Model Adaptation Activity Nano Roughness Project Part A

Successful completion of this project will enable you to: Gain more experience using MATLAB with the focus being on: o The use of control and conditional structures o The creation of an executive program and user-defined functions Continue to create plots of technical presentation quality Practice applying statistical analysis concepts Apply MATLAB skills to a problem based on a real-world situation Continue to develop effective teaming skills

PROJECT DESCRIPTION
Liguore Labs has analyzed your team's work thus far in determining roughness from nanoscale images. Kerry Prior has asked your team to develop a program in MATLAB that allows a user to calculate roughness of a nanoscale sample by several methods available. You have read how an AFM works, and Liguore Labs wants a method to visually display AFM datasets and calculate roughness using methods that are accepted within the industry. To satisfy the company's needs, your team must design a program that is functional and easy to use. In addition to developing the software tool, your team will document your procedures and demonstrate how your software tool can be used on a series of AFM data files. Your document must be written in complete sentences and should clarify the program completely, yet briefly, for your client. Your software tool will be viewed and evaluated by the managers at Liguore Labs. You may assume that the managers have some knowledge of science and math but are NOT engineers.

BACKGROUND INFORMATION
In Homework 11, you learned to use AFM data to make a digitized, grayscale image as in Figure 1. Note that this is not a picture of the surface, and you should not use "photograph" or "picture" in your report. These are digital "images" in which the brightness value of each pixel represents height. Figure 1 can be stored in MATLAB as a variable that contains an array of numbers, with each number referring to the gray scale value for each pixel of the image. A sub-sample of the complete Figure 1 file is shown in Table 1; this sub-sample shows the gray scale values for the square superimposed on Figure 1 and magnified by itself in Figure 2. Gray-scale values can range from 0 for black to 255 for white (as they do in Figure 1). You will place a line over this table of data, by choosing two random points to define the endpoints. This line can be horizontal, vertical, or at an angle. An example of a possible line is shown on the table as the underlined values (though it is not shown on the actual figure, to avoid obscuring the pixels that are used). You will determine gray values so you can make an image that acts like a "topographic map" of your AFM data, that will provide a visual representation of "depth".

Copyright 2004 Purdue University

Figure 1. Image made from AFM height data, with pixel color representing height at each location. to show (Remember that this is not a photograph.)

Figure 2. Close-up of area outlined in Figure 1, pixels and brightness.

Table 1. Digital file for sub-sample from AFM image shown in Figure 2, with possible angled line shown by underlined numbers. Note the dark "hole" in the middle of values < 100.
196 193 195 195 206 205 208 207 203 196 192 183 184 180 176 168 155 161 155 205 220 213 209 202 205 210 213 216 193 192 189 189 203 203 205 203 201 193 186 181 180 178 172 156 144 155 140 197 220 215 209 205 207 210 208 214 187 188 188 189 200 195 195 195 196 191 179 176 173 169 163 148 130 146 125 192 219 216 212 208 207 210 207 211 180 183 183 185 190 185 185 189 191 189 176 173 170 164 158 146 133 136 120 179 215 217 213 208 207 208 207 208 173 177 175 180 184 183 182 184 183 182 172 165 167 161 157 137 132 132 120 165 209 217 214 209 209 209 208 209 165 166 169 178 180 180 175 174 171 166 157 146 155 148 143 128 124 122 120 162 201 217 215 211 207 208 208 208 153 155 162 171 173 173 169 168 161 149 143 131 138 130 126 125 125 122 120 152 192 215 217 214 207 209 208 208 149 151 151 157 164 170 169 166 158 145 138 132 128 119 119 123 125 124 121 138 182 210 217 214 209 210 209 210 145 147 146 152 157 163 162 158 149 141 127 126 118 112 113 120 124 123 125 138 174 205 217 214 211 209 210 213 138 142 145 152 149 149 149 146 141 137 124 121 109 102 107 116 122 124 129 140 165 203 217 215 211 209 211 214 133 137 140 144 143 141 144 142 138 135 132 125 112 98 102 112 119 125 131 136 154 198 215 216 211 208 212 214 131 135 136 141 142 140 143 139 135 132 133 123 109 98 99 110 117 125 132 137 146 191 215 217 212 210 210 213 129 131 134 139 138 139 140 134 132 128 126 114 102 99 100 105 113 125 133 141 145 186 215 217 214 210 208 212 128 129 132 134 132 137 139 134 130 126 123 108 102 101 102 102 110 119 131 137 145 181 208 216 214 210 208 211 129 130 130 129 130 135 137 134 128 127 123 107 103 102 102 104 110 114 127 130 141 176 204 214 213 211 208 209 131 130 129 128 129 134 134 131 124 125 120 107 105 102 103 105 111 114 121 127 137 172 200 210 213 211 206 207 134 130 130 129 129 129 128 128 124 124 118 109 107 104 103 105 111 113 117 122 134 165 190 204 211 211 205 206 135 131 131 127 129 128 128 127 125 123 120 110 107 104 103 105 110 112 115 118 131 155 179 198 210 209 206 205 137 134 131 128 129 128 127 126 122 121 118 111 105 105 103 105 108 110 112 115 126 145 174 191 206 207 205 203 136 137 131 130 128 127 126 125 120 118 116 112 103 103 102 103 105 108 110 113 123 140 164 183 202 206 204 201

