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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 Saitousaitou.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 createdwith the analogy of selected area electron diffraction (SAED) on transmissionelectron microscope (TEM) which typically have up to two axes. However youcan 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 drawsthe 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, anddp_demo() has been opened withoutpairedcry_demo(), the CIF parameters of already openeddp_demo() will beused.

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, drawsthe 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, andcry_demo() has been opened withoutpaireddp_demo(), the CIF parameters of already openedcry_demo() will beused.

Interactive rotation, zooming, and panning of structures are possible usingthe 3D graphics libraryrgl. When the drag originates near the windowedge (within 5%), perform a Z-axis rotation.

This function also performs powder diffraction simulation and saves theresults to a file in the working directory. Currently, it doesn't accountfor 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. Thelabels and Miller indices of the selected atoms or lattice points will bedisplayed.

Usage

select(dev = NULL, verbose = TRUE)

Arguments

Details

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

Value

List of Miller indices or element labels.

Examples

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