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account for population masses to bulk velocity
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@nicolasaunai
nicolasaunai committed Nov 28, 2023
1 parent 43c40cc commit 3abf8c5
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Showing 4 changed files with 117 additions and 34 deletions.
1 change: 1 addition & 0 deletions src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -673,6 +673,7 @@ namespace amr
NiOldUser_.name, fieldRefineOp_, fieldTimeOp_,
info->modelIonDensity);


velGhostsRefiners_.addTimeRefiners(info->ghostBulkVelocity, info->modelIonBulkVelocity,
core::VecFieldNames{ViOld_}, fieldRefineOp_,
fieldTimeOp_);
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106 changes: 77 additions & 29 deletions src/core/data/ions/ions.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@ namespace core
public:
using field_type = typename IonPopulation::field_type;
using vecfield_type = typename IonPopulation::vecfield_type;
using Float = typename field_type::type;
using particle_array_type = typename IonPopulation::particle_array_type;
using ParticleInitializerFactoryT
= ParticleInitializerFactory<particle_array_type, GridLayout>;
Expand All @@ -48,6 +49,7 @@ namespace core
auto const& pop = dict["pop" + std::to_string(ipop)];
populations_.emplace_back(pop);
}
sameMasses_ = allSameMass_();
}


Expand All @@ -57,37 +59,29 @@ namespace core
NO_DISCARD field_type const& density() const
{
if (isUsable())
{
return *rho_;
}
else
{
throw std::runtime_error("Error - cannot access density data");
}
}



NO_DISCARD field_type& density()
{
if (isUsable())
{
return *rho_;
}
else
{
throw std::runtime_error("Error - cannot access density data");
}
}




NO_DISCARD vecfield_type const& velocity() const { return bulkVelocity_; }

NO_DISCARD vecfield_type& velocity() { return bulkVelocity_; }

NO_DISCARD std::string densityName() const { return "rho"; }
NO_DISCARD std::string massDensityName() const { return "massDensity"; }


void computeDensity()
Expand All @@ -102,43 +96,73 @@ namespace core

auto& popDensity = pop.density();
std::transform(std::begin(*rho_), std::end(*rho_), std::begin(popDensity),
std::begin(*rho_), std::plus<typename field_type::type>{});
std::begin(*rho_), std::plus<Float>{});
}
}
void computeMassDensity()
{
massDensity_->zero();

for (auto const& pop : populations_)
{
// we sum over all nodes contiguously, including ghosts
// nodes. This is more efficient and easier to code as we don't
// have to account for the field dimensionality.

auto& popDensity = pop.density();
std::transform(
std::begin(*massDensity_), std::end(*massDensity_), std::begin(popDensity),
std::begin(*massDensity_),
[&pop](auto const& n, auto const& pop_n) { return n + pop_n * pop.mass(); });
}
}


void computeBulkVelocity()
{
// the bulk velocity is sum(pop_mass * pop_flux) / sum(pop_mass * pop_density)
// if all populations have the same mass, this is equivalent to sum(pop_flux) /
// sum(pop_density) sum(pop_density) is rho_ and already known by the time we get here.
// sum(pop_mass * pop_flux) is massDensity_ and is computed by computeMassDensity() if
// needed
if (!sameMasses_)
computeMassDensity();
auto const& density = (sameMasses_) ? rho_ : massDensity_;

bulkVelocity_.zero();
auto& vx = bulkVelocity_.getComponent(Component::X);
auto& vy = bulkVelocity_.getComponent(Component::Y);
auto& vz = bulkVelocity_.getComponent(Component::Z);

for (auto& pop : populations_)
{
auto& flux = pop.flux();
auto& fx = flux.getComponent(Component::X);
auto& fy = flux.getComponent(Component::Y);
auto& fz = flux.getComponent(Component::Z);
// account for mass only if populations have different masses
std::function<Float(Float, Float)> plus = std::plus<Float>{};
std::function<Float(Float, Float)> plusMass
= [&pop](Float const& v, Float const& f) { return v + f * pop.mass(); };

auto const& flux = pop.flux();
auto&& [fx, fy, fz] = flux();


