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defects #59

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728b688
fix P BC and add DE1_lo/hi
Jul 11, 2024
efdf9a6
add noise
Jul 19, 2024
a79c9d4
add depolarization energy to tdgl
Jul 24, 2024
6bcfd40
defect
prkkumar Dec 6, 2024
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22 changes: 22 additions & 0 deletions Source/FerroX.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -184,9 +184,11 @@ int FerroX::plot_PhiDiff;

// multimaterial stack geometry
AMREX_GPU_MANAGED amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> FerroX::DE_lo;
AMREX_GPU_MANAGED amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> FerroX::DE1_lo;
AMREX_GPU_MANAGED amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> FerroX::FE_lo;
AMREX_GPU_MANAGED amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> FerroX::SC_lo;
AMREX_GPU_MANAGED amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> FerroX::DE_hi;
AMREX_GPU_MANAGED amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> FerroX::DE1_hi;
AMREX_GPU_MANAGED amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> FerroX::FE_hi;
AMREX_GPU_MANAGED amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> FerroX::SC_hi;
AMREX_GPU_MANAGED amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> FerroX::Channel_hi;
Expand Down Expand Up @@ -233,6 +235,8 @@ AMREX_GPU_MANAGED amrex::Real FerroX::lambda;
AMREX_GPU_MANAGED amrex::GpuArray<int, AMREX_SPACEDIM> FerroX::P_BC_flag_lo;
AMREX_GPU_MANAGED amrex::GpuArray<int, AMREX_SPACEDIM> FerroX::P_BC_flag_hi;
AMREX_GPU_MANAGED amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> FerroX::Remnant_P;
AMREX_GPU_MANAGED amrex::Real FerroX::noise_amplitude;
AMREX_GPU_MANAGED amrex::Real FerroX::theta_dep;

//problem type : initialization of P for 2D/3D/convergence problems
AMREX_GPU_MANAGED int FerroX::prob_type;
Expand Down Expand Up @@ -400,6 +404,12 @@ void InitializeFerroXNamespace(const amrex::GpuArray<amrex::Real, AMREX_SPACEDIM
num_Vapp_max = 1;
pp.query("num_Vapp_max",num_Vapp_max);

noise_amplitude = 0.0;
pp.query("noise_amplitude",noise_amplitude);

theta_dep = 1.0;
pp.query("theta_dep",theta_dep);

//stack dimensions in 3D. This is an alternate way of initializing the device geometry, which works in simpler scenarios.
//A more general way of initializing device geometry is accomplished through masks which use function parsers

Expand Down Expand Up @@ -447,6 +457,18 @@ void InitializeFerroXNamespace(const amrex::GpuArray<amrex::Real, AMREX_SPACEDIM
}
}

if (pp.queryarr("DE1_lo",temp)) {
for (int i=0; i<AMREX_SPACEDIM; ++i) {
DE1_lo[i] = temp[i];
}
}

if (pp.queryarr("DE1_hi",temp)) {
for (int i=0; i<AMREX_SPACEDIM; ++i) {
DE1_hi[i] = temp[i];
}
}

if (pp.queryarr("SC_lo",temp)) {
for (int i=0; i<AMREX_SPACEDIM; ++i) {
SC_lo[i] = temp[i];
Expand Down
5 changes: 4 additions & 1 deletion Source/FerroX_namespace.H
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Expand Up @@ -22,9 +22,11 @@ namespace FerroX {

// multimaterial stack geometry
extern AMREX_GPU_MANAGED amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> DE_lo;
extern AMREX_GPU_MANAGED amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> DE1_lo;
extern AMREX_GPU_MANAGED amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> FE_lo;
extern AMREX_GPU_MANAGED amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> SC_lo;
extern AMREX_GPU_MANAGED amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> DE_hi;
extern AMREX_GPU_MANAGED amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> DE1_hi;
extern AMREX_GPU_MANAGED amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> FE_hi;
extern AMREX_GPU_MANAGED amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> SC_hi;
extern AMREX_GPU_MANAGED amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> Channel_hi;
Expand Down Expand Up @@ -73,7 +75,8 @@ namespace FerroX {
extern AMREX_GPU_MANAGED amrex::GpuArray<int, AMREX_SPACEDIM> P_BC_flag_lo;
extern AMREX_GPU_MANAGED amrex::GpuArray<int, AMREX_SPACEDIM> P_BC_flag_hi;
extern AMREX_GPU_MANAGED amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> Remnant_P;

extern AMREX_GPU_MANAGED amrex::Real noise_amplitude;
extern AMREX_GPU_MANAGED amrex::Real theta_dep;

