LMFIT and Peak-Fitting of XRD peaks

I recently added the Non-Linear Least-Squares Minimization and Curve-Fitting (LMFIT) package to my Python. Lately I've made an effort to move away from MATLAB and use Python and the packages available for it to take on some of my scientific problems.

I've been using the Gaussian model and composite model feature of LMFIT to reproduce a fitted diffraction profile as close as possible to what the manufacturer's software provides me. In the software, the fitting procedure determines the position of 2theta to determine the d-spacing of the crystal structure by Bragg's law. The stress is then calculated based on the change in d-spacing or lattice strain (gross oversimplification). The software ignores the information that exists within the peak, such as peak width that can reflect a dislocation content or the peak shape that may influenced by the twin density. Hence my goal is to reproduce the fitting procedure and determine the peak characteristics such to hopefully find more information.

Below outlines my fun so far in trying to replicate what the manufacturer does for peak fitting. This is an example of a diffraction peak, that has been fitted with a Gaussian curve:

This is the output that the software reports:

One distinct difference right away is that two peaks are used to fit the diffraction profile. Obviously I'm already off to a bad start. For those curious, this is because both the K alpha1 and alpha2 are used during the measurement, so there is in fact two signals. This was my next attempt just using two Gaussian curves.

Not even close. Although the fit is actually better than the manufacturers, it has no physical reasoning. So I enforced some rules on the intensity of the two radiations as well as the expected separation of the two peaks and came out with this:

The constraints actually made my fit "worse" compared to when the summation of the two Gaussian curves were left unbounded, but at least now I'm little closer to what the manufacturer reports. The next constraint I added was to assume the interaction profile of both radiation types would be same same in terms of variance, which gave me this:

Then the end of the day rolled around and I called the quits =P

Overall though using LMFIT was pretty intuitive and seemed to offer a lot for optimized fitting routines. I'm hoping to use more of it in the future for my work.

CHiMaD Materials Design

Last week I participated in the CHiMaD Materials Design Workshop held on NIST. Greg Olsen gave a keynote talk to kick things off, introducing to us the concept of System Design Charts, specifically focused for materials science and engineering and focusing on the paradigm of processing, structure, properties (and sometimes performance). The idea is such design charts enable one to target the important areas of interest to investigate and focus on, but also being able to communicate better on what one is investigating. This makes sense from an industrial standpoint when one needs to talk with shareholders or clients of a consulting firm, but can also be applied academia so that members within a research group can keep track of what each person is working on specifically, while still seeing the big picture.

To be honest, there is nothing special with the System Design Charts. It's simply just another tool that one can use to organize their thoughts and convey their ideas on where to go next. It's a strategic planning tool (like SWOT or anything else) to keep groups focused on the important parts of the big picture, rather than investigating small parts of interest.

First, one lays out all the processing steps in a sequential manner. The processing steps will influence the structure of the material. This may be the literal crystal structure (if we're talking about metals), but also things such as phases, precipitates, or features like twins. The lines that connect the processing boxes and structure boxes are two-way, such that processing will directly influence structure, but the resultant structure can also influence subsequent processing. Properties sit on the side other structure, and highlight what structures are connected to what properties the most, again as a two-way connection. Optional is putting performance on the other side of properties.

Designing the chart this way, one attempts to solve the problem in determining how to optimize the processing to influence the properties of most interest, where the monetary interest lies. There's nothing special about this, except that the structure column clears up the historic blackboxes that we tried to directly correlate properties to processing. From what I understood, therein lies the materials design by considering the actual structure of the material and the impact it plays on the properties. As a materials science major, this is all something one learns in a first-year class. Looking from a bigger picture though, the tool tells you where money can be made, which for a scientist may not sit right.

Alternatively, it was introduced to us that such a concept can be applied to any science, which was the goal of the workshop. This was my attempt at a Monte-Carlo grain growth scheme (no money to be made here =P):

2016 DOE-AMR Vehicle Technologies

Last week I had the opportunity to participate as a reviewer for the Department of Energy (DOE) Annual Merit Review (AMR) in Vehicle Technologies, specifically propulsion materials. This past Friday, I finally submitted the two reviews assigned to me. 

With a combination of procrastinating and not being 100% efficient, two single reviews took me the entire afternoon. In my sample size of two, the second one was "easier" than the first one. I was talking to my lab director, and I mentioned that I did not think two reviews would take me so long.

