Python and C bindings

.github/workflows/rustbca_compile_check.yml

@@ -1,4 +1,4 @@
-name: rustBCA Compile check
+name: RustBCA Compile check
 
 on:
   push:
@@ -41,11 +41,11 @@ jobs:
     - name: Run Examples
       run: |
         cargo run --release 0D examples/boron_nitride_0D.toml
-        ./target/release/rustBCA 0D examples/titanium_dioxide_0D.toml
-        ./target/release/rustBCA 1D examples/layered_geometry_1D.toml
+        ./target/release/RustBCA 0D examples/titanium_dioxide_0D.toml
+        ./target/release/RustBCA 1D examples/layered_geometry_1D.toml
         cat 2000.0eV_0.0001deg_He_TiO2_Al_Sisummary.output
-        ./target/release/rustBCA examples/boron_nitride.toml
-        ./target/release/rustBCA examples/layered_geometry.toml
+        ./target/release/RustBCA examples/boron_nitride.toml
+        ./target/release/RustBCA examples/layered_geometry.toml
         cat 2000.0eV_0.0001deg_He_TiO2_Al_Sisummary.output
-        ./target/release/rustBCA SPHERE examples/boron_nitride_sphere.toml
+        ./target/release/RustBCA SPHERE examples/boron_nitride_sphere.toml
         cargo run --release --features parry3d TRIMESH examples/tungsten_twist_trimesh.toml

Cargo.toml

@@ -1,44 +1,53 @@
-[package]
-name = "rustBCA"
-version = "1.1.0"
-authors = ["Jon Drobny <drobny2@illinois.edu>"]
-edition = "2018"
-
-[[bin]]
-name="rustBCA"
-
-[dependencies]
-rand = "0.8.3"
-toml = "0.5.8"
-anyhow = "1.0.38"
-itertools = "0.10.0"
-rayon = "1.5.0"
-geo = {version = "0.17.1", optional = false}
-indicatif = {version = "0.15.0", features=["rayon"]}
-serde = { version = "1.0.123", features = ["derive"] }
-hdf5 = {version = "0.7.1", optional = true}
-openblas-src = {version  = "0.9", optional = true}
-netlib-src = {version  = "0.8", optional = true}
-intel-mkl-src = {version = "0.6.0", optional = true}
-rcpr = { git = "https://github.com/drobnyjt/rcpr", optional = true}
-ndarray = {version = "0.14.0", features = ["serde"], optional = true}
-parry3d-f64 = {version = "0.2.0", optional = true}
-
-[dev-dependencies]
-float-cmp = "0.8.0"
-
-[profile.release]
-lto = "fat"
-codegen-units = 1
-opt-level = 3
-debug = false
-
-[features]
-hdf5_input = ["hdf5"]
-cpr_rootfinder_openblas = ["rcpr", "openblas-src"]
-cpr_rootfinder_netlib = ["rcpr", "netlib-src"]
-cpr_rootfinder_intel_mkl = ["rcpr", "intel-mkl-src"]
-distributions = ["ndarray"]
-no_list_output = []
-parry3d = ["parry3d-f64"]
-accelerated_ions = []
+[package]
+name = "RustBCA"
+version = "1.1.0"
+authors = ["Jon Drobny <drobny2@illinois.edu>"]
+edition = "2018"
+
+[[bin]]
+name="RustBCA"
+
+[lib]
+name = "libRustBCA"
+path = "src/lib.rs"
+crate-type = ["cdylib"]
+
+[dependencies]
+rand = "0.8.3"
+toml = "0.5.8"
+anyhow = "1.0.38"
+itertools = "0.10.0"
+rayon = "1.5.0"
+geo = {version = "0.17.1", optional = false}
+indicatif = {version = "0.15.0", features=["rayon"]}
+serde = { version = "1.0.123", features = ["derive"] }
+hdf5 = {version = "0.7.1", optional = true}
+openblas-src = {version  = "0.9", optional = true}
+netlib-src = {version  = "0.8", optional = true}
+intel-mkl-src = {version = "0.6.0", optional = true}
+rcpr = { git = "https://github.com/drobnyjt/rcpr", optional = true}
+ndarray = {version = "0.14.0", features = ["serde"], optional = true}
+parry3d-f64 = {version = "0.2.0", optional = true}
+
+[dependencies.pyo3]
+version = "0.13.2"
+features = ["extension-module"]
+
+[dev-dependencies]
+float-cmp = "0.8.0"
+
+[profile.release]
+lto = "fat"
+codegen-units = 1
+opt-level = 3
+debug = false
+
+[features]
+hdf5_input = ["hdf5"]
+cpr_rootfinder_openblas = ["rcpr", "openblas-src"]
+cpr_rootfinder_netlib = ["rcpr", "netlib-src"]
+cpr_rootfinder_intel_mkl = ["rcpr", "intel-mkl-src"]
+distributions = ["ndarray"]
+no_list_output = []
+parry3d = ["parry3d-f64"]
+accelerated_ions = []

