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38 * \brief Implements gmx dump utility.
40 * \ingroup module_tools
53 #include "gromacs/commandline/cmdlineoptionsmodule.h"
54 #include "gromacs/fileio/checkpoint.h"
55 #include "gromacs/fileio/enxio.h"
56 #include "gromacs/fileio/filetypes.h"
57 #include "gromacs/fileio/gmxfio.h"
58 #include "gromacs/fileio/mtxio.h"
59 #include "gromacs/fileio/tngio.h"
60 #include "gromacs/fileio/tpxio.h"
61 #include "gromacs/fileio/trrio.h"
62 #include "gromacs/fileio/xtcio.h"
63 #include "gromacs/gmxpreprocess/gmxcpp.h"
64 #include "gromacs/math/vecdump.h"
65 #include "gromacs/mdrun/mdmodules.h"
66 #include "gromacs/mdtypes/forcerec.h"
67 #include "gromacs/mdtypes/inputrec.h"
68 #include "gromacs/mdtypes/md_enums.h"
69 #include "gromacs/mdtypes/state.h"
70 #include "gromacs/options/basicoptions.h"
71 #include "gromacs/options/filenameoption.h"
72 #include "gromacs/options/ioptionscontainer.h"
73 #include "gromacs/topology/mtop_util.h"
74 #include "gromacs/topology/topology.h"
75 #include "gromacs/trajectory/energyframe.h"
76 #include "gromacs/trajectory/trajectoryframe.h"
77 #include "gromacs/utility/arraysize.h"
78 #include "gromacs/utility/basedefinitions.h"
79 #include "gromacs/utility/fatalerror.h"
80 #include "gromacs/utility/futil.h"
81 #include "gromacs/utility/smalloc.h"
82 #include "gromacs/utility/txtdump.h"
91 void list_tpr(const char *fn
,
92 gmx_bool bShowNumbers
,
93 gmx_bool bShowParameters
,
96 gmx_bool bOriginalInputrec
)
105 read_tpxheader(fn
, &tpx
, TRUE
);
108 tpx
.bIr
? &ir
: nullptr,
110 tpx
.bTop
? &mtop
: nullptr);
111 if (tpx
.bIr
&& !bOriginalInputrec
)
113 MDModules().adjustInputrecBasedOnModules(&ir
);
116 if (mdpfn
&& tpx
.bIr
)
118 gp
= gmx_fio_fopen(mdpfn
, "w");
119 pr_inputrec(gp
, 0, nullptr, &ir
, TRUE
);
127 top
= gmx_mtop_t_to_t_topology(&mtop
, false);
130 if (available(stdout
, &tpx
, 0, fn
))
133 pr_title(stdout
, indent
, fn
);
134 pr_inputrec(stdout
, 0, "inputrec", tpx
.bIr
? &ir
: nullptr, FALSE
);
136 pr_tpxheader(stdout
, indent
, "header", &(tpx
));
140 pr_mtop(stdout
, indent
, "topology", &(mtop
), bShowNumbers
, bShowParameters
);
144 pr_top(stdout
, indent
, "topology", &(top
), bShowNumbers
, bShowParameters
);
147 pr_rvecs(stdout
, indent
, "box", tpx
.bBox
? state
.box
: nullptr, DIM
);
148 pr_rvecs(stdout
, indent
, "box_rel", tpx
.bBox
? state
.box_rel
: nullptr, DIM
);
149 pr_rvecs(stdout
, indent
, "boxv", tpx
.bBox
? state
.boxv
: nullptr, DIM
);
150 pr_rvecs(stdout
, indent
, "pres_prev", tpx
.bBox
? state
.pres_prev
: nullptr, DIM
);
151 pr_rvecs(stdout
, indent
, "svir_prev", tpx
.bBox
? state
.svir_prev
: nullptr, DIM
);
152 pr_rvecs(stdout
, indent
, "fvir_prev", tpx
.bBox
? state
.fvir_prev
: nullptr, DIM
);
153 /* leave nosehoover_xi in for now to match the tpr version */
154 pr_doubles(stdout
, indent
, "nosehoover_xi", state
.nosehoover_xi
.data(), state
.ngtc
);
155 /*pr_doubles(stdout,indent,"nosehoover_vxi",state.nosehoover_vxi,state.ngtc);*/
156 /*pr_doubles(stdout,indent,"therm_integral",state.therm_integral,state.ngtc);*/
157 pr_rvecs(stdout
, indent
, "x", tpx
