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Update hdf5/ndarray

This commit is contained in:
Magnus Ulimoen 2021-10-23 19:35:37 +00:00
parent 86275d2c2e
commit d16b274fe0
12 changed files with 41 additions and 42 deletions
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2
euler/Cargo.toml
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@ -11,7 +11,7 @@ expensive_tests = []
serde1 = ["serde", "arrayvec/serde"] serde1 = ["serde", "arrayvec/serde"]
[dependencies] [dependencies]
ndarray = "0.14.0" ndarray = "0.15.0"
sbp = { path = "../sbp" } sbp = { path = "../sbp" }
arrayvec = "0.6.0" arrayvec = "0.6.0"
serde = { version = "1.0.115", default-features = false, optional = true, features = ["derive"] } serde = { version = "1.0.115", default-features = false, optional = true, features = ["derive"] }

4
euler/src/lib.rs
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@ -227,14 +227,14 @@ impl Field {
pub(crate) fn slice<Do: Dimension>( pub(crate) fn slice<Do: Dimension>(
&self, &self,
info: &ndarray::SliceInfo<[ndarray::SliceOrIndex; 3], Do>, info: ndarray::SliceInfo<[ndarray::SliceInfoElem; 3], ndarray::Ix3, Do>,
) -> ArrayView<Float, Do> { ) -> ArrayView<Float, Do> {
self.0.slice(info) self.0.slice(info)
} }
pub(crate) fn slice_mut<Do: Dimension>( pub(crate) fn slice_mut<Do: Dimension>(
&mut self, &mut self,
info: &ndarray::SliceInfo<[ndarray::SliceOrIndex; 3], Do>, info: ndarray::SliceInfo<[ndarray::SliceInfoElem; 3], ndarray::Ix3, Do>,
) -> ArrayViewMut<Float, Do> { ) -> ArrayViewMut<Float, Do> {
self.0.slice_mut(info) self.0.slice_mut(info)
} }

2
gridgeneration/Cargo.toml
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@ -5,7 +5,7 @@ authors = ["Magnus Ulimoen <magnus@ulimoen.dev>"]
edition = "2018" edition = "2018"
[dependencies] [dependencies]
ndarray = { version = "0.14.0", default-features = false } ndarray = { version = "0.15.0", default-features = false }
plotters = { version = "0.3.0", default-features = false, features = ["svg_backend", "line_series", "point_series"] } plotters = { version = "0.3.0", default-features = false, features = ["svg_backend", "line_series", "point_series"] }
sbp = { path = "../sbp" } sbp = { path = "../sbp" }
json5 = { version = "0.2.8", optional = true } json5 = { version = "0.2.8", optional = true }

2
heat-equation/Cargo.toml
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@ -7,7 +7,7 @@ edition = "2018"
[dependencies] [dependencies]
sbp = { path = "../sbp", features = ["sparse"] } sbp = { path = "../sbp", features = ["sparse"] }
ndarray = "0.14.0" ndarray = "0.15.0"
plotters = { version = "0.3.0", default-features = false, features = ["bitmap_gif", "bitmap_backend", "line_series"] } plotters = { version = "0.3.0", default-features = false, features = ["bitmap_gif", "bitmap_backend", "line_series"] }
sprs = { version = "0.10.0", default-features = false } sprs = { version = "0.10.0", default-features = false }
integrate = { path = "../utils/integrate" } integrate = { path = "../utils/integrate" }

3
heat-equation/src/main.rs
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@ -11,9 +11,6 @@ struct Field(Array1<Float>);
impl integrate::Integrable for Field { impl integrate::Integrable for Field {
type State = Array1<Float>; type State = Array1<Float>;
type Diff = Array1<Float>; type Diff = Array1<Float>;
fn assign(s: &mut Self::State, o: &Self::State) {
s.assign(o)
}
fn scaled_add(s: &mut Self::State, o: &Self::Diff, scale: Float) { fn scaled_add(s: &mut Self::State, o: &Self::Diff, scale: Float) {
s.scaled_add(scale, o) s.scaled_add(scale, o)
} }

2
maxwell/Cargo.toml
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@ -8,7 +8,7 @@ edition = "2018"
sparse = ["sbp/sparse", "sprs"] sparse = ["sbp/sparse", "sprs"]
[dependencies] [dependencies]
ndarray = "0.14.0" ndarray = "0.15.0"
sbp = { path = "../sbp" } sbp = { path = "../sbp" }
sprs = { version = "0.10.0", optional = true, default-features = false } sprs = { version = "0.10.0", optional = true, default-features = false }
integrate = { path = "../utils/integrate" } integrate = { path = "../utils/integrate" }

