Flame.cpp

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#include "Flame.H"
#include "IO/ParmParse.H"
#include "BC/Constant.H"
#include "Numeric/Stencil.H"
#include "IC/Laminate.H"
#include "IC/Constant.H"
#include "IC/PointList.H"
#include "IC/PSRead.H"
#include "Numeric/Function.H"
#include "IC/Expression.H"
#include "IC/BMP.H"
#include "IC/PNG.H"
#include "Base/Mechanics.H"
#include "Util/Util.H"
#include "Model/Propellant/Propellant.H"
#include "Model/Propellant/FullFeedback.H"
#include "Model/Propellant/Homogenize.H"
#include <cmath>
 
namespace Integrator
{
 
Flame::Flame() : 
    Base::Mechanics<model_type>() {}
 
Flame::Flame(IO::ParmParse& pp) : Flame()
{
    pp_queryclass(*this);
}
 
 
void
Flame::Forbids(IO::ParmParse& pp)
{
    pp.forbid("pressure.P","use chamber.pressure instead");
 
    pp.forbid("geometry.x_len","This is specified by geometry.prob_lo/hi");
    pp.forbid("geometry.y_len","This is specified by geometry.prob_lo/hi");
    pp.forbid("amr.ghost_cells", "This should not be adjustable ");
 
    pp.forbid("pf.gamma","use propellant.powerlaw.gamma"); 
 
    pp.forbid("pressure.r_ap",   "use propellant.powerlaw.r_ap");
    pp.forbid("pressure.r_htpb", "use propellant.powerlaw.r_htpb");
    pp.forbid("pressure.r_comb", "use propellant.powerlaw.r_comb");
    pp.forbid("pressure.n_ap",   "use propellant.powerlaw.n_ap");
    pp.forbid("pressure.n_htpb", "use propellant.powerlaw.n_htpb");
    pp.forbid("pressure.n_comb", "use propellant.powerlaw.n_comb");
 
    pp.forbid("thermal.bound",   "use thermal.Tref");
    pp.forbid("thermal.T_fluid",   "use thermal.Tfluid (or nothing)");
    pp.forbid("thermal.m_ap",   "use propellant.fullfeedback.m_ap");
    pp.forbid("thermal.m_htpb", "use propellant.fullfeedback.m_htpb");
    pp.forbid("thermal.E_ap",   "use propellant.fullfeedback.E_ap");
    pp.forbid("thermal.E_htpb", "use propellant.fullfeedback.E_htpb");
    pp.forbid("thermal.modeling_ap",   "Old debug variable. Should equal 1 "); 
    pp.forbid("thermal.modeling_htpb", "Old debug variable. Should equal 1"); 
 
    pp.forbid("pressure.a1", "use propellant.fullfeedback.a1 instead");
    pp.forbid("pressure.a2", "use propellant.fullfeedback.a2 instead");
    pp.forbid("pressure.a3", "use propellant.fullfeedback.a3 instead");
    pp.forbid("pressure.b1", "use propellant.fullfeedback.b1 instead");
    pp.forbid("pressure.b2", "use propellant.fullfeedback.b2 instead");
    pp.forbid("pressure.b3", "use propellant.fullfeedback.b3 instead");
    pp.forbid("pressure.c1", "use propellant.fullfeedback.c1 instead");
    pp.forbid("pressure.mob_ap", "no longer used"); 
    pp.forbid("pressure.dependency", "use propellant.fullfeedback.pressure_dependency"); 
    pp.forbid("pressure.h1", "use propellant.homogenize.h1 instead"); 
    pp.forbid("pressure.h2", "use propellant.homogenize.h2 instead"); 
    pp.forbid("thermal.mlocal_ap", "use propellant.homogenize.mlocal_ap");
    pp.forbid("thermal.mlocal_comb", "use propellant.homogenize.mlocal_comb");
    pp.forbid("thermal.mlocal_htpb", "this actually did **nothing** - it was overridden by a hard code using massfraction.");
 
    pp.forbid("thermal.disperssion1", "use propellant.homogenize.dispersion1");
    pp.forbid("thermal.disperssion2", "use propellant.homogenize.dispersion2");
    pp.forbid("thermal.disperssion3", "use propellant.homogenize.dispersion3"); 
 
    pp.forbid("thermal.rho_ap", "use propellant.fullfeedback/homogenize.rho_ap ");
    pp.forbid("thermal.rho_htpb","use propellant.fullfeedback/homogenize.rho_htpb ");
    pp.forbid("thermal.k_ap",   "use propellant.fullfeedback/homogenize.k_ap ");
    pp.forbid("thermal.k_htpb", "use propellant.fullfeedback/homogenize.k_htpb ");
    pp.forbid("thermal.cp_ap", "use propellant.fullfeedback/homogenize.cp_ap ");
    pp.forbid("thermal.cp_htpb","use propellant.fullfeedback/homogenize.cp_htpb "); 
}
 