std::transform(std::begin(vx), std::end(vx), std::begin(fx), std::begin(vx),
std::plus<typename field_type::type>{});
sameMasses_ ? plus : plusMass);
std::transform(std::begin(vy), std::end(vy), std::begin(fy), std::begin(vy),
std::plus<typename field_type::type>{});
sameMasses_ ? plus : plusMass);
std::transform(std::begin(vz), std::end(vz), std::begin(fz), std::begin(vz),
std::plus<typename field_type::type>{});
sameMasses_ ? plus : plusMass);
}

std::transform(std::begin(vx), std::end(vx), std::begin(*rho_), std::begin(vx),
std::divides<typename field_type::type>{});
std::transform(std::begin(vy), std::end(vy), std::begin(*rho_), std::begin(vy),
std::divides<typename field_type::type>{});
std::transform(std::begin(vz), std::end(vz), std::begin(*rho_), std::begin(vz),
std::divides<typename field_type::type>{});

std::transform(std::begin(vx), std::end(vx), std::begin(*density), std::begin(vx),
std::divides<Float>{});
std::transform(std::begin(vy), std::end(vy), std::begin(*density), std::begin(vy),
std::divides<Float>{});
std::transform(std::begin(vz), std::end(vz), std::begin(*density), std::begin(vz),
std::divides<Float>{});
}


// TODO 3347 compute ion bulk velocity

NO_DISCARD auto begin() { return std::begin(populations_); }
NO_DISCARD auto end() { return std::end(populations_); }
Expand All @@ -147,6 +171,8 @@ namespace core
NO_DISCARD auto end() const { return std::end(populations_); }


// in the following isUsable and isSettable the massDensity_ is not checked
// because it is for internal use only so no object will ever need to access it.
NO_DISCARD bool isUsable() const
{
bool usable = rho_ != nullptr && bulkVelocity_.isUsable();
Expand Down Expand Up @@ -186,20 +212,25 @@ namespace core

NO_DISCARD MomentProperties getFieldNamesAndQuantities() const
{
return {{{densityName(), HybridQuantity::Scalar::rho}}};
return {{{densityName(), HybridQuantity::Scalar::rho},
{massDensityName(), HybridQuantity::Scalar::rho}}};
}



void setBuffer(std::string const& bufferName, field_type* field)
{
if (bufferName == "rho")
if (bufferName == densityName())
{
rho_ = field;
}
else if (bufferName == massDensityName())
{
massDensity_ = field;
}
else
{
throw std::runtime_error("Error - invalid density buffer name");
throw std::runtime_error("Error - invalid density buffer name : " + bufferName);
}
}

Expand Down Expand Up @@ -235,10 +266,27 @@ namespace core


private:
bool allSameMass_() const
{
auto const& firstPop = populations_.front();
return std::all_of(
std::begin(populations_), std::end(populations_), [&firstPop](auto const& pop) {
return std::abs(pop.mass() - firstPop.mass()) < 1e-10; // arbitrary small diff
});
}




field_type* rho_{nullptr};
field_type* massDensity_{nullptr};
vecfield_type bulkVelocity_;
std::vector<IonPopulation> populations_; // TODO we have to name this so they are unique
// although only 1 Ions should exist.
std::vector<IonPopulation> populations_;

// note this is set at construction when all populations are added
// in the future if some populations are dynamically created during the simulation
// this should be updated accordingly
bool sameMasses_{false};
};
} // namespace core
} // namespace PHARE
Expand Down
7 changes: 7 additions & 0 deletions tests/core/numerics/ion_updater/test_updater.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -227,6 +227,7 @@ struct IonsBuffers
using ParticleInitializerFactory = typename PHARETypes::ParticleInitializerFactory;

Field ionDensity;
Field ionMassDensity;
Field protonDensity;
Field alphaDensity;
Field protonFx;
Expand Down Expand Up @@ -258,6 +259,8 @@ struct IonsBuffers
IonsBuffers(GridLayout const& layout)
: ionDensity{"rho", HybridQuantity::Scalar::rho,
layout.allocSize(HybridQuantity::Scalar::rho)}
, ionMassDensity{"massDensity", HybridQuantity::Scalar::rho,
layout.allocSize(HybridQuantity::Scalar::rho)}
, protonDensity{"protons_rho", HybridQuantity::Scalar::rho,
layout.allocSize(HybridQuantity::Scalar::rho)}
, alphaDensity{"alpha_rho", HybridQuantity::Scalar::rho,
Expand Down Expand Up @@ -304,6 +307,8 @@ struct IonsBuffers
IonsBuffers(IonsBuffers const& source, GridLayout const& layout)
: ionDensity{"rho", HybridQuantity::Scalar::rho,
layout.allocSize(HybridQuantity::Scalar::rho)}
, ionMassDensity{"massDensity", HybridQuantity::Scalar::rho,
layout.allocSize(HybridQuantity::Scalar::rho)}
, protonDensity{"protons_rho", HybridQuantity::Scalar::rho,
layout.allocSize(HybridQuantity::Scalar::rho)}
, alphaDensity{"alpha_rho", HybridQuantity::Scalar::rho,
Expand Down Expand Up @@ -336,6 +341,7 @@ struct IonsBuffers