28
maxwell/src/lib.rs
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@ -44,14 +44,14 @@ impl Field {
pub(crate) fn slice<Do: Dimension>( pub(crate) fn slice<Do: Dimension>(
&self, &self,
info: &ndarray::SliceInfo<[ndarray::SliceOrIndex; 3], Do>, info: ndarray::SliceInfo<[ndarray::SliceInfoElem; 3], ndarray::Ix3, Do>,
) -> ArrayView<Float, Do> { ) -> ArrayView<Float, Do> {
self.0.slice(info) self.0.slice(info)
} }
pub(crate) fn slice_mut<Do: Dimension>( pub(crate) fn slice_mut<Do: Dimension>(
&mut self, &mut self,
info: &ndarray::SliceInfo<[ndarray::SliceOrIndex; 3], Do>, info: ndarray::SliceInfo<[ndarray::SliceInfoElem; 3], ndarray::Ix3, Do>,
) -> ArrayViewMut<Float, Do> { ) -> ArrayViewMut<Float, Do> {
self.0.slice_mut(info) self.0.slice_mut(info)
} }
@ -519,10 +519,10 @@ fn SAT_characteristics<SBP: SbpOperator2d>(
}; };
for ((((mut k, v), g), &kx), &ky) in k for ((((mut k, v), g), &kx), &ky) in k
.slice_mut(s![.., .., nx - 1]) .slice_mut(s![.., .., nx - 1])
.gencolumns_mut() .columns_mut()
.into_iter() .into_iter()
.zip(y.slice(s![.., .., nx - 1]).gencolumns()) .zip(y.slice(s![.., .., nx - 1]).columns())
.zip(g.gencolumns()) .zip(g.columns())
.zip(metrics.detj_dxi_dx().slice(s![.., nx - 1])) .zip(metrics.detj_dxi_dx().slice(s![.., nx - 1]))
.zip(metrics.detj_dxi_dy().slice(s![.., nx - 1])) .zip(metrics.detj_dxi_dy().slice(s![.., nx - 1]))
{ {
@ -557,10 +557,10 @@ fn SAT_characteristics<SBP: SbpOperator2d>(
}; };
for ((((mut k, v), g), &kx), &ky) in k for ((((mut k, v), g), &kx), &ky) in k
.slice_mut(s![.., .., 0]) .slice_mut(s![.., .., 0])
.gencolumns_mut() .columns_mut()
.into_iter() .into_iter()
.zip(y.slice(s![.., .., 0]).gencolumns()) .zip(y.slice(s![.., .., 0]).columns())
.zip(g.gencolumns()) .zip(g.columns())
.zip(metrics.detj_dxi_dx().slice(s![.., 0])) .zip(metrics.detj_dxi_dx().slice(s![.., 0]))
.zip(metrics.detj_dxi_dy().slice(s![.., 0])) .zip(metrics.detj_dxi_dy().slice(s![.., 0]))
{ {
@ -600,10 +600,10 @@ fn SAT_characteristics<SBP: SbpOperator2d>(
}; };
for ((((mut k, v), g), &kx), &ky) in k for ((((mut k, v), g), &kx), &ky) in k
.slice_mut(s![.., ny - 1, ..]) .slice_mut(s![.., ny - 1, ..])
.gencolumns_mut() .columns_mut()
.into_iter() .into_iter()
.zip(y.slice(s![.., ny - 1, ..]).gencolumns()) .zip(y.slice(s![.., ny - 1, ..]).columns())
.zip(g.gencolumns()) .zip(g.columns())
.zip(metrics.detj_deta_dx().slice(s![ny - 1, ..])) .zip(metrics.detj_deta_dx().slice(s![ny - 1, ..]))
.zip(metrics.detj_deta_dy().slice(s![ny - 1, ..])) .zip(metrics.detj_deta_dy().slice(s![ny - 1, ..]))
{ {
@ -637,10 +637,10 @@ fn SAT_characteristics<SBP: SbpOperator2d>(
}; };
for ((((mut k, v), g), &kx), &ky) in k for ((((mut k, v), g), &kx), &ky) in k
.slice_mut(s![.., 0, ..]) .slice_mut(s![.., 0, ..])
.gencolumns_mut() .columns_mut()
.into_iter() .into_iter()
.zip(y.slice(s![.., 0, ..]).gencolumns()) .zip(y.slice(s![.., 0, ..]).columns())
.zip(g.gencolumns()) .zip(g.columns())
.zip(metrics.detj_deta_dx().slice(s![0, ..])) .zip(metrics.detj_deta_dx().slice(s![0, ..]))
.zip(metrics.detj_deta_dy().slice(s![0, ..])) .zip(metrics.detj_deta_dy().slice(s![0, ..]))
{ {

4
multigrid/Cargo.toml
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@ -8,11 +8,11 @@ edition = "2018"
[dependencies] [dependencies]
sbp = { path = "../sbp", features = ["serde1"] } sbp = { path = "../sbp", features = ["serde1"] }
euler = { path = "../euler", features = ["serde1"] } euler = { path = "../euler", features = ["serde1"] }
hdf5 = "0.7.0" hdf5 = "0.8.0"
integrate = { path = "../utils/integrate" } integrate = { path = "../utils/integrate" }
rayon = "1.3.0" rayon = "1.3.0"
indicatif = "0.17.0-beta.1" indicatif = "0.17.0-beta.1"
ndarray = { version = "0.14.0", features = ["serde"] } ndarray = { version = "0.15.0", features = ["serde"] }
serde = { version = "1.0.115", features = ["derive"] } serde = { version = "1.0.115", features = ["derive"] }
json5 = "0.3.0" json5 = "0.3.0"
indexmap = { version = "1.5.2", features = ["serde-1"] } indexmap = { version = "1.5.2", features = ["serde-1"] }

