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rgl.cry

This is a use case for thecry andrglpackages. This package provides tools for selected area electrondiffraction (SAED) pattern and crystal structure visualization using thergl andcry packages. In particular, thecry_demo() anddp_demo() function read filesin CIF (Crystallographic Information Framework) format and display SAEDpatterns and crystal structures. Thedp_demo() functionalso performs simple simulations of powder X-ray diffraction (PXRD)patterns, and the results can be saved to a file in the workingdirectory.

The package has been tested on several platforms, including Linux onCrostini with a Core™ m3-8100Y Chromebook, I found that even on thislow-powered platform, the performance was acceptable.

Web Resources

https://saitoutoshihide.github.io/rgl.cry/

Installation

install.packages("rgl.cry")

Example

A CIF file is read, and a reciprocal lattice map with a cell widgetis drawn. In this example, a file is not specified, so the systemdefault is used.

dp_demo()

A CIF file is read, and a crystal structure with a axis widget isdrawn.

cry_demo()

Utility functions

The crystal and diffraction pattern are aligned and displayed.

align("a")align("ra")align("30 30")# x, y (deg)

Select one or more atoms or reciprocal lattice points in the window.The labels and Miller indices of the selected atoms or lattice pointswill be displayed.

>dp_demo()[1]1>select()To select points, use dragging the left mouse button.To finish, press ESC.. [1]"1 1 -3""1 0 -2""2 0 -2""1 1 -1""1 0 0""2 0 0""1 1 1""1 0 2">cry_demo()[1]2>select()To select points, use dragging the left mouse button.To finish, press ESC..[1]"Ti1""Ti1"

Extras

dp_demo() can perform PXRD pattern simulation. Theresult is saved as a file in the current directory by specifying optionslike this:

## Output the simulation results of the PXDR pattern as a file.dp_demo(xrd =TRUE)

The file looks like this:

References