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///////////////////////////////////////////////////////////////////////////////
//
// 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
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// in all copies or substantial portions of the Software.
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//
// 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

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#include <LibUtilities/BasicUtils/SessionReader.h>

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#include <iostream>
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#include <fstream>
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#include <string>
using namespace std;

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#include <boost/iostreams/filtering_streambuf.hpp>
#include <boost/iostreams/copy.hpp>
#include <boost/iostreams/filter/gzip.hpp>
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#include <boost/algorithm/string.hpp>
#include <tinyxml/tinyxml.h>
#include <LibUtilities/BasicUtils/ErrorUtil.hpp>
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#include <LibUtilities/BasicUtils/Equation.h>
#include <LibUtilities/Memory/NekMemoryManager.hpp>
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#include <LibUtilities/BasicUtils/MeshPartition.h>
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#include <LibUtilities/BasicUtils/ParseUtils.hpp>
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#include <LibUtilities/BasicUtils/FileSystem.h>
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#include <boost/program_options.hpp>
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#include <boost/format.hpp>
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namespace po = boost::program_options;
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namespace io = boost::iostreams;
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namespace Nektar
{
    namespace LibUtilities
    {
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        /**
         * @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.
         */

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        /**
         * 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.
         */
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        EnumMapList& SessionReader::GetSolverInfoEnums()
        {
            static EnumMapList solverInfoEnums;
            return solverInfoEnums;
        }
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        /**
         * 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.
         */
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        SolverInfoMap& SessionReader::GetSolverInfoDefaults()
        {
            static SolverInfoMap solverInfoMap;
            return solverInfoMap;
        }
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        /**
         * 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
         * solver for each variable. 
         */
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        GloSysSolnInfoList& SessionReader::GetGloSysSolnList()
        {
            static GloSysSolnInfoList gloSysSolnInfoList;
            return gloSysSolnInfoList;
        }
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        /**
         * 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.
         */
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        CmdLineArgMap& SessionReader::GetCmdLineArgMap()
        {
            static CmdLineArgMap cmdLineArguments;
            return cmdLineArguments;
        }
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        /**
         * 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
         */
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        SessionReader::SessionReader(int argc, char *argv[])
        {
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            m_xmlDoc    = 0;
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            m_filenames = ParseCommandLineArguments(argc, argv);
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            ASSERTL0(m_filenames.size() > 0, "No session file(s) given.");
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            m_filename    = m_filenames[0];
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            m_sessionName = m_filename.substr(0, m_filename.find_last_of('.'));
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            if (m_filename.size() > 3 &&
                m_filename.substr(m_filename.size() - 3, 3) == ".gz")
            {
                m_sessionName =
                    m_sessionName.substr(0, m_sessionName.find_last_of('.'));
            }
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            // Create communicator
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            CreateComm(argc, argv);
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            // If running in parallel change the default global sys solution
            // type.
            if (m_comm->GetSize() > 1)
            {
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                GetSolverInfoDefaults()["GLOBALSYSSOLN"] = 
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                    "IterativeStaticCond";
            }
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        }


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        /**
         *
         */
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        SessionReader::SessionReader(
            int                             argc, 
            char                           *argv[], 
            const std::vector<std::string> &pFilenames, 
            const CommSharedPtr            &pComm)
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        {
            ASSERTL0(pFilenames.size() > 0, "No filenames specified.");

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            ParseCommandLineArguments(argc, argv);
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            m_xmlDoc      = 0;
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            m_filenames   = pFilenames;
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            m_filename    = pFilenames[0];
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            m_sessionName = m_filename.substr(0, m_filename.find_last_of('.'));
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            if (m_filename.size() > 3 &&
                m_filename.substr(m_filename.size() - 3, 3) == ".gz")
            {
                m_sessionName =
                    m_sessionName.substr(0, m_sessionName.find_last_of('.'));
            }
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            // Create communicator
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            if (!pComm.get())
            {
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                CreateComm(argc, argv);
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            }
            else
            {
                m_comm = pComm;
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                if (m_comm->GetSize() > 1)
                {
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                    GetSolverInfoDefaults()["GLOBALSYSSOLN"] = 
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                        "IterativeStaticCond";
                }
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            }
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            // If running in parallel change the default global sys solution
            // type.
            if (m_comm->GetSize() > 1)
            {
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                GetSolverInfoDefaults()["GLOBALSYSSOLN"] = 
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                    "IterativeStaticCond";
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            }
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        }