 
// [parser]
void
Flame::Parse(Flame& value, IO::ParmParse& pp)
{
    BL_PROFILE("Integrator::Flame::Flame()");
 
    Forbids(pp);
 
    // Whether to include extra fields (such as mdot, etc) in the plot output
    pp.query_default("plot_field",value.plot_field,true); 
        
    //
    // PHASE FIELD VARIABLES
    //
        
    // Burn width thickness
    pp.query_default("pf.eps", value.pf.eps, "1.0_m", Unit::Length()); 
    // Interface energy param
    pp.query_default("pf.kappa", value.pf.kappa, "0.0_J/m^2", Unit::Energy() / Unit::Area()); 
    // Chemical potential multiplier
    pp.query_default("pf.lambda", value.pf.lambda, "0.0_J/m^2", Unit::Energy()/Unit::Area()); 
    // Unburned rest energy
    pp.query_default("pf.w1", value.pf.w1, "0.0",Unit::Less()); 
    // Barrier energy
    pp.query_default("pf.w12", value.pf.w12, "0.0", Unit::Less());  
    // Burned rest energy
    pp.query_default("pf.w0", value.pf.w0, "0.0",Unit::Less());    
 
    // Boundary conditions for phase field order params
    pp.select<BC::Constant>("pf.eta.bc", value.bc_eta, pp.forward_args(1));
    value.RegisterNewFab(value.eta_mf, value.bc_eta, 1, 2, "eta", true);
    value.RegisterNewFab(value.eta_old_mf, value.bc_eta, 1, 2, "eta_old", 0);
 
    // Inital value of eta that doesn't evolve and is used during refiment to set the updated values of eta with voids in the domain.
    // Used to fix a bug where duirn refinement, a void won't be updated correctly and would be a square, not a circle
    value.RegisterNewFab(value.eta_0_mf, value.bc_eta, 1, 2, "eta_0", 0);
 
    // value.RegisterNewFab(value.eta_mf_frozen, value.bc_eta, 1, 2, "eta_frozen", value.plot_field);
 
    // phase field initial condition
    pp.select<IC::Laminate,IC::Constant,IC::Expression,IC::BMP,IC::PNG, IC::PSRead>("pf.eta.ic",value.ic_eta,pp.forward_args(value.geom));
 
 
    // Select reduced order model to capture heat feedback
    pp.select<  Model::Propellant::PowerLaw, 
                Model::Propellant::FullFeedback,
                Model::Propellant::Homogenize>
        ("propellant",value.propellant);
 
 
    // Reference temperature
    // Used to set all other reference temperatures by default.
    pp_query_default("thermal.Tref", value.thermal.Tref, "300.0_K",Unit::Temperature());
 
    // Whether to use the Thermal Transport Model
    pp.query_if("thermal.on", [&](){
        value.thermal.on = true;
 
        // Used to change heat flux units
        pp_query_default("thermal.hc", value.thermal.hc, "1.0", Unit::Power()/Unit::Area());
 
        // Effective fluid temperature, temp of the eta = 0 (fluid) region
        pp_query_default("thermal.Tfluid", value.thermal.Tfluid, value.thermal.Tref);
 
        // Cutoff value for regression, if T < Tcutoff eta won't evolve/regress
        pp.query_default("thermal.Tcutoff", value.thermal.Tcutoff, "0.0", Unit::Temperature());
 
        // Switch time of the improved regridding where eta and the temperature field are both used. It is recommended to make this time ~10x the timestep.
        // Before this the refinement is based on the gradient of eta which helps the laser IC start correctly. A regrid is forced when this time is reached.
        pp.query_default("thermal.end_initial_refine_time", value.thermal.end_initial_refine_time, "0.0", Unit::Time());
 
        // Inital refinement of the phi field based on phi gradient. After time > end_initial_refine_time stops refining at these phi values.
        pp.query_default("thermal.phi_refinement_criterion_inital", value.thermal.phi_refinement_criterion_inital, 1.0e100);
 
