Fixes (#86)

* fix clippy warnings in test

* Removed useless loop statement in main

* highlight code with poor memory usage

* change in snap turtle implem

Now uses clamp() method; no perf diff but readability increased

* added check for particle density

* better MCGeneralPlane constructor

* moved mc_vector tests back to the src file

* removed dead code & simplified get_total_cross_section method

* small changes in tallies mod

* removed misc test

those did not concern fastiron, just verification of how Rust works

* added a match statement to handle CpuBindError

the bind doesn't work on m1 chip apparently

* small changes in simulation module

* renamed io_utils mod to input

* version bump + dependencies update

* fixed doc warning

* fixed cargo warning

* fixed doc example

Cargo.toml

@@ -1,5 +1,6 @@
 [workspace]
 
+resolver= "2"
 members = ["fastiron", "fastiron-stats"]
 
 [profile.release]

fastiron-stats/Cargo.toml

@@ -1,11 +1,11 @@
 [package]
 name = "fastiron-stats"
-version = "1.1.0"
+version = "1.1.1"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [dependencies]
-clap = {version="4.3.5", features=["cargo", "derive"]}
-csv = "1.2.2"
-gnuplot = "0.0.38"
+clap = { version = "*", features = ["cargo", "derive"] }
+csv = "*"
+gnuplot = "*"

fastiron-stats/src/structures/raw.rs

@@ -119,7 +119,7 @@ impl TalliedVariable {
     }
 }
 
-/// Returns the covariance of two given [FiniteDiscreteRV].
+/// Returns the covariance of two given [TalliedVariable].
 pub fn covariance(x: &TalliedVariable, y: &TalliedVariable) -> f64 {
     assert_eq!(x.n_val(), y.n_val());
     let iter = zip(x.values.iter(), y.values.iter());
@@ -128,11 +128,11 @@ pub fn covariance(x: &TalliedVariable, y: &TalliedVariable) -> f64 {
     cov
 }
 
-/// Returns the correlation coefficient of two given [FiniteDiscreteRV].
+/// Returns the correlation coefficient of two given [TalliedVariable].
 ///
 /// The function checks if `x` and `y` have non-zero variance. If this is the case,
 /// 0 is returned. It means variables are independent. While this may be technically
-/// false, it allows for generic computations
+/// false, it allows for generic computations.
 pub fn correlation(x: &TalliedVariable, y: &TalliedVariable) -> f64 {
     if (x.variance == 0.0) | (y.variance == 0.0) {
         //

fastiron/Cargo.toml

@@ -1,24 +1,24 @@
 [package]
 name = "fastiron"
-version = "1.3.0"
+version = "1.3.2"
 edition = "2021"
 
 # DEPENDENCIES
 
 [dependencies]
-clap = {version="4.3.5", features=["cargo", "derive"]}
-serde_yaml = {version="0.9.21", features=[]}
-num = {version="0.4.0"}
-rand = {version="0.8.5", features=["small_rng"]}
-tinyvec = {version="1.6.0"}
-rayon= {version="1.7.0"}
-atomic = {version="0.5.3"}
-hwloc2 = {version="2.2.0"}
-libc = {version="0.2.146"}
-rustc-hash = {version="1.1.0"}
+clap = { version = "*", features = ["cargo", "derive"] }
+serde_yaml = { version = "*", features = [] }
+num = { version = "*" }
+rand = { version = "*", features = ["small_rng"] }
+tinyvec = { version = "*" }
+rayon = { version = "*" }
+atomic = { version = "0.5.3" } # further upgrade == breaking change
+hwloc2 = { version = "2.2.0" }
+libc = { version = "*" }
+rustc-hash = { version = "*" }
 
 [dev-dependencies]
-criterion = {version="0.5.1", features=["html_reports"]}
+criterion = { version = "*", features = ["html_reports"] }
 
 # FEATURES
 [features]
@@ -33,3 +33,7 @@ harness = false
 [[bench]]
 name = "mct_cross_product"
 harness = false
+
+[[bench]]
+name = "snap_turtle"
+harness = false

fastiron/benches/snap_turtle.rs

@@ -0,0 +1,87 @@
+use criterion::{black_box, criterion_group, criterion_main, BenchmarkId, Criterion};
+use fastiron::constants::Tuple3;
+
+// Define the routines that are tested
+
+fn manual_snap(times: usize) {
+    let bounds: (usize, usize, usize) = (10, 10, 10);
+    fn snap(bounds: (usize, usize, usize), tt: (i32, i32, i32)) -> Tuple3 {
+        (
+            (tt.0.max(0) as usize).min(bounds.0 - 1),
+            (tt.1.max(0) as usize).min(bounds.1 - 1),
+            (tt.2.max(0) as usize).min(bounds.2 - 1),
+        )
+    }
+    let tt1 = (1, 3, 2); // nothing to snap
+    let tt2 = (-1, 3, 2); // 1 element
+    let tt3 = (-1, 11, 2); // 2 elements
+    let tt4 = (-1, 11, -1); // 3 elements
+    (0..times).for_each(|_| {
+        let res = snap(bounds, tt1);
+        black_box(res);
+    });
+    (0..times).for_each(|_| {
+        let res = snap(bounds, tt2);
+        black_box(res);
+    });
+    (0..times).for_each(|_| {
+        let res = snap(bounds, tt3);
+        black_box(res);
+    });
+    (0..times).for_each(|_| {
+        let res = snap(bounds, tt4);
+        black_box(res);
+    });
+}
+
+fn clamp_snap(times: usize) {
+    let bounds: (usize, usize, usize) = (10, 10, 10);
+    fn snap(bounds: (usize, usize, usize), tt: (i32, i32, i32)) -> Tuple3 {
+        (
+            tt.0.clamp(0, (bounds.0 - 1) as i32) as usize,
+            tt.1.clamp(0, (bounds.1 - 1) as i32) as usize,
+            tt.2.clamp(0, (bounds.2 - 1) as i32) as usize,
+        )
+    }
+    let tt1 = (1, 3, 2); // nothing to snap
+    let tt2 = (-1, 3, 2); // 1 element
+    let tt3 = (-1, 11, 2); // 2 elements
+    let tt4 = (-1, 11, -1); // 3 elements
+    (0..times).for_each(|_| {
+        let res = snap(bounds, tt1);
+        black_box(res);
+    });
+    (0..times).for_each(|_| {
+        let res = snap(bounds, tt2);
+        black_box(res);
+    });
+    (0..times).for_each(|_| {
+        let res = snap(bounds, tt3);
+        black_box(res);
+    });
+    (0..times).for_each(|_| {
+        let res = snap(bounds, tt4);
+        black_box(res);
+    });
+}
+
+pub fn criterion_benchmark(c: &mut Criterion) {
+    // Generate/Define the input
+    let n_iter: usize = 1000;
+
+    let mut group = c.benchmark_group("snap turtle implementation");
+    group.bench_with_input(
+        BenchmarkId::new("manual snap", "number of iterations/4"),
+        &n_iter,
+        |b, &n| b.iter(|| manual_snap(n)),
+    );
+    group.bench_with_input(
+        BenchmarkId::new("clamp snap", "number of iterations/4"),
+        &n_iter,
+        |b, &n| b.iter(|| clamp_snap(n)),
+    );
+    group.finish();
+}
+
+criterion_group!(benches, criterion_benchmark);
+criterion_main!(benches);