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use amu and k_B from microphysics instead of m_H and k_B in quokka
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@psharda
psharda committed Jul 24, 2023
1 parent dfef3f1 commit 607d203
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Showing 38 changed files with 104 additions and 106 deletions.
14 changes: 7 additions & 7 deletions src/CloudyCooling.hpp
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Expand Up @@ -81,7 +81,7 @@ AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE auto cloudy_cooling_function(Real const
{
// interpolate cooling rates from Cloudy tables
const Real rhoH = rho * cloudy_H_mass_fraction; // mass density of H species
const Real nH = rhoH / quokka::hydrogen_mass_cgs;
const Real nH = rhoH / C::m_u;
const Real log_nH = std::log10(nH);
const Real log_T = std::log10(T);

Expand All @@ -102,7 +102,7 @@ AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE auto cloudy_cooling_function(Real const

// compute electron density
// N.B. it is absolutely critical to include the metal contribution here!
double n_e = (rho / quokka::hydrogen_mass_cgs) * (1.0 - mu * (X + Y / 4. + Z / mean_metals_A)) / (mu - (electron_mass_cgs / quokka::hydrogen_mass_cgs));
double n_e = (rho / C::m_u) * (1.0 - mu * (X + Y / 4. + Z / mean_metals_A)) / (mu - (electron_mass_cgs / C::m_u));
// the approximation for the metals contribution to e- fails at high densities (~1e3 or higher)
n_e = std::max(n_e, 1.0e-4 * nH);

Expand All @@ -118,7 +118,7 @@ AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE auto cloudy_cooling_function(Real const
// Compton term (CMB photons)
// [e.g., Hirata 2018: doi:10.1093/mnras/stx2854]
constexpr double Gamma_C = (8. * sigma_T * E_cmb) / (3. * electron_mass_cgs * c_light_cgs_);
constexpr double C_n = Gamma_C * quokka::boltzmann_constant_cgs / (5. / 3. - 1.0);
constexpr double C_n = Gamma_C * C::k_B / (5. / 3. - 1.0);
const double compton_CMB = -C_n * (T - T_cmb) * n_e;
Edot += compton_CMB;

Expand All @@ -129,13 +129,13 @@ AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE auto ComputeEgasFromTgas(double rho, do
{
// convert Egas (internal gas energy) to temperature
const Real rhoH = rho * cloudy_H_mass_fraction;
const Real nH = rhoH / quokka::hydrogen_mass_cgs;
const Real nH = rhoH / C::m_u;

// compute mu from mu(T) table
const Real mu = interpolate2d(std::log10(nH), std::log10(Tgas), tables.log_nH, tables.log_Tgas, tables.meanMolWeight);

// compute thermal gas energy
const Real Egas = (rho / (quokka::hydrogen_mass_cgs * mu)) * quokka::boltzmann_constant_cgs * Tgas / (gamma - 1.);
const Real Egas = (rho / (C::m_u * mu)) * C::k_B * Tgas / (gamma - 1.);
return Egas;
}

Expand All @@ -157,12 +157,12 @@ AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE auto ComputeTgasFromEgas(double rho, do

// solve for temperature given Eint (with fixed adiabatic index gamma)
const Real rhoH = rho * cloudy_H_mass_fraction;
const Real nH = rhoH / quokka::hydrogen_mass_cgs;
const Real nH = rhoH / C::m_u;
const Real log_nH = std::log10(nH);

// mean molecular weight (in Grackle tables) is defined w/r/t
// hydrogen_mass_cgs_
const Real C = (gamma - 1.) * Egas / (quokka::boltzmann_constant_cgs * (rho / quokka::hydrogen_mass_cgs));
const Real C = (gamma - 1.) * Egas / (C::k_B * (rho / C::m_u));