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        /**
         *
         */
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        SessionReader::~SessionReader()
        {
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            delete m_xmlDoc;
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        }

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        /**
         * 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.
         */
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        void SessionReader::InitSession()
        {
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            m_exprEvaluator.SetRandomSeed((m_comm->GetRank() + 1) * time(NULL));

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            // Split up the communicator
            PartitionComm();

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            // Partition mesh
            PartitionMesh();

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            // Parse the XML data in #m_xmlDoc
            ParseDocument();
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            // Override SOLVERINFO and parameters with any specified on the
            // command line.
            CmdLineOverride();
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        }

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        /**
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         * @brief Parses the command-line arguments for known options and
         * filenames.
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         */
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        std::vector<std::string> SessionReader::ParseCommandLineArguments(
            int argc, char *argv[])
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        {
            // List the publically visible options (listed using --help)
            po::options_description desc("Allowed options");
            desc.add_options()
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                ("verbose,v",    "be verbose")
                ("help,h",       "print this help message")
                ("solverinfo,I", po::value<vector<std::string> >(), 
                                 "override a SOLVERINFO property")
                ("parameter,P",  po::value<vector<std::string> >(),
                                 "override a parameter")
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                ("shared-filesystem,s", "Using shared filesystem.")
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                ("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")
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                ("part-info",    "Output partition information")
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            ;
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            CmdLineArgMap::const_iterator cmdIt;
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            for (cmdIt  = GetCmdLineArgMap().begin();
                 cmdIt != GetCmdLineArgMap().end(); ++cmdIt)
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            {
                std::string names = cmdIt->first;
                if (cmdIt->second.shortName != "")
                {
                    names += "," + cmdIt->second.shortName;
                }
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                if (cmdIt->second.isFlag)
                {
                    desc.add_options()
                        (names.c_str(), cmdIt->second.description.c_str())
                    ;
                }
                else
                {
                    desc.add_options()
                        (names.c_str(), po::value<std::string>(),
                         cmdIt->second.description.c_str())
                    ;
                }
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            }
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            // 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()
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                    ("input-file", po::value< vector<string> >(), 
                                   "input filename")
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            ;

            // 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"))
            {
                cout << desc << endl;
                exit(0);
            }

            // Enable verbose mode
            if (m_cmdLineOptions.count("verbose"))
            {
                m_verbose = true;
            }
            else
            {
                m_verbose = false;
            }
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            // Print a warning for unknown options
            std::vector< po::basic_option<char> >::iterator x;
            for (x = parsed.options.begin(); x != parsed.options.end(); ++x)
            {
                if (x->unregistered)
                {
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                    cout << "Warning: Unknown option: " << x->string_key 
                         << endl;
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                }
            }

            // Return the vector of filename(s) given as positional options
            if (m_cmdLineOptions.count("input-file"))
            {
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                return m_cmdLineOptions["input-file"].as<
                    std::vector<std::string> >();
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            }
            else
            {
                return std::vector<std::string>();
            }
        }


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        /**
         *
         */
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        TiXmlDocument& SessionReader::GetDocument()
        {
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            ASSERTL1(m_xmlDoc, "XML Document not defined.");
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            return *m_xmlDoc;
        }

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        /**
         * 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.
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         *
         * @return Direct pointer to requested XML Element.
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         */
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        TiXmlElement* SessionReader::GetElement(const string& pPath)
        {
            std::string vPath = boost::to_upper_copy(pPath);
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            std::vector<std::string> st;
            boost::split(st, vPath, boost::is_any_of("\\/ "));
            ASSERTL0(st.size() > 0, "No path given in XML element request.");
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            TiXmlElement* vReturn = m_xmlDoc->FirstChildElement(st[0].c_str());
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            ASSERTL0(vReturn, std::string("Cannot find element '")
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                              + st[0] + std::string("'."));
            for (int i = 1; i < st.size(); ++i)
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            {
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                vReturn = vReturn->FirstChildElement(st[i].c_str());
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                ASSERTL0(vReturn, std::string("Cannot find element '")
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                                  + st[i] + std::string("'."));
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            }
            return vReturn;
        }

