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Geometry: Doc Strings #300

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Apr 25, 2024
Merged

Geometry: Doc Strings #300

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98 changes: 62 additions & 36 deletions src/Base/Geometry.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,22 +24,27 @@ void init_Geometry(py::module& m)
}
)
.def(py::init<>())
.def_readonly("prob_domain", &GeometryData::prob_domain)
.def_readonly("domain", &GeometryData::domain)
.def_readonly("coord", &GeometryData::coord)
.def_readonly("prob_domain", &GeometryData::prob_domain, "The problem domain (real).")
.def_readonly("domain", &GeometryData::domain, "The index domain.")
.def_readonly("coord", &GeometryData::coord, "The Coordinates type.")
.def_property_readonly("dx",
[](const GeometryData& gd){
std::array<Real,AMREX_SPACEDIM> dx {AMREX_D_DECL(
gd.dx[0], gd.dx[1], gd.dx[2]
)};
return dx;
})
},
"The cellsize for each coordinate direction."
)
.def_property_readonly("is_periodic",
[](const GeometryData& gd){
std::array<int,AMREX_SPACEDIM> per {AMREX_D_DECL(
gd.is_periodic[0], gd.is_periodic[1], gd.is_periodic[2]
)};
return per;})
return per;
},
"Returns whether the domain is periodic in each coordinate direction."
)
// ,
// [](GeometryData& gd, std::vector<Real> per_in) {
// AMREX_D_TERM(gd.is_periodic[0] = per_in[0];,
Expand Down Expand Up @@ -128,16 +133,18 @@ void init_Geometry(py::module& m)

.def("define", py::overload_cast<const Box&, const RealBox&,
int, Array<int,AMREX_SPACEDIM> const&>
(&Geometry::define), "Set geometry")

(&Geometry::define),
py::arg("dom"), py::arg("rb"), py::arg("coord"), py::arg("is_per"),
"Set geometry"
)

.def("ProbDomain", py::overload_cast<>(&Geometry::ProbDomain, py::const_),
"Return problem domain")
.def("ProbDomain", [](Geometry& gm, const RealBox& rb) {
if(gm.Ok()) { gm.ProbDomain(rb);}
else { throw std::runtime_error("Can't call ProbDomain on undefined Geometry; use Define");}
})
.def_property("prob_domain",
py::overload_cast<>(&Geometry::ProbDomain, py::const_),
py::overload_cast<RealBox const &>(&Geometry::ProbDomain),
"The problem domain (real)."
)
.def("ProbLo", py::overload_cast<int>(&Geometry::ProbLo, py::const_),
py::arg("dir"),
"Get the lo end of the problem domain in specified direction")
.def("ProbLo",
[](const Geometry& gm) {
Expand All @@ -147,6 +154,7 @@ void init_Geometry(py::module& m)
"Get the list of lo ends of the problem domain"
)
.def("ProbHi", py::overload_cast<int>(&Geometry::ProbHi, py::const_),
py::arg("dir"),
"Get the hi end of the problem domain in specified direction")
.def("ProbHi",
[](const Geometry& gm) {
Expand All @@ -157,11 +165,12 @@ void init_Geometry(py::module& m)
)
.def("ProbSize", &Geometry::ProbSize, "the overall size of the domain")
.def("ProbLength", &Geometry::ProbLength, "length of problem domain in specified dimension")
.def("Domain", py::overload_cast<>(&Geometry::Domain, py::const_), "Return rectangular domain")
// .def("Domain", py::overload_cast<const Box&>(&Geometry::Domain), "Set rectangular domain")
.def("Domain", [](Geometry& gm, const Box& bx) {
if(gm.Ok()) { gm.Domain(bx);}
else { throw std::runtime_error("Can't call Domain on undefined Geometry; use Define");}})

.def_property("domain",
py::overload_cast<>(&Geometry::Domain, py::const_),
py::overload_cast<Box const &>(&Geometry::Domain),
"The rectangular domain (index space)."
)

