structure_gauss: Structure of gaussian atoms

In jfoadi/crone: Structural Crystallography in 1d

Structure of gaussian atoms

Description

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)
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)

jfoadi/crone documentation built on Sept. 10, 2022, 4:34 p.m.