Good idea! I will certainly add it to my list. I warn you though, it will likely be a while before I have time. I am editing 3 different videos right now (using our new automatic sample changer, performing high-temperature experiments, and performing grazing incidence experiments). I need to get these three videos posted to help the users in my facility, which will reduce my workload a little bit since they will need my help less. This is especially important as we have just received a new single crystal diffractometer that I need to learn how to use, make a manual for, and make a basic training video for. We are also hoping to acquire funding very soon for upgrading one of our diffractometers to perform pair distribution function (PDF) experiments, which itself will be a very large project if funded. I am going to continue making videos through all of this because I love this channel and experience, but it may be slow going. It may or may not seem like it, but I put a lot of time into editing these videos (especially since I'm a novice and not that great at speaking when recorded), so that makes my release schedule much slower. All of that is to say that yes, I certainly take the suggestions people give me, but I may not be able to deliver on those suggestions as quickly as people may like. For that, I apologize!
How to quantify the phases in cement (which is a complex material containing tricalcium silicates, dicalcium silicates, tricalcium aluminates, tetracalcium alumino-ferrites, and others?
Very informative video sir. I have a question that in refinement control tab, where there is option of global variables, I cannot see the names of the phases
Hello. Great video, thanks for posting. One thing though; the Rietveld refinement won't run, I get a pop-up message instead saying "Automatic divergence slit scans are not valid for refinement". I'm puzzled a bit by this message ... Any suggestions how to fix this block? It would be highly appreciated
I'm happy it has helped so far! Regarding your question, automatic divergence slits are great as they allow you to reduce the amount of noise at higher angles of 2theta when compared to fixed divergence slits. However, Rietveld refinement is based upon the assumption that you have the same X-ray interaction volume throughout the experiment. This is true when using fixed divergence slits, but your interaction volume increases as 2theta increases when using automatic divergence slits (the slits continuously open more as 2theta increases to maintain X-ray interaction AREA). As a result, your relative intensities are "wrong" when using automatic divergence slits. Thankfully, HighScore can correct this. Go to Treatment, Corrections, and Convert Divergence Slits. You can then choose to convert the data to whatever divergence slit size you want (I typically choose 1/2 or 1/4, but it probably doesn't matter). Click ADS to FDS, click Replace, and then click Close. You should notice that your data look different now. When handling automatic divergence slit data, I recommend saving the original file with something like ADS in the title. After you complete the conversion in HighScore, I recommend going to File, Save As, choose the XRDML file extension, and then indicated in the filename that the data have been converted (e.g., put "ADS to FDS" in the filename). Do not save the converted data over the original data as you will lose some of the metadata that tells you what original hardware was used for data collection.
Hello Dr. Michael, Many thanks for such an instructive video. I have a question that I hope you can help me with: Can I use XRD data acquired from different equipment with highscore plus? I want to do the Rietveld refinement, but in the literature I see that there are several factors such as the scale factor which depend on the hardware and I am not sure if such factors are needed/used somewhere during the rietveld refinement. Many thanks.
You should be able to use HighScore Plus with data from other instruments. Back in my grad school days, I used HighScore Plus to refine data from a Bruker instrument.
Dear Dr. Koehler. I'm confused by a question in highscore plus. Usually doube-clicks on the pdf card show the detail of the phase information, right? but when I finished the phase identification, the double-click on the pdf card recieve nothing, and even cause a bug of no responce. what should l do?
Hmmmm...I have not run into that problem before, so I'm not sure. In this case, my suggestion would be to call Panalytical. I wish I could be of more help!
Excellent video! Is it necessary to do a process for instrument broadening before doing this Rietveld Analysis? I saw you did it for Crystallite size and microstrain analysis and now I am wondering if this step should be done before. Thank you for your response!
Thank you for the kind words! Regarding the instrument broadening, it certainly isn't a bad idea to do it for Rietveld refinements/phase quantification. I have tried it both with and without instrumental broadening, and my phase quantification results are the same. However, I suppose that the proper answer would be to do it. It is a good idea to get in the habit of doing it, that way you don't have to worry about forgetting to do it if you want to add crystallite size and microstrain to your phase quantification analysis. Excellent question!
Thank you so much for your very nice and didactical videos. One question. The program proposes to strip K-alpha2, which can be done before search peak. You did not comment the possible interest of such a step for next steps (phase identification & quantification, Rietveld, strain, etc.). What is your mind?
My apologies for the slow response, I was very busy preparing for and then taking a vacation. Regarding your question, I generally prefer to not strip K-alpha2. Maybe it would help to strip it for phase identification, but I have not tried it. Personally, I try to manipulate the data as little as possible so that I know I am not introducing a source of error from a poor stripping algorithm. Most (if not all) analysis software will account for the doublet peak during refinement anyway, so stripping the K-alpha2 peak is unnecessary.
This is not free software, so my only suggestion would be to reach out to Malvern Panalytical to purchase it from them directly. I wish I could give you cheaper advice!
Hi, I have watched most of your TH-cam video, but I can not find the "Crystallinity calculation" video from you by using the HighScore Plus. I know there is some basic information on the software, but it may be much helpful if you can do it by using an actual sample with step-by instructions as you do usually on the other videos. Could you please produce it? Anyway, thank you so much for all your works.
I think the Crystallography Open Database (COD) can provide files with structural information. I would suggest trying to use that. If you can save a .cif file with structural information, you can load that into HighScore Plus and refine it (I think you just have to do choose File, Insert, and then choose the .cif file).
Good suggestion! I don't think HighScore will report volume %, but I made a quick video on how to convert from weight % to volume % using Excel. I don't know if this is what you were hoping for, but I hope it helps. Note: I try to publish videos at the start of the week, so the video will be unlisted until Monday or Tuesday. However, you can view it with this link: th-cam.com/video/4iAEGTUyEmk/w-d-xo.html
Dear Dr.Koehler Excellent way to explain X'pert high score .can you explain me how i import just analysis Graph , I just want this analysis structure bcz I already have analysis data but I want to put this XRD graph in my paper that way I just want to pick up this analysis Graph of XRD
Thanks! As for your question, let me make sure I understand you correctly. Are you able to open the HighScore Plus file and see the graph? If so, you can save the graph by going to File, Save As, and choose JPEG as the file type. If you want to plot the data points, the refinement curve, and the background yourself in different plotting software, you can go to the Anchor Scan Data, highlight all rows, copy, and then paste into something like Excel or Origin. I think Anchor Scan Data has the raw data, the refinement curve, and the background data, but let me know if you can't find it in that tab; it's possible I'm thinking of a different tab. If I misunderstood your question, please let me know and try to ask it differently.
Hello, I am asking how exactly I can use the Rietveld method to determine if my experimental spectrum is comparable with the simulated one (a new CIF that I cannot find in the database)
Unfortunately, I have not found a way to load it into the HighScore Plus file so that you can see the stick pattern overlaid on your diffraction the same way you can when you find reference patterns in the database. However, if you go to File, Insert, and then select the CIF file, the software will load it as a phase. You can then choose to refine that phase in much the same way that you see in the video, and hopefully you will get a good fit if the CIF file matches your diffraction pattern. I hope this helps!
I'm glad that it helped so much, and I'm happy to see such excitement over XRD videos! I do not teach a course though :/ My time is dominated by helping users in my facility with training/data collection/analysis, budgets, proposals, learning new techniques as we get the hardware to perform them (XRF, single crystal diffraction, etc.). It's been so busy lately that I haven't even had the time to make the TH-cam videos I would like! I hope to have time to get back to them soon. If you have any questions though, feel free to leave them in the comment sections. I miss some comments, but I try to reply to as many as possible.
That is a difficult question to answer as there is no single answer; every sample is different, and the choice of detector can also affect it. I can tell you for step size, you want to have 8-12 data points above the full width half maximum (FWHM) of your peaks.
Good question! I would recommend reading this paper: Toby, B. H. R factors in Rietveld analysis: How good is good enough? Powder Diffraction 21(1), 67-70 (2006).
Sir I would like to ask you , I have done XRd to my material but when i do match , that materias show only 1 score , what does that mean ? i hope you can reply to my question . Thanks
Let's check this first. When you open the search and match window and click to edit the restriction set, do you see something towards the bottom of that window that says ### out of ### patterns? Can you tell me what those numbers are?
