Hello Rajeev, about the LP value: this is the Lorenz-Polarisation Factor and selected according to your monochromator for CuK radiation: Ge = 27.3, Graphite = 26.4, Quartz 26.6, unpolarized i.e. no monochramator = 90, fully polarised e.g. synchrotron = 0. We have a Goebel mirror, and Bruker haven't got a good answer fro what the LP factor should be, their suggestion was to use 0.1.

I have looked at your settings and files. I get a different error message and cannot reproduce your error, so I am not sure what is happening at your end. One thing you need to do is to go through the cif files and make a number adjustments before they can be used. As they are they will not work. Do you have the TOPAS Tutorial booklet that comes with the system?, Section 2.7.2.1, P. 79, goes through in some detail how to prepare cif files for use. If you don't I can walk you through it.

Do you have the TOPAS database?, as many of those structures are already present as .str files and it will save you a lot of time using these rather than .cif files.

I did try with that suite of phases but got quite poor fits. (I think the LP figure needs to set correctly - I am guessing no monochromator??) You also have a problem with the amorphous phase at low angles. I suspect this is from your plastic sample holder. It will mess up your background an you will need to use an SPV peaks phase to try and model this region, or better still, use a different holder, or restrict the beam so that it does not hit the holder at low angles.

I have attached a refinement using LP = 90, watch out for Cry size L moving to extreme values - these have no physical meaning, reset to a low value and re-refine. If it continually goes much above 1000 then switch it off. Sometimes its a bit like herding cats trying to get the Cry size L values at a realistic value. Switch on calculate errors and watch out for silly answers. You may need to use strain L. Use PO and look for values just below 1. 

I'll paste an image of attempt on your sample shortly. I'm working remotely at present and need to log in elsewhere...

Hello Rajeev, about the LP value: this is the Lorenz-Polarisation Factor and selected according to your monochromator for CuK radiation: Ge = 27.3, Graphite = 26.4, Quartz 26.6, unpolarized i.e. no monochramator = 90, fully polarised e.g. synchrotron = 0. We have a Goebel mirror, and Bruker haven't got a good answer fro what the LP factor should be, their suggestion was to use 0.1.

I have looked at your settings and files. I get a different error message and cannot reproduce your error, so I am not sure what is happening at your end. One thing you need to do is to go through the cif files and make a number adjustments before they can be used. As they are they will not work. Do you have the TOPAS Tutorial booklet that comes with the system?, Section 2.7.2.1, P. 79, goes through in some detail how to prepare cif files for use. If you don't I can walk you through it.

Do you have the TOPAS database?, as many of those structures are already present as .str files and it will save you a lot of time using these rather than .cif files.

I did try with that suite of phases but got quite poor fits. (I think the LP figure needs to set correctly - I am guessing no monochromator??) You also have a problem with the amorphous phase at low angles. I suspect this is from your plastic sample holder. It will mess up your background an you will need to use an SPV peaks phase to try and model this region, or better still, use a different holder, or restrict the beam so that it does not hit the holder at low angles.

I have attached a refinement using LP = 90, watch out for Cry size L moving to extreme values - these have no physical meaning, reset to a low value and re-refine. If it continually goes much above 1000 then switch it off. Sometimes its a bit like herding cats trying to get the Cry size L values at a realistic value. Switch on calculate errors and watch out for silly answers. You may need to use strain L. Use PO and look for values just below 1. 

I'll paste an image of attempt on your sample shortly. I'm working remotely at present and need to log in elsewhere...

here is an image of your sample analysed by TOPAS. Its not perfect, but it's shows it cane done. 

R-Values

Rexp : 2.06 Rwp : 6.73 Rp : 5.10 GOF : 3.28

Rexp`: 3.64 Rwp`: 11.93 Rp` : 10.07 DW : 0.26

Quantitative Analysis - Rietveld

Phase 1 : Brownmillerite 9.51(25) %

Phase 2 : "C3A cubic" 2.44(43) %

Phase 3 : "C3A Na cubic" 3.93(35) %

Phase 4 : Calcite 11.45(20) %

Phase 5 : "C3S monoclinic (NISHI)" 48.46(46) %

Phase 6 : Gypsum 3.26(11) %

Phase 7 : "C2S beta (MUMME)" 15.95(42) %

Phase 8 : Portlandite 2.19(17) %

Phase 9 : Quartz 0.352(51) %

Phase 10 : Bassanite 2.44(17) %

Thanks a lot Ian for your great help.

