SessionReader.cpp 83.5 KB
Newer Older
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
///////////////////////////////////////////////////////////////////////////////
//
// File SessionReader.cpp
//
// For more information, please see: http://www.nektar.info
//
// The MIT License
//
// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
// Department of Aeronautics, Imperial College London (UK), and Scientific
// Computing and Imaging Institute, University of Utah (USA).
//
// License for the specific language governing rights and limitations under
// Permission is hereby granted, free of charge, to any person obtaining a
// copy of this software and associated documentation files (the "Software"),
// to deal in the Software without restriction, including without limitation
// the rights to use, copy, modify, merge, publish, distribute, sublicense,
// and/or sell copies of the Software, and to permit persons to whom the
// Software is furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included
Dave Moxey's avatar
Dave Moxey committed
22
// in all copies or substantial portions of the Software.
23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
// DEALINGS IN THE SOFTWARE.
//
// Description: Session reader
//
///////////////////////////////////////////////////////////////////////////////

#ifndef TIXML_USE_STL
#define TIXML_USE_STL
#endif

40
#include <LibUtilities/BasicUtils/SessionReader.h>
41
#include <LibUtilities/BasicConst/GitRevision.h>
42

43
#include <iostream>
44
#include <fstream>
45 46 47
#include <string>
using namespace std;

48 49 50
#include <boost/iostreams/filtering_streambuf.hpp>
#include <boost/iostreams/copy.hpp>
#include <boost/iostreams/filter/gzip.hpp>
51
#include <boost/algorithm/string.hpp>
52
#include <tinyxml.h>
53
#include <LibUtilities/BasicUtils/ErrorUtil.hpp>
54 55
#include <LibUtilities/BasicUtils/Equation.h>
#include <LibUtilities/Memory/NekMemoryManager.hpp>
56
#include <LibUtilities/BasicUtils/ParseUtils.h>
57
#include <LibUtilities/BasicUtils/FileSystem.h>
58

59
#include <boost/program_options.hpp>
60
#include <boost/format.hpp>
61

62 63 64 65
#ifndef NEKTAR_VERSION
#define NEKTAR_VERSION "Unknown"
#endif

66
namespace po = boost::program_options;
67
namespace io = boost::iostreams;
68

69 70 71 72
namespace Nektar
{
    namespace LibUtilities
    {
73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110
        /**
         * @class SessionReader
         *
         * This class provides an interface to Nektar++-specific content in a
         * supplied XML document. It also initialises a Nektar++ session
         * including setting up communication for parallel execution and where
         * necessary partitioning the supplied mesh for running across multiple
         * processes.
         *
         * A session should be initialised at the beginning of a user's
         * application by passing the command-line arguments. This not only
         * allows the SessionReader to extract the name of the XML document to
         * load containing Nektar++ session information, but also supplies the
         * MPI arguments necessary for setting up parallel communication. The
         * SessionReader should be initialised using the #CreateInstance
         * function:
         * @code
         * LibUtilities::SessionReaderSharedPtr vSession
         *          = LibUtilities::SessionReader::CreateInstance(argc, argv);
         * @endcode
         * The instance \c vSession can now be passed to other key Nektar++
         * components during their construction.
         * @note At the end of the user application, it is important to call the
         * #Finalise routine in order to finalise any MPI communication and
         * correctly free resources.
         *
         * The SessionReader class provides streamlined, validated access to
         * session parameters, solver information and functions defined within a
         * Nektar++ XML document. The available routines and their usage is
         * documented below.
         *
         * In the case of solver information properties, the classes to which
         * these parameters are pertinent may register with the SessionReader
         * class the set of valid values for a given property. Such values may
         * also be associated with an enumeration value for more transparent use
         * of the property values in code.
         */

111 112 113 114 115 116 117 118 119 120 121 122 123
        /**
         * This map of maps stores the list of valid string values for a number
         * of solver information parameters. The top level map connects
         * different parameter names to their list of possible values. The list
         * of possible values is also a map, mapping a valid string to a
         * corresponding enum value.
         *
         * This list is populated through the #RegisterEnumValue static member
         * function which is called statically from various classes to register
         * the valid values for solver info parameters associated with them. The
         * map is therefore fully populated before the SessionReader class is
         * instantiated and a file is read in and parsed.
         */
124 125 126 127 128
        EnumMapList& SessionReader::GetSolverInfoEnums()
        {
            static EnumMapList solverInfoEnums;
            return solverInfoEnums;
        }
129 130 131 132 133 134 135 136 137 138


