src/gromacs/options/basicoptions.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  35 /*! \internal \file
  36  * \brief
  37  * Implements classes in basicoptions.h and basicoptionstorage.h.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_options
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "basicoptions.h"
  45
  46 #include <cerrno>
  47 #include <cstdio>
  48 #include <cstdlib>
  49
  50 #include <algorithm>
  51 #include <limits>
  52 #include <string>
  53 #include <vector>
  54
  55 #include "gromacs/utility/cstringutil.h"
  56 #include "gromacs/utility/exceptions.h"
  57 #include "gromacs/utility/strconvert.h"
  58 #include "gromacs/utility/stringutil.h"
  59
  60 #include "basicoptionstorage.h"
  61
  62 namespace
  63 {
  64
  65 /*! \brief
  66  * Expands a single value to a vector by copying the value.
  67  *
  68  * \tparam        ValueType  Type of values to process.
  69  * \param[in]     length     Length of the resulting vector.
  70  * \param[in,out] values     Values to process.
  71  * \throws   std::bad_alloc    if out of memory.
  72  * \throws   InvalidInputError if \p values has an invalid number of values.
  73  *
  74  * \p values should have 0, 1, or \p length values.
  75  * If \p values has 1 value, it is expanded such that it has \p length
  76  * identical values.  In other valid cases, nothing is done.
  77  *
  78  * \ingroup module_options
  79  */
  80 template <typename ValueType>
  81 void expandVector(size_t length, std::vector<ValueType> *values)
  82 {
  83     if (length > 0 && !values->empty() && values->size() != length)
  84     {
  85         if (values->size() != 1)
  86         {
  87             GMX_THROW(gmx::InvalidInputError(gmx::formatString(
  88                                                      "Expected 1 or %d values, got %d", length, values->size())));
  89         }
  90         const ValueType &value = (*values)[0];
  91         values->resize(length, value);
  92     }
  93 }
  94
  95 /*! \brief
  96  * Finds an enumerated value from the list of allowed values.
  97  *
  98  * \param[in] allowedValues  List of allowed values.
  99  * \param[in] value          Value to search for.
 100  * \throws    gmx::InvalidInputError if \p value does not match anything in
 101  *     \p allowedValues.
 102  * \returns   Iterator to the found value.
 103  *
 104  * \ingroup module_options
 105  */
 106 std::vector<std::string>::const_iterator
 107 findEnumValue(const std::vector<std::string> &allowedValues,
 108               const std::string              &value)
 109 {
 110     std::vector<std::string>::const_iterator  i;
 111     std::vector<std::string>::const_iterator  match = allowedValues.end();
 112     for (i = allowedValues.begin(); i != allowedValues.end(); ++i)
 113     {
 114         // TODO: Case independence.