Copyright 2004 Purdue University

216 215 215 214 214 213 211 213 214 213 211 210 209 209 209 209 208 207 204 203 211 214 216 216 218 220 219 217 216 216 214 210 209 210 209 208 207 206 206 206

Copyright 2004 Purdue University

MATLAB Code
Executive Function Your code will consist of a MATLAB executive program and a series of supporting MATLAB user-defined functions. An executive user-defined function is the main function that controls the overall order of computations and operations. This function has no input or output arguments. Your team will construct one executive user-defined function called nanorough.m which will control the order of the computations and calls to user-defined functions. For the duration of Project II, your team will add and modify sections of this function as you complete the supporting user-defined functions. This function is to execute when nanorough is entered at the MATLAB prompt. It will make calls to the supporting user-defined functions that your team creates. You will begin building the executive function in Lab 12, though you will have developed some of the supporting user-defined functions in Lab 11. In Part A, you will be writing introductory code that finds the height values needed to perform the roughness calculation. In Part B, you will be given information about the different formulas used to calculate roughness and will implement these calculations. Supporting User-Defined Functions Your team will construct user-defined functions that will perform the computations for the project. The executive function should route appropriate information to and from user-defined functions but perform minimal computations itself. All major computations (such as defining the endpoints of the line) and repetitive computations (such as converting height values to color values or finding the values of brightness along the line) must be handled by user-defined functions. A good rule-of-thumb is to create a user-defined function for any task or computation that takes more than 8 lines of code. Clearly indicate the author(s) of each function. There should be clear evidence that each member is contributing to the development of project code. Required Functionality of Code When the user of your code types nanorough at the MATLAB prompt, the user should be kept in the program until the user wishes to quit. This means that the user can continuously run AFM datasets without being forced to restart the program. Your team will work on this in Lab 12. Your code must be able to load an ASCII AFM dataset. Your code must also be general enough to handle any AFM dataset with X, Y, and height data in three columns. Your team will construct this piece of the project in Homework 11. During demonstrations of your code, your team will be asked to develop an image of a dataset your team has never seen before (though it will be of the same style as those you have used while developing your project). Sample Images and Determination of Pixel Color Value Three AFM datasets are provided for use by your team. The digitized files are called gold24.txt, afm2.txt, and afm3.txt and located in the engr106/FALL2003/PROJECTS subdirectory. Each dataset will be loaded and converted to an array of numbers. This will be covered in Homework 11. Each number in the array represents the height at the particular point. You will normalize this data to find a gray scale value for each pixel. These values range from 0 for black to 255 for white. Each of these 256 colors will represent a small range of heights.