{
ionDensity.copyData(source.ionDensity);
ionMassDensity.copyData(source.ionMassDensity);
protonDensity.copyData(source.protonDensity);
alphaDensity.copyData(source.alphaDensity);

Expand Down Expand Up @@ -366,6 +372,7 @@ struct IonsBuffers
void setBuffers(Ions& ions)
{
ions.setBuffer("rho", &ionDensity);
ions.setBuffer("massDensity", &ionMassDensity);
auto& v = ions.velocity();
v.setBuffer("bulkVel_x", &Vx);
v.setBuffer("bulkVel_y", &Vy);
Expand Down
37 changes: 32 additions & 5 deletions tests/simulator/test_restarts.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@

def permute(dic, expected_num_levels):
# from pyphare.pharein.simulation import supported_dimensions # eventually
dims = [1] # supported_dimensions()
dims = [1] # supported_dimensions()
return [
[dim, interp, dic, expected_num_levels] for dim in dims for interp in [1, 2, 3]
]
Expand Down Expand Up @@ -60,6 +60,9 @@ def vy(x):
def vz(x):
return 0.0

def vxalpha(x):
return 3.0

def vthxyz(x):
return T(x)

Expand All @@ -71,6 +74,14 @@ def vthxyz(x):
"vthy": vthxyz,
"vthz": vthxyz,
}
vvvalpha = {
"vbulkx": vxalpha,
"vbulky": vy,
"vbulkz": vz,
"vthx": vthxyz,
"vthy": vthxyz,
"vthz": vthxyz,
}
model = ph.MaxwellianFluidModel(
bx=bx,
by=by,
Expand All @@ -84,10 +95,10 @@ def vthxyz(x):
"init": {"seed": 1337},
},
alpha={
"mass": 4,
"mass": 4.0,
"charge": 1,
"density": density,
**vvv,
**vvvalpha,
"nbr_part_per_cell": ppc,
"init": {"seed": 2334},
},
Expand Down Expand Up @@ -160,6 +171,17 @@ def count_levels_and_patches(qty):
datahier0.level(0).patches[0].patch_datas.keys()
)

self.assertEqual(len(datahier0.levels()), len(datahier1.levels()))
for ilvl in range(len(datahier0.levels())):
self.assertEqual(
len(datahier0.level(ilvl).patches),
len(datahier1.level(ilvl).patches),
)
for patch0, patch1 in zip(
datahier0.level(ilvl).patches, datahier1.level(ilvl).patches
):
self.assertEqual(patch0.box, patch1.box)

self.assertGreater(len(datahier0.levels()), 0)

for ilvl, lvl0 in datahier0.levels().items():
Expand All @@ -170,7 +192,12 @@ def count_levels_and_patches(qty):
pd1 = patch1.patch_datas[pd_key]
self.assertNotEqual(id(pd0), id(pd1))
if "domain" in pd_key:
self.assertEqual(pd0.dataset, pd1.dataset)
try:
self.assertEqual(pd0.dataset, pd1.dataset)
except AssertionError:
print(
f"FAILED domain particles at time {time} {ilvl} {patch1.box} {patch0.box}"
)
else:
np.testing.assert_equal(pd0.dataset[:], pd1.dataset[:])
checks += 1
Expand Down Expand Up @@ -221,7 +248,7 @@ def test_restarts(self, ndim, interp, simInput, expected_num_levels):

restart_idx = 4
restart_time = time_step * restart_idx
timestamps = [time_step * restart_idx, time_step * time_step_nbr]
timestamps = [restart_time, time_step * time_step_nbr]

# first simulation
local_out = self.unique_diag_dir_for_test_case(f"{out}/test", ndim, interp)
Expand Down

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