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address a long-standing issue where sometimes its preferable to speci…
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…fy the avogadro number instead of Runiv.

If avogadro is supplied, then Runiv is set to avogadro * k_b

Default behavior is preserved as all codes presently set Runiv

The code will abort if you try to specify both.
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@ajnonaka
ajnonaka committed Aug 19, 2024
1 parent 17ed8fa commit 16d8018
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Showing 7 changed files with 21 additions and 14 deletions.
10 changes: 5 additions & 5 deletions exec/chemistry_testing/main.cpp
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Expand Up @@ -201,14 +201,14 @@ void main_main(const char* argv)

for (int n=0; n<nspecies; n++)
{
//amrex::Print() << ComputeSpatialMean(rho_old,n)*(Runiv/k_B)/molmass[n] << " ";
//amrex::Print() << ComputeSpatialMean(rho_old,n)*(avogadro)/molmass[n] << " ";
amrex::Print() << ComputeSpatialMean(rho_old,n) << " ";
}


for (int n=0; n<nspecies; n++)
{
//amrex::Print() << ComputeSpatialVariance(rho_old,n)*((Runiv/k_B)/molmass[n])*((Runiv/k_B)/molmass[n]) << " ";
//amrex::Print() << ComputeSpatialVariance(rho_old,n)*((avogadro)/molmass[n])*((avogadro)/molmass[n]) << " ";
amrex::Print() << ComputeSpatialVariance(rho_old,n) << " ";
}

Expand All @@ -235,7 +235,7 @@ void main_main(const char* argv)
{
GpuArray<amrex::Real,MAX_SPECIES> n_old;
GpuArray<amrex::Real,MAX_SPECIES> n_new;
for (int n=0; n<nspecies; n++) n_old[n] = rhoOld(i,j,k,n)*(Runiv/k_B)/molmass[n];
for (int n=0; n<nspecies; n++) n_old[n] = rhoOld(i,j,k,n)*(avogadro)/molmass[n];
switch(reaction_type){
case 0: // deterministic case
advance_reaction_det_cell(n_old,n_new,dt);
Expand Down Expand Up @@ -300,12 +300,12 @@ void main_main(const char* argv)
amrex::Print() << dt*step << " ";
for (int n=0; n<nspecies; n++)
{
//amrex::Print() << ComputeSpatialMean(rho_new,n)*(Runiv/k_B)/molmass[n] << " ";
//amrex::Print() << ComputeSpatialMean(rho_new,n)*(avogadro)/molmass[n] << " ";
amrex::Print() << ComputeSpatialMean(rho_new,n) << " ";
}
for (int n=0; n<nspecies; n++)
{
//amrex::Print() << ComputeSpatialVariance(rho_new,n)*((Runiv/k_B)/molmass[n])*((Runiv/k_B)/molmass[n]) << " ";
//amrex::Print() << ComputeSpatialVariance(rho_new,n)*((avogadro)/molmass[n])*((avogadro)/molmass[n]) << " ";
amrex::Print() << ComputeSpatialVariance(rho_new,n) << " ";
}
amrex::Print() << "\n";
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6 changes: 3 additions & 3 deletions src_chemistry/chemistry_functions.cpp
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Expand Up @@ -105,7 +105,7 @@ void compute_chemistry_source_CLE(amrex::Real dt, amrex::Real dV,
amrex::Real T = prim_arr(i,j,k,4);
amrex::Real T0 = T0_chem;
amrex::Real ctot = pres/Runiv/T;
amrex::Real Navo = Runiv/k_B;
amrex::Real Navo = avogadro;

GpuArray<amrex::Real,MAX_SPECIES> ck; // molar concentrations
for (int n=0; n<nspecies; n++) ck[n] = prim_arr(i,j,k,6+nspecies+n)*ctot;
Expand Down Expand Up @@ -176,7 +176,7 @@ void compute_chemistry_source_CLE_1(amrex::Real dt, amrex::Real dV,
if (reaction_type==2) amrex::Abort("ERROR: reaction_type=2 not implemented yet");

GpuArray<amrex::Real,MAX_SPECIES> m_s;
for (int n=0; n<nspecies; n++) m_s[n] = molmass[n]/(Runiv/k_B);
for (int n=0; n<nspecies; n++) m_s[n] = molmass[n]/(avogadro);

for (MFIter mfi(mf_in); mfi.isValid(); ++mfi)
{
Expand Down Expand Up @@ -229,7 +229,7 @@ void compute_chemistry_source_CLE_2(amrex::Real dt, amrex::Real dV,
if (reaction_type!=1) amrex::Abort("ERROR: compute_chemistry_source_CLE assumes reaction_type=1");