Copyright 2004 Purdue University

Thus, you will have two data arrays. The first, the Height Data Array, contains the height values for each point that will be used in all your calculations (most of which will be performed in Part B). The second array, the Pixel Color Array, will have the same number of rows and columns as the Height Data Array, but will have been "proportioned" or "normalized" to contain integer values between 0 and 255 and will be used as a visual representation to help the user "see" the roughness of the surface. This image will be Plot 1. Random Lines Each line is defined by a starting point and an ending point. The points must be randomly placed on the image. Your team will begin work on random generation of points in Lab 11, and will continue this in Labs 12 and 13 and Homework 12. Average Height Each pixel along the line will have a height value. You will calculate the average height of these points. You will plot the height at each point along the line as well as the average height. Refer to Question 7 of Homework 10. Your Plot 2 will look like the "Cross Section" plots. Required Output Results Your code should generate results that are easy to interpret. Graphical results are to include plots: Plot 1 is a figure showing the image made from the AFM data with all lines (though you are only required to have one for Part A) used to determine the roughness overlaid on the image. Plot 2 is a figure showing the height of each pixel along the line. It must be properly labeled and should display a line showing the average height (which is not shown on the plots in Homework 10, but is needed for calculations required for Part B). Additionally, a series of text-based key results must be displayed on the screen. These include: All user inputs (e.g., dataset name). All internally-measured values (e.g., size of dataset array, maximum and minimum height values). All internally-calculated values (e.g., "height resolution" of image the height difference between two pixels that differ by 1 out of the 256 shades of gray, the average height).

REPORTS
Your team will demonstrate the team's nanorough initial code in lab. Your code should be able to provide initial results (described below) for an AFM dataset never seen before. Your TA will select one team member to display the code, which is why every member should have access to the code and understand it. This demonstration will form part of the grade for Part A. Further, your team will submit an interim project report that includes the following items. Executive Summary. Write a one-page (1.5 spacing) executive summary to the managers of the Liguore Labs. The summary must include a description of your methodology for finding color values based on the AFM dataset and for finding the "addresses" of points (or pixels) that fall along the random line. The description should include enough detail for the manager of Liguor Labs to understand how the images are generated, what these images show, how the line is used, and what the "average" height represents Many of the calculations for Part B will be based on Copyright 2004 Purdue University 5

deviations from this "average" line. Also discuss the capabilities of MATLAB that make it useful for this type of analysis, as well as any shortcomings of MATLAB for this application that you may have identified. This should be written in the form of a memorandum as follows: MEMORANDUM To: Kerry Prior, Vice President of Research, Liguore Labs From: Team #: List all members of your team Re: AFM Roughness MATLAB Tool - Interim Report Date: Flow Chart(s). Draw one or more flowcharts to track the calculation of the pixel colors from the AFM height dataset, calculate the average height, and other tasks as necessary. These should be easy for the TA to follow. They may be neatly handwritten or electronic PowerPoint provides flowcharting capability, though you are allowed to do these by hand, which might be faster. Code and Documentation. Provide a typed list of all the functions that your team has written for Part A of the Project. For each function on the list, include the name of the function, the author(s), and a brief description of what the function does. Provide a description of the inputs and outputs. Note that most of this information is to be included in the help comments of each function. Submit a hard copy of each function written for Part A. Be sure the correct file name appears on each page. Adequately comment your code so your TA can easily follow your code. Initial Results. At the end of Part A, your code should do the following (and you will test that your code can develop these results on two of the three AFM datasets provided and submit your results): Convert a raw AFM height dataset into an image Generate one random line on the image Calculate the average height for the chosen line Display Plot 1 and Plot 2 to the screen in a single figure window using the subplot command Display to the screen the name of the AFM dataset being analyzed. Display all user inputs, assumed values, and key results that were required as part of the calculation. Your team will also submit a copy of the output printed to the screen by creating two diaries: one for each of two (out of the three) sample AFM datasets (use the diary command in MATLAB). Please suppress printing of all computation lines before running your simulation so that the diary will not be too long. Otherwise, trim extraneous lines in the diary text file before printing the hard copy. Your output should clearly indicate which dataset is being analyzed.