//problem type : initialization of P for 2D/3D/convergence problems
extern AMREX_GPU_MANAGED int prob_type;
Expand Down
20 changes: 12 additions & 8 deletions Source/Solver/DerivativeAlgorithm.H
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Expand Up @@ -193,8 +193,9 @@ using namespace FerroX;

} else if (P_BC_flag_lo[2] == 1){

Real F_lo = F(i,j,k)/(1 + dx[2]/2/lambda);
return (dx[2]*F_lo/lambda - F(i,j,k) + F(i,j,k+1))/(2.*dx[2]); // dP/dz = P_lo/lambda;
//Real F_lo = F(i,j,k)/(1 + dx[2]/2/lambda);
Real dF_lo = F(i,j,k)/lambda;
return (dx[2]*dF_lo - F(i,j,k) + F(i,j,k+1))/(2.*dx[2]); // dP/dz = P_lo/lambda;

// Real F_lo = (9. * F(i,j,k) - F(i,j,k+1)) / (3. * dx[2] / lambda + 8.); // derived with 2nd order one-sided 1st derivative
// return -(dx[2]*F_lo/lambda - F(i,j,k) + F(i,j,k+1))/(2.*dx[2]);// dP/dz = P_lo/lambda;
Expand Down Expand Up @@ -222,8 +223,9 @@ using namespace FerroX;

} else if (P_BC_flag_hi[2] == 1){

Real F_hi = F(i,j,k)/(1 - dx[2]/2/lambda);
return (dx[2]*F_hi/lambda + F(i,j,k) - F(i,j,k-1))/(2.*dx[2]);//dPdz = P_hi/lambda;
//Real F_hi = F(i,j,k)/(1 - dx[2]/2/lambda);
Real dF_hi = -F(i,j,k)/lambda;
return (dx[2]*dF_hi + F(i,j,k) - F(i,j,k-1))/(2.*dx[2]);//dPdz = P_hi/lambda;

// Real F_hi = (9. * F(i,j,k) - F(i,j,k-1)) / ( - 3. * dx[2] / lambda + 8.); // derived with 2nd order one-sided 1st derivative
// return -(dx[2]*F_hi/lambda + F(i,j,k) - F(i,j,k-1))/(2.*dx[2]);//dPdz = P_hi/lambda;
Expand Down Expand Up @@ -407,8 +409,9 @@ using namespace FerroX;

} else if (P_BC_flag_lo[2] == 1){

Real F_lo = F(i,j,k)/(1 + dx[2]/2/lambda);
return (-dx[2]*F_lo/lambda - F(i,j,k) + F(i,j,k+1))/dx[2]/dx[2];//dPdz = P_lo/lambda;
//Real F_lo = F(i,j,k)/(1 + dx[2]/2/lambda);
Real dF_lo = F(i,j,k)/lambda;
return (-dx[2]*dF_lo - F(i,j,k) + F(i,j,k+1))/dx[2]/dx[2];//dPdz = P_lo/lambda;

// Real F_lo = (9. * F(i,j,k) - F(i,j,k+1)) / (3. * dx[2] / lambda + 8.); // derived with 2nd order one-sided 1st derivative
// return (-dx[2]*F_lo/lambda - F(i,j,k) + F(i,j,k+1))/dx[2]/dx[2];// dPdz = P_lo/lambda;
Expand Down Expand Up @@ -436,8 +439,9 @@ using namespace FerroX;

} else if (P_BC_flag_hi[2] == 1){

Real F_hi = F(i,j,k)/(1 - dx[2]/2/lambda);
return (dx[2]*F_hi/lambda - F(i,j,k) + F(i,j,k-1))/dx[2]/dx[2];//dPdz = P_hi/lambda;
//Real F_hi = F(i,j,k)/(1 - dx[2]/2/lambda);
Real dF_hi = -F(i,j,k)/lambda;
return (dx[2]*dF_hi - F(i,j,k) + F(i,j,k-1))/dx[2]/dx[2];//dPdz = P_hi/lambda;

