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Add eos information to floors, misc UserWorkBeforeOutput fix #210

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merged 14 commits into from
Mar 20, 2024
Merged

Add eos information to floors, misc UserWorkBeforeOutput fix #210

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55be7e9
feat: threaded eos bounds into floors/ceilings. tweak ye logic
AstroBarker Mar 14, 2024
7e78834
leftover print
AstroBarker Mar 14, 2024
4e1391a
feat: pull ideal gas eos bounds from <eos> not from fixup
AstroBarker Mar 14, 2024
003d75c
bounds in moments_source
AstroBarker Mar 14, 2024
ed064de
feat: call SetEOSBnds
AstroBarker Mar 19, 2024
21a1753
fix: proper copy by value for Bounds
AstroBarker Mar 20, 2024
1162e41
feat: remove eos from Ceilings
AstroBarker Mar 20, 2024
f1af909
fix: pull package outside of kernel in UserWorkBeforeOutput
AstroBarker Mar 20, 2024
72a317e
fix: missed some -> to .
AstroBarker Mar 20, 2024
26b5971
fix: some missed bounds copies
AstroBarker Mar 20, 2024
ad10726
fix/feat: copy bounds into FluxState for riemann solve
AstroBarker Mar 20, 2024
ecd49fa
fix: remove unused vars
AstroBarker Mar 20, 2024
e445b09
fix: revert mystery unintended changes....
AstroBarker Mar 20, 2024
e6d5b4a
merge main fluid.hpp ....
AstroBarker Mar 20, 2024
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35 changes: 24 additions & 11 deletions src/fixup/fixup.cpp
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Expand Up @@ -49,6 +49,7 @@ namespace fixup {
std::shared_ptr<StateDescriptor> Initialize(ParameterInput *pin) {
auto fix = std::make_shared<StateDescriptor>("fixup");
Params &params = fix->AllParams();
auto mutable_param = parthenon::Params::Mutability::Mutable;

const bool enable_mhd = pin->GetOrAddBoolean("fluid", "mhd", false);
const bool enable_rad = pin->GetOrAddBoolean("physics", "rad", false);
Expand Down Expand Up @@ -273,7 +274,8 @@ std::shared_ptr<StateDescriptor> Initialize(ParameterInput *pin) {
Bounds(params.Get<Floors>("floor"), params.Get<Ceilings>("ceiling"),
params.Get<MHDCeilings>("mhd_ceiling"),
params.Get<RadiationFloors>("rad_floor"),
params.Get<RadiationCeilings>("rad_ceiling")));
params.Get<RadiationCeilings>("rad_ceiling")),
mutable_param);

return fix;
}
Expand Down Expand Up @@ -307,6 +309,9 @@ TaskStatus ApplyFloorsImpl(T *rc, IndexDomain domain = IndexDomain::entire) {

if (!enable_floors) return TaskStatus::complete;

const Real ye_min = eos_pkg->Param<Real>("ye_min");
const Real ye_max = eos_pkg->Param<Real>("ye_max");

const std::vector<std::string> vars(
{p::density::name(), c::density::name(), p::velocity::name(), c::momentum::name(),
p::energy::name(), c::energy::name(), p::bfield::name(), p::ye::name(),
Expand Down Expand Up @@ -344,7 +349,13 @@ TaskStatus ApplyFloorsImpl(T *rc, IndexDomain domain = IndexDomain::entire) {

auto eos = eos_pkg->Param<EOS>("d.EOS");
auto geom = Geometry::GetCoordinateSystem(rc);
auto bounds = fix_pkg->Param<Bounds>("bounds");
Bounds *pbounds = fix_pkg->MutableParam<Bounds>("bounds");

// BLB: Setting EOS bnds for Ceilings/Floors here.
pbounds->SetEOSBnds(eos_pkg);

