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moved density to new parthen variables machinery. updated parthenon a…
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…nd changed all the references to GetParentPointer that I needed to.
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@jonahm-LANL
jonahm-LANL committed Dec 5, 2023
1 parent ce9b81b commit ee84cbd
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Showing 54 changed files with 428 additions and 386 deletions.
2 changes: 1 addition & 1 deletion external/parthenon
Submodule parthenon updated from ec2d94 to a540d3
32 changes: 16 additions & 16 deletions src/analysis/history.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -24,17 +24,17 @@ Real ReduceMassAccretionRate(MeshData<Real> *md) {
const auto jb = md->GetBoundsJ(IndexDomain::interior);
const auto kb = md->GetBoundsK(IndexDomain::interior);

auto pmb = md->GetParentPointer();
auto &pars = pmb->packages.Get("geometry")->AllParams();
Mesh *pmesh = md->GetMeshPointer();
auto &pars = pmesh->packages.Get("geometry")->AllParams();
const Real xh = pars.Get<Real>("xh");

namespace p = fluid_prim;
const std::vector<std::string> vars({p::density, p::velocity});
const std::vector<std::string> vars({p::density::name(), p::velocity});

PackIndexMap imap;
auto pack = md->PackVariables(vars, imap);

const int prho = imap[p::density].first;
const int prho = imap[p::density::name()].first;
const int pvel_lo = imap[p::velocity].first;
const int pvel_hi = imap[p::velocity].second;

Expand Down Expand Up @@ -73,25 +73,25 @@ Real ReduceJetEnergyFlux(MeshData<Real> *md) {
const auto jb = md->GetBoundsJ(IndexDomain::interior);
const auto kb = md->GetBoundsK(IndexDomain::interior);

auto pmb = md->GetParentPointer();
auto &pars = pmb->packages.Get("geometry")->AllParams();
Mesh *pmesh = md->GetMeshPointer();
auto &pars = pmesh->packages.Get("geometry")->AllParams();
const Real xh = pars.Get<Real>("xh");

namespace p = fluid_prim;
const std::vector<std::string> vars({p::density, p::bfield, p::velocity});
const std::vector<std::string> vars({p::density::name(), p::bfield, p::velocity});

PackIndexMap imap;
auto pack = md->PackVariables(vars, imap);

const int prho = imap[p::density].first;
const int prho = imap[p::density::name()].first;
const int pvel_lo = imap[p::velocity].first;
const int pvel_hi = imap[p::velocity].second;
const int pb_lo = imap[p::bfield].first;
const int pb_hi = imap[p::bfield].second;

auto geom = Geometry::GetCoordinateSystem(md);

const Real sigma_cutoff = pmb->packages.Get("fluid")->Param<Real>("sigma_cutoff");
const Real sigma_cutoff = pmesh->packages.Get("fluid")->Param<Real>("sigma_cutoff");

Real result = 0.0;
parthenon::par_reduce(
Expand Down Expand Up @@ -132,25 +132,25 @@ Real ReduceJetMomentumFlux(MeshData<Real> *md) {
const auto jb = md->GetBoundsJ(IndexDomain::interior);
const auto kb = md->GetBoundsK(IndexDomain::interior);

auto pmb = md->GetParentPointer();
auto &pars = pmb->packages.Get("geometry")->AllParams();
Mesh *pmesh = md->GetMeshPointer();
auto &pars = pmesh->packages.Get("geometry")->AllParams();
const Real xh = pars.Get<Real>("xh");

namespace p = fluid_prim;
const std::vector<std::string> vars({p::density, p::bfield, p::velocity});
const std::vector<std::string> vars({p::density::name(), p::bfield, p::velocity});

PackIndexMap imap;
auto pack = md->PackVariables(vars, imap);

const int prho = imap[p::density].first;
const int prho = imap[p::density::name()].first;
const int pvel_lo = imap[p::velocity].first;
const int pvel_hi = imap[p::velocity].second;
const int pb_lo = imap[p::bfield].first;
const int pb_hi = imap[p::bfield].second;

auto geom = Geometry::GetCoordinateSystem(md);

const Real sigma_cutoff = pmb->packages.Get("fluid")->Param<Real>("sigma_cutoff");
const Real sigma_cutoff = pmesh->packages.Get("fluid")->Param<Real>("sigma_cutoff");

