomname
[i
]),
595 *(atoms
->resinfo
[atoms
->atom
[i
].resind
].name
),
596 atoms
->resinfo
[atoms
->atom
[i
].resind
].nr
, atom_vdw
[i
]);
597 for (j
= 0; (j
< DIM
); j
++)
599 fprintf(stderr
, " %6.3g", x
[i
][j
]);
601 fprintf(stderr
, "\n");
606 fprintf(stderr
, "(maybe more)\n");
610 fprintf(stderr
, "no atoms found outside box\n");
612 fprintf(stderr
, "\n");
617 static void chk_ndx(const char* fn
)
623 grps
= init_index(fn
, &grpname
);
626 pr_blocka(debug
, 0, fn
, grps
, FALSE
);
630 printf("Contents of index file %s\n", fn
);
631 printf("--------------------------------------------------\n");
632 printf("Nr. Group #Entries First Last\n");
633 for (i
= 0; (i
< grps
->nr
); i
++)
635 printf("%4d %-20s%8d%8d%8d\n", i
, grpname
[i
], grps
->index
[i
+ 1] - grps
->index
[i
],
636 grps
->a
[grps
->index
[i
]] + 1, grps
->a
[grps
->index
[i
+ 1] - 1] + 1);
639 for (i
= 0; (i
< grps
->nr
); i
++)
647 static void chk_enx(const char* fn
)
651 gmx_enxnm_t
* enm
= nullptr;
655 real t0
, old_t1
, old_t2
;
658 fprintf(stderr
, "Checking energy file %s\n\n", fn
);
660 in
= open_enx(fn
, "r");
661 do_enxnms(in
, &nre
, &enm
);
662 fprintf(stderr
, "%d groups in energy file", nre
);
671 while (do_enx(in
, fr
))
675 if (fabs((fr
->t
- old_t1
) - (old_t1
- old_t2
))
676 > 0.1 * (fabs(fr
->t
- old_t1
) + std::fabs(old_t1
- old_t2
)))
679 fprintf(stderr
, "\nTimesteps at t=%g don't match (%g, %g)\n", old_t1
,
680 old_t1
- old_t2
, fr
->t
- old_t1
);
692 fprintf(stderr
, "\rframe: %6s (index %6d), t: %10.3f\n", gmx_step_str(fr
->step
, buf
),
697 fprintf(stderr
, "\n\nFound %d frames", fnr
);
698 if (bShowTStep
&& fnr
> 1)
700 fprintf(stderr
, " with a timestep of %g ps", (old_t1
- t0
) / (fnr
- 1));
702 fprintf(stderr
, ".\n");
705 free_enxnms(nre
, enm
);
709 int gmx_check(int argc
, char* argv
[])
711 const char* desc
[] = {
712 "[THISMODULE] reads a trajectory ([REF].tng[ref], [REF].trr[ref] or ",
713 "[REF].xtc[ref]), an energy file ([REF].edr[ref])",
714 "or an index file ([REF].ndx[ref])",
715 "and prints out useful information about them.[PAR]",
716 "Option [TT]-c[tt] checks for presence of coordinates,",
717 "velocities and box in the file, for close contacts (smaller than",
718 "[TT]-vdwfac[tt] and not bonded, i.e. not between [TT]-bonlo[tt]",
719 "and [TT]-bonhi[tt], all relative to the sum of both Van der Waals",
720 "radii) and atoms outside the box (these may occur often and are",
721 "no problem). If velocities are present, an estimated temperature",
722 "will be calculated from them.[PAR]",
723 "If an index file, is given its contents will be summarized.[PAR]",
724 "If both a trajectory and a [REF].tpr[ref] file are given (with [TT]-s1[tt])",
725 "the program will check whether the bond lengths defined in the tpr",
726 "file are indeed correct in the trajectory. If not you may have",
727 "non-matching files due to e.g. deshuffling or due to problems with",
728 "virtual sites. With these flags, [TT]gmx check[tt] provides a quick check for ",
729 "such problems.[PAR]",
730 "The program can compare two run input ([REF].tpr[ref])",
732 "when both [TT]-s1[tt] and [TT]-s2[tt] are supplied. When comparing",
733 "run input files this way, the default relative tolerance is reduced",
734 "to 0.000001 and the absolute tolerance set to zero to find any differences",
735 "not due to minor compiler optimization differences, although you can",
736 "of course still set any other tolerances through the options.",