// GetVolume
// .def("GetVolume", py::overload_cast<MultiFab&>(&Geometry::GetVolume, py::const_))
Expand All @@ -178,30 +187,47 @@ void init_Geometry(py::module& m)
"Is domain periodic in all directions?")
.def("isPeriodic", py::overload_cast<>(&Geometry::isPeriodic, py::const_),
"Return list indicating whether domain is periodic in each direction")
.def("period", [](const Geometry& gm, const int dir) {
if(gm.isPeriodic(dir)){ return gm.period(dir); }
else { throw std::runtime_error("Geometry is not periodic in this direction."); }
}, "Return the period in the specified direction")
.def("periodicity", py::overload_cast<>(&Geometry::periodicity, py::const_)
)
.def("periodicity", py::overload_cast<const Box&>(&Geometry::periodicity, py::const_),
.def("period",
[](const Geometry& gm, const int dir) {
if(gm.isPeriodic(dir)){ return gm.period(dir); }
else { throw std::runtime_error("Geometry is not periodic in this direction."); }
},
py::arg("dir"),
"Return the period in the specified direction")
.def("periodicity",
py::overload_cast<>(&Geometry::periodicity, py::const_)
)
.def("periodicity",
py::overload_cast<const Box&>(&Geometry::periodicity, py::const_),
py::arg("b"),
"Return Periodicity object with lengths determined by input Box"
)
)

// .def("periodicShift", &Geometry::periodicShift)
.def("growNonPeriodicDomain", py::overload_cast<IntVect const&>(&Geometry::growNonPeriodicDomain, py::const_))
.def("growNonPeriodicDomain", py::overload_cast<int>(&Geometry::growNonPeriodicDomain, py::const_))
.def("growPeriodicDomain", py::overload_cast<IntVect const&>(&Geometry::growPeriodicDomain, py::const_))
.def("growPeriodicDomain", py::overload_cast<int>(&Geometry::growPeriodicDomain, py::const_))

.def("setPeriodicity", &Geometry::setPeriodicity)
.def("coarsen", &Geometry::coarsen)
.def("refine", &Geometry::refine)
.def("growNonPeriodicDomain", py::overload_cast<IntVect const&>(&Geometry::growNonPeriodicDomain, py::const_),
py::arg("ngrow"))
.def("growNonPeriodicDomain", py::overload_cast<int>(&Geometry::growNonPeriodicDomain, py::const_),
py::arg("ngrow"))
.def("growPeriodicDomain", py::overload_cast<IntVect const&>(&Geometry::growPeriodicDomain, py::const_),
py::arg("ngrow"))
.def("growPeriodicDomain", py::overload_cast<int>(&Geometry::growPeriodicDomain, py::const_),
py::arg("ngrow"))

.def("setPeriodicity",
&Geometry::setPeriodicity,
py::arg("period"),
"Set periodicity flags and return the old flags.\n"
"Note that, unlike Periodicity class, the flags are just boolean."
)
.def("coarsen", &Geometry::coarsen, py::arg("rr"))
.def("refine", &Geometry::refine, py::arg("rr"))
.def("outsideRoundOffDomain", py::overload_cast<AMREX_D_DECL(ParticleReal, ParticleReal, ParticleReal)>
(&Geometry::outsideRoundoffDomain, py::const_),
(&Geometry::outsideRoundoffDomain, py::const_),
AMREX_D_DECL(py::arg("x"), py::arg("y"), py::arg("z")),
"Returns true if a point is outside the roundoff domain. All particles with positions inside the roundoff domain are sure to be mapped to cells inside the Domain() box. Note that the same need not be true for all points inside ProbDomain()")
.def("insideRoundOffDomain", py::overload_cast<AMREX_D_DECL(ParticleReal, ParticleReal, ParticleReal)>
(&Geometry::insideRoundoffDomain, py::const_),
(&Geometry::insideRoundoffDomain, py::const_),
AMREX_D_DECL(py::arg("x"), py::arg("y"), py::arg("z")),
"Returns true if a point is inside the roundoff domain. All particles with positions inside the roundoff domain are sure to be mapped to cells inside the Domain() box. Note that the same need not be true for all points inside ProbDomain()")

