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small performance improvements

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Daniel Bauer
2018-10-08 09:48:22 +02:00
parent 5ea437db82
commit 23085ab6f1
1 changed files with 29 additions and 25 deletions
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54
src/lib.rs
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@@ -40,15 +40,11 @@ impl fmt::Display for Config {
// Checks for convergence between two WHAM iterations. WHAM is considered as
// converged if the absolute difference for the calculated bias offset is
// smaller then a tolerance value for each simulation window
// smaller then a tolerance value for every simulation window.
fn is_converged(old_F: &Vec<f32>, new_F: &Vec<f32>, tolerance: f32) -> bool {
for i in 0..old_F.len() {
let error = (new_F[i] - old_F[i]).abs();
if error > tolerance {
return false
}
}
true
!new_F.iter().zip(old_F.iter())
.map(|x| { (x.0-x.1).abs() })
.any(|diff| { diff > tolerance })
}
// estimate the probability of a bin of the histogram set based on F values
@@ -71,12 +67,11 @@ fn calc_bin_probability(bin: usize, ds: &Dataset, F: &Vec<f32>) -> f32 {
// estimate the bias offset F of the histogram based on given probabilities
// This evaluates the second WHAM equation for each window
fn calc_window_F(window: usize, ds: &Dataset, P: &Vec<f32>) -> f32 {
let mut ln_sum = 0.0;
for bin in 0..ds.num_bins {
let bias = ds.calc_bias(bin, window);
ln_sum += P[bin] * (-bias/ds.kT).exp()
}
-ds.kT * ln_sum.ln()
let bf_sum: f32 = (0..ds.num_bins).zip(P.iter()) // zip bins and P
.map(|x: (usize, &f32)| {
x.1 * (-ds.calc_bias(x.0, window)/ds.kT).exp()
}).sum();
-ds.kT * bf_sum.ln()
}
// One full WHAM iteration includes calculation of new probabilities P and
@@ -139,10 +134,10 @@ fn perform_wham_iteration(ds: &Dataset, F_prev: &Vec<f32>,F: &mut Vec<f32>, P: &
}
// normalize F
let norm = F[0];
for window in 0..ds.num_windows {
F[window] = F[window] - norm;
}
// let norm = F[0];
// for window in 0..ds.num_windows {
// F[window] = F[window] - norm;
// }
}
// get average difference between two bias offset sets
@@ -173,13 +168,13 @@ fn free_energy(ds: &Dataset, P: &mut Vec<f32>, A: &mut Vec<f32>) {
}
// Normalize P
let mut P_sum = 0.0;
for bin in 0..ds.num_bins {
P_sum += P[bin];
}
for bin in 0..ds.num_bins {
P[bin] /= P_sum;
}
// let mut P_sum = 0.0;
// for bin in 0..ds.num_bins {
// P_sum += P[bin];
// }
// for bin in 0..ds.num_bins {
// P[bin] /= P_sum;
// }
}
@@ -222,6 +217,15 @@ pub fn run(cfg: &Config) -> Result<(), Box<Error>>{
}
}
// Normalize P
// let mut P_sum = 0.0;
// for bin in 0..histograms.num_bins {
// P_sum += P[bin];
// }
// for bin in 0..histograms.num_bins {
// P[bin] /= P_sum;
// }
// final free energy calculation and state dump
println!("Finished. Dumping final PMF");
free_energy(&histograms, &mut P, &mut A);