.bX
? state
.x
.rvec_array() : nullptr, state
.natoms
);
158 pr_rvecs(stdout
, indent
, "v", tpx
.bV
? state
.v
.rvec_array() : nullptr, state
.natoms
);
161 const SimulationGroups
&groups
= mtop
.groups
;
163 gmx::EnumerationArray
< SimulationAtomGroupType
, std::vector
< int>> gcount
;
164 for (auto group
: keysOf(gcount
))
166 gcount
[group
].resize(groups
.groups
[group
].nr
);
169 for (int i
= 0; (i
< mtop
.natoms
); i
++)
171 for (auto group
: keysOf(gcount
))
173 gcount
[group
][getGroupType(groups
, group
, i
)]++;
176 printf("Group statistics\n");
177 for (auto group
: keysOf(gcount
))
180 printf("%-12s: ", shortName(group
));
181 for (int j
= 0; (j
< groups
.groups
[group
].nr
); j
++)
183 printf(" %5d", gcount
[group
][j
]);
184 atot
+= gcount
[group
][j
];
186 printf(" (total %d atoms)\n", atot
);
191 //! Dump a topology file
192 void list_top(const char *fn
)
195 // Legacy string length macro
198 char *cppopts
[] = { nullptr };
200 status
= cpp_open_file(fn
, &handle
, cppopts
);
203 gmx_fatal(FARGS
, "%s", cpp_error(&handle
, status
));
207 status
= cpp_read_line(&handle
, STRLEN
, buf
);
208 done
= static_cast<int>(status
== eCPP_EOF
);
211 if (status
!= eCPP_OK
)
213 gmx_fatal(FARGS
, "%s", cpp_error(&handle
, status
));
222 status
= cpp_close_file(&handle
);
223 if (status
!= eCPP_OK
)
225 gmx_fatal(FARGS
, "%s", cpp_error(&handle
, status
));
230 void list_trr(const char *fn
)
237 gmx_trr_header_t trrheader
;
240 fpread
= gmx_trr_open(fn
, "r");
243 while (gmx_trr_read_frame_header(fpread
, &trrheader
, &bOK
))
245 snew(x
, trrheader
.natoms
);
246 snew(v
, trrheader
.natoms
);
247 snew(f
, trrheader
.natoms
);
248 if (gmx_trr_read_frame_data(fpread
, &trrheader
,
249 trrheader
.box_size
? box
: nullptr,
250 trrheader
.x_size
? x
: nullptr,
251 trrheader
.v_size
? v
: nullptr,
252 trrheader
.f_size
? f
: nullptr))
254 sprintf(buf
, "%s frame %d", fn
, nframe
);
256 indent
= pr_title(stdout
, indent
, buf
);
257 pr_indent(stdout
, indent
);
258 fprintf(stdout
, "natoms=%10d step=%10" PRId64
" time=%12.7e lambda=%10g\n",
259 trrheader
.natoms
, trrheader
.step
, trrheader
.t
, trrheader
.lambda
);
260 if (trrheader
.box_size
)
262 pr_rvecs(stdout
, indent
, "box", box
, DIM
);
264 if (trrheader
.x_size
)
266 pr_rvecs(stdout
, indent
, "x", x
, trrheader
.natoms
);
268 if (trrheader
.v_size
)
270 pr_rvecs(stdout
, indent
, "v", v
, trrheader
.natoms
);
272 if (trrheader
.f_size
)
274 pr_rvecs(stdout
, indent
, "f", f
, trrheader
.natoms
);
279 fprintf(stderr
, "\nWARNING: Incomplete frame: nr %d, t=%g\n",
280 nframe
, trrheader
.t
);
290 fprintf(stderr
, "\nWARNING: Incomplete frame header: nr %d, t=%g\n",
291 nframe
, trrheader
.t
);
293 gmx_trr_close(fpread
);
297 void list_xtc(const char *fn
)
309 xd
= open_xtc(fn
, "r");
310 read_first_xtc(xd
, &natoms
, &step
, &time
, box
, &x
, &prec
, &bOK
);
315 sprintf(buf
, "%s frame %d", fn
, nframe
);
317 indent
= pr_title(stdout
, indent
, buf
);
318 pr_indent(stdout
, indent
);
319 fprintf(stdout
, "natoms=%10d step=%10" PRId64
" time=%12.7e prec=%10g\n",
320 natoms
, step
, time
, prec
);
321 pr_rvecs(stdout