Real result = 0.0;
parthenon::par_reduce(
Expand Down Expand Up @@ -191,8 +191,8 @@ Real ReduceMagneticFluxPhi(MeshData<Real> *md) {
const auto jb = md->GetBoundsJ(IndexDomain::interior);
const auto kb = md->GetBoundsK(IndexDomain::interior);

auto pmb = md->GetParentPointer();
auto &pars = pmb->packages.Get("geometry")->AllParams();
Mesh *pmesh = md->GetMeshPointer();
auto &pars = pmesh->packages.Get("geometry")->AllParams();
const Real xh = pars.Get<Real>("xh");

namespace c = fluid_cons;
Expand Down
36 changes: 18 additions & 18 deletions src/fixup/fixup.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -288,15 +288,15 @@ TaskStatus ApplyFloorsImpl(T *rc, IndexDomain domain = IndexDomain::entire) {
namespace cr = radmoment_cons;
namespace ir = radmoment_internal;
namespace impl = internal_variables;
auto *pmb = rc->GetParentPointer().get();
IndexRange ib = pmb->cellbounds.GetBoundsI(domain);
IndexRange jb = pmb->cellbounds.GetBoundsJ(domain);
IndexRange kb = pmb->cellbounds.GetBoundsK(domain);
auto *pmesh = rc->GetMeshPointer();
IndexRange ib = rc->GetBoundsI(domain);
IndexRange jb = rc->GetBoundsJ(domain);
IndexRange kb = rc->GetBoundsK(domain);

StateDescriptor *fix_pkg = pmb->packages.Get("fixup").get();
StateDescriptor *eos_pkg = pmb->packages.Get("eos").get();
StateDescriptor *fluid_pkg = pmb->packages.Get("fluid").get();
StateDescriptor *rad_pkg = pmb->packages.Get("radiation").get();
StateDescriptor *fix_pkg = pmesh->packages.Get("fixup").get();
StateDescriptor *eos_pkg = pmesh->packages.Get("eos").get();
StateDescriptor *fluid_pkg = pmesh->packages.Get("fluid").get();
StateDescriptor *rad_pkg = pmesh->packages.Get("radiation").get();

bool rad_active = rad_pkg->Param<bool>("active");

Expand All @@ -307,14 +307,14 @@ TaskStatus ApplyFloorsImpl(T *rc, IndexDomain domain = IndexDomain::entire) {
if (!enable_floors) return TaskStatus::complete;

const std::vector<std::string> vars(
{p::density, c::density, p::velocity, c::momentum, p::energy, c::energy, p::bfield,
p::ye, c::ye, p::pressure, p::temperature, p::gamma1, pr::J, pr::H, cr::E, cr::F,
impl::cell_signal_speed, impl::fail, ir::tilPi});
{p::density::name(), c::density, p::velocity, c::momentum, p::energy, c::energy,
p::bfield, p::ye, c::ye, p::pressure, p::temperature, p::gamma1, pr::J, pr::H,
cr::E, cr::F, impl::cell_signal_speed, impl::fail, ir::tilPi});

PackIndexMap imap;
auto v = rc->PackVariables(vars, imap);

const int prho = imap[p::density].first;
const int prho = imap[p::density::name()].first;
const int crho = imap[c::density].first;
const int pvel_lo = imap[p::velocity].first;
const int pvel_hi = imap[p::velocity].second;
Expand Down Expand Up @@ -352,7 +352,7 @@ TaskStatus ApplyFloorsImpl(T *rc, IndexDomain domain = IndexDomain::entire) {
c2p_floor_scale_fac, c2p_fail_on_floors,
c2p_fail_on_ceilings);