 115         if (gmx::startsWith(*i, value))
 116         {
 117             if (match == allowedValues.end() || i->size() < match->size())
 118             {
 119                 match = i;
 120             }
 121         }
 122     }
 123     if (match == allowedValues.end())
 124     {
 125         GMX_THROW(gmx::InvalidInputError("Invalid value: " + value));
 126     }
 127     return match;
 128 }
 129
 130 } // namespace
 131
 132 namespace gmx
 133 {
 134
 135 /********************************************************************
 136  * BooleanOptionStorage
 137  */
 138
 139 std::string BooleanOptionStorage::formatSingleValue(const bool &value) const
 140 {
 141     return value ? "yes" : "no";
 142 }
 143
 144 void BooleanOptionStorage::initConverter(ConverterType *converter)
 145 {
 146     converter->addConverter<std::string>(&fromStdString<bool>);
 147 }
 148
 149 /********************************************************************
 150  * BooleanOptionInfo
 151  */
 152
 153 BooleanOptionInfo::BooleanOptionInfo(BooleanOptionStorage *option)
 154     : OptionInfo(option)
 155 {
 156 }
 157
 158 const BooleanOptionStorage &BooleanOptionInfo::option() const
 159 {
 160     return static_cast<const BooleanOptionStorage &>(OptionInfo::option());
 161 }
 162
 163 bool BooleanOptionInfo::defaultValue() const
 164 {
 165     return option().defaultValue();
 166 }
 167
 168 /********************************************************************
 169  * BooleanOption
 170  */
 171
 172 AbstractOptionStorage *
 173 BooleanOption::createStorage(const OptionManagerContainer & /*managers*/) const
 174 {
 175     return new BooleanOptionStorage(*this);
 176 }
 177
 178
 179 /********************************************************************
 180  * IntegerOptionStorage
 181  */
 182
 183 std::string IntegerOptionStorage::formatSingleValue(const int &value) const
 184 {
 185     return formatString("%d", value);
 186 }
 187
 188 void IntegerOptionStorage::initConverter(ConverterType *converter)
 189 {
 190     converter->addConverter<std::string>(&fromStdString<int>);
 191 }
 192
 193 void IntegerOptionStorage::processSetValues(ValueList *values)
 194 {
 195     if (isVector())
 196     {
 197         expandVector(maxValueCount(), values);
 198     }
 199 }
 200
 201 /********************************************************************
 202  * IntegerOptionInfo
 203  */
 204
 205 IntegerOptionInfo::IntegerOptionInfo(IntegerOptionStorage *option)
 206     : OptionInfo(option)
 207 {
 208 }
 209
 210 /********************************************************************
 211  * IntegerOption
 212  */
 213
 214 AbstractOptionStorage *
 215 IntegerOption::createStorage(const OptionManagerContainer & /*managers*/) const
 216 {
 217     return new IntegerOptionStorage(*this);
 218 }
 219
 220
 221 /********************************************************************
 222  * Int64OptionStorage
 223  */
 224
 225 std::string Int64OptionStorage::formatSingleValue(const gmx_int64_t &value) const
 226 {
 227     return formatString("%" GMX_PRId64, value);
 228 }
 229
 230 void Int64OptionStorage::initConverter(ConverterType *converter)
 231 {
 232     converter->addConverter<std::string>(&fromStdString<gmx_int64_t>);
 233 }
 234
 235 /********************************************************************
 236  * Int64OptionInfo
 237  */
 238
 239 Int64OptionInfo::Int64OptionInfo(Int64OptionStorage *option)
 240     : OptionInfo(option)
 241 {
 242 }
 243
 244 /********************************************************************
 245  * Int64Option
 246  */
 247
 248 AbstractOptionStorage *
 249 Int64Option::createStorage(const OptionManagerContainer & /*managers*/) const
 250 {
 251     return new Int64OptionStorage(*this);
 252 }
 253
 254
 255 /********************************************************************
 256  * DoubleOptionStorage
 257  */
 258
 259 DoubleOptionStorage::DoubleOptionStorage(const DoubleOption &settings)
 260     : MyBase(settings), info_(this), bTime_(settings.bTime_), factor_(1.0)
 261 {
 262 }
 263
 264 std::string DoubleOptionStorage::typeString() const
 265 {
 266     return isVector() ? "vector" : (isTime() ? "time" : "real");
 267 }
 268
 269 std::string DoubleOptionStorage::formatSingleValue(const double &value) const
 270 {
 271     return formatString("%g", value / factor_);
 272 }
 273
 274 void DoubleOptionStorage::initConverter(ConverterType *converter)
 275 {
 276     converter->addConverter<std::string>(&fromStdString<double>);
 277     converter->addCastConversion<float>();
 278 }
 279
 280 double DoubleOptionStorage::processValue(const double &value) const
 281 {
 282     // TODO: Consider testing for overflow when scaling with factor_.
