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bootstrapping

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This commit is contained in:
Daniel Bauer
2018-11-12 15:16:06 +01:00
parent b86a9df7fb
commit fc776fd40e
12 changed files with 20449 additions and 10133 deletions
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37
src/lib.rs
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@@ -2,9 +2,12 @@
#[macro_use]
extern crate error_chain;
extern crate rand;
extern crate rgsl;
pub mod io;
pub mod histogram;
pub mod error_analysis;
use histogram::Dataset;
use std::f64;
@@ -32,12 +35,13 @@ pub struct Config {
pub temperature: f64,
pub cyclic: bool,
pub output: String,
pub bootstrap: usize,
}
impl fmt::Display for Config {
fn fmt(&self, f: &mut fmt::Formatter) -> fmt::Result {
write!(f, "Metadata={}, hist_min={:?}, hist_max={:?}, bins={:?} verbose={}, tolerance={}, iterations={}, temperature={}, cyclic={:?}", self.metadata_file, self.hist_min, self.hist_max, self.num_bins,
self.verbose, self.tolerance, self.max_iterations, self.temperature, self.cyclic)
write!(f, "Metadata={}, hist_min={:?}, hist_max={:?}, bins={:?} verbose={}, tolerance={}, iterations={}, temperature={}, cyclic={:?}, bootstrap={:?}", self.metadata_file, self.hist_min, self.hist_max, self.num_bins,
self.verbose, self.tolerance, self.max_iterations, self.temperature, self.cyclic, self.bootstrap)
}
}
@@ -54,11 +58,12 @@ fn is_converged(old_F: &[f64], new_F: &[f64], tolerance: f64) -> bool {
// This evaluates the first WHAM equation for each bin.
fn calc_bin_probability(bin: usize, dataset: &Dataset, F: &[f64]) -> f64 {
let mut denom_sum: f64 = 0.0;
let bin_count: f64 = dataset.get_weighted_bin_count(bin);
for (window, h) in dataset.histograms.iter().enumerate() {
let bias = dataset.calc_bias(bin, window);
denom_sum += (h.num_points as f64) * bias * F[window];
denom_sum += (dataset.weights[window] * h.num_points as f64) * bias * F[window];
}
dataset.bin_count[bin] / denom_sum
bin_count / denom_sum
}
// estimate the bias offset F of the histogram based on given probabilities.
@@ -150,12 +155,23 @@ pub fn run(cfg: &Config) -> Result<()>{
let (P, F, F_prev) = perform_wham(&cfg, &dataset)?;
let P_std: Vec<f64>;
let free_energy_std: Vec<f64>;
if cfg.bootstrap > 0 {
let error_est = error_analysis::run_bootstrap(&cfg, dataset.clone(), &P, cfg.bootstrap);
P_std = error_est.0;
free_energy_std = error_est.1;
} else {
P_std = vec![0.0; P.len()];
free_energy_std = vec![0.0; P.len()];
}
// calculate free energy and dump state
println!("Finished. Dumping final PMF");
let free_energy = calc_free_energy(&dataset, &P);
dump_state(&dataset, &F, &F_prev, &P, &free_energy);
dump_state(&dataset, &F, &F_prev, &P, &P_std, &free_energy, &free_energy_std);
io::write_results(&cfg.output, &dataset, &free_energy, &P)
io::write_results(&cfg.output, &dataset, &free_energy, &free_energy_std, &P, &P_std)
.chain_err(|| "Could not write results to output file")?;
Ok(())
@@ -191,16 +207,17 @@ fn calc_free_energy(dataset: &Dataset, P: &[f64]) -> Vec<f64> {
free_energy
}
fn dump_state(dataset: &Dataset, F: &[f64], F_prev: &[f64], P: &[f64], A: &[f64]) {
fn dump_state(dataset: &Dataset, F: &[f64], F_prev: &[f64], P: &[f64], P_std: &[f64], A: &[f64], A_std: &[f64]) {
// TODO fix output of F/F_prev
let out = std::io::stdout();
let mut lock = out.lock();
writeln!(lock, "# PMF");
writeln!(lock, "#bin\t\tFree Energy\t\tP(x)");
writeln!(lock, "#bin\t\tFree Energy\t\t+/-\t\tP(x)\t\t+/-");
for bin in 0..dataset.num_bins {
writeln!(lock, "{:9.5}\t{:9.5}\t{:9.5}", bin, A[bin], P[bin]);
writeln!(lock, "{:9.5}\t{:9.5}\t{:9.5}\t{:9.5}\t{:9.5}", bin, A[bin], A_std[bin], P[bin], P_std[bin]);
}
writeln!(lock, "# Bias offsets");
writeln!(lock, "#Window\t\tF\t\tdF");
writeln!(lock, "#Window\t\tF\t\tF_prev");
for window in 0..dataset.num_windows {
writeln!(lock, "{}\t{:9.5}\t{:8.8}", window, F[window], (F[window]-F_prev[window]).abs());
}