Thanks for this video. there is on question. i use high score plus, but don`t same your database. in particular there is no information about structure in reference pattern. except for structure, have all. I want to analyze the phase percentage ratio. please tell me add method to structure information. thank you so much!!
Please see this video (th-cam.com/video/yGQDXCXEaqY/w-d-xo.html). Option 2 in the video shows you where to find the structural information online in a .cif format. If you already know the structural information and are just looking for a way to enter it manually, option 3 in the video is what you want. If you look in the video description, you can skip to each option directly by clicking the time code. Please leave a comment in the other video if you have additional questions about it, and please let me know if it fixes your problem. Good luck!
@@IAMMDiffractionFacility thanks to your advice. i solved problem to structure information, percentage ratio. You recommended video, Nice!! thank you!!
I'll be honest, I don't really have experience with the RIR method as I have always used Rietveld refinement. Anything I told you would just be something that I found online. The ICDD has information on this method though: www.icdd.com/assets/tutorials/Quantitative-Analysis-RIR.pdf
Thank you for this tutorial. Please I would like to know how can we quantify the pourcentage of a cristalline phase in glass i tal about glass-ceramic ?
There are a number of methods for determining crystallinity. Please visit my website (www.jiamdiffraction.com/documents). If you look beneath Other Documents (it is likely on the right side of the screen), you should see a PDF button labeled "Methods for Quantifying Amorphous Content." Click the PDF button to view a document from Bruker. The description of the different methods begins on page 19, but the pages before that also have good information.
@@IAMMDiffractionFacility thank you for your reply. I was reading this document but i didn't know how i can apply it on the drx specta that i have. It contains a single crystallized phase and I would like to know the volume of this phase in the vitreous matrix.
You have a few options. Rietveld for amorphous phases...basically, you find a crystalline pattern that matches the wide amorphous humps for your glass. You then treat the wide peaks like crystalline phases but allow the refinement to greatly broaden the peaks. The refinement steps in the video should still work. The difficulty here is that there isn't always a good reference pattern to use. If the previous option doesn't work for you, you could try to collect another pattern. If you tested the glass as a solid piece the first time, grind it into a powder and add an internal standard (something that is as close to fully crystalline as possible and has as similar of a mass absorption coefficient to your sample as possible). You then perform quantitative analysis as I do in my video, and you use the weighed and calculated values of the internal standard to calculate the crystallinity. This is how I typically quantify amorphous content. You also have the degree of crystallinity option. In this one, you determine the area of the peaks contributed by the crystalline portion and the area of the peaks contributed by the amorphous portion. The degree of crystallinity is then the crystalline area divided by the total area. The difficulty I've found with this method is that you need to figure out how to fit the amorphous portion. One option is to make a completely amorphous glass and test that so that you can see what the amorphous contribution looks like. I know I haven't given you in-depth specifics, but it really depends upon your situation and what you have available in terms of XRD access, standards, and reference patterns. If you choose any method, I highly recommend trying it first on some samples for which you know the crystallinity. When I began quantifying amorphous content, I made a series of powder samples by mixing my internal standard, a semi-crystalline powder, and a completely amorphous powder. I then kept trying the internal standard method until my results matched what I had weighed the different components to be. I learned some important lessons by doing this though. Had I not done this, the analysis of my real samples would have been off.
Thank you for this video.I have a question about sample that no have CIF.If there is no CIF file of sample and this sample has not been created before and there is no information about the position of its atoms, how can we create the file related to that sample ourselves? Thanks in advance 🌺
Sorry, it was a busy day yesterday! You could load the Y3Fe5O12 CIF file, then go to the refinement tab, click the plus sign next to the phase, find...I believe it is atoms that you want. I think if you click atoms, you can enter new atoms and atomic positions. Assuming that the Sb substitutes for the Y atoms, you can give it the same Wyckoff position and then adjust the site occupancy factors (SOF) of both Sb and Y to reflect the amount each present.
@@IAMMDiffractionFacility Thanks a million for replying 💐💜💜 Wycjoff for Y is 24c, then I must use it for Sb. But how about x, y, z positions for that? 🤯 This data for Y is :0.125,0.000,0.2500. But I don't know how much to replace for x, y, z positions for Sb? And x,y,z positions for O in new structure?By the way, my structure has two other side phases (Sb2O4, Fe2O3) in addition to the main phase (Y3Fe5O12). Structural parameters of pure Y3Fe5O12 is:👇👇 Atom:Wyckoff: Position x ,y, z Fe(Octahedral) :16a: 0.0000 ,0.0000 ,0.0000 Fe(Tetrahedral): 24d :0.3750 ,0.0000, 0.2500 Y :24c: 0.1250 ,0.0000, 0.2500 O :96h: 0.9726 ,0.0572 ,0.1492 Thanks in advance💐🌺💚
If you are using the same Wyckoff position for Y and Sb, then the x, y, z positions should be the same. Again, this is assuming that the Sb atoms are substituting for the Y atoms. You could try changing the occupancy of Sb to 0.2/3 and of Y to 2.8/3. A good question to ask yourself is just how accurate do you need your analysis to be? You could spend a lot of time trying to get the atomic positions of all the elements correct, but if you are looking for a general idea as to phase quantification, that's likely a waste of time. You also have to keep in mind that there is going to be some sort of error bar associated with your quantification. It could be that trying to perfect your fit will change the results less than the error. Refining on the oxygen positions could be difficult as oxygen is such a light element. Your data would have to be very good.
@@IAMMDiffractionFacility Thanks for your tips dear Michael💐🌺 And sorry for the replay again Yes, I understand what you mean, I think the presence of side phases like Sb2O4 indicates that the Sb atoms are not substituting for the Y atoms. What I wanted to do was calculate the percentage of phases in the structure after Rietveld refinement and compare those to before Rietveld. And also measurement of bond length of Fe_Fe , Fe_O, Fe_O_Fe, Y_O,.. after substitution sb for Y. In my version of x'pert high score soft no exit information about XYZ wyck in reference patterns related to phases. And also after downloading CIF files , I realized that some of those files(related to phases of my structure) did not contain wykoff. Therefore, after Rietveld, the percentage of some of side phases was caculated as zero. I could not even use full prof software for this because of these problem 🤦🏻♀️ So I decided use the maud software . In this case I was able to calculate the percentage of side phases after Rietveld by importing the CIF file related to the phases.But now I have a problem and that is calculating the bond length and angles of Fe_Fe , Fe_O, Fe_O_Fe, Y_O,.. . I know software like FullProf, Vesta and crystal Maker can give me this information but after Rietveld , the maud software only generates files with (.par)s extension that I can not use it in any of the mentioned software😢😢🥺🥺 Thanks 💐
I can certainly try! Did you double click the pattern to see if there was structural information (such as atom positions, not lattice parameters) in it?
@@IAMMDiffractionFacility I tried but failed. So, Quantification requires the condition of the corresponding number of peaks. Due to background quite bad.
I don't think I understand. Can you send me an email at mkoehler@utk.edu and include a screenshot of whatever analysis you have been able to do so far?
Hi, Please I have issues with peak fitting as the software often displays " no structural data for simulation/refinement" and also refining the XRD peaks was not possible as well. Note that the data contains mixtures of compounds. Please, what am I doing wrong?
Hi Joshua...regarding the no structural data problem, please see this video: th-cam.com/video/yGQDXCXEaqY/w-d-xo.html. Regarding not being able to refine the XRD peaks, is this a problem you are having when you are trying to perform a profile fit or a Rietveld fit?
@@IAMMDiffractionFacility, I have followed the steps as explained in the video. Although my Xpert has more than 500,000 PDF, it cannot still display the structural data. Also, having inserted the CIF files the data did not sync with the Xpert database as they must be uploaded each time I want to do analysis. Also, I discovered that deleting the phases that do not have structural details left the peaks unidentified/unmatched. Please, what could be the issues?
Yeah, CIF files need to be loaded manually each time you use them, or you can copy the phase from one HPF file to the next, or save an HPF file with the CIF file loaded but no diffraction pattern loaded. There are a few options, but I don't know of any way to add it to a database. What database are you using? Some databases do not include atomic positions.
@@IAMMDiffractionFacility These are the database details: COD-Mar 2010 (HighScore plus 3.x) PDF 2 Release 2004 (HighScore plus 3.X) PANalytical Example database (HighScore Plus 2.x)
Can you tell me what version of HighScore you have (both the version number and if you have HighScore Plus or just HighScore)? Can you tell me what database you have?