        /**
         * List of default values for solver information parameters to be used
         * in the case of them not being provided.
         *
         * This list is populated through the #RegisterDefaultSolverInfo static
         * member variable which is called statically from various classes to
         * register the default value for a given parameter.
         */
139 140 141 142 143
        SolverInfoMap& SessionReader::GetSolverInfoDefaults()
        {
            static SolverInfoMap solverInfoMap;
            return solverInfoMap;
        }
144 145


146 147 148 149 150 151 152
        /**
         * List of values for GlobalSysSoln parameters to be used to override
         * details given in SolverInfo
         *
         * This list is populated by ReadGlobalSysSoln if the
         * GLOBALSYSSOLNINFO section is defined in the input file.
         * This List allows for details to define for the Global Sys
153
         * solver for each variable.
154
         */
155 156 157 158 159
        GloSysSolnInfoList& SessionReader::GetGloSysSolnList()
        {
            static GloSysSolnInfoList gloSysSolnInfoList;
            return gloSysSolnInfoList;
        }
160

161 162 163 164 165 166 167 168
        /**
         * Lists the possible command-line argument which can be specified for
         * this executable.
         *
         * This list is populated through the #RegisterCmdLineArgument static
         * member function which is called statically from various classes to
         * register command-line arguments they need.
         */
169 170 171 172 173
        CmdLineArgMap& SessionReader::GetCmdLineArgMap()
        {
            static CmdLineArgMap cmdLineArguments;
            return cmdLineArguments;
        }
174 175


176 177 178 179 180 181 182 183
        /**
         * This constructor parses the command-line arguments given to the user
         * application to set up any MPI communication, read supplied XML
         * session files, and partition meshes where necessary.
         *
         * @param   argc        Number of command-line arguments
         * @param   argv        Array of command-line arguments
         */
184 185
        SessionReader::SessionReader(int argc, char *argv[])
        {
Chris Cantwell's avatar
Chris Cantwell committed
186
            m_xmlDoc    = 0;
187
            m_filenames = ParseCommandLineArguments(argc, argv);
188

189
            ASSERTL0(m_filenames.size() > 0, "No session file(s) given.");
190

191
            m_sessionName = ParseSessionName(m_filenames);
192

193
            // Create communicator
194
            CreateComm(argc, argv);
195

196 197
            TestSharedFilesystem();

198 199 200 201
            // If running in parallel change the default global sys solution
            // type.
            if (m_comm->GetSize() > 1)
            {
202
                GetSolverInfoDefaults()["GLOBALSYSSOLN"] =
203 204
                    "IterativeStaticCond";
            }
205 206 207 208 209 210 211

            m_exprEvaluator = MemoryManager<AnalyticExpressionEvaluator>
                ::AllocateSharedPtr();
            m_exprEvaluator->SetRandomSeed((m_comm->GetRank() + 1) * time(NULL));

            // Split up the communicator
            PartitionComm();
212 213 214
        }


215 216 217
        /**
         *
         */
218
        SessionReader::SessionReader(
219 220 221
            int                             argc,
            char                           *argv[],
            const std::vector<std::string> &pFilenames,
222
            const CommSharedPtr            &pComm)
223 224 225
        {
            ASSERTL0(pFilenames.size() > 0, "No filenames specified.");

226
            ParseCommandLineArguments(argc, argv);
Chris Cantwell's avatar
Chris Cantwell committed
227
            m_xmlDoc      = 0;
228
            m_filenames   = pFilenames;
229

230
            m_sessionName = ParseSessionName(m_filenames);
231

232
            // Create communicator
233 234
            if (!pComm.get())
            {
235
                CreateComm(argc, argv);
236 237 238 239 240
            }
            else
            {
                m_comm = pComm;
            }
241

242 243
            TestSharedFilesystem();

244 245 246 247
            // If running in parallel change the default global sys solution
            // type.
            if (m_comm->GetSize() > 1)
            {
248
                GetSolverInfoDefaults()["GLOBALSYSSOLN"] =
249
                    "IterativeStaticCond";
250
            }
251 252 253 254 255 256 257

            m_exprEvaluator = MemoryManager<AnalyticExpressionEvaluator>
                ::AllocateSharedPtr();
            m_exprEvaluator->SetRandomSeed((m_comm->GetRank() + 1) * time(NULL));

            // Split up the communicator
            PartitionComm();
258 259 260
        }


261 262 263
        /**
         *
         */
264 265
        SessionReader::~SessionReader()
        {
266 267 268 269
            if (m_xmlDoc)
            {
                delete m_xmlDoc;
            }
270 271
        }

272 273 274 275 276 277 278

        /**
         * Performs the main initialisation of the object. The XML file provided
         * on the command-line is loaded and any mesh partitioning is done. The
         * resulting process-specific XML file (containing the process's
         * geometry partition) is then reloaded and parsed.
         */
279 280
        void SessionReader::InitSession(
            const std::vector<std::string> &filenames)
281
        {
282 283 284 285 286
            // Re-load filenames for session if required.
            if (filenames.size() > 0)
            {
                m_filenames = filenames;
            }
287