// Real F_hi = (9. * F(i,j,k) - F(i,j,k-1)) / ( - 3. * dx[2] / lambda + 8.); // derived with 2nd order one-sided 1st derivative
// return (dx[2]*F_hi/lambda - F(i,j,k) + F(i,j,k-1))/dx[2]/dx[2]; // dPdz = P_hi/lambda;
Expand Down
7 changes: 6 additions & 1 deletion Source/Solver/ElectrostaticSolver.H
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Expand Up @@ -63,18 +63,22 @@ void ComputePoissonRHS_Newton(MultiFab& PoissonRHS,
MultiFab& alpha_cc);

void SetPhiBC_z(MultiFab& PossonPhi, const amrex::GpuArray<int, AMREX_SPACEDIM>& n_cell, const Geometry& geom);
void SetPhiBC_z(MultiFab& PoissonPhi, Array<MultiFab, AMREX_SPACEDIM> &P_old, MultiFab& MaterialMask, const amrex::GpuArray<int, AMREX_SPACEDIM>& n_cell, const Geometry& geom);

void SetPoissonBC(c_FerroX& rFerroX, std::array<std::array<amrex::LinOpBCType,AMREX_SPACEDIM>,2>& LinOpBCType_2d, bool& all_homogeneous_boundaries, bool& some_functionbased_inhomogeneous_boundaries, bool& some_constant_inhomogeneous_boundaries);

void Fill_Constant_Inhomogeneous_Boundaries(c_FerroX& rFerroX, MultiFab& PoissonPhi);
void Fill_FunctionBased_Inhomogeneous_Boundaries(c_FerroX& rFerroX, MultiFab& PoissonPhi, amrex::Real& time);

void CheckSteadyState(MultiFab& PoissonPhi, MultiFab& PoissonPhi_Old, MultiFab& Phidiff, Real phi_tolerance, int step, int& steady_state_step, int& inc_step);
void SetNucleation(Array<MultiFab, AMREX_SPACEDIM> &P_old, MultiFab& NucleationMask, const amrex::GpuArray<int, AMREX_SPACEDIM>& n_cell);
void SetupMLMG(std::unique_ptr<amrex::MLMG>& pMLMG,
std::unique_ptr<amrex::MLABecLaplacian>& p_mlabec,
std::array<std::array<amrex::LinOpBCType,AMREX_SPACEDIM>,2>& LinOpBCType_2d,
const amrex::GpuArray<int, AMREX_SPACEDIM>& n_cell,
std::array< MultiFab, AMREX_SPACEDIM >& beta_face,
Array<MultiFab, AMREX_SPACEDIM>& P_old,
MultiFab& MaterialMask,
c_FerroX& rFerroX, MultiFab& PoissonPhi, amrex::Real& time, amrex::LPInfo& info);

#ifdef AMREX_USE_EB
Expand All @@ -101,7 +105,8 @@ void ComputePhi_Rho(std::unique_ptr<amrex::MLMG>& pMLMG,
MultiFab& MaterialMask,
MultiFab& angle_alpha, MultiFab& angle_beta, MultiFab& angle_theta,
const Geometry& geom,
const amrex::GpuArray<amrex::Real, AMREX_SPACEDIM>& prob_lo,
const amrex::GpuArray<int, AMREX_SPACEDIM>& n_cell,
const amrex::GpuArray<amrex::Real, AMREX_SPACEDIM>& prob_lo,
const amrex::GpuArray<amrex::Real, AMREX_SPACEDIM>& prob_hi);

#ifdef AMREX_USE_EB
Expand Down
135 changes: 130 additions & 5 deletions Source/Solver/ElectrostaticSolver.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
#include "ChargeDensity.H"
#include "Utils/eXstaticUtils/eXstaticUtil.H"
#include "Utils/FerroXUtils/FerroXUtil.H"

#include "TotalEnergyDensity.H"

void ComputePoissonRHS(MultiFab& PoissonRHS,
Array<MultiFab, AMREX_SPACEDIM> &P_old,
Expand All @@ -12,6 +12,18 @@ void ComputePoissonRHS(MultiFab& PoissonRHS,
MultiFab& angle_alpha, MultiFab& angle_beta, MultiFab& angle_theta,
const Geometry& geom)
{
//Real average_P_r = 0.;
//Real total_P_r = 0.;
//Real FE_index_counter = 0.;

//Compute_P_av(P_old, total_P_r, MaterialMask, FE_index_counter, average_P_r);

//Real FE_thickness = FE_hi[2] - FE_lo[2];
//Real one_m_theta = 1.0 - theta_dep;
//Real E_dep = average_P_r/(epsilonZ_fe*epsilon_0)*one_m_theta;