        //Temperature boundary condition
        pp.select_default<BC::Constant>("thermal.temp.bc", value.bc_temp, pp.forward_args(1, Unit::Temperature()));
            
        value.RegisterNewFab(value.temp_mf, value.bc_temp, 1, 3, "temp", true);
        value.RegisterNewFab(value.temp_old_mf, value.bc_temp, 1, 3, "temp_old", false);
        value.RegisterNewFab(value.temps_mf, value.bc_temp, 1, 0, "temps", false);
 
        value.RegisterNewFab(value.mdot_mf, value.bc_temp, 1, 0, "mdot", value.plot_field);
        value.RegisterNewFab(value.alpha_mf, value.bc_temp, 1, 0, "alpha", value.plot_field);
        value.RegisterNewFab(value.heatflux_mf, value.bc_temp, 1, 0, "heatflux", value.plot_field);
        value.RegisterNewFab(value.laser_mf, value.bc_temp, 1, 0, "laser", value.plot_field);
 
        value.RegisterIntegratedVariable(&value.chamber.volume, "volume");
        value.RegisterIntegratedVariable(&value.chamber.area, "area");
        value.RegisterIntegratedVariable(&value.chamber.massflux, "mass_flux");
        
        value.RegisterNewFab(value.thermal.has_exceeded_Tcutoff, value.bc_temp, 1, 2, "exceeded_Tcutoff", 0); // Used to determine where regression has started
 
        // laser initial condition
        pp.select_default<  IC::Constant,
                            IC::Expression  >
            ("laser.ic",value.ic_laser, pp.forward_args(value.geom, Unit::Power()/Unit::Area()));
 
        // thermal initial condition
        pp.select_default<  IC::Constant,
                            IC::Expression,
                            IC::BMP,
                            IC::PNG  >
            ("temp.ic",value.thermal.ic_temp,pp.forward_args(value.geom, Unit::Temperature()));
    });
 
 
    // Constant pressure value
    pp_query_default("chamber.pressure", value.chamber.pressure, "1.0_MPa", Unit::Pressure()); 
 
    // Whether to compute the pressure evolution
    pp_query_default("variable_pressure", value.variable_pressure, false);
 
    // Refinement criterion for eta field, if thermal is on, cells will only be tagged for refinement if T>0.9*TCutoff,
    // and the gradient of eta > m_refinement_criterion at each cell
    pp_query_default(   "amr.refinement_criterion", value.m_refinement_criterion, "0.001", 
                        Unit::Less());
 
    // Refinement criterion for temperature field    
    pp.query_default(   "amr.refinement_criterion_temp", value.t_refinement_criterion, "0.001_K",
                        Unit::Temperature());
 
    // Eta value to restrict the refinament for the temperature field 
    pp.query_default(   "amr.refinament_restriction", value.t_refinement_restriction, "0.1",
                        Unit::Less());
 
    // Refinement criterion for phi field [infinity]
    pp_query_default("amr.phi_refinement_criterion", value.phi_refinement_criterion, 1.0e100);
 
    // Minimum allowable threshold for $\eta$
    pp_query_default("small", value.small, 1.0e-8); 
 
    // Initial condition for $\phi$ field.
    pp.select_default<IC::Laminate,IC::Expression,IC::Constant,IC::BMP,IC::PNG, IC::PSRead>
        ("phi.ic",value.ic_phi,pp.forward_args(value.geom));
 
    value.RegisterNodalFab(value.phi_mf, 1, 2, "phi", true);
 
    // Whether to use Neo-hookean Elastic model
    value.m_type = Base::Mechanics<model_type>::Type::Disable;
    pp.query_if("elastic.on", [&]() {
        value.elastic.on = true;
 
        // Body force
        pp_query_default("elastic.traction", value.elastic.traction, 0.0);
 
        // Phi refinement criteria
        pp_query_default("elastic.phirefinement", value.elastic.phirefinement, 1);
 
        // Elastic integrator
        pp.queryclass<Base::Mechanics<model_type>>("elastic",value);
 
 
 
        // Reference temperature for thermal expansion 
        // (temperature at which the material is strain-free)
        pp_query_default("Telastic", value.elastic.Telastic, value.thermal.Tref);
        // elastic model of AP
        pp.queryclass<Model::Solid::Finite::NeoHookeanPredeformed>("model_ap", value.elastic.model_ap);
        // elastic model of HTPB
        pp.queryclass<Model::Solid::Finite::NeoHookeanPredeformed>("model_htpb", value.elastic.model_htpb);
 
        // eta cutoff value to stop applying the traction force and/or chamber pressure to the RHS.
        // Below this vlaue the RHS is set to 0.0
        pp.query_default("etacutoff",value.elastic.etacutoff, "0", Unit::Less());
 
        // Boolean value, when not 0 the chamber.pressure value is applied at the diffuse interface where t>Tcutoff
        pp.query_default("apply_chamber_pressure",value.elastic.apply_chamber_pressure, "0", Unit::Less());
 
        // Use our current eta field as the psi field for the solver
        value.psi_on = false;
        value.solver.setPsi(value.eta_mf);
 
        if (IO::ParmParse::InTraversalMode()) return;
 
        Util::AssertException(INFO, TEST(value.m_type != Disable), "You must specify elastic type to be dynamic or static");
    });
 
