CellBasedSimulationArchiver.hpp

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*/
 
#ifndef CELLBASEDSIMULATIONARCHIVER_HPP_
#define CELLBASEDSIMULATIONARCHIVER_HPP_
 
// Must be included before any other serialization headers
#include "CheckpointArchiveTypes.hpp"
 
#include <string>
 
// The headers below are needed by the templated implementation, which is in this header
#include <fstream>
#include <sstream>
 
#include "ArchiveLocationInfo.hpp"
#include "ArchiveOpener.hpp"
#include "FileFinder.hpp"
#include "SimulationTime.hpp"
 
template <unsigned ELEMENT_DIM, class SIM, unsigned SPACE_DIM = ELEMENT_DIM, class INPUT_ARCHIVE_TYPE = boost::archive::text_iarchive, class OUTPUT_ARCHIVE_TYPE = boost::archive::text_oarchive>
class CellBasedSimulationArchiver
{
public:
    static SIM* Load(const std::string& rArchiveDirectory, const double& rTimeStamp);
 
    static void Save(SIM* pSim);
};
 
template <unsigned ELEMENT_DIM, class SIM, unsigned SPACE_DIM, class INPUT_ARCHIVE_TYPE, class OUTPUT_ARCHIVE_TYPE>
SIM* CellBasedSimulationArchiver<ELEMENT_DIM, SIM, SPACE_DIM, INPUT_ARCHIVE_TYPE, OUTPUT_ARCHIVE_TYPE>::Load(const std::string& rArchiveDirectory, const double& rTimeStamp)
{
    std::ostringstream time_stamp;
    time_stamp << rTimeStamp;
    std::string archive_filename = "cell_population_sim_at_time_" + time_stamp.str() + ".arch";
    std::string mesh_filename = "mesh_" + time_stamp.str();
    FileFinder archive_dir(rArchiveDirectory + "/archive/", RelativeTo::ChasteTestOutput);
    ArchiveLocationInfo::SetMeshPathname(archive_dir, mesh_filename);
 
    // Create an input archive
    ArchiveOpener<INPUT_ARCHIVE_TYPE, std::ifstream> arch_opener(archive_dir, archive_filename);
    INPUT_ARCHIVE_TYPE* p_arch = arch_opener.GetCommonArchive();
 
    // Load the simulation
    SIM* p_sim;
    (*p_arch) >> p_sim;
    return p_sim;
}
 
template <unsigned ELEMENT_DIM, class SIM, unsigned SPACE_DIM, class INPUT_ARCHIVE_TYPE, class OUTPUT_ARCHIVE_TYPE>
void CellBasedSimulationArchiver<ELEMENT_DIM, SIM, SPACE_DIM, INPUT_ARCHIVE_TYPE, OUTPUT_ARCHIVE_TYPE>::Save(SIM* pSim)
{
    // Get the simulation time as a string
    const SimulationTime* p_sim_time = SimulationTime::Instance();
    assert(p_sim_time->IsStartTimeSetUp());
    std::ostringstream time_stamp;
    time_stamp << p_sim_time->GetTime();
 
    // Set up folder and filename of archive
    FileFinder archive_dir(pSim->GetOutputDirectory() + "/archive/", RelativeTo::ChasteTestOutput);
    std::string archive_filename = "cell_population_sim_at_time_" + time_stamp.str() + ".arch";
    ArchiveLocationInfo::SetMeshFilename(std::string("mesh_") + time_stamp.str());
 
    // Create output archive
    ArchiveOpener<OUTPUT_ARCHIVE_TYPE, std::ofstream> arch_opener(archive_dir, archive_filename);
    OUTPUT_ARCHIVE_TYPE* p_arch = arch_opener.GetCommonArchive();
 
    // Archive the simulation (const-ness would be a pain here)
    (*p_arch) & pSim;
}
 
/*
 * Specialization of the CellBasedSimulationArchiver for text based formats to reduce requirement to set both archive type template parameters
 */
template <unsigned ELEMENT_DIM, class SIM, unsigned SPACE_DIM = ELEMENT_DIM>
using CellBasedSimulationArchiverText = CellBasedSimulationArchiver<ELEMENT_DIM, SIM, SPACE_DIM, boost::archive::text_iarchive, boost::archive::text_oarchive>;
 
/*
 * Specialization of the CellBasedSimulationArchiver for binary based formats to reduce requirement to set both archive type template parameters
 */
template <unsigned ELEMENT_DIM, class SIM, unsigned SPACE_DIM = ELEMENT_DIM>
using CellBasedSimulationArchiverBinary = CellBasedSimulationArchiver<ELEMENT_DIM, SIM, SPACE_DIM, boost::archive::binary_iarchive, boost::archive::binary_oarchive>;
 
#endif /*CELLBASEDSIMULATIONARCHIVER_HPP_*/