Copyright 2004 Purdue University

Engineering Contexts and Concepts for Developing and Promoting Students' Higher Level Learning (NSF BEE 0342028) Model Adaptation Activity Nano Roughness Project Part B
Successful completion of this project will enable you to: Gain more experience using MATLAB with the focus being on: o The use of control and conditional structures o The creation of an executive program and user-defined functions Continue to create plots of technical presentation quality Practice applying statistical analysis concepts Apply MATLAB skills to a problem based on a real-world situation Continue to develop effective teaming skills

PROJECT DESCRIPTION
Liguore Labs is ready for your finished MATLAB code to calculate roughness of a nanoscale sample by several methods available. You have read how an AFM works, and Liguore Labs wants a method to visually display AFM datasets and calculate roughness using methods that are accepted within the industry. To satisfy the company's needs, your team must design a program that is functional and easy to use. In addition to developing the software tool, your team will document your procedures and demonstrate how your software tool can be used on a series of AFM data files. Your document must be written in complete sentences and should clarify the program completely, yet briefly, for your client. Your software tool will be evaluated by the managers at Liguore Labs, who have knowledge of science and math but are not engineers. Roughness Calculations: (based on www.veeco.com/appnotes/AN505.pdf)

Copyright 2004 Purdue University

The following methods of measuring roughness are generally accepted in the industry: Term Definition Calculation Use n Mean of height values of all This is a starting point for 1 Z Z = Zi heights along profile (where many of the other n i =1 "profile" is the line you draw) calculations n Roughness Average of the This simple method is often Ra 1 R = Z Z a i profile is the difference used to describe the n i =1 between each point and the roughness of machined average height surfaces. 2 Root Means Square Average of This more complicated Rq 1 n the profile is similar in concept Rq = method is ~1.11*Ra for many Zi Z n i =1 to linear regression surfaces, but not always Measure of highest and R p , Rv Maximum profile peak height, Measured Maximum profile valley depth lowest points Maximum Height of profile is Range of highest and lowest Rt Rt = R p + Rv difference between peak and points valley 5 Average Profile is the average Rz See picture and discussion 1 5 R = P + V i j below to define a maximum z found from the five greatest 10 i =1 j =1 peak and valley peaks and five greatest valleys. 3 Skewness measures the Used with a histogram (Plot Rsk 1 n R = Z Z assymetry of the profile about 3) to show if heights are sk i 3 nRq i =1 the mean line. normally distributed Positive skew indicates a predominance of peaks, while negative skew indicates a predominance of valleys.

Note that a peak, such as P1, prevents any other points on that "mountain" from being a peak until the height has gone below Z in both directions. Note this is also true of valleys (see V2, with a "local" valley just to the left of V2 that is not used). The label Rz has been used for other roughness measures, so you might find other equations if you search the Internet; use this one. The following image is provided only to help you see what skewness and the Rsk value indicate. Note that the ADF (Amplitude Distribution Function) is a histogram of all the heights. Again, you do not need to develop a figure like the one shown here. However, you will develop a histogram similar to the ADF curve (rotated 90) as Plot 3 (discussed in Required Output Results). To make this curve reasonably smooth, you will likely have 30 or more bins.

