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Squashed commit of the following:

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commit 07e5a0a1a5cef7b99ac8602fa39226ddce175b67
Author: Daniel Bauer <bauer@cbs.tu-darmstadt.de>
Date:   Thu Jul 22 12:48:35 2021 +0200

    version up

commit 4c58f5a42c091a480473809f8fdb5c4f361b8883
Author: Daniel Bauer <bauer@cbs.tu-darmstadt.de>
Date:   Thu Jul 22 12:22:01 2021 +0200

    test convdt needs start/end

commit fad1c0c4fca3cffe91db32c7e4d91139a6513a9f
Author: Daniel Bauer <bauer@cbs.tu-darmstadt.de>
Date:   Thu Jul 22 12:14:21 2021 +0200

    unit test for empty timeseries

commit cdf520aad6e70ea22d96363d28c1110d3d5bc3e0
Author: Daniel Bauer <bauer@cbs.tu-darmstadt.de>
Date:   Thu Jul 22 11:51:12 2021 +0200

    refractored convdt slices; fix issue with incomplete convdt slices

commit 5b33d9cb61b59ead4a22f03ae3981175feb25770
Author: Daniel Bauer <bauer@cbs.tu-darmstadt.de>
Date:   Thu Jul 22 10:37:13 2021 +0200

    test dataset for convdt

commit 023bba0a0d46929b3ea4c2ede075b851deb7b779
Author: Daniel Bauer <bauer@cbs.tu-darmstadt.de>
Date:   Thu Jul 22 10:36:45 2021 +0200

    force --start and --end with --convdt
This commit is contained in:
Daniel Bauer
2021-07-22 12:52:50 +02:00
parent b6f338058a
commit ec7024a285
14 changed files with 1680 additions and 89 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
Cargo.lock generated
View File

@@ -362,7 +362,7 @@ checksum = "cccddf32554fecc6acb585f82a32a72e28b48f8c4c1883ddfeeeaa96f7d8e519"
[[package]]
name = "wham"
version = "1.1.2"
version = "1.1.3"
dependencies = [
"assert_approx_eq",
"clap",

2
Cargo.toml
View File

@@ -1,6 +1,6 @@
[package]
name = "wham"
version = "1.1.2"
version = "1.1.3"
authors = ["Daniel Bauer <bauer@cbs.tu-darmstadt.de>"]
description = "An implementation of the weighted histogram analysis method"
license = "GPL-3.0"

4
src/cli.yml
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@@ -1,6 +1,6 @@
name: wham
version: "1.1.2"
author: D. Bauer <bauer@cbs.tu-darmstadt.de>
version: "1.1.3"
author: D. Bauer <bauer@bio.tu-darmstadt.de>
about: |
wham is a fast implementation of the weighted histogram analysis method (WHAM) written in Rust. It currently supports potential of mean force (PMF) calculations in multiple dimensions at constant temperature.

