Re: Problems using TOPAS R (Rietveld refinement)
Dear Lubomir Smrock, linear pattern analysis is _not_ Rietveld, this was a common QPA method prior to Rietveld QPA. In a Rietvel QPA, one must refine the lattice parameter at least. And that makes it nonlinear. Depending on the sample, one may decide to add more nonlinear details to the refinement. Of course, additional knowledge about the phases in the sample is welcome. For example: Stacking faults in clay minerals are known to be common from single crystal or electron microscopy investigations. Some phases are known to have sheet- or needle-like shape, e.g. from scanning electron microscopy; therefore anisotropic, hkl-dependant line broadening and/or strong preferred orientation must be concerned. Only seldom such phases real structure is derived from the pattern itself. But knowing them Rietveld QPA must introduce and refine them for good results. Regards Joerg Bergmann, Dresden Am Mittwoch, den 21.03.2007, 07:50 +0100 schrieb Lubomir Smrcok: Gentlemen, I've been listening for a week or so and I am really wondering what do you want to get ... Actually you are setting up a refinement, whose results will be, at least, inaccurate. I am always surprised by attempts to refine crystal structure of a disordered sheet silicate from powders, especially when it is known it hardly works with single crystal data. Yes, there are several models of disorder, but who has ever proved they are really good ? I do not mean here a graphical comparison of powder patterns with a calculated trace, but a comparison of structure factors or integrated intensities. (Which ones are to be selected is well described in the works of my colleague, S.Durovic and his co-workers.) As far as powders are concerned, all sheet silicates suffer from prefered orientation along 001. Until you have a pattern taken in a capillary or in transmission mode, this effect will be dominating and you can forget such noble problems like anisotropic broadening. Last but not least : quantitative phase analysis by Rietveld is (when only scale factors are on) nothing else but multiple linear regression. There is a huge volume of literature on the topic, especially which variables must, which should and which could be a part of your model. I really wonder why the authors of program do not add one option called QUAN, which could, upon convergence of highly sophisticated non-linear L-S, fix all parameters but scale factors and run standard tests or factor analysis. One more diagonalization is not very time consuming, is it ? To avoid numerical problems, I'd use SVD. This idea is free and if it helps people reporting 0.1% MgO (SiO2) in a mixture of 10 phases to think a little of the numbers they are getting, I would only be happy :-) Lubo P.S. Hereby I declare I have never used Topas and I am thus not familiar with all its advantages or disadvantages compared to other codes. On Wed, 21 Mar 2007, Reinhard Kleeberg wrote: Dear Leandro Bravo, some comments below: Leandro Bravo schrieb: In the refinement of chlorite minerals with well defined disordering (layers shifting by exactly b/3 along the three pseudohexagonal Y axis), you separate the peaks into k = 3.n (relative sharp, less intensive peak) and k #61625; 3.n (broadened or disappeared reflections). How did you determined this value k = 3.n and n = 0,1,2,3..., right? The occurence of stacking faults along the pseudohexagonal Y axes causes broadening of all reflections hkl with k unequal 3n (for example 110, 020, 111..) whereas the reflections with k equal 3n remain unaffected (001, 131, 060, 331...). This is clear from geometric conditions, and can be seen in single crystal XRD (oscillation photographs, Weissenberg photographs) as well in selected area electron diffraction patterns. The fact is known for a long time, and published and discussed in standard textbooks, for example *Brindley, G.W., Brown, G.: Crystal Structures of Clay Minerals and their X-ray Identification. Mineralogical Society, London, 1980.* First, the chlorite refinement. In the first refinement of chlorite you used no disordering models and used ´´cell parameters`` and ´´occupation of octahedra``. So you refined the lattice parameters and the occupancy of all atoms? Yes, the lattice parameters. Only the occupation/substitution of atoms with significant difference in scattering power can be refined in powder diffraction. In case of chlorites, the substitution Fe-Mg at the 4 octahedral positions can be refined. In the second refinement, you use na anisotropic line broadening ´´in the traditional way``. So you used a simple ellipsoidal model and/or spherical harmonics? Simple ellipsoidal model, assuming very thiny platy crystals. But it was clear that this model must fail, see above the known fact of disorder in layer stacking. And from microscopy it is clear that the crystals are
Re: Problems using TOPAS R (Rietveld refinement)
Dear colleagues, sorry, my mail should go directly to Leandro, but I used this damned reply buttom... My answer was related to Leandro's questions regarding these line broadening models. I realised that Leandro is going on to apply a Rietveld program for phase quantification, including kaolinite and later other clay minerals. I only tried to express my personal experience, that any inadequate profile description of a clay mineral will surely cause wrong QPA results, nothing else. This is a practical issue, and it is only partially related to structure refinement. Lubomir Smrcok is definitely right that other things like PO are frequently biasing a QPA result, but for the most of these problems working solutions do exist. But I disagree that anisotropic line broadening is a noble problem. In clay mineral mixtures, it is essentially to fit the profiles of the single phases as best as one can, to get any reasonable QPA result in a +-5 wt% interval. On the other hand, for the QPA purpose it is not so much important to find any sophisticated description of the microstructure of a phase. But the model should be flexible enough to cover the variablility of the profiles in a given system, and, on the other hand, stabil enough (not over-parametrised) to work in mixtures. The balancing out of these two issues could be the matter of an endless debate. And here I agree again, a better, more stable minimisation algorithm can help to keep a maximum of flexibility of the models. Best regards Reinhard Kleeberg Lubomir Smrcok schrieb: Gentlemen, I've been listening for a week or so and I am really wondering what do you want to get ... Actually you are setting up a refinement, whose results will be, at least, inaccurate. I am always surprised by attempts to refine crystal structure of a disordered sheet silicate from powders, especially when it is known it hardly works with single crystal data. Yes, there are several models of disorder, but who has ever proved they are really good ? I do not mean here a graphical comparison of powder patterns with a calculated trace, but a comparison of structure factors or integrated intensities. (Which ones are to be selected is well described in the works of my colleague, S.Durovic and