calcPDF {nanop}R Documentation

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 currently relatively time-consuming.

Usage

calcPDF(nanop, calpha = 1, dr = 0.01, minR = 1, maxR = 20, p = 1,
foranalcs=FALSE)

calcQDepPDF(nanop, dr=.1, minR=1, maxR=20, minQ=1, maxQ=20,
           a1 = 16.8819, b1=.4611, a2=18.5913, b2=8.6216,
           a3=25.5582, b3=1.48260, a4=5.86, b4=36.3956, c=12.0658) 

Arguments

nanop numeric matrix in which each row gives the coordinates of an atomic position in the nanoparticle
calpha numeric indicating the concentration of atoms of the type under consideration
dr numeric indicating the step size in r desired
minR numeric indicating the minimum value of r for which the function should be evaluated
maxR numeric indicating the maximum value of r for which the function should be evaluated
p numeric indicating the atomic number density or an approximation thereof
minQ numeric indicating the minimum value of Q for which the function should be evaluated
maxQ numeric indicating the maximum value of Q for which the function should be evaluated
a1 numeric X-ray scattering factor parameter; see details
b1 numeric X-ray scattering factor parameter; see details
a2 numeric X-ray scattering factor parameter; see details
b2 numeric X-ray scattering factor parameter; see details
a3 numeric X-ray scattering factor parameter; see details
b3 numeric X-ray scattering factor parameter; see details
a4 numeric X-ray scattering factor parameter; see details
b4 numeric X-ray scattering factor parameter; see details
c numeric X-ray scattering factor parameter; see details
foranalcs logical indicating whether the result will be used in combination with calculating analytical broadening for a core-shell particle using the function broadPDF

Details

The X-ray scattering factor is approximated by the function f(s)=a_1 * exp(-b_1 s) + a_2 * exp(-b_2 s) + a_3 * exp(-b_3 s) + a_4 * exp(-b_4 s) + c with s = \frac{Q}{4\pi}. The constants in the function are possible to specify as arguments. Their default values correspond to the values for Au.

Value

List with elements

Q numeric vector of values at which the function was evaluated
gQ numeric vector of function values

Note

calcQDepPDF and calcPDF do not use the same normalization; calcQDepPDF is currently very time-consuming.

See Also

simPart, displacePart

Examples

## simulate a particle 
aa <- simPart()
## uniform displacement of positions
ab <- displacePart(aa, sigma=.005)
## different displacement in core than shell 
ab1 <-  displacePart(aa, rcore=8, sigmacore=.005, sigmashell=.02)

## calculate and plot PDF associated with both particles 
ac <- calcPDF(ab)
ac1 <- calcPDF(ab1)
plot(ac$r, ac$gr, type="l")
lines(ac1$r, ac1$gr, col=2)


[Package nanop version 1.0 Index]