# Structure of gaussian atoms 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). ```r 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)` ## Returns 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 ```r # 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) ```

structure_gauss function