his co-workers.) As far as powders are concerned, all sheet silicates suffer from prefered orientation along 001. Until you have a pattern taken in a capillary or in transmission mode, this effect will be dominating and you can forget such noble problems like anisotropic broadening. Last but not least : quantitative phase analysis by Rietveld is (when only scale factors are on) nothing else but multiple linear regression. There is a huge volume of literature on the topic, especially which variables must, which should and which could be a part of your model. I really wonder why the authors of program do not add one option called QUAN, which could, upon convergence of highly sophisticated non-linear L-S, fix all parameters but scale factors and run standard tests or factor analysis. One more diagonalization is not very time consuming, is it ? To avoid numerical problems, I'd use SVD. This idea is free and if it helps people reporting 0.1% MgO (SiO2) in a mixture of 10 phases to think a little of the numbers they are getting, I would only be happy :-) Lubo P.S. Hereby I declare I have never used Topas and I am thus not familiar with all its advantages or disadvantages compared to other codes. On Wed, 21 Mar 2007, Reinhard Kleeberg wrote: Dear Leandro Bravo, some comments below: Leandro Bravo schrieb: In the refinement of chlorite minerals with well defined disordering (layers shifting by exactly b/3 along the three pseudohexagonal Y axis), you separate the peaks into k = 3.n (relative sharp, less intensive peak) and k #61625; 3.n (broadened or disappeared reflections). How did you determined this value k = 3.n and n = 0,1,2,3..., right? The occurence of stacking faults along the pseudohexagonal Y axes causes broadening of all reflections hkl with k unequal 3n (for example 110, 020, 111..) whereas the reflections with k equal 3n remain unaffected (001, 131, 060, 331...). This is clear from geometric conditions, and can be seen in single crystal XRD (oscillation photographs, Weissenberg photographs) as well in selected area electron diffraction patterns. The fact is known for a long time, and published and discussed in standard textbooks, for example *Brindley, G.W., Brown, G.: Crystal Structures of Clay Minerals and their X-ray Identification. Mineralogical Society, London, 1980.* First, the chlorite refinement. In the first refinement of chlorite you used no disordering models and used ´´cell parameters`` and ´´occupation of octahedra``. So you refined the lattice parameters and the occupancy of all atoms? Yes, the lattice parameters. Only the occupation/substitution of atoms with significant difference in scattering power can be refined in
RE: Problems using TOPAS R (Rietveld refinement)
Clay people I think the single crystal analysis of clays is interesting. I have not read the literature but in determining the intensities is overlap of the dots considered as I would have expected the dots to be very much smeared (5 to 10 degrees 2Th in my experience). If yes the fitting in two dimension would be better. Thus the question to ask is how accurate can QPA be for clays if the intensities can be accurately obtained; is this an open question or is the book closed on this. If as Reinhard Kleeberg mentioned that some directions are unaffected then it would seem plausible that something can be gained especially if one of those models work. Also, TOPAS simply offers a means of describing the peak shapes using a hkl dependent spherical harmonics. From my experiences it seems to work. Like Lubomir Smrcok remarked getting the intensities is critical. Another important point, again as Lubomir Smrcok mentioned, is preferred orientation. If there's very strong preferred orientation then the peak shapes will be affected due to axial divergence as well; it best to remove preferred orientation. Cheers Alan -Original Message- From: Reinhard Kleeberg [mailto:[EMAIL PROTECTED] Sent: Wednesday, 21 March 2007 7:48 PM To: rietveld_l@ill.fr Subject: Re: Problems using TOPAS R (Rietveld refinement) Dear colleagues, sorry, my mail should go directly to Leandro, but I used this damned reply buttom... My answer was related to Leandro's questions regarding these line broadening models. I realised that Leandro is going on to apply a Rietveld program for phase quantification, including kaolinite and later other clay minerals. I only tried to express my personal experience, that any inadequate profile description of a clay mineral will surely cause wrong QPA results, nothing else. This is a practical issue, and it is only partially related to structure refinement. Lubomir Smrcok is definitely right that other things like PO are frequently biasing a QPA result, but for the most of these problems working solutions do exist. But I disagree that anisotropic line broadening is a noble problem. In clay mineral mixtures, it is essentially to fit the profiles of the single phases as best as one can, to get any reasonable QPA result in a +-5 wt% interval. On the other hand, for the QPA purpose it is not so much important to find any sophisticated description of the microstructure of a phase. But the model should be flexible enough to cover the variablility of the profiles in a given system, and, on the other hand, stabil enough (not over-parametrised) to work in mixtures. The balancing out of these two issues could be the matter of an endless debate. And here I agree again, a better, more stable minimisation algorithm can help to keep a maximum of flexibility of the models. Best regards Reinhard Kleeberg Lubomir Smrcok schrieb: Gentlemen, I've been listening for a week or so and I am really wondering what do you want to get ... Actually you are setting up a refinement, whose results will be, at least, inaccurate. I am always surprised by attempts to refine crystal structure of a disordered sheet silicate from powders, especially when it is known it hardly works with single crystal data. Yes, there are several models of disorder, but who has ever proved they are really good ? I do not mean here a graphical comparison of powder patterns with a calculated trace, but a comparison of structure factors or integrated intensities. (Which ones are to be selected is well described in the works of my colleague, S.Durovic and his co-workers.) As far as powders are concerned, all sheet silicates suffer from prefered orientation along 001. Until you have a pattern taken in a capillary or in transmission mode, this effect will be dominating and you can forget such noble problems like anisotropic broadening. Last but not least : quantitative phase analysis by Rietveld is (when only scale factors are on) nothing else but multiple linear regression. There is a huge volume of literature on the topic, especially which variables must, which should and which could be a part of your model. I really wonder why the authors of program do not add one option called QUAN, which could, upon convergence of highly sophisticated non-linear L-S, fix all parameters but scale factors and run standard tests or factor analysis. One more diagonalization is not very time consuming, is it ? To avoid numerical problems, I'd use SVD. This idea is free and if it helps people reporting 0.1% MgO (SiO2) in a mixture of 10 phases to think a little of the numbers they are getting, I would only be happy :-) Lubo P.S. Hereby I declare I have never used Topas and I am thus not familiar with all its advantages or disadvantages compared to other codes. On Wed, 21 Mar 2007, Reinhard Kleeberg wrote: Dear Leandro Bravo, some comments below: Leandro Bravo schrieb: In the refinement of chlorite minerals with well defined
