Package 'rgl.cry'

Align crystal and diffraction pattern

Description

Align crystal and diffraction pattern and displayed.

Usage

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

Arguments

ax	An axis to align
dev	RGL device to apply. Defaults to current device.
verbose	logical: Should the report be suppressed?

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")
}

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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,
  abc = c(0, 0, 0),
  clipplanes = rbind(c(0, 0, 0, 0))
)

Arguments

file	Optional file in CIF formats. The file can also be specified by URL.
rf	A positive value indicating the scale factor of atom radius.
type	A style of atom displaying such like ball, fill and ball-stick but ball-stick is not implemented.
zoom	A positive value indicating the current scene magnification.
abc	A length-3 integer vector of repetitions along the a, b, c axes.
clipplanes	A list of numeric vectors representing clip planes. Each vector should contain four elements (a, b, c, d). Round the values to one decimal places before making the final determination in the internal process.

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"))

cry_demo(system.file("rhombohedral_r.cif", package = "rgl.cry"), abc = c(1,1,1),
  clipplanes = rbind(c(2.885490, 4.158112, -3.374928, -37.01),
                      c(2.885490, -5.082574, 1.687449, -37.01),
                      c(-5.7709802, 0.9244616, 1.6874797, -37.01),
                      c(-2.885490, -4.158112, 3.374928, -37.01),
                      c(-2.885490, 5.082574, -1.687449, -37.01),
                      c(5.7709802, -0.9244616, -1.6874797, -37.01),
                      c(5.771090, 8.316383, 15.180433, -332.92),
                      c(-5.771090, -8.316383, -15.180433, 0.01)))

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


  ## A rhombohedral crystal.
  cry_demo(system.file("rhombohedral_r.cif", package = "rgl.cry"))

  ## Extract crystal structure data from the internal processing of the package.
  library(pryr)
  lCIF <- rgl.cry:::pkg$inst[[nrow(rgl.cry:::pkg$inst), "lCIF"]]
  a <- lCIF$HEADER$CELL$A$VAL
  b <- lCIF$HEADER$CELL$B$VAL
  c <- lCIF$HEADER$CELL$C$VAL
  aa <- lCIF$HEADER$CELL$ALPHA$VAL # degree
  bb <- lCIF$HEADER$CELL$BETA$VAL
  cc <- lCIF$HEADER$CELL$GAMMA$VAL
  mat02 <- cry::xtal_mat02(a, b, c, aa, bb, cc)

  ea1 <- as.numeric(c(1, 0, 0) %*% mat02) # lattice vector
  ea2 <- as.numeric(c(0, 1, 0) %*% mat02)
  ea3 <- as.numeric(c(0, 0, 1) %*% mat02)
  ec3 <- ea1 + ea2 + ea3  # c-axis in a hexagonal crystal.

  ## a_hex is calculated as a - b, b_hex as b - c, and one of the clip planes is denoted as
  ## (a_hex + (a_hex + b_hex)) / 2 = a - b + a - b + b - c = 2a - b - c = a - (b + c) / 2.
  cp1 <- ea1 - (ea2 + ea3)/2
  cp2 <- ea2 - (ea3 + ea1)/2
  cp3 <- ea3 - (ea1 + ea2)/2

  cry_demo(system.file("rhombohedral_r.cif", package = "rgl.cry"), abc = c(1,1,1),
         clipplanes = rbind(
           c(cp1, -crossprod(cp1)),
           c(cp2, -crossprod(cp2)),
           c(cp3, -crossprod(cp3)),
           c(-cp1, -crossprod(cp1)),
           c(-cp2, -crossprod(cp2)),
           c(-cp3, -crossprod(cp3)),
           c(ec3, -crossprod(ec3)),
           c(-ec3, 0)))
}

---

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,
  hkl_labels = TRUE,
  xrd = FALSE
)

Arguments

file	Optional file in CIF formats.
reso	A real number. The highest data resolution, in angstroms. If the default value takes a long time to process displaying due to the large number of lattice points, you can expect to improve performance by increasing the value.
ews.r	Ewald sphere radius in angstrom^-1.
zoom	A positive value indicating the current scene magnification.
hkl_labels	A logical value indecating whether to show or hide the hkl index labels. Defaults to TRUE.
xrd	A logical value indicating whether to create an X-ray diffraction pattern simulation result file.

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")
}

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Examples of using the cry and rgl packages together.

Description

Output a lCIF.

Usage

getCIF(dev = NULL)

Arguments

dev	The device that is used to extract the lCIF. The default is current device.

Value

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

Examples

getCIF()

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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

dev	RGL device to apply. Defaults to current device.
verbose	logical: Should the report be suppressed?

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)
}

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