GpuArray<amrex::Real,MAX_SPECIES> m_s;
for (int n=0; n<nspecies; n++) m_s[n] = molmass[n]/(Runiv/k_B);
for (int n=0; n<nspecies; n++) m_s[n] = molmass[n]/(avogadro);

for (MFIter mfi(mf_in); mfi.isValid(); ++mfi)
{
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8 changes: 8 additions & 0 deletions src_common/common_functions.cpp
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Expand Up @@ -68,6 +68,7 @@ AMREX_GPU_MANAGED amrex::Real common::variance_coef_ener;
AMREX_GPU_MANAGED amrex::Real common::k_B;
AMREX_GPU_MANAGED amrex::Real common::h_bar;
AMREX_GPU_MANAGED amrex::Real common::Runiv;
AMREX_GPU_MANAGED amrex::Real common::avogadro;
AMREX_GPU_MANAGED amrex::GpuArray<amrex::Real, MAX_SPECIES> common::T_init;
AMREX_GPU_MANAGED int common::algorithm_type;
int common::barodiffusion_type;
Expand Down Expand Up @@ -764,6 +765,13 @@ void InitializeCommonNamespace() {
pp.query("k_B",k_B);
pp.query("h_bar",h_bar);
pp.query("Runiv",Runiv);
avogadro = Runiv / k_B;
if (pp.query("avogadro",avogadro) ) {
Runiv = k_B * avogadro;
}
if (pp.query("Runiv",Runiv) && pp.query("avogadro",avogadro)) {
Abort("Cannot specify both Runiv and avogadro");
}
if (pp.queryarr("T_init",temp)) {
for (int i=0; i<nspecies; ++i) {
T_init[i] = temp[i];
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1 change: 1 addition & 0 deletions src_common/common_namespace.H
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Expand Up @@ -86,6 +86,7 @@ namespace common {
extern AMREX_GPU_MANAGED amrex::Real k_B;
extern AMREX_GPU_MANAGED amrex::Real h_bar;
extern AMREX_GPU_MANAGED amrex::Real Runiv;
extern AMREX_GPU_MANAGED amrex::Real avogadro;
extern AMREX_GPU_MANAGED amrex::GpuArray<amrex::Real, MAX_SPECIES> T_init;

// Algorithm control / selection
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4 changes: 2 additions & 2 deletions src_compressible/compressible_functions.cpp
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Expand Up @@ -229,13 +229,13 @@ void InitConsVar(MultiFab& cons,
Real pscale = 884.147e3;

// rho0 = m * p / (k_B * T)
Real rhoscale = molmass[0] / (Runiv / k_B) * pscale / (k_B * T_init[0]);
Real rhoscale = molmass[0] / avogadro * pscale / (k_B * T_init[0]);

// compute pressure (needed to compute density)
Real pres = pscale+rhoscale*velscale*velscale*cos(2.*pi*x/Lf)*cos(4.*pi*y/Lf)*(cos(4.*pi*z/Lf)+2.);

// density
cu(i,j,k,0) = (molmass[0] / (Runiv / k_B)) * pres / (k_B * T_init[0]);
cu(i,j,k,0) = (molmass[0] / avogadro) * pres / (k_B * T_init[0]);

// momentum
cu(i,j,k,1) = velscale*cu(i,j,k,0)*sin(2.*pi*x/Lf)*cos(2.*pi*y/Lf)*cos(2.*pi*z/Lf);
Expand Down
2 changes: 1 addition & 1 deletion src_compressible/main_driver.cpp
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Expand Up @@ -337,7 +337,7 @@ void main_driver(const char* argv)

p0 = 884.147e3;
dProb = (AMREX_SPACEDIM==2) ? 1./(n_cells[0]*n_cells[1]) : 1./(n_cells[0]*n_cells[1]*n_cells[2]);
rho0 = molmass[0] / (Runiv / k_B) * p0 / (k_B * T_init[0]);
rho0 = molmass[0] / avogadro * p0 / (k_B * T_init[0]);
nu0 = 0.185;
}

Expand Down
4 changes: 1 addition & 3 deletions src_compressible_stag/reservoirStag.cpp
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Expand Up @@ -21,11 +21,9 @@ ComputeFluxMomReservoir(const MultiFab& cons0_in, const MultiFab& prim0_in,
const GpuArray<Real, AMREX_SPACEDIM> dx = geom.CellSizeArray();
Box dom(geom.Domain());

Real N_A = Runiv/k_B; // Avagadro's number

GpuArray<Real,MAX_SPECIES> mass;
for (int l=0;l<nspecies;++l) {
mass[l] = molmass[l]/(N_A);
mass[l] = molmass[l]/avogadro;
}

for (int d=0; d<AMREX_SPACEDIM; ++d) {
Expand Down

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