, indent
, "box", box
, DIM
);
322 pr_rvecs(stdout
, indent
, "x", x
, natoms
);
325 while (read_next_xtc(xd
, natoms
, &step
, &time
, box
, x
, &prec
, &bOK
) != 0);
328 fprintf(stderr
, "\nWARNING: Incomplete frame at time %g\n", time
);
336 /*! \brief Callback used by list_tng_for_gmx_dump. */
337 void list_tng_inner(const char *fn
,
338 gmx_bool bFirstFrame
,
342 int64_t n_values_per_frame
,
353 sprintf(buf
, "%s frame %" PRId64
, fn
, nframe
);
355 indent
= pr_title(stdout
, indent
, buf
);
356 pr_indent(stdout
, indent
);
357 fprintf(stdout
, "natoms=%10" PRId64
" step=%10" PRId64
" time=%12.7e",
358 n_atoms
, step
, frame_time
);
361 fprintf(stdout
, " prec=%10g", prec
);
363 fprintf(stdout
, "\n");
365 pr_reals_of_dim(stdout
, indent
, block_name
, values
, n_atoms
, n_values_per_frame
);
371 void list_tng(const char *fn
)
374 gmx_tng_trajectory_t tng
;
376 int64_t i
, *block_ids
= nullptr, step
, ndatablocks
;
378 real
*values
= nullptr;
380 gmx_tng_open(fn
, 'r', &tng
);
381 gmx_print_tng_molecule_system(tng
, stdout
);
383 bOK
= gmx_get_tng_data_block_types_of_next_frame(tng
, -1,
390 for (i
= 0; i
< ndatablocks
; i
++)
394 int64_t n_values_per_frame
, n_atoms
;
395 char block_name
[STRLEN
];
397 gmx_get_tng_data_next_frame_of_block_type(tng
, block_ids
[i
], &values
,
399 &n_values_per_frame
, &n_atoms
,
401 block_name
, STRLEN
, &bOK
);
404 /* Can't write any output because we don't know what
406 fprintf(stderr
, "\nWARNING: Incomplete frame at time %g, will not write output\n", frame_time
);
410 list_tng_inner(fn
, (0 == i
), values
, step
, frame_time
,
411 n_values_per_frame
, n_atoms
, prec
, nframe
, block_name
);
416 while (gmx_get_tng_data_block_types_of_next_frame(tng
, step
,
430 GMX_UNUSED_VALUE(fn
);
434 //! Dump a trajectory file
435 void list_trx(const char *fn
)
449 fprintf(stderr
, "File %s is of an unsupported type. Try using the command\n 'less %s'\n",
454 //! Dump an energy file
455 void list_ene(const char *fn
)
459 gmx_enxnm_t
*enm
= nullptr;
464 printf("gmx dump: %s\n", fn
);
465 in
= open_enx(fn
, "r");
466 do_enxnms(in
, &nre
, &enm
);
469 printf("energy components:\n");
470 for (i
= 0; (i
< nre
); i
++)
472 printf("%5d %-24s (%s)\n", i
, enm
[i
].name
, enm
[i
].unit
);
478 bCont
= do_enx(in
, fr
);
482 printf("\n%24s %12.5e %12s %12s\n", "time:",
483 fr
->t
, "step:", gmx_step_str(fr
->step
, buf
));
484 printf("%24s %12s %12s %12s\n",
485 "", "", "nsteps:", gmx_step_str(fr
->nsteps
, buf
));
486 printf("%24s %12.5e %12s %12s\n",
487 "delta_t:", fr
->dt
, "sum steps:", gmx_step_str(fr
->nsum
, buf
));
490 printf("%24s %12s %12s %12s\n",
491 "Component", "Energy", "Av. Energy", "Sum Energy");
494 for (i
= 0; (i
< nre
); i
++)
496 printf("%24s %12.5e %12.5e %12.5e\n",
497 enm
[i
].name
, fr
->ener
[i
].e
, fr
->ener
[i
].eav
,
503 for (i
= 0; (i
< nre
); i
++)
505 printf("%24s %12.5e\n",
506 enm
[i
].name
, fr
->ener
[i
].e
);
510 for (b
= 0; b
< fr
->nblock
; b
++)
512 const char *typestr
= "";
514 t_enxblock
*eb
= &(fr
->block
[b
]);
515 printf("Block data %2d (%3d subblocks, id=%d)\n",
516 b
, eb
->nsub
, eb
->id
);
520 typestr
