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fix xrb_layered trailing whitespace (#452)
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@zingale
zingale authored May 14, 2024
1 parent 53a9fea commit 3edbebe
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Showing 6 changed files with 44 additions and 44 deletions.
20 changes: 10 additions & 10 deletions Exec/science/xrb_layered/MaestroInitData.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ void Maestro::InitLevelData(const int lev, [[maybe_unused]] const Real time, con
const auto dx = geom[lev].CellSizeArray();

if (perturb_model) {

// Generate random seed (or get from input), and RNG
int seed = 0;
if (problem_rp::pert_seed != -1) {
Expand All @@ -49,14 +49,14 @@ void Maestro::InitLevelData(const int lev, [[maybe_unused]] const Real time, con
seed = r();
}
std::default_random_engine generator(seed);

// Gaussian distribution
std::normal_distribution<double> noise(1.0, 0.001); // mean of 1, std dev 10^-3

// Loop through data and perturb
const auto lo = amrex::lbound(tileBox);
const auto hi = amrex::ubound(tileBox);

// Why for and not parallelfor?
// Because RNG's are not thread safe. so if we wanted to use ParallelFor, we would have to create a new RNG inside
// every iteration, but that loses the ability to keep a fixed seed and be fully reproducible.. maybe that wouldn't be so bad
Expand All @@ -66,28 +66,28 @@ void Maestro::InitLevelData(const int lev, [[maybe_unused]] const Real time, con
for (int j = lo.y; j<= hi.y; j++) {
for (int i = lo.x; i<= hi.x; i++) {
int r = AMREX_SPACEDIM == 2 ? j : k; // j if 2D, k if 3D

Real t0 = s0_arr(lev, r, Temp);
Real temp = t0 * noise(generator);
Real temp = t0 * noise(generator);
Real dens = s0_arr(lev, r, Rho); // no change

// Create new eos object based on these modified values
eos_t eos_state;
eos_state.T = temp;
eos_state.p = p0_arr(lev, r);
eos_state.rho = dens;
for (auto comp = 0; comp < NumSpec; comp++) {
eos_state.xn[comp] =
eos_state.xn[comp] =
s0_arr(lev, r, FirstSpec + comp) / s0_arr(lev, r, Rho);
}

auto eos_input_flag = eos_input_tp; // temperature & pressure eos
eos(eos_input_flag, eos_state);
scal(i, j, k, Rho) = eos_state.rho;
scal(i, j, k, RhoH) = eos_state.rho * eos_state.h; // re-compute enthalpy
scal(i, j, k, Temp) = eos_state.T;
for (auto comp=0; comp < NumSpec; comp++) {
scal(i, j, k, FirstSpec + comp) =
scal(i, j, k, FirstSpec + comp) =
eos_state.rho * eos_state.xn[comp];
}
}
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2 changes: 1 addition & 1 deletion Exec/science/xrb_layered/MaestroTagging.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -67,5 +67,5 @@ void Maestro::StateError(TagBoxArray& tags, const MultiFab& state_mf,
tag_array_p[lev + max_lev * r] = TagBox::SET;
}
});
}
}
}
54 changes: 27 additions & 27 deletions Exec/science/xrb_layered/create_initial_model/toy_atm/init_1d.H
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Expand Up @@ -6,16 +6,16 @@
// (T_star) representing the NS, a hyperbolic tangent rise to a
// peak temperature (T_base) representing the base of an accreted
// layer at r=H_star, an isentropic profile representing the convective
// region at ignition, then a radiative profile from r=H_rad.
// Below, three different power-laws set the temperature profile
// region at ignition, then a radiative profile from r=H_rad.
// Below, three different power-laws set the temperature profile
// T = T0*(y/y0)^del
// where y is the column depth (=pressure/gravity) and, del is the power-law
// index, and T0 and y0 are the values at the beginning of a given region.
// Those regions have different physics: 1) an adiabatic zone
// where helium is burning and generating convection, 2) a stable region
// where nothing is burning, 3) a stable region with hot CNO burning.