// copy bounds by value for kernel
Bounds bounds = *pbounds;

const Real c2p_tol = fluid_pkg->Param<Real>("c2p_tol");
const int c2p_max_iter = fluid_pkg->Param<int>("c2p_max_iter");
Expand Down Expand Up @@ -437,16 +448,18 @@ TaskStatus ApplyFloorsImpl(T *rc, IndexDomain domain = IndexDomain::entire) {

if (floor_applied) {
Real vp_normalobs[3] = {0}; // Inject floors at rest in normal observer frame
Real ye_prim_default = 0.5;
eos_lambda[0] = ye_prim_default;
Real ye = 0.5;
if (pye > 0) {
ye = v(b, cye, k, j, i);
}
eos_lambda[0] = ye;
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Real dprs =
eos.PressureFromDensityInternalEnergy(drho, ratio(du, drho), eos_lambda);
Real dgm1 = ratio(
eos.BulkModulusFromDensityInternalEnergy(drho, ratio(du, drho), eos_lambda),
dprs);
prim2con::p2c(drho, vp_normalobs, bp, du, ye_prim_default, dprs, dgm1, gcov,
gammacon, betacon, alpha, sdetgam, dcrho, dS, dBcons, dtau,
dyecons);
prim2con::p2c(drho, vp_normalobs, bp, du, ye, dprs, dgm1, gcov, gammacon,
betacon, alpha, sdetgam, dcrho, dS, dBcons, dtau, dyecons);

// Update cons vars (not B field)
v(b, crho, k, j, i) += dcrho;
Expand All @@ -464,7 +477,7 @@ TaskStatus ApplyFloorsImpl(T *rc, IndexDomain domain = IndexDomain::entire) {
SPACELOOP(ii) { v(b, pvel_lo + ii, k, j, i) = vp_normalobs[ii]; }
v(b, peng, k, j, i) = du;
if (pye > 0) {
v(b, pye, k, j, i) = ye_prim_default;
v(b, pye, k, j, i) = ye_min;
}

// Update auxiliary primitives
Expand All @@ -476,9 +489,9 @@ TaskStatus ApplyFloorsImpl(T *rc, IndexDomain domain = IndexDomain::entire) {
eos_lambda);

// Update cons vars (not B field)
prim2con::p2c(drho, vp_normalobs, bp, du, ye_prim_default, dprs, dgm1, gcov,
gammacon, betacon, alpha, sdetgam, v(b, crho, k, j, i), dS,
dBcons, v(b, ceng, k, j, i), dyecons);
prim2con::p2c(drho, vp_normalobs, bp, du, ye, dprs, dgm1, gcov, gammacon,
betacon, alpha, sdetgam, v(b, crho, k, j, i), dS, dBcons,
v(b, ceng, k, j, i), dyecons);
SPACELOOP(ii) { v(b, cmom_lo + ii, k, j, i) = dS[ii]; }
if (pye > 0) {
v(b, cye, k, j, i) = dyecons;
Expand Down
42 changes: 36 additions & 6 deletions src/fixup/fixup.hpp
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Expand Up @@ -91,37 +91,60 @@ class Floors {
KOKKOS_INLINE_FUNCTION
void GetFloors(const Real x1, const Real x2, const Real x3, Real &rflr,
Real &sflr) const {
if (!eos_bnds_set_) {
PARTHENON_FAIL("EOS bounds not set in floors.");
}
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switch (floor_flag_) {
case FloorFlag::ConstantRhoSie:
rflr = r0_;
sflr = s0_;
rflr = std::max(rflr, rho_min_eos_);
sflr = std::max(sflr, sie_min_eos_);
break;
case FloorFlag::ExpX1RhoSie:
rflr = r0_ * std::exp(ralpha_ * x1);
sflr = s0_ * std::exp(salpha_ * x1);
rflr = std::max(rflr, rho_min_eos_);
sflr = std::max(sflr, sie_min_eos_);
break;
case FloorFlag::ExpX1RhoU: {
Real scratch = r0_ * std::exp(ralpha_ * x1);
sflr = s0_ * std::exp(salpha_ * x1) / std::max(rflr, scratch);
rflr = scratch;
rflr = std::max(rflr, rho_min_eos_);
sflr = std::max(sflr, sie_min_eos_);
} break;
case FloorFlag::X1RhoSie:
rflr = r0_ * std::min(1.0, std::pow(x1, ralpha_));
sflr = s0_ * std::min(1.0, std::pow(x1, salpha_));
rflr = std::max(rflr, rho_min_eos_);
sflr = std::max(sflr, sie_min_eos_);
break;
case FloorFlag::RRhoSie: {
Real r = std::sqrt(x1 * x1 + x2 * x2 + x3 * x3);
rflr = r0_ * std::min(1.0, std::pow(r, ralpha_));
sflr = s0_ * std::min(1.0, std::pow(r, salpha_));
rflr = std::max(rflr, rho_min_eos_);
sflr = std::max(sflr, sie_min_eos_);
} break;
default:
PARTHENON_FAIL("No valid floor set.");
}
}

