rgl.cry

This package provides tools for selected area electron diffraction (SAED) pattern and crystal structure visualization by using rgl and cry packages. In particular cry_demo() and dp_demo() read a file in CIF formats (Crystallographic Information Framework) and display SAED pattern and crystal structure. The function dp_demo() also performs simple simulation of powder X-ray diffraction (PXRD) pattern and it can be saved the results 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.

Installation

install.packages("rgl.cry")

Example

A CIF file is read. A reciprocal lattice map with a cell widget drawn. In this example, a file is not specified. Therefore, a system default is used.

dp_demo()

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

cry_demo()

Utility functions

The crystal and diffraction pattern are aligned and displayed.

align("a")
align("c*")
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 0 -2
1 0 0
1 0 2

> cry_demo()
[1] 2
> select()
To select points, use dragging the left mouse button.
To finish, press ESC.
...
O3 
O3 

Extras

dp_demo() can perform PXRD pattern simulation. The result is putted as a file on 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).