expand_to_cell: Expand content of asymmetric unit to whole unit cell

In crone: Structural Crystallography in 1d

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 read_x. 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.

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)

crone documentation built on Aug. 24, 2019, 5:03 p.m.