Sorry for the delay in getting back to you, i was sick for last couple of days.

I'll go through the TOPAS Tutorial Section 2.7.2.1, P. 79 and see if i manage to amend the CIF file. I'm not sure if our lab has got TOPAS database, i'll have a look, if it is there that will be great. Our lab otherwise has PDF2 database, which is good for identification but doesn't give out cif files to be used for quantitative analysis. I was using COD and American crystal structure database but i am going to buy ICSD database, 1 year license to carry out my analysis.

Thanks again for your great help

Hello Rajeev, if you have the database it will be in the folder C:\Topas4-2\Structure Database (or similar path). You will need PDF-4 from ICSD in order to get the structures. A good tip is once you have your cif files in a good state then you can save them as .str so don't have to keep going through that procedure

Thanks Ian for your good advice. I'll convert all cif files to str so that I don't have to keep on repeating the process

Make sure that they refine well before doing so. If you have samples with high proportion of, or pure phases, then use those to play with the cif before converting to str

Dear Rajeev,

I agree with Ian suggestions but I would like to add a new one: if you are interested in quantifying OPC (or any other material in a continous way with a lot of phases) is mandatory to add constraints to the cell parameters and crystallite size limits. I mean, once you have entered the crystal structure with a CIF file and before any refinement, it is highly recomended to add MIN and MAX values for the cell parameters (around 2-3% of the theoretical value) and for the crystallite size components. These constraints will avoid to get unreliable values of cell parameters and LVol-IB. If not, you can erroneously quantify nanoparticles in OPC or impossible crystal structures with bad cell parameters. 

A second suggestion: sample preparation for quantitative phase analysis is a crucial step that many times is underestimated. There is a lot of bibliography related with this subject. The presence of amorphous phase in OPC is possible but usualy is not detectable directly in the diffractogram.

Good luck!

Thanks Francesc for your valuable suggestion.

Sorry, i'm not fully conversant with the rietveld refinement and crystallography, could you please clarify, where can i get the crystal size information? Is it unit cell volume which is there in the crystal structure file?

You can estimate roughly the crystallite size by refining the parameters CS_L and/or CS_G once you have introduced the diffractometer description or the Instrumental Resolution Funcion. After refining these parameters, the term LVol_IB will be updated giving you a rough estimation of the crystallite size according to the Scherrer equation.

The crystallite size affects inverselly the peak width. The cell volume is affected by the peak position.

TOPAS software is a very powerful program that apparently makes easy something that needs a solid knowledge on crystallography. I mean, you can easily get a reasonable good refinement with TOPAS but without a crystallographic sense. So, I highly recommend you to go deep in the Rietveld method in order to take the maximum profit of TOPAS.

Here you have some starters for improving your refinements:

J. Appl. Cryst. (1999). 32, 36-50 [doi:10.1107/S0021889898009856]

J. Appl. Cryst. (2001). 34, 409-426 [doi:10.1107/S0021889801007476]

J. Appl. Cryst. (2002). 35, 383-400 [ doi:10.1107/S0021889802008798 ]

I have attached an image from TOPAS for quartz, showing the difference between the .str file and the .cif file. You will see that the cif does not have Min and Max values for the cell parameters a (A) and c (A), whereas the str files has these values already in place. Note also the cif has these as Fix rather than refine. Similarly there is no Min or Max value for the Cry Size. The str file has one Min value of 32, but no maximum. You could put a maximum value in. But I usually check these figures and see if any of them are stopping at the max or min, or if no max is in place whether the value is stupidly large. There gets a point where the limit on the instrumental broadening takes over from the very large Cry L size and this value becomes meaningless. This has happened in this example str file and Cry Size L has been switched off. Another thing to note are the cif file has an initial scale value that is too low. I usually start this at 0.001.