227
src/io.rs
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@@ -32,10 +32,17 @@ pub fn vprintln(s: String, verbose: bool) {
pub fn read_data(cfg: &Config) -> Result<Vec<Dataset>> {
let mut bias_pos: Vec<f64> = Vec::new();
let mut bias_fc: Vec<f64> = Vec::new();
let mut histograms: Vec<Vec<Histogram>> = Vec::new();
let mut timeseries_lengths: Vec<usize> = Vec::new();
let mut paths = Vec::new();
// Boundaries of individual histograms if convdt is set.
let dataset_boundaries: Vec<(f64, f64)> = get_convdt_boundaries(cfg.start, cfg.end, cfg.convdt);
let num_datasets = dataset_boundaries.len();
// for each timeseries, histograms are build for slices according to
// start..convdt, start..2*convdt, ...
let mut histograms = vec![Vec::new(); dataset_boundaries.len()];
let kT = cfg.temperature * k_B;
let bin_width: Vec<f64> = (0..cfg.dimens).map(|idx| {
(cfg.hist_max[idx] - cfg.hist_min[idx])/(cfg.num_bins[idx] as f64)
@@ -46,7 +53,6 @@ pub fn read_data(cfg: &Config) -> Result<Vec<Dataset>> {
let f = File::open(&cfg.metadata_file).chain_err(|| "Failed to open metadata file")?;
let buf = BufReader::new(&f);
// read each metadata file line and parse it
for (line_num,l) in buf.lines().enumerate() {
let line = l.chain_err(|| "Failed to read line")?;
@@ -80,47 +86,39 @@ pub fn read_data(cfg: &Config) -> Result<Vec<Dataset>> {
.chain_err(|| format!("Failed to read time series from {}", &path))?;
timeseries_lengths.push(timeseries_initial_lengths);
// for each timeseries, histograms are build for slices according to
// start..convdt, start..2*convdt, ...
histograms.push(Vec::new());
let h_idx = histograms.len()-1;
let convdt_stops = get_convdt_boundaries(&timeseries[0], &cfg);
for (idx, interval) in convdt_stops.iter().enumerate() {
for (idx, interval) in dataset_boundaries.iter().enumerate() {
// build histogram for slice start.._stop
let (start, stop) = interval;
let timeseries_mask: Vec<bool> = (0..timeseries[0].len()).map(|i| {
is_in_time_boundaries(timeseries[0][i], *start, *stop)
}).collect();
let hist = build_histogram_from_timeseries(&timeseries, &timeseries_mask, cfg);
histograms[h_idx].push(hist);
histograms[idx].push(hist);
if (cfg.convdt == 0.00) || idx+1 == convdt_stops.len() {
vprintln(format!("{}, {} data points added.", &path,
histograms[h_idx].last().unwrap().num_points), cfg.verbose);
if (cfg.convdt == 0.00) || idx+1 == num_datasets {
vprintln(format!("{}, {} data points added.",
&path, histograms[idx].last().unwrap().num_points), cfg.verbose);
break
}
}
}
// Datasets are created from histograms.
// Empty histograms result in an error when its the final dataset,
// and a warning otherwise.
let num_datasets: usize = histograms.iter().map(|h| h.len()).max().unwrap();
let dataset_boundaries: Vec<(f64, f64)> = (0..num_datasets).map(|idx| {
(cfg.start, cfg.start+(idx as f64 + 1.0)*cfg.convdt) }
).collect();
// Empty histograms result in an error when its the final dataset, and a warning otherwise.
vprintln(format!("Generating {} datasets from histograms.", num_datasets), cfg.verbose);
let datasets: Vec<Dataset> = (0..num_datasets).map(|idx| {
let mut dataset_histograms: Vec<Histogram> = Vec::with_capacity(histograms.len());
for (hs, path) in histograms.iter().zip(&paths) {
if hs.len() > idx {
dataset_histograms.push(hs[idx].clone())
} else {
let datasets: Vec<Dataset> = histograms.into_iter().enumerate().map(|(dataset_idx, dataset_histograms)| {
for (hs, path) in dataset_histograms.iter().zip(&paths) {
if hs.num_points == 0 {
let warning = format!("No data points for interval {}-{} in histogram boundaries: {}.",
dataset_boundaries[idx].0, dataset_boundaries[idx].1 ,&path);
if !cfg.ignore_empty && idx+1 == num_datasets {
bail!(warning + " This is the final dataset.");
dataset_boundaries[dataset_idx].0, dataset_boundaries[dataset_idx].1 ,&path);
if dataset_idx+1 == num_datasets {
let warning = warning + " This is the final dataset.";
if cfg.ignore_empty {
eprintln!("{}", warning);
} else {
bail!(warning);
}
} else {
eprintln!("{}", warning);
}
@@ -167,23 +165,20 @@ pub fn read_data(cfg: &Config) -> Result<Vec<Dataset>> {
}
}
// builds a time boundaries for datasets from convdt, timeseries start and end
fn get_convdt_boundaries(timeseries: &[f64], cfg: &Config) -> Vec<(f64, f64)> {
let mut last_timestep = *timeseries.last().unwrap();
if last_timestep > cfg.end {
last_timestep = cfg.end;
}
let mut first_timestep = *timeseries.first().unwrap();
if first_timestep < cfg.start {
first_timestep = cfg.start;
}
if cfg.convdt == 0.0 {
vec![(0.0, last_timestep)]
// builds a time boundaries for datasets from convdt, start and end
fn get_convdt_boundaries(start: f64, end: f64, convdt: f64) -> Vec<(f64, f64)> {
if convdt == 0.0 {
vec![(start, end)]
} else {
let intervals: usize = ((last_timestep - first_timestep) / cfg.convdt).ceil() as usize;
