cleanup

nano-optics · Jun 22, 2014 · 61dd965 · 61dd965
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diff --git a/NAMESPACE b/NAMESPACE
@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.0.0): do not edit by hand
+# Generated by roxygen2 (4.0.1.99): do not edit by hand
 
 export(La)
 export(alpha_kuwata)

diff --git a/R/dispersion.r b/R/dispersion.r
@@ -11,6 +11,7 @@
 ##' @param polarisation linear or circular polarisation
 ##' @param progress logical, display progress bar
 ##' @return data.frame
+##' @note The incident wavevector is along the z direction.
 ##' @export
 ##' @family user_level cda
 ##' @author baptiste Auguie

diff --git a/inst/doc/CD-theory.pdf b/inst/doc/CD-theory.pdf
diff --git a/man/G0.Rd b/man/G0.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \docType{data}
 \name{G0}
 \alias{G0}
@@ -11,12 +10,10 @@
    \item{\code{Gxx}}{ A complex vector}
  }}
 \description{
-Converged lattice sum G0 for an infinite 2D array of
-dipoles at normal incidence
+Converged lattice sum G0 for an infinite 2D array of dipoles at normal incidence
 }
 \details{
-The calculation was made using code from Prof. J. G. de
-Abajo (CSIC, Spain)
+The calculation was made using code from Prof. J. G. de Abajo (CSIC, Spain)
 }
 \examples{
 data(G0)

diff --git a/man/La.Rd b/man/La.Rd
@@ -1,17 +1,16 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{La}
 \alias{La}
 \title{La}
 \usage{
 La(a = 50, b = a, c = a)
 }
 \arguments{
-  \item{a}{semi-axis in nm}
+\item{a}{semi-axis in nm}
 
-  \item{b}{semi-axis in nm}
+\item{b}{semi-axis in nm}
 
-  \item{c}{semi-axis in nm}
+\item{c}{semi-axis in nm}
 }
 \value{
 shape factor along a
@@ -26,9 +25,9 @@ calculates the shape factor for a general ellipsoid
 baptiste Auguie
 }
 \seealso{
-Other user_level polarizability:
-\code{\link{alpha_kuwata}},
-\code{\link{inverse_polarizability}},
-\code{\link{polarizability_ellipsoid}}
+Other user_level polarizability: \code{\link{Kuwata.A}},
+  \code{\link{Kuwata.B}}, \code{\link{alpha_kuwata}};
+  \code{\link{inverse_polarizability}};
+  \code{\link{polarizability_ellipsoid}}
 }
 
diff --git a/man/alpha_kuwata.Rd b/man/alpha_kuwata.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{alpha_kuwata}
 \alias{Kuwata.A}
 \alias{Kuwata.B}
@@ -9,17 +8,17 @@
 alpha_kuwata(wavelength, epsilon, V, axis, L, medium = 1.33)
 }
 \arguments{
-  \item{wavelength}{wavelength}
+\item{wavelength}{wavelength}
 
-  \item{epsilon}{permittivity}
+\item{epsilon}{permittivity}
 
-  \item{V}{volume}
+\item{V}{volume}
 
-  \item{axis}{semi-axis along incident field}
+\item{axis}{semi-axis along incident field}
 
-  \item{L}{shape factor}
+\item{L}{shape factor}
 
-  \item{medium}{refractive index}
+\item{medium}{refractive index}
 }
 \value{
 polarizability
@@ -34,13 +33,11 @@ prescription from Kuwata
 baptiste Auguie
 }
 \references{
-Kuwata et al. Resonant light scattering from metal
-nanoparticles: Practical analysis beyond Rayleigh
-approximation Appl. Phys. Lett. 83, 22 (2003)
+Kuwata et al. Resonant light scattering from metal nanoparticles: Practical analysis beyond Rayleigh approximation Appl. Phys. Lett. 83, 22 (2003)
 }
 \seealso{
-Other user_level polarizability:
-\code{\link{inverse_polarizability}}, \code{\link{La}},
-\code{\link{polarizability_ellipsoid}}
+Other user_level polarizability: \code{\link{La}};
+  \code{\link{inverse_polarizability}};
+  \code{\link{polarizability_ellipsoid}}
 }
 