30
multigrid/src/system.rs
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@ -37,9 +37,9 @@ impl BaseSystem {
let output = hdf5::File::create(output).unwrap(); let output = hdf5::File::create(output).unwrap();
output output
.new_dataset::<u64>() .new_dataset::<u64>()
.resizable(true) .shape((0..,))
.chunk((1,)) .chunk((1,))
.create("t", (0,)) .create("t")
.unwrap(); .unwrap();
Self { Self {
names, names,
@ -92,8 +92,9 @@ impl BaseSystem {
let add_dim = |name| { let add_dim = |name| {
g.new_dataset::<Float>() g.new_dataset::<Float>()
.chunk((grid.ny(), grid.nx())) .chunk((grid.ny(), grid.nx()))
.gzip(9) .deflate(9)
.create(name, (grid.ny(), grid.nx())) .shape((grid.ny(), grid.nx()))
.create(name)
}; };
let xds = add_dim("x").unwrap(); let xds = add_dim("x").unwrap();
xds.write(grid.x()).unwrap(); xds.write(grid.x()).unwrap();
@ -102,11 +103,11 @@ impl BaseSystem {
let add_var = |name| { let add_var = |name| {
g.new_dataset::<Float>() g.new_dataset::<Float>()
.gzip(3) .shuffle()
.shuffle(true) .deflate(3)
.chunk((1, grid.ny(), grid.nx())) .chunk((1, grid.ny(), grid.nx()))
.resizable(true) .shape((0.., grid.ny(), grid.nx()))
.create(name, (0, grid.ny(), grid.nx())) .create(name)
}; };
add_var("rho").unwrap(); add_var("rho").unwrap();
add_var("rhou").unwrap(); add_var("rhou").unwrap();
@ -261,8 +262,9 @@ impl BaseSystem {
let add_dim = |name| { let add_dim = |name| {
g.new_dataset::<Float>() g.new_dataset::<Float>()
.chunk((grid.ny(), grid.nx())) .chunk((grid.ny(), grid.nx()))
.gzip(9) .deflate(9)
.create(name, (grid.ny(), grid.nx())) .shape((grid.ny(), grid.nx()))
.create(name)
}; };
let xds = add_dim("x").unwrap(); let xds = add_dim("x").unwrap();
xds.write(grid.x()).unwrap(); xds.write(grid.x()).unwrap();
@ -271,11 +273,11 @@ impl BaseSystem {
let add_var = |name| { let add_var = |name| {
g.new_dataset::<Float>() g.new_dataset::<Float>()
.gzip(3) .shuffle()
.shuffle(true) .deflate(3)
.chunk((1, grid.ny(), grid.nx())) .chunk((1, grid.ny(), grid.nx()))
.resizable(true) .shape((0.., grid.ny(), grid.nx()))
.create(name, (0, grid.ny(), grid.nx())) .create(name)
}; };
add_var("rho").unwrap(); add_var("rho").unwrap();
add_var("rhou").unwrap(); add_var("rhou").unwrap();

2
sbp/Cargo.toml
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@ -5,7 +5,7 @@ authors = ["Magnus Ulimoen <magnus@ulimoen.dev>"]
edition = "2018" edition = "2018"
[dependencies] [dependencies]
ndarray = { version = "0.14.0", features = ["approx"] } ndarray = { version = "0.15.0", features = ["approx"] }
approx = "0.4.0" approx = "0.4.0"
sprs = { version = "0.10.0", optional = true, default-features = false } sprs = { version = "0.10.0", optional = true, default-features = false }
serde = { version = "1.0.115", optional = true, default-features = false, features = ["derive"] } serde = { version = "1.0.115", optional = true, default-features = false, features = ["derive"] }

2
shallow_water/Cargo.toml
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@ -5,7 +5,7 @@ authors = ["Magnus Ulimoen <magnus@ulimoen.dev>"]
edition = "2018" edition = "2018"
[dependencies] [dependencies]
ndarray = "0.14.0" ndarray = "0.15.0"
sbp = { path = "../sbp" } sbp = { path = "../sbp" }
log = "0.4.8" log = "0.4.8"
integrate = { path = "../utils/integrate" } integrate = { path = "../utils/integrate" }

2
webfront/Cargo.toml
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@ -12,7 +12,7 @@ wasm-bindgen = "0.2.63"
console_error_panic_hook = "0.1.6" console_error_panic_hook = "0.1.6"
wee_alloc = "0.4.5" wee_alloc = "0.4.5"
sbp = { path = "../sbp", features = ["f32"] } sbp = { path = "../sbp", features = ["f32"] }
ndarray = "0.14.0" ndarray = "0.15.0"
euler = { path = "../euler" } euler = { path = "../euler" }
maxwell = { path = "../maxwell" } maxwell = { path = "../maxwell" }
shallow-water = { path = "../shallow_water" } shallow-water = { path = "../shallow_water" }