let intervals: usize = ((end - start) / convdt).ceil() as usize;
(1..intervals+1).map(|i| {
i as f64 * cfg.convdt + first_timestep
}).map(|end| { (first_timestep, end) }).collect()
let interval_end = i as f64 * convdt + start;
if interval_end > end {
end
} else {
interval_end
}
}).map(|interval_end| { (start, interval_end) }).collect()
}
}
@@ -273,7 +268,7 @@ fn read_window_file(window_file: &str, cfg: &Config) -> Result<(Vec<Vec<f64>>, u
timeseries = uncorrelate(timeseries, cfg);
}
if timeseries[0].is_empty() {
if timeseries[0].is_empty() && !cfg.ignore_empty {
bail!("Time series is empty")
}
@@ -465,6 +460,99 @@ mod tests {
assert_eq!(25, ds.histograms.len())
}
#[test]
fn read_data_empty() {
let mut cfg = cfg();
cfg.metadata_file = "tests/data/metadata_convdt.dat".to_string();
cfg.start = 2.5;
cfg.end = 9.0;
cfg.ignore_empty = false;
// should throw an error since one first timeseries ends at 2
let ds = super::read_data(&cfg);
if ds.is_ok() {
panic!()
}
// should not throw an error because ignore_empty is set
cfg.ignore_empty = true;
let ds = super::read_data(&cfg);
if ds.is_err() {
panic!()
}
}
// test if convdt results in correct parsing
// 6 timeseries are loaded ranging from:
// 1. 0-10, 500 datapoints
// 2. 0-2, 100 datapoints
// 3. 0-5, 250 datapoints
// 4. 5-10, 250 datapoints
// 5. 7-10, 150 datapoints
// 6 2-7, 250 datapoints
#[test]
fn read_data_convdt() {
let mut cfg = cfg();
cfg.metadata_file = "tests/data/metadata_convdt.dat".to_string();
cfg.convdt = 2.0;
cfg.start = 0.0;
cfg.end = 9.0;
let dss = super::read_data(&cfg).unwrap();
assert_eq!(5, dss.len());
for ds in &dss {
assert_eq!(6, ds.num_windows);
assert_eq!(6, ds.histograms.len());
}
let hist_points: Vec<u32> = dss.iter().map(|ds| {
ds.histograms.iter().map(|h| h.num_points).sum()
}).collect();
let expected_hist_points = vec![
300, // 0-2: 100+100+100+0+0
600, // 0-4: 200+100+200+0+0+100
900, // 0-6: 300+100+250+50+0+200
1200, // 0-8: 400+100+250+150+50+250
1350, // 0-9: 450+100+250+200+100+250
];
for (expected, actual) in expected_hist_points.iter().zip(hist_points.iter()) {
assert_eq!(expected, actual);
}
}
// test convdt with a single time series
#[test]
fn read_data_convdt_single() {
let mut cfg = cfg();
cfg.metadata_file = "tests/data/metadata_convdt_single.dat".to_string();
cfg.convdt = 2.0;
cfg.start = 0.0;
cfg.end = 9.0;
let dss = super::read_data(&cfg).unwrap();
assert_eq!(5, dss.len());
for ds in &dss {
assert_eq!(1, ds.num_windows);
assert_eq!(1, ds.histograms.len());
}
let hist_points: Vec<u32> = dss.iter().map(|ds| {
ds.histograms.iter().map(|h| h.num_points).sum()
}).collect();
let expected_hist_points = vec![
0, // 0-2
100, // 0-4
200, // 0-6
250, // 0-8
250, // 0-9
];
for (expected, actual) in expected_hist_points.iter().zip(hist_points.iter()) {
assert_eq!(expected, actual);
}
}
#[test]
fn get_relative_path() {
let path1 = "path/to/some_file.dat";
@@ -489,24 +577,13 @@ mod tests {
#[test]
fn get_convdt_boundaries() {
let mut cfg = cfg();
let timeseries: Vec<f64> = (0..31).map(|i| i as f64).collect();
println!("{:?}", timeseries);
cfg.start = 10.0;
cfg.end = 20.0;
cfg.convdt = 10.0;
let test = super::get_convdt_boundaries(&timeseries, &cfg);
let test = super::get_convdt_boundaries(10.0, 20.0, 10.0);
println!("{:?}", test);
assert!(test.len() == 1);
assert_approx_eq!(test[0].0, 10.0);
assert_approx_eq!(test[0].1, 20.0);
cfg.start = 10.0;
cfg.end = 20.0;
cfg.convdt = 5.0;
let test = super::get_convdt_boundaries(&timeseries, &cfg);
let test = super::get_convdt_boundaries(10.0, 20.0, 5.0);
println!("{:?}", test);
assert!(test.len() == 2);
assert_approx_eq!(test[0].0, 10.0);
@@ -514,34 +591,14 @@ mod tests {
assert_approx_eq!(test[1].0, 10.0);
assert_approx_eq!(test[1].1, 20.0);
let timeseries: Vec<f64> = (10..21).map(|i| i as f64).collect();
println!("{:?}", timeseries);
cfg.start = 10.0;
cfg.end = 20.0;
cfg.convdt = 10.0;
let test = super::get_convdt_boundaries(&timeseries, &cfg);
let test = super::get_convdt_boundaries(5.0, 30.0, 10.0);
println!("{:?}", test);
assert!(test.len() == 1);
assert_approx_eq!(test[0].0, 10.0);
assert_approx_eq!(test[0].1, 20.0);
cfg.start = 5.0;
cfg.end = 20.0;
cfg.convdt = 10.0;
let test = super::get_convdt_boundaries(&timeseries, &cfg);
println!("{:?}", test);
assert!(test.len() == 1);
assert_approx_eq!(test[0].0, 10.0);
assert_approx_eq!(test[0].1, 20.0);
cfg.start = 5.0;
cfg.end = 30.0;
cfg.convdt = 10.0;
let test = super::get_convdt_boundaries(&timeseries, &cfg);
println!("{:?}", test);
assert!(test.len() == 1);
assert_approx_eq!(test[0].0, 10.0);
assert_approx_eq!(test[0].1, 20.0);
assert!(test.len() == 3);
assert_approx_eq!(test[0].0, 5.0);
assert_approx_eq!(test[0].1, 15.0);
assert_approx_eq!(test[1].0, 5.0);
assert_approx_eq!(test[1].1, 25.0);
assert_approx_eq!(test[2].0, 5.0);
assert_approx_eq!(test[2].1, 30.0);
}
}