// solve for mu(T)*C == T.
// (Grackle does this with a fixed-point iteration. We use a more robust
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8 changes: 4 additions & 4 deletions src/Cooling/test_cooling.cpp
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Expand Up @@ -30,14 +30,14 @@ using amrex::Real;
struct CoolingTest {
}; // dummy type to allow compile-type polymorphism via template specialization

constexpr double m_H = quokka::hydrogen_mass_cgs;
constexpr double m_H = C::m_u;
constexpr double seconds_in_year = 3.154e7;

template <> struct quokka::EOS_Traits<CoolingTest> {
static constexpr double gamma = 5. / 3.; // default value
static constexpr double mean_molecular_weight = quokka::hydrogen_mass_cgs;
static constexpr double boltzmann_constant = quokka::boltzmann_constant_cgs;
static constexpr double hydrogen_mass_code_units = quokka::hydrogen_mass_cgs;
static constexpr double mean_molecular_weight = C::m_u;
static constexpr double boltzmann_constant = C::k_B;
static constexpr double mass_code_units = C::m_u;
};

template <> struct Physics_Traits<CoolingTest> {
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10 changes: 4 additions & 6 deletions src/EOS.hpp
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Expand Up @@ -26,17 +26,15 @@

namespace quokka
{
static constexpr double boltzmann_constant_cgs = C::k_B; // cgs
static constexpr double hydrogen_mass_cgs = C::m_p + C::m_e; // cgs

// specify default values for ideal gamma-law EOS
//
template <typename problem_t> struct EOS_Traits {
static constexpr double gamma = 5. / 3.; // default value
static constexpr double cs_isothermal = NAN; // only used when gamma = 1
static constexpr double mean_molecular_weight = NAN;
static constexpr double boltzmann_constant = boltzmann_constant_cgs;
static constexpr double hydrogen_mass_code_units = hydrogen_mass_cgs;
static constexpr double boltzmann_constant = C::k_B;
static constexpr double mass_code_units = C::m_u;
};

template <typename problem_t> class EOS
Expand All @@ -56,7 +54,7 @@ template <typename problem_t> class EOS
static constexpr amrex::Real gamma_ = EOS_Traits<problem_t>::gamma;
static constexpr amrex::Real boltzmann_constant_ = EOS_Traits<problem_t>::boltzmann_constant;
static constexpr amrex::Real mean_molecular_weight_ = EOS_Traits<problem_t>::mean_molecular_weight;
static constexpr amrex::Real hydrogen_mass_code_units_ = EOS_Traits<problem_t>::hydrogen_mass_code_units;
static constexpr amrex::Real mass_code_units_ = EOS_Traits<problem_t>::mass_code_units;
};

template <typename problem_t>
Expand Down Expand Up @@ -92,7 +90,7 @@ AMREX_FORCE_INLINE AMREX_GPU_HOST_DEVICE auto EOS<problem_t>::ComputeTgasFromEin
chem_eos_t estate;
estate.rho = rho;
estate.e = Eint / rho;
estate.mu = mean_molecular_weight_ / hydrogen_mass_code_units_;
estate.mu = mean_molecular_weight_ / mass_code_units_;
eos(eos_input_re, estate);
// scale returned temperature in case boltzmann constant is dimensionless
Tgas = estate.T * C::k_B / boltzmann_constant_;
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6 changes: 3 additions & 3 deletions src/FCQuantities/test_fc_quantities.cpp
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Expand Up @@ -27,9 +27,9 @@ struct FCQuantities {

template <> struct quokka::EOS_Traits<FCQuantities> {
static constexpr double gamma = 5. / 3.;
static constexpr double mean_molecular_weight = quokka::hydrogen_mass_cgs;
static constexpr double boltzmann_constant = quokka::boltzmann_constant_cgs;
static constexpr double hydrogen_mass_code_units = quokka::hydrogen_mass_cgs;
static constexpr double mean_molecular_weight = C::m_u;
static constexpr double boltzmann_constant = C::k_B;
static constexpr double mass_code_units = C::m_u;
};

template <> struct Physics_Traits<FCQuantities> {
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4 changes: 2 additions & 2 deletions src/HydroBlast2D/test_hydro2d_blast.cpp
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Expand Up @@ -28,8 +28,8 @@ struct BlastProblem {
template <> struct quokka::EOS_Traits<BlastProblem> {
static constexpr double gamma = 5. / 3.;
static constexpr double mean_molecular_weight = NAN;
static constexpr double boltzmann_constant = quokka::boltzmann_constant_cgs;
static constexpr double hydrogen_mass_code_units = quokka::hydrogen_mass_cgs;
static constexpr double boltzmann_constant = C::k_B;
static constexpr double mass_code_units = C::m_u;
};

