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bootstrapping

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This commit is contained in:
Daniel Bauer
2018-11-12 15:16:06 +01:00
parent b86a9df7fb
commit fc776fd40e
12 changed files with 20449 additions and 10133 deletions
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78
Cargo.lock generated
View File

@@ -1,3 +1,13 @@
[[package]]
name = "GSL"
version = "1.0.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
dependencies = [
"c_vec 1.0.12 (registry+https://github.com/rust-lang/crates.io-index)",
"libc 0.2.43 (registry+https://github.com/rust-lang/crates.io-index)",
"pkg-config 0.3.14 (registry+https://github.com/rust-lang/crates.io-index)",
]
[[package]]
name = "ansi_term"
version = "0.11.0"
@@ -42,6 +52,11 @@ name = "bitflags"
version = "1.0.4"
source = "registry+https://github.com/rust-lang/crates.io-index"
[[package]]
name = "c_vec"
version = "1.0.12"
source = "registry+https://github.com/rust-lang/crates.io-index"
[[package]]
name = "cc"
version = "1.0.25"
@@ -67,6 +82,14 @@ dependencies = [
"yaml-rust 0.3.5 (registry+https://github.com/rust-lang/crates.io-index)",
]
[[package]]
name = "cloudabi"
version = "0.0.3"
source = "registry+https://github.com/rust-lang/crates.io-index"
dependencies = [
"bitflags 1.0.4 (registry+https://github.com/rust-lang/crates.io-index)",
]
[[package]]
name = "error-chain"
version = "0.12.0"
@@ -75,11 +98,55 @@ dependencies = [
"backtrace 0.3.9 (registry+https://github.com/rust-lang/crates.io-index)",
]
[[package]]
name = "fuchsia-zircon"
version = "0.3.3"
source = "registry+https://github.com/rust-lang/crates.io-index"
dependencies = [
"bitflags 1.0.4 (registry+https://github.com/rust-lang/crates.io-index)",
"fuchsia-zircon-sys 0.3.3 (registry+https://github.com/rust-lang/crates.io-index)",
]
[[package]]
name = "fuchsia-zircon-sys"
version = "0.3.3"
source = "registry+https://github.com/rust-lang/crates.io-index"
[[package]]
name = "libc"
version = "0.2.43"
source = "registry+https://github.com/rust-lang/crates.io-index"
[[package]]
name = "pkg-config"
version = "0.3.14"
source = "registry+https://github.com/rust-lang/crates.io-index"
[[package]]
name = "rand"
version = "0.5.5"
source = "registry+https://github.com/rust-lang/crates.io-index"
dependencies = [
"cloudabi 0.0.3 (registry+https://github.com/rust-lang/crates.io-index)",
"fuchsia-zircon 0.3.3 (registry+https://github.com/rust-lang/crates.io-index)",
"libc 0.2.43 (registry+https://github.com/rust-lang/crates.io-index)",
"rand_core 0.2.2 (registry+https://github.com/rust-lang/crates.io-index)",
"winapi 0.3.6 (registry+https://github.com/rust-lang/crates.io-index)",
]
[[package]]
name = "rand_core"
version = "0.2.2"
source = "registry+https://github.com/rust-lang/crates.io-index"
dependencies = [
"rand_core 0.3.0 (registry+https://github.com/rust-lang/crates.io-index)",
]
[[package]]
name = "rand_core"
version = "0.3.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
[[package]]
name = "redox_syscall"
version = "0.1.40"
@@ -135,8 +202,10 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
name = "wham"
version = "0.9.0"
dependencies = [
"GSL 1.0.0 (registry+https://github.com/rust-lang/crates.io-index)",
"clap 2.32.0 (registry+https://github.com/rust-lang/crates.io-index)",
"error-chain 0.12.0 (registry+https://github.com/rust-lang/crates.io-index)",
"rand 0.5.5 (registry+https://github.com/rust-lang/crates.io-index)",
]
[[package]]
@@ -164,16 +233,25 @@ version = "0.3.5"