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        /**
         *
         */
        bool SessionReader::DefinesElement(const std::string &pPath) const
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        {
            std::string vPath = boost::to_upper_copy(pPath);
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            std::vector<std::string> st;
            boost::split(st, vPath, boost::is_any_of("\\/ "));
            ASSERTL0(st.size() > 0, "No path given in XML element request.");
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            TiXmlElement* vReturn = m_xmlDoc->FirstChildElement(st[0].c_str());
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            ASSERTL0(vReturn, std::string("Cannot find element '")
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                              + st[0] + std::string("'."));
            for (int i = 1; i < st.size(); ++i)
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            {
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                vReturn = vReturn->FirstChildElement(st[i].c_str());
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                if (!vReturn) return false;
            }
            return true;
        }

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        /**
         *
         */
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        const std::string& SessionReader::GetFilename() const
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        {
            return m_filename;
        }

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        /**
         *
         */
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        const std::string& SessionReader::GetSessionName() const
        {
            return m_sessionName;
        }

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        /**
         * Output is of the form [sessionName]_P[idx] where idx is the rank
         * of the process.
         */
        const std::string SessionReader::GetSessionNameRank() const
        {
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            std::string  dirname = m_sessionName + "_xml"; 
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            fs::path     pdirname(dirname);
            
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            std::string vFilename = "P" + boost::lexical_cast<std::string>(m_comm->GetRowComm()->GetRank());
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            fs::path    pFilename(vFilename);            
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            fs::path fullpath = pdirname / pFilename;

            return PortablePath(fullpath);
        }
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        /**
         *
         */
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        CommSharedPtr& SessionReader::GetComm()
        {
            return m_comm;
        }

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

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        /**
         *
         */
        bool SessionReader::DefinesParameter(const std::string& pName) const
        {
            std::string vName = boost::to_upper_copy(pName);
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            ParameterMap::const_iterator paramIter = m_parameters.find(vName);
            return (paramIter != m_parameters.end());
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        }

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        /**
         * 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.
         */
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        const NekDouble& SessionReader::GetParameter(
            const std::string& pName) const
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        {
            std::string vName = boost::to_upper_copy(pName);
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            ParameterMap::const_iterator paramIter = m_parameters.find(vName);
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            ASSERTL0(paramIter != m_parameters.end(),
                     "Unable to find requested parameter: " + pName);
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            return paramIter->second;
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        }

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        /**
         *
         */
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        void SessionReader::LoadParameter(
            const std::string &pName, int &pVar) const
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        {
            std::string vName = boost::to_upper_copy(pName);
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            ParameterMap::const_iterator paramIter = m_parameters.find(vName);
            ASSERTL0(paramIter != m_parameters.end(), "Required parameter '" + 
                     pName + "' not specified in session.");
            pVar = (int)floor(paramIter->second);
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        }

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        /**
         *
         */
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        void SessionReader::LoadParameter(
            const std::string &pName, int &pVar, const int &pDefault) const
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        {
            std::string vName = boost::to_upper_copy(pName);
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            ParameterMap::const_iterator paramIter = m_parameters.find(vName);
            if(paramIter != m_parameters.end())
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            {
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                pVar = (int)floor(paramIter->second);
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            }
            else
            {
                pVar  = pDefault;
            }
        }

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        /**
         *
         */
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        void SessionReader::LoadParameter(
            const std::string &pName, NekDouble& pVar) const
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        {
            std::string vName = boost::to_upper_copy(pName);
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            ParameterMap::const_iterator paramIter = m_parameters.find(vName);
            ASSERTL0(paramIter != m_parameters.end(), "Required parameter '" + 
                     pName + "' not specified in session.");
            pVar = paramIter->second;
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        }