RE: Re: Problems using TOPAS R (Rietveld refinement)
I have to disagree with that; at least on a practical front with lab XRD. I have done measurements myself with samples containing large portlandite plates (granted, not a silicate but lovely-looking plates in a SEM) for quantitative analysis. The whole point of the work was to see if capillary measurements would be worth it if the normal sample prep techniques would change the nature of the sample. The reflection measurements had awful orientation, but the portlandite spherical harmonics PO coefficients for the capillary data gave a texture index of 1, i.e. an ideal powder. The diffraction optics and detector were identical for reflection and transmission. The capillary data actually gave better quantitative results than the reflection. A reason might be that if the grains are large enough to orientate significantly they might be big enough to cause microabsorption effects that are best avoided (the Brindley correction assumes spherical particles so plates are a bit of a headache). It's just a thought, but the orientation in neutron and X-ray data might differ due to the difference in sample container size and orientation. Neutron cans are often mounted vertically and are pretty big so there won't be much advantage over reflection as the material settles. Lab capillaries are usually mounted horizontally and the capillary diameter is often quite small in relation to the grain size (compared to neutron sample cans). All bets are off for wollastonite though! I will shut up at this point as I trying to avoid doing clay analysis! Pam -Original Message- From: David L. Bish [mailto:[EMAIL PROTECTED] Sent: March 21, 2007 9:11 AM To: rietveld_l@ill.fr Subject: Re: Problems using TOPAS R (Rietveld refinement) One often hears of attempts to eliminate preferred orientation in diffraction patterns of layer silicates using transmission measurements. Keep in mind that if PO is a problem in reflection geometry, it will also affect transmission measurements, in a manner potentially similar to flat-plate samples. We did some TOF neutron measurements on phyllosilicates a few years ago with what amounts to capillary sample holders, and preferred orientation was a significant problem. If a material orients, it will do so in all mounts unless steps are taken to minimize it. Dave At 07:50 AM 3/21/2007 +0100, you wrote: Gentlemen, I've been listening for a week or so and I am really wondering what do you want to get ... Actually you are setting up a refinement, whose results will be, at least, inaccurate. I am always surprised by attempts to refine crystal structure of a disordered sheet silicate from powders, especially when it is known it hardly works with single crystal data. Yes, there are several models of disorder, but who has ever proved they are really good ? I do not mean here a graphical comparison of powder patterns with a calculated trace, but a comparison of structure factors or integrated intensities. (Which ones are to be selected is well described in the works of my colleague, S.Durovic and his co-workers.) As far as powders are concerned, all sheet silicates suffer from prefered orientation along 001. Until you have a pattern taken in a capillary or in transmission mode, this effect will be dominating and you can forget such noble problems like anisotropic broadening. Last but not least : quantitative phase analysis by Rietveld is (when only scale factors are on) nothing else but multiple linear regression. There is a huge volume of literature on the topic, especially which variables must, which should and which could be a part of your model. I really wonder why the authors of program do not add one option called QUAN, which could, upon convergence of highly sophisticated non-linear L-S, fix all parameters but scale factors and run standard tests or factor analysis. One more diagonalization is not very time consuming, is it ? To avoid numerical problems, I'd use SVD. This idea is free and if it helps people reporting 0.1% MgO (SiO2) in a mixture of 10 phases to think a little of the numbers they are getting, I would only be happy :-) Lubo P.S. Hereby I declare I have never used Topas and I am thus not familiar with all its advantages or disadvantages compared to other codes
RE: Problems using TOPAS R (Rietveld refinement)
Lubo SVD as you mentioned does avoid numerical problems as does other methods such as the conjugate gradient method. SVD minimizes on the residuals |A x - b| after solving the matrix equation A x = b. I would like to point out however that errors obtained from the covariance matrix are an approximation. The idea of fixing parameters as in SVD when a singular value is encountered is also a little arbitrary as it requires the user setting a lower limit. The A matrix is formed at a point in parameter space; when there are strong correlations (as SVD would report) then that point in space changes from one refinement to another after modifying the parameter slightly. If derivatives are numerically calculated, as is the case for convolution parameters, then the A matrix becomes a function of how the derivative are calculated; forward difference approximation for example gives different derivatives than both forward and backwards if the step size in the derivative is appreciable. For most convolutions and numerical derivatives in general then it needs to be appreciable for good convergence. Rietveld people may want to look at the re-sampling technique known as the bootstrap method of error determination. It gives similar errors to the covariance matrix when the correlations are weak; the maths journals are full of details. It requires some more computing time but it actually gives the distribution. And yes TOPAS has the bootstrap method; other code writers may wish to investigate it. Cheers Alan -Original Message- From: Lubomir Smrcok [mailto:[EMAIL PROTECTED] Sent: Wednesday, 21 March 2007 5:50 PM To: rietveld_l@ill.fr Subject: Re: Problems using TOPAS R (Rietveld refinement) Gentlemen, I've been listening for a week or so and I am really wondering what do you want to get ... Actually you are setting up a refinement, whose results will be, at least, inaccurate. I am always surprised by attempts to refine crystal structure of a disordered sheet silicate from powders, especially when it is known it hardly works with single crystal data. Yes, there are several models of disorder, but who has ever proved they are really good ? I do not mean here a graphical comparison of powder patterns with a calculated trace, but a comparison of structure factors or integrated intensities. (Which ones are to be selected