//amrex::Print() << " E_dep = " << E_dep << "\n";
//amrex::Print() << " FE_thickness = " << FE_thickness << "\n";
for ( MFIter mfi(PoissonRHS); mfi.isValid(); ++mfi )
{
const Box& bx = mfi.validbox();
Expand Down Expand Up @@ -73,7 +85,7 @@ void ComputePoissonRHS(MultiFab& PoissonRHS,
} else { //mask(i,j,k) == 0.0 FE region
RHS(i,j,k) = - (R_11*DPDx(pOld_p, mask, i, j, k, dx) + R_12*DPDy(pOld_p, mask, i, j, k, dx) + R_13*DPDz(pOld_p, mask, i, j, k, dx))
- (R_21*DPDx(pOld_q, mask, i, j, k, dx) + R_22*DPDy(pOld_q, mask, i, j, k, dx) + R_23*DPDz(pOld_q, mask, i, j, k, dx))
- (R_31*DPDx(pOld_r, mask, i, j, k, dx) + R_32*DPDy(pOld_r, mask, i, j, k, dx) + R_33*DPDz(pOld_r, mask, i, j, k, dx));
- (R_31*DPDx(pOld_r, mask, i, j, k, dx) + R_32*DPDy(pOld_r, mask, i, j, k, dx) + R_33*DPDz(pOld_r, mask, i, j, k, dx));// - E_dep*FE_thickness;

}

Expand Down Expand Up @@ -499,8 +511,47 @@ void Fill_FunctionBased_Inhomogeneous_Boundaries(c_FerroX& rFerroX, MultiFab& Po
}
}

void SetPhiBC_z(MultiFab& PoissonPhi, Array<MultiFab, AMREX_SPACEDIM> &P_old, MultiFab& MaterialMask, const amrex::GpuArray<int, AMREX_SPACEDIM>& n_cell, const Geometry& geom)
{
//
// Real average_P_r = 0.;
// Real total_P_r = 0.;
// Real FE_index_counter = 0.;
//
// Compute_P_av(P_old, total_P_r, MaterialMask, FE_index_counter, average_P_r);
//
// Real FE_thickness = FE_hi[2] - FE_lo[2];
// Real one_m_theta = 1.0 - theta_dep;
// Real E_dep = -1.0*average_P_r/(epsilonZ_fe*epsilon_0)*one_m_theta;
//
// amrex::Print() << "average_P_r = " << average_P_r << ", "<< ", E_dep = " << E_dep << ", theta = " << theta_dep << ", phi_Bc_hi" << Phi_Bc_hi << "\n";
//
for (MFIter mfi(PoissonPhi); mfi.isValid(); ++mfi)
{
const Box& bx = mfi.growntilebox(1);

const Array4<Real>& Phi = PoissonPhi.array(mfi);

amrex::ParallelFor(bx, [=] AMREX_GPU_DEVICE(int i, int j, int k)
{
if(k < 0) {
Phi(i,j,k) = Phi_Bc_lo;
} else if(k >= n_cell[2]){
amrex::Real Eg = bandgap;
amrex::Real Chi = affinity;
amrex::Real phi_ref = Chi + 0.5*Eg + 0.5*kb*T*log(Nc/Nv)/q;
amrex::Real phi_m = use_work_function ? metal_work_function : phi_ref; //in eV When not used, applied voltgae is set as the potential on the metal interface
Phi(i,j,k) = (Phi_Bc_hi - (phi_m - phi_ref))*theta_dep;// - E_dep*FE_thickness; //multiplying by theta_dep
//if(i == 5 && j == 5) amrex::Print() << "Phi(i,j,k) = "<< Phi(i,j,k) << std::endl;
}
});
}
PoissonPhi.FillBoundary(geom.periodicity());
}

void SetPhiBC_z(MultiFab& PoissonPhi, const amrex::GpuArray<int, AMREX_SPACEDIM>& n_cell, const Geometry& geom)
{

for (MFIter mfi(PoissonPhi); mfi.isValid(); ++mfi)
{
const Box& bx = mfi.growntilebox(1);
Expand All @@ -516,13 +567,81 @@ void SetPhiBC_z(MultiFab& PoissonPhi, const amrex::GpuArray<int, AMREX_SPACEDIM>
amrex::Real Chi = affinity;
amrex::Real phi_ref = Chi + 0.5*Eg + 0.5*kb*T*log(Nc/Nv)/q;
amrex::Real phi_m = use_work_function ? metal_work_function : phi_ref; //in eV When not used, applied voltgae is set as the potential on the metal interface
Phi(i,j,k) = Phi_Bc_hi - (phi_m - phi_ref);
Phi(i,j,k) = (Phi_Bc_hi - (phi_m - phi_ref));
//if(i == 5 && j == 5) amrex::Print() << "Phi(i,j,k) = "<< Phi(i,j,k) << std::endl;
}
});
}
PoissonPhi.FillBoundary(geom.periodicity());
}

