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48 #include "gromacs/commandline/cmdlinehelpcontext.h"
49 #include "gromacs/commandline/cmdlinehelpwriter.h"
50 #include "gromacs/commandline/cmdlineparser.h"
51 #include "gromacs/fileio/oenv.h"
52 #include "gromacs/fileio/timecontrol.h"
53 #include "gromacs/options/basicoptions.h"
54 #include "gromacs/options/behaviorcollection.h"
55 #include "gromacs/options/filenameoption.h"
56 #include "gromacs/options/filenameoptionmanager.h"
57 #include "gromacs/options/options.h"
58 #include "gromacs/options/timeunitmanager.h"
59 #include "gromacs/utility/arrayref.h"
60 #include "gromacs/utility/basenetwork.h"
61 #include "gromacs/utility/classhelpers.h"
62 #include "gromacs/utility/enumerationhelpers.h"
63 #include "gromacs/utility/exceptions.h"
64 #include "gromacs/utility/fatalerror.h"
65 #include "gromacs/utility/gmxassert.h"
66 #include "gromacs/utility/path.h"
67 #include "gromacs/utility/programcontext.h"
68 #include "gromacs/utility/stringutil.h"
70 /* The source code in this file should be thread-safe.
71 Please keep it that way. */
73 int nenum(const char* const enumc[])
78 /* we *can* compare pointers directly here! */
79 while (enumc[i] && enumc[0] != enumc[i])
87 int opt2parg_int(const char* option, int nparg, t_pargs pa[])
91 for (i = 0; (i < nparg); i++)
93 if (strcmp(pa[i].option, option) == 0)
99 gmx_fatal(FARGS, "No integer option %s in pargs", option);
102 gmx_bool opt2parg_bool(const char* option, int nparg, t_pargs pa[])
106 for (i = 0; (i < nparg); i++)
108 if (strcmp(pa[i].option, option) == 0)
114 gmx_fatal(FARGS, "No boolean option %s in pargs", option);
119 real opt2parg_real(const char* option, int nparg, t_pargs pa[])
123 for (i = 0; (i < nparg); i++)
125 if (strcmp(pa[i].option, option) == 0)
131 gmx_fatal(FARGS, "No real option %s in pargs", option);
134 const char* opt2parg_str(const char* option, int nparg, t_pargs pa[])
138 for (i = 0; (i < nparg); i++)
140 if (strcmp(pa[i].option, option) == 0)
146 gmx_fatal(FARGS, "No string option %s in pargs", option);
149 gmx_bool opt2parg_bSet(const char* option, int nparg, const t_pargs* pa)
153 for (i = 0; (i < nparg); i++)
155 if (strcmp(pa[i].option, option) == 0)
161 gmx_fatal(FARGS, "No such option %s in pargs", option);
163 return FALSE; /* Too make some compilers happy */
166 const char* opt2parg_enum(const char* option, int nparg, t_pargs pa[])
170 for (i = 0; (i < nparg); i++)
172 if (strcmp(pa[i].option, option) == 0)
178 gmx_fatal(FARGS, "No such option %s in pargs", option);
181 /********************************************************************
182 * parse_common_args()
191 //! Names for XvgFormat
192 const gmx::EnumerationArray<XvgFormat, const char*> c_xvgFormatNames = {
193 { "xmgrace", "xmgr", "none" }
196 /*! \brief Returns the default xvg format, as modified by GMX_VIEW_XVG
197 * if that environment variable is set.
199 * \ingroup module_commandline
201 XvgFormat getDefaultXvgFormat()
203 const char* const select = getenv("GMX_VIEW_XVG");
204 if (select != nullptr)
206 for (XvgFormat c : keysOf(c_xvgFormatNames))
208 if (std::strcmp(select, c_xvgFormatNames[c]) == 0)
213 return XvgFormat::None;
215 return XvgFormat::Xmgrace;
219 * Conversion helper between t_pargs/t_filenm and Options.
