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partial io for multidimensional WHAM

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This commit is contained in:
Daniel Bauer
2018-10-13 15:07:06 +02:00
parent 6450839c4a
commit 29d2dd2b03
4 changed files with 73 additions and 45 deletions
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75
src/io.rs
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@@ -29,7 +29,7 @@ pub fn vprintln(s: String, verbose: bool) {
// Read input data into a histogram set by iterating over input files
// given in the metadata file
pub fn read_data(cfg: &Config) -> Option<Dataset> {
let mut bias_x0: Vec<f64> = Vec::new();
let mut bias_pos: Vec<f64> = Vec::new();
let mut bias_fc: Vec<f64> = Vec::new();
let mut histograms: Vec<Histogram> = Vec::new();
let kT = cfg.temperature * k_B;
@@ -45,9 +45,11 @@ pub fn read_data(cfg: &Config) -> Option<Dataset> {
if line.starts_with("#") || line.len() == 0 {
continue;
}
let (path, x0, k) = scan_fmt!(&line, "{} {} {}", String, f64, f64);
let path = get_relative_path(&cfg.metadata_file, &path.unwrap());
let mut split = line.split_whitespace();
// parse histogram data
let path = get_relative_path(&cfg.metadata_file, split.next()?);
match read_window_file(&path, cfg) {
Some(h) => {
histograms.push(h);
@@ -55,25 +57,37 @@ pub fn read_data(cfg: &Config) -> Option<Dataset> {
},
None => {
eprintln!("No data points inside histogram boundaries: {}", &path);
continue; // goto next iteration and skip adding bias values
process::exit(1)
}
}
bias_x0.push(x0.unwrap_or_else(|| {
eprintln!("Failed to read coordinate from: {}", &line);
process::exit(1)
}));
bias_fc.push(k.unwrap_or_else(|| {
eprintln!("Failed to read bias value from: {}", &line);
process::exit(1)
}));
// parse bias force constants and positions
for _ in 0..cfg.dimens {
match split.next()?.parse() {
Ok(x) => bias_pos.push(x),
_ => {
eprintln!("Failed to read bias coordinate.");
process::exit(1);
}
}
}
for _ in 0..cfg.dimens {
match split.next()?.parse() {
Ok(x) => bias_fc.push(x),
_ => {
eprintln!("Failed to read bias force constant.");
process::exit(1);
}
}
}
}
if histograms.len() > 0 {
let bin_width = (cfg.hist_max - cfg.hist_min)/(cfg.num_bins as f64);
Some(Dataset::new(cfg.num_bins, bin_width, cfg.hist_min, cfg.hist_max, bias_x0, bias_fc, kT, histograms, cfg.cyclic))
let bin_width: Vec<f64> = (0..cfg.dimens).map(|idx| {
(cfg.hist_max[idx] - cfg.hist_min[idx])/(cfg.num_bins[idx] as f64)
}).collect();
Some(Dataset::new(cfg.num_bins[0], bin_width[0], cfg.hist_min[0], cfg.hist_max[0], bias_pos, bias_fc, kT, histograms, cfg.cyclic))
} else {
None
}
@@ -87,8 +101,8 @@ fn read_window_file(window_file: &str, cfg: &Config) -> Option<Histogram> {
});
let buf = BufReader::new(&f);
let mut global_hist = vec![0.0; cfg.num_bins];
let bin_width = (cfg.hist_max - cfg.hist_min)/(cfg.num_bins as f64);
let mut global_hist = vec![0.0; cfg.num_bins[0]];
let bin_width = (cfg.hist_max[0] - cfg.hist_min[0])/(cfg.num_bins[0] as f64);
for l in buf.lines() {
let line = l.unwrap();
// skip comments and empty lines
@@ -100,8 +114,8 @@ fn read_window_file(window_file: &str, cfg: &Config) -> Option<Histogram> {
match x {
Some(x) => {
if x > cfg.hist_min && x < cfg.hist_max {
let bin_ndx = ((x-cfg.hist_min) / bin_width) as usize;
if x > cfg.hist_min[0] && x < cfg.hist_max[0] {
let bin_ndx = ((x-cfg.hist_min[0]) / bin_width) as usize;
global_hist[bin_ndx] += 1.0;
}
}
@@ -113,7 +127,7 @@ fn read_window_file(window_file: &str, cfg: &Config) -> Option<Histogram> {
}
let mut max_bin: usize = 0;
let mut min_bin: usize =(cfg.num_bins-1) as usize;
let mut min_bin: usize =(cfg.num_bins[0]-1) as usize;
for bin in 0..global_hist.len() {
if global_hist[bin] != 0.0 && bin > max_bin {
max_bin = bin;
@@ -150,11 +164,12 @@ mod tests {
use super::*;
fn cfg() -> Config {
Config{
Config {
metadata_file: "tests/data/metadata.dat".to_string(),
hist_min: 0.0,
hist_max: 3.0,
num_bins: 30,
hist_min: vec![0.0],
hist_max: vec![3.0],
num_bins: vec![30],
dimens: 1,
verbose: false,
tolerance: 0.0,
max_iterations: 0,
@@ -187,13 +202,13 @@ mod tests {
let ds = ds.unwrap();
println!("{:?}", ds);
assert_eq!(2, ds.num_windows);
assert_eq!(cfg.num_bins, ds.num_bins);
assert_eq!(cfg.num_bins[0], ds.num_bins[0]);
// fields are private
// assert_eq!(cfg.hist_min, ds.hist_min);
// assert_eq!(cfg.hist_max, ds.hist_max);
// let expected_bin_width = (cfg.hist_max - cfg.hist_min)/cfg.num_bins as f64;
// assert_eq!(cfg.hist_min[0], ds.hist_min[0]);
// assert_eq!(cfg.hist_max[0], ds.hist_max[0]);
// let expected_bin_width = (cfg.hist_max[0] - cfg.hist_min[0])/cfg.num_bins[0] as f64;
// assert_eq!(expected_bin_width, ds.bin_width);
// assert_eq!(vec![0.0, 1.0], ds.bias_x0);
// assert_eq!(vec![0.0, 1.0], ds.bias_pos);
// assert_eq!(vec![100.0, 200.0], ds.bias_fc);
assert_eq!(cfg.temperature * k_B, ds.kT);
assert_eq!(2, ds.histograms.len())