MANIFEST.in

@@ -0,0 +1,2 @@
+include Cargo.toml
+recursive-include src *

RustBCA.h

@@ -0,0 +1,87 @@
+#include <cstdarg>
+#include <cstdint>
+#include <cstdlib>
+#include <ostream>
+#include <new>
+#include <cmath>
+
+static const double PI = M_PI;
+
+static const double FRAC_2_SQRT_PI = M_2_PI;
+
+static const double SQRT_2 = M_SQRT2;
+
+///Fundamental charge in Coulombs.
+static const double Q = 1.602176634e-19;
+
+/// One electron-volt in Joules.
+static const double EV = Q;
+
+/// One atomic mass unit in kilograms.
+static const double AMU = 1.66053906660e-27;
+
+/// One Angstrom in meters.
+static const double ANGSTROM = 1e-10;
+
+/// One micron in meters.
+static const double MICRON = 1e-6;
+
+/// One nanometer in meters.
+static const double NM = 1e-9;
+
+/// One centimeter in meters.
+static const double CM = 1e-2;
+
+/// Vacuum permitivity in Farads/meter.
+static const double EPS0 = 8.8541878128e-12;
+
+/// Bohr radius in meters.
+static const double A0 = 5.29177210903e-11;
+
+/// Electron mass in kilograms.
+static const double ME = 9.1093837015e-31;
+
+/// sqrt(pi).
+static const double SQRTPI = (2. / FRAC_2_SQRT_PI);
+
+/// sqrt(2 * pi).
+static const double SQRT2PI = ((2. * SQRT_2) / FRAC_2_SQRT_PI);
+
+/// Speed of light in meters/second.
+static const double C = 299792458.;
+
+/// Bethe-Bloch electronic stopping prefactor, in SI units.
+static const double BETHE_BLOCH_PREFACTOR = ((((((4. * PI) * ((Q * Q) / ((4. * PI) * EPS0))) * ((Q * Q) / ((4. * PI) * EPS0))) / ME) / C) / C);
+
+/// Lindhard-Scharff electronic stopping prefactor, in SI units.
+static const double LINDHARD_SCHARFF_PREFACTOR = (((1.212 * ANGSTROM) * ANGSTROM) * Q);
+
+/// Lindhard reduced energy prefactor, in SI units.
+static const double LINDHARD_REDUCED_ENERGY_PREFACTOR = ((((4. * PI) * EPS0) / Q) / Q);
+
+struct OutputBCA {
+  uintptr_t len;
+  double (*particles)[9];
+};
+
+extern "C" {
+
+OutputBCA simple_bca_c(double x,
+                       double y,
+                       double z,
+                       double ux,
+                       double uy,
+                       double uz,
+                       double E1,
+                       double Z1,
+                       double m1,
+                       double Ec1,
+                       double Es1,
+                       double Z2,
+                       double m2,
+                       double Ec2,
+                       double Es2,
+                       double n2,
+                       double Eb2);
+
+} // extern "C"

pyproject.toml

@@ -0,0 +1,2 @@
+[build-system]
+requires = ["setuptools", "setuptools-rust"]

setup.py

@@ -0,0 +1,9 @@
+from setuptools import setup
+from setuptools_rust import Binding, RustExtension
+
+setup(
+    name="RustBCA",
+    rust_extensions=[RustExtension("libRustBCA.pybca", binding=Binding.PyO3)],
+    # rust extensions are not zip safe, just like C-extensions.
+    zip_safe=False,
+)