bauer/lj_monte_carlo
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writing trajectories

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danijoo
2017-01-22 00:50:15 +01:00
parent 1d38e85964
commit 93bfc18b89
4 changed files with 220 additions and 26 deletions
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58
src/main.rs
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@@ -7,7 +7,10 @@ mod energy;
use energy::*;
use std::io::prelude::*;
extern crate argparse;
use argparse::{ArgumentParser, Store, StoreFalse};
use argparse::{ArgumentParser, Store, StoreFalse, StoreTrue};
mod trajectory;
use trajectory::*;
const LJ_EPS : f64 = 1.0;
const LJ_SIG : f64 = 1.0;
@@ -24,7 +27,10 @@ macro_rules! println_stderr(
} }
);
fn parse_cmd_args(NUM_STEPS: &mut usize, NUM_MINIM_STEPS: &mut usize, NUM_PARTICLES: &mut usize, DENSITY: &mut f64, TEMPERATURE: &mut f64, CUTOFF: &mut f64, MAX_DISP_START: &mut f64, SCALE: &mut bool, TAILCORR: &mut bool, SHIFT: &mut bool) {
fn parse_cmd_args(NUM_STEPS: &mut usize, NUM_MINIM_STEPS: &mut usize,
NUM_PARTICLES: &mut usize, DENSITY: &mut f64, TEMPERATURE: &mut f64,
CUTOFF: &mut f64, MAX_DISP_START: &mut f64, SCALE: &mut bool, TAILCORR: &mut bool, SHIFT: &mut bool,
OUTPUT_PREFIX: &mut String, OUTPUT_INTERVAL: &mut i64, OUTPUT_MINIM: &mut bool) {
let mut ap = ArgumentParser::new();
ap.set_description("LJ MC simulation.");
ap.refer(NUM_STEPS)
@@ -51,9 +57,15 @@ fn parse_cmd_args(NUM_STEPS: &mut usize, NUM_MINIM_STEPS: &mut usize, NUM_PARTIC
ap.refer(SCALE)
.add_option(&["--nodisplacementscale"], StoreFalse,
"Disable displacement scaling");
// ap.refer(TRAJECTORY_STEPSIZE)
// .add_option(&["--trj_steps"], Store,
// "Number of steps between writing to the trajectory file");
ap.refer(OUTPUT_PREFIX)
.add_option(&["-o", "--output"], Store,
"Output file prefix");
ap.refer(OUTPUT_INTERVAL)
.add_option(&["--osteps"], Store,
"Number of steps between writing to the trajectory file. -1 only writes last frame");
ap.refer(OUTPUT_MINIM)
.add_option(&["--writeminimization"], StoreTrue,
"Enables writing of minimization step to trajectory");
// ap.refer(VACUUM_DIMENSION)
// .add_option(&["--vacuum"], Store,
// "Dimension of vacuum space below and above the intial system.");
@@ -80,13 +92,16 @@ fn main() {
let mut displacement = 0.1;
let mut TAILCORR : bool = true;
let mut SHIFT: bool = false;
let mut SHIFT: bool = true;
let mut SCALE: bool = true;
let mut output_prefix = "montecarlo".to_string();
let mut output_interval : i64 = 100;
let mut output_minim : bool = false;
parse_cmd_args(&mut sample_steps, &mut minim_steps, &mut num_particles,
&mut density, &mut temperature,
&mut cutoff, &mut displacement, &mut SCALE, &mut TAILCORR, &mut SHIFT);
&mut cutoff, &mut displacement, &mut SCALE, &mut TAILCORR, &mut SHIFT,
&mut output_prefix, &mut output_interval, &mut output_minim);
println_stderr!("");
println_stderr!("################################################################");
@@ -116,6 +131,7 @@ fn main() {
if rx.len() == num_particles { break; }
}
let e_shift = if SHIFT { 4.0 * LJ_EPS * ( (LJ_SIG/cutoff).powi(12) - (LJ_SIG/cutoff).powi(6) ) } else { 0.0 };
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 };
@@ -123,9 +139,9 @@ fn main() {
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);
println_stderr!("Tailcorr: {:8.3}, Shift: {:8.3}, Pressurecprr: {:8.3}", e_corr, e_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, mut virial) = get_total_energy(&rx, &ry, &rz, num_particles, l_x, l_y, l_z, cutoff_squared, e_corr, e_shift);
let mut energy_sum = 0.0;
let mut virial_sum = 0.0;
let mut step_counter = 0;
@@ -137,6 +153,10 @@ fn main() {
println_stderr!("################################################################");
println_stderr!("");
// prepare and write first trajectory frame
let mut trajectory : XYZTrajectory = XYZTrajectory::new(&format!("{}.xyz", output_prefix));
if output_minim { trajectory.write(&rx, &ry, &rz, num_particles, l_x, l_y, l_z, temperature, LJ_EPS, LJ_SIG, cutoff, true); }
for step in 0..minim_steps+sample_steps {
// select rnd particle
@@ -148,7 +168,7 @@ fn main() {
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);
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, e_shift);
// rnd displacement and PBC
rx[rnd_index] += ( rng.gen::<f64>() - 0.5 ) * displacement;
@@ -162,14 +182,14 @@ fn main() {
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 (new_particle_energy, new_particle_virial) = get_particle_energy(&rx, &ry, &rz, rnd_index, num_particles, l_x, l_y, l_z, cutoff_squared, e_shift);
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);
let (e, v) = get_total_energy(&rx, &ry, &rz, num_particles, l_x, l_y, l_z, cutoff_squared, e_corr, e_shift);
energy = e;
virial = v;
} else {
@@ -220,7 +240,13 @@ fn main() {
if step > minim_steps && step_counter % 5000 == 0 {
println_stderr!("Step {:<10}Energy: {:<12.3}Virial: {:<12.3}", step_counter, energy, virial);
}
// write trajectory maybe
if step as i64 % output_interval == 0 {
if step > minim_steps || output_minim {
trajectory.write(&rx, &ry, &rz, num_particles, l_x, l_y, l_z, temperature, LJ_EPS, LJ_SIG, cutoff, true);
}
}
}
@@ -271,8 +297,8 @@ Pressure: {}",
minim_steps, sample_steps,
LJ_EPS, LJ_SIG, cutoff,
num_particles, density, temperature, volume, l_x, l_y, l_z, displacement,
e_corr, SHIFT, p_corr,
e_corr, e_shift, p_corr,
step_counter, accept_counter, final_acceptance_rate, final_energy, particle_energy, final_virial, pressure);
trajectory.write(&rx, &ry, &rz, num_particles, l_x, l_y, l_z, temperature, LJ_EPS, LJ_SIG, cutoff, true);
}