drafts/vignettes/averaging_method.R

In baptiste/cda: Coupled-Dipole Approximation for Electromagnetic Scattering by Three- Dimensional Clusters of Sub-Wavelength Particles

## ----demo, message=FALSE, echo=FALSE-------------------------------------
knitr::read_demo("quadrature", package="cda")
knitr::read_chunk("load.R")

## ----load, message=FALSE, echo=FALSE-------------------------------------
library(cda)
library(rgl)
library(ggplot2)
library(reshape2)
library(plyr)
library(dielectric)
library(knitr)
#require(microbenchmark)
#require(xtable)

## ----setup, message=FALSE, echo=FALSE------------------------------------
knit_hooks$set(rgl = function(before, options, envir) {
  # if a device was opened before this chunk, close it
  if (before && rgl.cur() > 0) rgl.close()
  hook_rgl(before, options, envir)
})

theme_set(theme_minimal())

display_benchmark <- function(x, unit = "t"){
  x$time <- microbenchmark:::convert_to_unit(x$time, unit)
  res <- aggregate(time ~ expr, x, function(.x) c(mean(.x), median(.x), min(.x), max(.x)))
  res <- cbind(res$expr, as.data.frame(res$time))
  colnames(res) <- c("expr",  "mean", "median", "min", "max")
  print(xtable(res), type = 'html', html.table.attributes = '')
}

## ----cluster, tidy=FALSE, fig.path='averaging-'--------------------------
gold <- epsAu(seq(600, 800))

cl <- cluster_dimer(d=100, 
              dihedral=10*pi/180, alpha1=20*pi/180, alpha2=0,
              a=35, b=12)

# achiral cluster (plane of symmetry)
cl2 <- cluster_dimer(d=100, 
              dihedral=0*pi/180, alpha1=20*pi/180, alpha2=0,
              a=35, b=12)

## ----comparison, tidy=FALSE, fig.path='averaging-'-----------------------
params <- expand.grid(Nq=c(5, 25, 50, 75, 100, 500),
                      quadrature=c("gl", "qmc", "random"),
                       stringsAsFactors=FALSE)

comparison <- mdply(params, spectrum_oa, cluster=cl, material=gold)
cheap <- spectrum_oa(cluster=cl, material=gold, quadrature="cheap")
converged <- spectrum_oa(cluster=cl, material=gold, quadrature="qmc", Nq=1000)

p <- 
  ggplot(subset(comparison, type == "dichroism" & variable == "extinction"),
         aes(wavelength, value)) + 
  facet_grid(quadrature~., scales="free")+
  geom_path(aes(colour=factor(Nq), group=Nq))+
  geom_path(data=subset(cheap, type == "dichroism" & variable == "extinction"), linetype=2)+
  geom_path(data=subset(converged, type == "dichroism" & variable == "extinction"), linetype=3)+
  labs(y=expression(sigma[ext]/nm^2),
       x=expression(wavelength/nm), colour=expression(N))

p

## ----achiral, tidy=FALSE, fig.path='averaging-'--------------------------