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        /**
         *
         */
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        void SessionReader::LoadParameter(
            const std::string &pName, 
                  NekDouble   &pVar, 
            const NekDouble   &pDefault) const
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        {
            std::string vName = boost::to_upper_copy(pName);
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            ParameterMap::const_iterator paramIter = m_parameters.find(vName);
            if(paramIter != m_parameters.end())
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            {
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                pVar = paramIter->second;
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            }
            else
            {
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                pVar = pDefault;
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            }
        }

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        /**
         *
         */
        void SessionReader::SetParameter(const std::string &pName, int &pVar) 
        {
            std::string vName = boost::to_upper_copy(pName);
            m_parameters[vName] = pVar;
        }


        /**
         *
         */
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        void SessionReader::SetParameter(
            const std::string &pName, NekDouble& pVar) 
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        {
            std::string vName = boost::to_upper_copy(pName);
            m_parameters[vName] = pVar;
        }



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        /**
         *
         */
        bool SessionReader::DefinesSolverInfo(const std::string &pName) const
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        {
            std::string vName = boost::to_upper_copy(pName);
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            SolverInfoMap::const_iterator infoIter = m_solverInfo.find(vName);
            return (infoIter != m_solverInfo.end());
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        }

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        /**
         *
         */
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        const std::string& SessionReader::GetSolverInfo(
            const std::string &pProperty) const
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        {
            std::string vProperty = boost::to_upper_copy(pProperty);
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            SolverInfoMap::const_iterator iter = m_solverInfo.find(vProperty);
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            ASSERTL1(iter != m_solverInfo.end(),
                     "Unable to find requested property: " + pProperty);
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            return iter->second;
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        }

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        /**
         *
         */
        void SessionReader::SetSolverInfo(
            const std::string &pProperty, const std::string &pValue) 
        {
            std::string vProperty = boost::to_upper_copy(pProperty);
            SolverInfoMap::iterator iter = m_solverInfo.find(vProperty);

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

            iter->second = pValue;
        }
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        /**
         *
         */
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        void SessionReader::LoadSolverInfo(
            const std::string &pName, 
                  std::string &pVar, 
            const std::string &pDefault) const
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        {
            std::string vName = boost::to_upper_copy(pName);
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            SolverInfoMap::const_iterator infoIter = m_solverInfo.find(vName);
            if(infoIter != m_solverInfo.end())
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            {
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                pVar = infoIter->second;
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            }
            else
            {
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                pVar = pDefault;
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            }
        }

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        /**
         *
         */
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        void SessionReader::MatchSolverInfo(
            const std::string &pName,
            const std::string &pTrueVal,
                  bool        &pVar,
            const bool        &pDefault) const
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        {
            std::string vName = boost::to_upper_copy(pName);
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            SolverInfoMap::const_iterator infoIter = m_solverInfo.find(vName);
            if(infoIter != m_solverInfo.end())
738
            {
739
                pVar = boost::iequals(infoIter->second, pTrueVal);
740 741 742
            }
            else
            {
743
                pVar = pDefault;
744 745 746
            }
        }

747 748 749 750

        /**
         *
         */
751 752 753
        bool SessionReader::MatchSolverInfo(
            const std::string &pName,
            const std::string &pTrueVal) const
754 755 756 757
        {
            if (DefinesSolverInfo(pName))
            {
                std::string vName = boost::to_upper_copy(pName);
758 759
                SolverInfoMap::const_iterator iter = m_solverInfo.find(vName);
                if(iter != m_solverInfo.end())
760 761 762 763 764 765 766 767
                {
                    return true;
                }
            }
            return false;
        }


768 769 770 771 772 773 774
        /**
         *
         */
        bool SessionReader::DefinesGlobalSysSolnInfo(const std::string &pVariable, 
                                                     const std::string &pProperty) const
        {

775 776 777
            GloSysSolnInfoList::const_iterator iter =
                    GetGloSysSolnList().find(pVariable);
            if(iter == GetGloSysSolnList().end())
778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800
            {
                return false;
            }

            std::string vProperty = boost::to_upper_copy(pProperty);
            
