Switch to parry2d

.github/workflows/rustbca_compile_check.yml

@@ -59,12 +59,12 @@ jobs:
         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
-        cat 2000.0eV_0.0001deg_He_TiO2_Al_Sisummary.output
+        echo "layered geometry 1D:"; cat 2000.0eV_0.0001deg_He_TiO2_Al_Sisummary.output
         ./target/release/RustBCA examples/layered_geometry.toml
-        cat 2000.0eV_0.0001deg_He_TiO2_Al_Sisummary.output
+        echo "layered geometry 2D:"; cat 2000.0eV_0.0001deg_He_TiO2_Al_Sisummary.output
         ./target/release/RustBCA SPHERE examples/boron_nitride_sphere.toml
         cargo run --release --features parry3d TRIMESH examples/tungsten_twist_trimesh.toml
         ./target/release/RustBCA examples/boron_nitride_wire.toml
-        cat boron_nitride_summary.output
+        echo "boron nitride 2D:"; cat boron_nitride_summary.output
         ./target/release/RustBCA HOMOGENEOUS2D examples/boron_nitride_wire_homogeneous.toml
-        cat boron_nitride_h_summary.output
+        echo "boron nitride 2D Homogeneous:"; cat boron_nitride_h_summary.output

Cargo.toml

@@ -5,6 +5,8 @@ default-run = "RustBCA"
 authors = ["Jon Drobny <[email protected]>", "Jon Drobny <[email protected]>"]
 edition = "2021"
 
+
+
 [[bin]]
 name = "RustBCA"
 path = "src/main.rs"
@@ -28,6 +30,7 @@ hdf5 = {version = "0.7.1", optional = true}
 rcpr = { git = "https://github.com/drobnyjt/rcpr", optional = true}
 ndarray = {version = "0.14.0", features = ["serde"], optional = true}
 parry3d-f64 = {optional = true, version="0.2.0"}
+parry2d-f64 = {optional = false, version="0.17.0"}
 
 [dependencies.pyo3]
 version = "0.19.0"
@@ -41,7 +44,7 @@ float-cmp = "0.8.0"
 lto = "fat"
 codegen-units = 1
 opt-level = 3
-debug = false
+debug = 1
 
 [features]
 hdf5_input = ["hdf5"]

README.md

@@ -12,9 +12,9 @@ By discretizing the collision cascade into a sequence of binary collisions,
 between an energetic ion and a target material. This includes reflection,
 implantation, and transmission of the incident ion, as well as sputtering
 and displacement damage of the target. Generally, [BCA] codes can be
-valid for incident ion energies between approximately ~1 eV/nucleon 
+valid for incident ion energies between approximately ~1 eV/nucleon
 to <1 GeV/nucleon. Improvements to RustBCA have expanded the regime
-of validity for some quantities, such as reflection coefficients, below 
+of validity for some quantities, such as reflection coefficients, below
 1 eV/nucleon.
 
 Check out the `RustBCA` [Wiki] for detailed information, installation
@@ -160,7 +160,7 @@ Windows, MacOS, and Linux systems.
 * [rcpr], a CPR and polynomial rootfinder, required for using attractive-repulsive interaction potentials such as Lennard-Jones or Morse.
 * For manipulating input files and running associated scripts, the following are required:
   * [Python] 3.6+
-  * The [Python] libraries: `numpy`, `matplotlib`, `toml` (must build from source), `shapely`, and `scipy`.
+  * The [Python] libraries: `numpy`, `matplotlib`, `toml`, `shapely`, and `scipy`.
 
 ### Detailed instructions for Ubuntu 18.04 LTS
 
@@ -187,36 +187,28 @@ git clone https://github.com/uiri/toml.git
 cd toml
 python3 setup.py install
 ```
-7. (Optional) Install software for [rcpr]:
-```bash
-sudo apt-get install gcc gfortran build-essential cmake liblapack-dev libblas-dev liblapacke-dev
-```
-8. (Optional - should come with rustup) Install `cargo`:
+7. (Optional - should come with rustup) Install `cargo`:
 ```bash
 sudo apt-get install cargo
 ```
-9. Build `RustBCA`:
+8. Build `RustBCA`:
 ```bash
 git clone https://github.com/lcpp-org/rustBCA
 cd RustBCA
 cargo build --release
 ```
-10. (Optional) Build `RustBCA` with optional dependencies, `hdf5` and/or `rcpr` (with your choice of backend: `openblas`, `netlib`, or `intel-mkl`):
+9. (Optional) Build `RustBCA` with optional dependencies, `hdf5` and/or `rcpr`:
 ```bash
-cargo build --release --features cpr_rootfinder_netlib,hdf5_input
-cargo build --release --features cpr_rootfinder_openblas,hdf5_input
-cargo build --release --features cpr_rootfinder_intel_mkl,hdf5_input
+cargo build --release --features cpr_rootfinder,hdf5_input
  ```
-11. `input.toml` is the input file - see [Usage](https://github.com/lcpp-org/RustBCA/wiki/Usage,-Input-File,-and-Output-Files) for more information
-12. Run the required tests using:
+10. `input.toml` is the input file - see [Usage](https://github.com/lcpp-org/RustBCA/wiki/Usage,-Input-File,-and-Output-Files) for more information
+11. Run the required tests using:
 ```bash
 cargo test
 ```
-13. (Optional) Run the required and optional tests for the desired backend(s):
+12. (Optional) Run the required and optional tests for the desired backend(s):
 ```bash
-cargo test --features cpr_rootfinder_netlib
-cargo test --features cpr_rootfinder_openblas
-cargo test --features cpr_rootfinder_intel_mkl
+cargo test --features cpr_rootfinder
 ```
 
 ### Detailed instructions for Fedora 33
@@ -275,7 +267,7 @@ command line argument.
 ./RustBCA /path/to/input.toml
 ```
 