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

parthenon::par_for(
DEFAULT_LOOP_PATTERN, "ApplyFloors", DevExecSpace(), 0, v.GetDim(5) - 1, kb.s, kb.e,
Expand Down Expand Up @@ -673,7 +673,7 @@ TaskStatus ApplyFloorsImpl(T *rc, IndexDomain domain = IndexDomain::entire) {

template <typename T>
TaskStatus ApplyFloors(T *rc) {
auto *pm = rc->GetParentPointer().get();
auto *pm = rc->GetMeshPointer();
StateDescriptor *rad_pkg = pm->packages.Get("radiation").get();
StateDescriptor *fix_pkg = pm->packages.Get("fixup").get();
const bool enable_rad_floors = fix_pkg->Param<bool>("enable_rad_floors");
Expand Down Expand Up @@ -706,7 +706,7 @@ template TaskStatus ApplyFloors<MeshBlockData<Real>>(MeshBlockData<Real> *rc);
TaskStatus FixFluxes(MeshBlockData<Real> *rc) {
using parthenon::BoundaryFace;
using parthenon::BoundaryFlag;
auto *pmb = rc->GetParentPointer().get();
auto *pmb = rc->GetParentPointer();
auto &fixup_pkg = pmb->packages.Get("fixup");
if (!fixup_pkg->Param<bool>("enable_flux_fixup")) return TaskStatus::complete;

Expand All @@ -723,9 +723,9 @@ TaskStatus FixFluxes(MeshBlockData<Real> *rc) {
}
auto moments_active = rad->Param<bool>("moments_active");

IndexRange ib = pmb->cellbounds.GetBoundsI(IndexDomain::interior);
IndexRange jb = pmb->cellbounds.GetBoundsJ(IndexDomain::interior);
IndexRange kb = pmb->cellbounds.GetBoundsK(IndexDomain::interior);
IndexRange ib = rc->GetBoundsI(IndexDomain::interior);
IndexRange jb = rc->GetBoundsJ(IndexDomain::interior);
IndexRange kb = rc->GetBoundsK(IndexDomain::interior);

const int ndim = pmb->pmy_mesh->ndim;
namespace p = fluid_prim;
Expand Down
36 changes: 18 additions & 18 deletions src/fixup/fixup_c2p.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -49,17 +49,17 @@ TaskStatus ConservedToPrimitiveFixupImpl(T *rc) {
namespace ir = radmoment_internal;
namespace pr = radmoment_prim;
namespace cr = radmoment_cons;
auto *pmb = rc->GetParentPointer().get();
IndexRange ib = pmb->cellbounds.GetBoundsI(IndexDomain::interior);
IndexRange jb = pmb->cellbounds.GetBoundsJ(IndexDomain::interior);
IndexRange kb = pmb->cellbounds.GetBoundsK(IndexDomain::interior);
Mesh *pmesh = rc->GetMeshPointer();
IndexRange ib = rc->GetBoundsI(IndexDomain::interior);
IndexRange jb = rc->GetBoundsJ(IndexDomain::interior);
IndexRange kb = rc->GetBoundsK(IndexDomain::interior);

StateDescriptor *fix_pkg = pmb->packages.Get("fixup").get();
StateDescriptor *fluid_pkg = pmb->packages.Get("fluid").get();
StateDescriptor *rad_pkg = pmb->packages.Get("radiation").get();
StateDescriptor *eos_pkg = pmb->packages.Get("eos").get();
StateDescriptor *fix_pkg = pmesh->packages.Get("fixup").get();
StateDescriptor *fluid_pkg = pmesh->packages.Get("fluid").get();
StateDescriptor *rad_pkg = pmesh->packages.Get("radiation").get();
StateDescriptor *eos_pkg = pmesh->packages.Get("eos").get();

const std::vector<std::string> vars({p::density,
const std::vector<std::string> vars({p::density::name(),
c::density,
p::velocity,
c::momentum,
Expand All @@ -85,7 +85,7 @@ TaskStatus ConservedToPrimitiveFixupImpl(T *rc) {
PackIndexMap imap;
auto v = rc->PackVariables(vars, imap);