 
 
    bool allow_unused;
    // Set this to true to allow unused inputs without error.
    // (Not recommended.)
    pp.query_default("allow_unused",allow_unused,false);
    if (!allow_unused && pp.AnyUnusedInputs())
    {
        Util::Warning(INFO,"The following inputs were specified but not used:");
        pp.AllUnusedInputs();
        Util::Exception(INFO,"Aborting. Specify 'allow_unused=True` to ignore this error.");
    }
}
 
void Flame::Initialize(int lev)
{
    BL_PROFILE("Integrator::Flame::Initialize");
    Base::Mechanics<model_type>::Initialize(lev);
 
    ic_eta->Initialize(lev, eta_mf);
    ic_eta->Initialize(lev, eta_old_mf);
    ic_phi->Initialize(lev, phi_mf);
    //ic_phicell->Initialize(lev, phicell_mf);
 
    if (elastic.on) {
        rhs_mf[lev]->setVal(Set::Vector::Zero());
    }
    if (thermal.on) {
        if (thermal.ic_temp)
        {
            thermal.ic_temp->Initialize(lev,temp_mf);
            thermal.ic_temp->Initialize(lev,temp_old_mf);
            thermal.ic_temp->Initialize(lev,temps_mf);
        }
        else
        {
            temp_mf[lev]->setVal(thermal.Tref);
            temp_old_mf[lev]->setVal(thermal.Tref);
            temps_mf[lev]->setVal(thermal.Tref);
        }
        alpha_mf[lev]->setVal(0.0);
        mdot_mf[lev]->setVal(0.0);
        heatflux_mf[lev]->setVal(0.0);
        ic_laser->Initialize(lev, laser_mf);
    }
    if (variable_pressure) chamber.pressure = 1.0;
}
 
void Flame::UpdateModel(int /*a_step*/, Set::Scalar /*a_time*/)
{
    if (m_type == Base::Mechanics<model_type>::Type::Disable) return;
 
    for (int lev = 0; lev <= finest_level; ++lev)
    {
        amrex::Box domain = this->geom[lev].Domain();
        domain.convert(amrex::IntVect::TheNodeVector());
        const Set::Scalar* DX = geom[lev].CellSize();
 
        phi_mf[lev]->FillBoundary();
        eta_mf[lev]->FillBoundary();
        temp_mf[lev]->FillBoundary();
 
        for (MFIter mfi(*model_mf[lev], false); mfi.isValid(); ++mfi)
        {
            amrex::Box smallbox = mfi.nodaltilebox();
            amrex::Box bx = mfi.grownnodaltilebox() & domain;
            Set::Patch<model_type>        model = model_mf.Patch(lev,mfi);
            Set::Patch<const Set::Scalar> phi   = phi_mf.Patch(lev,mfi);
            Set::Patch<const Set::Scalar> eta   = eta_mf.Patch(lev,mfi);
            Set::Patch<Set::Vector>       rhs   = rhs_mf.Patch(lev,mfi);
            Set::Scalar Tcutoff = thermal.Tcutoff;
 
            if (elastic.on)
            {
                Set::Patch <const Set::Scalar> temp = temp_mf.Patch(lev,mfi);
                amrex::ParallelFor(smallbox, [=] AMREX_GPU_DEVICE(int i, int j, int k)
 
                {   
                    Set::Vector grad_eta = Numeric::CellGradientOnNode(eta, i, j, k, 0, DX);
 
                    if (temp(i,j,k) > Tcutoff && eta(i,j,k) > elastic.etacutoff && elastic.apply_chamber_pressure)
                        {
                            rhs(i, j, k) = (elastic.traction) * grad_eta - chamber.pressure*grad_eta;
                            // std::cout << "Applying chamber pressure" << std::endl;
                        }
                    else if (temp(i,j,k) > Tcutoff && eta(i,j,k) > elastic.etacutoff && !elastic.apply_chamber_pressure)
                        {
                            rhs(i, j, k) = (elastic.traction) * grad_eta;
                            // std::cout << "Applying traction" << std::endl;
                        }
                    else
                            rhs(i, j, k) = 0.0 * grad_eta;
                            // std::cout << "Applying neither" << std::endl;
 
                });
                amrex::ParallelFor(bx, [=] AMREX_GPU_DEVICE(int i, int j, int k)
                {
                    Set::Scalar phi_avg = phi(i, j, k, 0);
                    Set::Scalar temp_avg = Numeric::Interpolate::CellToNodeAverage(temp, i, j, k, 0);
                    model_type model_ap = elastic.model_ap;
                    model_ap.F0 -= Set::Matrix::Identity();
                    model_ap.F0 *= (temp_avg - elastic.Telastic);
                    model_ap.F0 += Set::Matrix::Identity();
                    model_type model_htpb = elastic.model_htpb;
                    model_htpb.F0 -= Set::Matrix::Identity();
                    model_htpb.F0 *= (temp_avg - elastic.Telastic);
                    model_htpb.F0 += Set::Matrix::Identity();
 
