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danijoo
2017-01-21 14:03:08 +01:00
commit f95c1da06a
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23
Cargo.lock generated Normal file
View File

@@ -0,0 +1,23 @@
[root]
name = "mclj"
version = "0.1.0"
dependencies = [
"rand 0.3.15 (registry+https://github.com/rust-lang/crates.io-index)",
]
[[package]]
name = "libc"
version = "0.2.20"
source = "registry+https://github.com/rust-lang/crates.io-index"
[[package]]
name = "rand"
version = "0.3.15"
source = "registry+https://github.com/rust-lang/crates.io-index"
dependencies = [
"libc 0.2.20 (registry+https://github.com/rust-lang/crates.io-index)",
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"checksum libc 0.2.20 (registry+https://github.com/rust-lang/crates.io-index)" = "684f330624d8c3784fb9558ca46c4ce488073a8d22450415c5eb4f4cfb0d11b5"
"checksum rand 0.3.15 (registry+https://github.com/rust-lang/crates.io-index)" = "022e0636ec2519ddae48154b028864bdce4eaf7d35226ab8e65c611be97b189d"

14
Cargo.toml Normal file
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@@ -0,0 +1,14 @@
[package]
name = "mclj"
version = "0.1.0"
authors = ["Daniel Bauer <daniel.bauer@headlezz.net>"]
[dependencies]
rand = "0.3.15"
[profile.release]
lto = true
opt-level = 3

16
mclj.iml Normal file
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@@ -0,0 +1,16 @@
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88
src/energy.rs Normal file
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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);
}