source = "registry+https://github.com/rust-lang/crates.io-index"
[metadata]
"checksum GSL 1.0.0 (registry+https://github.com/rust-lang/crates.io-index)" = "2e70167131757876cda6ab95869b57ad6b55c627ff28421f5935f55f9b97d85c"
"checksum ansi_term 0.11.0 (registry+https://github.com/rust-lang/crates.io-index)" = "ee49baf6cb617b853aa8d93bf420db2383fab46d314482ca2803b40d5fde979b"
"checksum atty 0.2.11 (registry+https://github.com/rust-lang/crates.io-index)" = "9a7d5b8723950951411ee34d271d99dddcc2035a16ab25310ea2c8cfd4369652"
"checksum backtrace 0.3.9 (registry+https://github.com/rust-lang/crates.io-index)" = "89a47830402e9981c5c41223151efcced65a0510c13097c769cede7efb34782a"
"checksum backtrace-sys 0.1.24 (registry+https://github.com/rust-lang/crates.io-index)" = "c66d56ac8dabd07f6aacdaf633f4b8262f5b3601a810a0dcddffd5c22c69daa0"
"checksum bitflags 1.0.4 (registry+https://github.com/rust-lang/crates.io-index)" = "228047a76f468627ca71776ecdebd732a3423081fcf5125585bcd7c49886ce12"
"checksum c_vec 1.0.12 (registry+https://github.com/rust-lang/crates.io-index)" = "aa9e1d9f7d49e289f36f19effbf3d5a5e30163ecf9c7a3c9be94d5374dec5b9a"
"checksum cc 1.0.25 (registry+https://github.com/rust-lang/crates.io-index)" = "f159dfd43363c4d08055a07703eb7a3406b0dac4d0584d96965a3262db3c9d16"
"checksum cfg-if 0.1.6 (registry+https://github.com/rust-lang/crates.io-index)" = "082bb9b28e00d3c9d39cc03e64ce4cea0f1bb9b3fde493f0cbc008472d22bdf4"
"checksum clap 2.32.0 (registry+https://github.com/rust-lang/crates.io-index)" = "b957d88f4b6a63b9d70d5f454ac8011819c6efa7727858f458ab71c756ce2d3e"
"checksum cloudabi 0.0.3 (registry+https://github.com/rust-lang/crates.io-index)" = "ddfc5b9aa5d4507acaf872de71051dfd0e309860e88966e1051e462a077aac4f"
"checksum error-chain 0.12.0 (registry+https://github.com/rust-lang/crates.io-index)" = "07e791d3be96241c77c43846b665ef1384606da2cd2a48730abe606a12906e02"
"checksum fuchsia-zircon 0.3.3 (registry+https://github.com/rust-lang/crates.io-index)" = "2e9763c69ebaae630ba35f74888db465e49e259ba1bc0eda7d06f4a067615d82"
"checksum fuchsia-zircon-sys 0.3.3 (registry+https://github.com/rust-lang/crates.io-index)" = "3dcaa9ae7725d12cdb85b3ad99a434db70b468c09ded17e012d86b5c1010f7a7"
"checksum libc 0.2.43 (registry+https://github.com/rust-lang/crates.io-index)" = "76e3a3ef172f1a0b9a9ff0dd1491ae5e6c948b94479a3021819ba7d860c8645d"
"checksum pkg-config 0.3.14 (registry+https://github.com/rust-lang/crates.io-index)" = "676e8eb2b1b4c9043511a9b7bea0915320d7e502b0a079fb03f9635a5252b18c"
"checksum rand 0.5.5 (registry+https://github.com/rust-lang/crates.io-index)" = "e464cd887e869cddcae8792a4ee31d23c7edd516700695608f5b98c67ee0131c"
"checksum rand_core 0.2.2 (registry+https://github.com/rust-lang/crates.io-index)" = "1961a422c4d189dfb50ffa9320bf1f2a9bd54ecb92792fb9477f99a1045f3372"
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"checksum redox_syscall 0.1.40 (registry+https://github.com/rust-lang/crates.io-index)" = "c214e91d3ecf43e9a4e41e578973adeb14b474f2bee858742d127af75a0112b1"
"checksum redox_termios 0.1.1 (registry+https://github.com/rust-lang/crates.io-index)" = "7e891cfe48e9100a70a3b6eb652fef28920c117d366339687bd5576160db0f76"
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7
Cargo.toml
View File

@@ -6,6 +6,11 @@ authors = ["D. Bauer <bauer@bio.tu-darmstadt.de>"]
[dependencies]
clap = {version="2.32.0", features=['yaml']}
error-chain = "0.12.0"
rand = "0.5.5"
GSL = "1.0.0"
[profile.release]
opt-level = 2
opt-level = 2
[features]
default = ["GSL/v2"]