            GloSysInfoMap::const_iterator iter1 = iter->second.find(vProperty);
            if(iter1 == iter->second.end())
            {
                return false;
            }
            
            return true;
        }

        
        /**
         *
         */
        const std::string &SessionReader::GetGlobalSysSolnInfo(const std::string &pVariable, const std::string &pProperty) const
        {
            GloSysSolnInfoList::const_iterator iter; 

801 802
            ASSERTL0( (iter = GetGloSysSolnList().find(pVariable)) !=
                              GetGloSysSolnList().end(),
803 804 805 806 807 808 809 810 811 812 813
                      "Failed to find variable in GlobalSysSolnInfoList");

            std::string vProperty = boost::to_upper_copy(pProperty);
            GloSysInfoMap::const_iterator iter1; 

            ASSERTL0( (iter1 = iter->second.find(vProperty)) != iter->second.end(),
                      "Failed to find property: " + vProperty + " in GlobalSysSolnInfoList");
            
            return iter1->second;
        }
        
814 815 816 817
        /**
         *
         */
        bool SessionReader::DefinesGeometricInfo(const std::string &pName) const
818 819
        {
            std::string vName = boost::to_upper_copy(pName);
820 821
            GeometricInfoMap::const_iterator iter = m_geometricInfo.find(vName);
            return (iter != m_geometricInfo.end());
822 823
        }

824 825 826 827

        /**
         *
         */
828 829 830 831
        void SessionReader::LoadGeometricInfo(
            const std::string &pName,
                  std::string &pVar,
            const std::string &pDefault) const
832 833
        {
            std::string vName = boost::to_upper_copy(pName);
834 835
            GeometricInfoMap::const_iterator iter = m_geometricInfo.find(vName);
            if(iter != m_geometricInfo.end())
836
            {
837
                pVar = iter->second;
838 839 840
            }
            else
            {
841
                pVar = pDefault;
842 843 844
            }
        }

845 846 847 848

        /**
         *
         */
849 850 851 852
        void SessionReader::LoadGeometricInfo(
            const std::string &pName,
                  bool        &pVar,
            const bool        &pDefault) const
853 854
        {
            std::string vName = boost::to_upper_copy(pName);
855 856
            GeometricInfoMap::const_iterator iter = m_geometricInfo.find(vName);
            if(iter != m_geometricInfo.end())
857
            {
858
                if (iter->second == "TRUE")
859 860 861 862 863 864 865 866 867 868
                {
                    pVar = true;
                }
                else
                {
                    pVar = false;
                }
            }
            else
            {
869
                pVar = pDefault;
870 871 872
            }
        }

873

874 875 876
        /**
         *
         */
877 878 879 880
        void SessionReader::LoadGeometricInfo(
            const std::string &pName,
                  NekDouble   &pVar,
            const NekDouble   &pDefault) const
881 882
        {
            std::string vName = boost::to_upper_copy(pName);
883 884
            GeometricInfoMap::const_iterator iter = m_geometricInfo.find(vName);
            if(iter != m_geometricInfo.end())
885
            {
886
                pVar = std::atoi(iter->second.c_str());
887 888 889
            }
            else
            {
890
                pVar = pDefault;
891 892 893 894
            }
        }


895 896 897
        /**
         *
         */
898 899 900 901 902
        void SessionReader::MatchGeometricInfo(
            const std::string &pName,
            const std::string &pTrueVal,
                  bool        &pVar,
            const bool        &pDefault) const
903 904
        {
            std::string vName = boost::to_upper_copy(pName);
905 906
            GeometricInfoMap::const_iterator iter = m_geometricInfo.find(vName);
            if(iter != m_geometricInfo.end())
907
            {
908
                pVar = boost::iequals(iter->second, pTrueVal);
909 910 911 912 913 914 915 916
            }
            else
            {
                pVar  = pDefault;
            }
        }


