XRD + AFM data

library(projectRazo)
library(dataRazo)

Fernanda Razo M.S. Thesis Data v.0.2.1

AFM database FOUND: dataRazo-0.2.1.sqlite

library(pander)
library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

library(ggplot2)
library(nanoAFMr)
library(rigakuXRD)

Importing XRD Files

Au_05 = xrd.import(filename = "/Users/fern/Desktop/Data/20250811/20250811_AuRoughness_FR_XRD_FR20250624_2nmCr_5nmAu.rasx")
Au_10 = xrd.import(filename = "/Users/fern/Desktop/Data/20250807/20250807_AuRoughness_FR_XRD_FR20250624_2nmCr_10nmAu.rasx")
Au_30 = xrd.import(filename = "/Users/fern/Desktop/Data/20250721/20250721_AuRoughness_FR_XRD_FR20250624_2nmCr_30nmAu.rasx")
Au_60 = xrd.import(filename = "/Users/fern/Desktop/Data/20250811/20250811_AuRoughness_FR_XRD_FR20250624_2nmCr_60nmAu.rasx")

Importing AFM files

Au05nm_5x5 = AFM.import(filename = "/Users/fern/Desktop/Data/20250624/20250624_AuCr_FR_AFM_20250624_2nmCr_5nmAu__5.0x5.0+Topography_Forward_013.tiff")

Au10nm_2x2 = AFM.import(filename = "/Users/fern/Desktop/Data/20250709/20250709_FR_AuCr_AFM_20250624_2nmCr_30nmAu__2.0x2.0+Topography_Forward_012.tiff")
Au10nm_5x5 = AFM.import(filename = "/Users/fern/Desktop/Data/20250717/20250717_FR_AuCr_AFM_20250624_2nmCr_10nmAu__5.0x5.0+Topography_Forward_009.tiff")

Au30nm_2x2 = AFM.import(filename = "/Users/fern/Library/CloudStorage/OneDrive-SharedLibraries-csulb/Gredig Molecular Thin Film Lab - Fernanda - Fernanda/RAW/AFM/20250709/20250709_FR_AuCr_AFM_20250624_2nmCr_30nmAu__2.0x2.0+Topography_Forward_012.tiff")
Au30nm_5x5 = AFM.import(filename = "/Users/fern/Library/CloudStorage/OneDrive-SharedLibraries-csulb/Gredig Molecular Thin Film Lab - Fernanda - Fernanda/RAW/AFM/20250709/20250709_FR_AuCr_AFM_20250624_2nmCr_30nmAu__5.0x5.0+Topography_Forward_014.tiff")

Au60nm_2x2 = AFM.import(filename = "/Users/fern/Desktop/Data/20250716/20250716_FR_AuCr_AFM_20250624_2nmCr_60nmAu__2.0x2.0+Topography_Forward_009.tiff")
Au60nm_5x5 = AFM.import(filename = "/Users/fern/Desktop/Data/20250716/20250716_FR_AuCr_AFM_20250624_2nmCr_60nmAu__5.0x5.0+Topography_Forward_007.tiff")

Au75nm_2x2 = AFM.import(filename = "/Users/fern/Desktop/Data/20250811/20250811_FR_AuCr_AFM_20250624_4nmCr_75nmAu__2.0x2.0+Topography_Forward_010.tiff")
Au75nm_5x5 = AFM.import(filename = "/Users/fern/Desktop/Data/20250811/20250811_FR_AuCr_AFM_20250624_4nmCr_75nmAu__5.0x5.0+Topography_Forward_008.tiff")

Au 5nm

plot(Au_05$theta, Au_05$I.meas, log='y',col="blue", type='l', xlab="2θ",ylab="I [a.u]",main="5nm of Au ")

plot(Au05nm_5x5)

Graphing: Topography

afm_data <- AFM.import(filename = "/Users/fern/Desktop/Data/20250624/20250624_AuCr_FR_AFM_20250624_2nmCr_5nmAu__5.0x5.0+Topography_Forward_013.tiff")
params <- AFM.math.params(afm_data)
summary(params)

