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fix WHAM calculation by correctly setting F[0] to 0

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This commit is contained in:
Daniel Bauer
2018-10-06 00:12:38 +02:00
parent 03f8624e58
commit 6ee8eea1ab
1 changed files with 64 additions and 23 deletions
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87
src/lib.rs
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@@ -99,6 +99,44 @@ fn perform_wham_iteration(hs: &HistogramSet, F_prev: &Vec<f32>,F: &mut Vec<f32>,
F[window] = 0.0;
}
// for bin in 0..hs.num_bins {
// let x = get_x_for_bin(bin, hs.hist_min, hs.bin_width);
// let mut num = 0.0;
// let mut denom = 0.0;
// for window in 0..hs.num_windows {
// match hs.histograms[window].get_bin_count(bin) {
// Some(c) => num += c,
// _ => {}
// }
// let bias = calc_bias(
// hs.bias_fc[window],
// hs.bias_x0[window],
// x);
// let bf = ((F_prev[window]-bias) / hs.kT).exp();
// denom += hs.histograms[window].num_points as f32* bf
// }
// P[bin] = num / denom;
// for window in 0..hs.num_windows {
// let bias = calc_bias(
// hs.bias_fc[window],
// hs.bias_x0[window],
// x);
// let bf = (-bias/hs.kT).exp() * P[bin];
// F[window] += bf;
// }
// }
// for window in 0..hs.num_windows {
// F[window] = -hs.kT * F[window].ln();
// }
// let norm = F[0];
// for window in 0..hs.num_windows {
// F[window] = F[window] - norm;
// }
// evaluate first WHAM equation for each bin to
// estimage probabilities based on previous offsets (F_prev)
for bin in 0..hs.num_bins {
@@ -110,6 +148,12 @@ fn perform_wham_iteration(hs: &HistogramSet, F_prev: &Vec<f32>,F: &mut Vec<f32>,
for window in 0..hs.num_windows {
F[window] = calc_window_F(window, hs, P);
}
// normalize F
let norm = F[0];
for window in 0..hs.num_windows {
F[window] = F[window] - norm;
}
}
// get average difference between two bias offset sets
@@ -124,32 +168,30 @@ fn diff_avg(F: &Vec<f32>, F_prev: &Vec<f32>) -> f32 {
// calculate the normalized free energy from normalized probability values
fn free_energy(hs: &HistogramSet, P: &mut Vec<f32>, A: &mut Vec<f32>) {
// Normalize P
let mut P_sum = 0.0;
for bin in 0..hs.num_bins {
P_sum += P[bin];
}
for bin in 0..hs.num_bins {
P[bin] /= P_sum;
}
let mut bin_min = f32::MAX;
// Free energy calculation
for bin in 0..hs.num_bins {
A[bin] = -hs.kT*P[bin].ln();
}
// find min value
let mut min: f32 = f32::MAX;
for bin in 0..hs.num_bins {
if A[bin] < min {
min = A[bin]
if A[bin] < bin_min {
bin_min = A[bin];
}
}
// normalize A
// Make A relative to minimum
for bin in 0..hs.num_bins {
A[bin] -= min;
A[bin] -= bin_min;
}
// Normalize P
// let mut P_sum = 0.0;
// for bin in 0..hs.num_bins {
// P_sum += P[bin];
// }
// for bin in 0..hs.num_bins {
// P[bin] /= P_sum;
// }
}
pub fn run(cfg: &Config) -> Result<(), Box<Error>>{
@@ -157,7 +199,9 @@ pub fn run(cfg: &Config) -> Result<(), Box<Error>>{
// read input data into the histograms object
println!("Reading input files.");
let histograms = io::read_data(&cfg).unwrap();
let histograms = io::read_data(&cfg) // TODO nicer error handling for this
.expect("No datapoints in histogram boundaries.");
println!("{}",&histograms);
// allocate only once for better performance
@@ -169,9 +213,6 @@ pub fn run(cfg: &Config) -> Result<(), Box<Error>>{
// perform WHAM until convergence
let mut iteration = 0;
while !is_converged(&F_prev, &F, cfg.tolerance) && iteration < cfg.max_iterations {
use std::thread;
use std::time;
thread::sleep(time::Duration::from_millis(10));
iteration += 1;
// store F values before the next iteration
F_prev.copy_from_slice(&F[..]);
@@ -295,13 +336,13 @@ mod tests {
}
#[test]
fn test_perform_wham_iteration() {
fn perform_wham_iteration() {
let hs = create_test_hs();
let prev_F = vec![0.0; hs.num_windows];
let mut F = vec![0.0; hs.num_windows];
let mut P = vec![f32::NAN; hs.num_bins];
super::perform_wham_iteration(&hs, &prev_F, &mut F, &mut P);
let expected_F = vec!(0.596, -0.250);
let expected_F = vec!(0.0, -0.846);
let expected_P = vec!(0.959, 0.331, 0.656, 46.750);
for bin in 0..hs.num_bins {
assert_near(expected_P[bin], P[bin], 0.01)