Nothing
library(cda)
library(rgl)
library(ggplot2)
library(reshape2)
library(plyr)
theme_set(theme_bw() + theme(strip.background=element_blank()))
wavelength = seq(450,650)
medium <- 1.33
dye = alpha_bare(wavelength)
model_dimer <- function(d, orientation="side", ...){
if(orientation=="side-by-side")
cl = cluster_dimer(d, 1, 0, 0, 0, 0, 0) else
cl = cluster_dimer(d, 0, 0, 1, 0, 0, 0)
xsec = spectrum_oa(cl, dye, ..., quadrature = 'qmc', Nq = 100, method = "solve")
}
dimers <- mdply(expand.grid(d=c(seq(0.7, 2, by=0.2)),
orientation=c("head-to-head", "side-by-side"),
stringsAsFactors = FALSE),
model_dimer, medium=medium)
cl <- cluster_single(1,0,0)
ref <- spectrum_oa(cl, dye, medium=medium, quadrature = 'qmc', Nq = 100, method = "solve")
p <- ggplot(subset(dimers, type=="cross-section" & variable =="extinction"),
aes(wavelength, value)) +
geom_line(aes(colour=factor(d))) +
facet_grid(.~orientation)+
# geom_line(data=manual) +
geom_line(data=subset(ref, type=="cross-section" & variable =="extinction"),
map=aes(wavelength, value),lty=2) +
labs(x = "wavelength /nm", y = expression(sigma[abs]/nm^2),
colour = "d /nm")
p
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