The overall experience was interesting. The presentations that I attended were allotted 30 minutes each, with the presentation to be about 20 minutes and 10 minutes for questions and answers, with priority given to the reviewers. Unsurprisingly, some presenters still clearly went over the the 20 minute mark, like in any other conference. Although this was not like any other conference. For one, there was no conference fee. Secondly, the contents of the presentation were organized in a way that made the review process challenging for me as a first-timer.

Reviews needed to cover their approach, their technical content, their collaborations, and their future work. Often collaborations are quickly glanced over and rated on a scale of 1-4 but almost seemed to be more of a check-box. The approach was where the objective of the project was generalized such that anybody could understand, and since most of these talks dealt with Integrated Computational Materials Engineering (ICME), typically presented a flow diagram as well. The technical content focused on what was achieved that year, and finally the future work covered what will be done for the next year, which at times seemed relevant to the technical content presented or other times seemed out of place before you realized you needed to look at the big picture.

Therein lied the challenge for me being a first-time review. I was reviewing projects that were both somewhere half-way complete, so in my head I couldn't see the complete picture at times of what had been accomplished before. And even in the technical content, it was a quick overview glance at the most major achievements, without digging deeper into the science at times. This made the merit of the future work even harder to judge. Lastly, I approach science with mostly a positive mindset (until I learn more and become a pessimist), so I think all approaches are generally valid and very cool. Then to score and comment each one of these categories on an arbitrary scale from 1-4...

Reviewing a project based a 20 minute presentation was unlike a reviewing a paper where you did have all the details. And as a scientist, details are important to us. I started making the effort to look up papers had been published, but most of this could not be found since it was all recent work. It took me awhile before I finally conceded and took a step back and judge the review based on what was presented to me (as well as last year's presentation. I realized I had to judge the project, and not necessarily the science (although it is a large part of it). I gave my input on the things I was impressed with, but also on what I thought could be use some more work or consideration. I hope in the future if I do this again, I'll also be able to give input on what I found was lacking (which comes with years of knowledge in the field...)

It was an experience to sit on the other side and be presented to, rather than making the presentations for my advisor as I had once done during graduate school. 

NADDRG 2016 Spring

Last Thursday I went to the North America Deep Drawing Research Group Spring Symposium.

It was the first "conference" I've gone to since I've started my new position. I've placed conference in quotations since it was a single day of talks starting from 8:30am and ending at 6:00pm (although originally planned for 5:00pm). In that essence, it was like a conference in which some talks ran a little long, and there were always too many questions asked. Neither of which is bad, as the content was always interesting (at least in my opinion) and the questions brought up discussions between the audience. Furthermore, since there is only one talk at a time, there is no scramble from one room to the next like at the typical conference.

The speakers were well divided between industry and academia (and no one from a National Lab). The industry talks turned out to be equally as interesting as the academic ones. Sales pitches are not allowed, so the talks are typically focused on addressing an engineering problem or challenge without any superfluous information. Furthermore, the talks are designed to be either updates or works in progress (this is attributes for the large discussion aspect from the audience).

Two things that stood out for from these talks is the lack of microstructure characterization and discussion of crystal plasticity. It was a reminder that I was in a room of mostly mechanical engineers and not materials scientists. However during one of my side discussions with an engineer at Aleris, he expressed his surprise on just how things at the microscale influence the macroscale behavior. (Context: They found that special grain boundaries played a major role in crash-worthiness in aluminum. However I didn't get the chance to ask if these were Sigma3 boundaries or not, which would've been very interesting...).

My takeaway from all of this was the (micro)structure to property and performance relationships is equally important during forming/processing operations, and there is a large room for the development of these understandings.

5% Done...

It's scary that time is already passing by so quickly at my new job. While two-years seems like a long time for a post-doc, I am repeatedly reminded that two years will pass by in a flash. It seems ridiculous, although when I look back at graduate school, I can't disagree. There were times where I wasn't sure if I was a third or fourth year graduate student when research is the only thing you focus on and you topic or findings don't change significantly from one month to the next.