Copyright 2004 Purdue University

MATLAB Code
Executive Function Your code will consist of a MATLAB executive function and a series of supporting user-defined functions. The executive function, called nanorough.m, will control the order of computations and calls to user-defined functions. This function is to execute when nanorough is entered at the MATLAB prompt. The executive function should route appropriate information to and from user-defined functions but perform minimal computations itself. Supporting User-Defined Functions Your team will construct user-defined functions that will perform the computations for the project. In the "Roughness Calculations" section above, you have been given information about the different formulas used to calculate roughness and will implement these calculations. For additional information, visit www.htskorea.com/tech/spm/profile.pdf (particularly pages 6-7, 1113, 33-37, and 41-42). Much of this site is based on www.predev.com/smg/parameters.htm). All major computations (such as defining the endpoints of the line or solving the roughness equations) and repetitive computations (such as converting height values to color values or finding the five peaks and valleys) must be handled by user-defined functions. A good rule-ofthumb is to create a user-defined function for any task or computation that takes more than 8 lines of code. Clearly indicate the author(s) of each function. There should be clear evidence that each member is contributing to the development of project code. Required Functionality of Code When the user of your code types nanorough at the MATLAB prompt, the user should be kept in the program until the user wishes to quit. This means that the user is to be allowed to run one AFM dataset after another, after another without being forced to restart the program.

Copyright 2004 Purdue University

Your code must be general enough to load any AFM dataset with X, Y, and height data in three columns. During the final demonstration of your code, your team will be asked to calculate roughness of a dataset your team has never seen before (though it will be of the same style as those you have used while developing your project). Random Lines Each line is defined by a starting point and an ending point that allows at least 200 data points to be found between them. The starting and ending points must be randomly placed on the image. User Choice of Parameter The user should be given a choice of which roughness value will be found. The user should also be given the choice to find all measurements at once, if desired, rather than having to choose all of them one by one. Once the user makes a selection, the MATLAB code should calculate that value and display it to the screen. As soon as the user enters a name of an AFM dataset, Plot 1 should appear. When the user chooses any of the measurements, Plots 1 and 2 should appear in a single figure using the subplot command. If the user chooses to find the skewness, Plots 1 and 3 should appear in a single figure. If the user chooses to see all calculations, then Plots 1, 2, and 3 should appear in a single figure. (Plots are discussed in Required Output Results below.) Consistency and Reliability "Consistency" is the sameness of parts of the whole. Some AFM datasets are "consistent", in that if you are calculating Rz, and you place seven random lines on your data, you get similar values for each of the seven lines. The roughness measure is similar over each measured part. Other datasets will be highly variable, in that a line placed in one location will result in a very different roughness value from another line, and could be called "inconsistent". It is up to your team to define similar. You should discuss the concept of consistency of the datasets in your summary. "Reliability" is defined as an ability to collect the same results on repeated trials. The roughness calculation made for a single line may not be a good representation of the dataset since there may be a high degree of variability depending on where the line is superimposed on the dataset. To get high reliability, several lines with different starting and end points should be used on the dataset. Your team will decide how many lines are needed to attain "reasonable reliability" of the roughness for a given dataset. To do this, your team will need to come to a consensus on what constitutes "reasonable reliability". If you take readings on seven lines, it may not make sense to average those seven readings. You might choose to use the mode roughness value (which is difficult with continuous values; how many decimal places are appropriate for your roughness value?), a trimmed mean where you drop the highest and lowest values (or three highest and three lowest values), or some method other than simple arithmetic average. Develop a procedure for determining roughness values that ensures that your measurements on a dataset meet your team's definition of "reasonable reliability." Implement your procedure in your project code - your team will need to decide what results need to be presented to the user. Discuss your analysis of reliability in your report. Consistency and reliability are related topics, so there may be an amount of overlap in your discussion of each topic.