// The composition transitions from pure ash, to helium and CNO, to a solar
// The composition transitions from pure ash, to helium and CNO, to a solar
// mixture including hydrogen, with initial hydrogen fraction X0 and CNO fraction
// Zcno (inputs file). The CNO is split between o14 and o15 with ratio
// determined by their beta decay times (70.621/122.266). Because hot CNO burns
Expand All @@ -40,23 +40,23 @@
// | . . +__
// | . . . `--- T ~ y^del_2
// | . . . `---+
// | . . . .`-
// | . . . .`-
// | . . . . `- T ~ y^del_3
// | . . . . `-
// | . . . . `-
// +-----+---+-----+---------------------> r
// | \ /
// | delta
// |< H_star>|
// |-----<y_2>----|
// |----------<y_3>---------|
// |-----<y_2>----|
// |----------<y_3>---------|
//
// The composition profile is:
//
// X
// ^
// | star | reg 1 | reg 2 | region 3
// 1.0 +--------*----------
// | star | reg 1 | reg 2 | region 3
// 1.0 +--------*----------
// | ash . \
// | . \ +--------- X0 (hydrogen)
// | . \ /
Expand All @@ -66,8 +66,8 @@
// | . / +--------- 1-X0-Zcno (helium)
// | .----------/--------------- Zcno (o14/o15)
// 0.0 +--------+---------+-----------------> r
// |<H_star>|
// |------<y_d>------|
// |<H_star>|
// |------<y_d>------|
// |
//
// The transition from ash to fuel is a hyperbolic tangent, parametrized
Expand Down Expand Up @@ -140,7 +140,7 @@ AMREX_INLINE void init_1d()
}
if (std::abs(sum) - 1.0_rt > NumSpec * smallx) {
amrex::Error("ERROR: fuel mass fractions don't sum to 1");
}
}



Expand Down Expand Up @@ -196,7 +196,7 @@ AMREX_INLINE void init_1d()
if (error < err_min) {
err_min = error;
n_best = n;
}
}
}

Real dens_base = (1.3 + n_best*0.001)*1.e6;
Expand All @@ -217,10 +217,10 @@ AMREX_INLINE void init_1d()

// Composition
for (int n = 0; n < NumSpec; ++n) {
model_hse(i, ispec+n) = xn_star[n] +
model_hse(i, ispec+n) = xn_star[n] +
0.5_rt * (xn_base[n] - xn_star[n]) *
(1.0_rt + std::tanh((xzn_hse(i) - (problem_rp::xmin + problem_rp::H_star - problem_rp::delta) + problem_rp::delta) / problem_rp::delta));
}
(1.0_rt + std::tanh((xzn_hse(i) - (problem_rp::xmin + problem_rp::H_star - problem_rp::delta) + problem_rp::delta) / problem_rp::delta));
}

// Temperature
model_hse(i, itemp) = problem_rp::T_star + 0.5_rt * (problem_rp::T_base - problem_rp::T_star) *
Expand All @@ -241,7 +241,7 @@ AMREX_INLINE void init_1d()
for (int i = 0; i < problem_rp::nx; ++i) {
if (model_hse(i, itemp) > 0.9995 * problem_rp::T_base) {
index_base = i+1;
break;
break;
}
}
} else {
Expand Down Expand Up @@ -348,9 +348,9 @@ AMREX_INLINE void init_1d()

// set to isothermal if hit threshold
if (temp_zone < problem_rp::T_lo) {
temp_zone = problem_rp::T_lo;
temp_zone = problem_rp::T_lo;
}

// std::cout << "T=" << temp_zone << std::endl;
}

Expand Down Expand Up @@ -400,7 +400,7 @@ AMREX_INLINE void init_1d()

// call the EOS one more time for this zone and then go on to the next
// (t, rho) -> (p)

eos_state.T = temp_zone;
eos_state.rho = dens_zone;
for (int n = 0; n < NumSpec; ++n) {
Expand Down Expand Up @@ -447,7 +447,7 @@ AMREX_INLINE void init_1d()