 283     return value * factor_;
 284 }
 285
 286 void DoubleOptionStorage::processSetValues(ValueList *values)
 287 {
 288     if (isVector())
 289     {
 290         expandVector(maxValueCount(), values);
 291     }
 292 }
 293
 294 void DoubleOptionStorage::setScaleFactor(double factor)
 295 {
 296     GMX_RELEASE_ASSERT(factor > 0.0, "Invalid scaling factor");
 297     if (!hasFlag(efOption_HasDefaultValue))
 298     {
 299         double scale = factor / factor_;
 300         for (double &value : values())
 301         {
 302             value *= scale;
 303         }
 304     }
 305     factor_ = factor;
 306 }
 307
 308 /********************************************************************
 309  * DoubleOptionInfo
 310  */
 311
 312 DoubleOptionInfo::DoubleOptionInfo(DoubleOptionStorage *option)
 313     : OptionInfo(option)
 314 {
 315 }
 316
 317 DoubleOptionStorage &DoubleOptionInfo::option()
 318 {
 319     return static_cast<DoubleOptionStorage &>(OptionInfo::option());
 320 }
 321
 322 const DoubleOptionStorage &DoubleOptionInfo::option() const
 323 {
 324     return static_cast<const DoubleOptionStorage &>(OptionInfo::option());
 325 }
 326
 327 bool DoubleOptionInfo::isTime() const
 328 {
 329     return option().isTime();
 330 }
 331
 332 void DoubleOptionInfo::setScaleFactor(double factor)
 333 {
 334     option().setScaleFactor(factor);
 335 }
 336
 337 /********************************************************************
 338  * DoubleOption
 339  */
 340
 341 AbstractOptionStorage *
 342 DoubleOption::createStorage(const OptionManagerContainer & /*managers*/) const
 343 {
 344     return new DoubleOptionStorage(*this);
 345 }
 346
 347
 348 /********************************************************************
 349  * FloatOptionStorage
 350  */
 351
 352 FloatOptionStorage::FloatOptionStorage(const FloatOption &settings)
 353     : MyBase(settings), info_(this), bTime_(settings.bTime_), factor_(1.0)
 354 {
 355 }
 356
 357 std::string FloatOptionStorage::typeString() const
 358 {
 359     return isVector() ? "vector" : (isTime() ? "time" : "real");
 360 }
 361
 362 std::string FloatOptionStorage::formatSingleValue(const float &value) const
 363 {
 364     return formatString("%g", value / factor_);
 365 }
 366
 367 void FloatOptionStorage::initConverter(ConverterType *converter)
 368 {
 369     converter->addConverter<std::string>(&fromStdString<float>);
 370     converter->addCastConversion<double>();
 371 }
 372
 373 float FloatOptionStorage::processValue(const float &value) const
 374 {
 375     // TODO: Consider testing for overflow when scaling with factor_.
 376     return value * factor_;
 377 }
 378
 379 void FloatOptionStorage::processSetValues(ValueList *values)
 380 {
 381     if (isVector())
 382     {
 383         expandVector(maxValueCount(), values);
 384     }
 385 }
 386
 387 void FloatOptionStorage::setScaleFactor(double factor)
 388 {
 389     GMX_RELEASE_ASSERT(factor > 0.0, "Invalid scaling factor");
 390     if (!hasFlag(efOption_HasDefaultValue))
 391     {
 392         float scale = factor / factor_;
 393         for (float &value : values())
 394         {
 395             value *= scale;
 396         }
 397     }
 398     factor_ = factor;
 399 }
 400
 401 /********************************************************************
 402  * FloatOptionInfo
 403  */
 404
 405 FloatOptionInfo::FloatOptionInfo(FloatOptionStorage *option)
 406     : OptionInfo(option)
 407 {
 408 }
 409
 410 FloatOptionStorage &FloatOptionInfo::option()
 411 {
 412     return static_cast<FloatOptionStorage &>(OptionInfo::option());
 413 }
 414
 415 const FloatOptionStorage &FloatOptionInfo::option() const
 416 {
 417     return static_cast<const FloatOptionStorage &>(OptionInfo::option());
 418 }
 419
 420 bool FloatOptionInfo::isTime() const