So far the new job has gone from intimidating to nostalgic and finally a little bit of fun. The intimidation comes from starting a completely new research project, where my first few days and weeks were completely focused on reviewing the current literature (to which I am still doing). Starting a new topic has made me feel like a graduate student again even though I just completed my PhD a few months ago. I just finished being an expert in one topic and then I'm thrown into something completely new again. While it is refreshing to change topics, it is also intimidating as everyone else expects you to become the expert. However, this is where everyone is correct on the PhD:

Getting your PhD is a sign that you know how to learn the important information in a new field, design the relevant experiments to test new ideas, and evaluate those findings to continue moving on.

The nostalgia, as I've already hinted at, is feeling like a new graduate student again with a new topic. Similarly I have a new "advisor" again as well as a research group (although with far more independence here). Although in the past few weeks I've had to taught how to using the mechanical testing frames, how to spray-paint for digital image correlation, and how to properly use the wet chemical fume hood for metal etching, all under the constant supervision of my sponsor. This reminded me of my undergraduate years, where each of my steps were carefully monitored. However instead of being tested for whether I was competent or not, it was just being taught for safe operating procedures. But nonetheless, to top it all off, I was told to wash beakers and cylinders.

The fun has been coming from the start of our mechanical testing of a TWIP steel sheet from a major supplier to better understand its forming limits. However, at the moment the material has not been been behaving as we expected. But I'm breaking a lot of stuff! And for an engineering, there's nothing better than that.

7.5x7.5 in. square sheets (1mm) of TWIP steel subjected to balanced bi-axial testing in a Marciniak set-up. Failure is occurring on the lip or bend, rather than the center as desired.

The Exit Interview

Overall I had an enjoyable graduate school experience in the Department of Materials Science and Engineering at Carnegie Mellon University. There were things I enjoyed a lot, although other things which I had some grievances too. That being said, no program is perfect and every one is unique.

Last Friday I had my "exit interview" with the department head. Having not been in any other programs, I don't know if this exclusively unique to our department alone or happens for many others. For every graduating PhD student, the department head tries to make a one hour appointment to before they permanently leave to cover a variety of topics. The generally cover the following:

• What class was most useful to you?
• What has provided you with the most professional development?
• What was your overall opinion of the program and structure?
• What do you feel was lacking or your least favorite thing in the program?

I've had an exit interview with my advisor. A mix of awkwardness of these are things that you did really well, there are the things that you can still continue improving, what are the things that I (the advisor) can do better, and then these are papers I (the advisor) want you to consider working on still. (The question that never goes away!)

For a department head to ask the similar set of questions shows a desire to improve the program based on a statistical collection of students opinion, rather that just hiring a professor with lots of potential and encouraging the department to increase the number of high impact journal publications. This is a department that will continue to strive to be better not based on research alone, but how it trains the next generation of scientists. Obviously, if you ask the opinion of my classmates, it's not perfect. And it never will be.

In retrospect, I wish I did a similar sort of thing with each and every undergraduate who worked under me as well as all the graduate students with whom I have collaborated with. I won't be the best scientist at the end of the day, but I'll be a better one than I was before.

The Gordon Research Conference

My first "encounter" with the Gordon Research Conference (GRC) series was from Professor Michael Plewa. In my undergraduate research with virucidal materials for water purification, we started a collaboration with Professor Plewa for testing the cytotoxicity of our metal-oxide materials on mammalian cells. During that summer, we were rushing for results in one particular week as he was going to absent the next week for this Gordon Conference. (As we were working in his lab and his equipment, we needed to be under his supervision).

One of those days, Professor Plewa exclaimed his excitement for the upcoming conference. Of course, I had to ask what it was as I had neither heard of it nor thought anyone could get that excited over a single conference. The discussion was short, but memorable as he gave a brief summary that a GRC was one of the best things ever.

In pure delight, he told us that you had the best scientific talks in the morning,  then open scientific discussion in the afternoon, then more talks in the evening, and then you drink the rest of the evening.

To make it better, you repeat all of this over the next few days.

The way he spoke of this made it seem to be the holy land of the scientific community. (Where as the holy grail would be publishing in Science or Nature I suppose). Not only was he going to be attending, but two of his students would be presenting posters as well. Professor Plewa was excited about attending, but also for his two students attending!

The last words he told us on this topic was, "If you ever have the chance, make sure you attend one."




So last week I attended my first Gordon Research Conference in Physical Metallurgy, and hopefully not my last one.