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Daniel Bauer
2021-07-17 14:44:09 +02:00
parent c27dbb7ab5
commit c05becea22
4 changed files with 10 additions and 6 deletions
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2
Cargo.lock generated
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@@ -362,7 +362,7 @@ checksum = "cccddf32554fecc6acb585f82a32a72e28b48f8c4c1883ddfeeeaa96f7d8e519"
[[package]] [[package]]
name = "wham" name = "wham"
version = "1.0.0" version = "1.1.0"
dependencies = [ dependencies = [
"assert_approx_eq", "assert_approx_eq",
"clap", "clap",

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Cargo.toml
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@@ -1,6 +1,6 @@
[package] [package]
name = "wham" name = "wham"
version = "1.0.0" version = "1.1.0"
authors = ["Daniel Bauer <bauer@cbs.tu-darmstadt.de>"] authors = ["Daniel Bauer <bauer@cbs.tu-darmstadt.de>"]
description = "An implementation of the weighted histogram analysis method" description = "An implementation of the weighted histogram analysis method"
license = "GPL-3.0" license = "GPL-3.0"

10
README.md
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@@ -34,8 +34,8 @@ wham has a convenient command line interface. You can see all options with
```wham -h```: ```wham -h```:
``` ```
wham 1.0.0 wham 1.1.0
D. Bauer <bauer@bio.tu-darmstadt.de> 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 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. potential of mean force (PMF) calculations in multiple dimensions at constant temperature.
@@ -56,7 +56,7 @@ The first column will be ignored and is followed by N reaction coordinates x.
Shipped under the GPLv3 license. Shipped under the GPLv3 license.
USAGE: USAGE:
wham [FLAGS] [OPTIONS] --bins <BINS> --max <HIST_MAX> --file <METADATA> --min <HIST_MIN> --temperature <temperature> wham [FLAGS] [OPTIONS] --bins <BINS> --max <HIST_MAX> --file <METADATA> --min <HIST_MIN> --temperature <temperature>
FLAGS: FLAGS:
-c, --cyclic For periodic reaction coordinates. If this is set, the first and last coordinate bin in each -c, --cyclic For periodic reaction coordinates. If this is set, the first and last coordinate bin in each
@@ -72,6 +72,10 @@ OPTIONS:
--bt <bootstrap> Number of bayesian bootstrapping runs for error analysis by assigning random --bt <bootstrap> Number of bayesian bootstrapping runs for error analysis by assigning random
weights (defaults to 0). weights (defaults to 0).
--seed <bootstrap_seed> Random seed for bootstrapping runs. --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) --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). -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". --max <HIST_MAX> Histogram maxima (comma separated). Also accepts "pi".

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src/cli.yml
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@@ -1,5 +1,5 @@
name: wham name: wham
version: "1.0.0" version: "1.1.0"
author: D. Bauer <bauer@cbs.tu-darmstadt.de> author: D. Bauer <bauer@cbs.tu-darmstadt.de>
about: | 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. 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.