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Compare commits
7 Commits
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2
Cargo.lock
generated
2
Cargo.lock
generated
@@ -362,7 +362,7 @@ checksum = "cccddf32554fecc6acb585f82a32a72e28b48f8c4c1883ddfeeeaa96f7d8e519"
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[[package]]
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name = "wham"
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version = "1.1.0"
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version = "1.1.2"
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dependencies = [
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"assert_approx_eq",
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"clap",
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@@ -1,6 +1,6 @@
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[package]
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name = "wham"
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version = "1.1.0"
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version = "1.1.2"
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authors = ["Daniel Bauer <bauer@cbs.tu-darmstadt.de>"]
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description = "An implementation of the weighted histogram analysis method"
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license = "GPL-3.0"
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@@ -1,101 +1,101 @@
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#coord1 Free Energy +/- Probability +/-
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101
example/1d_cyclic/wham_bt.out
Normal file
101
example/1d_cyclic/wham_bt.out
Normal file
@@ -0,0 +1,101 @@
|
||||
#coord1 Free Energy +/- Probability +/-
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|
||||
0.031416 35.561946 0.118225 0.000000 0.000000
|
||||
0.094248 35.382089 0.108652 0.000000 0.000000
|
||||
0.157080 34.934827 0.118384 0.000000 0.000000
|
||||
0.219911 33.673460 0.119195 0.000000 0.000000
|
||||
0.282743 32.731563 0.121592 0.000000 0.000000
|
||||
0.345575 31.261855 0.129698 0.000000 0.000000
|
||||
0.408407 29.717377 0.139789 0.000000 0.000000
|
||||
0.471239 28.076620 0.137289 0.000001 0.000000
|
||||
0.534071 26.481097 0.135712 0.000002 0.000000
|
||||
0.596903 24.487358 0.135156 0.000003 0.000000
|
||||
0.659734 22.344251 0.131027 0.000008 0.000000
|
||||
0.722566 20.241543 0.133145 0.000018 0.000001
|
||||
0.785398 18.341869 0.131952 0.000039 0.000002
|
||||
0.848230 16.261582 0.134676 0.000091 0.000006
|
||||
0.911062 14.301801 0.134417 0.000199 0.000013
|
||||
0.973894 12.603788 0.131018 0.000394 0.000024
|
||||
1.036726 11.249601 0.131276 0.000678 0.000043
|
||||
1.099557 10.087886 0.132498 0.001079 0.000070
|
||||
1.162389 9.443303 0.132990 0.001398 0.000092
|
||||
1.225221 9.152799 0.132250 0.001570 0.000104
|
||||
1.288053 9.331937 0.133178 0.001462 0.000099
|
||||
1.350885 9.905546 0.133357 0.001161 0.000078
|
||||
1.413717 11.042050 0.133807 0.000736 0.000051
|
||||
1.476549 12.598167 0.132722 0.000395 0.000027
|
||||
1.539380 14.520167 0.131816 0.000183 0.000012
|
||||
1.602212 16.569783 0.131773 0.000080 0.000005
|
||||
1.665044 18.687390 0.132601 0.000034 0.000002
|
||||
1.727876 20.775408 0.133867 0.000015 0.000001
|
||||
1.790708 22.905200 0.129265 0.000006 0.000000
|
||||
1.853540 24.643852 0.128894 0.000003 0.000000
|
||||
1.916372 26.301740 0.130266 0.000002 0.000000
|
||||
1.979203 27.372071 0.128620 0.000001 0.000000
|
||||
2.042035 28.697726 0.133263 0.000001 0.000000
|
||||
2.104867 29.417901 0.133513 0.000000 0.000000
|
||||
2.167699 30.008351 0.130925 0.000000 0.000000
|
||||
2.230531 30.406016 0.124398 0.000000 0.000000
|
||||
2.293363 30.171275 0.122493 0.000000 0.000000
|
||||
2.356194 29.884646 0.130278 0.000000 0.000000
|
||||
2.419026 29.428153 0.130844 0.000000 0.000000
|
||||
2.481858 28.546982 0.148114 0.000001 0.000000
|
||||
2.544690 27.757520 0.133045 0.000001 0.000000
|
||||
2.607522 26.505787 0.134364 0.000001 0.000000
|
||||
2.670354 24.491866 0.115061 0.000003 0.000000
|
||||
2.733186 22.320664 0.110036 0.000008 0.000000
|
||||
2.796017 20.052723 0.107894 0.000020 0.000001
|
||||
2.858849 17.655650 0.105964 0.000052 0.000002
|
||||
2.921681 15.471590 0.107005 0.000125 0.000005
|
||||
2.984513 13.138167 0.099378 0.000318 0.000012
|
||||
3.047345 11.092386 0.087770 0.000722 0.000022
|
||||
3.110177 9.065722 0.077092 0.001626 0.000038
|
||||
@@ -1,5 +1,5 @@
|
||||
name: wham
|
||||
version: "1.1.0"
|
||||
version: "1.1.2"
|
||||
author: D. Bauer <bauer@cbs.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.