Thanks for the video. One question is that for a few particular phases that I use have very old version of pdf cards that do not have crystal structure info and no new pdf of the phase can be found as replacement, so the phases cannot be quantified at all based on your methods unfortunately. The crystal info of the phases is not hard to find but is it possible to add these info in the old pdf card in highscore plus to make the quantification workable in highscore? THanks!
You can certainly add info to make it usable. You should begin by converting the pattern to a phase. Then go to the Refinement Control tab and expand the phase that you want to add information to (click the + sign next to it). Click on Atomic Coordinates. If there are no atoms present shown in the Object Inspector (probably the right panel on your screen), right click in the Object Inspector and choose Add New Atom. Add information to the element, oxidation, and name fields. Don't worry about the Wyckoff, Multiplicity, and other fields just yet (in my version, I can't change them even if they are blank). Do this for each atom that you need. In the Refinement tab, click on the name of the phase again. In the Object Inspector, you should see different sections such as Phase Display, General Phase Info, Symmetry/Space Group, etc. You want to expand the Symmetry/Space Group section (click the + sign next to it). Make sure that the Space Group Number is correct based upon what you found in other resources. If you click on Atomic Coordinates again under the phase you are changing in the Refinement Control tab, you should now see that each of your atoms has a Wyckoff position and atomic coordinates. If any of these values are wrong, you can now change them. Good luck, and please let me know if this works for you!
When you open the search and match window and click to edit the restriction set, do you see something towards the bottom of that window that says ### out of ### patterns? Can you tell me what those numbers are?
@Ana Maria Ferrari My apologies for the slow reply, I didn't see your comment until just now. So there are 64 possible matches according to the window, but when you actually perform the search, no candidates appear?
Hello, thanks a lot for this tutorial. I was wondering if this procedure could be enough accurate for clays phase quantification, or if I should use an internal standard ? Thank you for your reply !
Honestly, I do not have much experience with clay samples, so I do not want to give an answer that I am not 100% confident in. However, I did a little research, and there are numerous papers online on the topic. A couple are "XRD-based quantitative analysis of clay minerals using reference intensity ratios, mineral intensity factors, Rietveld, and full pattern summation methods: A critical review" and "Accurate quantitative analysis of clay and other minerals in sandstones by XRD: comparison of a Rietveld and a reference intensity ratio (RIR) method and the importance of sample preparation." The second paper seems to conclude that both RIR with an internal standard and Rietveld (without an internal standard, if I am reading it correctly) give similar results. However, the importance of sample preparation can't be overstated.
Hi there, Thank you so much for the videos. These are amazing. I have a query- What if you dont have the structural features in any of the pattern? How would you run the Rietveld then? I dont have the structural features in any of the pattern and is kind of in a fix what to do? Any suggestions would have been really helpful. Thank you so much again for all the videos and trust me these are helping me a lot.
First off, thank you for the kind words! They really do mean a lot and are appreciated. Next, if there are no structural features (i.e., atomic positions), there is an option called charge flipping. It is a feature present in both HighScore Plus and GSAS-II. However, it is not something I have done before, so I will not be any help with it. I could be wrong, but I don't think it is very easy. I want to learn it, but the difficulty is finding the time! I'm sure that is how it is for most people though. It sounds like your situation may be that atomic positions exist for the patterns, but your database does not have atomic positions. Is this correct? If so, you could try to find such information on the Crystallography Open Database (COD). The link is www.crystallography.net/cod/search.html. Please let me know which situation you are in and if you were able to get your problem solved. Good luck!
@@IAMMDiffractionFacility Thank you so much for your sharp response. I do see the crystallographic data in the springer crystallographic doc available online but those are not embedded in the available pattern in the highscore plus I am using just like the way you have in yours. I think I will have to manually set all those data? What's your thought on that? Thank you so much again.
Do you mean that you found your phase on DOC but you can't download a .cif file for it? If so, what phase are you trying to find? I can look into it further.
In addition to my previous reply from a minute ago, I will say that you can certainly manually enter the information into HighScore Plus to build your own phase. That is a perfectly valid option, it is just slower than if you can easily find a .cif file.
One option is that you have only HighScore, not HighScore Plus. I believe regular HighScore does not perform Rietveld. Another option is that your database does not contain atomic positions for the reference patterns. Those are the two most likely reasons that I can think of.
I'm happy you like the videos, and excellent question! There are numerous methods for determining the amorphous content. A good place to start to learn a bit more about the different options can be found here: www.icdd.com/assets/ppxrd/presentations/13/PPXRD-13-Dinnebier-WS.pdf. I haven't done too much with amorphous quantification (edited...I mistakenly wrote phase quantification originally), but I've found the internal standard method to work pretty well. For this method, I'll mix about 50% standard with 50% sample...before I go on, let me add a few notes: (1) you want to use a balance and record the weights, (2) the standard should be as close to 100% crystalline as possible, and (3) I can't guarantee that a 50%/50% mixture will be best for you. You then perform phase quantification just like in the video, but add whatever phase your standard is. The refinement should give a phase fraction for the standard that is larger than what you measured. You can then use the refined value and the actual value for the phase fraction to calculate the amorphous content. Whichever method you choose, I recommend preparing some samples for which you know how much amorphous content is present, perform the analysis, and then make sure you get the correct answer. This way, you can make sure that your general method is at least close to being correct.
@@IAMMDiffractionFacility I am sorry to bother you again. None of the cards in the database of Xpert High Scorer plus I am using have structural details: the position of atoms. Hence, I cant do quantification or refinement. Any Solution to that ?
Don't worry, it's not a bother. Unfortunately, databases do exist that don't have atomic positions. There are a few solutions. (1) Find someone who does have access to a database with atomic positions and get them to send you the .cif files for your phases. (2) Find the atomic positions in a journal article, and then create a new phase in HighScore Plus so that you can enter the space group, lattice parameters, atomic positions, etc. (basically, you enter all of the phase information yourself instead of having it provided by the card). (3) Check out the Crystallography Open Database (COD) (www.crystallography.net/cod/search.html) to see if they have the phases that you need. From COD, you can get .cif files. I hope this helps! Let me know if you need any more information/advice on these possible solutions.
Hi can you help regarding where to find values of rwp rp rb in xpert highscore as iam not able to find it after refinement.Also it is not shown in additional graphics window.
I'm not sure what version you are using, but you should see the values if you left-click Global Variables in the Refinement Control tab. If you go to 2:53 in the video, you should see the values in the right side of the screen. Let me know if you don't see the values there in your version.
@@IAMMDiffractionFacility Thank you for your reply. I Am using version 3 of the software.Sorry but iam not able to see values of rwp, rp, rb in your video also. Exactly which values are ones corresponding to rwp, rp, rb. Please help
If you look under agreement indices at 2:53 in the video, you will see "Weighted R profile" (which corresponds to Rwp) and "R profile" (which corresponds to Rp). I don't see anything for Rb though.
Okay. First, make a copy of the file in case what I tell you messes it up! On the copied file, change the extension from .txt to .asc. Now try to open the file using HighScore. It worked when I tried it, but let me know if it works for you.
Thank you very much for these videos, in fact I am following the same steps as you but I cannot determine the Miller hkl indices, is the database file of COD_2016_Conv45.hsrdb not suitable for determining them? Thank you
Just to clarify, are you able to identify your phases (you found reference patterns that match your diffraction pattern) but you can't determine the hkl indices of the peaks? Or are you unable to identify the correct phases?
I do not feel qualified to say whether or not it is the best as I have not tried all of the others, but I do really like it. There are free options (like GSAS-ii) that give excellent results as well (my boss loves GSAS-ii), but the graphical user interface and customization options of HighScore Plus make the cost well worth it, in my opinion. I have also recently helped a user analyze in situ battery data, and the results turned out very well.
A pattern is basically just a list of peak locations and relative intensities, which makes them great for phase identification. HighScore Plus takes all of the necessary information (e.g., crystal structure, lattice parameters, etc.) from the pattern file and allows you to alter/refine it to best fit your specific sample. If we didn't convert our patterns to phases, we couldn't perform phase quantification. If you only have one phase, phase quantification will, of course, give you 100% of that phase. However, converting a pattern to a phase also helps if you want to determine the lattice parameters, crystallite size, and microstrain of your phase(s). Hopefully that answered your question. Please let me know if it seems that I misunderstood what you were asking.