221 * This class holds the necessary mapping between the old C structures and
222 * the new C++ options to allow copying values back after parsing for cases
223 * where the C++ options do not directly provide the type of value required for
226 * \ingroup module_commandline
232 * Initializes the adapter to convert from a specified command line.
234 * The command line is required, because t_pargs wants to return
235 * strings by reference to the original command line.
236 * OptionsAdapter creates a copy of the `argv` array (but not the
237 * strings) to make this possible, even if the parser removes
238 * options it has recognized.
240 OptionsAdapter(int argc, const char* const argv[]) : argv_(argv, argv + argc) {}
243 * Converts a t_filenm option into an Options option.
245 * \param options Options object to add the new option to.
246 * \param fnm t_filenm option to convert.
248 void filenmToOptions(Options* options, t_filenm* fnm);
250 * Converts a t_pargs option into an Options option.
252 * \param options Options object to add the new option to.
253 * \param pa t_pargs option to convert.
255 void pargsToOptions(Options* options, t_pargs* pa);
258 * Copies values back from options to t_pargs/t_filenm.
265 //! Creates a conversion helper for a given `t_filenm` struct.
266 explicit FileNameData(t_filenm* fnm) : fnm(fnm), optionInfo(nullptr) {}
268 //! t_filenm structure to receive the final values.
270 //! Option info object for the created FileNameOption.
271 FileNameOptionInfo* optionInfo;
272 //! Value storage for the created FileNameOption.
273 std::vector<std::string> values;
275 struct ProgramArgData
277 //! Creates a conversion helper for a given `t_pargs` struct.
278 explicit ProgramArgData(t_pargs* pa) :
286 //! t_pargs structure to receive the final values.
288 //! Option info object for the created option.
289 OptionInfo* optionInfo;
290 //! Value storage for a non-enum StringOption (unused for other types).
291 std::string stringValue;
292 //! Value storage for an enum option (unused for other types).
294 //! Value storage for a BooleanOption (unused for other types).
298 std::vector<const char*> argv_;
299 // These are lists instead of vectors to avoid relocating existing
300 // objects in case the container is reallocated (the Options object
301 // contains pointes to members of the objects, which would get
303 std::list<FileNameData> fileNameOptions_;
304 std::list<ProgramArgData> programArgs_;
306 GMX_DISALLOW_COPY_AND_ASSIGN(OptionsAdapter);
309 void OptionsAdapter::filenmToOptions(Options* options, t_filenm* fnm)
311 const bool bRead = ((fnm->flag & ffREAD) != 0);
312 const bool bWrite = ((fnm->flag & ffWRITE) != 0);
313 const bool bOptional = ((fnm->flag & ffOPT) != 0);
314 const bool bLibrary = ((fnm->flag & ffLIB) != 0);
315 const bool bMultiple = ((fnm->flag & ffMULT) != 0);
316 const bool bMissing = ((fnm->flag & ffALLOW_MISSING) != 0);
317 const char* const name = (fnm->opt ? &fnm->opt[1] : &ftp2defopt(fnm->ftp)[1]);
318 const char* defName = fnm->fn;
320 if (defName == nullptr)
322 defName = ftp2defnm(fnm->ftp);
324 else if (Path::hasExtension(defName))
326 defType = fn2ftp(defName);
327 GMX_RELEASE_ASSERT(defType != efNR, "File name option specifies an invalid extension");