template <> struct Physics_Traits<BlastProblem> {
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4 changes: 2 additions & 2 deletions src/HydroBlast3D/test_hydro3d_blast.cpp
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Expand Up @@ -35,8 +35,8 @@ bool test_passes = false; // if one of the energy checks fails, set to false
template <> struct quokka::EOS_Traits<SedovProblem> {
static constexpr double gamma = 1.4;
static constexpr double mean_molecular_weight = NAN;
static constexpr double boltzmann_constant = quokka::boltzmann_constant_cgs;
static constexpr double hydrogen_mass_code_units = quokka::hydrogen_mass_cgs;
static constexpr double boltzmann_constant = C::k_B;
static constexpr double mass_code_units = C::m_u;
};

template <> struct HydroSystem_Traits<SedovProblem> {
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6 changes: 3 additions & 3 deletions src/HydroContact/test_hydro_contact.cpp
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Expand Up @@ -23,9 +23,9 @@ struct ContactProblem {

template <> struct quokka::EOS_Traits<ContactProblem> {
static constexpr double gamma = 1.4;
static constexpr double mean_molecular_weight = quokka::hydrogen_mass_cgs;
static constexpr double boltzmann_constant = quokka::boltzmann_constant_cgs;
static constexpr double hydrogen_mass_code_units = quokka::hydrogen_mass_cgs;
static constexpr double mean_molecular_weight = C::m_u;
static constexpr double boltzmann_constant = C::k_B;
static constexpr double mass_code_units = C::m_u;
};

template <> struct Physics_Traits<ContactProblem> {
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4 changes: 2 additions & 2 deletions src/HydroHighMach/test_hydro_highmach.cpp
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Expand Up @@ -31,8 +31,8 @@ struct HighMachProblem {
template <> struct quokka::EOS_Traits<HighMachProblem> {
static constexpr double gamma = 5. / 3.;
static constexpr double mean_molecular_weight = NAN;
static constexpr double boltzmann_constant = quokka::boltzmann_constant_cgs;
static constexpr double hydrogen_mass_code_units = quokka::hydrogen_mass_cgs;
static constexpr double boltzmann_constant = C::k_B;
static constexpr double mass_code_units = C::m_u;
};

template <> struct Physics_Traits<HighMachProblem> {
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4 changes: 2 additions & 2 deletions src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
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Expand Up @@ -25,8 +25,8 @@ struct KelvinHelmholzProblem {
template <> struct quokka::EOS_Traits<KelvinHelmholzProblem> {
static constexpr double gamma = 1.4;
static constexpr double mean_molecular_weight = NAN;
static constexpr double boltzmann_constant = quokka::boltzmann_constant_cgs;
static constexpr double hydrogen_mass_code_units = quokka::hydrogen_mass_cgs;
static constexpr double boltzmann_constant = C::k_B;
static constexpr double mass_code_units = C::m_u;
};

template <> struct HydroSystem_Traits<KelvinHelmholzProblem> {
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6 changes: 3 additions & 3 deletions src/HydroLeblanc/test_hydro_leblanc.cpp
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Expand Up @@ -30,9 +30,9 @@ struct ShocktubeProblem {

template <> struct quokka::EOS_Traits<ShocktubeProblem> {
static constexpr double gamma = (5. / 3.);
static constexpr double mean_molecular_weight = quokka::hydrogen_mass_cgs;
static constexpr double boltzmann_constant = quokka::boltzmann_constant_cgs;
static constexpr double hydrogen_mass_code_units = quokka::hydrogen_mass_cgs;
static constexpr double mean_molecular_weight = C::m_u;
static constexpr double boltzmann_constant = C::k_B;
static constexpr double mass_code_units = C::m_u;
};

