Package 'terms'

Clusters of particles

Description

Defines various cluster geometries and exports in a format suitable for TERMS

Helix of particles

Chain of particles

Core-satellite cluster of spheres

Usage

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, ...)

Arguments

N	number of particles
cl_fun	cluster function
radius	particle radius
label	particle material label
...	extra arguments passed to cl_fun
out	filename
digits	accuracy
a	semi-axis
b	semi-axis
c	semi-axis
R0	helix radius
pitch	chain pitch
delta	helix angle step
delta0	helix start angle
hand	helix handedness
rot	rotation matrix applied to each particle
Rcore	core radius
Rsat	satellite radius
gap	gap distance
exclusion	minimum exclusion distance for hc positions

Value

returns scatterers positions and sizes for an input file

Functions

• cluster_positions(): write cluster positions to input file

• cluster_helix(): helical cluster

• cluster_chain(): linear chain cluster

• cluster_satellite(): core-satellite cluster

Examples

cluster_positions()
cluster_helix()
cluster_chain()
cluster_satellite()

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Utility functions

Description

Matrix of equal sizes

Matrix of equal angles

Combined T-matrix index

T-matrix indices

Unpack T-matrix indices

Unpack T-matrix indices

Wrap staged matrices into a list of T-matrix like objects

Read T-matrix into long-format data.frame

Display staged matrix

Display T-matrix

Display prestaged matrix

Generate an incidence file for spherical cubature

Generate a dielectric function in suitable format for TERMS

Euler rotation matrix

Euler rotation matrix

Axis-angle rotation from Euler angles

Extend a range symmetrically about 0

Extract geometry information from input file

Wrap geometry information into a 'cluster' structure

Visualise a 'cluster' structure

Usage

equal_sizes(a, b, c, N)

equal_angles(phi, theta, gamma, N)

p_index(in1, in2)

indices(n_max = 3, n_part = 1)

unpack_indices(n_max = 3, j_max = 2)

read_amat(f)

amat_to_tmatlist(a, n_max = 3, n_part = 2)

read_tmat(f, save = FALSE)

display_amat(l)

display_tmat(s)

display_prestaged(a, n_max = 3, n_part = 2, draw = TRUE)

export_cubature(q = cubs::cubs(N = 10, cubature = "lebedev"), out = "")

export_dielectric(m = dielectric::epsAu(seq(400, 800)), out = "")

rotation_euler_passive(phi, theta, psi)

rotation_euler_active(phi, theta, psi)

euler_to_axisangle(a, b, c)

symmetric_range(range)

get_geometry(input = "input")

cluster_geometry(ge)

visualise_rgl(cl, outfile = NULL, show_core = FALSE, ...)

Arguments

a	Euler angle
b	Euler angle
c	Euler angle
N	number of particles
phi	Euler angle
theta	Euler angle
gamma	Euler angle
in1	index
in2	index
n_max	maximum order
n_part	number of particles
j_max	size of collective T-matrix
f	filename
save	store result as Rds file
l	list of T-matrices, from amat_to_tmatlist
s	T-matrices, from read_tmat
draw	logical, draw output
q	data.frame with angles and weights, from cubs::cubs()
out	filename
m	data.frame with wavelength and epsilon, e.g. from dielectric::epsAu()
psi	Euler angle
range	range (2-vector)
input	filename
ge	geometry, from get_geometry
cl	'cluster' object
outfile	optional output snapshot
show_core	display a core sphere if 'R0' field present
...	additional parameters passed to rgl.ellipsoids

Functions

• equal_sizes(): equal sizes

• equal_angles(): equal angles

• p_index(): p-index

• indices(): indices

• unpack_indices(): unpack indices

• read_amat(): unpack indices

• amat_to_tmatlist(): wrap staged matrices

• read_tmat(): read T-matrix

• display_amat(): display staged matrix

• display_tmat(): display T-matrix

• display_prestaged(): display prestaged matrix

• export_cubature(): export a spherical cubature

• export_dielectric(): export a dielectric function

• rotation_euler_passive(): passive rotation matrix

• rotation_euler_active(): active rotation matrix

• euler_to_axisangle(): axis-angle rotation

• symmetric_range(): symmetric range

• get_geometry(): extract geometry information from input file

• cluster_geometry(): wrap geometry information obtained from input file

• visualise_rgl(): rgl visualisation of a cluster

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Extract timings from log files

Description

Parses a log file to extract timing information from subroutines (verbosity-dependent)

Usage

extract_time(log = "log")

Arguments

log

filename

Value

returns a tibble of timings

Functions

• extract_time(): extract timings from log files

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sample_fibonacci

Description

Fibonacci coverage of a sphere

Usage

sample_fibonacci(N = 301)

Arguments

N	number of points

Details

Produces a set of points that covers rather uniformly the unit sphere with N points with a spiral-like pattern based on a Fibonacci sequence

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Reshape cross-section results into a convenient format for post-processing and plotting

Description

Read and store plain text cross-sections

Extracts commonly-used information from a HDF5 file storing far-field cross-sections (Mode=2), and reshapes the data into long-format data.frames suitable for plotting

Extracts partial absorption cross-sections from a HDF5 file storing far-field cross-sections (Mode=2), and reshapes the data into long-format data.frames suitable for plotting

Usage

store_xsec(..., out = "xsec.rds")

consolidate_xsec(hdf5, verbose = TRUE, ...)

consolidate_partials(hdf5, verbose = TRUE)

Arguments

...	extra arguments passed to the final list
out	output Rds filename
hdf5	filename
verbose	logical: print attributes

Value

returns a list containing data.frames in long format

Functions

• store_xsec(): store plain text cross-sections

• consolidate_xsec(): consolidate cross-sections

• consolidate_partials(): consolidate partial absorption cross-sections for multilayered spheres

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Interactive display of cluster geometries

Description

Displays a cluster in X3D format

Usage

x3d_scene(
  cl,
  viewpoint = c(0, 0, 100),
  orientation = NULL,
  width = "300px",
  height = "300px",
  scale = 100,
  ...
)

Arguments

cl	cluster
viewpoint	viewpoint position (3-vector)
orientation	optional viewpoint orientation (axis-angle vector: x,y,z,angle)
width	display width
height	display height
scale	size of axes
...	extra arguments passed to cluster_to_x3d

Value

returns X3D object to embed in a html document with suitable X3D support

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