rgl.cry

This is a use case for the cry and rgl packages. This package provides tools for selected area electron diffraction (SAED) pattern and crystal structure visualization using the rgl and cry packages. In particular, the cry_demo() and dp_demo() function read files in CIF (Crystallographic Information Framework) format and display SAED patterns and crystal structures. The dp_demo() function also performs simple simulations of powder X-ray diffraction (PXRD) patterns, and the results can be saved to a file in the working directory.

The package has been tested on several platforms, including Linux on Crostini with a Core™ m3-8100Y Chromebook, I found that even on this low-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 widget is drawn. In this example, a file is not specified, so the system default is used.

dp_demo()

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

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 points will 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. The result is saved as a file in the current directory by specifying options like this:

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

The file looks like this:

% sort -n +7 rgl.cry.dp.demo.2024-02-26_000000.dat
     h  k  l        d       absF         lp twotheta
137  0  0  0      Inf 308.117522        Inf  0.00000
136 -1  0  0 5.583222  17.389409 101.955123 15.87322
138  1  0  0 5.583222  17.389409 101.955123 15.87322
128  0 -2  0 4.453238  40.628676  63.820476 19.93782
146  0  2  0 4.453238  40.628676  63.820476 19.93782
129  1 -2  0 4.142661  17.444203  54.849532 21.44963
145 -1  2  0 4.142661  17.444203  54.849532 21.44963

References

Acknowledgment

I would like to express my gratitude to the rgl, cry packages, and R for making this work possible. The data for the scattering factors is based on the data from the KEK Report (Hanashima). For the coloring of the atoms, I used (Helmenstine 2019), and for the atomic radii, I used (Wikipedia contributors 2023).