template <> struct Physics_Traits<ShocktubeProblem> {
Expand Down
4 changes: 2 additions & 2 deletions src/HydroQuirk/test_quirk.cpp
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Expand Up @@ -44,8 +44,8 @@ struct QuirkProblem {
template <> struct quokka::EOS_Traits<QuirkProblem> {
static constexpr double gamma = 5. / 3.;
static constexpr double mean_molecular_weight = NAN;
static constexpr double boltzmann_constant = quokka::boltzmann_constant_cgs;
static constexpr double hydrogen_mass_code_units = quokka::hydrogen_mass_cgs;
static constexpr double boltzmann_constant = C::k_B;
static constexpr double mass_code_units = C::m_u;
};

template <> struct HydroSystem_Traits<QuirkProblem> {
Expand Down
4 changes: 2 additions & 2 deletions src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
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Expand Up @@ -24,8 +24,8 @@ struct RichtmeyerMeshkovProblem {
template <> struct quokka::EOS_Traits<RichtmeyerMeshkovProblem> {
static constexpr double gamma = 1.4;
static constexpr double mean_molecular_weight = NAN;
static constexpr double boltzmann_constant = quokka::boltzmann_constant_cgs;
static constexpr double hydrogen_mass_code_units = quokka::hydrogen_mass_cgs;
static constexpr double boltzmann_constant = C::k_B;
static constexpr double mass_code_units = C::m_u;
};

template <> struct HydroSystem_Traits<RichtmeyerMeshkovProblem> {
Expand Down
6 changes: 3 additions & 3 deletions src/HydroSMS/test_hydro_sms.cpp
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Expand Up @@ -23,9 +23,9 @@ struct ShocktubeProblem {

template <> struct quokka::EOS_Traits<ShocktubeProblem> {
static constexpr double gamma = 1.4;
static constexpr double mean_molecular_weight = quokka::hydrogen_mass_cgs;
static constexpr double boltzmann_constant = quokka::boltzmann_constant_cgs;
static constexpr double hydrogen_mass_code_units = quokka::hydrogen_mass_cgs;
static constexpr double mean_molecular_weight = C::m_u;
static constexpr double boltzmann_constant = C::k_B;
static constexpr double mass_code_units = C::m_u;
};

template <> struct Physics_Traits<ShocktubeProblem> {
Expand Down
4 changes: 2 additions & 2 deletions src/HydroShocktube/test_hydro_shocktube.cpp
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Expand Up @@ -29,8 +29,8 @@ struct ShocktubeProblem {
template <> struct quokka::EOS_Traits<ShocktubeProblem> {
static constexpr double gamma = 1.4;
static constexpr double mean_molecular_weight = NAN;
static constexpr double boltzmann_constant = quokka::boltzmann_constant_cgs;
static constexpr double hydrogen_mass_code_units = quokka::hydrogen_mass_cgs;
static constexpr double boltzmann_constant = C::k_B;
static constexpr double mass_code_units = C::m_u;
};

template <> struct Physics_Traits<ShocktubeProblem> {
Expand Down
4 changes: 2 additions & 2 deletions src/HydroShocktubeCMA/test_hydro_shocktube_cma.cpp
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Expand Up @@ -34,8 +34,8 @@ template <> struct SimulationData<ShocktubeProblem> {
template <> struct quokka::EOS_Traits<ShocktubeProblem> {
static constexpr double gamma = 1.4;
static constexpr double mean_molecular_weight = NAN;
static constexpr double boltzmann_constant = quokka::boltzmann_constant_cgs;
static constexpr double hydrogen_mass_code_units = quokka::hydrogen_mass_cgs;
static constexpr double boltzmann_constant = C::k_B;
static constexpr double mass_code_units = C::m_u;
};

template <> struct Physics_Traits<ShocktubeProblem> {
Expand Down
6 changes: 3 additions & 3 deletions src/HydroShuOsher/test_hydro_shuosher.cpp
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Expand Up @@ -25,9 +25,9 @@ struct ShocktubeProblem {