Copyright 2004 Purdue University

10

Required Output Results Your code should generate results that are easy to interpret. Graphical results are to include plots: Plot 1 is a figure showing the image made from the AFM data with all lines used to determine the roughness overlaid on the image. Plot 2 is a figure showing the height of each pixel along the line. In Part A, the x-axis showed pixels along the line; for Part B, the x-axis should show the actual distance in nanometers along the line. Use proper labels and display a line showing the average height. Plot 3 is a histogram of the height values found for one of the lines used, with approximately 30 bins and with bin edges defined to help illustrate the skew of the roughness value. Additionally, a series of text-based key results must be displayed on the screen. These include: All user inputs (e.g., dataset name). All internally-measured values (e.g., size of dataset, maximum and minimum height values, reliability related measured values). All internally-calculated values (e.g., "height resolution" of image the height difference between two pixels that differ by 1 out of the 256 shades of gray, the average height, the computed roughness value(s) desired by the user, reliability related calculated values).

REPORTS
Your team will demonstrate the team's nanorough code in lab. Your code should be able to provide full results (described below) for an AFM dataset never seen before. Your TA will select one team member to display the code, which is why every member should have access to the code and understand it. This demonstration will form part of the grade for Part B. Further, your team will submit a final project report that includes the following items. Executive Summary. Write maximum three-page (1.5 spacing) executive summary to the managers of the Liguore Labs. The executive summary should include: A brief description of the problem your team is solving and an explanation of why methods for measuring nanoscale roughness are important/useful. Your team must include a paragraph that discusses why there are so many roughness measures, i.e., why a single roughness measure will not work for all datasets. You may wish to refer to the datasets you were provided. A discussion of consistency and/or reliability in general terms. You may certainly refer to the three datasets provided, but do not discuss consistency and reliability in terms of those three images only; your discussion should be general so it would be useful for the managers as they look at other datasets. A brief response to any problems that were noted on Part A of the project (e.g. clarify missing or unclear material). A 1-2 paragraph description of the functionality and use of the program you have developed. The description should include enough detail for the manager of Liguor Labs to understand what a "roughness" value indicates about the surface, as well as what "skewness" represents and how to read your histogram. Your description should note how your team had chosen to define consistency and a procedure for how it is achieved in the determination of roughness measures.

Copyright 2004 Purdue University

11

A comparison of two of the provided datasets; results should be presented in table format. (The table will not count towards your three page limit).

Write the summary in the form of a memorandum as follows: MEMORANDUM To: Kerry Prior, Vice President of Research, Liguore Labs From: Team #: List all members of your team Re: AFM Roughness MATLAB Tool - Final Report Date: Flow Chart(s). Draw one or more flowcharts to track allowing the user to choose the desired calculation, finding the five peaks and valleys, or other important code functionality. Code and Documentation. Provide a typed list of all the functions that your team has written for the Project. For each function on the list, include the name of the function, the author(s), and a brief description of what the function does. Provide a description of the inputs and outputs. Note that most of this information is to be included in the help comments of each function. Submit a hard copy of each function written for Part B. Be sure the correct file name appears on each page. Adequately comment your code so your TA can easily follow your code. Final Results. At the end of Part B, your code should do the following (and you will test that your code can develop these results on two of the three AFM datasets provided and submit your results): Convert a raw AFM height dataset into an image Generate one random line on the image that allows at least 200 data points along its length Calculate the Mean and the Average Roughness for the chosen line Print all required plots to the screen in a single figure window (the histogram is not required to have "nice" bin edges, but it must have at least 30 bins to make a "smooth" curve) Print all user inputs, assumed values, and key results that required as part of the calculation. Display Plots 1, 2, and 3 (as appropriate based on the user input) to the screen in a single figure window using the subplot command Display to the screen the name of the AFM dataset being analyzed. Display all user inputs, assumed values, and key results that were required as part of the calculation. Your team will also submit a copy of the output printed to the screen by creating two diaries: one for each of two (out of the three) sample AFM datasets (use the diary command in MATLAB). Please suppress printing of all computation lines before running your simulation so that the diary will not be too long. Otherwise, trim extraneous lines in the diary text file before printing the hard copy. Your output should clearly indicate which dataset is being analyzed.

Copyright 2004 Purdue University

12