bauer/lj_monte_carlo
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forgot what this commit is about

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This commit is contained in:
Daniel Bauer
2017-01-27 15:11:29 +01:00
parent b68e4be2a3
commit 98bd75ebfd
3 changed files with 113 additions and 108 deletions
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4
src/main.rs
View File

@@ -223,7 +223,8 @@ fn main() {
if step < minim_steps && step_counter % 5000 == 0 && step != 0 {
let tries_per_step : f64 = step_counter as f64 /accept_counter as f64;
let acceptance_rate = 1.0/tries_per_step * 100.0;
println_stderr!("Minim {:<10} Energy: {:<30.3} Accept.: {:<4.1}% dr: {:.3}", step+1, energy, acceptance_rate, displacement);
let avg_energy = energy_sum / step_counter as f64;
println_stderr!("Minim {:<10} Energy: {:<30.3} Accept.: {:<4.1}% dr: {:.3}", step+1, avg_energy, acceptance_rate, displacement);
if SCALE {
let scale_factor = (TRIES_INTENDED/tries_per_step * DISP_SCALE_FACTOR).abs();
@@ -234,6 +235,7 @@ fn main() {
}
step_counter = 0;
accept_counter = 0;
energy_sum = 0.0;
}
}

17
src/trajectory.rs
View File

@@ -6,7 +6,7 @@ use std::error::Error;
use std::io::prelude::*;
use std::fs::File;
use std::path::Path;
use std::fmt;
use std::io::BufReader;
@@ -60,6 +60,21 @@ pub struct Frame {
pub lj_cutoff: f64,
}
impl fmt::Debug for Frame {
fn fmt(&self, fmt: &mut fmt::Formatter) -> fmt::Result {
fmt.debug_struct("Frame")
.field("num_particles", &self.num_particles)
.field("box_x", &self.box_x)
.field("box_y", &self.box_y)
.field("box_z", &self.box_z)
.field("temperature", &self.temperature)
.field("lj_eps", &self.lj_eps)
.field("lj_sig", &self.lj_sig)
.field("lj_cutoff", &self.lj_cutoff)
.finish()
}
}
pub struct TrjReader {
pub reader: BufReader<File>,
}