void SetNucleation(Array<MultiFab, AMREX_SPACEDIM> &P_old, MultiFab& NucleationMask, const amrex::GpuArray<int, AMREX_SPACEDIM>& n_cell)
{
int seed = random_seed;

int nprocs = ParallelDescriptor::NProcs();

if (prob_type == 1) {
amrex::InitRandom(seed , nprocs, seed ); // give all MPI ranks the same seed
} else {
amrex::InitRandom(seed+ParallelDescriptor::MyProc(), nprocs, seed+ParallelDescriptor::MyProc()); // give all MPI ranks a different seed
}

int nrand = n_cell[0]*n_cell[2];
amrex::Gpu::ManagedVector<Real> rngs(nrand, 0.0);

// generate random numbers on the host
for (int i=0; i<nrand; ++i) {
//rngs[i] = amrex::RandomNormal(0.,1.); // zero mean, unit variance
rngs[i] = amrex::Random(); // uniform [0,1] option
}

for (MFIter mfi(P_old[0]); mfi.isValid(); ++mfi)
{
const Box& bx = mfi.tilebox();

const Array4<Real> &pOld_p = P_old[0].array(mfi);
const Array4<Real> &pOld_q = P_old[1].array(mfi);
const Array4<Real> &pOld_r = P_old[2].array(mfi);
const Array4<Real>& mask = NucleationMask.array(mfi);

Real* rng = rngs.data();

amrex::ParallelForRNG(bx, [=] AMREX_GPU_DEVICE(int i, int j, int k, amrex::RandomEngine const& engine) noexcept
{
if (mask(i,j,k) == 0.) {
if (prob_type == 1) { //2D
if (rng[i + k*n_cell[2]] <= 0.02){
pOld_p(i,j,k) = Remnant_P[0];
pOld_q(i,j,k) = Remnant_P[1];
pOld_r(i,j,k) = Remnant_P[2];
} else if (rng[i + k*n_cell[2]] <= 0.04){
pOld_p(i,j,k) = -Remnant_P[0];
pOld_q(i,j,k) = -Remnant_P[1];
pOld_r(i,j,k) = -Remnant_P[2];
} else {
pOld_p(i,j,k) += (-1.0 + 2.0*rng[i + k*n_cell[2]])*Remnant_P[0]*noise_amplitude;
pOld_q(i,j,k) += (-1.0 + 2.0*rng[i + k*n_cell[2]])*Remnant_P[1]*noise_amplitude;
pOld_r(i,j,k) += (-1.0 + 2.0*rng[i + k*n_cell[2]])*Remnant_P[2]*noise_amplitude;
}
} else if (prob_type == 2) { //3D
Real rand = Random(engine);
if (rand <= 0.04) {
pOld_p(i,j,k) = Remnant_P[0];
pOld_q(i,j,k) = Remnant_P[1];
pOld_r(i,j,k) = Remnant_P[2];
} else {
pOld_p(i,j,k) += (-1.0 + 2.0*rand)*Remnant_P[0]*noise_amplitude;
pOld_q(i,j,k) += (-1.0 + 2.0*rand)*Remnant_P[1]*noise_amplitude;
pOld_r(i,j,k) += (-1.0 + 2.0*rand)*Remnant_P[2]*noise_amplitude;
}
}
}
});
}

}

void CheckSteadyState(MultiFab& PoissonPhi, MultiFab& PoissonPhi_Old, MultiFab& Phidiff, Real phi_tolerance, int step, int& steady_state_step, int& inc_step)
{

Expand Down Expand Up @@ -564,6 +683,8 @@ void SetupMLMG(std::unique_ptr<amrex::MLMG>& pMLMG,
std::array<std::array<amrex::LinOpBCType,AMREX_SPACEDIM>,2>& LinOpBCType_2d,
const amrex::GpuArray<int, AMREX_SPACEDIM>& n_cell,
std::array< MultiFab, AMREX_SPACEDIM >& beta_face,
Array<MultiFab, AMREX_SPACEDIM>& P_old,
MultiFab& MaterialMask,
c_FerroX& rFerroX, MultiFab& PoissonPhi, amrex::Real& time, amrex::LPInfo& info)
{
auto& rGprop = rFerroX.get_GeometryProperties();
Expand Down Expand Up @@ -597,7 +718,8 @@ void SetupMLMG(std::unique_ptr<amrex::MLMG>& pMLMG,
PoissonPhi.FillBoundary(geom.periodicity());