|
||||
@@ -112,3 +112,8 @@ args:
|
||||
help: "Performs WHAM for slices with the given delta in time and returns an output file for each slice. THis is useful to check the result for convergence. Example: with --convdt 100 and a timeseries ranging from 0-300, free energy surfaces for slices 0-100, 0-200 and 0-300 will be given returned."
|
||||
takes_value: true
|
||||
required: false
|
||||
- ignore_empty:
|
||||
long: ignore_empty
|
||||
help: If this is set, do not fail if a histogram is empty.
|
||||
takes_value: false
|
||||
required: false
|
||||
|
||||
20
src/io.rs
20
src/io.rs
@@ -103,19 +103,24 @@ pub fn read_data(cfg: &Config) -> Result<Vec<Dataset>> {
|
||||
}
|
||||
}
|
||||
|
||||
// Histograms are stored as timeseries x convdt right now,
|
||||
// but we need convdt x timeseries to create Datasets
|
||||
// this transposes the data
|
||||
// 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();
|
||||
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 warning = format!("No data points in histogram boundaries: {}", &path);
|
||||
if idx+1 == num_datasets {
|
||||
bail!(warning);
|
||||
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.");
|
||||
} else {
|
||||
eprintln!("{}", warning);
|
||||
}
|
||||
@@ -172,12 +177,10 @@ fn get_convdt_boundaries(timeseries: &[f64], cfg: &Config) -> Vec<(f64, f64)> {
|
||||
if first_timestep < cfg.start {
|
||||
first_timestep = cfg.start;
|
||||
}
|
||||
println!("{} to {} with dt={}", first_timestep, last_timestep, cfg.convdt);
|
||||
if cfg.convdt == 0.0 {
|
||||
vec![(0.0, last_timestep)]
|
||||
} else {
|
||||
let intervals: usize = ((last_timestep - first_timestep) / cfg.convdt).ceil() as usize;
|
||||
println!("{:?}", intervals);
|
||||
(1..intervals+1).map(|i| {
|
||||
i as f64 * cfg.convdt + first_timestep
|
||||
}).map(|end| { (first_timestep, end) }).collect()
|
||||
@@ -407,6 +410,7 @@ mod tests {
|
||||
end: 1e+20,
|
||||
uncorr: false,
|
||||
convdt: 0.0,
|
||||
ignore_empty: false,
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@@ -48,6 +48,7 @@ pub struct Config {
|
||||
pub end: f64,
|
||||
pub uncorr: bool,
|
||||
pub convdt: f64,
|
||||
pub ignore_empty: bool
|
||||
}
|
||||
|
||||
impl fmt::Display for Config {
|
||||
@@ -55,11 +56,11 @@ impl fmt::Display for Config {
|
||||
write!(f, "Metadata={}, hist_min={:?}, hist_max={:?}, bins={:?},
|
||||
verbose={}, tolerance={}, iterations={}, temperature={},
|
||||
cyclic={:?}, uncorr={:?}, bootstrap={:?}, seed={:?},
|
||||
uncorr={:?}, start={:?}, end={:?}, convdt={:?}",
|
||||
uncorr={:?}, start={:?}, end={:?}, convdt={:?}, ignore_empty={:?}",
|
||||
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.uncorr, self.start, self.end, self.convdt)
|
||||
self.uncorr, self.start, self.end, self.convdt, self.ignore_empty)
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@@ -71,9 +71,11 @@ fn cli() -> Result<Config> {
|
||||
let convdt: f64 = matches.value_of("convdt").unwrap_or("0").parse()
|
||||
.chain_err(|| "Cannot parse convdt.")?;
|
||||
|
||||
let ignore_empty: bool = matches.is_present("ignore_empty");
|
||||
|
||||
Ok(wham::Config{metadata_file, hist_min, hist_max, num_bins, dimens,
|
||||
verbose, tolerance, max_iterations, temperature, cyclic, output,
|
||||