917 918 919
        /**
         *
         */
920 921
        const std::string& SessionReader::GetVariable(
            const unsigned int &idx) const
922 923 924 925 926
        {
            ASSERTL0(idx < m_variables.size(), "Variable index out of range.");
            return m_variables[idx];
        }

927

928 929 930 931 932 933 934 935 936 937 938 939

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


940 941 942
        /**
         *
         */
943 944 945 946 947
        std::vector<std::string> SessionReader::GetVariables() const
        {
            return m_variables;
        }

948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967

        /**
         *
         */
        bool SessionReader::DefinesFunction(const std::string &pName) const
        {
            FunctionMap::const_iterator it1;
            std::string vName = boost::to_upper_copy(pName);

            if ((it1 = m_functions.find(vName)) != m_functions.end())
            {
                return true;
            }
            return false;
        }


        /**
         *
         */
968 969
        bool SessionReader::DefinesFunction(
            const std::string &pName,
970 971
            const std::string &pVariable,
            const int pDomain) const
972 973
        {
            FunctionMap::const_iterator it1;
974
            FunctionVariableMap::const_iterator it2;
975 976
            std::string vName = boost::to_upper_copy(pName);

977 978
            // Check function exists
            if ((it1 = m_functions.find(vName))     != m_functions.end())
979
            {
980 981
                pair<std::string, int> key(pVariable,pDomain);
                pair<std::string, int> defkey("*",pDomain);
982
                bool varExists =
983 984
                    (it2 = it1->second.find(key)) != it1->second.end() ||
                    (it2 = it1->second.find(defkey)) != it1->second.end();
985
                return varExists;
986 987 988 989 990 991 992 993
            }
            return false;
        }


        /**
         *
         */
994 995
        EquationSharedPtr SessionReader::GetFunction(
            const std::string &pName,
996 997
            const std::string &pVariable,
            const int pDomain) const
998 999
        {
            FunctionMap::const_iterator it1;
1000
            FunctionVariableMap::const_iterator it2, it3;
1001 1002 1003 1004 1005
            std::string vName = boost::to_upper_copy(pName);

            ASSERTL0((it1 = m_functions.find(vName)) != m_functions.end(),
                     std::string("No such function '") + pName
                     + std::string("' has been defined in the session file."));
1006 1007

            // Check for specific and wildcard definitions
1008 1009 1010 1011 1012 1013
            pair<std::string,int> key(pVariable,pDomain);
            pair<std::string,int> defkey("*",pDomain);
            bool specific = (it2 = it1->second.find(key)) !=
                it1->second.end();
            bool wildcard = (it3 = it1->second.find(defkey)) !=
                it1->second.end();
1014 1015 1016

            // Check function is defined somewhere
            ASSERTL0(specific || wildcard,
1017 1018 1019 1020
                     "No such variable " + pVariable
                     + " in domain " + boost::lexical_cast<string>(pDomain) 
                     + " defined for function " + pName
                     + " in session file.");
1021 1022 1023 1024 1025 1026 1027

            // If not specific, must be wildcard
            if (!specific)
            {
                it2 = it3;
            }

1028
            ASSERTL0((it2->second.m_type == eFunctionTypeExpression),
1029
                    std::string("Function is defined by a file."));
1030
            return it2->second.m_expression;
1031 1032
        }

1033 1034 1035 1036

        /**
         *
         */
1037 1038
        EquationSharedPtr SessionReader::GetFunction(
            const std::string  &pName,
1039 1040
            const unsigned int &pVar,
            const int pDomain) const
1041 1042
        {
            ASSERTL0(pVar < m_variables.size(), "Variable index out of range.");
1043
            return GetFunction(pName, m_variables[pVar],pDomain);
1044 1045
        }

1046 1047 1048 1049

        /**
         *
         */
1050 1051
        enum FunctionType SessionReader::GetFunctionType(
            const std::string &pName,
1052 1053
            const std::string &pVariable,
            const int pDomain) const
1054 1055
        {
            FunctionMap::const_iterator it1;
1056
            FunctionVariableMap::const_iterator it2, it3;
1057 1058 1059 1060 1061 1062
            std::string vName = boost::to_upper_copy(pName);

            it1 = m_functions.find(vName);
            ASSERTL0 (it1 != m_functions.end(),
                      std::string("Function '") + pName
                      + std::string("' not found."));
1063 1064

