R/polarisability-package.r

In baptiste/polarisability: Polarisability of small particles for electromagnetic scattering

##' Coupled dipole approximation in electromagnetic scattering
##'
##' The cda package implements the coupled-dipole approximation for electromagnetic scattering by sparse collections of subwavelength particles, with a particular focus on plasmonic nanoparticles in the visible regime. The interaction matrix, and the solution of the linear system of coupled-dipole equations are executed in C++ code for speed; convenient wrapper functions are provided at the R level to generate the particle clusters, calculate the extinction, scattering, and absorption of light by particles with linearly and circularly polarised light. Functions are also provided to calculate orientation-averaged circular dichroism, and display clusters of nanoparticles in three dimensions using OpenGL or povray.
##'
##' 
##' @name cda-package
##' @docType package
##' @useDynLib cda
##' @import Rcpp
##' @title cda
##' @keywords package
##' @author baptiste Auguie \email{baptiste.auguie@@gmail.com}
##' @references
##' Draine BT. The discrete-dipole approximation and its application to interstellar graphite grains. Astrophysical Journal. 1988.
##' 
##' Schatz GC, Duyne RP. Discrete dipole approximation for calculating extinction and Raman intensities for small particles with arbitrary shapes. Journal of Chemical Physics. 1995.
##' 
##' Gunnarsson L, Zou S, Schatz GC, et al. Confined plasmons in nanofabricated single silver particle pairs: Experimental observations of strong interparticle interactions. Journal of Physical Chemistry B. 2005.
##' 
##' ## Any one of the following references may (should) be used to cite and acknowledge this package.
##' 
##' A. Guerrero-Martinez, B. Auguie, J.L. Alonso-Gomez, Z. Dzolic, S. Gomez-Grana, M. Zinic, M.M. Cid, L.M. Liz-Marzan. Intense Optical Activity from three-Dimensional Chiral Ordering of Plasmonic Nanoantennas. Angew. Chem. Int. Ed.50 (2011)
##' 
##' B. Auguie, J.L. Alonso-Gomez, A. Guerrero-Martinez, L.M. Liz-Marzan. Fingers crossed: circular dichroism with a dimer of plasmonic nanorods. J. Phys. Chem. Lett. 2, (2011)
##' 
##' B. Auguie, W.L. Barnes. Diffractive coupling in gold nanoparticle arrays and the effect of disorder. Optics Letters (2009)
##' 
##' B. Auguie, W.L. Barnes. Collective resonances in gold nanoparticle arrays. Physical Review Letters (2008)
##' @keywords packagelibrary
##' 
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##' Rcpp module: array
##' 
##' Exposes a C++ calculation of the array factor.
##' @name array
##' @docType data
##' @export
##' @details
##' \itemize{
##'  \item{array_factor}{ truncated lattice sum for a finite 2D square array}
##' }
##' @examples
##' show( array )
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##' Rcpp module: cd
##' 
##' Exposes a calculation of orientation-averaged circular dichroism within the coupled-dipole approximation.
##' @name cd
##' @docType data
##' @export
##' @details
##' \itemize{
##'  \item{circular_dichroism_spectrum}{Loop over wavelenghts and calculate the orientation averaging of the difference in extinction, absorption, scattering for left/right circularly polarised light}
##' }
##' @examples
##' show( cd )
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##' Rcpp module: cda
##' 
##' Exposes basic C++ functions used in the coupled-dipole approximation.
##' @name cda
##' @docType data
##' @export
##' @details
##' \itemize{
##'   \item{absorption}{absorption cross-section}
##'   \item{euler}{ 3D rotation matrix parametrized by Euler angles }
##'   \item{extinction}{ extinction cross-section }
##'   \item{interaction_matrix}{ build the coupled-dipole interaction matrix }
##' }
##' @examples
##' show( cda )
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##' Rcpp module: linear
##' 
##' Exposes C++ calculation of scattering and absorption of dipolar particles by linearly polarised light in fixed orientation.
##' @name linear
##' @docType data
##' @export
##' @details
##' \itemize{
##'   \item{linear_extinction_spectrum}{Returns extinction spectra for x and y polarisation at one fixed incidence } 
##'   \item{dispersion}{Returns absorption and extinction cross-sections for x and y polarisation at multiple angles of incidence, fixed wavelength (subroutine)} 
##'   \item{dispersion_spectrum}{Returns absorption and extinction spectra for x and y polarisation at multiple angles of incidence.} 
##' }
##' @examples
##' show( linear )
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##' Lattice sum
##' 
##' Converged lattice sum G0 for an infinite 2D array of dipoles at normal incidence
##' @name G0
##' @aliases gfun
##' @docType data
##' @details
##' The calculation was made using code from Prof. J. G. de Abajo (CSIC, Spain)
##' @format
##'   \describe{
##'    \item{\code{wavelength}}{a numeric vector}
##'    \item{\code{Qx}}{a numeric vector}
##'    \item{\code{Gxx}}{a complex vector}
##'  }
##' @examples
##' data(G0)
##' \dontrun{demo(lattice_sum)}
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