const int prho = imap[p::density].first;
const int prho = imap[p::density::name()].first;
const int crho = imap[c::density].first;
const int pvel_lo = imap[p::velocity].first;
const int pvel_hi = imap[p::velocity].second;
Expand Down Expand Up @@ -134,9 +134,9 @@ TaskStatus ConservedToPrimitiveFixupImpl(T *rc) {
},
Kokkos::Sum<int>(nfail_total));
printf("total nfail: %i\n", nfail_total);
IndexRange ibi = pmb->cellbounds.GetBoundsI(IndexDomain::interior);
IndexRange jbi = pmb->cellbounds.GetBoundsJ(IndexDomain::interior);
IndexRange kbi = pmb->cellbounds.GetBoundsK(IndexDomain::interior);
IndexRange ibi = rc->GetBoundsI(IndexDomain::interior);
IndexRange jbi = rc->GetBoundsJ(IndexDomain::interior);
IndexRange kbi = rc->GetBoundsK(IndexDomain::interior);
nfail_total = 0;
parthenon::par_reduce(
parthenon::loop_pattern_mdrange_tag, "Rad ConToPrim::Solve fixup failures",
Expand All @@ -150,13 +150,13 @@ TaskStatus ConservedToPrimitiveFixupImpl(T *rc) {
printf("total interior nfail: %i\n", nfail_total);
}

const int ndim = pmb->pmy_mesh->ndim;
const int ndim = pmesh->ndim;

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

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

auto fluid_c2p_failure_strategy =
fix_pkg->Param<FAILURE_STRATEGY>("fluid_c2p_failure_strategy");
Expand Down Expand Up @@ -356,9 +356,9 @@ TaskStatus ConservedToPrimitiveFixupImpl(T *rc) {

template <typename T>
TaskStatus ConservedToPrimitiveFixup(T *rc) {
auto *pm = rc->GetParentPointer().get();
StateDescriptor *rad_pkg = pm->packages.Get("radiation").get();
StateDescriptor *fix_pkg = pm->packages.Get("fixup").get();
Mesh *pmesh = rc->GetMeshPointer();
StateDescriptor *rad_pkg = pmesh->packages.Get("radiation").get();
StateDescriptor *fix_pkg = pmesh->packages.Get("fixup").get();
const bool enable_rad_floors = fix_pkg->Param<bool>("enable_rad_floors");
std::string method;
if (enable_rad_floors) {
Expand Down
10 changes: 5 additions & 5 deletions src/fixup/fixup_netfield.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ namespace fixup {

TaskStatus SumMdotPhiForNetFieldScaling(MeshData<Real> *md, const Real t, const int stage,
std::vector<Real> *sums) {
auto *pm = md->GetParentPointer();
Mesh *pm = md->GetMeshPointer();
StateDescriptor *fix_pkg = pm->packages.Get("fixup").get();

const bool enable_phi_enforcement = fix_pkg->Param<bool>("enable_phi_enforcement");
Expand All @@ -64,7 +64,7 @@ TaskStatus SumMdotPhiForNetFieldScaling(MeshData<Real> *md, const Real t, const

TaskStatus NetFieldStartReduce(MeshData<Real> *md, const Real t, const int stage,
AllReduce<std::vector<Real>> *net_field_totals) {
auto *pm = md->GetParentPointer();
Mesh *pm = md->GetMeshPointer();
StateDescriptor *fix_pkg = pm->packages.Get("fixup").get();

const bool enable_phi_enforcement = fix_pkg->Param<bool>("enable_phi_enforcement");
Expand All @@ -88,7 +88,7 @@ TaskStatus NetFieldCheckReduce(MeshData<Real> *md, const Real t, const int stage
return TaskStatus::complete;
}

auto *pm = md->GetParentPointer();
Mesh *pm = md->GetMeshPointer();
StateDescriptor *fix_pkg = pm->packages.Get("fixup").get();

const bool enable_phi_enforcement = fix_pkg->Param<bool>("enable_phi_enforcement");
Expand All @@ -112,7 +112,7 @@ TaskStatus UpdateNetFieldScaleControls(MeshData<Real> *md, const Real t, const R
if (stage != 1) {
return TaskStatus::complete;
}
auto *pm = md->GetParentPointer();
Mesh *pm = md->GetMeshPointer();
StateDescriptor *fix_pkg = pm->packages.Get("fixup").get();

const bool enable_phi_enforcement = fix_pkg->Param<bool>("enable_phi_enforcement");
Expand Down Expand Up @@ -158,7 +158,7 @@ TaskStatus ModifyNetField(MeshData<Real> *md, const Real t, const Real dt,
if (stage != 1 && fiducial) {
return TaskStatus::complete;
}
auto *pm = md->GetParentPointer();
Mesh *pm = md->GetMeshPointer();
StateDescriptor *fix_pkg = pm->packages.Get("fixup").get();

