From ec7024a285dc1d0e19001296fc19e04c77b1e9be Mon Sep 17 00:00:00 2001 From: Daniel Bauer Date: Thu, 22 Jul 2021 12:52:50 +0200 Subject: [PATCH] Squashed commit of the following: commit 07e5a0a1a5cef7b99ac8602fa39226ddce175b67 Author: Daniel Bauer Date: Thu Jul 22 12:48:35 2021 +0200 version up commit 4c58f5a42c091a480473809f8fdb5c4f361b8883 Author: Daniel Bauer Date: Thu Jul 22 12:22:01 2021 +0200 test convdt needs start/end commit fad1c0c4fca3cffe91db32c7e4d91139a6513a9f Author: Daniel Bauer Date: Thu Jul 22 12:14:21 2021 +0200 unit test for empty timeseries commit cdf520aad6e70ea22d96363d28c1110d3d5bc3e0 Author: Daniel Bauer Date: Thu Jul 22 11:51:12 2021 +0200 refractored convdt slices; fix issue with incomplete convdt slices commit 5b33d9cb61b59ead4a22f03ae3981175feb25770 Author: Daniel Bauer Date: Thu Jul 22 10:37:13 2021 +0200 test dataset for convdt commit 023bba0a0d46929b3ea4c2ede075b851deb7b779 Author: Daniel Bauer Date: Thu Jul 22 10:36:45 2021 +0200 force --start and --end with --convdt --- Cargo.lock | 2 +- Cargo.toml | 2 +- src/cli.yml | 4 +- src/io.rs | 227 +++++++----- src/main.rs | 5 + tests/cli.rs | 16 + tests/data/COLVAR_0-10.xvg | 500 ++++++++++++++++++++++++++ tests/data/COLVAR_0-2.xvg | 100 ++++++ tests/data/COLVAR_0-5.xvg | 250 +++++++++++++ tests/data/COLVAR_2-7.xvg | 250 +++++++++++++ tests/data/COLVAR_5-10.xvg | 250 +++++++++++++ tests/data/COLVAR_7-10.xvg | 150 ++++++++ tests/data/metadata_convdt.dat | 12 + tests/data/metadata_convdt_single.dat | 1 + 14 files changed, 1680 insertions(+), 89 deletions(-) create mode 100644 tests/data/COLVAR_0-10.xvg create mode 100644 tests/data/COLVAR_0-2.xvg create mode 100644 tests/data/COLVAR_0-5.xvg create mode 100644 tests/data/COLVAR_2-7.xvg create mode 100644 tests/data/COLVAR_5-10.xvg create mode 100644 tests/data/COLVAR_7-10.xvg create mode 100644 tests/data/metadata_convdt.dat create mode 100644 tests/data/metadata_convdt_single.dat diff --git a/Cargo.lock b/Cargo.lock index c7dea20..3671459 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -362,7 +362,7 @@ checksum = "cccddf32554fecc6acb585f82a32a72e28b48f8c4c1883ddfeeeaa96f7d8e519" [[package]] name = "wham" -version = "1.1.2" +version = "1.1.3" dependencies = [ "assert_approx_eq", "clap", diff --git a/Cargo.toml b/Cargo.toml index 058001a..9e4d419 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "wham" -version = "1.1.2" +version = "1.1.3" authors = ["Daniel Bauer "] description = "An implementation of the weighted histogram analysis method" license = "GPL-3.0" diff --git a/src/cli.yml b/src/cli.yml index 3cbe997..31c37f3 100644 --- a/src/cli.yml +++ b/src/cli.yml @@ -1,6 +1,6 @@ name: wham -version: "1.1.2" -author: D. Bauer +version: "1.1.3" +author: D. Bauer 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. diff --git a/src/io.rs b/src/io.rs index bef559f..e46d20e 100644 --- a/src/io.rs +++ b/src/io.rs @@ -32,10 +32,17 @@ pub fn vprintln(s: String, verbose: bool) { pub fn read_data(cfg: &Config) -> Result> { let mut bias_pos: Vec = Vec::new(); let mut bias_fc: Vec = Vec::new(); - let mut histograms: Vec> = Vec::new(); let mut timeseries_lengths: Vec = 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 = (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> { 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> { .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(×eries[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 = (0..timeseries[0].len()).map(|i| { is_in_time_boundaries(timeseries[0][i], *start, *stop) }).collect(); let hist = build_histogram_from_timeseries(×eries, ×eries_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 = (0..num_datasets).map(|idx| { - let mut dataset_histograms: Vec = 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 = 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> { } } -// 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>, 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 = 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 = 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 = (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(×eries, &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(×eries, &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 = (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(×eries, &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(×eries, &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(×eries, &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); } } \ No newline at end of file diff --git a/src/main.rs b/src/main.rs index aa8cff4..0e81f7a 100644 --- a/src/main.rs +++ b/src/main.rs @@ -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 { } 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.")?; diff --git a/tests/cli.rs b/tests/cli.rs index 1e3bb8e..879dfed 100644 --- a/tests/cli.rs +++ b/tests/cli.rs @@ -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" + )); + } + } \ No newline at end of file diff --git a/tests/data/COLVAR_0-10.xvg b/tests/data/COLVAR_0-10.xvg new file mode 100644 index 0000000..7801b2f --- /dev/null +++ b/tests/data/COLVAR_0-10.xvg @@ -0,0 +1,500 @@ +0.020000 -0.377860 +0.040000 0.010992 +0.060000 0.123074 +0.080000 0.108291 +0.100000 0.261607 +0.120000 0.185592 +0.140000 0.398266 +0.160000 0.461779 +0.180000 0.105976 +0.200000 0.214612 +0.220000 0.239492 +0.240000 0.320299 +0.260000 0.344827 +0.280000 0.223717 +0.300000 0.445152 +0.320000 0.487640 +0.340000 0.568231 +0.360000 0.264504 +0.380000 0.156700 +0.400000 0.339014 +0.420000 0.007749 +0.440000 -0.024582 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+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 \ No newline at end of file diff --git a/tests/data/metadata_convdt_single.dat b/tests/data/metadata_convdt_single.dat new file mode 100644 index 0000000..01f1a8d --- /dev/null +++ b/tests/data/metadata_convdt_single.dat @@ -0,0 +1 @@ +COLVAR_2-7.xvg 0.0 100