is well described in the works of my colleague, S.Durovic and his co-workers.) As far as powders are concerned, all sheet silicates suffer from prefered orientation along 001. Until you have a pattern taken in a capillary or in transmission mode, this effect will be dominating and you can forget such noble problems like anisotropic broadening. Last but not least : quantitative phase analysis by Rietveld is (when only scale factors are on) nothing else but multiple linear regression. There is a huge volume of literature on the topic, especially which variables must, which should and which could be a part of your model. I really wonder why the authors of program do not add one option called QUAN, which could, upon convergence of highly sophisticated non-linear L-S, fix all parameters but scale factors and run standard tests or factor analysis. One more diagonalization is not very time consuming, is it ? To avoid numerical problems, I'd use SVD. This idea is free and if it helps people reporting 0.1% MgO (SiO2) in a mixture of 10 phases to think a little of the numbers they are getting, I would only be happy :-) Lubo P.S. Hereby I declare I have never used Topas and I am thus not familiar with all its advantages or disadvantages compared to other codes. On Wed, 21 Mar 2007, Reinhard Kleeberg wrote: Dear Leandro Bravo, some comments below: Leandro Bravo schrieb: In the refinement of chlorite minerals with well defined disordering (layers shifting by exactly b/3 along the three pseudohexagonal Y axis), you separate the peaks into k = 3.n (relative sharp, less intensive peak) and k #61625; 3.n (broadened or disappeared reflections). How did you determined this value k = 3.n and n = 0,1,2,3..., right? The occurence of stacking faults along the pseudohexagonal Y axes causes broadening of all reflections hkl with k unequal 3n (for example 110, 020, 111..) whereas the reflections with k equal 3n remain unaffected (001, 131, 060, 331...). This is clear from geometric conditions, and can be seen in single crystal XRD (oscillation photographs, Weissenberg photographs) as well in selected area electron diffraction patterns. The fact is known for a long time, and published and discussed in standard textbooks, for example *Brindley, G.W., Brown, G.: Crystal Structures of Clay Minerals and their X-ray Identification. Mineralogical Society, London, 1980.* First, the chlorite refinement. In the first refinement of chlorite you used no disordering models and used ´´cell parameters`` and ´´occupation of octahedra``. So you refined the lattice parameters
Re: Problems using TOPAS R (Rietveld refinement)
My limited experience with X-ray capillary measurements of ultra fine clay minerals suggests that you could have significant preferred orientation along the b* axis. It is actually a good way of determining aspect ratios in phyllosilicates. Dipo Omotoso From: Whitfield, Pamela [mailto:[EMAIL PROTECTED] Sent: Wednesday, March 21, 2007 7:51 AM To: rietveld_l@ill.fr Subject: RE: Re: Problems using TOPAS R (Rietveld refinement) I have to disagree with that; at least on a practical front with lab XRD. I have done measurements myself with samples containing large portlandite plates (granted, not a silicate but lovely-looking plates in a SEM) for quantitative analysis. The whole point of the work was to see if capillary measurements would be worth it if the normal sample prep techniques would change the nature of the sample. The reflection measurements had awful orientation, but the portlandite spherical harmonics PO coefficients for the capillary data gave a texture index of 1, i.e. an ideal powder. The diffraction optics and detector were identical for reflection and transmission. The capillary data actually gave better quantitative results than the reflection. A reason might be that if the grains are large enough to orientate significantly they might be big enough to cause microabsorption effects that are best avoided (the Brindley correction assumes spherical particles so plates are a bit of a headache). It's just a thought, but the orientation in neutron and X-ray data might differ due to the difference in sample container size and orientation. Neutron cans are often mounted vertically and are pretty big so there won't be much advantage over reflection as the material settles. Lab capillaries are usually mounted horizontally and the capillary diameter is often quite small in relation to the grain size (compared to neutron sample cans). All bets are off for wollastonite though! I will shut up at this point as I trying to avoid doing clay analysis! Pam -Original Message- From: David L. Bish [mailto:[EMAIL PROTECTED] Sent: March 21, 2007 9:11 AM To: rietveld_l@ill.fr Subject: Re: Problems using TOPAS R (Rietveld refinement) One often hears of attempts to eliminate preferred orientation in diffraction patterns of layer silicates using transmission measurements. Keep in mind that if PO is a problem in reflection geometry, it will also affect transmission measurements, in a manner potentially similar to flat-plate samples. We did some TOF neutron measurements on phyllosilicates a few years ago with what amounts to capillary sample holders, and preferred orientation was a significant problem. If a material orients, it will do so in all mounts unless steps are taken to minimize it. Dave At 07:50 AM 3/21/2007 +0100, you wrote: Gentlemen, I've been listening for a week or so and I am really wondering what do you want to get ... Actually you are setting up a refinement, whose results will be, at least, inaccurate. I am always surprised by attempts to refine crystal structure of a disordered sheet silicate from powders, especially when it is known it hardly works with single crystal data. Yes, there are several models of disorder, but who has ever proved they are really good ? I do not mean here a graphical comparison of powder patterns with a calculated trace, but a comparison of structure factors or integrated intensities. (Which ones are to be selected is well described in the works of my colleague, S.Durovic and his co-workers.) As far as powders are concerned, all sheet silicates suffer from prefered orientation along 001. Until you have a pattern taken in a capillary or in transmission mode, this effect will be dominating and you can forget such noble problems like anisotropic broadening. Last but not least : quantitative phase analysis by Rietveld is (when only scale factors are on) nothing else but multiple linear regression. There is a huge volume of literature on the topic, especially which variables must, which should and which could be a part of your model. I really wonder why the authors of program do not add one option called QUAN, which could, upon convergence of highly sophisticated non-linear L-S, fix all parameters but scale factors and run standard tests or factor analysis. One more diagonalization is not very time consuming, is it ? To avoid numerical problems, I'd use SVD. This idea is free and if it helps people reporting 0.1% MgO (SiO2) in a mixture of 10 phases to think a little of the numbers they are getting, I would only be happy :-) Lubo