void SetEOSBnds(StateDescriptor *eos_pkg) {
if (!eos_bnds_set_) {
rho_min_eos_ = eos_pkg->Param<Real>("rho_min");
sie_min_eos_ = eos_pkg->Param<Real>("sie_min");
eos_bnds_set_ = true;
}
}

private:
Real r0_, s0_, ralpha_, salpha_;
Real r0_, s0_, ralpha_, salpha_, rho_min_eos_, sie_min_eos_;
const FloorFlag floor_flag_;
bool eos_bnds_set_;
};

static struct ConstantJFloor {
Expand Down Expand Up @@ -173,6 +196,7 @@ class Ceilings {
KOKKOS_INLINE_FUNCTION
void GetCeilings(const Real x1, const Real x2, const Real x3, Real &gmax,
Real &smax) const {

switch (ceiling_flag_) {
case 1:
gmax = g0_;
Expand All @@ -184,8 +208,9 @@ class Ceilings {
}

private:
Real g0_, s0_;
Real g0_, s0_, sie_max_eos_;
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const int ceiling_flag_;
bool eos_bnds_set_;
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};

static struct ConstantBsqRatCeiling {
Expand Down Expand Up @@ -257,13 +282,18 @@ class Bounds {
const RadiationFloors &rfl, const RadiationCeilings &rcl)
: floors_(fl), ceilings_(cl), mhd_ceilings_(mcl), radiation_floors_(rfl),
radiation_ceilings_(rcl) {}
explicit Bounds(const Floors &fl)
explicit Bounds(Floors &fl)
: floors_(fl), ceilings_(Ceilings()), mhd_ceilings_(MHDCeilings()),
radiation_floors_(RadiationFloors()), radiation_ceilings_(RadiationCeilings()) {}
explicit Bounds(const Ceilings &cl)
explicit Bounds(Ceilings &cl)
: floors_(Floors()), ceilings_(cl), mhd_ceilings_(MHDCeilings()),
radiation_floors_(RadiationFloors()), radiation_ceilings_(RadiationCeilings()) {}

template <class... Args>
void SetEOSBnds(Args &&...args) {
floors_.SetEOSBnds(std::forward<Args>(args)...);
}

template <class... Args>
KOKKOS_INLINE_FUNCTION void GetFloors(Args &&...args) const {
floors_.GetFloors(std::forward<Args>(args)...);
Expand All @@ -290,8 +320,8 @@ class Bounds {
}

private:
const Floors floors_;
const Ceilings ceilings_;
Floors floors_;
Ceilings ceilings_;
const MHDCeilings mhd_ceilings_;
const RadiationFloors radiation_floors_;
const RadiationCeilings radiation_ceilings_;
Expand Down
3 changes: 2 additions & 1 deletion src/fixup/fixup_c2p.cpp
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Expand Up @@ -155,7 +155,8 @@ TaskStatus ConservedToPrimitiveFixupImpl(T *rc) {

auto eos = eos_pkg->Param<Microphysics::EOS::EOS>("d.EOS");
auto geom = Geometry::GetCoordinateSystem(rc);
auto bounds = fix_pkg->Param<Bounds>("bounds");
Bounds *pbounds = fix_pkg->MutableParam<Bounds>("bounds");
Bounds bounds = *pbounds;