329 fileNameOptions_.emplace_back(fnm);
330 FileNameData& data = fileNameOptions_.back();
331 data.optionInfo = options->addOption(FileNameOption(name)
332 .storeVector(&data.values)
333 .defaultBasename(defName)
334 .defaultType(defType)
335 .legacyType(fnm->ftp)
336 .legacyOptionalBehavior()
337 .readWriteFlags(bRead, bWrite)
338 .required(!bOptional)
339 .libraryFile(bLibrary)
340 .multiValue(bMultiple)
341 .allowMissing(bMissing)
342 .description(ftp2desc(fnm->ftp)));
345 void OptionsAdapter::pargsToOptions(Options* options, t_pargs* pa)
347 const bool bHidden = startsWith(pa->desc, "HIDDEN");
348 const char* const name = &pa->option[1];
349 const char* const desc = (bHidden ? &pa->desc[6] : pa->desc);
350 programArgs_.emplace_back(pa);
351 ProgramArgData& data = programArgs_.back();
355 data.optionInfo = options->addOption(
356 IntegerOption(name).store(pa->u.i).description(desc).hidden(bHidden));
359 data.optionInfo = options->addOption(
360 Int64Option(name).store(pa->u.is).description(desc).hidden(bHidden));
364 options->addOption(RealOption(name).store(pa->u.r).description(desc).hidden(bHidden));
367 data.optionInfo = options->addOption(
368 RealOption(name).store(pa->u.r).timeValue().description(desc).hidden(bHidden));
372 const char* const defValue = (*pa->u.c != nullptr ? *pa->u.c : "");
373 data.optionInfo = options->addOption(StringOption(name)
374 .store(&data.stringValue)
375 .defaultValue(defValue)
381 data.optionInfo = options->addOption(BooleanOption(name)
382 .store(&data.boolValue)
383 .defaultValue(*pa->u.b)
388 data.optionInfo = options->addOption(
389 RealOption(name).store(*pa->u.rv).vector().description(desc).hidden(bHidden));
393 // TODO This is the only use of LegacyEnumOption. It
394 // exists to support dozens of analysis tools use that
395 // don't make sense to fix without either test coverage or
396 // automated refactoring. No new uses of LegacyEnumOption
398 const int defaultIndex = (pa->u.c[0] != nullptr ? nenum(pa->u.c) - 1 : 0);
399 data.optionInfo = options->addOption(LegacyEnumOption<int>(name)
400 .store(&data.enumIndex)
401 .defaultValue(defaultIndex)
402 .enumValueFromNullTerminatedArray(pa->u.c + 1)
408 GMX_THROW(NotImplementedError("Argument type not implemented"));
411 void OptionsAdapter::copyValues()
413 std::list<FileNameData>::const_iterator file;
414 for (file = fileNameOptions_.begin(); file != fileNameOptions_.end(); ++file)
416 if (file->optionInfo->isSet())
418 file->fnm->flag |= ffSET;
420 file->fnm->filenames = file->values;
422 std::list<ProgramArgData>::const_iterator arg;
423 for (arg = programArgs_.begin(); arg != programArgs_.end(); ++arg)
425 arg->pa->bSet = arg->optionInfo->isSet();
426 switch (arg->pa->type)
432 std::vector<const char*>::const_iterator pos =
433 std::find(argv_.begin(), argv_.end(), arg->stringValue);
434 GMX_RELEASE_ASSERT(pos != argv_.end(),
435 "String argument got a value not in argv");
436 *arg->pa->u.c = *pos;
440 case etBOOL: *arg->pa->u.b = arg->boolValue; break;
441 case etENUM: *arg->pa->u.c = arg->pa->u.c[arg->enumIndex + 1]; break;
443 // For other types, there is nothing type-specific to do.
453 gmx_bool parse_common_args(int* argc,
464 gmx_output_env_t** oenv)
466 // Lambda function to test the (local) Flags parameter against a bit mask.
