mirror of
https://github.com/dnlbauer/WHAM.git
synced 2026-09-10 22:25:31 +00:00
Compare commits
9 Commits
| Author | SHA1 | Date | |
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87f3cceb6a |
157
Cargo.lock
generated
157
Cargo.lock
generated
@@ -60,12 +60,12 @@ checksum = "cdb031dd78e28731d87d56cc8ffef4a8f36ca26c38fe2de700543e627f8a464a"
|
||||
|
||||
[[package]]
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
"addr2line",
|
||||
"cfg-if",
|
||||
"cfg-if 1.0.0",
|
||||
"libc",
|
||||
"miniz_oxide",
|
||||
"object",
|
||||
@@ -90,6 +90,12 @@ version = "0.1.10"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "4785bdd1c96b2a846b2bd7cc02e86b6b3dbf14e7e53446c4f54c92a361040822"
|
||||
|
||||
[[package]]
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
|
||||
[[package]]
|
||||
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|
||||
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|
||||
@@ -107,66 +113,63 @@ dependencies = [
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "cloudabi"
|
||||
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|
||||
name = "const_fn"
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
"bitflags",
|
||||
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|
||||
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|
||||
|
||||
[[package]]
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
dependencies = [
|
||||
"cfg-if 1.0.0",
|
||||
"crossbeam-utils",
|
||||
"maybe-uninit",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "crossbeam-deque"
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
dependencies = [
|
||||
"cfg-if 1.0.0",
|
||||
"crossbeam-epoch",
|
||||
"crossbeam-utils",
|
||||
"maybe-uninit",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
dependencies = [
|
||||
"autocfg",
|
||||
"cfg-if",
|
||||
"cfg-if 1.0.0",
|
||||
"const_fn",
|
||||
"crossbeam-utils",
|
||||
"lazy_static",
|
||||
"maybe-uninit",
|
||||
"memoffset",
|
||||
"scopeguard",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "crossbeam-utils"
|
||||
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|
||||
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|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
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|
||||
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|
||||
dependencies = [
|
||||
"autocfg",
|
||||
"cfg-if",
|
||||
"cfg-if 1.0.0",
|
||||
"const_fn",
|
||||
"lazy_static",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
|
||||
[[package]]
|
||||
name = "error-chain"
|
||||
@@ -179,10 +182,15 @@ dependencies = [
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "fuchsia-cprng"
|
||||
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|
||||
name = "getrandom"
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
dependencies = [
|
||||
"cfg-if 0.1.10",
|
||||
"libc",
|
||||
"wasi",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "gimli"
|
||||
@@ -192,9 +200,9 @@ checksum = "aaf91faf136cb47367fa430cd46e37a788775e7fa104f8b4bcb3861dc389b724"
|
||||
|
||||
[[package]]
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
dependencies = [
|
||||
"libc",
|
||||
]
|
||||
@@ -207,30 +215,24 @@ checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646"
|
||||
|
||||
[[package]]
|
||||
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|
||||
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||||
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|
||||
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||||
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|
||||
|
||||
[[package]]
|
||||
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||||
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||||
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||||
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||||
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||||
|
||||
[[package]]
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||||
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|
||||
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||||
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|
||||
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||||
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|
||||
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|
||||
dependencies = [
|
||||
"autocfg",
|
||||
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|
||||
|
||||
[[package]]
|
||||
name = "miniz_oxide"
|
||||
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|
||||
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|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
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||||
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||||
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|
||||
dependencies = [
|
||||
"adler",
|
||||
"autocfg",
|
||||
@@ -248,49 +250,68 @@ dependencies = [
|
||||
|
||||
[[package]]
|
||||
name = "object"
|
||||
version = "0.20.0"
|
||||
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|
||||
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||||
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||||
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||||
|
||||
[[package]]
|
||||
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||||
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||||
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||||
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||||
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||||
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||||
[[package]]
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||||
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||||
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||||
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||||
[[package]]
|
||||
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||||
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||||
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|
||||
dependencies = [
|
||||
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|
||||
"fuchsia-cprng",
|
||||
"getrandom",
|
||||
"libc",
|
||||
"rand_core 0.3.1",
|
||||
"winapi",
|
||||
"rand_chacha",
|
||||
"rand_core",
|
||||
"rand_hc",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
"ppv-lite86",
|
||||
"rand_core",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
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|
||||
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||||
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||||
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|
||||
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||||
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|
||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
|
||||
[[package]]
|
||||
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|
||||
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||||
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dependencies = [
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||||
"autocfg",
|
||||
"crossbeam-deque",
|
||||
@@ -300,9 +321,9 @@ dependencies = [
|
||||
|
||||
[[package]]
|
||||
name = "rayon-core"
|
||||
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||||
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||||
dependencies = [
|
||||
"crossbeam-channel",
|
||||
"crossbeam-deque",
|
||||
@@ -313,9 +334,9 @@ dependencies = [
|
||||
|
||||
[[package]]
|
||||
name = "rustc-demangle"
|
||||
version = "0.1.16"
|
||||
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|
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||||
|
||||
[[package]]
|
||||
name = "scopeguard"
|
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@@ -356,9 +377,15 @@ version = "0.9.2"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "b5a972e5669d67ba988ce3dc826706fb0a8b01471c088cb0b6110b805cc36aed"
|
||||
|
||||
[[package]]
|
||||
name = "wasi"
|
||||
version = "0.9.0+wasi-snapshot-preview1"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
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|
||||
|
||||
[[package]]
|
||||
name = "wham"
|
||||
version = "0.9.8"
|
||||
version = "0.9.9"
|
||||
dependencies = [
|
||||
"GSL",
|
||||
"assert_approx_eq",
|
||||
|
||||
13
Cargo.toml
13
Cargo.toml
@@ -1,23 +1,24 @@
|
||||
[package]
|
||||
name = "wham"
|
||||
version = "0.9.8"
|
||||
version = "0.9.9"
|
||||
authors = ["Daniel Bauer <bauer@cbs.tu-darmstadt.de>"]
|
||||
description = "An implementation of the weighted histogram analysis method"
|
||||
license = "GPL-3.0"
|
||||
repository = "https://github.com/danijoo/WHAM"
|
||||
readme = "README.md"
|
||||
categories = ["science", "command-line-utilities", "molecular-dynamics", "algorithms"]
|
||||
keywords = ["math", "statistics", "histogram", "bioinformatics", "molecular-dynamics"]
|
||||
|
||||
[dependencies]
|
||||
clap = {version="2.32.0", features=['yaml']}
|
||||
error-chain = "0.12.0"
|
||||
rand = "0.5.5"
|
||||
GSL = "1.0.0"
|
||||
rand = "0.7.*"
|
||||
GSL = "1.1"
|
||||
rayon = "1.0.3"
|
||||
|
||||
[dev-dependencies]
|
||||
assert_approx_eq = "1.1.0"
|
||||
|
||||
[profile.release]
|
||||
opt-level = 2
|
||||
opt-level = 3
|
||||
|
||||
[features]
|
||||
default = ["GSL/v2"]
|
||||
|
||||
51
README.md
51
README.md
@@ -38,6 +38,56 @@ Usage
|
||||
wham has a convenient command line interface. You can see all options with
|
||||
```wham -h```:
|
||||
|
||||
```
|
||||
wham 0.9.9
|
||||
D. Bauer <bauer@bio.tu-darmstadt.de>
|
||||
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.
|
||||
|
||||
Metadata file format:
|
||||
/path/to/timeseries_file1 x_1 x_2 x_N fc_1 fc_2 fc_N
|
||||
/path/to/timeseries_file2 x_1 x_2 x_N fc_1 fc_2 fc_N
|
||||
/path/to/timeseries_file3 x_1 x_2 x_N fc_1 fc_2 fc_N
|
||||
The first column is a path to a timeseries file _relative_ to the metadata file (see below). This is followed by the
|
||||
position of the umbrella potential x in N dimensions and the force constant fc in each dimension. Lines starting with a
|
||||
# are treated as comments and will not be parsed.
|
||||
|
||||
Timeseries file format:
|
||||
time x_1 x_2 x_N
|
||||
time x_1 x_2 x_N
|
||||
time x_1 x_2 x_N
|
||||
The first column will be ignored and is followed by N reaction coordinates x.
|
||||
|
||||
Shipped under the GPLv3 license.
|
||||
|
||||
USAGE:
|
||||
wham [FLAGS] [OPTIONS] --bins <BINS> --max <HIST_MAX> --file <METADATA> --min <HIST_MIN> --temperature <temperature>
|
||||
|
||||
FLAGS:
|
||||
-c, --cyclic 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.
|
||||
-h, --help Prints help information
|
||||
-V, --version Prints version information
|
||||
-v, --verbose Enables verbose output.
|
||||
|
||||
OPTIONS:
|
||||
-b, --bins <BINS> Number of histogram bins (comma separated).
|
||||
--bt <bootstrap> Number of bayesian bootstrapping runs for error analysis by assigning random
|
||||
weights (defaults to 0).
|
||||
--seed <bootstrap_seed> Random seed for bootstrapping runs.
|
||||
--end <end> Skip rows in timeseries with an index larger than this value (defaults to 1e+20)
|
||||
-i, --iterations <ITERATIONS> Stop WHAM after this many iterations without convergence (defaults to 100,000).
|
||||
--max <HIST_MAX> Histogram maxima (comma separated). Also accepts "pi".
|
||||
-f, --file <METADATA> Path to the metadata file.
|
||||
--min <HIST_MIN> Histogram minima (comma separated for multiple dimensions). Also accepts "pi".
|
||||
-o, --output <output> Free energy output file (defaults to wham.out).
|
||||
--start <start> Skip rows in timeseries with an index smaller than this value (defaults to 0)
|
||||
-T, --temperature <temperature> WHAM temperature in Kelvin.
|
||||
-t, --tolerance <TOLERANCE> Abortion criteria for WHAM calculation. WHAM stops if abs(F_new - F_old) <
|
||||
tolerance (defaults to 0.000001).
|
||||
|
||||
```
|
||||
|
||||
To run the two dimensional example (simulation of dialanine phi and psi angle):
|
||||
```bash
|
||||
wham --max 3.14,3.14 --min -3.14,-3.14 -T 300 --bins 100,100 --cyclic -f example/2d/metadata.dat
|
||||
@@ -94,7 +144,6 @@ The example folder contains input and output files for two simple test systems:
|
||||
|
||||
TODO
|
||||
---
|
||||
- better error estimation
|
||||
- Autocorrelation
|
||||
- Replica exchange
|
||||
|
||||
|
||||
@@ -1,101 +1,101 @@
|
||||
#coord1 Free Energy +/- Probability +/-
|
||||
-3.110177 7.158102 0.069244 0.003494 0.000067
|
||||
-3.047345 5.365727 0.068503 0.007168 0.000135
|
||||
-2.984513 3.873190 0.065883 0.013039 0.000226
|
||||
-2.921681 2.953162 0.066856 0.018855 0.000334
|
||||
-2.858849 1.949554 0.066705 0.028195 0.000501
|
||||
-2.796017 1.391747 0.064012 0.035261 0.000576
|
||||
-2.733186 1.128270 0.061522 0.039189 0.000598
|
||||
-2.670354 0.839970 0.060810 0.043991 0.000653
|
||||
-2.607522 0.624769 0.061888 0.047955 0.000733
|
||||
-2.544690 0.663757 0.062566 0.047211 0.000736
|
||||
-2.481858 1.051932 0.061093 0.040407 0.000616
|
||||
-2.419026 1.463048 0.062547 0.034267 0.000543
|
||||
-2.356194 1.990616 0.057022 0.027734 0.000373
|
||||
-2.293363 2.190692 0.044029 0.025597 0.000202
|
||||
-2.230531 2.553036 0.041867 0.022136 0.000157
|
||||
-2.167699 2.572522 0.044817 0.021964 0.000184
|
||||
-2.104867 2.472360 0.038778 0.022863 0.000155
|
||||
-2.042035 2.517562 0.030296 0.022453 0.000150
|
||||
-1.979203 2.469778 0.025852 0.022887 0.000167
|
||||
-1.916372 2.223125 0.030799 0.025266 0.000411
|
||||
-1.853540 2.080157 0.024928 0.026756 0.000365
|
||||
-1.790708 1.793841 0.027529 0.030011 0.000475
|
||||
-1.727876 1.458784 0.026130 0.034326 0.000462
|
||||
-1.665044 0.914441 0.024774 0.042697 0.000576
|
||||
-1.602212 0.303813 0.020400 0.054540 0.000701
|
||||
-1.539380 0.268335 0.020423 0.055321 0.000733
|
||||
-1.476549 0.000000 0.020271 0.061604 0.000835
|
||||
-1.413717 0.537061 0.023895 0.049671 0.000735
|
||||
-1.350885 1.439940 0.023678 0.034586 0.000528
|
||||
-1.288053 2.391838 0.025951 0.023614 0.000386
|
||||
-1.225221 3.779470 0.026215 0.013538 0.000224
|
||||
-1.162389 5.685555 0.028543 0.006305 0.000109
|
||||
-1.099557 7.661896 0.030579 0.002855 0.000051
|
||||
-1.036726 9.946594 0.039243 0.001142 0.000022
|
||||
-0.973894 12.359408 0.054067 0.000434 0.000009
|
||||
-0.911062 14.954655 0.066597 0.000153 0.000004
|
||||
-0.848230 17.742242 0.073582 0.000050 0.000002
|
||||
-0.785398 20.555785 0.074644 0.000016 0.000001
|
||||
-0.722566 22.811160 0.078503 0.000007 0.000000
|
||||
-0.659734 25.178094 0.088961 0.000003 0.000000
|
||||
-0.596903 26.442288 0.093509 0.000002 0.000000
|
||||
-0.534071 27.897565 0.091353 0.000001 0.000000
|
||||
-0.471239 29.062473 0.086244 0.000001 0.000000
|
||||
-0.408407 30.384521 0.084285 0.000000 0.000000
|
||||
-0.345575 31.638454 0.084871 0.000000 0.000000
|
||||
-0.282743 32.817727 0.092750 0.000000 0.000000
|
||||
-0.219911 33.770369 0.094479 0.000000 0.000000
|
||||
-0.157080 34.505503 0.095774 0.000000 0.000000
|
||||
-0.094248 35.431659 0.107598 0.000000 0.000000
|
||||
-0.031416 35.615810 0.108959 0.000000 0.000000
|
||||
0.031416 35.561946 0.107382 0.000000 0.000000
|
||||
0.094248 35.382089 0.096643 0.000000 0.000000
|
||||
0.157080 34.934827 0.107624 0.000000 0.000000
|
||||
0.219911 33.673460 0.100231 0.000000 0.000000
|
||||
0.282743 32.731563 0.096604 0.000000 0.000000
|
||||
0.345575 31.261855 0.099036 0.000000 0.000000
|
||||
0.408407 29.717377 0.107915 0.000000 0.000000
|
||||
0.471239 28.076620 0.104513 0.000001 0.000000
|
||||
0.534071 26.481097 0.103164 0.000002 0.000000
|
||||
0.596903 24.487358 0.103039 0.000003 0.000000
|
||||
0.659734 22.344251 0.100666 0.000008 0.000000
|
||||
0.722566 20.241543 0.102150 0.000018 0.000001
|
||||
0.785398 18.341869 0.101957 0.000039 0.000002
|
||||
0.848230 16.261582 0.105391 0.000091 0.000005
|
||||
0.911062 14.301801 0.107389 0.000199 0.000010
|
||||
0.973894 12.603788 0.105487 0.000394 0.000020
|
||||
1.036726 11.249601 0.106308 0.000678 0.000035
|
||||
1.099557 10.087886 0.106741 0.001079 0.000055
|
||||
1.162389 9.443303 0.106957 0.001398 0.000071
|
||||
1.225221 9.152799 0.105940 0.001570 0.000079
|
||||
1.288053 9.331937 0.105860 0.001462 0.000074
|
||||
1.350885 9.905546 0.105389 0.001161 0.000058
|
||||
1.413717 11.042050 0.105466 0.000736 0.000037
|
||||
1.476549 12.598167 0.105119 0.000395 0.000020
|
||||
1.539380 14.520167 0.104367 0.000183 0.000009
|
||||
1.602212 16.569783 0.104184 0.000080 0.000004
|
||||
1.665044 18.687390 0.104276 0.000034 0.000002
|
||||
1.727876 20.775408 0.104944 0.000015 0.000001
|
||||
1.790708 22.905200 0.101547 0.000006 0.000000
|
||||
1.853540 24.643852 0.103914 0.000003 0.000000
|
||||
1.916372 26.301740 0.101973 0.000002 0.000000
|
||||
1.979203 27.372071 0.101762 0.000001 0.000000
|
||||
2.042035 28.697726 0.105177 0.000001 0.000000
|
||||
2.104867 29.417901 0.100003 0.000000 0.000000
|
||||
2.167699 30.008351 0.100038 0.000000 0.000000
|
||||
2.230531 30.406016 0.096233 0.000000 0.000000
|
||||
2.293363 30.171275 0.096428 0.000000 0.000000
|
||||
2.356194 29.884646 0.108339 0.000000 0.000000
|
||||
2.419026 29.428153 0.106679 0.000000 0.000000
|
||||
2.481858 28.546982 0.123259 0.000001 0.000000
|
||||
2.544690 27.757520 0.108526 0.000001 0.000000
|
||||
2.607522 26.505787 0.111134 0.000001 0.000000
|
||||
2.670354 24.491866 0.095963 0.000003 0.000000
|
||||
2.733186 22.320664 0.096576 0.000008 0.000000
|
||||
2.796017 20.052723 0.098813 0.000020 0.000001
|
||||
2.858849 17.655650 0.097052 0.000052 0.000002
|
||||
2.921681 15.471590 0.100497 0.000125 0.000005
|
||||
2.984513 13.138167 0.092102 0.000318 0.000011
|
||||
3.047345 11.092386 0.081862 0.000722 0.000020
|
||||
3.110177 9.065722 0.072111 0.001626 0.000034
|
||||
-3.110177 7.158102 0.071438 0.003494 0.000068
|
||||
-3.047345 5.365727 0.069449 0.007168 0.000135
|
||||
-2.984513 3.873190 0.067495 0.013039 0.000232
|
||||
-2.921681 2.953162 0.067589 0.018855 0.000343
|
||||
-2.858849 1.949554 0.064640 0.028195 0.000480
|
||||
-2.796017 1.391747 0.063570 0.035261 0.000584
|
||||
-2.733186 1.128270 0.061710 0.039189 0.000620
|
||||
-2.670354 0.839970 0.060445 0.043991 0.000667
|
||||
-2.607522 0.624769 0.060762 0.047955 0.000739
|
||||
-2.544690 0.663757 0.060786 0.047211 0.000731
|
||||
-2.481858 1.051932 0.059774 0.040407 0.000617
|
||||
-2.419026 1.463048 0.060422 0.034267 0.000527
|
||||
-2.356194 1.990616 0.055242 0.027734 0.000360
|
||||
-2.293363 2.190692 0.044458 0.025597 0.000210
|
||||
-2.230531 2.553036 0.042144 0.022136 0.000159
|
||||
-2.167699 2.572522 0.043313 0.021964 0.000165
|
||||
-2.104867 2.472360 0.039799 0.022863 0.000157
|
||||
-2.042035 2.517562 0.036792 0.022453 0.000203
|
||||
-1.979203 2.469778 0.036324 0.022887 0.000237
|
||||
-1.916372 2.223125 0.049496 0.025266 0.000565
|
||||
-1.853540 2.080157 0.039205 0.026756 0.000453
|
||||
-1.790708 1.793841 0.041488 0.030011 0.000558
|
||||
-1.727876 1.458784 0.042362 0.034326 0.000565
|
||||
-1.665044 0.914441 0.037561 0.042697 0.000682
|
||||
-1.602212 0.303813 0.028701 0.054540 0.000761
|
||||
-1.539380 0.268335 0.025765 0.055321 0.000771
|
||||
-1.476549 0.000000 0.023371 0.061604 0.000866
|
||||
-1.413717 0.537061 0.026370 0.049671 0.000715
|
||||
-1.350885 1.439940 0.025620 0.034586 0.000547
|
||||
-1.288053 2.391838 0.027653 0.023614 0.000393
|
||||
-1.225221 3.779470 0.027093 0.013538 0.000229
|
||||
-1.162389 5.685555 0.027762 0.006305 0.000111
|
||||
-1.099557 7.661896 0.028996 0.002855 0.000051
|
||||
-1.036726 9.946594 0.032118 0.001142 0.000021
|
||||
-0.973894 12.359408 0.042801 0.000434 0.000009
|
||||
-0.911062 14.954655 0.052443 0.000153 0.000004
|
||||
-0.848230 17.742242 0.063261 0.000050 0.000002
|
||||
-0.785398 20.555785 0.068133 0.000016 0.000001
|
||||
-0.722566 22.811160 0.075518 0.000007 0.000000
|
||||
-0.659734 25.178094 0.086226 0.000003 0.000000
|
||||
-0.596903 26.442288 0.091783 0.000002 0.000000
|
||||
-0.534071 27.897565 0.093175 0.000001 0.000000
|
||||
-0.471239 29.062473 0.096027 0.000001 0.000000
|
||||
-0.408407 30.384521 0.096855 0.000000 0.000000
|
||||
-0.345575 31.638454 0.099956 0.000000 0.000000
|
||||
-0.282743 32.817727 0.107689 0.000000 0.000000
|
||||
-0.219911 33.770369 0.108946 0.000000 0.000000
|
||||
-0.157080 34.505503 0.112902 0.000000 0.000000
|
||||
-0.094248 35.431659 0.120856 0.000000 0.000000
|
||||
-0.031416 35.615810 0.122046 0.000000 0.000000
|
||||
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: "0.9.0"
|
||||
version: "0.9.9"
|
||||
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.
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
use rand::{SeedableRng, StdRng, Rng};
|
||||
use rand::prelude::*;
|
||||
use super::histogram::{Dataset};
|
||||
use super::perform_wham;
|
||||
use super::{Config,calc_free_energy};
|
||||
|
||||
@@ -3,6 +3,7 @@ extern crate wham;
|
||||
extern crate clap;
|
||||
extern crate rand;
|
||||
|
||||
use rand::prelude::*;
|
||||
use clap::App;
|
||||
use wham::Config;
|
||||
use wham::errors::*;
|
||||
@@ -49,7 +50,6 @@ fn cli() -> Result<Config> {
|
||||
.chain_err(|| "Cannot parse bootstrap iteration.")?;
|
||||
let bootstrap_seed: u64 = matches.value_of("bootstrap_seed")
|
||||
.unwrap_or({
|
||||
use rand::Rng;
|
||||
let mut rng = rand::thread_rng();
|
||||
&rng.gen::<u32>().to_string()
|
||||
}).parse()
|
||||
|
||||
Reference in New Issue
Block a user