Coordinates_t coords = rc->GetParentPointer()->coords;

Expand Down
6 changes: 3 additions & 3 deletions src/fixup/fixup_radc2p.cpp
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Expand Up @@ -113,7 +113,7 @@ TaskStatus RadConservedToPrimitiveFixupImpl(T *rc) {
}

auto geom = Geometry::GetCoordinateSystem(rc);
auto bounds = fix_pkg->Param<Bounds>("bounds");
Bounds *bounds = fix_pkg->MutableParam<Bounds>("bounds");

Coordinates_t coords = rc->GetParentPointer()->coords;

Expand All @@ -129,8 +129,8 @@ TaskStatus RadConservedToPrimitiveFixupImpl(T *rc) {
KOKKOS_LAMBDA(const int b, const int k, const int j, const int i) {
Real xi_max;
Real garbage;
bounds.GetRadiationCeilings(coords.Xc<1>(k, j, i), coords.Xc<2>(k, j, i),
coords.Xc<3>(k, j, i), xi_max, garbage);
bounds->GetRadiationCeilings(coords.Xc<1>(k, j, i), coords.Xc<2>(k, j, i),
coords.Xc<3>(k, j, i), xi_max, garbage);

// It is assumed that the fluid is already fixed up
auto fail = [&](const int k, const int j, const int i) {
Expand Down
10 changes: 5 additions & 5 deletions src/fixup/fixup_src.cpp
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Expand Up @@ -73,7 +73,7 @@ TaskStatus SourceFixupImpl(T *rc) {
}

auto eos = eos_pkg->Param<EOS>("d.EOS");
auto bounds = fix_pkg->Param<Bounds>("bounds");
Bounds *bounds = fix_pkg->MutableParam<Bounds>("bounds");

const std::vector<std::string> vars(
{p::density::name(), c::density::name(), p::velocity::name(), c::momentum::name(),
Expand Down Expand Up @@ -151,12 +151,12 @@ TaskStatus SourceFixupImpl(T *rc) {
kb.e, jb.s, jb.e, ib.s, ib.e,
KOKKOS_LAMBDA(const int b, const int k, const int j, const int i) {
double gamma_max, e_max;
bounds.GetCeilings(coords.Xc<1>(k, j, i), coords.Xc<2>(k, j, i),
coords.Xc<3>(k, j, i), gamma_max, e_max);
bounds->GetCeilings(coords.Xc<1>(k, j, i), coords.Xc<2>(k, j, i),
coords.Xc<3>(k, j, i), gamma_max, e_max);
Real xi_max;
Real garbage;
bounds.GetRadiationCeilings(coords.Xc<1>(k, j, i), coords.Xc<2>(k, j, i),
coords.Xc<3>(k, j, i), xi_max, garbage);
bounds->GetRadiationCeilings(coords.Xc<1>(k, j, i), coords.Xc<2>(k, j, i),
coords.Xc<3>(k, j, i), xi_max, garbage);

double eos_lambda[2]; // used for stellarcollapse eos and other EOS's that require
// root finding.
Expand Down
2 changes: 1 addition & 1 deletion src/fluid/con2prim_robust.hpp
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Expand Up @@ -164,7 +164,7 @@ class Residual {
private:
const Real D_, q_, bsq_, bsq_rpsq_, rsq_, rbsq_, v0sq_;
const Microphysics::EOS::EOS &eos_;
const fixup::Bounds &bounds_;
const fixup::Bounds bounds_;
const Real x1_, x2_, x3_;
const Real floor_scale_fac_;
Real lambda_[2];
Expand Down
27 changes: 5 additions & 22 deletions src/fluid/fluid.cpp
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Expand Up @@ -13,7 +13,6 @@

