https://github.com/vitroid/genice-twist
Twist order parameter module for GenIce.
https://github.com/vitroid/genice-twist
Last synced: over 1 year ago
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Twist order parameter module for GenIce.
- Host: GitHub
- URL: https://github.com/vitroid/genice-twist
- Owner: vitroid
- Created: 2019-07-24T18:37:24.000Z (almost 7 years ago)
- Default Branch: main
- Last Pushed: 2021-01-27T07:01:26.000Z (over 5 years ago)
- Last Synced: 2025-02-21T17:19:27.476Z (over 1 year ago)
- Language: Python
- Size: 780 KB
- Stars: 0
- Watchers: 2
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
```shell
genice2 CRN1 -f twist[svg] > sample.svg
```
# [genice2_twist](https://github.com/vitroid/genice-twist/)
Draw the structure with twist order parameter.
version 2.0
## Requirements
* genice2
* genice2-svg>=0.7
* twist-op>=0.2
* sklearn
## Installation from PyPI
```shell
% pip install genice2_twist
```
## Manual Installation
### System-wide installation
```shell
% make install
```
### Private installation
Copy the files in genice2_twist/formats/ into your local formats/ folder.
## Usage
usage:
genice II -f twist[options:separated:by:colons] > file
Output the twist values for all the hydrogen-bonded pairs.
options:
png Draw the hydrogen bonds with a rainbow palette according to the twist value in PNG format.
png:CM Draw the hydrogen bonds with color-mixing scheme in PNG format.
png:DB Draw the hydrogen bonds with decision-boundary coloring scheme in PNG format.
png:SB Draw the hydrogen bonds with simple boundary coloring scheme in PNG format.
svg Draw the hydrogen bonds with a rainbow palette according to the twist value in SVG format.
svg:CM Draw the hydrogen bonds with color-mixing scheme in SVG format.
svg:DB Draw the hydrogen bonds with decision-boundary coloring scheme in SVG format.
svg:SB Draw the hydrogen bonds with simple boundary coloring scheme in SVG format.
yaplot Draw the hydrogen bonds with a rainbow palette according to the twist value in YaPlot format.
shadow Draw shadows to the atoms (PNG and SVG)
Ih=filename.twhist Specify the (two-dimensional) histogram of twist parameter in pure ice Ih.
Ic=filename.twhist Specify the (two-dimensional) histogram of twist parameter in pure ice Ic.
LDL=filename.twhist Specify the (two-dimensional) histogram of twist parameter in pure LDL.
HDL=filename.twhist Specify the (two-dimensional) histogram of twist parameter in pure HDL.
rotatex=30 Rotate the picture (SVG and PNG)
rotatey=30 Rotate the picture (SVG and PNG)
rotatez=30 Rotate the picture (SVG and PNG)
## Auxiliary Files
* IhST2.twhist
* IcST2.twhist
* LDLST2.twhist
* HDLST2.twhist
They are two-dimensional (i.e. real and imaginary) histograms of twist order parameter of ST2 water at 235 K, 0.98 g cm-3. You have to prepare the appropriate histogram if you want to apply CM (color-mixing) or DB (decision-boundary) coloring scheme to other water models or in other conditions.
## Test in place
```shell
% make test
```
## Reference
* Matsumoto, M., Yagasaki, T. & Tanaka, H. A Bayesian approach for identification of ice Ih, ice Ic, high density, and low density liquid water with a torsional order parameter. J. Chem. Phys. 150, 214504 (2019).