rgl.cry: 'cry' and 'rgl' — Applications in Crystallography

Description

Visualizing crystal structures and selected area electron diffraction (SAED) patterns. It provides functions cry_demo() and dp_demo() to load a file in 'CIF' (Crystallographic Information Framework) formats and display crystal structures and electron diffraction patterns. The function dp_demo() also performs simple simulation 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. T. Hanashima (2001) https://www2.kek.jp/imss/pf/tools/sasaki/sinram/sinram.html Todd Helmenstine (2019) https://sciencenotes.org/molecule-atom-colors-cpk-colors/ Wikipedia contributors (2023) https://en.wikipedia.org/w/index.php?title=Atomic_radius&oldid=1179864711.

Author(s)

Maintainer: Toshihide Saitou saitou.toshihide@gmail.com [copyright holder]

See Also

Useful links:

• https://github.com/SaitouToshihide/rgl.cry/

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

Align crystal and diffraction pattern

Description

Align crystal and diffraction pattern and displayed.

Usage

align(ax, dev = NULL, verbose = TRUE)

Arguments

Details

There is no z-axis alignment support because the visualization was created with the analogy of selected area electron diffraction (SAED) on transmission electron microscope (TEM) which typically have up to two axes. However you can rotate around the z-axis by the drag originates near the window edge.

Value

No return value, called for side effects.

Examples

if (interactive()) {
 align("a")
 align("rb")
 align("1 1 0")
 align("60 -30")
 align(dev = 123, "a")
}

Examples of using the cry and rgl packages together.

Description

Read a file in CIF formats, set the parameters, calculates them, and draws the crystal structure with an axis widget.

Usage

cry_demo(file = NULL, rf = 1, type = "b", zoom = 1)

Arguments

Details

If no file argument is provided, and dp_demo() has been opened without paired cry_demo(), the CIF parameters of already opened dp_demo() will be used.

Value

An integer the device number of the currently window.

Examples

cry_demo()
cry_demo(system.file("orthorhombic_p.cif", package = "rgl.cry"))


if (interactive()) {
 cry_demo(file, type = "fill", zoom = 0.5)
 cry_demo("https://www.crystallography.net/cod/foo.cif")
}

Examples of using the cry and rgl packages together.

Description

Read a file in CIF formats, set and the parameters, calculates them, draws the reciprocal lattice map with a cell widget.

Usage

dp_demo(file = NULL, reso = 1.2, ews.r = 40, zoom = 0.5, xrd = FALSE)

Arguments

Details

If no file argument is provided, and cry_demo() has been opened without paired dp_demo(), the CIF parameters of already opened cry_demo() will be used.

Interactive rotation, zooming, and panning of structures are possible using the 3D graphics library rgl. When the drag originates near the window edge (within 5%), perform a Z-axis rotation.

This function also performs powder diffraction simulation and saves the results to a file in the working directory. Currently, it doesn't account for atomic ionization and uses standard atomic scattering factors.

Value

An integer the device number of the currently window.

Examples

dp_demo()
dp_demo(system.file("orthorhombic_p.cif", package = "rgl.cry"))
dp_demo(system.file("orthorhombic_p.cif", package = "rgl.cry"), res = 2.0)


if (interactive()) {
 dp_demo(file, zoom = 0.5)
 dp_demo("https://www.crystallography.net/cod/foo.cif")
}

Examples of using the cry and rgl packages together.

Description

Output a lCIF.

Usage

getCIF(dev = NULL)

Arguments

Value

A named list, the same as that of 'cry::readCIF.'

Examples

getCIF()

Select atoms or reciprocal lattice points.

Description

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.

Usage

select(dev = NULL, verbose = TRUE)

Arguments

Details

Selecting atoms or lattice points in the window will include all z-coordinates. If you do not want to include all z-coordinates, you will need to modify the code.

Value

List of Miller indices or element labels.

Examples

if (interactive()) {
 select()
 select(dev = 123)
}