                    model(i, j, k) = (model_ap * phi_avg + model_htpb * (1. - phi_avg));
                });
            }
            else
            {
                amrex::ParallelFor(bx, [=] AMREX_GPU_DEVICE(int i, int j, int k)
                {
                    Set::Scalar phi_avg = Numeric::Interpolate::CellToNodeAverage(phi, i, j, k, 0);
                    //phi_avg = phi(i,j,k,0);
                    model_type model_ap = elastic.model_ap;
                    model_ap.F0 *= Set::Matrix::Zero();
                    model_type model_htpb = elastic.model_htpb;
                    model_htpb.F0 *= Set::Matrix::Zero();
                    model(i, j, k) = (model_ap * phi_avg + model_htpb * (1. - phi_avg));
                });
            }
        }
        Util::RealFillBoundary(*model_mf[lev], geom[lev]);
 
    }
}
 
void Flame::TimeStepBegin(Set::Scalar a_time, int a_iter)
{
    BL_PROFILE("Integrator::Flame::TimeStepBegin");
    Base::Mechanics<model_type>::TimeStepBegin(a_time, a_iter);
    if (thermal.on) {
        for (int lev = 0; lev <= finest_level; ++lev)
            ic_laser->Initialize(lev, laser_mf, a_time);
    }
 
    if (a_time > thermal.end_initial_refine_time)
    {   
        if (!end_initial_refine) {
            for (int lev = 0; lev <= finest_level; ++lev)
                Flame::Regrid(lev, a_time);
            end_initial_refine = 1;
        }
 
        prev_finest_ba = grids[finest_level];
        prev_finest_level = finest_level;
    }
}
 
void Flame::TimeStepComplete(Set::Scalar /*a_time*/, int /*a_iter*/)
{
    BL_PROFILE("Integrator::Flame::TimeStepComplete");
    if (variable_pressure) {
        //Set::Scalar x_len = geom[0].ProbDomain().length(0);
        //Set::Scalar y_len = geom[0].ProbDomain().length(1);
        // Set::Scalar domain_area = x_len * y_len;
        Util::Message(INFO, "Mass = ", chamber.massflux);
        Util::Message(INFO, "Pressure = ", chamber.pressure);
    }
}
 
void Flame::Advance(int lev, Set::Scalar time, Set::Scalar dt)
{
    BL_PROFILE("Integrador::Flame::Advance");
    Base::Mechanics<model_type>::Advance(lev, time, dt);
    const Set::Scalar* DX = geom[lev].CellSize();
 
    std::swap(eta_old_mf[lev], eta_mf[lev]);
 
    //
    // Chamber pressure update
    //
    if (variable_pressure) {
        chamber.pressure = exp(0.00075 * chamber.massflux);
        if (chamber.pressure > 10.0) {
            chamber.pressure = 10.0;
        }
        else if (chamber.pressure <= 0.99) {
            chamber.pressure = 0.99;
        }
        elastic.traction = chamber.pressure;
    }
 
 
    //
    // Multi-well chemical potential
    //
    Numeric::Function::Polynomial<4> w( pf.w0,
                                        0.0,
                                        -5.0 * pf.w1 + 16.0 * pf.w12 - 11.0 * pf.w0,
                                        14.0 * pf.w1 - 32.0 * pf.w12 + 18.0 * pf.w0,
                                        -8.0 * pf.w1 + 16.0 * pf.w12 - 8.0 * pf.w0);
    Numeric::Function::Polynomial<3> dw = w.D();
 
    propellant.set_pressure(chamber.pressure);
 
    for (amrex::MFIter mfi(*eta_mf[lev], true); mfi.isValid(); ++mfi)
    {
        const amrex::Box& bx = mfi.tilebox();
        // Phase fields
        Set::Patch<Set::Scalar> etanew    = eta_mf.Patch(lev,mfi);
        Set::Patch<const Set::Scalar> eta = eta_old_mf.Patch(lev,mfi);
        Set::Patch<const Set::Scalar> phi = phi_mf.Patch(lev,mfi);
        // Heat transfer fields
        Set::Patch<const Set::Scalar> temp = temp_mf.Patch(lev,mfi);
        Set::Patch<Set::Scalar>       alpha = alpha_mf.Patch(lev,mfi);
        Set::Patch<Set::Scalar>       laser = laser_mf.Patch(lev,mfi);
        // Diagnostic fields
        Set::Patch<Set::Scalar> mdot     = mdot_mf.Patch(lev,mfi);
        Set::Patch<Set::Scalar> heatflux = heatflux_mf.Patch(lev,mfi);
 