template <> struct quokka::EOS_Traits<ShocktubeProblem> {
static constexpr double gamma = 1.4;
static constexpr double mean_molecular_weight = quokka::hydrogen_mass_cgs;
static constexpr double boltzmann_constant = quokka::boltzmann_constant_cgs;
static constexpr double hydrogen_mass_code_units = quokka::hydrogen_mass_cgs;
static constexpr double mean_molecular_weight = C::m_u;
static constexpr double boltzmann_constant = C::k_B;
static constexpr double mass_code_units = C::m_u;
};

template <> struct Physics_Traits<ShocktubeProblem> {
Expand Down
4 changes: 2 additions & 2 deletions src/HydroVacuum/test_hydro_vacuum.cpp
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Expand Up @@ -28,8 +28,8 @@ struct ShocktubeProblem {
template <> struct quokka::EOS_Traits<ShocktubeProblem> {
static constexpr double gamma = 1.4;
static constexpr double mean_molecular_weight = NAN;
static constexpr double boltzmann_constant = quokka::boltzmann_constant_cgs;
static constexpr double hydrogen_mass_code_units = quokka::hydrogen_mass_cgs;
static constexpr double boltzmann_constant = C::k_B;
static constexpr double mass_code_units = C::m_u;
};

template <> struct Physics_Traits<ShocktubeProblem> {
Expand Down
6 changes: 3 additions & 3 deletions src/HydroWave/test_hydro_wave.cpp
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Expand Up @@ -23,9 +23,9 @@ struct WaveProblem {

template <> struct quokka::EOS_Traits<WaveProblem> {
static constexpr double gamma = 5. / 3.;
static constexpr double mean_molecular_weight = quokka::hydrogen_mass_cgs;
static constexpr double boltzmann_constant = quokka::boltzmann_constant_cgs;
static constexpr double hydrogen_mass_code_units = quokka::hydrogen_mass_cgs;
static constexpr double mean_molecular_weight = C::m_u;
static constexpr double boltzmann_constant = C::k_B;
static constexpr double mass_code_units = C::m_u;
};

template <> struct Physics_Traits<WaveProblem> {
Expand Down
10 changes: 5 additions & 5 deletions src/ODEIntegration/test_ode.cpp
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Expand Up @@ -15,13 +15,13 @@
using amrex::Real;

constexpr double Tgas0 = 6000.; // K
constexpr double rho0 = 0.01 * quokka::hydrogen_mass_cgs; // g cm^-3
constexpr double rho0 = 0.01 * C::m_u; // g cm^-3

template <> struct quokka::EOS_Traits<ODETest> {
static constexpr double mean_molecular_weight = quokka::hydrogen_mass_cgs;
static constexpr double boltzmann_constant = quokka::boltzmann_constant_cgs;
static constexpr double mean_molecular_weight = C::m_u;
static constexpr double boltzmann_constant = C::k_B;
static constexpr double gamma = 5. / 3.;
static constexpr double hydrogen_mass_code_units = quokka::hydrogen_mass_cgs;
static constexpr double mass_code_units = C::m_u;
};

struct ODEUserData {
Expand All @@ -33,7 +33,7 @@ AMREX_GPU_HOST_DEVICE AMREX_FORCE_INLINE auto cooling_function(Real const rho, R
// use fitting function from Koyama & Inutsuka (2002)
Real gamma_heat = 2.0e-26;
Real lambda_cool = gamma_heat * (1.0e7 * std::exp(-114800. / (T + 1000.)) + 14. * std::sqrt(T) * std::exp(-92. / T));
Real rho_over_mh = rho / quokka::hydrogen_mass_cgs;
Real rho_over_mh = rho / C::m_u;
Real cooling_source_term = rho_over_mh * gamma_heat - (rho_over_mh * rho_over_mh) * lambda_cool;
return cooling_source_term;
}
Expand Down
6 changes: 3 additions & 3 deletions src/PassiveScalar/test_scalars.cpp
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Expand Up @@ -25,9 +25,9 @@ struct ScalarProblem {

template <> struct quokka::EOS_Traits<ScalarProblem> {
static constexpr double gamma = 1.4;
static constexpr double mean_molecular_weight = quokka::hydrogen_mass_cgs;
static constexpr double boltzmann_constant = quokka::boltzmann_constant_cgs;
static constexpr double hydrogen_mass_code_units = quokka::hydrogen_mass_cgs;
static constexpr double mean_molecular_weight = C::m_u;
static constexpr double boltzmann_constant = C::k_B;
static constexpr double mass_code_units = C::m_u;
};