101
example/1d/wham.bs.out Normal file
View File

@@ -0,0 +1,101 @@
#coord1 Free Energy +/- Probability +/-
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0.282600 32.686511 3.077967 0.000000 0.000000
0.345400 31.211777 3.305545 0.000000 0.000000
0.408200 29.680451 4.240068 0.000000 0.000001
0.471000 28.032242 4.472562 0.000001 0.000001
0.533800 26.439599 4.654827 0.000002 0.000003
0.596600 24.432467 4.574666 0.000003 0.000006
0.659400 22.309893 4.862061 0.000008 0.000016
0.722200 20.186040 4.828795 0.000019 0.000037
0.785000 18.295046 5.011677 0.000040 0.000081
0.847800 16.221232 4.936856 0.000093 0.000183
0.910600 14.251911 5.036745 0.000204 0.000412
0.973400 12.562353 5.358431 0.000402 0.000863
1.036200 11.184029 5.447495 0.000698 0.001524
1.099000 10.040677 5.503065 0.001103 0.002434
1.161800 9.369064 5.732528 0.001444 0.003320
1.224600 9.095392 5.840210 0.001612 0.003774
1.287400 9.256035 6.090900 0.001511 0.003691
1.350200 9.814068 6.280131 0.001208 0.003042
1.413000 10.945207 6.508250 0.000768 0.002003
1.475800 12.518898 6.775260 0.000409 0.001110
1.538600 14.409744 6.965926 0.000191 0.000535
1.601400 16.451965 7.139771 0.000084 0.000242
1.664200 18.589166 7.587443 0.000036 0.000109
1.727000 20.669504 7.985190 0.000016 0.000050
1.789800 22.804791 7.785886 0.000007 0.000021
1.852600 24.531690 10.770791 0.000003 0.000014
1.915400 26.182612 7.778636 0.000002 0.000005
1.978200 27.279439 7.317796 0.000001 0.000003
2.041000 28.571380 3.941626 0.000001 0.000001
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2.920200 15.420138 0.930646 0.000128 0.000048
2.983000 13.069599 0.868684 0.000328 0.000114
3.045800 11.036085 0.791301 0.000740 0.000235
3.108600 9.015657 0.747120 0.001664 0.000498