 421 {
 422     return option().isTime();
 423 }
 424
 425 void FloatOptionInfo::setScaleFactor(double factor)
 426 {
 427     option().setScaleFactor(factor);
 428 }
 429
 430 /********************************************************************
 431  * FloatOption
 432  */
 433
 434 AbstractOptionStorage *
 435 FloatOption::createStorage(const OptionManagerContainer & /*managers*/) const
 436 {
 437     return new FloatOptionStorage(*this);
 438 }
 439
 440
 441 /********************************************************************
 442  * StringOptionStorage
 443  */
 444
 445 StringOptionStorage::StringOptionStorage(const StringOption &settings)
 446     : MyBase(settings), info_(this)
 447 {
 448     if (settings.defaultEnumIndex_ >= 0 && settings.enumValues_ == nullptr)
 449     {
 450         GMX_THROW(APIError("Cannot set default enum index without enum values"));
 451     }
 452     if (settings.enumValues_ != nullptr)
 453     {
 454         int count = settings.enumValuesCount_;
 455         if (count < 0)
 456         {
 457             count = 0;
 458             while (settings.enumValues_[count] != nullptr)
 459             {
 460                 ++count;
 461             }
 462         }
 463         for (int i = 0; i < count; ++i)
 464         {
 465             if (settings.enumValues_[i] == nullptr)
 466             {
 467                 GMX_THROW(APIError("Enumeration value cannot be NULL"));
 468             }
 469             allowed_.emplace_back(settings.enumValues_[i]);
 470         }
 471         if (settings.defaultEnumIndex_ >= 0)
 472         {
 473             if (settings.defaultEnumIndex_ >= count)
 474             {
 475                 GMX_THROW(APIError("Default enumeration index is out of range"));
 476             }
 477             const std::string *defaultValue = settings.defaultValue();
 478             if (defaultValue != nullptr && *defaultValue != allowed_[settings.defaultEnumIndex_])
 479             {
 480                 GMX_THROW(APIError("Conflicting default values"));
 481             }
 482             setDefaultValue(allowed_[settings.defaultEnumIndex_]);
 483         }
 484     }
 485 }
 486
 487 std::string StringOptionStorage::formatExtraDescription() const
 488 {
 489     std::string result;
 490     if (!allowed_.empty())
 491     {
 492         result.append(": ");
 493         result.append(joinStrings(allowed_, ", "));
 494     }
 495     return result;
 496 }
 497
 498 std::string StringOptionStorage::formatSingleValue(const std::string &value) const
 499 {
 500     return value;
 501 }
 502
 503 void StringOptionStorage::initConverter(ConverterType * /*converter*/)
 504 {
 505 }
 506
 507 std::string StringOptionStorage::processValue(const std::string &value) const
 508 {
 509     if (allowed_.size() > 0)
 510     {
 511         return *findEnumValue(this->allowed_, value);
 512     }
 513     return value;
 514 }
 515
 516 /********************************************************************
 517  * StringOptionInfo
 518  */
 519
 520 StringOptionInfo::StringOptionInfo(StringOptionStorage *option)
 521     : OptionInfo(option)
 522 {
 523 }
 524
 525 const StringOptionStorage &StringOptionInfo::option() const
 526 {
 527     return static_cast<const StringOptionStorage &>(OptionInfo::option());
 528 }
 529
 530 bool StringOptionInfo::isEnumerated() const
 531 {
 532     return !allowedValues().empty();
 533 }
 534
 535 const std::vector<std::string> &StringOptionInfo::allowedValues() const
 536 {
 537     return option().allowedValues();
 538 }
 539
 540 /********************************************************************
 541  * StringOption
 542  */
 543
 544 AbstractOptionStorage *
 545 StringOption::createStorage(const OptionManagerContainer & /*managers*/) const
 546 {