= enx_block_id_name
[eb
->id
];
522 printf(" id='%s'\n", typestr
);
523 for (i
= 0; i
< eb
->nsub
; i
++)
525 t_enxsubblock
*sb
= &(eb
->sub
[i
]);
526 printf(" Sub block %3d (%5d elems, type=%s) values:\n",
527 i
, sb
->nr
, xdr_datatype_names
[sb
->type
]);
531 case xdr_datatype_float
:
532 for (j
= 0; j
< sb
->nr
; j
++)
534 printf("%14d %8.4f\n", j
, sb
->fval
[j
]);
537 case xdr_datatype_double
:
538 for (j
= 0; j
< sb
->nr
; j
++)
540 printf("%14d %10.6f\n", j
, sb
->dval
[j
]);
543 case xdr_datatype_int
:
544 for (j
= 0; j
< sb
->nr
; j
++)
546 printf("%14d %10d\n", j
, sb
->ival
[j
]);
549 case xdr_datatype_int64
:
550 for (j
= 0; j
< sb
->nr
; j
++)
553 j
, gmx_step_str(sb
->lval
[j
], buf
));
556 case xdr_datatype_char
:
557 for (j
= 0; j
< sb
->nr
; j
++)
559 printf("%14d %1c\n", j
, sb
->cval
[j
]);
562 case xdr_datatype_string
:
563 for (j
= 0; j
< sb
->nr
; j
++)
565 printf("%14d %80s\n", j
, sb
->sval
[j
]);
569 gmx_incons("Unknown subblock type");
584 //! Dump a (Hessian) matrix file
585 void list_mtx(const char *fn
)
587 int nrow
, ncol
, i
, j
, k
;
588 real
*full
= nullptr, value
;
589 gmx_sparsematrix_t
* sparse
= nullptr;
591 gmx_mtxio_read(fn
, &nrow
, &ncol
, &full
, &sparse
);
595 snew(full
, nrow
*ncol
);
596 for (i
= 0; i
< nrow
*ncol
; i
++)
601 for (i
= 0; i
< sparse
->nrow
; i
++)
603 for (j
= 0; j
< sparse
->ndata
[i
]; j
++)
605 k
= sparse
->data
[i
][j
].col
;
606 value
= sparse
->data
[i
][j
].value
;
607 full
[i
*ncol
+k
] = value
;
608 full
[k
*ncol
+i
] = value
;
611 gmx_sparsematrix_destroy(sparse
);
614 printf("%d %d\n", nrow
, ncol
);
615 for (i
= 0; i
< nrow
; i
++)
617 for (j
= 0; j
< ncol
; j
++)
619 printf(" %g", full
[i
*ncol
+j
]);
627 class Dump
: public ICommandLineOptionsModule
633 // From ICommandLineOptionsModule
634 void init(CommandLineModuleSettings
* /*settings*/) override
638 void initOptions(IOptionsContainer
*options
,
639 ICommandLineOptionsModuleSettings
*settings
) override
;
641 void optionsFinished() override
;
646 //! Commandline options
648 bool bShowNumbers_
= true;
649 bool bShowParams_
= false;
650 bool bSysTop_
= false;
651 bool bOriginalInputrec_
= false;
653 //! Commandline file options
655 std::string inputTprFilename_
;
656 std::string inputTrajectoryFilename_
;
657 std::string inputEnergyFilename_
;
658 std::string inputCheckpointFilename_
;
659 std::string inputTopologyFilename_
;
660 std::string inputMatrixFilename_
;
661 std::string outputMdpFilename_
;
665 void Dump::initOptions(IOptionsContainer
*options
,
666 ICommandLineOptionsModuleSettings
*settings
)
668 const char *desc
[] = {
669 "[THISMODULE] reads a run input file ([REF].tpr[ref]),",
670 "a trajectory ([REF].trr[ref]/[REF].xtc[ref]/[TT]tng[tt]), an energy",
671 "file ([REF].edr[ref]), a checkpoint file ([REF].cpt[ref])",
672 "or topology file ([REF].top[ref])",
673 "and prints that to standard output in a readable format.",
674 "This program is essential for checking your run input file in case of",
677 settings
->setHelpText(desc
);
678 // TODO If this ancient note acknowledging a bug is still true,
679 // fix it or block that run path:
680 // Position restraint output from -sys -s is broken
682 options
->addOption(FileNameOption("s")
683 .filetype(eftRunInput
).inputFile()
684 .store(&inputTprFilename_
)
685 .description("Run input file to dump"));
686 options
->addOption(FileNameOption("f")
687 .filetype(eftTrajectory
).inputFile()
688 .store(&inputTrajectoryFilename_
)
689 .description("Trajectory file to dump"));
690 options
->addOption(FileNameOption("e")
691 .filetype(eftEnergy
).inputFile()
692 .store(&inputEnergyFilename_
)
693 .description("Energy file to dump"));
694 options
->addOption(FileNameOption("cp")
695 .legacyType(efCPT
).inputFile()
696 .store(&inputCheckpointFilename_
)
697 .description("Checkpoint file to dump"));
698 options
->addOption(FileNameOption("p")
699 .legacyType(efTOP
).inputFile()
700 .store(&inputTopologyFilename_
)
701 .description("Topology file to dump"));
702 options
->addOption(FileNameOption("mtx")
703 .legacyType(efMTX
).inputFile()
704 .store(&inputMatrixFilename_
)
705 .description("Hessian matrix to dump"));
706 options
->addOption(FileNameOption("om")
707 .legacyType(efMDP
).outputFile()
708 .store(&outputMdpFilename_
)
709 .description("grompp input file from run input file"));
711 options
->addOption(BooleanOption("nr")
712 .store(&bShowNumbers_
).defaultValue(true)
713 .description("Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)"));
714 options
->addOption(BooleanOption("param")
715 .store(&bShowParams_
).defaultValue(false)
716 .description("Show parameters for each bonded interaction (for comparing dumps, it is useful to combine this with -nonr)"));
717 options
->addOption(BooleanOption("sys")
718 .store(&bShowParams_
).defaultValue(false)
719 .description("List the atoms and bonded interactions for the whole system instead of for each molecule type"));
720 options
->addOption(BooleanOption("orgir")
721 .store(&bShowParams_
).defaultValue(false)
722 .description("Show input parameters from tpr as they were written by the version that produced the file, instead of how the current version reads them"));
725 void Dump::optionsFinished()
727 // TODO Currently gmx dump ignores user input that seeks to dump
728 // multiple files. Here, we could enforce that the user only asks
734 if (!inputTprFilename_
.empty())
736 list_tpr(inputTprFilename_
.c_str(), bShowNumbers_
, bShowParams_
,
737 outputMdpFilename_
.c_str(), bSysTop_
, bOriginalInputrec_
);
739 else if (!inputTrajectoryFilename_
.empty())
741 list_trx(inputTrajectoryFilename_
.c_str());
743 else if (!inputEnergyFilename_
.empty())
745 list_ene(inputEnergyFilename_
.c_str());
747 else if (!inputCheckpointFilename_
.empty())
749 list_checkpoint(inputCheckpointFilename_
.c_str(), stdout
);
751 else if (!inputTopologyFilename_
.empty())
753 list_top(inputTopologyFilename_
.c_str());
755 else if (!inputMatrixFilename_
.empty())
757 list_mtx(inputMatrixFilename_
.c_str());
765 const char DumpInfo::name
[] = "dump";
766 const char DumpInfo::shortDescription
[] =
767 "Make binary files human readable";
768 ICommandLineOptionsModulePointer
DumpInfo::create()
770 return std::make_unique
<Dump
>();