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Description:

genicetwist 0.1.2

genice-twist
Draw the structure with twist order parameter.
version 0.1.2
Requirements

genice<2.0
genice-svg>=0.4
twist-op>=0.2
sklearn

Installation from PyPI
% pip install genice_twist

Manual Installation
System-wide installation
% make install

Private Installation
Copy the files in 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
% 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).