// .def("computeRoundoffDomain")
Expand Down
20 changes: 10 additions & 10 deletions tests/test_geometry.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,7 @@ def test_probDomain(box, real_box):
lo = [0, -1, 1]
hi = [1, 0, 2]
rb = amr.RealBox(lo, hi)
gm.ProbDomain(rb)
gm.prob_domain = rb
assert (
np.isclose(gm.ProbLo(0), lo[0])
and np.isclose(gm.ProbLo(1), lo[1])
Expand Down Expand Up @@ -105,8 +105,8 @@ def test_domain(box, real_box):
gm.define(box, real_box, coord, is_periodic)
assert gm.ok()

gm.Domain(bx)
assert gm.Domain().small_end == bx.small_end and gm.Domain().big_end == bx.big_end
gm.domain = bx
assert gm.domain.small_end == bx.small_end and gm.domain.big_end == bx.big_end


@pytest.mark.skipif(amr.Config.spacedim != 3, reason="Requires AMREX_SPACEDIM = 3")
Expand All @@ -130,7 +130,7 @@ def test_periodic_queries(box, real_box):
@pytest.mark.skipif(amr.Config.spacedim != 3, reason="Requires AMREX_SPACEDIM = 3")
def test_periodicity(geometry):
gm = geometry
bx = gm.Domain()
bx = gm.domain

for _non_periodic_coord in [0, 1]:
error_thrown = False
Expand Down Expand Up @@ -166,8 +166,8 @@ def test_data(geometry, box, real_box):
geometry_data = geometry.data()
gd = geometry_data

assert gd.domain.small_end == box.small_end == gd.Domain().small_end
assert gd.domain.big_end == box.big_end == gd.Domain().big_end
assert gd.domain.small_end == box.small_end == gd.domain.small_end
assert gd.domain.big_end == box.big_end == gd.domain.big_end

assert amr.AlmostEqual(gd.prob_domain, real_box)
assert np.allclose(real_box.lo(), gd.prob_domain.lo())
Expand Down Expand Up @@ -219,14 +219,14 @@ def test_coarsen_refine(geometry):
gmc = amr.Geometry(bx, rb, 1, [0, 0, 1])
cv = amr.IntVect(2, 2, 1)
gmc.coarsen(cv)
assert gmc.Domain().small_end == amr.IntVect(-1, -1, -3)
assert gmc.Domain().big_end == amr.IntVect(2, 2, 6)
assert gmc.domain.small_end == amr.IntVect(-1, -1, -3)
assert gmc.domain.big_end == amr.IntVect(2, 2, 6)

gmr = amr.Geometry(bx, rb, 1, [0, 0, 1])
rv = amr.IntVect(2, 2, 3)
gmr.refine(rv)
assert gmr.Domain().small_end == amr.IntVect(-2, -4, -9)
assert gmr.Domain().big_end == amr.IntVect(9, 11, 20)
assert gmr.domain.small_end == amr.IntVect(-2, -4, -9)
assert gmr.domain.big_end == amr.IntVect(9, 11, 20)


@pytest.mark.skipif(amr.Config.spacedim != 3, reason="Requires AMREX_SPACEDIM = 3")
Expand Down
2 changes: 1 addition & 1 deletion tests/test_particleContainer.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -330,7 +330,7 @@ def test_per_cell(empty_particle_container, std_geometry, std_particle):
real_arrays = pt.get_struct_of_arrays().get_real_data()
sum_1 += np.sum(real_arrays[1])
print(sum_1)
ncells = std_geometry.Domain().numPts()
ncells = std_geometry.domain.numPts()
print("ncells from box", ncells)
print("NumberOfParticles", pc.number_of_particles_at_level(0))
assert (
Expand Down
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