genice2 CRN1 -f twist[svg] > sample.svg

genice2_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

% pip install genice2_twist

Manual Installation

System-wide installation

% 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

% 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).