 547     return new StringOptionStorage(*this);
 548 }
 549
 550
 551 /********************************************************************
 552  * EnumOptionStorage
 553  */
 554
 555 EnumOptionStorage::EnumOptionStorage(const AbstractOption &settings,
 556                                      const char *const *enumValues, int count,
 557                                      int defaultValue, int defaultValueIfSet,
 558                                      StorePointer store)
 559     : MyBase(settings, std::move(store)), info_(this)
 560 {
 561     if (enumValues == nullptr)
 562     {
 563         GMX_THROW(APIError("Allowed values must be provided to EnumOption"));
 564     }
 565
 566     if (count < 0)
 567     {
 568         count = 0;
 569         while (enumValues[count] != nullptr)
 570         {
 571             ++count;
 572         }
 573     }
 574     for (int i = 0; i < count; ++i)
 575     {
 576         if (enumValues[i] == nullptr)
 577         {
 578             GMX_THROW(APIError("Enumeration value cannot be NULL"));
 579         }
 580         allowed_.emplace_back(enumValues[i]);
 581     }
 582
 583     GMX_ASSERT(defaultValue < count, "Default enumeration value is out of range");
 584     GMX_ASSERT(defaultValueIfSet < count, "Default enumeration value is out of range");
 585     setFlag(efOption_HasDefaultValue);
 586     if (defaultValue >= 0)
 587     {
 588         setDefaultValue(defaultValue);
 589     }
 590     if (defaultValueIfSet >= 0)
 591     {
 592         setDefaultValueIfSet(defaultValueIfSet);
 593     }
 594 }
 595
 596 std::string EnumOptionStorage::formatExtraDescription() const
 597 {
 598     std::string result;
 599     result.append(": ");
 600     result.append(joinStrings(allowed_, ", "));
 601     return result;
 602 }
 603
 604 std::string EnumOptionStorage::formatSingleValue(const int &value) const
 605 {
 606     if (value < 0 || value >= static_cast<int>(allowed_.size()))
 607     {
 608         return std::string();
 609     }
 610     return allowed_[value];
 611 }
 612
 613 Variant EnumOptionStorage::normalizeValue(const int &value) const
 614 {
 615     return Variant::create<std::string>(formatSingleValue(value));
 616 }
 617
 618 void EnumOptionStorage::initConverter(ConverterType *converter)
 619 {
 620     converter->addConverter<std::string>(
 621             [this] (const std::string &value)
 622             {
 623                 return findEnumValue(this->allowed_, value) - this->allowed_.begin();
 624             });
 625 }
 626
 627 /********************************************************************
 628  * EnumOptionInfo
 629  */
 630
 631 EnumOptionInfo::EnumOptionInfo(EnumOptionStorage *option)
 632     : OptionInfo(option)
 633 {
 634 }
 635
 636 const EnumOptionStorage &EnumOptionInfo::option() const
 637 {
 638     return static_cast<const EnumOptionStorage &>(OptionInfo::option());
 639 }
 640
 641 const std::vector<std::string> &EnumOptionInfo::allowedValues() const
 642 {
 643     return option().allowedValues();
 644 }
 645
 646 /********************************************************************
 647  * EnumOption helpers
 648  */
 649
 650 namespace internal
 651 {
 652
 653 //! \cond internal
 654 AbstractOptionStorage *
 655 createEnumOptionStorage(const AbstractOption &option,
 656                         const char *const *enumValues, int count,
 657                         int defaultValue, int defaultValueIfSet,
 658                         IOptionValueStore<int> *store)
 659 {
 660     std::unique_ptr<IOptionValueStore<int> > storePtr(store);
 661     return new EnumOptionStorage(option, enumValues, count, defaultValue,
 662                                  defaultValueIfSet, move(storePtr));
 663 }
 664 //! \endcond
 665
 666 } // namespace internal
 667
 668 } // namespace gmx