        Set::Patch<Set::Scalar> exceeded_Tcutoff = thermal.has_exceeded_Tcutoff.Patch(lev, mfi);
        Set::Scalar Tcutoff = thermal.Tcutoff;
 
 
        amrex::ParallelFor(bx, [=] AMREX_GPU_DEVICE(int i, int j, int k)
        {
            //
            // CALCULATE PHI-AVERAGED QUANTITIES
            //
            Set::Scalar phi_avg = Numeric::Interpolate::NodeToCellAverage(phi, i, j, k, 0);
            Set::Scalar T = thermal.on ? temp(i,j,k) : NAN;
 
            Set::Scalar K = propellant.get_K(phi_avg);
 
            Set::Scalar rho = propellant.get_rho(phi_avg);
 
            Set::Scalar cp = propellant.get_cp(phi_avg);
 
            //
            // CALCULATE MOBILITY
            // 
            Set::Scalar L = propellant.get_L(  phi_avg, T);
 
            // 
            // EVOLVE PHASE FIELD (ETA)
            // 
 
            Set::Scalar eta_lap = Numeric::Laplacian(eta, i, j, k, 0, DX);
            Set::Scalar df_deta = ((pf.lambda / pf.eps) * dw(eta(i, j, k)) - pf.eps * pf.kappa * eta_lap);
            
            if (df_deta < 0) {
                // Prevent eta from increasing/healing. A bug was found where if the diffuse thickness was too large compared to a void
                // (region of eta = 0), eta would heal/increase in a non-physcial way, this statement stops that behavior 
                df_deta = 0.0;
            }
            if (thermal.on && T < thermal.Tcutoff) {
                // If the temperature is lower then the cutoff temperature don't evolve the eta field
                df_deta = 0.0;
            }
            etanew(i, j, k) = eta(i, j, k) - L * dt * df_deta;
            
            if (etanew(i, j, k) <= small) etanew(i, j, k) = small;
 
            if (thermal.on)
            {
                //
                // Calculate thermal diffisivity and store for later gradient
                //
 
                alpha(i, j, k) = K / rho / cp; 
 
                //
                // CALCULATE MASS FLUX BASED ON EVOLVING ETA
                //
            
                mdot(i, j, k) = rho * fabs(eta(i, j, k) - etanew(i, j, k)) / dt; 
 
                //
                // CALCULATE HEAT FLUX BASED ON THE CALCULATED MASS FLUX
                //
 
                Set::Scalar q0 = propellant.get_qdot(mdot(i,j,k), phi_avg);
                heatflux(i,j,k) = ( thermal.hc*q0 + laser(i,j,k) ) / K;
 
                if (temp(i,j,k) > Tcutoff)
                {
                    exceeded_Tcutoff(i,j,k) = 1;
                }
 
            }
 
        });
 
    } // MFi For loop 
 
 
    //
    // THERMAL TRANSPORT
    // 
    if (thermal.on)
    {
        std::swap(temp_old_mf[lev], temp_mf[lev]);
 
        for (amrex::MFIter mfi(*eta_mf[lev], true); mfi.isValid(); ++mfi)
        {
            const amrex::Box& bx = mfi.tilebox();
 
            Set::Patch<Set::Scalar>       tempnew = temp_mf.Patch(lev,mfi);
            Set::Patch<const Set::Scalar> temp = temp_old_mf.Patch(lev,mfi);
            Set::Patch<const Set::Scalar> alpha = alpha_mf.Patch(lev,mfi);
 
            Set::Patch<Set::Scalar>       temps = temps_mf.Patch(lev,mfi);
 
 
            // Phase field
            Set::Patch<Set::Scalar>       etanew = (*eta_mf[lev]).array(mfi);
            Set::Patch<const Set::Scalar> eta = (*eta_old_mf[lev]).array(mfi);
            // Diagnostic fields
            Set::Patch<const Set::Scalar> heatflux = heatflux_mf.Patch(lev,mfi);
 
            amrex::ParallelFor(bx, [=] AMREX_GPU_DEVICE(int i, int j, int k)
            {
                auto sten = Numeric::GetStencil(i, j, k, bx);
                Set::Vector grad_eta = Numeric::Gradient(eta, i, j, k, 0, DX);
                Set::Vector grad_temp = Numeric::Gradient(temp, i, j, k, 0, DX);
                Set::Scalar lap_temp = Numeric::Laplacian(temp, i, j, k, 0, DX);
                Set::Scalar grad_eta_mag = grad_eta.lpNorm<2>();
                Set::Vector grad_alpha = Numeric::Gradient(alpha, i, j, k, 0, DX, sten);
                Set::Scalar dTdt = 0.0;
                dTdt += grad_eta.dot(grad_temp * alpha(i, j, k));
                dTdt += grad_alpha.dot(eta(i, j, k) * grad_temp);
                dTdt += eta(i, j, k) * alpha(i, j, k) * lap_temp;
                dTdt += alpha(i, j, k) * heatflux(i, j, k) * grad_eta_mag;
 