-Additionally, `RustBCA` accepts an input file type (one of: `0D`, `1D`, `2D`, `TRIMESH`, `SPHERE` - see the wiki for more details):
+Additionally, `RustBCA` accepts an input file type (one of: `0D`, `1D`, `2D`, `TRIMESH`, `SPHERE`, `HOMOGENEOUS2D` - see the wiki for more details):
 ```bash
 ./RustBCA 0D /path/to/input.toml
 ```

examples/boron_nitride_wire_homogeneous.toml

@@ -1,4 +1,4 @@
-#Use with 0D geometry option only
+#Use with HOMOGENEOUS geometry option only
 [options]
 name = "boron_nitride_h_"
 weak_collision_order = 0

examples/layered_geometry.toml

@@ -1,7 +1,7 @@
 #Use with 2D geometry option only
 [options]
 name = "2000.0eV_0.0001deg_He_TiO2_Al_Si"
-track_trajectories = false
+track_trajectories = true
 track_recoils = true
 track_recoil_trajectories = false
 write_buffer_size = 8000
@@ -54,7 +54,8 @@ points = [[0.0, -0.5], [0.01, -0.5], [0.04, -0.5], [0.5, -0.5], [0.5, 0.5], [0.0
 triangles = [[0, 1, 6], [0, 6, 7], [1, 2, 5], [1, 5, 6], [2, 3, 4], [2, 4, 5]]
 densities = [ [ 3.0e+10, 6.0e+10, 0.0, 0.0,], [ 3.0e+10, 6.0e+10, 0.0, 0.0,], [ 0.0, 0.0, 6.026e+10, 0.0,], [ 0.0, 0.0, 6.026e+10, 0.0,], [ 0.0, 0.0, 0.0, 4.996e+10,], [ 0.0, 0.0, 0.0, 4.996e+10,],]
 boundary = [0, 3, 4, 7]
-simulation_boundary_points = [ [ 0.6, -0.6,], [ -0.1, -0.6,], [ -0.1, 0.6,], [ 0.6, 0.6,], [ 0.6, -0.6,],]
+#simulation_boundary_points = [ [ 0.6, -0.6,], [ -0.1, -0.6,], [ -0.1, 0.6,], [ 0.6, 0.6,],]
+simulation_boundary_points = [[0.6, 0.6], [-0.1, 0.6], [-0.1, -0.6], [0.6, -0.6]]
 electronic_stopping_correction_factors = [1.0, 1.0, 1.0, 1.0, 1.0, 1.0]
 energy_barrier_thickness = 2.2E-4
 

examples/multiple_interaction_potentials.toml

@@ -48,7 +48,7 @@ length_unit = "MICRON"
 triangles = [ [ 0.0, 0.01, 0.0, 0.5, 0.5, -0.5,], [ 0.0, 0.01, 0.01, -0.5, 0.5, -0.5,], [ 0.01, 0.01, 0.04, -0.5, 0.5, -0.5,], [ 0.01, 0.04, 0.04, 0.5, 0.5, -0.5,], [ 0.04, 0.5, 0.04, 0.5, 0.5, -0.5,], [ 0.04, 0.5, 0.5, -0.5, 0.5, -0.5,],]
 densities = [ [ 3.0e+10, 6.0e+10, 0.0, 0.0,], [ 3.0e+10, 6.0e+10, 0.0, 0.0,], [ 0.0, 0.0, 6.026e+10, 0.0,], [ 0.0, 0.0, 6.026e+10, 0.0,], [ 0.0, 0.0, 0.0, 4.996e+10,], [ 0.0, 0.0, 0.0, 4.996e+10,],]
 material_boundary_points = [ [ 0.0, 0.5,], [ 0.5, 0.5,], [ 0.5, -0.5,], [ 0.0, -0.5,],]
-simulation_boundary_points = [ [ 0.6, -0.6,], [ -0.1, -0.6,], [ -0.1, 0.6,], [ 0.6, 0.6,], [ 0.6, -0.6,],]
+simulation_boundary_points = [ [ 0.6, -0.6,], [ -0.1, -0.6,], [ -0.1, 0.6,], [ 0.6, 0.6,],]
 electronic_stopping_correction_factors = [1.0, 1.0, 1.0, 1.0, 1.0, 1.0]
 
 [material_parameters]

src/enums.rs

@@ -3,13 +3,13 @@ use super::*;
 pub enum MaterialType {
     MESH0D(material::Material<geometry::Mesh0D>),
     MESH1D(material::Material<geometry::Mesh1D>),
-    MESH2D(material::Material<geometry::Mesh2D>),
+    MESH2D(material::Material<geometry::ParryMesh2D>),
     SPHERE(material::Material<sphere::Sphere>),
     #[cfg(feature = "parry3d")]
     BALL(material::Material<parry::ParryBall>),
     #[cfg(feature = "parry3d")]
     TRIMESH(material::Material<parry::ParryTriMesh>),
-    HOMOGENEOUS2D(material::Material<geometry::HomogeneousMesh2D>)
+    HOMOGENEOUS2D(material::Material<geometry::ParryHomogeneousMesh2D>)
 }
 
 #[derive(Deserialize, PartialEq, Clone, Copy)]