202
example/1d/wham.out
View File

@@ -1,101 +1,101 @@
#coord1 Free Energy Probability
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1.413000 10.945207 0.000768
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1.538600 14.409744 0.000191
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1.664200 18.589166 0.000036
1.727000 20.669504 0.000016
1.789800 22.804791 0.000007
1.852600 24.531690 0.000003
1.915400 26.182612 0.000002
1.978200 27.279439 0.000001
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2.794600 19.958407 0.000021
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3.045800 11.036085 0.000740
3.108600 9.015657 0.001664
#coord1 Free Energy +/- Probability +/-
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-0.847800 17.745327 0.000000 0.000050 0.000000
-0.785000 20.559461 0.000000 0.000016 0.000000
-0.722200 22.783560 0.000000 0.000007 0.000000
-0.659400 25.175865 0.000000 0.000003 0.000000
-0.596600 26.419980 0.000000 0.000002 0.000000
-0.533800 27.885999 0.000000 0.000001 0.000000
-0.471000 29.029334 0.000000 0.000001 0.000000
-0.408200 30.366556 0.000000 0.000000 0.000000
-0.345400 31.615252 0.000000 0.000000 0.000000
-0.282600 32.781716 0.000000 0.000000 0.000000
-0.219800 33.731378 0.000000 0.000000 0.000000
-0.157000 34.476014 0.000000 0.000000 0.000000
-0.094200 35.387300 0.000000 0.000000 0.000000
-0.031400 35.579756 0.000000 0.000000 0.000000
0.031400 35.520194 0.000000 0.000000 0.000000
0.094200 35.344763 0.000000 0.000000 0.000000
0.157000 34.886460 0.000000 0.000000 0.000000
0.219800 33.633998 0.000000 0.000000 0.000000
0.282600 32.686511 0.000000 0.000000 0.000000
0.345400 31.211777 0.000000 0.000000 0.000000
0.408200 29.680451 0.000000 0.000000 0.000000
0.471000 28.032242 0.000000 0.000001 0.000000
0.533800 26.439599 0.000000 0.000002 0.000000
0.596600 24.432467 0.000000 0.000003 0.000000
0.659400 22.309893 0.000000 0.000008 0.000000
0.722200 20.186040 0.000000 0.000019 0.000000
0.785000 18.295046 0.000000 0.000040 0.000000
0.847800 16.221232 0.000000 0.000093 0.000000
0.910600 14.251911 0.000000 0.000204 0.000000
0.973400 12.562353 0.000000 0.000402 0.000000
1.036200 11.184029 0.000000 0.000698 0.000000
1.099000 10.040677 0.000000 0.001103 0.000000
1.161800 9.369064 0.000000 0.001444 0.000000
1.224600 9.095392 0.000000 0.001612 0.000000
1.287400 9.256035 0.000000 0.001511 0.000000
1.350200 9.814068 0.000000 0.001208 0.000000
1.413000 10.945207 0.000000 0.000768 0.000000
1.475800 12.518898 0.000000 0.000409 0.000000
1.538600 14.409744 0.000000 0.000191 0.000000
1.601400 16.451965 0.000000 0.000084 0.000000
1.664200 18.589166 0.000000 0.000036 0.000000
1.727000 20.669504 0.000000 0.000016 0.000000
1.789800 22.804791 0.000000 0.000007 0.000000
1.852600 24.531690 0.000000 0.000003 0.000000
1.915400 26.182612 0.000000 0.000002 0.000000
1.978200 27.279439 0.000000 0.000001 0.000000
2.041000 28.571380 0.000000 0.000001 0.000000
2.103800 29.328969 0.000000 0.000000 0.000000
2.166600 29.897739 0.000000 0.000000 0.000000
2.229400 30.320908 0.000000 0.000000 0.000000
2.292200 30.065391 0.000000 0.000000 0.000000
2.355000 29.809137 0.000000 0.000000 0.000000
2.417800 29.340601 0.000000 0.000000 0.000000
2.480600 28.473346 0.000000 0.000001 0.000000
2.543400 27.679353 0.000000 0.000001 0.000000
2.606200 26.453160 0.000000 0.000002 0.000000
2.669000 24.424649 0.000000 0.000003 0.000000
2.731800 22.285933 0.000000 0.000008 0.000000
2.794600 19.958407 0.000000 0.000021 0.000000
2.857400 17.606291 0.000000 0.000053 0.000000
2.920200 15.420138 0.000000 0.000128 0.000000
2.983000 13.069599 0.000000 0.000328 0.000000
3.045800 11.036085 0.000000 0.000740 0.000000
3.108600 9.015657 0.000000 0.001664 0.000000

10001
example/2d/wham.bs.out Normal file
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20002
example/2d/wham.out
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12
src/cli.yml
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@@ -61,6 +61,7 @@ args:
required: false
help: Stop WHAM after this many iterations without convergence (defaults to 100,000).
- cyclic:
short: c
long: cyclic
help: For periodic reaction coordinates. If this is set, the first and last coordinate bin in each dimension are treated as neighbors for the bias calculation.
- verbose:
@@ -71,12 +72,17 @@ args:
- temperature:
short: T
long: temperature
help: WHAM temperature in Kelvin
help: WHAM temperature in Kelvin.
takes_value: true
required: true
- output:
short: o
long: output
help: Free energy output file (defaults to wham.out)
help: Free energy output file (defaults to wham.out).
takes_value: true
required: false
required: false
- bootstrap:
long: bt
help: Number of bayesian bootstrapping runs for error analysis by assigning random weights (defaults to 0).
takes_value: true
required: false

95
src/error_analysis.rs Normal file
View File

@@ -0,0 +1,95 @@
use rand;
use super::histogram::{Dataset,Histogram};
use super::k_B;
use super::perform_wham;
use super::Config;
use rgsl::statistics;
fn generate_random_weights(num_windows: usize) -> Vec<f64> {
// TODO this is ugly.
// create a list of num_windows - 1 sorted random numbers and append/prepend 0 and 1
let mut tmp = (0..num_windows-1).map(|_| rand::random::<f64>()).collect::<Vec<f64>>();
tmp.sort_by(|a,b| { a.partial_cmp(b).unwrap() });
let mut rnds = vec![0.0];
rnds.append(&mut tmp);
rnds.append(&mut vec![1.0]);
// weights of window i is the difference between rnd[i+1] and rnd[i]
let mut weights = vec![0.0; num_windows];
for i in 0..num_windows {
weights[i] = rnds[i+1] - rnds[i]
}
return weights
}
fn generate_random_weighted_dataset(ds: Dataset) -> Dataset {
let weights = generate_random_weights(ds.num_windows);
Dataset::new_weighted(ds, weights )
}
pub fn run_bootstrap(cfg: &Config, ds: Dataset, P: &[f64], num_runs: usize) -> (Vec<f64>,Vec<f64>) {
let Ps: Vec<Vec<f64>> = (0..num_runs).map(|x| {
println!("Bootstrap run {}/{}", x, num_runs);
let rnd_weighted_dataset = generate_random_weighted_dataset(ds.clone());
perform_wham(cfg, &rnd_weighted_dataset).unwrap().0
}).collect();
let mut P_std = vec![0.0; ds.num_bins];
for bin in 0..ds.num_bins {
let Ps = Ps.iter().map(|window| window[bin]).collect::<Vec<f64>>();
P_std[bin] = statistics::sd(&Ps, 1, num_runs);
}
let A_std = P_std.iter().zip(P.iter()).map(|(std,P)| ds.kT*1.0/P*std).collect();
(P_std, A_std)
}
mod tests {
use super::*;
fn build_hist() -> Histogram {
Histogram::new(
22, // num_points
vec![1.0, 1.0, 3.0, 5.0, 12.0] // bins
)
}
fn build_hist_set() -> Dataset {
let h1 = build_hist();
let h2 = build_hist();
let h3 = build_hist();
Dataset::new(
5, // num bins
vec![3],
vec![1.0], // bin width
vec![0.0], // hist min
vec![9.0], // hist max
vec![4.5, 4.5, 4.5], // x0
vec![10.0, 10.0, 10.0], // fc
300.0*k_B, // kT
vec![h1, h2, h3], // hists
false // cyclic
)
}
#[test]
fn random_weights() {
let num_windows = 5;
let weights = generate_random_weights(num_windows);
assert_eq!(num_windows, weights.len());
for w in weights {
assert!(0.0 < w && w < 1.0);
}
}
#[test]
fn random_weighted_dataset() {
let ds = build_hist_set();
let rnd_weights_ds = generate_random_weighted_dataset(ds);
println!("{:?}", rnd_weights_ds.weights);
for w in rnd_weights_ds.weights {
assert!(w > 0.0);
assert!(w < 1.0);
}
}
}

35
src/histogram.rs
View File

@@ -2,7 +2,7 @@ use std::fmt;
use std::cell::RefCell;
// One histogram
#[derive(Debug)]
#[derive(Debug,Clone)]
pub struct Histogram {
// total number of data points stored in the histogram
pub num_points: u32,
@@ -18,7 +18,7 @@ impl Histogram {
}
// a set of histograms
#[derive(Debug)]
#[derive(Debug,Clone)]
pub struct Dataset {
// number of histogram windows (number of simulations)
pub num_windows: usize,
@@ -56,8 +56,8 @@ pub struct Dataset {
// bias value cache
bias: RefCell<Vec<Option<f64>>>,
// sum of bin count for windows
pub bin_count: Vec<f64>
// histogram weight
pub weights: Vec<f64>,
}
impl Dataset {
@@ -65,9 +65,7 @@ impl Dataset {
pub fn new(num_bins: usize, dimens_lengths: Vec<usize>, bin_width: Vec<f64>, hist_min: Vec<f64>, hist_max: Vec<f64>, bias_pos: Vec<f64>, bias_fc: Vec<f64>, kT: f64, histograms: Vec<Histogram>, cyclic: bool) -> Dataset {
let num_windows = histograms.len();
let bias: RefCell<Vec<Option<f64>>> = RefCell::new(vec![None; num_bins*num_windows]);
let bin_count = (0..num_bins).map(|bin| {
histograms.iter().map(|h| h.bins[bin]).sum()
}).collect();
let weights = vec![1.0; num_windows];
Dataset{
num_windows,
num_bins,
@@ -81,10 +79,21 @@ impl Dataset {
bias_pos,
bias_fc,
bias,
bin_count,
weights
}
}
pub fn new_weighted(ds: Dataset, weights: Vec<f64>) -> Dataset {
Dataset {
weights: weights,
..ds
}
}
pub fn get_weighted_bin_count(&self, bin: usize) -> f64 {
self.histograms.iter().enumerate().map(|(idx,h)| self.weights[idx]*h.bins[bin]).sum()
}
fn expand_index(&self, bin: usize, lengths: &[usize]) -> Vec<usize> {
let mut tmp = bin;
let mut idx = vec![0; lengths.len()];
@@ -247,10 +256,10 @@ mod tests {
vec![build_hist(), build_hist()], // hists
false // cyclic
);
assert_delta!(2.0, ds.bin_count[0], 0.0000000001);
assert_delta!(2.0, ds.bin_count[1], 0.0000000001);
assert_delta!(6.0, ds.bin_count[2], 0.0000000001);
assert_delta!(10.0, ds.bin_count[3], 0.0000000001);
assert_delta!(24.0, ds.bin_count[4], 0.0000000001);
assert_delta!(2.0, ds.get_weighted_bin_count(0), 0.0000000001);
assert_delta!(2.0, ds.get_weighted_bin_count(1), 0.0000000001);
assert_delta!(6.0, ds.get_weighted_bin_count(2), 0.0000000001);
assert_delta!(10.0, ds.get_weighted_bin_count(3), 0.0000000001);
assert_delta!(24.0, ds.get_weighted_bin_count(4), 0.0000000001);
}
}

7
src/io.rs
View File

@@ -158,20 +158,20 @@ fn read_window_file(window_file: &str, cfg: &Config) -> Result<Histogram> {
}
// Write WHAM calculation results to out_file.
pub fn write_results(out_file: &str, ds: &Dataset, free: &Vec<f64>, prob: &Vec<f64>) -> Result<()> {
pub fn write_results(out_file: &str, ds: &Dataset, free: &Vec<f64>, free_std: &Vec<f64>, prob: &Vec<f64>, prob_std: &Vec<f64>) -> Result<()> {
let output = File::create(out_file)
.chain_err(|| format!("Failed to create file with path {}", out_file))?;
let mut buf = BufWriter::new(output);
let header: String = (0..ds.dimens_lengths.len()).map(|d| format!("coord{}", d+1))
.collect::<Vec<String>>().join(" ");
writeln!(buf, "#{} {} {}", header, "Free Energy", "Probability");
writeln!(buf, "#{} {} {} {} {}", header, "Free Energy", "+/-", "Probability", "+/-");
for bin in 0..free.len() {
let coords = ds.get_coords_for_bin(bin);
let coords_str: String = coords.iter().map(|c| {format!("{:8.6} ", c)})
.collect::<Vec<String>>().join("\t");
writeln!(buf, "{}{:8.6} {:8.6}", coords_str, free[bin], prob[bin])
writeln!(buf, "{}{:8.6} {:8.6} {:8.6} {:8.6}", coords_str, free[bin], free_std[bin], prob[bin], prob_std[bin])
.chain_err(|| "Failed to write to file.")?;
}
Ok(())
@@ -194,6 +194,7 @@ mod tests {
temperature: 300.0,
cyclic: false,
output: "qwert".to_string(),
bootstrap: 0,
}
}

37
src/lib.rs
View File

@@ -2,9 +2,12 @@
#[macro_use]
extern crate error_chain;
extern crate rand;
extern crate rgsl;
pub mod io;
pub mod histogram;
pub mod error_analysis;
use histogram::Dataset;
use std::f64;
@@ -32,12 +35,13 @@ pub struct Config {
pub temperature: f64,
pub cyclic: bool,
pub output: String,
pub bootstrap: usize,
}
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={:?}", self.metadata_file, self.hist_min, self.hist_max, self.num_bins,
self.verbose, self.tolerance, self.max_iterations, self.temperature, self.cyclic)
write!(f, "Metadata={}, hist_min={:?}, hist_max={:?}, bins={:?} verbose={}, tolerance={}, iterations={}, temperature={}, cyclic={:?}, bootstrap={:?}", self.metadata_file, self.hist_min, self.hist_max, self.num_bins,
self.verbose, self.tolerance, self.max_iterations, self.temperature, self.cyclic, self.bootstrap)
}
}
@@ -54,11 +58,12 @@ fn is_converged(old_F: &[f64], new_F: &[f64], tolerance: f64) -> bool {
// This evaluates the first WHAM equation for each bin.
fn calc_bin_probability(bin: usize, dataset: &Dataset, F: &[f64]) -> f64 {
let mut denom_sum: f64 = 0.0;
let bin_count: f64 = dataset.get_weighted_bin_count(bin);
for (window, h) in dataset.histograms.iter().enumerate() {
let bias = dataset.calc_bias(bin, window);
denom_sum += (h.num_points as f64) * bias * F[window];
denom_sum += (dataset.weights[window] * h.num_points as f64) * bias * F[window];
}
dataset.bin_count[bin] / denom_sum
bin_count / denom_sum
}
// estimate the bias offset F of the histogram based on given probabilities.
@@ -150,12 +155,23 @@ pub fn run(cfg: &Config) -> Result<()>{
let (P, F, F_prev) = perform_wham(&cfg, &dataset)?;
let P_std: Vec<f64>;
let free_energy_std: Vec<f64>;
if cfg.bootstrap > 0 {
let error_est = error_analysis::run_bootstrap(&cfg, dataset.clone(), &P, cfg.bootstrap);
P_std = error_est.0;
free_energy_std = error_est.1;
} else {
P_std = vec![0.0; P.len()];
free_energy_std = 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, &free_energy);
dump_state(&dataset, &F, &F_prev, &P, &P_std, &free_energy, &free_energy_std);
io::write_results(&cfg.output, &dataset, &free_energy, &P)
io::write_results(&cfg.output, &dataset, &free_energy, &free_energy_std, &P, &P_std)
.chain_err(|| "Could not write results to output file")?;
Ok(())
@@ -191,16 +207,17 @@ fn calc_free_energy(dataset: &Dataset, P: &[f64]) -> Vec<f64> {
free_energy
}
fn dump_state(dataset: &Dataset, F: &[f64], F_prev: &[f64], P: &[f64], A: &[f64]) {
fn dump_state(dataset: &Dataset, F: &[f64], F_prev: &[f64], P: &[f64], P_std: &[f64], A: &[f64], A_std: &[f64]) {
// TODO fix output of F/F_prev
let out = std::io::stdout();
let mut lock = out.lock();
writeln!(lock, "# PMF");
writeln!(lock, "#bin\t\tFree Energy\t\tP(x)");
writeln!(lock, "#bin\t\tFree Energy\t\t+/-\t\tP(x)\t\t+/-");
for bin in 0..dataset.num_bins {
writeln!(lock, "{:9.5}\t{:9.5}\t{:9.5}", bin, A[bin], P[bin]);
writeln!(lock, "{:9.5}\t{:9.5}\t{:9.5}\t{:9.5}\t{:9.5}", bin, A[bin], A_std[bin], P[bin], P_std[bin]);
}
writeln!(lock, "# Bias offsets");
writeln!(lock, "#Window\t\tF\t\tdF");
writeln!(lock, "#Window\t\tF\t\tF_prev");
for window in 0..dataset.num_windows {
writeln!(lock, "{}\t{:9.5}\t{:8.8}", window, F[window], (F[window]-F_prev[window]).abs());
}

5
src/main.rs
View File

@@ -28,6 +28,8 @@ fn cli() -> Result<Config> {
.split(',').map(|x| { x.parse().unwrap() }).collect();
let num_bins: Vec<usize> = matches.value_of("bins").unwrap()
.split(',').map(|x| { x.parse().unwrap() }).collect();
let bootstrap: usize = matches.value_of("bootstrap").unwrap_or("0").parse()
.chain_err(|| "Cannot parse bootstrap iteration.")?;
if num_bins.len() != hist_max.len() || num_bins.len() != hist_max.len() {
eprintln!("Input dimensions do not match (min: {}, max: {}, bins: {})",
@@ -38,7 +40,8 @@ fn cli() -> Result<Config> {
let dimens = num_bins.len();
Ok(wham::Config{metadata_file, hist_min, hist_max, num_bins, dimens,
verbose, tolerance, max_iterations, temperature, cyclic, output})
verbose, tolerance, max_iterations, temperature, cyclic, output,
bootstrap})
}
fn main() {