288 289 290 291 292
            // Merge document if required.
            if (m_xmlDoc)
            {
                delete m_xmlDoc;
            }
293

Dave Moxey's avatar
Dave Moxey committed
294
            m_xmlDoc = MergeDoc(m_filenames);
295

296 297
            // Parse the XML data in #m_xmlDoc
            ParseDocument();
298 299 300 301

            // Override SOLVERINFO and parameters with any specified on the
            // command line.
            CmdLineOverride();
302

303 304 305
            // Verify SOLVERINFO values
            VerifySolverInfo();

306 307 308
            // In verbose mode, print out parameters and solver info sections
            if (m_verbose && m_comm)
            {
309
                if (m_comm->TreatAsRankZero() && m_parameters.size() > 0)
310 311
                {
                    cout << "Parameters:" << endl;
312
                    for (auto &x : m_parameters)
313
                    {
314
                        cout << "\t" << x.first << " = " << x.second << endl;
315 316 317 318
                    }
                    cout << endl;
                }

319
                if (m_comm->TreatAsRankZero() && m_solverInfo.size() > 0)
320 321
                {
                    cout << "Solver Info:" << endl;
322
                    for (auto &x : m_solverInfo)
323
                    {
324
                        cout << "\t" << x.first << " = " << x.second << endl;
325 326 327 328
                    }
                    cout << endl;
                }
            }
329 330
        }

331 332 333 334 335 336 337 338
        void SessionReader::TestSharedFilesystem()
        {
            m_sharedFilesystem = false;

            if (m_comm->GetSize() > 1)
            {
                if (m_comm->GetRank() == 0)
                {
Kilian Lackhove's avatar
Kilian Lackhove committed
339
                    std::ofstream testfile("shared-fs-testfile");
340
                    testfile << "" << std::endl;
Kilian Lackhove's avatar
Kilian Lackhove committed
341
                    ASSERTL1(!testfile.fail(), "Test file creation failed");
342 343 344 345
                    testfile.close();
                }
                m_comm->Block();

Kilian Lackhove's avatar
Kilian Lackhove committed
346
                int exists = (bool)boost::filesystem::exists("shared-fs-testfile");
347 348 349 350
                m_comm->AllReduce(exists, LibUtilities::ReduceSum);

                m_sharedFilesystem = (exists == m_comm->GetSize());

Kilian Lackhove's avatar
Kilian Lackhove committed
351 352
                if ((m_sharedFilesystem && m_comm->GetRank() == 0) ||
                    !m_sharedFilesystem)
353 354 355 356 357 358 359 360 361 362 363
                {
                    std::remove("shared-fs-testfile");
                }
            }
            else
            {
                m_sharedFilesystem = false;
            }

            if (m_verbose && m_comm->GetRank() == 0 && m_sharedFilesystem)
            {
Kilian Lackhove's avatar
Kilian Lackhove committed
364
                cout << "Shared filesystem detected" << endl;
365 366 367 368
            }
        }


369
        /**
370 371
         * @brief Parses the command-line arguments for known options and
         * filenames.
372
         */
373 374
        std::vector<std::string> SessionReader::ParseCommandLineArguments(
            int argc, char *argv[])
375 376 377 378
        {
            // List the publically visible options (listed using --help)
            po::options_description desc("Allowed options");
            desc.add_options()
379
                ("verbose,v",    "be verbose")
380
                ("version,V",    "print version information")
381
                ("help,h",       "print this help message")
382
                ("solverinfo,I", po::value<vector<std::string> >(),
383 384 385
                                 "override a SOLVERINFO property")
                ("parameter,P",  po::value<vector<std::string> >(),
                                 "override a parameter")
386 387 388 389 390 391
                ("npx",          po::value<int>(),
                                 "number of procs in X-dir")
                ("npy",          po::value<int>(),
                                 "number of procs in Y-dir")
                ("npz",          po::value<int>(),
                                 "number of procs in Z-dir")
392
                ("nsz",          po::value<int>(),
393
                                 "number of slices in Z-dir")
394 395
                ("part-only",    po::value<int>(),
                                 "only partition mesh into N partitions.")
396 397
                ("part-only-overlapping",    po::value<int>(),
                                 "only partition mesh into N overlapping partitions.")
398
                ("part-info",    "Output partition information")
399
#ifdef NEKTAR_USE_CWIPI
400 401
                ("cwipi",        po::value<std::string>(),
                                 "set CWIPI name")
402
#endif
403
            ;
404