Basename: 20250624_AuCr_FR_AFM_20250624_2nmCr_5nmAu__5.0x5.0+Topography_Forward_013.tiff 
Roughness Ra ............: 0.3807944  nm 
Roughness Rq ............: 0.4985521  nm 
Skewness Rsk ............: -0.003367199  
Kurtosis K ..............: 4.539809  
Binder Cumulant U4 ......: -5.088288  
Std. Dev of Height Hsd ..: 0.4985531  nm 
Deep Area Ratio .........: 0.00403595 

Au 10nm

plot(Au_10$theta, Au_10$I.meas, log='y',col="blue", type='l', xlab="2θ",ylab="I [a.u]",main="10 nm of Au")

plot(Au10nm_2x2)

Graphing: Topography

plot(Au10nm_5x5)

Graphing: Topography

#For the 2x2 
afm_data <- AFM.import(filename = "/Users/fern/Desktop/Data/20250709/20250709_FR_AuCr_AFM_20250624_2nmCr_30nmAu__2.0x2.0+Topography_Forward_012.tiff")
params <- AFM.math.params(afm_data)
summary(params)

Basename: 20250709_FR_AuCr_AFM_20250624_2nmCr_30nmAu__2.0x2.0+Topography_Forward_012.tiff 
Roughness Ra ............: 0.5056806  nm 
Roughness Rq ............: 0.6342873  nm 
Skewness Rsk ............: 0.3310548  
Kurtosis K ..............: 3.101414  
Binder Cumulant U4 ......: -1.569605  
Std. Dev of Height Hsd ..: 0.6342922  nm 
Deep Area Ratio .........: 0.0003509521 

#for the 5x5
afm_data <- AFM.import(filename = "/Users/fern/Desktop/Data/20250717/20250717_FR_AuCr_AFM_20250624_2nmCr_10nmAu__5.0x5.0+Topography_Forward_009.tiff")
params <- AFM.math.params(afm_data)
summary(params)

Basename: 20250717_FR_AuCr_AFM_20250624_2nmCr_10nmAu__5.0x5.0+Topography_Forward_009.tiff 
Roughness Ra ............: 0.2959693  nm 
Roughness Rq ............: 0.3873544  nm 
Skewness Rsk ............: 0.6644707  
Kurtosis K ..............: 5.702704  
Binder Cumulant U4 ......: -11.66901  
Std. Dev of Height Hsd ..: 0.3873552  nm 
Deep Area Ratio .........: 0.001285553 

note: the 2x2 and 5x5 have a higher variance in their Rq because they were not taken on the same day, so different location with different parameters 🤧

Au 30nm

plot(Au_30$theta, Au_30$I.meas, log='y',col="blue", type='l', xlab="2θ",ylab="I [a.u]",main="30 nm of Au")

plot(Au30nm_2x2)

Graphing: Topography

plot(Au30nm_5x5)

Graphing: Topography

#For the 2x2 
afm_data <- AFM.import(filename = "/Users/fern/Library/CloudStorage/OneDrive-SharedLibraries-csulb/Gredig Molecular Thin Film Lab - Fernanda - Fernanda/RAW/AFM/20250709/20250709_FR_AuCr_AFM_20250624_2nmCr_30nmAu__2.0x2.0+Topography_Forward_012.tiff")
params <- AFM.math.params(afm_data)
summary(params)

Basename: 20250709_FR_AuCr_AFM_20250624_2nmCr_30nmAu__2.0x2.0+Topography_Forward_012.tiff 
Roughness Ra ............: 0.5056806  nm 
Roughness Rq ............: 0.6342873  nm 
Skewness Rsk ............: 0.3310548  
Kurtosis K ..............: 3.101414  
Binder Cumulant U4 ......: -1.569605  
Std. Dev of Height Hsd ..: 0.6342922  nm 
Deep Area Ratio .........: 0.0003509521 

#for the 5x5
afm_data <- AFM.import(filename = "/Users/fern/Library/CloudStorage/OneDrive-SharedLibraries-csulb/Gredig Molecular Thin Film Lab - Fernanda - Fernanda/RAW/AFM/20250709/20250709_FR_AuCr_AFM_20250624_2nmCr_30nmAu__5.0x5.0+Topography_Forward_014.tiff")
params <- AFM.math.params(afm_data)
summary(params)