            // Check for specific and wildcard definitions
1065 1066 1067
            pair<std::string,int> key(pVariable,pDomain);
            pair<std::string,int> defkey("*",pDomain);
            bool specific = (it2 = it1->second.find(key)) !=
1068
                            it1->second.end();
1069
            bool wildcard = (it3 = it1->second.find(defkey)) !=
1070 1071 1072 1073
                            it1->second.end();

            // Check function is defined somewhere
            ASSERTL0(specific || wildcard,
1074 1075 1076 1077
                     "No such variable " + pVariable
                     + " in domain " + boost::lexical_cast<string>(pDomain) 
                     + " defined for function " + pName
                     + " in session file.");
1078 1079 1080 1081 1082 1083 1084

            // If not specific, must be wildcard
            if (!specific)
            {
                it2 = it3;
            }

1085
            return it2->second.m_type;
1086 1087
        }

1088 1089 1090 1091

        /**
         *
         */
1092 1093
        enum FunctionType SessionReader::GetFunctionType(
            const std::string  &pName,
1094 1095
            const unsigned int &pVar,
            const int pDomain) const
1096 1097
        {
            ASSERTL0(pVar < m_variables.size(), "Variable index out of range.");
1098
            return GetFunctionType(pName, m_variables[pVar],pDomain);
1099 1100 1101 1102 1103 1104
        }


        /**
         *
         */
1105 1106
        std::string SessionReader::GetFunctionFilename(
            const std::string &pName, 
1107 1108
            const std::string &pVariable,
            const int pDomain) const
1109 1110
        {
            FunctionMap::const_iterator it1;
1111
            FunctionVariableMap::const_iterator it2, it3;
1112 1113 1114 1115 1116 1117
            std::string vName = boost::to_upper_copy(pName);

            it1 = m_functions.find(vName);
            ASSERTL0 (it1 != m_functions.end(),
                      std::string("Function '") + pName
                      + std::string("' not found."));
1118 1119

            // Check for specific and wildcard definitions
1120 1121 1122
            pair<std::string,int> key(pVariable,pDomain);
            pair<std::string,int> defkey("*",pDomain);
            bool specific = (it2 = it1->second.find(key)) !=
1123
                            it1->second.end();
1124
            bool wildcard = (it3 = it1->second.find(defkey)) !=
1125 1126 1127 1128
                            it1->second.end();

            // Check function is defined somewhere
            ASSERTL0(specific || wildcard,
1129 1130 1131 1132 1133
                     "No such variable " + pVariable
                     + " in domain " + boost::lexical_cast<string>(pDomain) 
                     + " defined for function " + pName
                     + " in session file.");
            
1134 1135 1136 1137 1138 1139
            // If not specific, must be wildcard
            if (!specific)
            {
                it2 = it3;
            }

1140 1141 1142 1143 1144 1145 1146
            return it2->second.m_filename;
        }


        /**
         *
         */
1147 1148
        std::string SessionReader::GetFunctionFilename(
            const std::string  &pName, 
1149 1150
            const unsigned int &pVar,
            const int pDomain) const
1151 1152
        {
            ASSERTL0(pVar < m_variables.size(), "Variable index out of range.");
1153
            return GetFunctionFilename(pName, m_variables[pVar],pDomain);
1154 1155 1156
        }


1157 1158 1159 1160 1161 1162 1163 1164 1165
        /**
         *
         */
        AnalyticExpressionEvaluator& SessionReader::GetExpressionEvaluator()
        {
            return m_exprEvaluator;
        }


1166 1167 1168 1169
        /**
         *
         */
        bool SessionReader::DefinesTag(const std::string &pName) const
1170 1171
        {
            std::string vName = boost::to_upper_copy(pName);
1172
            TagMap::const_iterator vTagIterator = m_tags.find(vName);
1173 1174 1175
            return (vTagIterator != m_tags.end());
        }