// integrate down -- using the temperature profile defined above

for (int i = index_base-1; i >= 0; --i) {

Real delx = xzn_hse(i+1) - xzn_hse(i);
Expand All @@ -459,7 +459,7 @@ AMREX_INLINE void init_1d()
}

// use our previous initial guess for density

dens_zone = model_hse(i+1, idens);


Expand All @@ -477,7 +477,7 @@ AMREX_INLINE void init_1d()
// find the density and pressure that are consistent

// HSE differencing

p_want = model_hse(i+1, ipres) -
delx * 0.5_rt * (dens_zone + model_hse(i+1, idens)) * problem_rp::g_const;

Expand Down Expand Up @@ -541,7 +541,7 @@ AMREX_INLINE void init_1d()

}


// auto deltastr = num_to_unitstring(delta);
auto dxstr = num_to_unitstring(dCoord);

Expand Down Expand Up @@ -576,7 +576,7 @@ AMREX_INLINE void init_1d()

of.close();

std::cout << "Saved model to " << outfile << std::endl;
std::cout << "Saved model to " << outfile << std::endl;

// some metadata
of << "# generated by toy_atm_layered" << std::endl;
Expand All @@ -600,11 +600,11 @@ AMREX_INLINE void init_1d()

of2 << std::setprecision(12) << std::setw(20) << xzn_hse(i) << std::endl;
of2 << std::setprecision(12) << std::setw(20) << eos_state.s << std::endl;
of2 << std::setprecision(12) << std::setw(20) << eos_state.cs << std::endl;
of2 << std::setprecision(12) << std::setw(20) << eos_state.cs << std::endl;
}

// compute the maximum HSE error

Real max_hse_error = -1.e30;

for (int i = 1; i < problem_rp::nx-1; ++i) {
Expand All @@ -620,5 +620,5 @@ AMREX_INLINE void init_1d()
}

std::cout << "maximum HSE error = " << max_hse_error << std::endl;

}
2 changes: 1 addition & 1 deletion Exec/science/xrb_layered/create_initial_model/toy_atm/main.cpp
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Expand Up @@ -42,7 +42,7 @@ main (int argc,
// std::cout << "inputs file is " << inputs_name << std::endl;
}
} else {
std::cout << "No input file. Using defaults" << inputs_name << std::endl;
std::cout << "No input file. Using defaults" << inputs_name << std::endl;
}


Expand Down
6 changes: 3 additions & 3 deletions Exec/science/xrb_layered/plotfile_derive/main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -94,7 +94,7 @@ void main_main()
varnames = pf.varNames();

// find variable indices
// We want:
// We want:
// density, temperature, pressure, species
// vertical velocity, temperature perturbation
// we will assume here that the species are contiguous, so we will find
Expand Down Expand Up @@ -476,10 +476,10 @@ void main_main()
// Fluxes

// Convective heat flux : "Fconv_dT"
ga(i,j,k,4) = rho * cp * vely * delT;
ga(i,j,k,4) = rho * cp * vely * delT;

// Alternate version that should be equivalent : "Fconv_T"
// because <vdT> = <v(T-T0)> = <vT> - <v>T0 = <vT> (the vertical velocity averages to zero)
// because <vdT> = <v(T-T0)> = <vT> - <v>T0 = <vT> (the vertical velocity averages to zero)
ga(i,j,k,5) = rho * cp * vely * temp;

// MLT heat flux in the efficient regime : "Fconv_mlt"
Expand Down
4 changes: 2 additions & 2 deletions Exec/science/xrb_layered/scripts/chainslurm.sh
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Expand Up @@ -31,9 +31,9 @@ fi
firstcount=1

if [ $oldjob -eq "-1" ]
then
then
echo chaining $numjobs jobs

echo starting job 1 with no dependency
aout=`sbatch --parsable ${script}`
echo " " jobid: $aout
Expand Down

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