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Expand content of asymmetric unit to whole unit cell

expand_to_cell.Rd

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
#> $a
#> [1] 10
#> 
#> $SG
#> [1] "P-1"
#> 
#> $x0
#> [1] 1 2 4 6 8 9
#> 
#> $Z
#> [1] 6 8 6 6 8 6
#> 
#> $B
#> [1] 1.0 1.2 1.1 1.1 1.2 1.0
#> 
#> $occ
#> [1] 1.0 1.0 0.8 0.8 1.0 1.0
#> 

# Nothing changes if imposed SG is "P1" (but you get a warning!)
ltmp <- expand_to_cell(sdata,SG="P1")
#> Warning: Chosen space group different from input data one.
print(ltmp)
#> $a
#> [1] 10
#> 
#> $SG
#> [1] "P1"
#> 
#> $x0
#> [1] 1 2 4
#> 
#> $Z
#> [1] 6 8 6
#> 
#> $B
#> [1] 1.0 1.2 1.1
#> 
#> $occ
#> [1] 1.0 1.0 0.8
#>