405
            for (auto &cmdIt : GetCmdLineArgMap())
406
            {
407 408
                std::string names = cmdIt.first;
                if (cmdIt.second.shortName != "")
409
                {
410
                    names += "," + cmdIt.second.shortName;
411
                }
412
                if (cmdIt.second.isFlag)
413 414
                {
                    desc.add_options()
415
                        (names.c_str(), cmdIt.second.description.c_str())
416 417 418 419 420 421
                    ;
                }
                else
                {
                    desc.add_options()
                        (names.c_str(), po::value<std::string>(),
422
                         cmdIt.second.description.c_str())
423 424
                    ;
                }
425
            }
426 427 428 429 430

            // List hidden options (e.g. session file arguments are not actually
            // specified using the input-file option by the user).
            po::options_description hidden("Hidden options");
            hidden.add_options()
431
                    ("input-file", po::value< vector<string> >(),
432
                                   "input filename")
433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456
            ;

            // Combine all options for the parser
            po::options_description all("All options");
            all.add(desc).add(hidden);

            // Session file is a positional option
            po::positional_options_description p;
            p.add("input-file", -1);

            // Parse the command-line options
            po::parsed_options parsed = po::command_line_parser(argc, argv).
                                                options(all).
                                                positional(p).
                                                allow_unregistered().
                                                run();

            // Extract known options to map and update
            po::store(parsed, m_cmdLineOptions);
            po::notify(m_cmdLineOptions);

            // Help message
            if (m_cmdLineOptions.count("help"))
            {
457 458 459 460 461 462 463 464 465 466 467 468 469 470 471
                cout << desc;
                exit(0);
            }

            // Version information
            if (m_cmdLineOptions.count("version"))
            {
                cout << "Nektar++ version " << NEKTAR_VERSION;

                if (NekConstants::kGitSha1 != "GITDIR-NOTFOUND")
                {
                    string sha1(NekConstants::kGitSha1);
                    string branch(NekConstants::kGitBranch);
                    boost::replace_all(branch, "refs/heads/", "");

Dave Moxey's avatar
Dave Moxey committed
472 473 474 475 476 477 478 479 480 481 482 483
                    cout << " (git changeset " << sha1.substr(0, 8) << ", ";

                    if (branch == "")
                    {
                        cout << "detached head";
                    }
                    else
                    {
                        cout << "head " << branch;
                    }

                    cout << ")";
484 485 486
                }

                cout << endl;
487 488 489 490 491 492 493 494 495 496 497 498
                exit(0);
            }

            // Enable verbose mode
            if (m_cmdLineOptions.count("verbose"))
            {
                m_verbose = true;
            }
            else
            {
                m_verbose = false;
            }
499

500
            // Print a warning for unknown options
501
            for (auto &x : parsed.options)
502
            {
503
                if (x.unregistered)
504
                {
505
                    cout << "Warning: Unknown option: " << x.string_key
506
                         << endl;
507 508 509 510 511 512
                }
            }

            // Return the vector of filename(s) given as positional options
            if (m_cmdLineOptions.count("input-file"))
            {
513 514
                return m_cmdLineOptions["input-file"].as<
                    std::vector<std::string> >();
515 516 517 518 519 520 521 522
            }
            else
            {
                return std::vector<std::string>();
            }
        }


523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560
        /**
         *
         */
        std::string SessionReader::ParseSessionName(
                std::vector<std::string> &filenames)
        {
            ASSERTL0(!filenames.empty(),
                     "At least one filename expected.");

            std::string retval = "";

            // First input file defines the session name
            std::string fname = filenames[0];

            // If loading a pre-partitioned mesh, remove _xml extension
            if (fname.size() > 4 &&
                fname.substr(fname.size() - 4, 4) == "_xml")
            {
                retval = fname.substr(0, fname.find_last_of("_"));
            }
            // otherwise remove the .xml extension
            else if (fname.size() > 4 &&
                fname.substr(fname.size() - 4, 4) == ".xml")
            {
                retval = fname.substr(0, fname.find_last_of("."));
            }
            // If compressed .xml.gz, remove both extensions
            else if (fname.size() > 7 &&
                fname.substr(fname.size() - 7, 7) == ".xml.gz")
            {
                retval = fname.substr(0, fname.find_last_of("."));
                retval = retval.substr(0, retval.find_last_of("."));
            }

            return retval;
        }


561 562 563
        /**
         *
         */
564 565
        TiXmlDocument& SessionReader::GetDocument()
        {
566
            ASSERTL1(m_xmlDoc, "XML Document not defined.");
567 568 569
            return *m_xmlDoc;
        }