200
src/widom.rs
View File

@@ -4,6 +4,7 @@ mod energy;
use energy::*;
extern crate rand;
use rand::Rng;
use std::env;
const LJ_EPS : f64 = 1.0;
const LJ_SIG : f64 = 1.0;
@@ -11,22 +12,104 @@ const LJ_SIG : f64 = 1.0;
static MKSA_PLANCKS_CONSTANT_H : f64 = 1.0;
static MASS : f64 = 1.0;
const INSERTIONS_PER_STEP : usize = 10;
const RUN_AVG_SIZE : usize = 100;
const INSERTIONS_PER_STEP : usize = 1000;
const RUN_AVG_SIZE : usize = 10;
const SHIFT : bool = true;
// returns number of particles in liquid and gas phase as tuble
fn count_particles(rz: &[f64], num_particles: usize, liquid_height: f64) -> (usize, usize) {
let mut liquid_count = 0;
let mut gas_count = 0;
for i in 0..num_particles {
if rz[i] < liquid_height { liquid_count += 1; }
else { gas_count += 1; }
fn main() {
// open file
let args: Vec<String> = env::args().collect();
let mut trj_reader = TrjReader::new(&args[1]);
let mut frame = trj_reader.next_frame();
println!("{:?}", frame);
// get some non changing values
let volume = frame.box_x * frame.box_y * frame.box_z;
let beta = 1.0/frame.temperature;
let cutoff_sqr = frame.lj_cutoff * frame.lj_cutoff;
// account for gas phase slab
let gas_slab = args[2].parse::<f64>().unwrap();
let liquid_height = frame.box_z / (gas_slab + 1.0);
let liquid_volume = volume / (gas_slab + 1.0);
let gas_volume = volume - liquid_volume;
let wave = MKSA_PLANCKS_CONSTANT_H / (2.0 * std::f64::consts::PI * MASS * frame.temperature / frame.lj_eps).sqrt();
let e_shift = if SHIFT { 4.0 * LJ_EPS * ( (LJ_SIG/frame.lj_cutoff).powi(12) - (LJ_SIG/frame.lj_cutoff).powi(6) ) } else { 0.0 };
let mut rng = rand::thread_rng();
// average counters
let mut frame_count = 0;
let mut widom_sum_gas = 0.0;
let mut ideal_sum_gas = 0.0;
let mut widom_sum_liquid = 0.0;
let mut ideal_sum_liquid = 0.0;
// loop over frames
let mut avg_count = 0;
loop {
frame_count += 1;
// calculate number of particles in each phase
let mut liquid_count = 0.0;
let mut gas_count = 0.0;
for i in 0..frame.num_particles {
if frame.rz[i] < liquid_height { liquid_count += 1.0; }
else { gas_count += 1.0; }
}
// test particle insertion multiple times
for i in 0..INSERTIONS_PER_STEP {
avg_count += 1;
// liquid test partciles
let lx = frame.box_x * rng.gen::<f64>();
let ly = frame.box_y * rng.gen::<f64>();
let lz = liquid_height * rng.gen::<f64>();
let widom_e_liquid = get_particle_insertion_energy(&frame.rx, &frame.ry, &frame.rz, frame.num_particles, lx, ly, lz, frame.box_x, frame.box_y, frame.box_z, cutoff_sqr, e_shift);
widom_sum_liquid += (-beta*widom_e_liquid).exp();
// test particle gas energy
let gx = frame.box_x * rng.gen::<f64>();
let gy = frame.box_y * rng.gen::<f64>();
let gz = ((frame.box_z - liquid_height) * rng.gen::<f64>()) + liquid_height;
let widom_e_gas = get_particle_insertion_energy(&frame.rx, &frame.ry, &frame.rz, frame.num_particles, gx, gy, gz, frame.box_x, frame.box_y, frame.box_z, cutoff_sqr, e_shift);
widom_sum_gas += (-beta*widom_e_gas).exp();
// calculate ideal gas potential for both phases
ideal_sum_gas += frame.temperature / frame.lj_eps * (gas_volume/(wave.powi(3)* gas_count)).ln();
ideal_sum_liquid += frame.temperature / frame.lj_eps * (liquid_volume/(wave.powi(3)* liquid_count)).ln();
}
// print running averages
if avg_count / INSERTIONS_PER_STEP > RUN_AVG_SIZE {
let ideal_gas = ideal_sum_gas / avg_count as f64;
let ideal_liquid = ideal_sum_liquid / avg_count as f64;
let excess_gas = -(widom_sum_gas/avg_count as f64).ln()/beta;
let excess_liquid = -(widom_sum_liquid/avg_count as f64).ln()/beta;
println!("Frame {}\tgas {}\tliquid {}\t particles gas/liquid:{}/{}", frame_count, ideal_gas + excess_gas, ideal_liquid + excess_liquid, gas_count, liquid_count);
// reset averages for next round
avg_count = 0;
ideal_sum_gas = 0.0;
ideal_sum_liquid = 0.0;