RE: Re: Problems using TOPAS R (Rietveld refinement)
Makes sense with ultra-fines. My portlandite grains were 5 microns upwards. I'm working to avoid ultra-fines even harder than the bigger stuff :-) Pam From: Omotoso, Oladipo [mailto:[EMAIL PROTECTED] Sent: Wed 21/03/2007 10:47 AM To: rietveld_l@ill.fr Subject: Re: Problems using TOPAS R (Rietveld refinement) My limited experience with X-ray capillary measurements of ultra fine clay minerals suggests that you could have significant preferred orientation along the b* axis. It is actually a good way of determining aspect ratios in phyllosilicates. Dipo Omotoso From: Whitfield, Pamela [mailto:[EMAIL PROTECTED] Sent: Wednesday, March 21, 2007 7:51 AM To: rietveld_l@ill.fr Subject: RE: Re: Problems using TOPAS R (Rietveld refinement) I have to disagree with that; at least on a practical front with lab XRD. I have done measurements myself with samples containing large portlandite plates (granted, not a silicate but lovely-looking plates in a SEM) for quantitative analysis. The whole point of the work was to see if capillary measurements would be worth it if the normal sample prep techniques would change the nature of the sample. The reflection measurements had awful orientation, but the portlandite spherical harmonics PO coefficients for the capillary data gave a texture index of 1, i.e. an ideal powder. The diffraction optics and detector were identical for reflection and transmission. The capillary data actually gave better quantitative results than the reflection. A reason might be that if the grains are large enough to orientate significantly they might be big enough to cause microabsorption effects that are best avoided (the Brindley correction assumes spherical particles so plates are a bit of a headache). It's just a thought, but the orientation in neutron and X-ray data might differ due to the difference in sample container size and orientation. Neutron cans are often mounted vertically and are pretty big so there won't be much advantage over reflection as the material settles. Lab capillaries are usually mounted horizontally and the capillary diameter is often quite small in relation to the grain size (compared to neutron sample cans). All bets are off for wollastonite though! I will shut up at this point as I trying to avoid doing clay analysis! Pam -Original Message- From: David L. Bish [mailto:[EMAIL PROTECTED] Sent: March 21, 2007 9:11 AM To: rietveld_l@ill.fr Subject: Re: Problems using TOPAS R (Rietveld refinement) One often hears of attempts to eliminate preferred orientation in diffraction patterns of layer silicates using transmission measurements. Keep in mind that if PO is a problem in reflection geometry, it will also affect transmission measurements, in a manner potentially similar to flat-plate samples. We did some TOF neutron measurements on phyllosilicates a few years ago with what amounts to capillary sample holders, and preferred orientation was a significant problem. If a material orients, it will do so in all mounts unless steps are taken to minimize it. Dave At 07:50 AM 3/21/2007 +0100, you wrote: Gentlemen, I've been listening for a week or so and I am really wondering what do you want to get ... Actually you are setting up a refinement, whose results will be, at least, inaccurate. I am always surprised by attempts to refine crystal structure of a disordered sheet silicate from powders, especially when it is known it hardly works with single crystal data. Yes, there are several models of disorder, but who has ever proved they are really good ? I do not mean here a graphical comparison of powder patterns with a calculated trace, but a comparison of structure factors or integrated intensities. (Which ones are to be selected is well described in the works of my colleague, S.Durovic and his co-workers.) As far as powders are concerned, all sheet silicates suffer from prefered orientation along 001. Until you have a pattern taken in a capillary or in transmission mode, this effect will be dominating and you can forget such noble problems like anisotropic broadening. Last but not least : quantitative phase analysis by Rietveld is (when only scale factors are on) nothing else but multiple linear regression. There is a huge volume of literature on the topic, especially which variables must, which should and which could be a part of your model. I really wonder why the authors of program do not add one option called QUAN, which could, upon convergence of highly sophisticated non-linear L-S, fix all parameters but scale factors and run standard tests
Re: Problems using TOPAS R (Rietveld refinement)
Dear Leandro Bravo, some comments below: Leandro Bravo schrieb: In the refinement of chlorite minerals with well defined disordering (layers shifting by exactly b/3 along the three pseudohexagonal Y axis), you separate the peaks into k = 3.n (relative sharp, less intensive peak) and k #61625; 3.n (broadened or disappeared reflections). How did you determined this value k = 3.n and n = 0,1,2,3..., right? The occurence of stacking faults along the pseudohexagonal Y axes causes broadening of all reflections hkl with k unequal 3n (for example 110, 020, 111..) whereas the reflections with k equal 3n remain unaffected (001, 131, 060, 331...). This is clear from geometric conditions, and can be seen in single crystal XRD (oscillation photographs, Weissenberg photographs) as well in selected area electron diffraction patterns. The fact is known for a long time, and published and discussed in standard textbooks, for example *Brindley, G.W., Brown, G.: Crystal Structures of Clay Minerals and their X-ray Identification. Mineralogical Society, London, 1980.* First, the chlorite refinement. In the first refinement of chlorite you used no disordering models and used ´´cell parameters`` and ´´occupation of octahedra``. So you refined the lattice parameters and the occupancy of all atoms? Yes, the lattice parameters. Only the occupation/substitution of atoms with significant difference in scattering power can be refined in powder diffraction. In case of chlorites, the substitution Fe-Mg at the 4 octahedral positions can be refined. In the second refinement, you use na anisotropic line broadening ´´in the traditional way``. So you used a simple ellipsoidal model and/or spherical harmonics? Simple ellipsoidal model, assuming very thiny platy crystals. But it was clear that this model must fail, see above the known fact of disorder in layer stacking. And from microscopy it is clear that the crystals are much too large to produce significant line broadening from size effects. You can see this for a lot of clay minerals: If the ellipsoidal crystallite shape model would be ok, the 00l reflections would have the broadest lines, and the 110, 020 and so on should be the sharpest ones. But this is not true in practice, mostly the hkl are terribly broadenend and smeared, but the 00l are still sharp. The last refinement, describing a real structure. You used for the reflections k #61625; 3.n (broadened peaks) a ´´rod-like intensity distribution``, with the rod being projected by the cosine of the direction on the