HeartConfigDefaults.hpp

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*/
 
#ifndef HEARTCONFIGDEFAULTS_HPP_
#define HEARTCONFIGDEFAULTS_HPP_
 
boost::shared_ptr<cp::chaste_parameters_type> CreateDefaultParameters()
{
    // Simulation parameters
    cp::simulation_type simulation_params;
    simulation_params.SpaceDimension().set(3);
    cp::domain_type domain("Mono");
    simulation_params.Domain().set(domain);
    cp::ionic_model_selection_type default_ionic_model;
    cp::ionic_models_available_type ionic_model("LuoRudyI");
    default_ionic_model.Hardcoded().set(ionic_model);
    cp::ionic_models_type ionic_models(default_ionic_model);
    simulation_params.IonicModels().set(ionic_models);
    simulation_params.OutputDirectory().set("ChasteResults");
    simulation_params.OutputFilenamePrefix().set("SimulationResults");
 
    // Physiological parameters
    cp::physiological_type phys_params;
    XSD_CREATE_WITH_FIXED_ATTR3(cp::conductivities_type, intra_conductivities,
                                1.75, 1.75, 1.75, "mS/cm");
    phys_params.IntracellularConductivities().set(intra_conductivities);
    XSD_CREATE_WITH_FIXED_ATTR3(cp::conductivities_type, extra_conductivities,
                                7.0, 7.0, 7.0, "mS/cm");
    phys_params.ExtracellularConductivities().set(extra_conductivities);
    XSD_CREATE_WITH_FIXED_ATTR1(cp::conductivity_type, bath_conductivity, 7.0, "mS/cm");
    phys_params.BathConductivity().set(bath_conductivity);
    XSD_CREATE_WITH_FIXED_ATTR1(cp::inverse_length_type, surface_area_to_volume_ratio, 1400, "1/cm");
    phys_params.SurfaceAreaToVolumeRatio().set(surface_area_to_volume_ratio);
    XSD_CREATE_WITH_FIXED_ATTR1(cp::capacitance_type, capacitance, 1.0, "uF/cm^2");
    phys_params.Capacitance().set(capacitance);
 
    cp::purkinje_physiological_type purkinje_phys_params;
    XSD_CREATE_WITH_FIXED_ATTR1(cp::inverse_length_type, purkinje_Am, 2800, "1/cm");
    purkinje_phys_params.SurfaceAreaToVolumeRatio().set(purkinje_Am);
    XSD_CREATE_WITH_FIXED_ATTR1(cp::capacitance_type, purkinje_Cm, 1.0, "uF/cm^2");
    purkinje_phys_params.Capacitance().set(purkinje_Cm);
    XSD_CREATE_WITH_FIXED_ATTR1(cp::conductivity_type, purkinje_conductivity, 1.75, "mS/cm");
    purkinje_phys_params.Conductivity().set(purkinje_conductivity);
    phys_params.Purkinje().set(purkinje_phys_params);
 
    // Numerical parameters
    cp::numerical_type numerical_params;
    XSD_CREATE_WITH_FIXED_ATTR3(cp::time_steps_type, timesteps, 0.01, 0.01, 0.01, "ms");
    cp::ksp_tolerances_type tolerances;
    tolerances.KSPAbsolute().set(2e-4);
    cp::ksp_solver_type ksp_solver("cg");
    cp::ksp_preconditioner_type ksp_precond("bjacobi");
    cp::mesh_partitioning_type mesh_partitioning("parmetis");
    numerical_params.TimeSteps().set(timesteps);
    numerical_params.KSPTolerances().set(tolerances);
    numerical_params.KSPSolver().set(ksp_solver);
    numerical_params.KSPPreconditioner().set(ksp_precond);
    numerical_params.MeshPartitioning().set(mesh_partitioning);
    numerical_params.UseStateVariableInterpolation().set(cp::yesno_type::no);
 
    // Postprocessing - empty is equivalent to missing, so don't include it
    //cp::postprocessing_type postproc;
 
    // Full default parameters
    boost::shared_ptr<cp::chaste_parameters_type> p_defaults(new cp::chaste_parameters_type(phys_params, numerical_params));
    p_defaults->Simulation().set(simulation_params);
    //p_defaults->PostProcessing().set(postproc);
    return p_defaults;
}
 
 
#define MERGE_PARAM(path)                                 \
    if (!pParams->path().present()) {                     \
        if (pDefaults->path().present()) {                \
            pParams->path().set(pDefaults->path().get()); \
        }                                                 \
    }
#define ELSE_IF_DEFAULT(path)                             \
    else if (pDefaults->path().present())
 
void MergeDefaults(boost::shared_ptr<cp::chaste_parameters_type> pParams,
                   boost::shared_ptr<cp::chaste_parameters_type> pDefaults)
{
    // Simulation and ResumeSimulation are mutually exclusive
    if (!pParams->ResumeSimulation().present())
    {
        MERGE_PARAM(Simulation)
        ELSE_IF_DEFAULT(Simulation) // Simulation() exists in both
        {
            MERGE_PARAM(Simulation()->SpaceDimension)
            MERGE_PARAM(Simulation()->Domain)
            MERGE_PARAM(Simulation()->IonicModels)
            ELSE_IF_DEFAULT(Simulation()->IonicModels) // Simulation()->IonicModels() exists in both
            {
                //MERGE_PARAM(Simulation()->IonicModels()->Default) // This must be present if IonicModels is
            }
            MERGE_PARAM(Simulation()->OutputDirectory)
            MERGE_PARAM(Simulation()->OutputFilenamePrefix)
        }
 
        // Physiological() is mandatory
        //MERGE_PARAM(Physiological)
        //ELSE_IF_DEFAULT(Physiological) // Physiological() exists in both
        {
            MERGE_PARAM(Physiological().IntracellularConductivities)
            MERGE_PARAM(Physiological().ExtracellularConductivities)
            MERGE_PARAM(Physiological().BathConductivity)
            MERGE_PARAM(Physiological().SurfaceAreaToVolumeRatio)
            MERGE_PARAM(Physiological().Capacitance)
            MERGE_PARAM(Physiological().Purkinje)
            ELSE_IF_DEFAULT(Physiological().Purkinje) // Physiological()->Purkinje() exists in both
            {
                MERGE_PARAM(Physiological().Purkinje()->SurfaceAreaToVolumeRatio)
                MERGE_PARAM(Physiological().Purkinje()->Capacitance)
                MERGE_PARAM(Physiological().Purkinje()->Conductivity)
            }
        }
 
        // Numerical() is mandatory
        //MERGE_PARAM(Numerical)
        //ELSE_IF_DEFAULT(Numerical) // Numerical() exists in both
        {
            MERGE_PARAM(Numerical().TimeSteps)
            MERGE_PARAM(Numerical().KSPTolerances)
            ELSE_IF_DEFAULT(Numerical().KSPTolerances) // Numerical()->KSPTolerances() exists in both
            {
                // Note that we aren't allowed both absolute and relative tolerances
                if (!pParams->Numerical().KSPTolerances()->KSPRelative().present())
                {
                    MERGE_PARAM(Numerical().KSPTolerances()->KSPAbsolute)
                }
            }
            MERGE_PARAM(Numerical().KSPSolver)
            MERGE_PARAM(Numerical().KSPPreconditioner)
            MERGE_PARAM(Numerical().MeshPartitioning)
            MERGE_PARAM(Numerical().UseStateVariableInterpolation)
        }
    }
}
 
#endif /*HEARTCONFIGDEFAULTS_HPP_*/