Description Usage Arguments Value See Also Examples
Function to simulate termination ripples in the PDF calculated as the Fourier transform of the total scattering function that arise due to the finite value of the upper integration limit Qmax.
1 2 |
pdf |
numeric vector containing PDF. |
Qmax |
numeric indicating value of |
dr |
numeric indicating the step size in |
maxR |
numeric indicating the maximum value of |
maxRTermRip |
numeric indicating the maximum value of |
numeric vector of function values.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 | ## simulate a particle
Cu <- createAtom("Cu")
part <- simPart(atoms=list(Cu), atomsShell=list(Cu), r=12,
rcore=10, latticep=4.08, latticepShell=3.89)
## calculate the PDF
gr1 <- calcPDF(part, maxR=24, scatterLength=c(4.87, 7.97))
gr1 <- broadPDF(gr1, sigma=c(.01, .01), nAtomTypes=2)
## normalization
gr1$gr <- 4*pi*gr1$r*gr1$gr
## calculate and substract the baseline term
gQSAS <- calcTotalScatt(part, type="neutron", minQ=0.001,
maxQ=0.771, dQ=0.005, scatterLength=c(4.87, 7.97),
sigma=c(.01, .01))
gammaR <- calcQDepPDF(minR=0.01, maxR=24, dr=0.01, maxQ=.771,
minQ=0.001, verbose=50,
preTotalScat=list(Q=gQSAS$Q, gQ=gQSAS$gQ))
gr1$gr <- gr1$gr - gammaR$gr
plot(gr1$r, gr1$gr, type="l", xlim=c(0,10))
## simulate termination ripples
rvector <- gr1$r
gr1 <- termRip(gr1$gr, Qmax=11.881, dr=0.01, maxR=24, maxRTermRip=16)
## plot the PDF with simulated termination ripples:
lines(rvector, gr1, col=2)
#### compare with ripples due to finite value of Qmax:
## calculate scattering function
gQ <- calcTotalScatt(part, type="neutron",
scatterLength=c(4.87, 7.97), sigma=c(.01, .01))
## set Qmax to a value between 11 and 13 at which scattering function reaches
## minimum:
t1 <- which(gQ$Q > 11)[1]
t2 <- which(gQ$Q > 13)[1]
cut <- gQ$Q[t1:t2][which(abs(gQ$gQ[t1:t2])
==min(abs(gQ$gQ[t1:t2]) ))[1]]
## calculate Q-dependent PDF
gr3 <- calcQDepPDF(minR=0.01, maxR=24, dr=0.01, minQ=.771,
maxQ=cut, verbose=50, preTotalScat=list(Q=gQ$Q, gQ=gQ$gQ))
## add Q-dependent PDF to plot:
lines(gr3$r, gr3$gr, col=4)
legend(5,7,c("PDF as returned by calcPDF", "PDF with simulated
termination ripples", "PDF as Fourier transform"), lty=1,
col=c(1,2,4))
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DIM BASE 1 4
DIM BASE 1 4
Finished computing r= 0.5
Finished computing r= 1
Finished computing r= 1.5
Finished computing r= 2
Finished computing r= 2.5
Finished computing r= 3
Finished computing r= 3.5
Finished computing r= 4
Finished computing r= 4.5
Finished computing r= 5
Finished computing r= 5.5
Finished computing r= 6
Finished computing r= 6.5
Finished computing r= 7
Finished computing r= 7.5
Finished computing r= 8
Finished computing r= 8.5
Finished computing r= 9
Finished computing r= 9.5
Finished computing r= 10
Finished computing r= 10.5
Finished computing r= 11
Finished computing r= 11.5
Finished computing r= 12
Finished computing r= 12.5
Finished computing r= 13
Finished computing r= 13.5
Finished computing r= 14
Finished computing r= 14.5
Finished computing r= 15
Finished computing r= 15.5
Finished computing r= 16
Finished computing r= 16.5
Finished computing r= 17
Finished computing r= 17.5
Finished computing r= 18
Finished computing r= 18.5
Finished computing r= 19
Finished computing r= 19.5
Finished computing r= 20
Finished computing r= 20.5
Finished computing r= 21
Finished computing r= 21.5
Finished computing r= 22
Finished computing r= 22.5
Finished computing r= 23
Finished computing r= 23.5
Finished computing r= 24
Finished computing r= 0.5
Finished computing r= 1
Finished computing r= 1.5
Finished computing r= 2
Finished computing r= 2.5
Finished computing r= 3
Finished computing r= 3.5
Finished computing r= 4
Finished computing r= 4.5
Finished computing r= 5
Finished computing r= 5.5
Finished computing r= 6
Finished computing r= 6.5
Finished computing r= 7
Finished computing r= 7.5
Finished computing r= 8
Finished computing r= 8.5
Finished computing r= 9
Finished computing r= 9.5
Finished computing r= 10
Finished computing r= 10.5
Finished computing r= 11
Finished computing r= 11.5
Finished computing r= 12
Finished computing r= 12.5
Finished computing r= 13
Finished computing r= 13.5
Finished computing r= 14
Finished computing r= 14.5
Finished computing r= 15
Finished computing r= 15.5
Finished computing r= 16
Finished computing r= 16.5
Finished computing r= 17
Finished computing r= 17.5
Finished computing r= 18
Finished computing r= 18.5
Finished computing r= 19
Finished computing r= 19.5
Finished computing r= 20
Finished computing r= 20.5
Finished computing r= 21
Finished computing r= 21.5
Finished computing r= 22
Finished computing r= 22.5
Finished computing r= 23
Finished computing r= 23.5
Finished computing r= 24
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