diffractogram. You used also the lenghts of the rods as a parameter, so as the dimension of the rods for 0k0 with k #61625; 3.n. I would like to know how did you ´´project`` these rods and use them in the refinement. For the k = 3.n reflections, you used an anisotropic broadening model (aniso crystallyte size) and and isotropic broadening model (microstrain broadening). But you said that crystallite size is an isotropic line broadening in my kaolinite refinement and I should not use it. So I use or not the cry size? Yes, we used an additional ellipsoidal broadening in order to describe any potential thinning of the crystals. But this broadening model was not significant because the broadening was dominated by the stacking faults. A microstrain makes sense because of natural chlorits are sometimes zoned in their chemical composition and a distribution of the lattice constants may occur. In one of your mails you mentioned crysize gave reasonable numbers with low error, and from that I assumed you looked only on the errors of the isotropic crysize as defined in Topas. You must know what model you did apply. But it is clear that any crysize model is inadequate to describe the line broadening of kaolinite. Now the kaolinite refinement. In the first refinement was used fixed atomic positions and a conventional anisotropic peak broadening. This conventional anisotropic peak broadening would be the simple ellipsoidal model and/or spherical harmonics?! Only ellipsoidal model, assuming a platy crystal shape, see above. Only for comparision. After that you use the introduced model of disorfering. Is this model the same of the chlorite (rods for k #61625; 3.n and microstrain broadening and anisotropic crystallite size? Not exactly the same like in chlorite, because the disorder in kaolinite is much more complicated like in chlorites. See also the textbook cited above, and extensive works of Plancon and Tchoubar. Thus, most of the natural kaolinites show stacking faults along b/3 as well as along a, and additional random faults. Thus, more broadening parameters had to be defined, and this is not completely perfect until now. See the presentation I sent you last week. Best regards Reinhard Kleeberg begin:vcard fn:Reinhard Kleeberg n:Kleeberg;Reinhard org;quoted-printable:TU Bergakademie Freiberg;Institut f=C3=BCr Mineralogie
Re: Problems using TOPAS R (Rietveld refinement)
Gentlemen, I've been listening for a week or so and I am really wondering what do you want to get ... Actually you are setting up a refinement, whose results will be, at least, inaccurate. I am always surprised by attempts to refine crystal structure of a disordered sheet silicate from powders, especially when it is known it hardly works with single crystal data. Yes, there are several models of disorder, but who has ever proved they are really good ? I do not mean here a graphical comparison of powder patterns with a calculated trace, but a comparison of structure factors or integrated intensities. (Which ones are to be selected is well described in the works of my colleague, S.Durovic and his co-workers.) As far as powders are concerned, all sheet silicates suffer from prefered orientation along 001. Until you have a pattern taken in a capillary or in transmission mode, this effect will be dominating and you can forget such noble problems like anisotropic broadening. Last but not least : quantitative phase analysis by Rietveld is (when only scale factors are on) nothing else but multiple linear regression. There is a huge volume of literature on the topic, especially which variables must, which should and which could be a part of your model. I really wonder why the authors of program do not add one option called QUAN, which could, upon convergence of highly sophisticated non-linear L-S, fix all parameters but scale factors and run standard tests or factor analysis. One more diagonalization is not very time consuming, is it ? To avoid numerical problems, I'd use SVD. This idea is free and if it helps people reporting 0.1% MgO (SiO2) in a mixture of 10 phases to think a little of the numbers they are getting, I would only be happy :-) Lubo P.S. Hereby I declare I have never used Topas and I am thus not familiar with all its advantages or disadvantages compared to other codes. On Wed, 21 Mar 2007, Reinhard Kleeberg wrote: Dear Leandro Bravo, some comments below: Leandro Bravo schrieb: In the refinement of chlorite minerals with well defined disordering (layers shifting by exactly b/3 along the three pseudohexagonal Y axis), you separate the peaks into k = 3.n (relative sharp, less intensive peak) and k #61625; 3.n (broadened or disappeared reflections). How did you determined this value k = 3.n and n = 0,1,2,3..., right? The occurence of stacking faults along the pseudohexagonal Y axes causes broadening of all reflections hkl with k unequal 3n (for example 110, 020, 111..) whereas the reflections with k equal 3n remain unaffected (001, 131, 060, 331...). This is clear from geometric conditions, and can be seen in single crystal XRD (oscillation photographs, Weissenberg photographs) as well in selected area electron diffraction patterns. The fact is known for a long time, and published and discussed in standard textbooks, for example *Brindley, G.W., Brown, G.: Crystal Structures of Clay Minerals and their X-ray Identification. Mineralogical Society, London, 1980.* First, the chlorite refinement. In the first refinement of chlorite you used no disordering models and used ´´cell parameters`` and ´´occupation of octahedra``. So you refined the lattice parameters and the occupancy of all atoms? Yes, the lattice parameters. Only the occupation/substitution of atoms with significant difference in scattering power can be refined in powder diffraction. In case of chlorites, the substitution Fe-Mg at the 4 octahedral positions can be refined. In the second refinement, you use na anisotropic line broadening ´´in the traditional way``. So you used a simple ellipsoidal model and/or spherical harmonics? Simple ellipsoidal model, assuming very thiny platy crystals. But it was clear that this model must fail, see above the known fact of disorder in layer stacking. And from microscopy it is clear that the crystals are much too large to produce significant line broadening from size effects. You can see this for a lot of clay minerals: If the ellipsoidal crystallite shape model would be ok, the 00l reflections would have the broadest lines, and the 110, 020 and so on should be the sharpest ones. But this is not true in practice, mostly the hkl are terribly broadenend and smeared, but the 00l are still sharp. The last refinement, describing a real structure. You used for the reflections k #61625; 3.n (broadened peaks) a ´´rod-like intensity distribution``, with the rod being projected by the cosine of the direction on the diffractogram. You used also the lenghts of the rods as a parameter, so as the dimension of the rods for 0k0 with k #61625; 3.n. I would like to know how did you ´´project`` these rods and use them in the refinement. For the k = 3.n reflections, you used an anisotropic broadening model (aniso crystallyte size) and and isotropic broadening model (microstrain broadening). But you said that crystallite size is an