#include "fluid.hpp"

#include "analysis/analysis.hpp"
#include "analysis/history.hpp"
#include "con2prim.hpp"
#include "con2prim_robust.hpp"
Expand Down Expand Up @@ -208,8 +207,6 @@ std::shared_ptr<StateDescriptor> Initialize(ParameterInput *pin) {
physics->AddField(p::entropy::name(), mprim_scalar);
physics->AddField(p::cs::name(), mprim_scalar);
physics->AddField(diag::ratio_divv_cs::name(), mprim_scalar);
// physics->AddField(diag::localization_function::name(), mprim_scalar);
// (MG) currently not in use, turn on when needed.
physics->AddField(diag::entropy_z_0::name(), mprim_scalar);
physics->AddField(p::gamma1::name(), mprim_scalar);
if (ye) {
Expand Down Expand Up @@ -312,8 +309,6 @@ std::shared_ptr<StateDescriptor> Initialize(ParameterInput *pin) {
// Reductions
// By default compute integrated value of scalar conserved vars
auto HstSum = parthenon::UserHistoryOperation::sum;
auto HstMax = parthenon::UserHistoryOperation::max;
using History::ReduceInGain;
using History::ReduceOneVar;
using parthenon::HistoryOutputVar;
parthenon::HstVar_list hst_vars = {};
Expand All @@ -324,11 +319,6 @@ std::shared_ptr<StateDescriptor> Initialize(ParameterInput *pin) {
auto ReduceEn = [](MeshData<Real> *md) {
return ReduceOneVar<Kokkos::Sum<Real>>(md, fluid_cons::energy::name(), 0);
};
auto MaxDensity = [](MeshData<Real> *md) {
return ReduceOneVar<Kokkos::Max<Real>>(md, fluid_prim::density::name(), 0);
};

hst_vars.emplace_back(HistoryOutputVar(HstMax, MaxDensity, "maximum density"));
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Looks like this branch might be out of date with main... double check you and @mari2895 are in sync so your PRs don't undo each other.

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Looks like this is the same as current main, unless I missed something.

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Why is there a diff showing here then? Odd.

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Oh I see it now... not sure why it's different from main, don't think I did this myself..

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maybe just merge main in again... see if that fixes it?

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@AstroBarker Looks the same on my branch too. Don't see anything different.

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but why is it deleted? should not be deleted

hst_vars.emplace_back(HistoryOutputVar(HstSum, ReduceMass, "total baryon number"));
hst_vars.emplace_back(HistoryOutputVar(HstSum, ReduceEn, "total conserved energy tau"));

Expand Down Expand Up @@ -451,15 +441,6 @@ TaskStatus ConservedToPrimitiveRegion(T *rc, const IndexRange &ib, const IndexRa
auto c2p = pkg->Param<c2p_type<T>>("c2p_func");
return c2p(rc, ib, jb, kb);
}
// JMM: Must specialize function for both potential use cases so we
// can keep it in this file.
template TaskStatus ConservedToPrimitiveRegion<MeshData<Real>>(MeshData<Real> *rc,
const IndexRange &ib,
const IndexRange &jb,
const IndexRange &kb);
template TaskStatus ConservedToPrimitiveRegion<MeshBlockData<Real>>(
MeshBlockData<Real> *rc, const IndexRange &ib, const IndexRange &jb,
const IndexRange &kb);

template <typename T>
TaskStatus ConservedToPrimitive(T *rc) {
Expand All @@ -476,7 +457,10 @@ TaskStatus ConservedToPrimitiveRobust(T *rc, const IndexRange &ib, const IndexRa
auto *pmb = rc->GetParentPointer();

StateDescriptor *fix_pkg = pmb->packages.Get("fixup").get();
auto bounds = fix_pkg->Param<fixup::Bounds>("bounds");
StateDescriptor *eos_pkg = pmb->packages.Get("eos").get();
fixup::Bounds *pbounds = fix_pkg->MutableParam<fixup::Bounds>("bounds");
pbounds->SetEOSBnds(eos_pkg);
fixup::Bounds bounds = *pbounds;