diff --git a/man/array.Rd b/man/array.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \docType{data}
 \name{array}
 \alias{array}
@@ -8,8 +7,9 @@
 Exposes a C++ calculation of the array factor.
 }
 \details{
-\itemize{ \item{array_factor}{ Truncated lattice sum for a
-finite 2D square array} }
+\itemize{
+ \item{array_factor}{ Truncated lattice sum for a finite 2D square array}
+}
 }
 \examples{
 show( array )

diff --git a/man/array_factor.Rd b/man/array_factor.Rd
@@ -1,17 +1,16 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{array_factor}
 \alias{array_factor}
 \title{array factor}
 \usage{
 array_factor(wavelength, N, pitch)
 }
 \arguments{
-  \item{wavelength}{wavelength in nm}
+\item{wavelength}{wavelength in nm}
 
-  \item{N}{half number of dipoles along one side}
+\item{N}{half number of dipoles along one side}
 
-  \item{pitch}{pitch in nm}
+\item{pitch}{pitch in nm}
 }
 \value{
 S
@@ -20,8 +19,7 @@ S
 C++ calculation of the array factor
 }
 \details{
-Brute-force numerical evaluation of the truncated 2D sum of
-dipole fields
+Brute-force numerical evaluation of the truncated 2D sum of dipole fields
 }
 \examples{
 S <- array_factor(seq(400, 600),  10,  500)

diff --git a/man/cd.Rd b/man/cd.Rd
@@ -1,18 +1,15 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \docType{data}
 \name{cd}
 \alias{cd}
 \title{Rcpp module: cd}
 \description{
-Exposes a calculation of orientation-averaged circular
-dichroism within the coupled-dipole approximation.
+Exposes a calculation of orientation-averaged circular dichroism within the coupled-dipole approximation.
 }
 \details{
-\itemize{ \item{average_spectrum}{ Loop over wavelengths
-and calculate the orientation averaging of the difference
-in extinction, absorption, scattering for left/right
-circularly polarised light} }
+\itemize{
+ \item{average_spectrum}{ Loop over wavelengths and calculate the orientation averaging of the difference in extinction, absorption, scattering for left/right circularly polarised light}
+}
 }
 \examples{
 show( cd )

diff --git a/man/cda-package.Rd b/man/cda-package.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \docType{package}
 \name{cda-package}
 \alias{cda-package}
@@ -8,52 +7,31 @@
 Coupled dipole approximation in electromagnetic scattering
 }
 \details{
-Solves the electromagnetic problem of coupled-dipoles
-(scattering and absorption by a cluster of subwavelength
-particles in arbitrary 3D configuration) by direct
-inversion of the interaction matrix. Functions are provided
-for linear polarisation with varying angle of incidence, as
-well as circular polarisation with angular averaging
-(optical activity). Retardation is included in the
-interaction.
+Solves the electromagnetic problem of coupled-dipoles (scattering and absorption by a cluster of subwavelength particles in arbitrary 3D configuration) by direct inversion of the interaction matrix. Functions are provided for linear polarisation with varying angle of incidence, as well as circular polarisation with angular averaging (optical activity). Retardation is included in the interaction.
 }
 \author{
 baptiste Auguie
 }
 \references{
-Draine BT. The discrete-dipole approximation and its
-application to interstellar graphite grains. Astrophysical
-Journal. 1988.
+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.
+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.
+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 should be used to
-cite and acknowledge the use of this package.
+## Any one of the following references should be used to cite and acknowledge the use of this package.
 
 Circular dichroism:
 
-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, 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)
 
 Linear extinction:
 
-B. Auguie, W.L. Barnes. Diffractive coupling in gold
-nanoparticle arrays and the effect of disorder. Optics
-Letters (2009)
+B. Auguie, W.L. Barnes. Diffractive coupling in gold nanoparticle arrays and the effect of disorder. Optics Letters (2009)
 
 Array factor (infinite case):
 
