Merge development branch towards RustBCA 1.1.0

.github/workflows/rustbca_compile_check.yml

@@ -1,4 +1,4 @@
-name: rustBCA Compile check
+name: RustBCA Compile check
 
 on:
   push:
@@ -37,15 +37,15 @@ jobs:
         sudo apt install libhdf5-dev
     - name: Test RustBCA
       run: |
-        cargo test --features cpr_rootfinder_netlib,hdf5_input,distributions
+        cargo test --features cpr_rootfinder_netlib,hdf5_input,distributions,parry3d
     - 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

@@ -1,11 +1,16 @@
 [package]
-name = "rustBCA"
-version = "1.0.0"
+name = "RustBCA"
+version = "1.1.0"
 authors = ["Jon Drobny <drobny2@illinois.edu>"]
 edition = "2018"
 
 [[bin]]
-name="rustBCA"
+name="RustBCA"
+
+[lib]
+name = "libRustBCA"
+path = "src/lib.rs"
+crate-type = ["cdylib"]
 
 [dependencies]
 rand = "0.8.3"
@@ -22,6 +27,11 @@ 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"
@@ -39,3 +49,5 @@ 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 +1,105 @@
+#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];
+};
+
+struct InputSimpleBCA {
+  uintptr_t len;
+  // vx vy vz [m/s]
+  double (*velocities)[3];
+  double Z1;
+  double m1;
+  double Ec1;
+  double Es1;
+  double Z2;
+  double m2;
+  double n2;
+  double Ec2;
+  double Es2;
+  double Eb2;
+};
+
+extern "C" {
+
+OutputBCA simple_bca_list_c(InputSimpleBCA input);
+
+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"

examples/tungsten_tiles_trimesh.toml

@@ -0,0 +1,105 @@
+[options]
+name = "tungsten_tiles_"
+track_trajectories = true
+track_recoils = true
+track_recoil_trajectories = true
+write_buffer_size = 8000
+weak_collision_order = 0
+suppress_deep_recoils = false
+high_energy_free_flight_paths = false
+num_threads = 4
+num_chunks = 5
+use_hdf5 = false
+electronic_stopping_mode = "LOW_ENERGY_NONLOCAL"
+mean_free_path_model = "LIQUID"
+interaction_potential = [["KR_C"]]
+scattering_integral = [["MENDENHALL_WELLER"]]
+root_finder = [[{"NEWTON"={max_iterations=100, tolerance=1E-3}}]]
+track_displacements = false
+track_energy_losses = false
+
+[material_parameters]
+energy_unit = "EV"
+mass_unit = "AMU"
+Eb = [ 3.0,]
+Es = [ 8.79,]
+Ec = [ 1.0,]
+Z = [ 74 ]
+m = [ 183.84 ]
+interaction_index = [0]
+surface_binding_model = {"PLANAR"={calculation="TARGET"}}
+bulk_binding_model = "AVERAGE"
+
+[particle_parameters]
+length_unit = "1e-8"
+energy_unit = "EV"
+mass_unit = "AMU"
+N = [ 10 ]
+m = [ 4.008 ]
+Z = [ 2 ]
+E = [ 250.0 ]
+Ec = [ 1.0 ]
+Es = [ 0.0 ]
+pos = [ [ 0.35, 1.0, 0.5,] ]
+dir = [ [ 0.98, -0.3, 0.0,] ]
+interaction_index = [ 0 ]
+
+[geometry_input]
+length_unit = "1e-8"
+electronic_stopping_correction_factor = 1.0
+densities = [60000]
+vertices = [
+  [0.00000000, 0.00000000, 0.00000000],
+  [0.00000000, 0.00000000, 0.20000000],
+  [0.00000000, 0.00000000, 0.40000000],
+  [0.00000000, 0.00000000, 0.60000000],
+  [0.00000000, 0.00000000, 0.80000000],
+  [0.00000000, 0.00000000, 1.00000000],
+  [0.00000000, 1.00000000, 0.00000000],
+  [0.00000000, 1.00000000, 0.20000000],
+  [0.00000000, 1.00000000, 0.40000000],
+  [0.00000000, 1.00000000, 0.60000000],
+  [0.00000000, 1.00000000, 0.80000000],
+  [0.00000000, 1.00000000, 1.00000000],
+  [0.20000000, 0.55000000, 0.00000000],
+  [0.20000000, 0.55000000, 1.00000000],
+  [0.40000000, 0.20000000, 0.00000000],
+  [0.40000000, 0.20000000, 0.20000000],
+  [0.40000000, 0.20000000, 0.40000000],
+  [0.40000000, 0.20000000, 0.60000000],
+  [0.40000000, 0.20000000, 0.80000000],
+  [0.40000000, 0.20000000, 1.00000000],
+  [0.40000000, 1.00000000, 0.00000000],
+  [0.40000000, 1.00000000, 0.20000000],
+  [0.40000000, 1.00000000, 0.40000000],
+  [0.40000000, 1.00000000, 0.60000000],
+  [0.40000000, 1.00000000, 0.80000000],
+  [0.40000000, 1.00000000, 1.00000000],
+  [0.60000000, 0.20000000, 0.00000000],
+  [0.60000000, 0.20000000, 0.20000000],
+  [0.60000000, 0.20000000, 0.40000000],
+  [0.60000000, 0.20000000, 0.60000000],
+  [0.60000000, 0.20000000, 0.80000000],
+  [0.60000000, 0.20000000, 1.00000000],
+  [0.60000000, 1.00000000, 0.00000000],
+  [0.60000000, 1.00000000, 0.20000000],
+  [0.60000000, 1.00000000, 0.40000000],
+  [0.60000000, 1.00000000, 0.60000000],
+  [0.60000000, 1.00000000, 0.80000000],
+  [0.60000000, 1.00000000, 1.00000000],
+  [0.80000000, 0.55000000, 0.00000000],
+  [0.80000000, 0.55000000, 1.00000000],
+  [1.00000000, 0.00000000, 0.00000000],
+  [1.00000000, 0.00000000, 0.20000000],
+  [1.00000000, 0.00000000, 0.40000000],
+  [1.00000000, 0.00000000, 0.60000000],
+  [1.00000000, 0.00000000, 0.80000000],
+  [1.00000000, 0.00000000, 1.00000000],
+  [1.00000000, 1.00000000, 0.00000000],
+  [1.00000000, 1.00000000, 0.20000000],
+  [1.00000000, 1.00000000, 0.40000000],
+  [1.00000000, 1.00000000, 0.60000000],
+  [1.00000000, 1.00000000, 0.80000000],
+  [1.00000000, 1.00000000, 1.00000000],
+]
+indices = [[0, 14, 12], [26, 40, 38], [46, 32, 38], [20, 6, 12], [0, 40, 14], [6, 0, 12], [40, 46, 38], [40, 26, 14], [32, 26, 38], [14, 20, 12], [1, 0, 40], [1, 40, 41], [2, 1, 41], [2, 41, 42], [3, 2, 42], [3, 42, 43], [4, 3, 43], [4, 43, 44], [5, 4, 44], [5, 44, 45], [41, 40, 46], [41, 46, 47], [42, 41, 47], [42, 47, 48], [43, 42, 48], [43, 48, 49], [44, 43, 49], [44, 49, 50], [45, 44, 50], [45, 50, 51], [47, 46, 32], [47, 32, 33], [48, 47, 33], [48, 33, 34], [49, 48, 34], [49, 34, 35], [50, 49, 35], [50, 35, 36], [51, 50, 36], [51, 36, 37], [33, 32, 26], [33, 26, 27], [34, 33, 27], [34, 27, 28], [35, 34, 28], [35, 28, 29], [36, 35, 29], [36, 29, 30], [37, 36, 30], [37, 30, 31], [27, 26, 15], [26, 14, 15], [28, 27, 16], [27, 15, 16], [29, 28, 17], [28, 16, 17], [30, 29, 18], [29, 17, 18], [31, 30, 19], [30, 18, 19], [15, 14, 20], [15, 20, 21], [16, 15, 21], [16, 21, 22], [17, 16, 22], [17, 22, 23], [18, 17, 23], [18, 23, 24], [19, 18, 24], [19, 24, 25], [21, 20, 6], [21, 6, 7], [22, 21, 7], [22, 7, 8], [23, 22, 8], [23, 8, 9], [24, 23, 9], [24, 9, 10], [25, 24, 10], [25, 10, 11], [7, 6, 0], [7, 0, 1], [8, 7, 1], [8, 1, 2], [9, 8, 2], [9, 2, 3], [10, 9, 3], [10, 3, 4], [11, 10, 4], [11, 4, 5], [5, 19, 13], [31, 45, 39], [51, 37, 39], [25, 11, 13], [5, 45, 19], [11, 5, 13], [45, 51, 39], [45, 31, 19], [37, 31, 39], [19, 25, 13]]