bootstrap, bootstrap_seed, start, end, uncorr, convdt})
|
||||
bootstrap, bootstrap_seed, start, end, uncorr, convdt, ignore_empty})
|
||||
}
|
||||
|
||||
fn main() {
|
||||
|
||||
@@ -6,64 +6,154 @@ mod integration {
|
||||
use std::process::Command;
|
||||
use std::fs;
|
||||
use super::command::get_command;
|
||||
use std::fs::OpenOptions;
|
||||
use std::io::prelude::*;
|
||||
|
||||
#[test]
|
||||
fn wham_1d_cyclic() {
|
||||
let output_file = "/tmp/wham_test_1d_cyclic.out";
|
||||
get_command()
|
||||
.args(&["--bins", "100", "--max", "pi", "--min", "-pi", "-T", "300", "--cyclic"])
|
||||
.args(&["--bt", "100", "--seed", "1234"])
|
||||
.args(&["--seed", "1234"])
|
||||
.args(&["-f", "example/1d_cyclic/metadata.dat"])
|
||||
.args(&["-o", "/tmp/wham_test_1d_cyclic.out"])
|
||||
.args(&["-o", output_file])
|
||||
.output()
|
||||
.expect("failed to execute process");
|
||||
|
||||
assert!(fs::metadata("/tmp/wham_test_1d_cyclic.out").is_ok());
|
||||
assert!(fs::metadata(output_file).is_ok());
|
||||
let output = Command::new("diff")
|
||||
.arg("/tmp/wham_test_1d_cyclic.out")
|
||||
.arg(output_file)
|
||||
.arg("example/1d_cyclic/wham.out")
|
||||
.output()
|
||||
.expect("failed to run diff");
|
||||
let output_len = String::from_utf8_lossy(&output.stdout).len();
|
||||
assert_eq!(output_len, 0);
|
||||
std::fs::remove_file(output_file).unwrap();
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn wham_1d_cyclic_uncorrelated() {
|
||||
let output_file = "/tmp/wham_test_1d_cyclic.out";
|
||||
get_command()
|
||||
.args(&["--bins", "100", "--max", "pi", "--min", "-pi", "-T", "300", "--cyclic", "--uncorr"])
|
||||
.args(&["--seed", "1234"])
|
||||
.args(&["-f", "example/1d_cyclic/metadata.dat"])
|
||||
.args(&["-o", "/tmp/wham_test_1d_cyclic.out"])
|
||||
.args(&["-o", output_file])
|
||||
.output()
|
||||
.expect("failed to execute process");
|
||||
|
||||
assert!(fs::metadata("/tmp/wham_test_1d_cyclic.out").is_ok());
|
||||
let output = Command::new("diff")
|
||||
.arg("/tmp/wham_test_1d_cyclic.out")
|
||||
.arg(output_file)
|
||||
.arg("example/1d_cyclic/wham_uncorrelated.out")
|
||||
.output()
|
||||
.expect("failed to run diff");
|
||||
let output_len = String::from_utf8_lossy(&output.stdout).len();
|
||||
assert_eq!(output_len, 0);
|
||||
std::fs::remove_file(output_file).unwrap();
|
||||
}
|
||||
|
||||
#[test]
|
||||
// Test if convdt runs have the same result as normal runs
|
||||
fn wham_convdt() {
|
||||
// run wham with convdt
|
||||
let output_file = "/tmp/wham_test_convdt.out";
|
||||
get_command()
|
||||
.args(&["--bins", "10", "--max", "pi", "--min", "-pi", "-T", "300", "--cyclic"])
|
||||
.args(&["--seed", "1234", "--tolerance", "0.001"])
|
||||
.args(&["--start", "0", "--end", "10"])
|
||||
.args(&["--convdt", "1"])
|
||||
.args(&["-f", "example/1d_cyclic/metadata.dat"])
|
||||
.args(&["-o", output_file])
|
||||
.output()
|
||||
.expect("failed to execute process");
|
||||
assert!(fs::metadata(output_file).is_ok());
|
||||
|
||||
// run wham for individual sets
|
||||
for i in 1..11 {
|
||||
let output_file_single = format!("/tmp/wham_test_convdt_{}.out", i);
|
||||
get_command()
|
||||
.args(&["--bins", "10", "--max", "pi", "--min", "-pi", "-T", "300", "--cyclic"])
|