JIAM Diffraction Facility thanks a lot I'm starting learning sample identification by x-ray difraction and one of the aims is to perform rietveld refinement (manually).
Okay, I see. If you haven't already, be sure to check out the phase identification video that I have. That is a good starting point. If you want to perform rietveld manually, you'll just want to go into the refinement tab (which you can see in the video) and choose which items to refine. HighScore Plus gives a nice user interface, so finding the different items to refine isn't too difficult. If you do have problems figuring out how to refine a certain parameter, I'll be happy to help if you post another question. Good luck!
For zeolites, you could select aluminum, oxygen, hydrogen, sodium, potassium, magnesium, and calcium as possible elements. My understanding is that gismondine is also a zeolite, so the same search should work for it. Essentially, find what elements are in the phases that you think are in your sample, and then enter those in the periodic table screen that I show in the video. Depending on your version of HighScore Plus, you might have a couple more options in the Edit Restriction Set window. You can go to the Strings tab and enter the compound name or mineral name to narrow down the search results. The second additional option is to go to the Mineral/Zeolite Class tab. Under Mineral Classification, you can scroll all the way to the bottom and choose ZEO - Zeolite (Family). Under Zeolite Classification, you can scroll down and choose GIS - Gismondine.
Dear Dr. Koehler. Thank you for the video. I have one question. Is it possible to determine the size of nanoparticles from a xrd pattern/ Rietveld refinement ? I am not talking about the crystallite size but the mean size of nanoparticles such as gold or other crystaline nanostructure. Thanks again!
Unfortunately, XRD does not give you information about particle size, just crystallite size. You may want to look into an electron microscopy technique, that may give you the information that you are looking for.
My pleasure! As far as free software for Rietveld refinements go, I would suggest GSAS-II. You can download it from subversion.xray.aps.anl.gov/trac/pyGSAS. There are some great tutorials available at subversion.xray.aps.anl.gov/pyGSAS/trunk/help/Tutorials.html. I feel like the best two tutorials to start with for learning to refine are "Fitting laboratory X-ray powder data for fluoroapatite" and "Determining Starting Profile Parameters from a Standard."
@@IAMMDiffractionFacility Thanks a lot. What I concluded that we can do phase quantification with crystalline material. And my composit contains some amorphous material that's why phase quantification will not work with my prepared composite.
thank you so much. I am a post-doctor in the HUST of china. I have learned a lot from your tutorial. there is one problem that I cant find the entry of solver tolerance under 'General property' in my HSP. So the Rietveld refinement just executed for a few steps and then stopped, which cause the difference between the calculated profile and obs is still very high. I will be greatly appreciated if you could give me some advice to fix this problem. Regards.
Thank you for the kind words! Once your refinement is finished running and you still have a large difference, does the fit get any better if you click the "Execute Fitting" button again? If you don't see solver tolerance when you go to Refinement Control - Global Variables and look under general fit properties, do you see "Max No. of Fit Cycles" or "Solver Time Limit [sec]" fields there?
@@IAMMDiffractionFacility Thank you so much. After a second click on the button of 'start rietveld refinement ', the fit showed almost no change. I can see the entry of 'Max. No of Least-Squares Cycles', but no entries of 'solver tolerance' or 'solver Time Limit' under 'General Properties'. Besides, the content in Refinement control/Global variables and object inspector/general properties show some difference from yours. I wonder that is due to a different version of the HSP? mine version is 3.0d(3.0.4)
In addition to the question regarding your value for "Max No. of Least-Squares Cycles," I have a couple of others to help find the problem. (1) Are you performing an automatic refinement or a manual refinement? (2) What parameters (such as scale factor, lattice parameters, etc.) are being refined? You can figure out which parameters are being refined by clicking the plus sign next to the phase and seeing which parameters have check marks in the "Refine" box (sorry for explaining if you already know how to do this).
Do you mean that you only have HighScore but not HighScore Plus? If so, I don't think you can do Rietveld with just HighScore. You can perform phase identification though. Once you know the phases you have, you may be able to export .cif files and use those and your data to perform Rietveld using GSAS-II. There are some nice written tutorials on GSAS-II (subversion.xray.aps.anl.gov/pyGSAS/trunk/help/Tutorials.html).
I only have experience with the ICDD databases in HighScore Plus. If I'm not mistaken, you would need something like PDF-4+ for phase quantification. There is a PDF-2 that is good for phase identification, but it doesn't seem to have the information necessary for phase quantification. You can find more information at www.icdd.com/pdf-product-summary/
Hello! Thanks for this video it's very helpful. I have a question about the phase quantification : if there is another method to calculate concentration of each phase manually because i haven't the structural information in my pdf phase ? and I see in another video who speak about the "RIR Information" to quantify phases, any explanation about this please?
Unfortunately, I cannot share the software and database, they both require licenses (HighScore Plus from Malvern Panalytical and the PDF-4+ database from ICDD). HighScore Plus is really nice if you have the money for it, but there are free options such as GSAS-II and FullProf that can perform Rietveld refinements. I've used GSAS-II a bit, and while I prefer the user interface and automation of HighScore, GSAS-II's interface isn't bad. There are also some really nice written tutorials that you can find on anl.gov (just google gsas-II tutorial). You do need to import a .cif file or enter the structural information for the phase in GSAS-II though.
Sir, when i click convert pattern to phase I am not getting any percentages only phases appeared. Could you please help me ? How I can get phase percentages?
Again above and beyond expectations. Thank you
Can you pls post a video for the Rietveld refinement for the quantification of cement and hydrates and/or any more complex amorphous phases
hi, your explanation is very helpful.. can you post a video with a complex pattern and semiauto or manual mode of refinement?
Yes, this is a good question
Good idea! I will certainly add it to my list. I warn you though, it will likely be a while before I have time. I am editing 3 different videos right now (using our new automatic sample changer, performing high-temperature experiments, and performing grazing incidence experiments). I need to get these three videos posted to help the users in my facility, which will reduce my workload a little bit since they will need my help less. This is especially important as we have just received a new single crystal diffractometer that I need to learn how to use, make a manual for, and make a basic training video for. We are also hoping to acquire funding very soon for upgrading one of our diffractometers to perform pair distribution function (PDF) experiments, which itself will be a very large project if funded.
I am going to continue making videos through all of this because I love this channel and experience, but it may be slow going. It may or may not seem like it, but I put a lot of time into editing these videos (especially since I'm a novice and not that great at speaking when recorded), so that makes my release schedule much slower. All of that is to say that yes, I certainly take the suggestions people give me, but I may not be able to deliver on those suggestions as quickly as people may like. For that, I apologize!
@@IAMMDiffractionFacility thanks for the reply... I believe it would be worth to wait for your videos.
How to quantify the phases in cement (which is a complex material containing tricalcium silicates, dicalcium silicates, tricalcium aluminates, tetracalcium alumino-ferrites, and others?
I can help you
Very informative video sir. I have a question that in refinement control tab, where there is option of global variables, I cannot see the names of the phases
In the Patterns tab, did you select the phases of interest, right click, and then choose "Convert Pattern to Phase"?
Hi which model is used use in Xpert high score, most of the options are not shown in my software
Hello. Great video, thanks for posting. One thing though; the Rietveld refinement won't run, I get a pop-up message instead saying "Automatic divergence slit scans are not valid for refinement". I'm puzzled a bit by this message ... Any suggestions how to fix this block? It would be highly appreciated
I'm happy it has helped so far! Regarding your question, automatic divergence slits are great as they allow you to reduce the amount of noise at higher angles of 2theta when compared to fixed divergence slits. However, Rietveld refinement is based upon the assumption that you have the same X-ray interaction volume throughout the experiment. This is true when using fixed divergence slits, but your interaction volume increases as 2theta increases when using automatic divergence slits (the slits continuously open more as 2theta increases to maintain X-ray interaction AREA). As a result, your relative intensities are "wrong" when using automatic divergence slits.
Thankfully, HighScore can correct this. Go to Treatment, Corrections, and Convert Divergence Slits. You can then choose to convert the data to whatever divergence slit size you want (I typically choose 1/2 or 1/4, but it probably doesn't matter). Click ADS to FDS, click Replace, and then click Close. You should notice that your data look different now.
When handling automatic divergence slit data, I recommend saving the original file with something like ADS in the title. After you complete the conversion in HighScore, I recommend going to File, Save As, choose the XRDML file extension, and then indicated in the filename that the data have been converted (e.g., put "ADS to FDS" in the filename). Do not save the converted data over the original data as you will lose some of the metadata that tells you what original hardware was used for data collection.