5
src/main.rs
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@@ -2,6 +2,8 @@ extern crate wham;
#[macro_use]
extern crate clap;
extern crate rand;
#[macro_use]
extern crate error_chain;
use rand::prelude::*;
use clap::App;
@@ -68,6 +70,9 @@ fn cli() -> Result<Config> {
}
let dimens = num_bins.len();
if matches.is_present("convdt") && (!matches.is_present("start") || !matches.is_present("end")) {
bail!("--convdt requires --start and --end to be set.")
}
let convdt: f64 = matches.value_of("convdt").unwrap_or("0").parse()
.chain_err(|| "Cannot parse convdt.")?;

16
tests/cli.rs
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@@ -108,4 +108,20 @@ mod integration {
));
}
#[test]
fn convdt_needs_start_end() {
let output = get_command()
.args(&["--bins", "100", "--min", "-3.0", "--max", "3.0", "-T", "300"])
.args(&["-f", "tests/data/metadata_unparseable1.dat"])
.args(&["-o", "/dev/null"])
.args(&["--convdt", "100"])
.output()
.expect("failed to execute process");
let output = String::from_utf8_lossy(&output.stderr);
println!("{}", output);
assert!(output.to_string().contains(
"--convdt requires --start and --end to be set"
));
}
}

500
tests/data/COLVAR_0-10.xvg Normal file
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tests/data/metadata_convdt.dat Normal file
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# 500 pts
COLVAR_0-10.xvg 0.0 100
# 100 pts
COLVAR_0-2.xvg 0.0 100
# 250 pts
COLVAR_0-5.xvg 0.0 100
# 250 pts
COLVAR_5-10.xvg 0.0 100
# 150 pts
COLVAR_7-10.xvg 0.0 100
# 250 pts
COLVAR_2-7.xvg 0.0 100

1
tests/data/metadata_convdt_single.dat Normal file
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COLVAR_2-7.xvg 0.0 100