737 "Similarly a pair of trajectory files can be compared (using the [TT]-f2[tt]",
738 "option), or a pair of energy files (using the [TT]-e2[tt] option).[PAR]",
739 "For free energy simulations the A and B state topology from one",
740 "run input file can be compared with options [TT]-s1[tt] and [TT]-ab[tt].[PAR]"
742 t_filenm fnm
[] = { { efTRX
, "-f", nullptr, ffOPTRD
}, { efTRX
, "-f2", nullptr, ffOPTRD
},
743 { efTPR
, "-s1", "top1", ffOPTRD
}, { efTPR
, "-s2", "top2", ffOPTRD
},
744 { efTPS
, "-c", nullptr, ffOPTRD
}, { efEDR
, "-e", nullptr, ffOPTRD
},
745 { efEDR
, "-e2", "ener2", ffOPTRD
}, { efNDX
, "-n", nullptr, ffOPTRD
},
746 { efTEX
, "-m", nullptr, ffOPTWR
} };
747 #define NFILE asize(fnm)
748 const char *fn1
= nullptr, *fn2
= nullptr, *tex
= nullptr;
750 gmx_output_env_t
* oenv
;
751 static real vdw_fac
= 0.8;
752 static real bon_lo
= 0.4;
753 static real bon_hi
= 0.7;
754 static gmx_bool bRMSD
= FALSE
;
755 static real ftol
= 0.001;
756 static real abstol
= 0.001;
757 static gmx_bool bCompAB
= FALSE
;
758 static char* lastener
= nullptr;
759 static t_pargs pa
[] = {
764 "Fraction of sum of VdW radii used as warning cutoff" },
765 { "-bonlo", FALSE
, etREAL
, { &bon_lo
}, "Min. fract. of sum of VdW radii for bonded atoms" },
766 { "-bonhi", FALSE
, etREAL
, { &bon_hi
}, "Max. fract. of sum of VdW radii for bonded atoms" },
767 { "-rmsd", FALSE
, etBOOL
, { &bRMSD
}, "Print RMSD for x, v and f" },
772 "Relative tolerance for comparing real values defined as "
773 "[MATH]2*(a-b)/([MAG]a[mag]+[MAG]b[mag])[math]" },
778 "Absolute tolerance, useful when sums are close to zero." },
779 { "-ab", FALSE
, etBOOL
, { &bCompAB
}, "Compare the A and B topology from one file" },
784 "Last energy term to compare (if not given all are tested). It makes sense to go up "
785 "until the Pressure." }
788 if (!parse_common_args(&argc
, argv
, 0, NFILE
, fnm
, asize(pa
), pa
, asize(desc
), desc
, 0, nullptr, &oenv
))
793 fn1
= opt2fn_null("-f", NFILE
, fnm
);
794 fn2
= opt2fn_null("-f2", NFILE
, fnm
);
795 tex
= opt2fn_null("-m", NFILE
, fnm
);
800 "LaTeX file writing has been removed from gmx check. "
801 "Please use gmx report-methods instead for it.\n");
805 comp_trx(oenv
, fn1
, fn2
, bRMSD
, ftol
, abstol
);
809 chk_trj(oenv
, fn1
, opt2fn_null("-s1", NFILE
, fnm
), ftol
);
813 fprintf(stderr
, "Please give me TWO trajectory (.xtc/.trr/.tng) files!\n");
816 fn1
= opt2fn_null("-s1", NFILE
, fnm
);
817 fn2
= opt2fn_null("-s2", NFILE
, fnm
);
818 if ((fn1
&& fn2
) || bCompAB
)
824 gmx_fatal(FARGS
, "With -ab you need to set the -s1 option");
829 fprintf(stderr
, "Note: When comparing run input files, default tolerances are reduced.\n");
830 if (!opt2parg_bSet("-tol", asize(pa
), pa
))
834 if (!opt2parg_bSet("-abstol", asize(pa
), pa
))
838 comp_tpx(fn1
, fn2
, bRMSD
, ftol
, abstol
);
840 else if ((fn1
&& !opt2fn_null("-f", NFILE
, fnm
)) || (!fn1
&& fn2
))
842 fprintf(stderr
, "Please give me TWO run input (.tpr) files\n");
845 fn1
= opt2fn_null("-e", NFILE
, fnm
);
846 fn2
= opt2fn_null("-e2", NFILE
, fnm
);
849 comp_enx(fn1
, fn2
, ftol
, abstol
, lastener
);
853 chk_enx(ftp2fn(efEDR
, NFILE
, fnm
));
857 fprintf(stderr
, "Please give me TWO energy (.edr/.ene) files!\n");
860 if (ftp2bSet(efTPS
, NFILE
, fnm
))
862 chk_tps(ftp2fn(efTPS
, NFILE
, fnm
), vdw_fac
, bon_lo
, bon_hi
);
865 if (ftp2bSet(efNDX
, NFILE
, fnm
))
867 chk_ndx(ftp2fn(efNDX
, NFILE
, fnm
));