Basename: 20250709_FR_AuCr_AFM_20250624_2nmCr_30nmAu__5.0x5.0+Topography_Forward_014.tiff 
Roughness Ra ............: 0.5265953  nm 
Roughness Rq ............: 0.6618933  nm 
Skewness Rsk ............: 0.4410237  
Kurtosis K ..............: 3.90379  
Binder Cumulant U4 ......: -1.970224  
Std. Dev of Height Hsd ..: 0.6618946  nm 
Deep Area Ratio .........: 0.000289917 

Au 60nm

plot(Au_60$theta, Au_60$I.meas, log='y',col="blue", type='l', xlab="2θ",ylab="I [a.u]",main="60 nm of Au")

plot(Au60nm_2x2)

Graphing: Topography

plot(Au60nm_5x5)

Graphing: Topography

#For the 2x2 
afm_data <- AFM.import(filename = "/Users/fern/Desktop/Data/20250716/20250716_FR_AuCr_AFM_20250624_2nmCr_60nmAu__2.0x2.0+Topography_Forward_009.tiff")
params <- AFM.math.params(afm_data)
summary(params)

Basename: 20250716_FR_AuCr_AFM_20250624_2nmCr_60nmAu__2.0x2.0+Topography_Forward_009.tiff 
Roughness Ra ............: 1.123509  nm 
Roughness Rq ............: 1.391271  nm 
Skewness Rsk ............: 0.3587928  
Kurtosis K ..............: 2.831975  
Binder Cumulant U4 ......: 0.5123088  
Std. Dev of Height Hsd ..: 1.391281  nm 
Deep Area Ratio .........: 0.0001983643 

#for the 5x5
afm_data <- AFM.import(filename = "/Users/fern/Desktop/Data/20250716/20250716_FR_AuCr_AFM_20250624_2nmCr_60nmAu__5.0x5.0+Topography_Forward_007.tiff")
params <- AFM.math.params(afm_data)
summary(params)

Basename: 20250716_FR_AuCr_AFM_20250624_2nmCr_60nmAu__5.0x5.0+Topography_Forward_007.tiff 
Roughness Ra ............: 1.056472  nm 
Roughness Rq ............: 1.30228  nm 
Skewness Rsk ............: 0.3938286  
Kurtosis K ..............: 2.771381  
Binder Cumulant U4 ......: 0.4552893  
Std. Dev of Height Hsd ..: 1.302283  nm 
Deep Area Ratio .........: 3.814697e-06 

Au 75nm

no xrd data 😔

#For the 2x2 
afm_data <- AFM.import(filename = "/Users/fern/Desktop/Data/20250811/20250811_FR_AuCr_AFM_20250624_4nmCr_75nmAu__2.0x2.0+Topography_Forward_010.tiff")
params <- AFM.math.params(afm_data)
summary(params)

Basename: 20250811_FR_AuCr_AFM_20250624_4nmCr_75nmAu__2.0x2.0+Topography_Forward_010.tiff 
Roughness Ra ............: 1.611074  nm 
Roughness Rq ............: 2.036822  nm 
Skewness Rsk ............: 0.5870996  
Kurtosis K ..............: 3.528666  
Binder Cumulant U4 ......: 0.7164804  
Std. Dev of Height Hsd ..: 2.036838  nm 
Deep Area Ratio .........: 6.103516e-05 

#for the 5x5
afm_data <- AFM.import(filename = "/Users/fern/Desktop/Data/20250811/20250811_FR_AuCr_AFM_20250624_4nmCr_75nmAu__5.0x5.0+Topography_Forward_008.tiff")
params <- AFM.math.params(afm_data)
summary(params)

Basename: 20250811_FR_AuCr_AFM_20250624_4nmCr_75nmAu__5.0x5.0+Topography_Forward_008.tiff 
Roughness Ra ............: 1.562363  nm 
Roughness Rq ............: 2.013378  nm 
Skewness Rsk ............: 0.8103764  
Kurtosis K ..............: 4.568334  
Binder Cumulant U4 ......: 0.6243479  
Std. Dev of Height Hsd ..: 2.013382  nm 
Deep Area Ratio .........: 3.433228e-05 