570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589

        /**
         * The single parameter specifies a path to the requested element in a
         * similar format to the filesystem path. Given the following XML:
         * @code
         * <NEKTAR>
         *   <CONDITIONS>
         *     <PARAMETERS>
         *     ...
         *     </PARAMETERS>
         *   </CONDITIONS>
         * </NEKTAR>
         * @endcode
         * the PARAMETERS element would be retrieved by requesting the path:
         * @code
         * Nektar/Conditions/Parameters
         * @endcode
         * @note Paths are case-insensitive.
         *
         * @param   pPath       Path to requested element.
590 591
         *
         * @return Direct pointer to requested XML Element.
592
         */
593 594 595
        TiXmlElement* SessionReader::GetElement(const string& pPath)
        {
            std::string vPath = boost::to_upper_copy(pPath);
596 597 598
            std::vector<std::string> st;
            boost::split(st, vPath, boost::is_any_of("\\/ "));
            ASSERTL0(st.size() > 0, "No path given in XML element request.");
599

600
            TiXmlElement* vReturn = m_xmlDoc->FirstChildElement(st[0].c_str());
601
            ASSERTL0(vReturn, std::string("Cannot find element '")
602 603
                              + st[0] + std::string("'."));
            for (int i = 1; i < st.size(); ++i)
604
            {
605
                vReturn = vReturn->FirstChildElement(st[i].c_str());
606
                ASSERTL0(vReturn, std::string("Cannot find element '")
607
                                  + st[i] + std::string("'."));
608 609 610 611
            }
            return vReturn;
        }

612 613 614 615 616

        /**
         *
         */
        bool SessionReader::DefinesElement(const std::string &pPath) const
617 618
        {
            std::string vPath = boost::to_upper_copy(pPath);
619 620 621
            std::vector<std::string> st;
            boost::split(st, vPath, boost::is_any_of("\\/ "));
            ASSERTL0(st.size() > 0, "No path given in XML element request.");
622

623
            TiXmlElement* vReturn = m_xmlDoc->FirstChildElement(st[0].c_str());
624
            ASSERTL0(vReturn, std::string("Cannot find element '")
625 626
                              + st[0] + std::string("'."));
            for (int i = 1; i < st.size(); ++i)
627
            {
628
                vReturn = vReturn->FirstChildElement(st[i].c_str());
629 630 631 632 633
                if (!vReturn) return false;
            }
            return true;
        }

634 635 636 637

        /**
         *
         */
638
        const std::vector<std::string>& SessionReader::GetFilenames() const
639
        {
640
            return m_filenames;
641 642
        }

643 644 645 646

        /**
         *
         */
647 648 649 650 651
        const std::string& SessionReader::GetSessionName() const
        {
            return m_sessionName;
        }

652

653 654 655 656 657 658
        /**
         * Output is of the form [sessionName]_P[idx] where idx is the rank
         * of the process.
         */
        const std::string SessionReader::GetSessionNameRank() const
        {
659
            std::string  dirname = m_sessionName + "_xml";
660
            fs::path     pdirname(dirname);
661

662
            std::string vFilename = "P" + boost::lexical_cast<std::string>(m_comm->GetRowComm()->GetRank());
663
            fs::path    pFilename(vFilename);
664

665 666 667 668
            fs::path fullpath = pdirname / pFilename;

            return PortablePath(fullpath);
        }
669

670 671 672
        /**
         *
         */
673 674 675 676 677
        CommSharedPtr& SessionReader::GetComm()
        {
            return m_comm;
        }

678 679 680 681
        bool SessionReader::GetSharedFilesystem()
        {
            return m_sharedFilesystem;
        }
682 683 684 685 686 687 688

        /**
         * This routine finalises any parallel communication.
         *
         * @note This routine should be called at the very end of a users
         * application.
         */
689 690 691 692 693
        void SessionReader::Finalise()
        {
            m_comm->Finalise();
        }

694

695 696 697 698 699 700
        /**
         *
         */
        bool SessionReader::DefinesParameter(const std::string& pName) const
        {
            std::string vName = boost::to_upper_copy(pName);
701
            return m_parameters.find(vName) != m_parameters.end();
702 703
        }

704 705 706 707 708 709 710 711 712

        /**
         * If the parameter is not defined, termination occurs. Therefore, the
         * parameters existence should be tested for using #DefinesParameter
         * before calling this function.
         *
         * @param   pName       The name of a floating-point parameter.
         * @returns The value of the floating-point parameter.
         */
713 714
        const NekDouble& SessionReader::GetParameter(
            const std::string& pName) const
715 716
        {
            std::string vName = boost::to_upper_copy(pName);
717
            auto paramIter = m_parameters.find(vName);
718

719 720
            ASSERTL0(paramIter != m_parameters.end(),
                     "Unable to find requested parameter: " + pName);
721