const bool enable_phi_enforcement = fix_pkg->Param<bool>("enable_phi_enforcement");
Expand Down
30 changes: 15 additions & 15 deletions src/fixup/fixup_radc2p.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -50,14 +50,14 @@ TaskStatus RadConservedToPrimitiveFixupImpl(T *rc) {
namespace pr = radmoment_prim;
namespace cr = radmoment_cons;

auto *pmb = rc->GetParentPointer().get();
IndexRange ib = pmb->cellbounds.GetBoundsI(IndexDomain::interior);
IndexRange jb = pmb->cellbounds.GetBoundsJ(IndexDomain::interior);
IndexRange kb = pmb->cellbounds.GetBoundsK(IndexDomain::interior);
Mesh *pmesh = rc->GetMeshPointer();
IndexRange ib = rc->GetBoundsI(IndexDomain::interior);
IndexRange jb = rc->GetBoundsJ(IndexDomain::interior);
IndexRange kb = rc->GetBoundsK(IndexDomain::interior);

StateDescriptor *fix_pkg = pmb->packages.Get("fixup").get();
StateDescriptor *eos_pkg = pmb->packages.Get("eos").get();
StateDescriptor *rad_pkg = pmb->packages.Get("radiation").get();
StateDescriptor *fix_pkg = pmesh->packages.Get("fixup").get();
StateDescriptor *eos_pkg = pmesh->packages.Get("eos").get();
StateDescriptor *rad_pkg = pmesh->packages.Get("radiation").get();

bool enable_c2p_fixup = fix_pkg->Param<bool>("enable_c2p_fixup");
bool update_rad = rad_pkg->Param<bool>("active");
Expand Down Expand Up @@ -93,9 +93,9 @@ TaskStatus RadConservedToPrimitiveFixupImpl(T *rc) {
},
Kokkos::Sum<int>(nfail_total));
printf("total rad nfail: %i\n", nfail_total);
IndexRange ibi = pmb->cellbounds.GetBoundsI(IndexDomain::interior);
IndexRange jbi = pmb->cellbounds.GetBoundsJ(IndexDomain::interior);
IndexRange kbi = pmb->cellbounds.GetBoundsK(IndexDomain::interior);
IndexRange ibi = rc->GetBoundsI(IndexDomain::interior);
IndexRange jbi = rc->GetBoundsJ(IndexDomain::interior);
IndexRange kbi = rc->GetBoundsK(IndexDomain::interior);
nfail_total = 0;
parthenon::par_reduce(
parthenon::loop_pattern_mdrange_tag, "Rad ConToPrim::Solve fixup failures",
Expand All @@ -112,10 +112,10 @@ TaskStatus RadConservedToPrimitiveFixupImpl(T *rc) {
auto geom = Geometry::GetCoordinateSystem(rc);
auto bounds = fix_pkg->Param<Bounds>("bounds");

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

const int nspec = idx_E.DimSize(1);
const int ndim = pmb->pmy_mesh->ndim;
const int ndim = pmesh->ndim;

auto rad_c2p_failure_strategy =
fix_pkg->Param<FAILURE_STRATEGY>("rad_c2p_failure_strategy");
Expand Down Expand Up @@ -223,9 +223,9 @@ TaskStatus RadConservedToPrimitiveFixupImpl(T *rc) {

template <typename T>
TaskStatus RadConservedToPrimitiveFixup(T *rc) {
auto *pm = rc->GetParentPointer().get();
StateDescriptor *rad_pkg = pm->packages.Get("radiation").get();
StateDescriptor *fix_pkg = pm->packages.Get("fixup").get();
Mesh *pmesh = rc->GetMeshPointer();
StateDescriptor *rad_pkg = pmesh->packages.Get("radiation").get();
StateDescriptor *fix_pkg = pmesh->packages.Get("fixup").get();
const bool enable_rad_floors = fix_pkg->Param<bool>("enable_rad_floors");
std::string method;
if (enable_rad_floors) {
Expand Down
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