CardiacSimulation.cpp

/*
 
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OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
*/
 
#include "CardiacSimulationArchiver.hpp"  // Must go first
#include "CardiacSimulation.hpp"
 
 
boost::shared_ptr<AbstractUntemplatedCardiacProblem> CardiacSimulation::GetSavedProblem()
{
    return mSavedProblem;
}
 
std::string CardiacSimulation::BoolToString(bool yesNo)
{
    std::string result;
    if (yesNo)
    {
        result = "yes";
    }
    else
    {
        result = "no";
    }
    return result;
}
 
void CardiacSimulation::CreateResumeXmlFile(const std::string& rOutputDirectory, const std::string& rArchiveDirectory)
{
    OutputFileHandler handler(rOutputDirectory, false);
    if (PetscTools::AmMaster())
    {
        out_stream p_file = handler.OpenOutputFile("ResumeParameters.xml");
        (*p_file) << "<?xml version='1.0' encoding='UTF-8'?>" << std::endl;
        (*p_file) << "<ChasteParameters xmlns='https://chaste.comlab.ox.ac.uk/nss/parameters/3_0' "
                  << "xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance' "
                  << "xsi:schemaLocation='https://chaste.comlab.ox.ac.uk/nss/parameters/3_0 ChasteParameters_3_0.xsd'>" << std::endl;
        (*p_file) << std::endl;
        (*p_file) << "    <ResumeSimulation>" << std::endl;
        (*p_file) << "        <ArchiveDirectory relative_to='this_file'>" << rArchiveDirectory << "</ArchiveDirectory>" << std::endl;
        (*p_file) << "        <SpaceDimension>" << HeartConfig::Instance()->GetSpaceDimension() << "</SpaceDimension>" << std::endl;
        (*p_file) << "        <SimulationDuration unit='ms'>0.0</SimulationDuration> <!-- Edit with new simulation duration. Please "
                  << "note that the simulation does not restart at t=0 but at the time where the checkpoint was created.-->" << std::endl;
        (*p_file) << "        <Domain>" << HeartConfig::Instance()->GetDomain() << "</Domain>" << std::endl;
        (*p_file) << "        <CheckpointSimulation timestep='" << HeartConfig::Instance()->GetCheckpointTimestep()
                  << "' unit='ms' max_checkpoints_on_disk='" << HeartConfig::Instance()->GetMaxCheckpointsOnDisk()
                  << "'/> <!-- This is optional; if not given, the loaded simulation will NOT itself be checkpointed -->" << std::endl;
        (*p_file) << "        <OutputVisualizer meshalyzer='" << BoolToString(HeartConfig::Instance()->GetVisualizeWithMeshalyzer())
                  << "' vtk='" << BoolToString(HeartConfig::Instance()->GetVisualizeWithVtk())
                  << "' parallel_vtk='" << BoolToString(HeartConfig::Instance()->GetVisualizeWithParallelVtk())
                  << "' cmgui='" << BoolToString(HeartConfig::Instance()->GetVisualizeWithCmgui()) << "'/>" << std::endl;
        (*p_file) << "    </ResumeSimulation>" << std::endl;
        (*p_file) << std::endl;
        (*p_file) << "    <!-- These elements must exist, but their contents are ignored -->" << std::endl;
        (*p_file) << "    <Physiological/>" << std::endl;
        (*p_file) << "    <Numerical/>" << std::endl;
        (*p_file) << "</ChasteParameters>" << std::endl;
        p_file->close();
    }
 
    TRY_IF_MASTER(HeartConfig::Instance()->CopySchema(handler.GetOutputDirectoryFullPath()));
}
 
CardiacSimulation::CardiacSimulation(std::string parameterFileName,
                                     bool writeProvenanceInfo,
                                     bool saveProblemInstance)
    : mSaveProblemInstance(saveProblemInstance)
{
    // If we have been passed an XML file then parse the XML file, otherwise throw
    if (parameterFileName == "")
    {
        EXCEPTION("No XML file name given");
    }
    ReadParametersFromFile(parameterFileName);
    Run();
    HeartEventHandler::Headings();
    HeartEventHandler::Report();
    if (writeProvenanceInfo)
    {
        ExecutableSupport::SetOutputDirectory(HeartConfig::Instance()->GetOutputDirectory());
        ExecutableSupport::WriteProvenanceInfoFile();
        ExecutableSupport::WriteMachineInfoFile("machine_info");
    }
}
 
void CardiacSimulation::ReadParametersFromFile(std::string parameterFileName)
{
    // Ensure the singleton is in a clean state
    HeartConfig::Reset();
    try
    {
        // Try the hardcoded schema location first
        HeartConfig::Instance()->SetUseFixedSchemaLocation(true);
        HeartConfig::Instance()->SetParametersFile(parameterFileName);
    }
    catch (Exception& e)
    {
        if (e.CheckShortMessageContains("Missing file parsing configuration") == "")
        {
            // Try using the schema location given in the XML
            HeartConfig::Reset();
            HeartConfig::Instance()->SetUseFixedSchemaLocation(false);
            HeartConfig::Instance()->SetParametersFile(parameterFileName);
        }
        else
        {
            throw e;
        }
    }
}
 
 
#define DOMAIN_CASE(VALUE, CLASS, DIM)    \
    case VALUE:                           \
    {                                     \
        CreateAndRun<CLASS<DIM>, DIM>();  \
        break;                            \
    }
 
#define DOMAIN_SWITCH(DIM)                                                     \
    switch (HeartConfig::Instance()->GetDomain())                              \
    {                                                                          \
        DOMAIN_CASE(cp::domain_type::Mono, MonodomainProblem, DIM)             \
        DOMAIN_CASE(cp::domain_type::Bi, BidomainProblem, DIM)                 \
        DOMAIN_CASE(cp::domain_type::BiWithBath, BidomainWithBathProblem, DIM) \
        default:                                                               \
            NEVER_REACHED;                                                     \
    }                                                                          \
    break
// Note that if the domain is not set correctly then the XML parser will have picked it up before now!
// Missing semi-colon after break so we can put it after the macro call.
 
void CardiacSimulation::Run()
{
    switch (HeartConfig::Instance()->GetSpaceDimension())
    {
        case 3:
        {
            DOMAIN_SWITCH(3);
        }
        case 2:
        {
            DOMAIN_SWITCH(2);
        }
        case 1:
        {
            DOMAIN_SWITCH(1);
        }
        default:
            // We could check for this too in the XML Schema...
            EXCEPTION("Space dimension not supported: should be 1, 2 or 3");
    }
}
 
// These aren't needed externally
#undef DOMAIN_SWITCH
#undef DOMAIN_CASE