722
            return paramIter->second;
723 724
        }

725 726 727 728

        /**
         *
         */
729 730
        void SessionReader::LoadParameter(
            const std::string &pName, int &pVar) const
731 732
        {
            std::string vName = boost::to_upper_copy(pName);
733
            auto paramIter = m_parameters.find(vName);
734
            ASSERTL0(paramIter != m_parameters.end(), "Required parameter '" +
735
                     pName + "' not specified in session.");
736
            pVar = (int)round(paramIter->second);
737 738
        }

739 740 741 742

        /**
         *
         */
743 744
        void SessionReader::LoadParameter(
            const std::string &pName, int &pVar, const int &pDefault) const
745 746
        {
            std::string vName = boost::to_upper_copy(pName);
747
            auto paramIter = m_parameters.find(vName);
748
            if(paramIter != m_parameters.end())
749
            {
750
                pVar = (int)round(paramIter->second);
751 752 753 754 755 756 757
            }
            else
            {
                pVar  = pDefault;
            }
        }

758 759 760 761

        /**
         *
         */
762 763
        void SessionReader::LoadParameter(
            const std::string &pName, NekDouble& pVar) const
764 765
        {
            std::string vName = boost::to_upper_copy(pName);
766
            auto paramIter = m_parameters.find(vName);
767
            ASSERTL0(paramIter != m_parameters.end(), "Required parameter '" +
768 769
                     pName + "' not specified in session.");
            pVar = paramIter->second;
770 771
        }

772 773 774 775

        /**
         *
         */
776
        void SessionReader::LoadParameter(
777 778
            const std::string &pName,
                  NekDouble   &pVar,
779
            const NekDouble   &pDefault) const
780 781
        {
            std::string vName = boost::to_upper_copy(pName);
782
            auto paramIter = m_parameters.find(vName);
783
            if(paramIter != m_parameters.end())
784
            {
785
                pVar = paramIter->second;
786 787 788
            }
            else
            {
789
                pVar = pDefault;
790 791 792
            }
        }

793

Spencer Sherwin's avatar
Spencer Sherwin committed
794 795 796 797

        /**
         *
         */
798
        void SessionReader::SetParameter(const std::string &pName, int &pVar)
Spencer Sherwin's avatar
Spencer Sherwin committed
799 800 801 802 803 804 805 806 807
        {
            std::string vName = boost::to_upper_copy(pName);
            m_parameters[vName] = pVar;
        }


        /**
         *
         */
808
        void SessionReader::SetParameter(
809
            const std::string &pName, NekDouble& pVar)
Spencer Sherwin's avatar
Spencer Sherwin committed
810 811 812 813 814 815 816
        {
            std::string vName = boost::to_upper_copy(pName);
            m_parameters[vName] = pVar;
        }



817 818 819 820
        /**
         *
         */
        bool SessionReader::DefinesSolverInfo(const std::string &pName) const
821 822
        {
            std::string vName = boost::to_upper_copy(pName);
823
            auto infoIter = m_solverInfo.find(vName);
824
            return (infoIter != m_solverInfo.end());
825 826
        }

827 828 829 830

        /**
         *
         */
831 832
        const std::string& SessionReader::GetSolverInfo(
            const std::string &pProperty) const
833 834
        {
            std::string vProperty = boost::to_upper_copy(pProperty);
835
            auto iter = m_solverInfo.find(vProperty);
836

837 838
            ASSERTL1(iter != m_solverInfo.end(),
                     "Unable to find requested property: " + pProperty);
839

840
            return iter->second;
841 842
        }

843 844 845 846
        /**
         *
         */
        void SessionReader::SetSolverInfo(
847
            const std::string &pProperty, const std::string &pValue)
848 849
        {
            std::string vProperty = boost::to_upper_copy(pProperty);
850
            auto iter = m_solverInfo.find(vProperty);
851 852 853 854 855 856

            ASSERTL1(iter != m_solverInfo.end(),
                     "Unable to find requested property: " + pProperty);

            iter->second = pValue;
        }
857 858 859 860

        /**
         *
         */
861
        void SessionReader::LoadSolverInfo(
862 863
            const std::string &pName,
                  std::string &pVar,
864
            const std::string &pDefault) const
865 866
        {
            std::string vName = boost::to_upper_copy(pName);
867
            auto infoIter = m_solverInfo.find(vName);
868
            if(infoIter != m_solverInfo.end())
869
            {
870
                pVar = infoIter->second;
871 872 873
            }
            else
            {
874
                pVar = pDefault;
875 876 877
            }
        }