template <> struct Physics_Traits<ScalarProblem> {
Expand Down
4 changes: 2 additions & 2 deletions src/RadBeam/test_radiation_beam.cpp
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Expand Up @@ -33,10 +33,10 @@ constexpr double a_rad = 7.5646e-15; // erg cm^-3 K^-4
constexpr double c = 2.99792458e10; // cm s^-1

template <> struct quokka::EOS_Traits<BeamProblem> {
static constexpr double mean_molecular_weight = quokka::hydrogen_mass_cgs;
static constexpr double mean_molecular_weight = C::m_u;
static constexpr double boltzmann_constant = quokka::boltzmann_constant_cgs;
static constexpr double gamma = 5. / 3.;
static constexpr double hydrogen_mass_code_units = quokka::hydrogen_mass_cgs;
static constexpr double mass_code_units = C::m_u;
};

template <> struct RadSystem_Traits<BeamProblem> {
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6 changes: 3 additions & 3 deletions src/RadForce/test_radiation_force.cpp
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Expand Up @@ -29,7 +29,7 @@ struct TubeProblem {
};

constexpr double kappa0 = 5.0; // cm^2 g^-1
constexpr double mu = 2.33 * quokka::hydrogen_mass_cgs; // g
constexpr double mu = 2.33 * C::m_u; // g
constexpr double gamma_gas = 1.0; // isothermal gas EOS
constexpr double a0 = 0.2e5; // cm s^-1
constexpr double tau = 1.0e-6; // optical depth (dimensionless)
Expand All @@ -45,10 +45,10 @@ constexpr double Lx = (a0 * a0) / g0; // cm

template <> struct quokka::EOS_Traits<TubeProblem> {
static constexpr double mean_molecular_weight = mu;
static constexpr double boltzmann_constant = quokka::boltzmann_constant_cgs;
static constexpr double boltzmann_constant = C::k_B;
static constexpr double gamma = gamma_gas;
static constexpr double cs_isothermal = a0; // only used when gamma = 1
static constexpr double hydrogen_mass_code_units = quokka::hydrogen_mass_cgs;
static constexpr double mass_code_units = C::m_u;
};

template <> struct RadSystem_Traits<TubeProblem> {
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2 changes: 1 addition & 1 deletion src/RadMarshak/test_radiation_marshak.cpp
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Expand Up @@ -34,7 +34,7 @@ template <> struct quokka::EOS_Traits<SuOlsonProblem> {
static constexpr double mean_molecular_mass = 1.0;
static constexpr double boltzmann_constant = 1.0;
static constexpr double gamma = 5. / 3.;
static constexpr double hydrogen_mass_code_units = 1.0 / C::n_A;
static constexpr double mass_code_units = C::m_u;
};

template <> struct RadSystem_Traits<SuOlsonProblem> {
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8 changes: 4 additions & 4 deletions src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
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Expand Up @@ -23,13 +23,13 @@ constexpr double T_initial = 300.; // K

// constexpr double kelvin_to_eV = 8.617385e-5;
constexpr double a_rad = radiation_constant_cgs_;
constexpr double c_v = (quokka::boltzmann_constant_cgs / quokka::hydrogen_mass_cgs) / (5. / 3. - 1.);
constexpr double c_v = (C::k_B / C::m_u) / (5. / 3. - 1.);

template <> struct quokka::EOS_Traits<SuOlsonProblemCgs> {
static constexpr double mean_molecular_weight = quokka::hydrogen_mass_cgs;
static constexpr double boltzmann_constant = quokka::boltzmann_constant_cgs;
static constexpr double mean_molecular_weight = C::m_u;
static constexpr double boltzmann_constant = C::k_B;
static constexpr double gamma = 5. / 3.;
static constexpr double hydrogen_mass_code_units = quokka::hydrogen_mass_cgs;
static constexpr double mass_code_units = C::m_u;
};

template <> struct RadSystem_Traits<SuOlsonProblemCgs> {
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