Hello Dr. Michael,
Many thanks for such an instructive video. I have a question that I hope you can help me with: Can I use XRD data acquired from different equipment with highscore plus? I want to do the Rietveld refinement, but in the literature I see that there are several factors such as the scale factor which depend on the hardware and I am not sure if such factors are needed/used somewhere during the rietveld refinement.
Many thanks.
You should be able to use HighScore Plus with data from other instruments. Back in my grad school days, I used HighScore Plus to refine data from a Bruker instrument.
Dear Dr. Koehler. I'm confused by a question in highscore plus. Usually doube-clicks on the pdf card show the detail of the phase information, right? but when I finished the phase identification, the double-click on the pdf card recieve nothing, and even cause a bug of no responce. what should l do?
Hmmmm...I have not run into that problem before, so I'm not sure. In this case, my suggestion would be to call Panalytical. I wish I could be of more help!
Excellent video! Is it necessary to do a process for instrument broadening before doing this Rietveld Analysis? I saw you did it for Crystallite size and microstrain analysis and now I am wondering if this step should be done before. Thank you for your response!
Thank you for the kind words! Regarding the instrument broadening, it certainly isn't a bad idea to do it for Rietveld refinements/phase quantification. I have tried it both with and without instrumental broadening, and my phase quantification results are the same. However, I suppose that the proper answer would be to do it. It is a good idea to get in the habit of doing it, that way you don't have to worry about forgetting to do it if you want to add crystallite size and microstrain to your phase quantification analysis. Excellent question!
@@IAMMDiffractionFacility Thank you for taking the time to respond! I'll keep it in mind for my analysis.
Thank you so much for your very nice and didactical videos. One question. The program proposes to strip K-alpha2, which can be done before search peak. You did not comment the possible interest of such a step for next steps (phase identification & quantification, Rietveld, strain, etc.). What is your mind?
My apologies for the slow response, I was very busy preparing for and then taking a vacation. Regarding your question, I generally prefer to not strip K-alpha2. Maybe it would help to strip it for phase identification, but I have not tried it. Personally, I try to manipulate the data as little as possible so that I know I am not introducing a source of error from a poor stripping algorithm. Most (if not all) analysis software will account for the doublet peak during refinement anyway, so stripping the K-alpha2 peak is unnecessary.
Could you please provide me any link from where i can download the exact version of highscore plus you used in this video?
This is not free software, so my only suggestion would be to reach out to Malvern Panalytical to purchase it from them directly. I wish I could give you cheaper advice!
Hi, I have watched most of your TH-cam video, but I can not find the "Crystallinity calculation" video from you by using the HighScore Plus. I know there is some basic information on the software, but it may be much helpful if you can do it by using an actual sample with step-by instructions as you do usually on the other videos. Could you please produce it? Anyway, thank you so much for all your works.
hello, thank you for your explanation and video. For some samples, some people add internal standards in the powder. Why it is necessary?
Hello. Many thanks for such an instructive video.
I wanted to know what is your software version?
there is no structural information for any of my phase, could you please tell me how to get the structural information???
I think the Crystallography Open Database (COD) can provide files with structural information. I would suggest trying to use that. If you can save a .cif file with structural information, you can load that into HighScore Plus and refine it (I think you just have to do choose File, Insert, and then choose the .cif file).
Sir can we use Rietveld parameter in organic field
Thanks for the video. The quantification is based on weight or mol ?
Apologies for the slow response, it is weight %
Hi, Sir. Could you post a guide to build a PONKCS phases to quantify the amorphous content in Highscore? Seems no such guide online.
Sir, do I need any required stuff in addition to my XRD file? I watched fully your video but just wanna make sure
While reitveld refinement I get an error stating too many data points for reitveld module. How to deal with it Sir? Pls help.
Is that all it says? Can you type the exact error you get, word for word? And are you running a default Rietveld refinement?
nice work sir, could you please make a video how to calculate volume fraction of each phase , if already exist please share the link. Thanks!
Good suggestion! I don't think HighScore will report volume %, but I made a quick video on how to convert from weight % to volume % using Excel. I don't know if this is what you were hoping for, but I hope it helps.
Note: I try to publish videos at the start of the week, so the video will be unlisted until Monday or Tuesday. However, you can view it with this link: th-cam.com/video/4iAEGTUyEmk/w-d-xo.html
Dear Dr.Koehler Excellent way to explain X'pert high score .can you explain me how i import just analysis Graph , I just want this analysis structure bcz I already have analysis data but I want to put this XRD graph in my paper that way I just want to pick up this analysis Graph of XRD
Thanks! As for your question, let me make sure I understand you correctly. Are you able to open the HighScore Plus file and see the graph? If so, you can save the graph by going to File, Save As, and choose JPEG as the file type. If you want to plot the data points, the refinement curve, and the background yourself in different plotting software, you can go to the Anchor Scan Data, highlight all rows, copy, and then paste into something like Excel or Origin. I think Anchor Scan Data has the raw data, the refinement curve, and the background data, but let me know if you can't find it in that tab; it's possible I'm thinking of a different tab.
If I misunderstood your question, please let me know and try to ask it differently.
Hello, I am asking how exactly I can use the Rietveld method to determine if my experimental spectrum is comparable with the simulated one (a new CIF that I cannot find in the database)
Unfortunately, I have not found a way to load it into the HighScore Plus file so that you can see the stick pattern overlaid on your diffraction the same way you can when you find reference patterns in the database.
However, if you go to File, Insert, and then select the CIF file, the software will load it as a phase. You can then choose to refine that phase in much the same way that you see in the video, and hopefully you will get a good fit if the CIF file matches your diffraction pattern.
I hope this helps!
Oh good gosh! I am so happy to have found this site! This is a great help to me. Do you teach a course I could take???
I'm glad that it helped so much, and I'm happy to see such excitement over XRD videos! I do not teach a course though :/ My time is dominated by helping users in my facility with training/data collection/analysis, budgets, proposals, learning new techniques as we get the hardware to perform them (XRF, single crystal diffraction, etc.). It's been so busy lately that I haven't even had the time to make the TH-cam videos I would like! I hope to have time to get back to them soon. If you have any questions though, feel free to leave them in the comment sections. I miss some comments, but I try to reply to as many as possible.
First thanks for a very informative tutorial. Could you please tell the minimum step size and step time to perform a reasonable rietveld analysis?
That is a difficult question to answer as there is no single answer; every sample is different, and the choice of detector can also affect it. I can tell you for step size, you want to have 8-12 data points above the full width half maximum (FWHM) of your peaks.
Thank you so much for your very informative video.
I'm glad it was helpful!
Hello sir, can I know what criteria u consider to stop rietveld refinement? How u know that your rietveld refinement doing well?
Good question! I would recommend reading this paper: Toby, B. H. R factors in Rietveld analysis: How good is good enough? Powder Diffraction 21(1), 67-70 (2006).
@@IAMMDiffractionFacility okey Thank You sir.. or did you have use standard sample as a reference to do rietveld?
My apologies, but I don't think I understand your question. For what reason do you ask about a standard sample?
What to do when none of the database standards does not contain the structure table, in the rietvled quantification?
I give a few different suggestions in this video: th-cam.com/video/yGQDXCXEaqY/w-d-xo.html
Sir I would like to ask you , I have done XRd to my material but when i do match , that materias show only 1 score , what does that mean ? i hope you can reply to my question . Thanks
other candidates close it but not that my main material
Let's check this first. When you open the search and match window and click to edit the restriction set, do you see something towards the bottom of that window that says ### out of ### patterns? Can you tell me what those numbers are?
Thanks for this video. there is on question. i use high score plus, but don`t same your database. in particular there is no information about structure in reference pattern.
except for structure, have all. I want to analyze the phase percentage ratio. please tell me add method to structure information. thank you so much!!
Please see this video (th-cam.com/video/yGQDXCXEaqY/w-d-xo.html). Option 2 in the video shows you where to find the structural information online in a .cif format. If you already know the structural information and are just looking for a way to enter it manually, option 3 in the video is what you want. If you look in the video description, you can skip to each option directly by clicking the time code.
Please leave a comment in the other video if you have additional questions about it, and please let me know if it fixes your problem. Good luck!