widom_sum_gas = 0.0;
widom_sum_liquid = 0.0;
}
if !trj_reader.update_with_next(&mut frame) {
break;
}
}
return (liquid_count, gas_count);
}
fn get_particle_insertion_energy(rx: &[f64], ry: &[f64], rz: &[f64], num_particles: usize, x: f64, y: f64, z: f64, l_x: f64,l_y: f64, l_z: f64, cutoff_sqr: f64, e_shift: f64) -> f64 {
let mut energy = 0.0;
let half_l_x = l_x/2.0;
@@ -36,103 +119,8 @@ fn get_particle_insertion_energy(rx: &[f64], ry: &[f64], rz: &[f64], num_particl
let dist_squared = get_particle_distance_squared(x, y, z, rx[i],ry[i],rz[i], l_x, l_y, l_z, half_l_x, half_l_y, half_l_z);
if dist_squared < cutoff_sqr {
let (e,v) = eval_pair_energy(dist_squared, e_shift);
energy += e;
energy += eval_pair_energy(dist_squared, e_shift).0;
}
}
return energy;
}
fn main() {
let mut trj_reader = TrjReader::new(&"2phases/10k_1step.xyz".to_string());
let mut frame = trj_reader.next_frame();
let volume = frame.box_x * frame.box_y * frame.box_z;
let beta = 1.0/frame.temperature;
let cutoff_sqr = frame.lj_cutoff * frame.lj_cutoff;
let mut gas_slab = 2.0;
let mut liquid_height = frame.box_z / (gas_slab + 1.0);
let liquid_volume = volume / (gas_slab + 1.0);
let gas_volume = volume - liquid_volume;
let wave = MKSA_PLANCKS_CONSTANT_H / (2.0 * std::f64::consts::PI * MASS * frame.temperature / frame.lj_eps).sqrt();
let mut rng = rand::thread_rng();
let e_shift = if SHIFT { 4.0 * LJ_EPS * ( (LJ_SIG/frame.lj_cutoff).powi(12) - (LJ_SIG/frame.lj_cutoff).powi(6) ) } else { 0.0 };
let mut frame_count = 0;
let mut widom_sum_gas = 0.0;
let mut ideal_sum_gas = 0.0;
let mut widom_sum_liquid = 0.0;
let mut ideal_sum_liquid = 0.0;
let mut avg_count = 0;
loop {
frame_count += 1;
avg_count += 1;
// test particle liquid energy
let lx = frame.box_x * rng.gen::<f64>();
let ly = frame.box_y * rng.gen::<f64>();
let lz = liquid_height * rng.gen::<f64>();
let widom_e_liquid = get_particle_insertion_energy(&frame.rx, &frame.ry, &frame.rz, frame.num_particles, lx, ly, lz, frame.box_x, frame.box_y, frame.box_z, cutoff_sqr, e_shift);
widom_sum_liquid += (-beta*widom_e_liquid).exp();
// test particle gas energy
let gx = frame.box_x * rng.gen::<f64>();
let gy = frame.box_y * rng.gen::<f64>();
let gz = ((frame.box_z - liquid_height) * rng.gen::<f64>()) + liquid_height;
let widom_e_gas = get_particle_insertion_energy(&frame.rx, &frame.ry, &frame.rz, frame.num_particles, gx, gy, gz, frame.box_x, frame.box_y, frame.box_z, cutoff_sqr, e_shift);
widom_sum_gas += (-beta*widom_e_gas).exp();
// calculate number of particles in each phase
let mut liquid_count = 0.0;
let mut gas_count = 0.0;
for i in 0..frame.num_particles {
if frame.rz[i] < liquid_height { liquid_count += 1.0; }
else { gas_count += 1.0; }
}
// calculate ideal gas potential for both phases
let wave = MKSA_PLANCKS_CONSTANT_H / (2.0 * std::f64::consts::PI * MASS * frame.temperature / frame.lj_eps).sqrt();
ideal_sum_gas += frame.temperature / frame.lj_eps * (gas_volume/(wave.powi(3)* gas_count)).ln();
ideal_sum_liquid += frame.temperature / frame.lj_eps * (liquid_volume/(wave.powi(3)* liquid_count)).ln();
if avg_count == RUN_AVG_SIZE {
let ideal_gas = ideal_sum_gas / avg_count as f64;
let ideal_liquid = ideal_sum_liquid / avg_count as f64;
let excess_gas = -(widom_sum_gas/avg_count as f64).ln()/beta;
let excess_liquid = -(widom_sum_liquid/avg_count as f64).ln()/beta;
println!("Frame {} gas {} liquid {} particlecount:{}/{}", frame_count, ideal_gas + excess_gas, ideal_liquid + excess_liquid, gas_count, liquid_count);
avg_count = 0;
ideal_sum_gas = 0.0;
ideal_sum_liquid = 0.0;
widom_sum_gas = 0.0;
widom_sum_liquid = 0.0;
}
// liquid_gas_sum = 0.0;
// excess_liquid_sum = 0.0;
// gas_gas_sum = 0.0;
// excess_gas_sum = 0.0;
// avg_count = 0;
if !trj_reader.update_with_next(&mut frame) { break }
}
}