// set Dirichlet BC by reading in the ghost cell values
SetPhiBC_z(PoissonPhi, n_cell, geom);
SetPhiBC_z(PoissonPhi, n_cell, geom);
//SetPhiBC_z(PoissonPhi, P_old, MaterialMask, n_cell, geom);
p_mlabec->setLevelBC(amrlev, &PoissonPhi);

// (A*alpha_cc - B * div beta grad) phi = rhs
Expand Down Expand Up @@ -689,7 +811,8 @@ void ComputePhi_Rho(std::unique_ptr<amrex::MLMG>& pMLMG,
MultiFab& MaterialMask,
MultiFab& angle_alpha, MultiFab& angle_beta, MultiFab& angle_theta,
const Geometry& geom,
const amrex::GpuArray<amrex::Real, AMREX_SPACEDIM>& prob_lo,
const amrex::GpuArray<int, AMREX_SPACEDIM>& n_cell,
const amrex::GpuArray<amrex::Real, AMREX_SPACEDIM>& prob_lo,
const amrex::GpuArray<amrex::Real, AMREX_SPACEDIM>& prob_hi)

{
Expand All @@ -714,6 +837,8 @@ void ComputePhi_Rho(std::unique_ptr<amrex::MLMG>& pMLMG,

//Initial guess for phi
PoissonPhi.setVal(0.);
SetPhiBC_z(PoissonPhi, n_cell, geom);
//SetPhiBC_z(PoissonPhi, P_old, MaterialMask, n_cell, geom);

//Poisson Solve
pMLMG->solve({&PoissonPhi}, {&PoissonRHS}, 1.e-10, -1);
Expand Down
5 changes: 4 additions & 1 deletion Source/Solver/Initialization.cpp
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Expand Up @@ -192,6 +192,8 @@ void InitializeMaterialMask(MultiFab& MaterialMask,
mask(i,j,k) = 0.;
} else if (x <= DE_hi[0] && x >= DE_lo[0] && y <= DE_hi[1] && y >= DE_lo[1] && z <= DE_hi[2] && z >= DE_lo[2]) {
mask(i,j,k) = 1.;
} else if (x <= DE1_hi[0] && x >= DE1_lo[0] && y <= DE1_hi[1] && y >= DE1_lo[1] && z <= DE1_hi[2] && z >= DE1_lo[2]) {
mask(i,j,k) = 1.;
} else if (x <= SC_hi[0] && x >= SC_lo[0] && y <= SC_hi[1] && y >= SC_lo[1] && z <= SC_hi[2] && z >= SC_lo[2]) {
mask(i,j,k) = 2.;
if (x <= Channel_hi[0] && x >= Channel_lo[0] && y <= Channel_hi[1] && y >= Channel_lo[1] && z <= Channel_hi[2] && z >= Channel_lo[2]){
Expand All @@ -218,7 +220,8 @@ void InitializeMaterialMask(c_FerroX& rFerroX, const Geometry& geom, MultiFab& M
for (MFIter mfi(MaterialMask, TilingIfNotGPU()); mfi.isValid(); ++mfi)
{
const auto& mask_arr = MaterialMask.array(mfi);
const auto& bx = mfi.tilebox();
// const auto& bx = mfi.tilebox();
const Box& bx = mfi.growntilebox(MaterialMask.nGrow());

std::string m_mask_s;
std::unique_ptr<amrex::Parser> m_mask_parser;
Expand Down
6 changes: 6 additions & 0 deletions Source/Solver/TotalEnergyDensity.H
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Original file line number Diff line number Diff line change
Expand Up @@ -16,3 +16,9 @@ void CalculateTDGL_RHS(Array<MultiFab, AMREX_SPACEDIM> &GL_rhs,
const Geometry& geom,
const amrex::GpuArray<amrex::Real, AMREX_SPACEDIM>& prob_lo,
const amrex::GpuArray<amrex::Real, AMREX_SPACEDIM>& prob_hi);

void Compute_P_Sum(const std::array<MultiFab, AMREX_SPACEDIM>& P, Real& sum);

void Compute_P_index_Sum(const MultiFab& MaterialMask, Real& count);

void Compute_P_av(const std::array<MultiFab, AMREX_SPACEDIM>& P, Real& sum, const MultiFab& MaterialMask, Real& count, Real &P_av_z);
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