initial

src/energy.rs

@@ -0,0 +1,88 @@
+
+pub fn get_total_energy(rx: &[f64], ry: &[f64], rz: &[f64], num_particles: usize, l_x: f64, l_y: f64, l_z: f64, cutoff_squared: f64, e_corr: f64) -> (f64, f64) {
+    let mut energy = 0.0;
+    let mut virial = 0.0;
+    let hl_x = l_x / 2.0;
+    let hl_y = l_y / 2.0;
+    let hl_z = l_z / 2.0;
+    for i in 0..num_particles-1 {
+        for j in i+1..num_particles-1 {
+            let dist_squared = get_particle_distance_squared(rx[i], ry[i],rz[i],rx[j],ry[j],rz[j], l_x, l_y, l_z, hl_x, hl_y, hl_z);
+            if dist_squared < cutoff_squared {
+                let (e,v) = eval_pair_energy(dist_squared);
+                energy += e;
+                virial += v;
+            }
+        }
+    }
+    energy += num_particles as f64 * e_corr;
+    return (energy, virial);
+}
+
+pub fn get_particle_energy(rx: &[f64], ry: &[f64], rz: &[f64], p_index: usize, num_particles: usize, l_x: f64, l_y: f64, l_z: f64, cutoff_squared: f64) -> (f64, f64) {
+    let mut energy = 0.0;
+    let mut virial = 0.0;
+    let hl_x = l_x / 2.0;
+    let hl_y = l_y / 2.0;
+    let hl_z = l_z / 2.0;
+    for i in 0..num_particles-1 {
+        if i == p_index { continue; }
+
+        let dist_squared = get_particle_distance_squared(rx[i], ry[i], rz[i], rx[p_index], ry[p_index], rz[p_index], l_x, l_y, l_z, hl_x, hl_y, hl_z);
+        if dist_squared < cutoff_squared {
+            let (e,v) = eval_pair_energy(dist_squared);
+            energy += e;
+            virial += v;
+        }
+    }
+    return (energy, virial);
+}
+
+fn get_particle_distance_squared(x1: f64,y1: f64,z1: f64,x2: f64,y2: f64,z2: f64, l_x: f64, l_y: f64, l_z: f64, hl_x: f64, hl_y: f64, hl_z: f64) -> f64 {
+    let mut dx = x1 - x2;
+    let mut dy = y1 - y2;
+    let mut dz = z1 - z2;
+
+    if dx > hl_x { dx -= l_x }
+        else if dx < -hl_x{ dx += -l_x}
+    if dy > hl_y { dy -= l_y }
+        else if dy < -hl_y{ dy += -l_y}
+    if dz > hl_z { dz -= l_z }
+        else if dz < -hl_z{ dz += -l_z}
+
+    return dx*dx + dy*dy + dz*dz;
+}
+
+#[test]
+fn test_get_particle_distance_squared() {
+    let (x1, y1, z1) = (0.0, 0.0, 0.0);
+    let (x2, y2, z2) = (5.0, 0.0, 0.0);
+
+    // no pbc
+    let dist = get_particle_distance_squared(x1,y1,y1,y2,z2,z2, 20.0, 20.0, 20.0, 10.0, 10.0, 10.0);
+    assert!( (dist - 25.0) < 0.00001, "{}", dist);
+
+    // with pbc
+    let dist = get_particle_distance_squared(x1,y1,y1,y2,z1,z2, 9.0, 9.0, 9.0, 4.5, 4.5, 4.5);
+    assert!( (dist - 16.0) < 0.00001, "{}", dist);
+}
+
+fn eval_pair_energy(dist_squared: f64) -> (f64, f64) {
+    let r6 = ::LJ_SIG/(dist_squared * dist_squared * dist_squared);
+    let r62 = r6*r6;
+    let energy = 4.0 * ::LJ_EPS * (r62 - r6);
+    let virial = 48.0 * ::LJ_EPS * ( r62 - 0.5 * r6 );
+    return (energy, virial);
+}
+
+#[test]
+fn test_eval_pair_energy() {
+    let (e,v) = eval_pair_energy(1.0);
+    assert!( (e - 0.0).abs() < 0.00001, "{}",  e);
+
+    let (e,v) = eval_pair_energy(2.0);
+    assert!( (e - -0.4375).abs() < 0.00001, "{}",  e);
+
+    let (e,v) = eval_pair_energy(0.5);
+    assert!( (e - 224.0).abs() < 0.00001, "{}",  e);
+}