@@IAMMDiffractionFacility thanks to your advice. i solved problem to structure information, percentage ratio. You recommended video, Nice!! thank you!!
This video talks about Rietveld refinement. I want some info about the RIR method to quantity phases. Can you help??
I'll be honest, I don't really have experience with the RIR method as I have always used Rietveld refinement. Anything I told you would just be something that I found online. The ICDD has information on this method though: www.icdd.com/assets/tutorials/Quantitative-Analysis-RIR.pdf
Thank you for this tutorial. Please I would like to know how can we quantify the pourcentage of a cristalline phase in glass i tal about glass-ceramic ?
There are a number of methods for determining crystallinity. Please visit my website (www.jiamdiffraction.com/documents). If you look beneath Other Documents (it is likely on the right side of the screen), you should see a PDF button labeled "Methods for Quantifying Amorphous Content." Click the PDF button to view a document from Bruker. The description of the different methods begins on page 19, but the pages before that also have good information.
@@IAMMDiffractionFacility thank you for your reply. I was reading this document but i didn't know how i can apply it on the drx specta that i have. It contains a single crystallized phase and I would like to know the volume of this phase in the vitreous matrix.
You have a few options. Rietveld for amorphous phases...basically, you find a crystalline pattern that matches the wide amorphous humps for your glass. You then treat the wide peaks like crystalline phases but allow the refinement to greatly broaden the peaks. The refinement steps in the video should still work. The difficulty here is that there isn't always a good reference pattern to use.
If the previous option doesn't work for you, you could try to collect another pattern. If you tested the glass as a solid piece the first time, grind it into a powder and add an internal standard (something that is as close to fully crystalline as possible and has as similar of a mass absorption coefficient to your sample as possible). You then perform quantitative analysis as I do in my video, and you use the weighed and calculated values of the internal standard to calculate the crystallinity. This is how I typically quantify amorphous content.
You also have the degree of crystallinity option. In this one, you determine the area of the peaks contributed by the crystalline portion and the area of the peaks contributed by the amorphous portion. The degree of crystallinity is then the crystalline area divided by the total area. The difficulty I've found with this method is that you need to figure out how to fit the amorphous portion. One option is to make a completely amorphous glass and test that so that you can see what the amorphous contribution looks like.
I know I haven't given you in-depth specifics, but it really depends upon your situation and what you have available in terms of XRD access, standards, and reference patterns. If you choose any method, I highly recommend trying it first on some samples for which you know the crystallinity. When I began quantifying amorphous content, I made a series of powder samples by mixing my internal standard, a semi-crystalline powder, and a completely amorphous powder. I then kept trying the internal standard method until my results matched what I had weighed the different components to be. I learned some important lessons by doing this though. Had I not done this, the analysis of my real samples would have been off.
@@IAMMDiffractionFacility i undrestand you thank you so much for your information and y2help
Thank you for this video.I have a question about sample that no have CIF.If there is no CIF file of sample and this sample has not been created before and there is no information about the position of its atoms, how can we create the file related to that sample ourselves? Thanks in advance 🌺
Please help me 🥺🙏🥺😢
I have CIF file of Y3Fe5O12 but I need cif file for Sb0.2Y2.8Fe5O12 that no exit information about that, thank you
Sorry, it was a busy day yesterday! You could load the Y3Fe5O12 CIF file, then go to the refinement tab, click the plus sign next to the phase, find...I believe it is atoms that you want. I think if you click atoms, you can enter new atoms and atomic positions. Assuming that the Sb substitutes for the Y atoms, you can give it the same Wyckoff position and then adjust the site occupancy factors (SOF) of both Sb and Y to reflect the amount each present.
@@IAMMDiffractionFacility
Thanks a million for replying 💐💜💜
Wycjoff for Y is 24c, then I must use it for Sb. But how about x, y, z positions for that? 🤯
This data for Y is :0.125,0.000,0.2500.
But I don't know how much to replace for x, y, z positions for Sb? And x,y,z positions for O in new structure?By the way, my structure has two other side phases (Sb2O4, Fe2O3) in addition to the main phase (Y3Fe5O12).
Structural parameters of pure Y3Fe5O12 is:👇👇
Atom:Wyckoff: Position x ,y, z
Fe(Octahedral) :16a: 0.0000 ,0.0000 ,0.0000
Fe(Tetrahedral): 24d :0.3750 ,0.0000, 0.2500
Y :24c: 0.1250 ,0.0000, 0.2500
O :96h: 0.9726 ,0.0572 ,0.1492
Thanks in advance💐🌺💚
If you are using the same Wyckoff position for Y and Sb, then the x, y, z positions should be the same. Again, this is assuming that the Sb atoms are substituting for the Y atoms. You could try changing the occupancy of Sb to 0.2/3 and of Y to 2.8/3.
A good question to ask yourself is just how accurate do you need your analysis to be? You could spend a lot of time trying to get the atomic positions of all the elements correct, but if you are looking for a general idea as to phase quantification, that's likely a waste of time. You also have to keep in mind that there is going to be some sort of error bar associated with your quantification. It could be that trying to perfect your fit will change the results less than the error. Refining on the oxygen positions could be difficult as oxygen is such a light element. Your data would have to be very good.
@@IAMMDiffractionFacility Thanks for your tips dear Michael💐🌺
And sorry for the replay again
Yes, I understand what you mean, I think the presence of side phases like Sb2O4 indicates that the Sb atoms are not substituting for the Y atoms.
What I wanted to do was calculate the percentage of phases in the structure after Rietveld refinement and compare those to before Rietveld. And also measurement of bond length of Fe_Fe , Fe_O, Fe_O_Fe, Y_O,.. after substitution sb for Y.
In my version of x'pert high score soft no exit information about XYZ wyck in reference patterns related to phases. And also after downloading CIF files , I realized that some of those files(related to phases of my structure) did not contain wykoff. Therefore, after Rietveld, the percentage of some of side phases was caculated as zero. I could not even use full prof software for this because of these problem 🤦🏻♀️
So I decided use the maud software . In this case I was able to calculate the percentage of side phases after Rietveld by importing the CIF file related to the phases.But now I have a problem and that is calculating the bond length and angles of Fe_Fe , Fe_O, Fe_O_Fe, Y_O,.. .
I know software like FullProf, Vesta and crystal Maker can give me this information but after Rietveld , the maud software only generates files with (.par)s extension that I can not use it in any of the mentioned software😢😢🥺🥺
Thanks 💐
Thanks for the video. I took the same steps to quantify the phase as you do but it shows only phase name, not percent. Can you help me ?
I can certainly try! Did you double click the pattern to see if there was structural information (such as atom positions, not lattice parameters) in it?
@@IAMMDiffractionFacility I tried but failed. So, Quantification requires the condition of the corresponding number of peaks. Due to background quite bad.
I don't think I understand. Can you send me an email at mkoehler@utk.edu and include a screenshot of whatever analysis you have been able to do so far?
Hi,
Please I have issues with peak fitting as the software often displays " no structural data for simulation/refinement" and also refining the XRD peaks was not possible as well.
Note that the data contains mixtures of compounds. Please, what am I doing wrong?
Hi Joshua...regarding the no structural data problem, please see this video: th-cam.com/video/yGQDXCXEaqY/w-d-xo.html.
Regarding not being able to refine the XRD peaks, is this a problem you are having when you are trying to perform a profile fit or a Rietveld fit?
@@IAMMDiffractionFacility, thanks for the prompt response. I usually encounter this problem when trying to perform Rietveld fit.
@@IAMMDiffractionFacility,
I have followed the steps as explained in the video. Although my Xpert has more than 500,000 PDF, it cannot still display the structural data. Also, having inserted the CIF files the data did not sync with the Xpert database as they must be uploaded each time I want to do analysis.
Also, I discovered that deleting the phases that do not have structural details left the peaks unidentified/unmatched.
Please, what could be the issues?
Yeah, CIF files need to be loaded manually each time you use them, or you can copy the phase from one HPF file to the next, or save an HPF file with the CIF file loaded but no diffraction pattern loaded. There are a few options, but I don't know of any way to add it to a database.
What database are you using? Some databases do not include atomic positions.
@@IAMMDiffractionFacility
These are the database details:
COD-Mar 2010 (HighScore plus 3.x)
PDF 2 Release 2004 (HighScore plus 3.X)
PANalytical Example database (HighScore Plus 2.x)
My X'pert highscore, dont show the structure , could please help me why ?
Can you tell me what version of HighScore you have (both the version number and if you have HighScore Plus or just HighScore)? Can you tell me what database you have?
Thanks for the video. One question is that for a few particular phases that I use have very old version of pdf cards that do not have crystal structure info and no new pdf of the phase can be found as replacement, so the phases cannot be quantified at all based on your methods unfortunately. The crystal info of the phases is not hard to find but is it possible to add these info in the old pdf card in highscore plus to make the quantification workable in highscore? THanks!
You can certainly add info to make it usable. You should begin by converting the pattern to a phase. Then go to the Refinement Control tab and expand the phase that you want to add information to (click the + sign next to it). Click on Atomic Coordinates. If there are no atoms present shown in the Object Inspector (probably the right panel on your screen), right click in the Object Inspector and choose Add New Atom. Add information to the element, oxidation, and name fields. Don't worry about the Wyckoff, Multiplicity, and other fields just yet (in my version, I can't change them even if they are blank). Do this for each atom that you need.
In the Refinement tab, click on the name of the phase again. In the Object Inspector, you should see different sections such as Phase Display, General Phase Info, Symmetry/Space Group, etc. You want to expand the Symmetry/Space Group section (click the + sign next to it). Make sure that the Space Group Number is correct based upon what you found in other resources.
If you click on Atomic Coordinates again under the phase you are changing in the Refinement Control tab, you should now see that each of your atoms has a Wyckoff position and atomic coordinates. If any of these values are wrong, you can now change them.
Good luck, and please let me know if this works for you!
Hi sir, I tried to search and match peak but the software said no candidate found. Can you please help me to deal with the issue?
When you open the search and match window and click to edit the restriction set, do you see something towards the bottom of that window that says ### out of ### patterns? Can you tell me what those numbers are?
@@IAMMDiffractionFacility the same happens to me. The window says 64 patterns of 131574. Could you help me please?
@Ana Maria Ferrari My apologies for the slow reply, I didn't see your comment until just now. So there are 64 possible matches according to the window, but when you actually perform the search, no candidates appear?
Hello, thanks a lot for this tutorial. I was wondering if this procedure could be enough accurate for clays phase quantification, or if I should use an internal standard ? Thank you for your reply !
Honestly, I do not have much experience with clay samples, so I do not want to give an answer that I am not 100% confident in. However, I did a little research, and there are numerous papers online on the topic. A couple are "XRD-based quantitative analysis of clay minerals using reference intensity ratios, mineral intensity factors, Rietveld, and full pattern summation methods: A critical review" and "Accurate quantitative analysis of clay and other minerals in sandstones by XRD: comparison of a Rietveld and a reference intensity ratio (RIR) method and the importance of sample preparation." The second paper seems to conclude that both RIR with an internal standard and Rietveld (without an internal standard, if I am reading it correctly) give similar results. However, the importance of sample preparation can't be overstated.
@@IAMMDiffractionFacility Thx for the advice, I'll read them and see what is the most suitable to my samples
Hi there,
Thank you so much for the videos. These are amazing. I have a query-
What if you dont have the structural features in any of the pattern? How would you run the Rietveld then? I dont have the structural features in any of the pattern and is kind of in a fix what to do? Any suggestions would have been really helpful. Thank you so much again for all the videos and trust me these are helping me a lot.
First off, thank you for the kind words! They really do mean a lot and are appreciated.
Next, if there are no structural features (i.e., atomic positions), there is an option called charge flipping. It is a feature present in both HighScore Plus and GSAS-II. However, it is not something I have done before, so I will not be any help with it. I could be wrong, but I don't think it is very easy. I want to learn it, but the difficulty is finding the time! I'm sure that is how it is for most people though.
It sounds like your situation may be that atomic positions exist for the patterns, but your database does not have atomic positions. Is this correct? If so, you could try to find such information on the Crystallography Open Database (COD). The link is www.crystallography.net/cod/search.html.
Please let me know which situation you are in and if you were able to get your problem solved. Good luck!
@@IAMMDiffractionFacility Thank you so much for your sharp response. I do see the crystallographic data in the springer crystallographic doc available online but those are not embedded in the available pattern in the highscore plus I am using just like the way you have in yours. I think I will have to manually set all those data? What's your thought on that? Thank you so much again.
Do you mean that you found your phase on DOC but you can't download a .cif file for it? If so, what phase are you trying to find? I can look into it further.
In addition to my previous reply from a minute ago, I will say that you can certainly manually enter the information into HighScore Plus to build your own phase. That is a perfectly valid option, it is just slower than if you can easily find a .cif file.
hello thanks for the video and i want to ask, why there is all no structure in my peak list so that i cant do rietveld to show the number
One option is that you have only HighScore, not HighScore Plus. I believe regular HighScore does not perform Rietveld. Another option is that your database does not contain atomic positions for the reference patterns. Those are the two most likely reasons that I can think of.
thanks a million for such nice videos. how to quantify amorphousness of in a system, using the same process ?
I'm happy you like the videos, and excellent question! There are numerous methods for determining the amorphous content. A good place to start to learn a bit more about the different options can be found here: www.icdd.com/assets/ppxrd/presentations/13/PPXRD-13-Dinnebier-WS.pdf.
I haven't done too much with amorphous quantification (edited...I mistakenly wrote phase quantification originally), but I've found the internal standard method to work pretty well. For this method, I'll mix about 50% standard with 50% sample...before I go on, let me add a few notes: (1) you want to use a balance and record the weights, (2) the standard should be as close to 100% crystalline as possible, and (3) I can't guarantee that a 50%/50% mixture will be best for you.
You then perform phase quantification just like in the video, but add whatever phase your standard is. The refinement should give a phase fraction for the standard that is larger than what you measured. You can then use the refined value and the actual value for the phase fraction to calculate the amorphous content.
Whichever method you choose, I recommend preparing some samples for which you know how much amorphous content is present, perform the analysis, and then make sure you get the correct answer. This way, you can make sure that your general method is at least close to being correct.
@@IAMMDiffractionFacility out of words to say how grateful I am. Thank you so much 💓. I am very sure what I need to do now.
Great! If you have any other questions in the future, always feel free to ask, and I'll do my best to answer.
@@IAMMDiffractionFacility I am sorry to bother you again. None of the cards in the database of Xpert High Scorer plus I am using have structural details: the position of atoms. Hence, I cant do quantification or refinement. Any Solution to that ?
Don't worry, it's not a bother. Unfortunately, databases do exist that don't have atomic positions. There are a few solutions. (1) Find someone who does have access to a database with atomic positions and get them to send you the .cif files for your phases. (2) Find the atomic positions in a journal article, and then create a new phase in HighScore Plus so that you can enter the space group, lattice parameters, atomic positions, etc. (basically, you enter all of the phase information yourself instead of having it provided by the card). (3) Check out the Crystallography Open Database (COD) (www.crystallography.net/cod/search.html) to see if they have the phases that you need. From COD, you can get .cif files.
I hope this helps! Let me know if you need any more information/advice on these possible solutions.
Hi can you help regarding where to find values of rwp rp rb in xpert highscore as iam not able to find it after refinement.Also it is not shown in additional graphics window.
I'm not sure what version you are using, but you should see the values if you left-click Global Variables in the Refinement Control tab. If you go to 2:53 in the video, you should see the values in the right side of the screen. Let me know if you don't see the values there in your version.
@@IAMMDiffractionFacility Thank you for your reply. I Am using version 3 of the software.Sorry but iam not able to see values of rwp, rp, rb in your video also. Exactly which values are ones corresponding to rwp, rp, rb. Please help
If you look under agreement indices at 2:53 in the video, you will see "Weighted R profile" (which corresponds to Rwp) and "R profile" (which corresponds to Rp). I don't see anything for Rb though.
@@IAMMDiffractionFacility yes i got it.Thank you for your help.
Thank you for explain.
I got x data as a text file. How can I get it into the program?
Can you help me . Pleas
So it is a .txt file? What does it look like? For example, is it just two columns of data?
@@IAMMDiffractionFacility
Yes it is 2 columns
but it is txt file . So the program don't able the file
Okay. First, make a copy of the file in case what I tell you messes it up! On the copied file, change the extension from .txt to .asc. Now try to open the file using HighScore. It worked when I tried it, but let me know if it works for you.
@@IAMMDiffractionFacility
Did you mean this information for my research?
If that is the question then the answer is yes the works for me
I'm glad it fixed the problem, and thank you for letting me know!
Thank you very much for these videos, in fact I am following the same steps as you but I cannot determine the Miller hkl indices, is the database file of COD_2016_Conv45.hsrdb not suitable for determining them?
Thank you
Just to clarify, are you able to identify your phases (you found reference patterns that match your diffraction pattern) but you can't determine the hkl indices of the peaks? Or are you unable to identify the correct phases?
Dear Sir, Is this software best for analysis of xrd data of materials ? (Li-ion battery cathode materials)
I do not feel qualified to say whether or not it is the best as I have not tried all of the others, but I do really like it. There are free options (like GSAS-ii) that give excellent results as well (my boss loves GSAS-ii), but the graphical user interface and customization options of HighScore Plus make the cost well worth it, in my opinion. I have also recently helped a user analyze in situ battery data, and the results turned out very well.
Hello, I would like to know why do you convert pattern to phase?
A pattern is basically just a list of peak locations and relative intensities, which makes them great for phase identification. HighScore Plus takes all of the necessary information (e.g., crystal structure, lattice parameters, etc.) from the pattern file and allows you to alter/refine it to best fit your specific sample. If we didn't convert our patterns to phases, we couldn't perform phase quantification.
If you only have one phase, phase quantification will, of course, give you 100% of that phase. However, converting a pattern to a phase also helps if you want to determine the lattice parameters, crystallite size, and microstrain of your phase(s).
Hopefully that answered your question. Please let me know if it seems that I misunderstood what you were asking.
JIAM Diffraction Facility thanks a lot I'm starting learning sample identification by x-ray difraction and one of the aims is to perform rietveld refinement (manually).
Okay, I see. If you haven't already, be sure to check out the phase identification video that I have. That is a good starting point. If you want to perform rietveld manually, you'll just want to go into the refinement tab (which you can see in the video) and choose which items to refine. HighScore Plus gives a nice user interface, so finding the different items to refine isn't too difficult. If you do have problems figuring out how to refine a certain parameter, I'll be happy to help if you post another question.
Good luck!
could you please explain how to find zeolite and gismondine phases in XRD pattern using Xpert high score.
For zeolites, you could select aluminum, oxygen, hydrogen, sodium, potassium, magnesium, and calcium as possible elements. My understanding is that gismondine is also a zeolite, so the same search should work for it. Essentially, find what elements are in the phases that you think are in your sample, and then enter those in the periodic table screen that I show in the video.
Depending on your version of HighScore Plus, you might have a couple more options in the Edit Restriction Set window. You can go to the Strings tab and enter the compound name or mineral name to narrow down the search results. The second additional option is to go to the Mineral/Zeolite Class tab. Under Mineral Classification, you can scroll all the way to the bottom and choose ZEO - Zeolite (Family). Under Zeolite Classification, you can scroll down and choose GIS - Gismondine.
Dear Dr. Koehler. Thank you for the video. I have one question. Is it possible to determine the size of nanoparticles from a xrd pattern/ Rietveld refinement ? I am not talking about the crystallite size but the mean size of nanoparticles such as gold or other crystaline nanostructure. Thanks again!
Unfortunately, XRD does not give you information about particle size, just crystallite size. You may want to look into an electron microscopy technique, that may give you the information that you are looking for.
@@IAMMDiffractionFacility thank you very much. Could you suggest a free software for refinement?
My pleasure! As far as free software for Rietveld refinements go, I would suggest GSAS-II. You can download it from subversion.xray.aps.anl.gov/trac/pyGSAS.
There are some great tutorials available at subversion.xray.aps.anl.gov/pyGSAS/trunk/help/Tutorials.html. I feel like the best two tutorials to start with for learning to refine are "Fitting laboratory X-ray powder data for fluoroapatite" and "Determining Starting Profile Parameters from a Standard."
@@IAMMDiffractionFacility Thank you very much!
hi, can phase quantification of composite materials (polypyrrole and bismuth on the surface of GO)do by reitveld refinement?
I'm not familiar with all the materials you listed, but if you can detect the different crystalline phases, phase quantification should work.
@@IAMMDiffractionFacility Thanks a lot. What I concluded that we can do phase quantification with crystalline material. And my composit contains some amorphous material that's why phase quantification will not work with my prepared composite.
can you remove the synthetic label ?
Sure! Instructions for how to change the title of a phase can be found around 05:50.
thank you so much. I am a post-doctor in the HUST of china. I have learned a lot from your tutorial. there is one problem that I cant find the entry of solver tolerance under 'General property' in my HSP. So the Rietveld refinement just executed for a few steps and then stopped, which cause the difference between the calculated profile and obs is still very high. I will be greatly appreciated if you could give me some advice to fix this problem. Regards.
Thank you for the kind words! Once your refinement is finished running and you still have a large difference, does the fit get any better if you click the "Execute Fitting" button again?
If you don't see solver tolerance when you go to Refinement Control - Global Variables and look under general fit properties, do you see "Max No. of Fit Cycles" or "Solver Time Limit [sec]" fields there?
@@IAMMDiffractionFacility Thank you so much. After a second click on the button of 'start rietveld refinement ', the fit showed almost no change.
I can see the entry of 'Max. No of Least-Squares Cycles', but no entries of 'solver tolerance' or 'solver Time Limit' under 'General Properties'.
Besides, the content in Refinement control/Global variables and object inspector/general properties show some difference from yours. I wonder that is due to a different version of the HSP? mine version is 3.0d(3.0.4)
Yeah, my version is much newer (4.7). What value do you have for "Max No. of Least-Squares Cycles?"
In addition to the question regarding your value for "Max No. of Least-Squares Cycles," I have a couple of others to help find the problem. (1) Are you performing an automatic refinement or a manual refinement? (2) What parameters (such as scale factor, lattice parameters, etc.) are being refined? You can figure out which parameters are being refined by clicking the plus sign next to the phase and seeing which parameters have check marks in the "Refine" box (sorry for explaining if you already know how to do this).
@@IAMMDiffractionFacility 20, and i also tried higher value (eg. 100) for "Max No. of Least-Squares Cycles?", but the result is the same
this method valid only for HighScore Plus but for HighScore which are not either, you can help me because I don't have the option
Do you mean that you only have HighScore but not HighScore Plus? If so, I don't think you can do Rietveld with just HighScore. You can perform phase identification though. Once you know the phases you have, you may be able to export .cif files and use those and your data to perform Rietveld using GSAS-II. There are some nice written tutorials on GSAS-II (subversion.xray.aps.anl.gov/pyGSAS/trunk/help/Tutorials.html).
@@IAMMDiffractionFacility I did not understand is it possible to give me your gmail
If you would like to discuss more outside of TH-cam, please contact me at mkoehler@utk.edu.
Can I know wich database schoud I use to quantify?
I only have experience with the ICDD databases in HighScore Plus. If I'm not mistaken, you would need something like PDF-4+ for phase quantification. There is a PDF-2 that is good for phase identification, but it doesn't seem to have the information necessary for phase quantification. You can find more information at www.icdd.com/pdf-product-summary/
Hello!
Thanks for this video it's very helpful.
I have a question about the phase quantification : if there is another method to calculate concentration of each phase manually because i haven't the structural information in my pdf phase ?
and I see in another video who speak about the "RIR Information" to quantify phases, any explanation about this please?
Thank you very much for the tutorial. Is it possible share The software and database?
Unfortunately, I cannot share the software and database, they both require licenses (HighScore Plus from Malvern Panalytical and the PDF-4+ database from ICDD). HighScore Plus is really nice if you have the money for it, but there are free options such as GSAS-II and FullProf that can perform Rietveld refinements. I've used GSAS-II a bit, and while I prefer the user interface and automation of HighScore, GSAS-II's interface isn't bad. There are also some really nice written tutorials that you can find on anl.gov (just google gsas-II tutorial). You do need to import a .cif file or enter the structural information for the phase in GSAS-II though.
Are the percentages wt% ?
They are.
Sir, I have sent you an email requesting help. If you received it Please kindly help.
Will You please provide me your email. I am facing some problems to fit some sample and I need your help
Sir, when i click convert pattern to phase I am not getting any percentages only phases appeared. Could you please help me ? How I can get phase percentages?
I recommend you watch this video of ours (th-cam.com/video/yGQDXCXEaqY/w-d-xo.html) and let me know if it solves your problem.