XRD plots Overlayed

plot(Au_05$theta, Au_05$I.meas, log='y', col="blue", type='l', 
     xlab="2θ", ylab="I [a.u]",main = "Full XRD plot", xlim=c(20,80))
lines(Au_10$theta, Au_10$I.meas, col="red", lwd=1)
lines(Au_30$theta, Au_30$I.meas, col="blueviolet", lwd=1)
lines(Au_60$theta, Au_60$I.meas, col="darkgreen", lwd=1)

legend("topright", legend = c("Au_05", "Au_10","Au_30","Au60"), col = c("blue", "red","blueviolet","darkgreen"), lwd = 3)

plot(Au_05$theta, Au_05$I.meas, log='y', col="blue", type='l', 
     xlab="2θ", ylab="I [a.u]",main="~33° peak", xlim=c(30,35))
lines(Au_10$theta, Au_10$I.meas, col="red", lwd=1)
lines(Au_30$theta, Au_30$I.meas, col="blueviolet", lwd=1)
lines(Au_60$theta, Au_60$I.meas, col="darkgreen", lwd=1)

this one was weird 🥸 has the same sort of trend as silicon so I’m thinking its that it’s a chromium peak

plot(Au_05$theta, Au_05$I.meas, log='y', col="blue", type='l', main="~38° peak",
     xlab="2θ", ylab="I [a.u]",xlim=c(35,40))
lines(Au_10$theta, Au_10$I.meas, col="red", lwd=1)
lines(Au_30$theta, Au_30$I.meas, col="blueviolet", lwd=1)
lines(Au_60$theta, Au_60$I.meas, col="darkgreen", lwd=1)

Corresponds with Au(111) peak

plot(Au_05$theta, Au_05$I.meas, log='y', col="blue", type='l', main="~44° peak",
     xlab="2θ", ylab="I [a.u]",xlim=c(43,46))
lines(Au_10$theta, Au_10$I.meas, col="red", lwd=1)
lines(Au_30$theta, Au_30$I.meas, col="blueviolet", lwd=1)
lines(Au_60$theta, Au_60$I.meas, col="darkgreen", lwd=1)

Corresponds with Au(200) peak

plot(Au_05$theta, Au_05$I.meas, log='y', col="blue", type='l', main="~61° peak",
     xlab="2θ", ylab="I [a.u]",xlim=c(61,63))
lines(Au_10$theta, Au_10$I.meas, col="red", lwd=1)
lines(Au_30$theta, Au_30$I.meas, col="blueviolet", lwd=1)
lines(Au_60$theta, Au_60$I.meas, col="darkgreen", lwd=1)

plot(Au_05$theta, Au_05$I.meas, log='y', col="blue", type='l', main="~70° peak",
     xlab="2θ", ylab="I [a.u]",xlim=c(65,76),ylim=c(5e+01,5e+05))
lines(Au_10$theta, Au_10$I.meas, col="red", lwd=1)
lines(Au_30$theta, Au_30$I.meas, col="blueviolet", lwd=1)
lines(Au_60$theta, Au_60$I.meas, col="darkgreen", lwd=1)

Corresponds with Si(400) peak

plot(Au_05$theta, Au_05$I.meas, log='y', col="blue", type='l', , main="~77° peak",
     xlab="2θ", ylab="I [a.u]",xlim=c(77,80),ylim=c(5e+01,1e+03))
lines(Au_10$theta, Au_10$I.meas, col="red", lwd=1)
lines(Au_30$theta, Au_30$I.meas, col="blueviolet", lwd=1)
lines(Au_60$theta, Au_60$I.meas, col="darkgreen", lwd=1)

Corresponds with Au(311) peak

plot(Au_05$theta, Au_05$I.meas, log='y', col="blue", type='l', 
     xlab="2θ", ylab="I [a.u]",main = "Full XRD plot", xlim=c(20,80))
lines(Au_10$theta, Au_10$I.meas, col="red", lwd=1)
lines(Au_30$theta, Au_30$I.meas, col="blueviolet", lwd=1)
lines(Au_60$theta, Au_60$I.meas, col="darkgreen", lwd=1)
legend("topright", legend = c("Au_05", "Au_10","Au_30","Au_60"), col = c("blue", "red","blueviolet","darkgreen"), lwd = 1)