README.md

In thomasgredig/rigakuXRD: X-Ray Diffraction Data Analysis Package for Rigaku Data Sets

rigakuXRD

The goal of rigakuXRD is to analyze x-ray diffraction data from the Rigaku Smartlab x-ray diffractometer; mostly for low-angle reflectivity data and Bragg-Brentano diffractive data sets.

Installation

You can install the released version of rigakuXRD from GitHub with:

# install.packages("devtools")
devtools::install_github("thomasgredig/rigakuXRD")

The first line installs the popular devtools package that you can use to install R packages from (Github)[http://www.github.com]. The second lines installs the latest version of the rigakuXRD package.

Import XRD Data

The package comes with several sample data files, which can be found with the function xrd.getSampleFiles(). A general example of loading a sample XRD file:

library(rigakuXRD)
d = xrd.import(filename = xrd.getSampleFiles()[1])

The data can be graphed, typically on a semi-log graph:

plot(d$theta, d$I.meas, log='y')

If you are loading a text file without a header, you could use the following approach:

d = xrd.read.TXTnoheader('xrd.txt')
plot(d$theta, d$I.meas, log='y')

Importing RAS or RASX Files

In addition to .asc files, .ras or .rasx files are also text files and contain a header information, followed by the data. Here is an example:

fileName = xrd.getSampleFiles(fileExt = 'rasx')[1]
d = xrd.import(fileName)

Peak Analsysis

The largest peak in a sub dataset is found with the xrd.peakEstimate() function. It is not a fit, but an estimate to find the parameters of the largest peak in the data set.

Finding the precise peak position, you need to provide a starting angle (see xrd.peakEstimate()). The xrd.find.Peak() function attempts to fit a Gaussian function to the main peak. Here is an example:

fileName = xrd.getSampleFiles(fileExt = 'asc')[1]
d = xrd.import(fileName)

library(dplyr)
d %>% filter(theta < 42 & theta > 32) -> d1
p = xrd.peakEstimate(d1$theta, d1$I)

# is there a Au peak ?
xrd.find.Peak(d$theta, d$I, p[3])

# is there a Si substrate peak ?
xrd.find.Peak(d$theta, d$I, 44, Try.Sigma = c(0.05,0.1) )

You can search for all the prominent peaks, using the following function, which returns a vector with all the peaks.

xrd.get.AllPeaks(d$theta, d$I)

Peak Analysis

After finding the peaks, the peak amplitude is compared to the background to check the prominence of the peak, it should rise above 5%:

peak.stats = xrd.get.PeakStats(d$theta, d$I, 38.217)
peak.prom = xrd.get.PeakProminence(peak.stats)
paste0("Peak prominence: ",signif(peak.prom,3),"%.")

You can also get the thickness or grain size using the Debye-Scherrer analysis.

peak.d = xrd.get.DebyeScherrer(peak.stats)
paste("Debye-Scherrer thickness from peak:", peak.d/10, "nm")

thomasgredig/rigakuXRD documentation built on Feb. 3, 2024, 10:49 p.m.