                Set::Scalar Tsolid = dTdt + temps(i, j, k) * (etanew(i, j, k) - eta(i, j, k)) / dt;
                temps(i, j, k) = temps(i, j, k) + dt * Tsolid;
                tempnew(i, j, k) = etanew(i, j, k) * temps(i, j, k) + (1.0 - etanew(i, j, k)) * thermal.Tfluid;
            });
        }
    }
 
} //Function
 
 
void Flame::TagCellsForRefinement(int lev, amrex::TagBoxArray& a_tags, Set::Scalar time, int ngrow)
{
    BL_PROFILE("Integrator::Flame::TagCellsForRefinement");
    Base::Mechanics<model_type>::TagCellsForRefinement(lev, a_tags, time, ngrow);
 
    const Set::Scalar* DX = geom[lev].CellSize();
    Set::Scalar dr = sqrt(AMREX_D_TERM(DX[0] * DX[0], +DX[1] * DX[1], +DX[2] * DX[2]));
 
    // Eta criterion for refinement
    for (amrex::MFIter mfi(*eta_mf[lev], true); mfi.isValid(); ++mfi)
    {
        const amrex::Box& bx = mfi.tilebox();
        amrex::Array4<char> const& tags = a_tags.array(mfi);
        Set::Patch<const Set::Scalar> eta = eta_mf.Patch(lev,mfi);
        Set::Patch<const Set::Scalar> temp = temp_mf.Patch(lev,mfi);
 
        if (thermal.on) {
        amrex::ParallelFor(bx, [=] AMREX_GPU_DEVICE(int i, int j, int k)
        {
            Set::Vector gradeta = Numeric::Gradient(eta, i, j, k, 0, DX);
            if (gradeta.lpNorm<2>() * dr * 2 > m_refinement_criterion && eta(i, j, k) >= t_refinement_restriction && temp(i,j,k) > thermal.Tcutoff*0.9)
                tags(i, j, k) = amrex::TagBox::SET;
        });
 
        } else {
        amrex::ParallelFor(bx, [=] AMREX_GPU_DEVICE(int i, int j, int k)
        {
            Set::Vector gradeta = Numeric::Gradient(eta, i, j, k, 0, DX);
            if (gradeta.lpNorm<2>() * dr * 2 > m_refinement_criterion && eta(i, j, k) >= t_refinement_restriction)
                tags(i, j, k) = amrex::TagBox::SET;
        });
        }
    }
 
    // Phi criterion for refinement 
    if (elastic.phirefinement) {
        for (amrex::MFIter mfi(*eta_mf[lev], true); mfi.isValid(); ++mfi)
        {
            const amrex::Box& bx = mfi.tilebox();
            amrex::Array4<char> const& tags = a_tags.array(mfi);
            Set::Patch<const Set::Scalar> phi = phi_mf.Patch(lev,mfi);
 
            amrex::ParallelFor(bx, [=] AMREX_GPU_DEVICE(int i, int j, int k)
            {
                Set::Vector gradphi = Numeric::Gradient(phi, i, j, k, 0, DX);
                if (gradphi.lpNorm<2>() * dr >= phi_refinement_criterion)
                    tags(i, j, k) = amrex::TagBox::SET;
            });
        }
    }
 
 
    // Thermal criterion for refinement 
    if (thermal.on) {
        for (amrex::MFIter mfi(*temp_mf[lev], true); mfi.isValid(); ++mfi)
        {
            const amrex::Box& bx = mfi.tilebox();
            amrex::Array4<char> const& tags = a_tags.array(mfi);
            Set::Patch<const Set::Scalar> temp = temp_mf.Patch(lev,mfi);
            Set::Patch<const Set::Scalar> eta  = eta_mf.Patch(lev,mfi);
            amrex::ParallelFor(bx, [=] AMREX_GPU_DEVICE(int i, int j, int k)
            {
                Set::Vector tempgrad = Numeric::Gradient(temp, i, j, k, 0, DX);
                if (tempgrad.lpNorm<2>() * dr > t_refinement_criterion && eta(i, j, k) >= t_refinement_restriction)
                    tags(i, j, k) = amrex::TagBox::SET;
            });
        }
    }
 