-B. Auguie, W.L. Barnes. Collective resonances in gold
-nanoparticle arrays. Physical Review Letters (2008)
+B. Auguie, W.L. Barnes. Collective resonances in gold nanoparticle arrays. Physical Review Letters (2008)
 }
 \keyword{package}
 \keyword{packagelibrary}

diff --git a/man/cda.Rd b/man/cda.Rd
@@ -1,24 +1,22 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \docType{data}
 \name{cda}
 \alias{cda}
 \title{Rcpp module: cda}
 \description{
-Exposes basic C++ functions used in the coupled-dipole
-approximation.
+Exposes basic C++ functions used in the coupled-dipole approximation.
 }
 \details{
-\itemize{ \item{absorption}{ Absorption cross-section}
-\item{extinction}{ Extinction cross-section }
-\item{axis_rotation}{ 3D rotation matrix parametrized by
-axis + angle} \item{euler}{ 3D rotation matrix parametrized
-by Euler angles } \item{interaction_matrix}{ Build the
-coupled-dipole interaction matrix } \item{block_diagonal}{
-Diagonal blocks of the coupled-dipole interaction matrix }
-\item{incident_field}{ Construct the incident fields for
-specific Euler angles} \item{multiple_incident_field}{
-Construct the incident fields for specific axes+angles} }
+\itemize{
+  \item{absorption}{ Absorption cross-section}
+  \item{extinction}{ Extinction cross-section }
+  \item{axis_rotation}{ 3D rotation matrix parametrized by axis + angle}
+  \item{euler}{ 3D rotation matrix parametrized by Euler angles }
+  \item{interaction_matrix}{ Build the coupled-dipole interaction matrix }
+  \item{block_diagonal}{ Diagonal blocks of the coupled-dipole interaction matrix }
+  \item{incident_field}{ Construct the incident fields for specific Euler angles}
+  \item{multiple_incident_field}{ Construct the incident fields for specific axes+angles}
+}
 }
 \examples{
 show( cda )

diff --git a/man/circular_dichroism_spectrum.Rd b/man/circular_dichroism_spectrum.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{circular_dichroism_spectrum}
 \alias{circular_dichroism_spectrum}
 \title{circular_dichroism_spectrum}
@@ -10,37 +9,31 @@ circular_dichroism_spectrum(cluster, material, medium = 1.33, Nquad = 100,
   progress = FALSE, verbose = TRUE, result.matrix = FALSE)
 }
 \arguments{
-  \item{cluster}{cluster (list)}
+\item{cluster}{cluster (list)}
 
-  \item{material}{material}
+\item{material}{material}
 
-  \item{medium}{refractive index medium}
+\item{medium}{refractive index medium}
 
-  \item{Nquad}{number of integration points}
+\item{Nquad}{number of integration points}
 
-  \item{averaging}{averaging method, using either Gauss
-  Legendre quadrature (default), Quasi Monte Carlo, regular
-  grid, or "cheap" (3 axes)}
+\item{averaging}{averaging method, using either Gauss Legendre quadrature (default), Quasi Monte Carlo, regular grid, or "cheap" (3 axes)}
 
-  \item{iterative}{logical, increase N until convergence
-  (QMC only)}
+\item{iterative}{logical, increase N until convergence (QMC only)}
 
-  \item{precision}{relative diff between two runs (QMC
-  only)}
+\item{precision}{relative diff between two runs (QMC only)}
 
-  \item{Nmax}{maximum N if convergence not attained (QMC
-  only)}
+\item{Nmax}{maximum N if convergence not attained (QMC only)}
 
-  \item{dN}{iterative increase in N (QMC only)}
+\item{dN}{iterative increase in N (QMC only)}
 
-  \item{full}{logical use full (retarded) dipolar field}
+\item{full}{logical use full (retarded) dipolar field}
 
-  \item{progress}{print progress lines}
+\item{progress}{print progress lines}
 
-  \item{verbose}{display messages}
+\item{verbose}{display messages}
 
-  \item{result.matrix}{logical return the results as a
-  matrix}
+\item{result.matrix}{logical return the results as a matrix}
 }
 \description{
 Simulate a CD spectrum
@@ -52,9 +45,6 @@ CD spectrum
 baptiste Auguie
 }
 \references{
-Y. Okada, Efficient numerical orientation averaging of
-light scattering properties with a quasi-Monte-Carlo
-method, Journal of Quantitative Spectroscopy and Radiative
-Transfer, Volume 109, Issue 9, June 2008, Pages 1719-1742.
+Y. Okada, Efficient numerical orientation averaging of light scattering properties with a quasi-Monte-Carlo method, Journal of Quantitative Spectroscopy and Radiative Transfer, Volume 109, Issue 9, June 2008, Pages 1719-1742.
 }