878 879 880 881

        /**
         *
         */
882 883 884 885 886
        void SessionReader::MatchSolverInfo(
            const std::string &pName,
            const std::string &pTrueVal,
                  bool        &pVar,
            const bool        &pDefault) const
887 888
        {
            std::string vName = boost::to_upper_copy(pName);
889
            auto infoIter = m_solverInfo.find(vName);
890
            if(infoIter != m_solverInfo.end())
891
            {
892
                pVar = boost::iequals(infoIter->second, pTrueVal);
893 894 895
            }
            else
            {
896
                pVar = pDefault;
897 898 899
            }
        }

900 901 902 903

        /**
         *
         */
904 905 906
        bool SessionReader::MatchSolverInfo(
            const std::string &pName,
            const std::string &pTrueVal) const
907 908 909 910
        {
            if (DefinesSolverInfo(pName))
            {
                std::string vName = boost::to_upper_copy(pName);
911
                auto iter = m_solverInfo.find(vName);
912
                if(iter != m_solverInfo.end())
913 914 915 916 917 918 919 920
                {
                    return true;
                }
            }
            return false;
        }


921 922 923
        /**
         *
         */
924
        bool SessionReader::DefinesGlobalSysSolnInfo(const std::string &pVariable,
925 926
                                                     const std::string &pProperty) const
        {
927
            auto iter = GetGloSysSolnList().find(pVariable);
928
            if(iter == GetGloSysSolnList().end())
929 930 931 932 933
            {
                return false;
            }

            std::string vProperty = boost::to_upper_copy(pProperty);
934

935
            auto iter1 = iter->second.find(vProperty);
936 937 938 939
            if(iter1 == iter->second.end())
            {
                return false;
            }
940

941 942 943
            return true;
        }

944

945 946 947 948 949
        /**
         *
         */
        const std::string &SessionReader::GetGlobalSysSolnInfo(const std::string &pVariable, const std::string &pProperty) const
        {
950 951 952
            auto iter = GetGloSysSolnList().find(pVariable);
            ASSERTL0(iter != GetGloSysSolnList().end(),
                     "Failed to find variable in GlobalSysSolnInfoList");
953 954

            std::string vProperty = boost::to_upper_copy(pProperty);
955
            auto iter1 = iter->second.find(vProperty);
956

957 958
            ASSERTL0(iter1 != iter->second.end(),
                     "Failed to find property: " + vProperty + " in GlobalSysSolnInfoList");
959

960 961
            return iter1->second;
        }
962

963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995
        std::string SessionReader::GetGeometryType() const
        {
            TiXmlElement *xmlGeom = m_xmlDoc->FirstChildElement("NEKTAR")
                ->FirstChildElement("GEOMETRY");
            TiXmlAttribute *attr  = xmlGeom->FirstAttribute();
            while (attr)
            {
                std::string attrName(attr->Name());
                if (attrName == "HDF5FILE")
                {
                    // there is a file pointer, therefore is HDF5
                    return "HDF5";
                }
                // Get the next attribute.
                attr = attr->Next();
            }

            // Check the VERTEX block. If this is compressed, assume the file is
            // compressed, otherwise assume uncompressed.
            TiXmlElement *element = xmlGeom->FirstChildElement("VERTEX");
            string IsCompressed;
            element->QueryStringAttribute("COMPRESSED", &IsCompressed);

            if (IsCompressed.size() > 0)
            {
                return "XmlCompressed";
            }

            // no file pointer or compressed, just standard xml
            return "Xml";
        }

       /**
996 997 998
         *
         */
        bool SessionReader::DefinesGeometricInfo(const std::string &pName) const
999 1000
        {
            std::string vName = boost::to_upper_copy(pName);
1001
            return m_geometricInfo.find(vName) != m_geometricInfo.end();
1002 1003
        }

1004 1005 1006 1007

        /**
         *
         */
1008 1009 1010 1011
        void SessionReader::LoadGeometricInfo(
            const std::string &pName,
                  std::string &pVar,
            const std::string &pDefault) const
1012 1013
        {
            std::string vName = boost::to_upper_copy(pName);
1014
            auto iter = m_geometricInfo.find(vName);
1015
            if(iter != m_geometricInfo.end())
1016
            {
1017
                pVar = iter->second;
1018 1019 1020
            }
            else
            {
1021
                pVar = pDefault;
1022 1023 1024
            }
        }

1025 1026 1027 1028

        /**
         *
         */
1029 1030 1031 1032
        void SessionReader::LoadGeometricInfo(
            const std::string &pName,
                  bool        &pVar,
            const bool        &pDefault) const
1033 1034
        {
            std::string vName = boost::to_upper_copy(pName);
1035
            auto iter = m_geometricInfo.find(vName);
1036
            if(iter != m_geometricInfo.end())
1037
            {
1038
                if (iter->second == "TRUE")
1039 1040 1041 1042 1043 1044 1045 1046 1047 1048
                {
                    pVar = true;
                }
                else
                {
                    pVar = false;
                }
            }
            else
            {
1049
                pVar = pDefault;
1050 1051 1052
            }
        }

