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Reduce content of unit cell to asymmetric unit.

reduce_to_asu.Rd

Atom types, B factors and occupancies are restricted to those corresponding to positions in the asymmetric unit, if the input space group (SG) is P-1. Otherwise they are only sorted according to increasing atom positions. If the starting positions do not correspond to a properly symmetry-expanded set, then a warning is issued. If no symmetry is used (P1) the starting set is forced to have values inside the unit cell and it is sorted according to increasing atom positions.

Usage

reduce_to_asu(adata, SG = NULL)

Arguments

adata

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:

  • x0. Vector of real numerics indicating the reduced atomic positions in the asymmetric unit.

  • Z. Vector of integers indicating the reduced atomic numbers for all atoms in the asymmetric unit.

  • B. Vector of real numerics indicating the reduced B factors for all atoms in the asymmetric unit.

  • occ. Vector of real numerics indicating the reduced occupancies for all atoms in the asymmetric unit.

Examples

# Asymmetric unit includes 4 atoms between 0 and a/2, 1 in special position
a <- 10
SG <- "P-1"
x0 <- c(1,2,4,5)
Z <- c(6,8,6,16)
B <- c(1,1.2,1.1,0.8)
occ <- c(1,1,1,0.5)
adata <- standardise_sdata(a,SG,x0,Z,B,occ)
ltmp <- expand_to_cell(adata)
print(ltmp)  # Positions, atomic numbers, etc. have doubled
#> $a
#> [1] 10
#> 
#> $SG
#> [1] "P-1"
#> 
#> $x0
#> [1] 1 2 4 5 6 8 9
#> 
#> $Z
#> [1]  6  8  6 16  6  8  6
#> 
#> $B
#> [1] 1.0 1.2 1.1 0.8 1.1 1.2 1.0
#> 
#> $occ
#> [1] 1 1 1 1 1 1 1
#> 

# Now these expanded values are used as input for reduction
ltmp2 <- reduce_to_asu(ltmp)

# Compare
print(x0)
#> [1] 1 2 4 5
print(ltmp2$x0)
#> [1] 1 2 4 5

# SG is "P1"
a <- 16
SG <- "P1"
x0 <- c(1,2,7,9,12,16)
Z <- c(6,6,8,8,7,6)
B <- c(0,0,0,0,0,0)
occ <- c(1,1,1,1,1,1)
adata <- standardise_sdata(a,SG,x0,Z,B,occ)
ltmp3 <- reduce_to_asu(adata)
print(ltmp3) # Now all positions are inside the unit cell
#> $a
#> [1] 16
#> 
#> $SG
#> [1] "P1"
#> 
#> $x0
#> [1]  0  1  2  7  9 12
#> 
#> $Z
#> [1] 6 6 6 8 8 7
#> 
#> $B
#> [1] 0 0 0 0 0 0
#> 
#> $occ
#> [1] 1 1 1 1 1 1
#>