| expand_to_cell {crone} | R Documentation |
Expand content of asymmetric unit to whole unit cell
Description
Atom positions, types, B factors and occupancies are duplicated if input space group (SG) is P-1; otherwise they are left untouched (space group P1). Value of the occupancy for special positions is barely checked for values outside [0,1] range. Extra-care needed.
Usage
expand_to_cell(sdata, SG = NULL)
Arguments
sdata |
A named list, normally obtained through the use of
function
|
SG |
2-letters character string. There are only two symmetries possible when working within 1D crystallography, P1 (no symmetry) and P-1 (inversion through the origin). SG can be either "P1" or "P-1" for this function. Default is NULL, in which case the space group is assumed to be equal to the one of the input structure. |
Value
A named list with the following elements:
a. Real numeric. The size of the unit cell.
SG. Character string. Name of the space group, 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.
Examples
# Asymmetric unit includes 3 atoms between 0 and a/2
a <- 10
SG <- "P-1"
x0 <- c(1,2,4)
Z <- c(6,8,6)
B <- c(1,1.2,1.1)
occ <- c(1,1,0.8)
sdata <- standardise_sdata(a,SG,x0,Z,B,occ)
ltmp <- expand_to_cell(sdata)
print(ltmp) # Positions, atomic numbers, etc. have doubled
# Nothing changes if imposed SG is "P1" (but you get a warning!)
ltmp <- expand_to_cell(sdata,SG="P1")
print(ltmp)