nanop (version 2.0-1)

calcPDF: Functions to calculate the PDF

Description

Functions to calculate the pair distribution function (PDF) and Q-dependent PDF given a matrix of atomic positions. The latter is relatively time-consuming.

Usage

calcPDF(nanop, dr=.01, minR=.01, maxR=20, 
        scatterLength=NA, scatterFactor=NA,  
        type="neutron", Qmin=1e-16)
	 
calcQDepPDF(nanop, dr=.1, minR=1, maxR=20, dQ=.01, minQ=1, maxQ=20,
            verbose=0, subdivisions = 100,
            rel.tol=.Machine$double.eps^.7,
            addNoise=FALSE, noiseFun=NA, 
            totalScattParams=list(), preTotalScat=NA, ...)

Value

list with elementsrnumeric vector of values at which the function was evaluated,grnumeric vector of function values.

Rdversion

1.1

Details

If preTotalScat is not NA calcQDepPDF function calculates Fourier transform of the vector gQ$preTotalScat. Otherwise it uses parameters specified in totalScattParams to generate total scattering function first.

See Also

simPart, displacePart

Examples

## simulate a particle 
Cu <- createAtom("Cu")
part <- simPart(atoms=list(Cu), atomsShell=list(Cu), r=12, 
    rcore=10, latticep=4.08, latticepShell=3.89)
## uniform displacement of positions
partx1 <- displacePart(part, sigma=c(.005, 0.005))
## different displacement in core than shell 
partx2 <-  displacePart(part, sigma=c(.005, .02))

## calculate and plot PDF associated with both particles 
gr1 <- calcPDF(partx1, maxR=24, scatterLength=c(4.87, 7.97))
gr2 <- calcPDF(partx2, maxR=24, scatterLength=c(4.87, 7.97))

plot(gr1$r, gr1$gr, type="l")
lines(gr2$r, gr2$gr, col=2)

## calculate scattering fucntion
gQ <- calcTotalScatt(part, type="neutron", dr=.01,
    scatterLength=c(4.87, 7.97), sigma=c(.005, .02))
t1 <- which(gQ$Q > 30)[1]
t2 <- which(gQ$Q > 34.9)[1]
cut <- gQ$Q[t1:t2][which(abs(gQ$gQ[t1:t2])
    ==min(abs(gQ$gQ[t1:t2]) ))[1]]
## calculate Q-dependent PDF
gr3 <- calcQDepPDF(part, minR=0, maxR=24, dr=0.01, minQ=.771, maxQ=cut,
    verbose=100, preTotalScat=list(Q=gQ$Q, gQ=gQ$gQ) )
## compare results with that obtained by calcPDF:
## ...normalization:
gr2 <- 4*pi*gr2$r*gr2$gr
## calculate and subtract gamma term:
gQSAS <- calcTotalScatt(part, type="neutron",  minQ=0.001, 
    maxQ=0.771, dQ=0.005,  dr=.01, 
    scatterLength=c(4.87, 7.97), sigma=c(.005, .02))
gammaR <- calcQDepPDF(part, minR=0.01, maxR=24,
    maxQ=.771, minQ=0.001, dr=.01,
    verbose=100, preTotalScat=list(Q=gQSAS$Q, gQ=gQSAS$gQ))
gr2 <- gr2 - gammaR$gr

## plot pair distribution functions associated with both technique:
plot(gr1$r, gr2, type="l")
lines(gr3$r, gr3$gr, col=2, lwd=2)