467 auto isFlagSet = [Flags](unsigned long bits) { return (Flags & bits) == bits; };
471 double tbegin = 0.0, tend = 0.0, tdelta = 0.0;
472 bool bBeginTimeSet = false, bEndTimeSet = false, bDtSet = false;
474 gmx::OptionsAdapter adapter(*argc, argv);
475 gmx::Options options;
476 gmx::OptionsBehaviorCollection behaviors(&options);
477 gmx::FileNameOptionManager fileOptManager;
479 fileOptManager.disableInputOptionChecking(isFlagSet(PCA_DISABLE_INPUT_FILE_CHECKING));
480 options.addManager(&fileOptManager);
482 if (isFlagSet(PCA_CAN_SET_DEFFNM))
484 fileOptManager.addDefaultFileNameOption(&options, "deffnm");
486 if (isFlagSet(PCA_CAN_BEGIN))
489 gmx::DoubleOption("b").store(&tbegin).storeIsSet(&bBeginTimeSet).timeValue().description("Time of first frame to read from trajectory (default unit %t)"));
491 if (isFlagSet(PCA_CAN_END))
494 gmx::DoubleOption("e").store(&tend).storeIsSet(&bEndTimeSet).timeValue().description("Time of last frame to read from trajectory (default unit %t)"));
496 if (isFlagSet(PCA_CAN_DT))
498 options.addOption(gmx::DoubleOption("dt").store(&tdelta).storeIsSet(&bDtSet).timeValue().description(
499 "Only use frame when t MOD dt = first time (default unit %t)"));
501 gmx::TimeUnit timeUnit = gmx::TimeUnit::Default;
502 if (isFlagSet(PCA_TIME_UNIT))
504 std::shared_ptr<gmx::TimeUnitBehavior> timeUnitBehavior(new gmx::TimeUnitBehavior());
505 timeUnitBehavior->setTimeUnitStore(&timeUnit);
506 timeUnitBehavior->setTimeUnitFromEnvironment();
507 timeUnitBehavior->addTimeUnitOption(&options, "tu");
508 behaviors.addBehavior(timeUnitBehavior);
510 if (isFlagSet(PCA_CAN_VIEW))
512 options.addOption(gmx::BooleanOption("w").store(&bView).description(
513 "View output [REF].xvg[ref], [REF].xpm[ref], "
514 "[REF].eps[ref] and [REF].pdb[ref] files"));
518 for (int i = 0; i < nfile; i++)
520 bXvgr = bXvgr || (fnm[i].ftp == efXVG);
522 XvgFormat xvgFormat = gmx::getDefaultXvgFormat();
525 options.addOption(gmx::EnumOption<XvgFormat>("xvg")
526 .enumValue(gmx::c_xvgFormatNames)
528 .description("xvg plot formatting"));
531 /* Now append the program specific arguments */
532 for (int i = 0; i < nfile; i++)
534 adapter.filenmToOptions(&options, &fnm[i]);
536 for (int i = 0; i < npargs; i++)
538 adapter.pargsToOptions(&options, &pa[i]);
541 const gmx::CommandLineHelpContext* context = gmx::GlobalCommandLineHelpContext::get();
542 if (context != nullptr)
544 GMX_RELEASE_ASSERT(gmx_node_rank() == 0,
545 "Help output should be handled higher up and "
546 "only get called only on the master rank");
547 gmx::CommandLineHelpWriter(options)
548 .setHelpText(gmx::constArrayRefFromArray<const char*>(desc, ndesc))
549 .setKnownIssues(gmx::constArrayRefFromArray(bugs, nbugs))
550 .writeHelp(*context);
554 /* Now parse all the command-line options */
555 gmx::CommandLineParser(&options)
556 .skipUnknown(isFlagSet(PCA_NOEXIT_ON_ARGS))
557 .allowPositionalArguments(isFlagSet(PCA_NOEXIT_ON_ARGS))
559 behaviors.optionsFinishing();
562 /* set program name, command line, and default values for output options */
563 // NOLINTNEXTLINE(bugprone-misplaced-widening-cast)
564 output_env_init(oenv, gmx::getProgramContext(), timeUnit, bView, xvgFormat, 0);
566 /* Extract Time info from arguments */
569 setTimeValue(TBEGIN, tbegin);
573 setTimeValue(TEND, tend);
577 setTimeValue(TDELTA, tdelta);
580 adapter.copyValues();
584 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR