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7
.github/dependabot.yml
vendored
Normal file
7
.github/dependabot.yml
vendored
Normal file
@@ -0,0 +1,7 @@
|
||||
version: 2
|
||||
updates:
|
||||
- package-ecosystem: "cargo"
|
||||
directory: "/"
|
||||
schedule:
|
||||
interval: "monthly"
|
||||
rebase-strategy: "disabled"
|
||||
45
.github/workflows/build.yml
vendored
Normal file
45
.github/workflows/build.yml
vendored
Normal file
@@ -0,0 +1,45 @@
|
||||
name: Cargo Build and Test
|
||||
on:
|
||||
push:
|
||||
branches: [ "main" ]
|
||||
pull_request:
|
||||
|
||||
concurrency:
|
||||
group: ${{ github.head_ref || github.run_id }}
|
||||
cancel-in-progress: true
|
||||
|
||||
env:
|
||||
CARGO_TERM_COLOR: always
|
||||
|
||||
jobs:
|
||||
build_and_test:
|
||||
name: WHAM Test
|
||||
runs-on: ubuntu-latest
|
||||
strategy:
|
||||
matrix:
|
||||
toolchain:
|
||||
- stable
|
||||
- beta
|
||||
- nightly
|
||||
steps:
|
||||
- uses: actions/checkout@v3
|
||||
- run: rustup update ${{ matrix.toolchain }} && rustup default ${{ matrix.toolchain }}
|
||||
- run: cargo build --verbose
|
||||
- run: cargo test --verbose
|
||||
|
||||
publish:
|
||||
name: WHAM Publish
|
||||
runs-on: ubuntu-latest
|
||||
needs: [build_and_test]
|
||||
steps:
|
||||
- uses: actions/checkout@v3
|
||||
- uses: actions-rs/toolchain@v1
|
||||
with:
|
||||
toolchain: stable
|
||||
override: true
|
||||
- uses: katyo/publish-crates@v2
|
||||
with:
|
||||
registry-token: ${{ secrets.CARGO_REGISTRY_TOKEN }}
|
||||
ignore-unpublished-changes: true
|
||||
dry-run: ${{ github.event_name != 'push' }}
|
||||
|
||||
3
.gitignore
vendored
3
.gitignore
vendored
@@ -1,4 +1,5 @@
|
||||
target
|
||||
reference
|
||||
.idea
|
||||
bench.sh
|
||||
*bench.*
|
||||
*.sublime*
|
||||
406
Cargo.lock
generated
406
Cargo.lock
generated
@@ -1,266 +1,396 @@
|
||||
# This file is automatically @generated by Cargo.
|
||||
# It is not intended for manual editing.
|
||||
version = 3
|
||||
|
||||
[[package]]
|
||||
name = "GSL"
|
||||
version = "1.0.0"
|
||||
name = "addr2line"
|
||||
version = "0.21.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
"pkg-config 0.3.14 (registry+https://github.com/rust-lang/crates.io-index)",
|
||||
"gimli",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "ansi_term"
|
||||
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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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|
||||
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|
||||
|
||||
[[package]]
|
||||
name = "atty"
|
||||
version = "0.2.11"
|
||||
version = "0.2.14"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "d9b39be18770d11421cdb1b9947a45dd3f37e93092cbf377614828a319d5fee8"
|
||||
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|
||||
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|
||||
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|
||||
"winapi 0.3.6 (registry+https://github.com/rust-lang/crates.io-index)",
|
||||
"hermit-abi",
|
||||
"libc",
|
||||
"winapi",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "autocfg"
|
||||
version = "1.1.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "d468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa"
|
||||
|
||||
[[package]]
|
||||
name = "backtrace"
|
||||
version = "0.3.9"
|
||||
version = "0.3.69"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "2089b7e3f35b9dd2d0ed921ead4f6d318c27680d4a5bd167b3ee120edb105837"
|
||||
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|
||||
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|
||||
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|
||||
"libc 0.2.43 (registry+https://github.com/rust-lang/crates.io-index)",
|
||||
"rustc-demangle 0.1.9 (registry+https://github.com/rust-lang/crates.io-index)",
|
||||
"winapi 0.3.6 (registry+https://github.com/rust-lang/crates.io-index)",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "backtrace-sys"
|
||||
version = "0.1.24"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
dependencies = [
|
||||
"cc 1.0.25 (registry+https://github.com/rust-lang/crates.io-index)",
|
||||
"libc 0.2.43 (registry+https://github.com/rust-lang/crates.io-index)",
|
||||
"addr2line",
|
||||
"cc",
|
||||
"cfg-if",
|
||||
"libc",
|
||||
"miniz_oxide",
|
||||
"object",
|
||||
"rustc-demangle",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "bitflags"
|
||||
version = "1.0.4"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
|
||||
[[package]]
|
||||
name = "c_vec"
|
||||
version = "1.0.12"
|
||||
version = "1.3.2"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a"
|
||||
|
||||
[[package]]
|
||||
name = "cc"
|
||||
version = "1.0.25"
|
||||
version = "1.0.83"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "f1174fb0b6ec23863f8b971027804a42614e347eafb0a95bf0b12cdae21fc4d0"
|
||||
dependencies = [
|
||||
"libc",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "cfg-if"
|
||||
version = "0.1.6"
|
||||
version = "1.0.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd"
|
||||
|
||||
[[package]]
|
||||
name = "clap"
|
||||
version = "2.32.0"
|
||||
version = "3.2.25"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "4ea181bf566f71cb9a5d17a59e1871af638180a18fb0035c92ae62b705207123"
|
||||
dependencies = [
|
||||
"ansi_term 0.11.0 (registry+https://github.com/rust-lang/crates.io-index)",
|
||||
"atty 0.2.11 (registry+https://github.com/rust-lang/crates.io-index)",
|
||||
"bitflags 1.0.4 (registry+https://github.com/rust-lang/crates.io-index)",
|
||||
"strsim 0.7.0 (registry+https://github.com/rust-lang/crates.io-index)",
|
||||
"textwrap 0.10.0 (registry+https://github.com/rust-lang/crates.io-index)",
|
||||
"unicode-width 0.1.5 (registry+https://github.com/rust-lang/crates.io-index)",
|
||||
"vec_map 0.8.1 (registry+https://github.com/rust-lang/crates.io-index)",
|
||||
"yaml-rust 0.3.5 (registry+https://github.com/rust-lang/crates.io-index)",
|
||||
"atty",
|
||||
"bitflags",
|
||||
"clap_lex",
|
||||
"indexmap",
|
||||
"strsim",
|
||||
"termcolor",
|
||||
"textwrap",
|
||||
"yaml-rust",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "cloudabi"
|
||||
version = "0.0.3"
|
||||
name = "clap_lex"
|
||||
version = "0.2.4"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "2850f2f5a82cbf437dd5af4d49848fbdfc27c157c3d010345776f952765261c5"
|
||||
dependencies = [
|
||||
"bitflags 1.0.4 (registry+https://github.com/rust-lang/crates.io-index)",
|
||||
"os_str_bytes",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "crossbeam-deque"
|
||||
version = "0.8.3"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "ce6fd6f855243022dcecf8702fef0c297d4338e226845fe067f6341ad9fa0cef"
|
||||
dependencies = [
|
||||
"cfg-if",
|
||||
"crossbeam-epoch",
|
||||
"crossbeam-utils",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "crossbeam-epoch"
|
||||
version = "0.9.15"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "ae211234986c545741a7dc064309f67ee1e5ad243d0e48335adc0484d960bcc7"
|
||||
dependencies = [
|
||||
"autocfg",
|
||||
"cfg-if",
|
||||
"crossbeam-utils",
|
||||
"memoffset",
|
||||
"scopeguard",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "crossbeam-utils"
|
||||
version = "0.8.16"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "5a22b2d63d4d1dc0b7f1b6b2747dd0088008a9be28b6ddf0b1e7d335e3037294"
|
||||
dependencies = [
|
||||
"cfg-if",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "either"
|
||||
version = "1.9.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "a26ae43d7bcc3b814de94796a5e736d4029efb0ee900c12e2d54c993ad1a1e07"
|
||||
|
||||
[[package]]
|
||||
name = "error-chain"
|
||||
version = "0.12.0"
|
||||
version = "0.12.4"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "2d2f06b9cac1506ece98fe3231e3cc9c4410ec3d5b1f24ae1c8946f0742cdefc"
|
||||
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|
||||
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|
||||
"backtrace",
|
||||
"version_check",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "fuchsia-zircon"
|
||||
version = "0.3.3"
|
||||
name = "getrandom"
|
||||
version = "0.2.10"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
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|
||||
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|
||||
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||||
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|
||||
"cfg-if",
|
||||
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|
||||
"wasi",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "fuchsia-zircon-sys"
|
||||
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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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|
||||
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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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|
||||
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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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|
||||
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||||
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||||
|
||||
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||||
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||||
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|
||||
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23
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23
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@@ -1,19 +1,26 @@
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[features]
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|
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112
README.md
112
README.md
@@ -1,4 +1,6 @@
|
||||
[](https://travis-ci.com/danijoo/WHAM) [](https://www.crates.io/crates/wham)
|
||||
[](https://travis-ci.com/danijoo/WHAM) [](https://www.crates.io/crates/wham) [](https://doi.org/10.5281/zenodo.1488597)
|
||||
|
||||
|
||||
|
||||
Weighted Histogram Analysis Method (WHAM)
|
||||
===
|
||||
@@ -10,18 +12,14 @@ from umbrella sampling simulations. For more details on the method, I suggest *R
|
||||
Features
|
||||
---
|
||||
- Fast, especially for small systems
|
||||
- Multidimensional
|
||||
- Error analysis
|
||||
- Multithreaded (automatically runs on all available cores)
|
||||
- Multidimensional (any number of collective variables are possible)
|
||||
- Autocorrelation to remove correlated samples
|
||||
- Error analysis via bootstrapping
|
||||
- Unit tested
|
||||
|
||||
Installation
|
||||
---
|
||||
WHAM requires the GSL library to be installed:
|
||||
```bash
|
||||
# on debian/ubuntu:
|
||||
sudo apt-get install libgsl0-dev
|
||||
```
|
||||
|
||||
Installation from source via cargo:
|
||||
```bash
|
||||
# cargo installation
|
||||
@@ -35,7 +33,71 @@ Usage
|
||||
wham has a convenient command line interface. You can see all options with
|
||||
```wham -h```:
|
||||
|
||||
To run the two dimensional example (simulation of dialanine phi and psi angle):
|
||||
```
|
||||
wham 1.1.0
|
||||
D. Bauer <bauer@cbs.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
|
||||
-g, --uncorr Estimates statistical inefficiency of each timeseries via autocorrelation and removes correlated
|
||||
samples (default is off).
|
||||
-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.
|
||||
--convdt <convdt> 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.
|
||||
--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).
|
||||
```
|
||||
|
||||
Examples
|
||||
---
|
||||
The example folder contains input and output files for two simple test systems:
|
||||
|
||||
- 1d_cyclic: Phi torsion angle of dialanine in vaccum
|
||||
- 2d_cyclic: Phi and psi torsion angles of the same system
|
||||
|
||||
The command below will run the two dimensional example (simulation of dialanine phi and psi angle) and calculate the free energy based on the two collective variables
|
||||
in the range of -3.14 to 3.14, with 100 bins in each dimension and periodic collective variables:
|
||||
|
||||
```bash
|
||||
wham --max 3.14,3.14 --min -3.14,-3.14 -T 300 --bins 100,100 --cyclic -f example/2d/metadata.dat
|
||||
> Supplied WHAM options: Metadata=example/2d/metadata.dat, hist_min=[-3.14, -3.14], hist_max=[3.14, 3.14], bins=[100, 100] verbose=false, tolerance=0.000001, iterations=100000, temperature=300, cyclic=true
|
||||
@@ -52,7 +114,6 @@ wham --max 3.14,3.14 --min -3.14,-3.14 -T 300 --bins 100,100 --cyclic -f example
|
||||
```
|
||||
After convergence, final bias offsets (F) and the free energy will be dumped to stdout and the output file is written.
|
||||
|
||||
|
||||
The output file contains the free energy and probability for each bin. Probabilities are normalized to sum to P=1.0 and
|
||||
the smallest free energy is set to 0 (with other free energies based on that).
|
||||
```
|
||||
@@ -72,33 +133,32 @@ the smallest free energy is set to 0 (with other free energies based on that).
|
||||
Error analysis
|
||||
---
|
||||
WHAM can perform error analysis using the bayesian bootstrapping method. Every simulation window is assumed to be an
|
||||
individual set of data point. By calculating probabilities N times with randomly assigned weights for each window,
|
||||
individual set of data points. By calculating probabilities N times with randomly assigned weights for each window,
|
||||
one can estimate the error as standard deviation between the N bootstrapping runs. For more details see
|
||||
*Van der Spoel, D. et al. (2010). g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and
|
||||
Autocorrelation Estimates, JCTC, 6(12), 3713-3720*.
|
||||
|
||||
To perform bayesian bootstrapping in WHAM, use the ```-bt <RUNS>``` flag to perform <RUNS> individual bootstrapping
|
||||
runs. The error estimates of bin probabilities and free energy will be given as separate column (+/-) in the output file.
|
||||
If no error analysis is performed, these columns are set to 0.0.
|
||||
runs. The error estimates of bin probabilities and free energy will be given as standard error (SE) in a
|
||||
separate column (+/-) in the output file. If no error analysis is performed, these columns are set to 0.0.
|
||||
|
||||
Examples
|
||||
Autocorrelation analysis
|
||||
---
|
||||
The example folder contains input and output files for two simple test systems:
|
||||
With the ```--uncorr``` flag, WHAM calculates the autocorrelation time ```tau``` for all timeseries and all collective
|
||||
variables. Timeseries are then filtered based on their highest autocorrelation time to remove correlated samples from
|
||||
the dataset. This reduces the number of data points but can improve the accuracy of the result.
|
||||
|
||||
- 1d: Phi torsion angle of dialanine in vaccum
|
||||
- 2d: Phi and psi torsion angles of the same system
|
||||
For filtering, the statistical inefficiency `g` is calculated: ```g = 1 + 2*tau```, and only every `g`th element of the
|
||||
timeseries is used for unbiasing. A more detailed description of the method can be found in
|
||||
*Chodera, J.D. et al. (2007). Use of the weighted histogram analysis method for the analysis of simulated and parallel
|
||||
tempering simulations, JCTC 3(1):26-41*
|
||||
|
||||
|
||||
TODO
|
||||
---
|
||||
- Multithreading (?)
|
||||
- Autocorrelation
|
||||
- Replica exchange
|
||||
|
||||
License
|
||||
License & Citing
|
||||
---
|
||||
WHAM is licensed under the GPL-3.0 license. Please read the LICENSE file in this
|
||||
repository for more information.
|
||||
|
||||
There's no publication for this WHAM implementation. However, there is a citeabe DOI. If you use this software for your work, please consider citing it: *Bauer, D., WHAM - An efficient weighted histogram analysis implementation written in Rust, Zenodo. https://doi.org/10.5281/zenodo.1488597*
|
||||
|
||||
Parts of this work, especially some perfomance optimizations and the I/O format, are inspired by the
|
||||
implementation of A. Grossfield (*Grossfield, A, WHAM: the weighted histogram analysis method, http://membrane.urmc.rochester.edu/content/wham*).
|
||||
|
||||
@@ -1,101 +0,0 @@
|
||||
#coord1 Free Energy +/- Probability +/-
|
||||
-3.108600 7.118166 0.000000 0.003561 0.000000
|
||||
-3.045800 5.331290 0.000000 0.007290 0.000000
|
||||
-2.983000 3.879241 0.000000 0.013048 0.000000
|
||||
-2.920200 2.968659 0.000000 0.018796 0.000000
|
||||
-2.857400 1.942494 0.000000 0.028362 0.000000
|
||||
-2.794600 1.418408 0.000000 0.034994 0.000000
|
||||
-2.731800 1.169398 0.000000 0.038668 0.000000
|
||||
-2.669000 0.843024 0.000000 0.044073 0.000000
|
||||
-2.606200 0.636021 0.000000 0.047887 0.000000
|
||||
-2.543400 0.720123 0.000000 0.046299 0.000000
|
||||
-2.480600 1.066434 0.000000 0.040297 0.000000
|
||||
-2.417800 1.509855 0.000000 0.033734 0.000000
|
||||
-2.355000 2.015549 0.000000 0.027544 0.000000
|
||||
-2.292200 2.226942 0.000000 0.025306 0.000000
|
||||
-2.229400 2.573176 0.000000 0.022026 0.000000
|
||||
-2.166600 2.591946 0.000000 0.021861 0.000000
|
||||
-2.103800 2.476835 0.000000 0.022893 0.000000
|
||||
-2.041000 2.513953 0.000000 0.022555 0.000000
|
||||
-1.978200 2.470032 0.000000 0.022956 0.000000
|
||||
-1.915400 2.227585 0.000000 0.025299 0.000000
|
||||
-1.852600 2.105310 0.000000 0.026570 0.000000
|
||||
-1.789800 1.778779 0.000000 0.030286 0.000000
|
||||
-1.727000 1.447127 0.000000 0.034593 0.000000
|
||||
-1.664200 0.906384 0.000000 0.042968 0.000000
|
||||
-1.601400 0.304263 0.000000 0.054699 0.000000
|
||||
-1.538600 0.247397 0.000000 0.055960 0.000000
|
||||
-1.475800 0.000000 0.000000 0.061795 0.000000
|
||||
-1.413000 0.536142 0.000000 0.049843 0.000000
|
||||
-1.350200 1.428046 0.000000 0.034859 0.000000
|
||||
-1.287400 2.398149 0.000000 0.023627 0.000000
|
||||
-1.224600 3.784647 0.000000 0.013552 0.000000
|
||||
-1.161800 5.696583 0.000000 0.006297 0.000000
|
||||
-1.099000 7.656158 0.000000 0.002870 0.000000
|
||||
-1.036200 9.955000 0.000000 0.001142 0.000000
|
||||
-0.973400 12.357407 0.000000 0.000436 0.000000
|
||||
-0.910600 14.954254 0.000000 0.000154 0.000000
|
||||
-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
|
||||
9
example/1d_cyclic/README.txt
Normal file
9
example/1d_cyclic/README.txt
Normal file
@@ -0,0 +1,9 @@
|
||||
Example data: Dialanine torsion angle at 300K
|
||||
wham.out was produced with the folling settings:
|
||||
|
||||
wham --max pi --min -pi --cyclic\
|
||||
--bins 100 \
|
||||
-T 300 \
|
||||
-f metadata.dat \
|
||||
-o wham.out \
|
||||
--bt 100 --seed 1234
|
||||
101
example/1d_cyclic/wham.out
Normal file
101
example/1d_cyclic/wham.out
Normal file
@@ -0,0 +1,101 @@
|
||||
#coord1 Free Energy +/- Probability +/-
|
||||
-3.110177 7.158102 0.000000 0.003494 0.000000
|
||||
-3.047345 5.365727 0.000000 0.007168 0.000000
|
||||
-2.984513 3.873190 0.000000 0.013039 0.000000
|
||||
-2.921681 2.953162 0.000000 0.018855 0.000000
|
||||
-2.858849 1.949554 0.000000 0.028195 0.000000
|
||||
-2.796017 1.391747 0.000000 0.035261 0.000000
|
||||
-2.733186 1.128270 0.000000 0.039189 0.000000
|
||||
-2.670354 0.839970 0.000000 0.043991 0.000000
|
||||
-2.607522 0.624769 0.000000 0.047955 0.000000
|
||||
-2.544690 0.663757 0.000000 0.047211 0.000000
|
||||
-2.481858 1.051932 0.000000 0.040407 0.000000
|
||||
-2.419026 1.463048 0.000000 0.034267 0.000000
|
||||
-2.356194 1.990616 0.000000 0.027734 0.000000
|
||||
-2.293363 2.190692 0.000000 0.025597 0.000000
|
||||
-2.230531 2.553036 0.000000 0.022136 0.000000
|
||||
-2.167699 2.572522 0.000000 0.021964 0.000000
|
||||
-2.104867 2.472360 0.000000 0.022863 0.000000
|
||||
-2.042035 2.517562 0.000000 0.022453 0.000000
|
||||
-1.979203 2.469778 0.000000 0.022887 0.000000
|
||||
-1.916372 2.223125 0.000000 0.025266 0.000000
|
||||
-1.853540 2.080157 0.000000 0.026756 0.000000
|
||||
-1.790708 1.793841 0.000000 0.030011 0.000000
|
||||
-1.727876 1.458784 0.000000 0.034326 0.000000
|
||||
-1.665044 0.914441 0.000000 0.042697 0.000000
|
||||
-1.602212 0.303813 0.000000 0.054540 0.000000
|
||||
-1.539380 0.268335 0.000000 0.055321 0.000000
|
||||
-1.476549 0.000000 0.000000 0.061604 0.000000
|
||||
-1.413717 0.537061 0.000000 0.049671 0.000000
|
||||
-1.350885 1.439940 0.000000 0.034586 0.000000
|
||||
-1.288053 2.391838 0.000000 0.023614 0.000000
|
||||
-1.225221 3.779470 0.000000 0.013538 0.000000
|
||||
-1.162389 5.685555 0.000000 0.006305 0.000000
|
||||
-1.099557 7.661896 0.000000 0.002855 0.000000
|
||||
-1.036726 9.946594 0.000000 0.001142 0.000000
|
||||
-0.973894 12.359408 0.000000 0.000434 0.000000
|
||||
-0.911062 14.954655 0.000000 0.000153 0.000000
|
||||
-0.848230 17.742242 0.000000 0.000050 0.000000
|
||||
-0.785398 20.555785 0.000000 0.000016 0.000000
|
||||
-0.722566 22.811160 0.000000 0.000007 0.000000
|
||||
-0.659734 25.178094 0.000000 0.000003 0.000000
|
||||
-0.596903 26.442288 0.000000 0.000002 0.000000
|
||||
-0.534071 27.897565 0.000000 0.000001 0.000000
|
||||
-0.471239 29.062473 0.000000 0.000001 0.000000
|
||||
-0.408407 30.384521 0.000000 0.000000 0.000000
|
||||
-0.345575 31.638454 0.000000 0.000000 0.000000
|
||||
-0.282743 32.817727 0.000000 0.000000 0.000000
|
||||
-0.219911 33.770369 0.000000 0.000000 0.000000
|
||||
-0.157080 34.505503 0.000000 0.000000 0.000000
|
||||
-0.094248 35.431659 0.000000 0.000000 0.000000
|
||||
-0.031416 35.615810 0.000000 0.000000 0.000000
|
||||
0.031416 35.561946 0.000000 0.000000 0.000000
|
||||
0.094248 35.382089 0.000000 0.000000 0.000000
|
||||
0.157080 34.934827 0.000000 0.000000 0.000000
|
||||
0.219911 33.673460 0.000000 0.000000 0.000000
|
||||
0.282743 32.731563 0.000000 0.000000 0.000000
|
||||
0.345575 31.261855 0.000000 0.000000 0.000000
|
||||
0.408407 29.717377 0.000000 0.000000 0.000000
|
||||
0.471239 28.076620 0.000000 0.000001 0.000000
|
||||
0.534071 26.481097 0.000000 0.000002 0.000000
|
||||
0.596903 24.487358 0.000000 0.000003 0.000000
|
||||
0.659734 22.344251 0.000000 0.000008 0.000000
|
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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 +/-
|
||||
-3.110177 7.158102 0.066061 0.003494 0.000070
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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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|
||||
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||||
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|
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|
||||
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|
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|
||||
1.539380 14.520167 0.110164 0.000183 0.000010
|
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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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|
||||
3.047345 11.092386 0.074513 0.000722 0.000020
|
||||
3.110177 9.065722 0.068298 0.001626 0.000036
|
||||
101
example/1d_cyclic/wham_uncorrelated.out
Normal file
101
example/1d_cyclic/wham_uncorrelated.out
Normal file
@@ -0,0 +1,101 @@
|
||||
#coord1 Free Energy +/- Probability +/-
|
||||
-3.110177 7.531315 0.000000 0.003080 0.000000
|
||||
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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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|
||||
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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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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
10001
example/2d/wham.out
10001
example/2d/wham.out
File diff suppressed because it is too large
Load Diff
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user