StateDescriptor *pkg = pmb->packages.Get("fluid").get();
const Real c2p_tol = pkg->Param<Real>("c2p_tol");
Expand All @@ -488,7 +472,6 @@ TaskStatus ConservedToPrimitiveRobust(T *rc, const IndexRange &ib, const IndexRa
c2p_floor_scale_fac, c2p_fail_on_floors,
c2p_fail_on_ceilings);

StateDescriptor *eos_pkg = pmb->packages.Get("eos").get();
auto eos = eos_pkg->Param<Microphysics::EOS::EOS>("d.EOS");
auto geom = Geometry::GetCoordinateSystem(rc);
auto coords = pmb->coords;
Expand Down Expand Up @@ -516,7 +499,7 @@ TaskStatus ConservedToPrimitiveClassic(T *rc, const IndexRange &ib, const IndexR
auto *pmesh = rc->GetMeshPointer();

StateDescriptor *fix_pkg = pmesh->packages.Get("fixup").get();
auto bounds = fix_pkg->Param<fixup::Bounds>("bounds");
fixup::Bounds *bounds = fix_pkg->MutableParam<fixup::Bounds>("bounds");

StateDescriptor *pkg = pmesh->packages.Get("fluid").get();
const Real c2p_tol = pkg->Param<Real>("c2p_tol");
Expand Down
10 changes: 0 additions & 10 deletions src/fluid/fluid.hpp
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Expand Up @@ -29,19 +29,9 @@ std::shared_ptr<StateDescriptor> Initialize(ParameterInput *pin);
TaskStatus PrimitiveToConserved(MeshBlockData<Real> *rc);
TaskStatus PrimitiveToConservedRegion(MeshBlockData<Real> *rc, const IndexRange &ib,
const IndexRange &jb, const IndexRange &kb);
// JMM: Not sure how the templated value here worked in the first
// place. But proper solution is need to tell the linker it's
// available elsewhere.
template <typename T>
TaskStatus ConservedToPrimitiveRegion(T *rc, const IndexRange &ib, const IndexRange &jb,
const IndexRange &kb);
extern template TaskStatus
ConservedToPrimitiveRegion<MeshData<Real>>(MeshData<Real> *rc, const IndexRange &ib,
const IndexRange &jb, const IndexRange &kb);
extern template TaskStatus ConservedToPrimitiveRegion<MeshBlockData<Real>>(
MeshBlockData<Real> *rc, const IndexRange &ib, const IndexRange &jb,
const IndexRange &kb);

template <typename T>
TaskStatus ConservedToPrimitive(T *rc);
template <typename T>
Expand Down
9 changes: 6 additions & 3 deletions src/fluid/riemann.hpp
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Expand Up @@ -205,6 +205,7 @@ class FluxState {
const ParArrayND<Real> qr;
const Geometry::CoordSysMeshBlock geom;
const Coordinates_t coords;
fixup::Bounds *pbounds;
fixup::Bounds bounds;

private:
Expand All @@ -216,9 +217,11 @@ class FluxState {
ql(rc->Get("ql").data), qr(rc->Get("qr").data),
geom(Geometry::GetCoordinateSystem(rc)),
coords(rc->GetParentPointer()->coords), // problem for packs
bounds(rc->GetParentPointer()->packages.Get("fixup").get()->Param<fixup::Bounds>(
"bounds")),
prho(imap[fluid_prim::density::name()].first),
pbounds(rc->GetParentPointer()
->packages.Get("fixup")
.get()
->MutableParam<fixup::Bounds>("bounds")),
bounds(*pbounds), prho(imap[fluid_prim::density::name()].first),
pvel_lo(imap[fluid_prim::velocity::name()].first),
peng(imap[fluid_prim::energy::name()].first),
pb_lo(imap[fluid_prim::bfield::name()].first),
Expand Down
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