Re: Problems using TOPAS R (Rietveld refinement)
Mr. Kleeberg, Read the paper that you send to me, ´´RIETVELD ANALYSIS OF DISORDERED LAYER SILICATES``, and I have some questions about it. In the refinement of chlorite minerals with well defined disordering (layers shifting by exactly b/3 along the three pseudohexagonal Y axis), you separate the peaks into k = 3.n (relative sharp, less intensive peak) and k #61625; 3.n (broadened or disappeared reflections). How did you determined this value k = 3.n and n = 0,1,2,3..., right? First, the chlorite refinement. In the first refinement of chlorite you used no disordering models and used ´´cell parameters`` and ´´occupation of octahedra``. So you refined the lattice parameters and the occupancy of all atoms? In the second refinement, you use na anisotropic line broadening ´´in the traditional way``. So you used a simple ellipsoidal model and/or spherical harmonics? The last refinement, describing a real structure. You used for the reflections k #61625; 3.n (broadened peaks) a ´´rod-like intensity distribution``, with the rod being projected by the cosine of the direction on the diffractogram. You used also the lenghts of the rods as a parameter, so as the dimension of the rods for 0k0 with k #61625; 3.n. I would like to know how did you ´´project`` these rods and use them in the refinement. For the k = 3.n reflections, you used an anisotropic broadening model (aniso crystallyte size) and and isotropic broadening model (microstrain broadening). But you said that crystallite size is an isotropic line broadening in my kaolinite refinement and I should not use it. So I use or not the cry size? Now the kaolinite refinement. In the first refinement was used fixed atomic positions and a conventional anisotropic peak broadening. This conventional anisotropic peak broadening would be the simple ellipsoidal model and/or spherical harmonics?! After that you use the introduced model of disorfering. Is this model the same of the chlorite (rods for k #61625; 3.n and microstrain broadening and anisotropic crystallite size? Thank you very much. Regards, Leandro _ Seja um dos primeiros a testar o novo Windows Live Mail Beta- grátis. Acesse http://www.ideas.live.com/programpage.aspx?versionId=5d21c51a-b161-4314-9b0e-4911fb2b2e6d
RE: Problems using TOPAS R (Rietveld refinement)
Leandro I would suggest that you use an internal standard to get a handle on your sources of uncertainty. I would suggest Baikalox corundum CR1 - while I don't know its non-diffracting content, it is probably low. I would suggest that you use the technique outlined in Pratapa et. al. Powder Diffraction 13(3) 166-170, and measure the diffractometer constant, then look at the relationship between s (scale factor) and phase concentration. If you want more details, contact me directly. regards, Tony Raftery At 02:59 AM 18/03/2007, you wrote: My purpose is really quantification. And I´m getting erros of about 5% in each phase (in the quantification part). I´m using samples that I made by mixing calcite, dolomite and kaolinite (18, 55 and 26 or near it). It is valid to mix the sample with a known standard if you are analysing a unknown sample (quantitatively). But I´d like to know more about this method to determine the amount of amorphous content using a standard. I´m using now a beq. of 20 in all atoms, and they are fix. Could you discriminate each variable of the equation that you send to me?! prm b 0 scale_pks = Exp(-b /D_spacing^2) Does it give reasonable values!? Regards, Leandro From: AlanCoelho [EMAIL PROTECTED] Reply-To: rietveld_l@ill.fr To: rietveld_l@ill.fr Subject: RE: Problems using TOPAS R (Rietveld refinement) Date: Fri, 16 Mar 2007 09:56:33 +1100 Leandro Not sure what the purpose of your refinement is but if it's quantification then your results would probably be in error to a large extent. The references given by Alan Hewat and Lubo Smrcok is probably a good starting point. Data quality and model errors typically mean that atomic positions should not be refined for clays; especially for Kaolinite. Also, use a common beq value for all sites or take them from literature. A gobal beq could then be superimposed using something like prm b 0 scale_pks = Exp(-b / D_spacing^2);. For quantification try spiking the sample with a standard to determine the amorphous content. It is possible to get the peak shapes without changing peak intensities; if you need assistance then contact me off the list. Cheers Alan -Original Message- From: Leandro Bravo [ mailto:[EMAIL PROTECTED]] Sent: Friday, 16 March 2007 9:15 AM To: rietveld_l@ill.fr Subject: Re: Problems using TOPAS R (Rietveld refinement) Ok, I´m starting to have sucess in the kaolinite refinement, the quantification is giving me reasonable values. I´m refining the thermal factors, all the atoms positions in the kaolinite, the lattice parameters and the cystallite size. Lattice parameters and crystallite size are giving me very good numbers, with very low errors (about 0,09). In the thermal factors, I realized that alll of them tend to 20, so after all refinements I put them to 20, and refine all over again. I don´t care that much for atoms positions, I´m only using them because refining only lattice, thermal and cry size wasn´t enough to make a good calculated pattern to compare with the measured one. In the calcite and dolomite I refine: lattice parameters, cry size and thermal factors. And use on both a preferred orientation correction (spherical harmonics 4 th order). The RWP is about 16. I´d to hear some opinions about this strategy of refinement, if you think that I can spare some refining cycles or even fix some values to reduce erros in the refinement. _ Descubra como mandar Torpedos SMS do seu Messenger para o celular dos seus amigos. http://mobile.msn.com/ _ Descubra como mandar Torpedos do Messenger para o celular! http://mobile.msn.com/ Tony Raftery Senior Technologist AEMF XAF, R Block Faculty of Science, GP Queensland University of Technology c/- AEMF, R Block Gardens Point Road, Brisbane, 4000 (or) GPO Box 2434 Brisbane 4001 AUSTRALIA ph+61 7 3138 2271 fax +61 7 3138 5100 email[EMAIL PROTECTED] http://www.xaf.qut.edu.au/ please note new phone number from 16/10/2006
RE: Problems using TOPAS R (Rietveld refinement)