As for the crystallite size - the usual start value is 200. It is helpful to look at the individual calculated profiles to see if they make sense, if the Cry Size is going too low (you get a very wavy line that makes no sense and the % is way too high) or too high (a set of peaks that are very sharp when compared with the data). Sometimes when I am working with clays, I allow the Cry Size L to go right down as these can have very disordered structures. But for most well-crystalline material I would expect values in the region of 64-500.

I have to disagree with Francesc that - while LVol-IB is the correct measure to report for crystallite size - it is not a result of the Scherrer equation. This implementation is using integral breadth measurement using both Gaussian and Lorentzian component convolutions and not a single measure at FWHM as used in Scherrer equation. The integral breadth measure also does away with the K constant in the Scherrer equation.

Thanks a lot Ian for a very detailed explanation. Things are much clearer now. i'm working to a trial run with cif to str conversion and use that on some standard material until i receive ICSD database. Thanks a lot for all your help

Hi Rajeev and all,

I have gone through your problem. I have faced similar kind of problem based on error s given by Topas software.

I am giving the results here but the error is showing large within bracket.

R-Values

Rexp : 7.15 Rwp : 11.49 Rp : 8.83 GOF : 1.61

Rexp`: 4.42 Rwp`: 7.11 Rp` : 5.58 DW : 0.84

Quantitative Analysis - Rietveld

Phase 1 : CaO 0.418(46) %

Phase 2 : gamma 21.44(14) %

Phase 3 : beta 71.03(20) %

Phase 4 : C3S2 0.00(13) %

Phase 5 : C3S 0.23(11) %

Phase 6 : SiO2 0.000(30) %

Phase 7 : CaTiO3 6.876(90) %

Could you please help me out why it is coming?

Thanks,

Sanat

Hi Sanat,

I suggest, you do Thermogravimetric analysis as well. I found it very helpful. My OPC sample had calcite content as well, which has a peak overlap with calcium silicate in XRD. But with TGA I managed to identify that, moreover I had portlandite as well in my cement sample. You can also identify if the gypsum content in your cement is in which form i.e. CaSO4.2H2O (gypsum) or CaSO4 (Anhydrite). Conducting TGA will help you in identifying many phases correctly in your XRD. In addition, you will have to check whether the other phases that you have identified are correct. Once you are fully confident, then you can concentrate on your analysis part. One thing that helped me in the analysis was the crystallite size of the identified phases. Calculate the approximate size of the crystal and provide a range ±5% approx. to restrict your crystallite size otherwise sometimes it starts gettings ridiculous values, which does affect the results as well. When you refine atomic parameters, do one by one element, I was making a mistake of refining all in one go, then I figured out that only some of them needed refinement and the others were negatively affecting the RBragg values. 

Another thing I suggest if yoy can do is to conduct an XRF of your sample, with that you can identify the elements present in your sample, which would help you in correctly identifying the phases correctly in XRD.

The process is tedious but it really helps a lot. Moreover, I had raised many questions on this topic, you can go through, you may find many interesting answers from the researchers who helped me in my analysis.

Thanks Rajeev for your suggestions.

Sanat, It is not explained in the TOPAS manuals exactly what these figures in brackets are. But I have spoken to Bruker about these in the past and it appears they are not error values at all but extra decimal places that are not considered to be significant - note that the number of places changes. So don't worry about them.

What you do need to worry about is getting the correct structures in your refinement. it is reporting C3S2 as 0.00(13)% and SiO2 as 0.000(30)%. You should switch these structures off.

Also while you have a good GoF value it is down to having a poor Rexp value. I suspect from this that you have poor data with a high or noisy background.

Can you post your data so that I can check?

Thank you very much for clearing my doubt on error. Actually I am comparing the all phases with different samples so I keep all these phases.

Right now I do not have the raw data with me. I will post the raw data as soon as I will get that.

Thank you once again.