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commit eaebf0dcbb259decbc0d8f5bbffa62244303f6c7
Author: Daniel Bauer <bauer@cbs.tu-darmstadt.de>
Date:   Sat Jul 17 14:12:30 2021 +0200

    error for empty timeseries

commit 1fe5383c5079ca6c0ad102d4e2cb32d5b1227e80
Author: Daniel Bauer <bauer@cbs.tu-darmstadt.de>
Date:   Sat Jul 17 14:09:13 2021 +0200

    refractored convdt slices calculation

commit 0b1fb7fb6a72edc50b013b59623551b2ccab6913
Author: Daniel Bauer <bauer@cbs.tu-darmstadt.de>
Date:   Sat Jul 17 13:27:59 2021 +0200

    fix histogram building without convdt

commit f9882ca4cece57451cd2971d0993a2d3621b0cdf
Author: Daniel Bauer <bauer@cbs.tu-darmstadt.de>
Date:   Sat Jul 17 12:53:06 2021 +0200

    fix tests not compiling

commit e6550e20bde3824f8199432b08777be41fc79fa8
Author: Daniel Bauer <bauer@cbs.tu-darmstadt.de>
Date:   Sat Jul 17 12:43:36 2021 +0200

    refractoring

commit 18c77a9b6694d491ef23cebb3918ccda8fcc44a5
Author: Daniel Bauer <bauer@cbs.tu-darmstadt.de>
Date:   Fri Jul 16 08:16:34 2021 +0200

    run and output for multiple datasets

commit 069f318f72207c416387007435eeff9867494e7a
Author: Daniel Bauer <bauer@cbs.tu-darmstadt.de>
Date:   Fri Jul 16 07:58:01 2021 +0200

    cleanup io.rs

commit 10efa428a0c6bf490c9f2d7a4c1df185de402a11
Author: Daniel Bauer <bauer@cbs.tu-darmstadt.de>
Date:   Thu Jul 15 19:27:22 2021 +0200

    parse multiple datasets with convdt
This commit is contained in:
Daniel Bauer
2021-07-17 14:14:25 +02:00
parent 0b5d0ebecd
commit c9e18ebda9
4 changed files with 285 additions and 86 deletions
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54
src/lib.rs
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@@ -47,16 +47,19 @@ pub struct Config {
pub start: f64,
pub end: f64,
pub uncorr: bool,
pub convdt: f64,
}
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={:?}, uncorr={:?}, bootstrap={:?}, seed={:?}",
cyclic={:?}, uncorr={:?}, bootstrap={:?}, seed={:?},
uncorr={:?}, start={:?}, end={:?}, convdt={:?}",
self.metadata_file, self.hist_min, self.hist_max, self.num_bins,
self.verbose, self.tolerance, self.max_iterations, self.temperature,
self.cyclic, self.uncorr, self.bootstrap, self.bootstrap_seed)
self.cyclic, self.uncorr, self.bootstrap, self.bootstrap_seed,
self.uncorr, self.start, self.end, self.convdt)
}
}
@@ -183,27 +186,40 @@ pub fn run(cfg: &Config) -> Result<()>{
println!("Supplied WHAM options: {}", &cfg);
println!("Reading input files.");
let dataset = io::read_data(&cfg).chain_err(|| "Failed to create histogram.")?;
println!("{}", &dataset);
let datasets = io::read_data(&cfg).chain_err(|| "Failed to read data.")?;
let (P, F, F_prev) = perform_wham(&cfg, &dataset)?;
println!("WHAM converged.");
for (idx, dataset) in datasets.iter().enumerate() {
if datasets.len() > 1 {
println!("Dataset {}/{}: {}", idx+1, datasets.len(), &dataset);
}
else {
println!("{}", &dataset);
}
let (P, F, F_prev) = perform_wham(&cfg, &dataset)?;
println!("WHAM converged.");
let (P_std, free_energy_std) = if cfg.bootstrap > 0 {
println!("Bootstrapping..");
error_analysis::run_bootstrap(&cfg, dataset.clone(), cfg.bootstrap)
} else {
(vec![0.0; P.len()], vec![0.0; P.len()])
};
let (P_std, free_energy_std) = if cfg.bootstrap > 0 {
println!("Bootstrapping..");
error_analysis::run_bootstrap(&cfg, dataset.clone(), cfg.bootstrap)
} else {
(vec![0.0; P.len()], 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, &P_std, &free_energy, &free_energy_std);
io::write_results(&cfg.output, &dataset, &free_energy, &free_energy_std, &P, &P_std)
.chain_err(|| "Could not write results to output file")?;
// calculate free energy and dump state
println!("Finished. Dumping PMF");
let free_energy = calc_free_energy(&dataset, &P);
dump_state(&dataset, &F, &F_prev, &P, &P_std, &free_energy, &free_energy_std);
let append = idx > 0 && datasets.len() > 1;
let index = if datasets.len() > 1 {
Some(idx)
} else {
None
};
io::write_results(&cfg.output, append, &dataset, &free_energy, &free_energy_std, &P, &P_std, index)
.chain_err(|| "Could not write results to output file")?;
}
Ok(())
}