1053

1054 1055 1056
        /**
         *
         */
1057 1058 1059 1060
        void SessionReader::LoadGeometricInfo(
            const std::string &pName,
                  NekDouble   &pVar,
            const NekDouble   &pDefault) const
1061 1062
        {
            std::string vName = boost::to_upper_copy(pName);
1063
            auto iter = m_geometricInfo.find(vName);
1064
            if(iter != m_geometricInfo.end())
1065
            {
1066
                pVar = std::atoi(iter->second.c_str());
1067 1068 1069
            }
            else
            {
1070
                pVar = pDefault;
1071 1072 1073 1074
            }
        }


1075 1076 1077
        /**
         *
         */
1078 1079 1080 1081 1082
        void SessionReader::MatchGeometricInfo(
            const std::string &pName,
            const std::string &pTrueVal,
                  bool        &pVar,
            const bool        &pDefault) const
1083 1084
        {
            std::string vName = boost::to_upper_copy(pName);
1085
            auto iter = m_geometricInfo.find(vName);
1086
            if(iter != m_geometricInfo.end())
1087
            {
1088
                pVar = boost::iequals(iter->second, pTrueVal);
1089 1090 1091 1092 1093 1094 1095 1096
            }
            else
            {
                pVar  = pDefault;
            }
        }


1097 1098 1099
        /**
         *
         */
1100 1101
        const std::string& SessionReader::GetVariable(
            const unsigned int &idx) const
1102 1103 1104 1105 1106
        {
            ASSERTL0(idx < m_variables.size(), "Variable index out of range.");
            return m_variables[idx];
        }

1107

1108 1109 1110 1111

        /**
         *
         */
1112 1113
        void SessionReader::SetVariable(const unsigned int &idx,
                                        std::string newname)
1114 1115 1116 1117 1118 1119
        {
            ASSERTL0(idx < m_variables.size(), "Variable index out of range.");
            m_variables[idx] = newname;
        }


1120 1121 1122
        /**
         *
         */
1123 1124 1125 1126 1127
        std::vector<std::string> SessionReader::GetVariables() const
        {
            return m_variables;
        }

1128 1129 1130 1131 1132 1133 1134

        /**
         *
         */
        bool SessionReader::DefinesFunction(const std::string &pName) const
        {
            std::string vName = boost::to_upper_copy(pName);
1135
            return m_functions.find(vName) != m_functions.end();
1136 1137 1138 1139 1140 1141
        }


        /**
         *
         */
1142 1143
        bool SessionReader::DefinesFunction(
            const std::string &pName,
1144 1145
            const std::string &pVariable,
            const int pDomain) const
1146 1147 1148
        {
            std::string vName = boost::to_upper_copy(pName);

1149
            // Check function exists
1150 1151
            auto it1 = m_functions.find(vName);
            if (it1 != m_functions.end())
1152
            {
1153 1154
                pair<std::string, int> key(pVariable,pDomain);
                pair<std::string, int> defkey("*",pDomain);
1155
                bool varExists =
1156 1157
                    it1->second.find(key)    != it1->second.end() ||
                    it1->second.find(defkey) != it1->second.end();
1158
                return varExists;
1159 1160 1161 1162 1163 1164 1165 1166
            }
            return false;
        }


        /**
         *
         */
1167 1168
        EquationSharedPtr SessionReader::GetFunction(
            const std::string &pName,
1169 1170
            const std::string &pVariable,
            const int pDomain) const
1171 1172
        {
            std::string vName = boost::to_upper_copy(pName);
1173
            auto it1 = m_functions.find(vName);
1174

1175
            ASSERTL0(it1 != m_functions.end(),
1176 1177
                     std::string("No such function '") + pName
                     + std::string("' has been defined in the session file."));
1178 1179

            // Check for specific and wildcard definitions
1180 1181
            pair<std::string,int> key(pVariable,pDomain);
            pair<std::string,int> defkey("*",pDomain);
1182 1183 1184 1185 1186

            auto it2 = it1->second.find(key);
            auto it3 = it1->second.find(defkey);
            bool specific = it2 != it1->second.end();
            bool wildcard = it3 != it1->second.end();
1187 1188 1189

            // Check function is defined somewhere
            ASSERTL0(specific || wildcard,
1190
                     "No such variable " + pVariable
1191
                     + " in domain " + boost::lexical_cast<string>(pDomain)
1192 1193
                     + " defined for function " + pName
                     + " in session file.");
1194 1195 1196 1197 1198 1199 1200