1176 1177 1178 1179

        /**
         *
         */
1180 1181 1182
        void SessionReader::SetTag(
            const std::string &pName, 
            const std::string &pValue)
1183 1184 1185 1186 1187
        {
            std::string vName = boost::to_upper_copy(pName);
            m_tags[vName] = pValue;
        }

1188 1189 1190 1191 1192

        /**
         *
         */
        const std::string &SessionReader::GetTag(const std::string& pName) const
1193 1194
        {
            std::string vName = boost::to_upper_copy(pName);
1195
            TagMap::const_iterator vTagIterator = m_tags.find(vName);
1196 1197 1198 1199 1200
            ASSERTL0(vTagIterator != m_tags.end(),
                     "Requested tag does not exist.");
            return vTagIterator->second;
        }

1201

1202 1203 1204 1205 1206 1207 1208 1209 1210
        /**
         *
         */
        const FilterMap &SessionReader::GetFilters() const
        {
            return m_filters;
        }


1211 1212 1213
        /**
         *
         */
1214 1215
        bool SessionReader::DefinesCmdLineArgument(
            const std::string& pName) const
1216 1217 1218 1219 1220
        {
            return (m_cmdLineOptions.find(pName) != m_cmdLineOptions.end());
        }


1221 1222 1223 1224 1225 1226
        /**
         *
         */
        void SessionReader::SubstituteExpressions(std::string& pExpr)
        {
            ExpressionMap::iterator exprIter;
1227 1228
            for (exprIter  = m_expressions.begin(); 
                 exprIter != m_expressions.end(); ++exprIter)
1229 1230 1231 1232 1233
            {
                boost::replace_all(pExpr, exprIter->first, exprIter->second);
            }
        }

1234 1235 1236 1237
        CompositeOrdering SessionReader::GetCompositeOrdering() const
        {
            return m_compOrder;
        }
1238

1239 1240 1241 1242 1243
        BndRegionOrdering SessionReader::GetBndRegionOrdering() const
        {
            return m_bndRegOrder;
        }

1244 1245 1246 1247 1248 1249 1250
        /**
         *
         */
        void SessionReader::LoadDoc(
            const std::string &pFilename,
            TiXmlDocument* pDoc) const
        {
1251 1252
            if (pFilename.size() > 3 &&
                pFilename.substr(pFilename.size() - 3, 3) == ".gz")
1253
            {
1254 1255 1256
                ifstream file(pFilename.c_str(),
                              ios_base::in | ios_base::binary);
                ASSERTL0(file.good(), "Unable to open file: " + pFilename);
1257
                stringstream ss;
1258 1259
                io::filtering_streambuf<io::input> in;
                in.push(io::gzip_decompressor());
1260
                in.push(file);
1261 1262 1263 1264 1265 1266 1267 1268 1269 1270
                try
                {
                    io::copy(in, ss);
                    ss >> (*pDoc);
                }
                catch (io::gzip_error& e)
                {
                    ASSERTL0(false,
                             "Error: File '" + pFilename + "' is corrupt.");
                }
1271 1272 1273
            }
            else
            {
1274 1275 1276
                ifstream file(pFilename.c_str());
                ASSERTL0(file.good(), "Unable to open file: " + pFilename);
                file >> (*pDoc);
1277 1278 1279
            }
        }

1280 1281 1282
        /**
         *
         */
1283 1284
        TiXmlDocument *SessionReader::MergeDoc(
            const std::vector<std::string> &pFilenames) const
1285
        {
1286 1287
            ASSERTL0(pFilenames.size() > 0, "No filenames for merging.");

1288
            // Read the first document
1289 1290 1291
            TiXmlDocument *vMainDoc = new TiXmlDocument;
            LoadDoc(pFilenames[0], vMainDoc);

1292
            TiXmlHandle vMainHandle(vMainDoc);
1293 1294
            TiXmlElement* vMainNektar = 
                vMainHandle.FirstChildElement("NEKTAR").Element();
1295 1296 1297 1298

            // Read all subsequent XML documents.
            // For each element within the NEKTAR tag, use it to replace the
            // version already present in the loaded XML data.