Defines various cluster geometries and exports in a format suitable for TERMS
Helix of particles
Chain of particles
Core-satellite cluster of spheres
cluster_positions(
N = 5,
cl_fun = cluster_chain,
radius = 50,
label = "Au",
...,
out = "",
digits = 8
)
cluster_helix(
N = 5,
a = 10,
b = 10,
c = 50,
R0 = 100,
pitch = 200,
delta = pi/5,
delta0 = 0,
hand = 1,
...
)
cluster_chain(
N = 5,
pitch = 500,
a = 50,
b = 30,
c = b,
rot = rotation_euler_passive(0, 0, 0)
)
cluster_satellite(N = 30, Rcore = 30, Rsat = 4, gap = 0.1, exclusion = 10, ...)number of particles
cluster function
particle radius
particle material label
extra arguments passed to cl_fun
filename
accuracy
semi-axis
semi-axis
semi-axis
helix radius
chain pitch
helix angle step
helix start angle
helix handedness
rotation matrix applied to each particle
core radius
satellite radius
gap distance
minimum exclusion distance for hc positions
returns scatterers positions and sizes for an input file
cluster_positions(): write cluster positions to input file
cluster_helix(): helical cluster
cluster_chain(): linear chain cluster
cluster_satellite(): core-satellite cluster
cluster_positions()
#> Au -1000 0 0 50
#> Au -500 0 0 50
#> Au 0 0 0 50
#> Au 500 0 0 50
#> Au 1000 0 0 50
cluster_helix()
#> $positions
#> [,1] [,2] [,3] [,4] [,5]
#> x 100 80.90170 30.90170 -30.90170 -80.90170
#> y 0 58.77853 95.10565 95.10565 58.77853
#> z -40 -20.00000 0.00000 20.00000 40.00000
#>
#> $sizes
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 10 10 10 10 10
#> [2,] 10 10 10 10 10
#> [3,] 50 50 50 50 50
#>
#> $angles
#> [,1] [,2] [,3] [,4] [,5]
#> phi 1.570796 2.199115 2.827433 -2.827433 -2.199115
#> theta 1.262627 1.262627 1.262627 1.262627 1.262627
#> psi 0.000000 0.000000 0.000000 0.000000 0.000000
#>
#> $R0
#> [1] 100
#>
#> attr(,"class")
#> [1] "cluster"
cluster_chain()
#> $positions
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] -1000 -500 0 500 1000
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#>
#> $sizes
#> [,1] [,2] [,3] [,4] [,5]
#> a 50 50 50 50 50
#> b 30 30 30 30 30
#> c 30 30 30 30 30
#>
#> $angles
#> [,1] [,2] [,3] [,4] [,5]
#> phi 0 0 0 0 0
#> theta 0 0 0 0 0
#> gamma 0 0 0 0 0
#>
#> attr(,"class")
#> [1] "cluster"
cluster_satellite()
#> $positions
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7]
#> x 8.476599 -8.235287 -2.89900 17.09593 -24.297840 18.22398 -0.5805691
#> y 2.091872 -12.373922 18.62522 -13.67718 -1.627288 19.08614 -28.0905986
#> z -32.963333 -30.690000 -28.41667 -26.14333 -23.870000 -21.59667 -19.3233333
#> [,8] [,9] [,10] [,11] [,12] [,13] [,14]
#> x -19.49400 30.552344 -25.57048 6.326701 17.215306 -32.282993 30.42701
#> y 22.18313 -3.318795 -18.77837 31.908149 -28.339631 9.397770 15.01263
#> z -17.05000 -14.776667 -12.50333 -10.230000 -7.956667 -5.683333 -3.41000
#> [,15] [,16] [,17] [,18] [,19] [,20] [,21]
#> x -12.350117 -12.350117 30.42701 -32.282993 17.215306 6.326701 -25.57048
#> y -31.764644 31.764644 -15.01263 -9.397770 28.339631 -31.908149 18.77837
#> z -1.136667 1.136667 3.41000 5.683333 7.956667 10.230000 12.50333
#> [,22] [,23] [,24] [,25] [,26] [,27] [,28]
#> x 30.552344 -19.49400 -0.5805691 18.22398 -24.297840 17.09593 -2.89900
#> y 3.318795 -22.18313 28.0905986 -19.08614 1.627288 13.67718 -18.62522
#> z 14.776667 17.05000 19.3233333 21.59667 23.870000 26.14333 28.41667
#> [,29] [,30]
#> x -8.235287 8.476599
#> y 12.373922 -2.091872
#> z 30.690000 32.963333
#>
#> $sizes
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
#> x 4 4 4 4 4 4 4 4 4 4 4 4 4 4
#> y 4 4 4 4 4 4 4 4 4 4 4 4 4 4
#> z 4 4 4 4 4 4 4 4 4 4 4 4 4 4
#> [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26] [,27]
#> x 4 4 4 4 4 4 4 4 4 4 4 4 4
#> y 4 4 4 4 4 4 4 4 4 4 4 4 4
#> z 4 4 4 4 4 4 4 4 4 4 4 4 4
#> [,28] [,29] [,30]
#> x 4 4 4
#> y 4 4 4
#> z 4 4 4
#>
#> $angles
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
#> x 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> y 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> z 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26] [,27]
#> x 0 0 0 0 0 0 0 0 0 0 0 0 0
#> y 0 0 0 0 0 0 0 0 0 0 0 0 0
#> z 0 0 0 0 0 0 0 0 0 0 0 0 0
#> [,28] [,29] [,30]
#> x 0 0 0
#> y 0 0 0
#> z 0 0 0
#>
#> $R0
#> [1] 30
#>
#> attr(,"class")
#> [1] "cluster"