package.py

@@ -0,0 +1,47 @@
+# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+# ----------------------------------------------------------------------------
+# If you submit this package back to Spack as a pull request,
+# please first remove this boilerplate and all FIXME comments.
+#
+# This is a template package file for Spack.  We've put "FIXME"
+# next to all the things you'll want to change. Once you've handled
+# them, you can save this file and test your package like this:
+#
+#     spack install rustbca
+#
+# You can edit this file again by typing:
+#
+#     spack edit rustbca
+#
+# See the Spack documentation for more information on packaging.
+# ----------------------------------------------------------------------------
+
+from spack import *
+
+
+class Rustbca(Package):
+    """FIXME: Put a proper description of your package here."""
+
+    # FIXME: Add a proper url for your package's homepage here.
+    homepage = "https://www.github.com/lcpp-org/RustBCA/wiki"
+    url      = "https://github.com/lcpp-org/RustBCA/archive/refs/tags/v1.0.0.tar.gz"
+    git      = "https://www.github.com/lcpp-org/RustBCA.git"
+
+    # FIXME: Add a list of GitHub accounts to
+    # notify when the package is updated.
+    # maintainers = ['github_user1', 'github_user2']
+
+    version('dev', branch='dev')
+    version('1.0.0', sha256='99dcac7c7a78e6cd17da63a0dcbb3c36bca523ffafbb0425128b0c971b1a6829')
+    depends_on('rust')
+
+    # FIXME: Add dependencies if required.
+    # depends_on('foo')
+
+    def install(self, spec, prefix):
+        cargo = which('cargo')
+        cargo('build', '--release', '--lib', '--target-dir', prefix)

pyproject.toml

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

scripts/materials.py

@@ -21,6 +21,17 @@
     'Es': 1.5,
 }
 
+lithium = {
+    'symbol': 'Li',
+    'name': 'lithium',
+    'Z': 3,
+    'm': 6.941,
+    'Ec': 1.0,
+    'Es': 1.64,
+    'Eb': 0.0,
+    'n': 4.63E28
+}
+
 nitrogen = {
     'symbol': 'N',
     'name': 'nitrogen',