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Structure of gaussian atoms

structure_gauss.Rd

Structure formed by all gaussian atoms in the unit cell. Positions, atomic numbers and thermal factors are given by vectors of a same length. Each atom forming the structure is also characterised by a given occupancy (between 0 and 1).

Usage

structure_gauss(sdata, x = NULL, N = NULL, k = ksigma)

Arguments

sdata

A named list, normally obtained through the use of function read_x or standardise_sdata. The list names correspond to different object types:

  • a. Real numeric. The size of the unit cell.

  • SG. Character string. Space group symbol; either "P1" or "P-1"

  • x0. Vector of real numerics indicating the expanded atomic positions in the unit cell.

  • Z. Vector of integers indicating the expanded atomic numbers for all atoms in the unit cell.

  • B. Vector of real numerics indicating the expanded B factors for all atoms in the unit cell.

  • occ. Vector of real numerics indicating the expanded occupancies for all atoms in the unit cell.

x

Point in the 1D cell at which this function is calculated. Default is NULL, in which case a grid is set up internally.

N

Integer. Number of points in the regular grid, if the grid is not provided directly.

k

A real number. It controls the standard deviation of the gaussian function describing the atom and, thus, the shape of the associated peak. The standard deviation sigma is given by: sigma = k * sqrt(Z)

Value

A named list of length 2: x is the grid (either input by user or set up internally), rr is a vector of length equal to the length of vector x, with values equal to the evaluated gaussian atoms.

Examples

# Cell, atom types, positions and B factors
a <- 10
SG <- "P1"
x0 <- c(2,5,7)
Z <- c(6,16,8)
B <- c(0,0,0)

# All occupancies to 1
occ <- c(1,1,1)

# Standard data format
sdata <- standardise_sdata(a,SG,x0,Z,B,occ)

# Grid for unit cell
x <- seq(0,a,length=1000)

# Structure density
rtmp <- structure_gauss(sdata,x)
#> Warning: Out-of-scale occupancies produced!
plot(rtmp$x,rtmp$rr,type="l",xlab="x",ylab=expression(rho))

# Now reduce occupancy of sulphur
occ[2] <- 0.5
sdata <- standardise_sdata(a,SG,x0,Z,B,occ)
rtmp <- structure_gauss(sdata,x)
points(rtmp$x,rtmp$rr,type="l",col=2)

# Increase temperature of oxygen
B[3] <- 10
sdata <- standardise_sdata(a,SG,x0,Z,B,occ)
rtmp <- structure_gauss(sdata,x)
points(rtmp$x,rtmp$rr,type="l",col=3)