        // Refine at start
    for (amrex::MFIter mfi(*eta_mf[lev], true); mfi.isValid(); ++mfi)
    {
        const amrex::Box& bx = mfi.tilebox();
        amrex::Array4<char> const& tags = a_tags.array(mfi);
        Set::Patch<const Set::Scalar> eta = eta_mf.Patch(lev,mfi);
        Set::Patch<const Set::Scalar> phi = phi_mf.Patch(lev,mfi);
 
        amrex::ParallelFor(bx, [=] AMREX_GPU_DEVICE(int i, int j, int k)
        {
            Set::Vector gradeta = Numeric::Gradient(eta, i, j, k, 0, DX);
            Set::Vector gradphi = Numeric::Gradient(phi, i, j, k, 0, DX);
            if ((gradeta.lpNorm<2>() * dr * 2 > m_refinement_criterion || gradphi.lpNorm<2>() * dr >= thermal.phi_refinement_criterion_inital) && time < thermal.end_initial_refine_time)
                tags(i, j, k) = amrex::TagBox::SET;
        });
    }
}
 
void Flame::Regrid(int lev, Set::Scalar time)
{   
    BL_PROFILE("Integrator::Flame::Regrid");
 
    ic_phi->Initialize(lev, phi_mf, time);
    ic_eta->Initialize(lev, eta_0_mf, time);
 
    if (thermal.on) {
    /* 
    This regrid function works by using the "has_exceeded_Tcutoff" field. If the temperature in a cell is greater than Tcutoff,
    eta will change and when regridding won't use the initial eta field. If T < T_cutoff, when regriding happens it applies the inital 
    eta field condition. This gives at leat a 4x speed improvement in 2D when doing regression with voids. This is because orgionally
    there was a bug where when regridding, the orgional eta field wouldn't be applied, so there would be "squares" of voids instead of
    circles/spheres when using .xyzr files as the inital condition.
    */
    for (amrex::MFIter mfi(*eta_mf[lev], true); mfi.isValid(); ++mfi)
    {
        const amrex::Box &bx = mfi.tilebox();
        Set::Patch<Set::Scalar> eta    = eta_mf.Patch(lev, mfi);
        Set::Patch<const Set::Scalar> temp = temp_mf.Patch(lev, mfi);
        Set::Patch<const Set::Scalar> eta_0 = eta_0_mf.Patch(lev, mfi);
        Set::Patch<Set::Scalar> exceeded_Tcutoff = thermal.has_exceeded_Tcutoff.Patch(lev, mfi);
 
        Set::Scalar Tcutoff = thermal.Tcutoff;
 
        amrex::BoxList boxes_to_update;
        if (lev == finest_level && prev_finest_level == finest_level)
            boxes_to_update = amrex::complementIn(bx, prev_finest_ba).boxList();
        else
            boxes_to_update.push_back(bx);
 
        for (const amrex::Box &box : boxes_to_update)
            amrex::ParallelFor(box, [=] AMREX_GPU_DEVICE(int i, int j, int k)
            {
 
                if (!exceeded_Tcutoff(i,j,k) && temp(i,j,k) < Tcutoff)
                {
                        eta(i, j, k) = eta_0(i, j, k);
                }
            });
    }
 
    if (lev == finest_level)
    {
        prev_finest_ba    = grids[finest_level];
        prev_finest_level = finest_level;
    }
    }
}
 
void Flame::Integrate(int amrlev, Set::Scalar time, int /*step*/,
    const amrex::MFIter& mfi, const amrex::Box& box)
{
    BL_PROFILE("Flame::Integrate");
    
    Base::Mechanics<model_type>::Integrate(amrlev,time,timestep,mfi,box);
 
    const Set::Scalar* DX = geom[amrlev].CellSize();
    Set::Scalar dv = AMREX_D_TERM(DX[0], *DX[1], *DX[2]);
    Set::Patch<const Set::Scalar> eta  = eta_mf.Patch(amrlev,mfi);
    Set::Patch<const Set::Scalar> mdot = mdot_mf.Patch(amrlev,mfi);
    if (variable_pressure) {
        amrex::ParallelFor(box, [=] AMREX_GPU_DEVICE(int i, int j, int k)
        {
            chamber.volume += eta(i, j, k, 0) * dv;
            Set::Vector grad = Numeric::Gradient(eta, i, j, k, 0, DX);
            Set::Scalar normgrad = grad.lpNorm<2>();
            Set::Scalar da = normgrad * dv;
            chamber.area += da;
 
            Set::Vector mgrad = Numeric::Gradient(mdot, i, j, k, 0, DX);
            Set::Scalar mnormgrad = mgrad.lpNorm<2>();
            Set::Scalar dm = mnormgrad * dv;
            chamber.massflux += dm;
 
        });
    }
    else {
        amrex::ParallelFor(box, [=] AMREX_GPU_DEVICE(int i, int j, int k)
        {
            chamber.volume += eta(i, j, k, 0) * dv;
            Set::Vector grad = Numeric::Gradient(eta, i, j, k, 0, DX);
            Set::Scalar normgrad = grad.lpNorm<2>();
            Set::Scalar da = normgrad * dv;
            chamber.area += da;
        });
    }
    // time dependent pressure data from experimenta -> p = 0.0954521220950523 * exp(15.289993148880678 * t)
}
} // namespace Integrator