167
src/main.rs Normal file
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#![allow(non_snake_case)]
extern crate rand;
use rand::Rng;
use rand::distributions::{IndependentSample, Range};
mod energy;
use energy::*;
use std::io::prelude::*;
const LJ_EPS : f64 = 1.0;
const LJ_SIG : f64 = 1.0;
const TAILCORR : bool = true;
const SHIFT: bool = false;
// easy printing to stderr
macro_rules! println_stderr(
($($arg:tt)*) => { {
let r = writeln!(&mut ::std::io::stderr(), $($arg)*);
r.expect("failed printing to stderr");
} }
);
fn main() {
// define all the stuff
let sample_steps = 1000000;
let minim_steps = 1000000;
let num_particles: usize = 512;
let density = 0.7;
let temperature = 0.9;
let cutoff = 3.0;
let displacement = 0.1;
println_stderr!("");
println_stderr!("################################################################");
println_stderr!("################## LJ Monte Carlo Simulation #################");
println_stderr!("################################################################");
println_stderr!("");
// initialize stuff
let beta = 1.0/temperature;
let volume = (num_particles as f64)/ density;
let l_x = volume.cbrt();
let l_y = l_x;
let l_z = l_x;
let cutoff_squared = cutoff * cutoff;
let mut rng = rand::thread_rng();
let particle_range = Range::new(0, num_particles-1);
let mut rx : Vec<f64> = vec![];
let mut ry : Vec<f64> = vec![];
let mut rz : Vec<f64> = vec![];
loop {
rx.push(l_x * rng.gen::<f64>());
ry.push(l_y * rng.gen::<f64>());
rz.push(l_z * rng.gen::<f64>());
if rx.len() == num_particles { break; }
}
let e_corr = if TAILCORR { 8.0/3.0*std::f64::consts::PI*density*LJ_EPS*LJ_SIG.powi(3)*((1.0/3.0*(LJ_SIG/cutoff).powi(9)) - (LJ_SIG/cutoff).powi(3)) } else { 0.0 };
let p_corr = if TAILCORR { 16.0/3.0*std::f64::consts::PI*density.powi(2)*LJ_EPS*LJ_SIG.powi(3)*((2.0/3.0*(LJ_SIG/cutoff).powi(9)) - (LJ_SIG/cutoff).powi(3)) } else { 0.0 };
println_stderr!("Particles: {}, Density: {}, Temperature: {}", num_particles, density, temperature);
println_stderr!("System volume: {:8.3}, Dimensions {:.3}/{:.3}/{:.3}", volume, l_x, l_y, l_z,);
println_stderr!("Minimization steps: {}, Sampling steps: {}", minim_steps, sample_steps);
println_stderr!("LJ params eps: {}, sigma: {}, cutoff: {}", LJ_EPS, LJ_SIG, cutoff);
println_stderr!("Tailcorr: {:8.3}, Shift: {:8.3}, Pressurecprr: {:8.3}", e_corr, SHIFT, p_corr);
let (mut energy, mut virial) = get_total_energy(&rx, &ry, &rz, num_particles, l_x, l_y, l_z, cutoff_squared, e_corr);
let mut energy_sum = 0.0;
let mut virial_sum = 0.0;
let mut step_counter = 0;
let mut accept_counter = 0;
println_stderr!("");
println_stderr!("################################################################");
println_stderr!("##################### Energy Minimization ####################");
println_stderr!("################################################################");
println_stderr!("");
for step in 0..minim_steps+sample_steps {
// select rnd particle
let rnd_index = particle_range.ind_sample(&mut rng);
// store old position
let oldX = rx[rnd_index];
let oldY = ry[rnd_index];
let oldZ = rz[rnd_index];
// old particle energy
let (old_particle_energy, old_particle_virial) = get_particle_energy(&rx, &ry, &rz, rnd_index, num_particles, l_x, l_y, l_z, cutoff_squared);
// rnd displacement and PBC
rx[rnd_index] += ( rng.gen::<f64>() - 0.5 ) * displacement;
ry[rnd_index] += ( rng.gen::<f64>() - 0.5 ) * displacement;
rz[rnd_index] += ( rng.gen::<f64>() - 0.5 ) * displacement;
if rx[rnd_index] < 0.0 { rx[rnd_index] += l_x }
if rx[rnd_index] > l_x { rx[rnd_index] -= l_x }
if ry[rnd_index] < 0.0 { ry[rnd_index] += l_y }
if ry[rnd_index] > l_y { ry[rnd_index] -= l_y }
if rz[rnd_index] < 0.0 { rz[rnd_index] += l_z }
if rz[rnd_index] > l_z { rz[rnd_index] -= l_z }
// calculate energy difference
let (new_particle_energy, new_particle_virial) = get_particle_energy(&rx, &ry, &rz, rnd_index, num_particles, l_x, l_y, l_z, cutoff_squared);
let dE = new_particle_energy - old_particle_energy;
//accept move
if rng.gen::<f64>() < (-beta * dE).exp() {
accept_counter += 1;
if step % 1000 == 0 { // calculate total energy every 1000 steps to account for rounding errors
let (e, v) = get_total_energy(&rx, &ry, &rz, num_particles, l_x, l_y, l_z, cutoff_squared, e_corr);
energy = e;
virial = v;
} else {
energy += dE;
virial += new_particle_virial - old_particle_virial;
}
} else { // or restore old position
rx[rnd_index] = oldX;
ry[rnd_index] = oldY;
rz[rnd_index] = oldZ;
}
// update sums for averaging
step_counter += 1;
energy_sum += energy;
virial_sum += virial;
if step_counter % 5000 == 0 && step < minim_steps {
println!("Minim {}\tEnergy: {:.3}\tVirial: {:.3}\tAcceptance:{:.1}\tDisplacement: {:.3}", step_counter, energy, virial, 666, displacement);
}
// reset sums for sampling
if step == minim_steps-1 {
println!("Starting averaging!");
step_counter = 0;
energy_sum = 0.0;
virial_sum = 0.0;
}
}
let final_energy = energy_sum/step_counter as f64;
let particle_energy = final_energy / num_particles as f64;
let final_virial = virial_sum / 3.0 / step_counter as f64 / num_particles as f64 / volume;
let pressure = virial_sum / 3.0 / step_counter as f64 / volume + density * temperature + p_corr;
println!("Steps: {}", step_counter );
println!("Avg Energy: {:.3}", final_energy);
println!("Energy/Particle: {:.3}", particle_energy);
println!("Virial: {:.3}", final_virial);
println!("Pressure: {:.3}", pressure);
}