||||
.args(&["--seed", "1234", "--tolerance", "0.001"])
|
||||
.args(&["--start", "0", "--end", &i.to_string()])
|
||||
.args(&["-f", "example/1d_cyclic/metadata.dat"])
|
||||
.args(&["-o", &output_file_single])
|
||||
.output()
|
||||
.expect("failed to execute process");
|
||||
assert!(fs::metadata(output_file_single).is_ok());
|
||||
}
|
||||
|
||||
// combine individual runs
|
||||
let output_combined = "/tmp/wham_test_convdt_combined.out";
|
||||
let mut file = OpenOptions::new()
|
||||
.create(true)
|
||||
.write(true)
|
||||
.open(output_combined)
|
||||
.unwrap();
|
||||
for i in 1..11 {
|
||||
let output_file_single = format!("/tmp/wham_test_convdt_{}.out", i);
|
||||
println!("{}", output_file_single);
|
||||
file.write_all(format!("#Dataset {}\n", i-1).as_bytes()).unwrap();
|
||||
file.write_all(fs::read_to_string(output_file_single.clone()).unwrap().as_bytes()).unwrap();
|
||||
std::fs::remove_file(output_file_single).unwrap();
|
||||
}
|
||||
|
||||
// compare combined runs with single run
|
||||
let output = Command::new("diff")
|
||||
.arg(output_file)
|
||||
.arg(output_combined)
|
||||
.output()
|
||||
.expect("failed to run diff");
|
||||
let output_len = String::from_utf8_lossy(&output.stdout).len();
|
||||
assert_eq!(output_len, 0);
|
||||
|
||||
std::fs::remove_file(output_combined).unwrap();
|
||||
std::fs::remove_file(output_file).unwrap();
|
||||
|
||||
}
|
||||
|
||||
#[test]
|
||||
#[ignore]
|
||||
fn wham_1d_cyclic_bootstrap() {
|
||||
let output_file = "/tmp/wham_test_1d_cyclic_bt.out";
|
||||
get_command()
|
||||
.args(&["--bins", "100", "--max", "pi", "--min", "-pi", "-T", "300", "--cyclic"])
|
||||
.args(&["--seed", "1234", "--bt", "100"])
|
||||
.args(&["-f", "example/1d_cyclic/metadata.dat"])
|
||||
.args(&["-o", output_file])
|
||||
.output()
|
||||
.expect("failed to execute process");
|
||||
|
||||
assert!(fs::metadata(output_file).is_ok());
|
||||
let output = Command::new("diff")
|
||||
.arg(output_file)
|
||||
.arg("example/1d_cyclic/wham_bt.out")
|
||||
.output()
|
||||
.expect("failed to run diff");
|
||||
let output_len = String::from_utf8_lossy(&output.stdout).len();
|
||||
assert_eq!(output_len, 0);
|
||||
std::fs::remove_file(output_file).unwrap();
|
||||
}
|
||||
|
||||
#[test]
|
||||
#[ignore] // expensive
|
||||
fn wham_2d_cyclic() {
|
||||
let output_file = "/tmp/wham_test_2d_cyclic.out";
|
||||
get_command()
|
||||
.args(&["--bins", "100,100", "--max", "pi,pi", "--min", "-pi,-pi", "-T", "300", "--cyclic"])
|
||||
.args(&["-f", "example/2d_cyclic/metadata.dat"])
|
||||
.args(&["-o", "/tmp/wham_test_2d_cyclic.out"])
|
||||
.args(&["-o", output_file])
|
||||
.output()
|
||||
.expect("failed to execute process");
|
||||
|
||||
assert!(fs::metadata("/tmp/wham_test_2d_cyclic.out").is_ok());
|
||||
assert!(fs::metadata(output_file).is_ok());
|
||||
let output = Command::new("diff")
|
||||
.arg("/tmp/wham_test_2d_cyclic.out")
|
||||
.arg(output_file)
|
||||
.arg("example/2d_cyclic/wham.out")
|
||||
.output()
|
||||
.expect("failed to run diff");
|
||||
let output_len = String::from_utf8_lossy(&output.stdout).len();
|
||||
assert_eq!(output_len, 0);
|
||||
std::fs::remove_file(output_file).unwrap();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user