Replicate Atomic Coordinates
Replicate atomic coordinates using periodic boundary conditions.
replicate(x, ...) ## S3 method for class 'coords' replicate(x, cryst1 = NULL, a.ind = 0, b.ind = 0, c.ind = 0, ...) ## S3 method for class 'atoms' replicate(x, cryst1 = NULL, a.ind = 0, b.ind = 0, c.ind = 0, ...) ## S3 method for class 'pdb' replicate(x, a.ind = 0, b.ind = 0, c.ind = 0, cryst1 = NULL, ...)
x |
an R object containing atomic coordinates to be replicated. |
cryst1 |
an object of class ‘cryst1’ containing periodical boundary conditions used for replicating. |
a.ind |
a vector of integers indicating the positions of the replicated cells along the a-axis. |
b.ind |
a vector of integers indicating the positions of the replicated cells along the b-axis. |
c.ind |
a vector of integers indicating the positions of the replicated cells along the c-axis. |
... |
further arguments passed to or from other methods. |
The replicate function replicate a unit cell along the lattice vectors a, b and c
as as many times as indicated by the a.ind, b.ind and c.ind arguments.
Discontinuous integer vectors can be used for a.ind, b.ind and c.ind
to create layered supercells (See examples).
Return an object of class ‘pdb’ with replicated atomic coordinates.
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb",package="Rpdb"))
# Create a 3x3 supercell
y <- replicate(x, a.ind= 0:2, b.ind = 0:2, c.ind = 0:2)
# Create a 3x3 supercell which might need to be wrapped (some molecules are ouside the cell)
y <- replicate(x, a.ind= -1:1, b.ind = -1:1, c.ind = -1:1)
# Create a layered supercell with a vacuum layer in the bc-plan
y <- replicate(x, a.ind= c(0,2), b.ind = 0:2, c.ind = 0:2)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.