My purpose is really quantification. And I´m getting erros of about 5% in each phase (in the quantification part). I´m using samples that I made by mixing calcite, dolomite and kaolinite (18, 55 and 26 or near it). It is valid to mix the sample with a known standard if you are analysing a unknown sample (quantitatively). But I´d like to know more about this method to determine the amount of amorphous content using a standard. I´m using now a beq. of 20 in all atoms, and they are fix. Could you discriminate each variable of the equation that you send to me?! prm b 0 scale_pks = Exp(-b /D_spacing^2) Does it give reasonable values!? Regards, Leandro From: AlanCoelho [EMAIL PROTECTED] Reply-To: rietveld_l@ill.fr To: rietveld_l@ill.fr Subject: RE: Problems using TOPAS R (Rietveld refinement) Date: Fri, 16 Mar 2007 09:56:33 +1100 Leandro Not sure what the purpose of your refinement is but if it's quantification then your results would probably be in error to a large extent. The references given by Alan Hewat and Lubo Smrcok is probably a good starting point. Data quality and model errors typically mean that atomic positions should not be refined for clays; especially for Kaolinite. Also, use a common beq value for all sites or take them from literature. A gobal beq could then be superimposed using something like prm b 0 scale_pks = Exp(-b / D_spacing^2);. For quantification try spiking the sample with a standard to determine the amorphous content. It is possible to get the peak shapes without changing peak intensities; if you need assistance then contact me off the list. Cheers Alan -Original Message- From: Leandro Bravo [mailto:[EMAIL PROTECTED] Sent: Friday, 16 March 2007 9:15 AM To: rietveld_l@ill.fr Subject: Re: Problems using TOPAS R (Rietveld refinement) Ok, I´m starting to have sucess in the kaolinite refinement, the quantification is giving me reasonable values. I´m refining the thermal factors, all the atoms positions in the kaolinite, the lattice parameters and the cystallite size. Lattice parameters and crystallite size are giving me very good numbers, with very low errors (about 0,09). In the thermal factors, I realized that alll of them tend to 20, so after all refinements I put them to 20, and refine all over again. I don´t care that much for atoms positions, I´m only using them because refining only lattice, thermal and cry size wasn´t enough to make a good calculated pattern to compare with the measured one. In the calcite and dolomite I refine: lattice parameters, cry size and thermal factors. And use on both a preferred orientation correction (spherical harmonics 4 th order). The RWP is about 16. I´d to hear some opinions about this strategy of refinement, if you think that I can spare some refining cycles or even fix some values to reduce erros in the refinement. _ Descubra como mandar Torpedos SMS do seu Messenger para o celular dos seus amigos. http://mobile.msn.com/ _ Descubra como mandar Torpedos do Messenger para o celular! http://mobile.msn.com/
Re: Problems using TOPAS R (Rietveld refinement)
Dear Leandro, some comments: Leandro Bravo schrieb: I know that refining the atoms positions is ´´too much´´, exagerated. But is the only way I can make the calculated DRX pattern fit with the measured one. There must a problem in the instrument details since I´m using Fundamental Parameters (FP) for peak shape, the values I put in the instrument description play a major role in FP, am I right? No. The misfit in your Rietveld refinement of kaolinite you get by using published atomic coordinates and temperature factors does definitely not arise from wrong published structure date and probably not significantly from any error in your instrumental parameters. Kaolinite diffraction pattern can not be described by simple isotropic line broadening as you tried by the crystallite size parameter. The different types and amounts of stacking faults in kaolinite are the reason for different kinds of smearing of the reciprocal lattice points. It makes no sense to refine atomic coordinates and temperature factors in an ideal cell to get a better Rwp of a disordered structure: One will of course get a better fit, but this is reached by variations of intensity by meaningless atomic positions. I made a new scan, of the same sample, with range from 10° to 80°, step size 0,02 and count time 4 seconds. The old one was from 5° to 120,° maybe it is prejudicing the background refining. Tomorrow I´m gonna to scrap this old pattern and work with the new one. I´m having a good response refining the calcite and teh dolomite in the sample only refining lattice parameters, cry size and beq. I think that refining this is what we can call a ´´normal refining method``. Now the kaolinite... The major problem is that I have a sample from a laterite with hydroxyapatite, calcite, dolomite, vermiculite and other phases. The vermiculite is very alterated and in the DRX pattern we can confuse it with other ``layered silicates``, it will be a huge problem. But I will only put my hands on these samples after finishing with the kaolinite. Altered vermiculite is probably a mixed-layered clay mineral? If yes, I'm in doubt that you can quantify this by the Rietveld method. See: Omotoso, O., McCarty, D.K., Hillier, S., Kleeberg, R. (2006) Some successful approaches to quantitative mineral analysis as revealed by the 3^rd Reynolds Cup contest. Clays and Clay Minerals, 54 (6), 751-763. One question, these ´´models`` and ´´trials`` that you talk about regarding the kaolinite is used in the CIF part of the refinement, am I right?! It´s not a part of the TOPAS itself. right? I think he CIF part you are referring is from the database you used (ICSD), right? These data refer to the ideal cell. One must introduce any models regarding line broadening or supercell coordinates into your structure model (*.str ?) what is used in your refinement. You will not find such models in a crystallographic database, specific formulations are necessary, depending on your disorder problem and on the capabilities of your Rietveld program. Best regards Reinhard Thank you, Leandro _ Chegou o Windows Live Spaces com rede social. Confira http://spaces.live.com/ begin:vcard fn:Reinhard Kleeberg n:Kleeberg;Reinhard org;quoted-printable:TU Bergakademie Freiberg;Institut f=C3=BCr Mineralogie adr:;;Brennhausgasse 14;Freiberg;Sachsen;D-09596;Germany email;internet:[EMAIL PROTECTED] title:Dr. tel;work:(+49) (0)3731 393244 tel;fax:(+49)(0)3731 393129 url:http://www.mineral.tu-freiberg.de/mineralogie/roelabor/ version:2.1 end:vcard
RE: Re: Problems using TOPAS R (Rietveld refinement)
Leandro, You probably should consult the references suggested by Alan Hewat and Reinhard Kleeberg before you read anything into your reasonable Rwp. Kaolinite is grossly over-parametized in your refinement strategy. If you are stuck with TOPAS, you may want to contact Arnt Kern (Bruker) about last year's TOPAS workshop. I recall that there was a paper on refinement strategies for disordered clays. Dipo Omotoso CANMET Energy Technology Centre - Devon Energy Technology and Programs Sector Natural Resources Canada #1 Oil Patch Drive, Devon, AB. Canada Groupe des techniques perfectionnées de séparation Centre de la technologie de l'énergie de CANMET - Devon Secteur de la technologie et des programmes de l'énergie Ressources naturelles Canada -Original Message- From: Leandro Bravo [mailto:[EMAIL PROTECTED] Sent: Thursday, March 15, 2007 4:15 PM To: rietveld_l@ill.fr Subject: Re: Problems using TOPAS R (Rietveld refinement) Ok, I´m starting to have sucess in the kaolinite refinement, the quantification is giving me reasonable values. I´m refining the thermal factors, all the atoms positions in the kaolinite, the lattice parameters and the cystallite size. Lattice parameters and crystallite size are giving me very good numbers, with very low errors (about 0,09). In the thermal factors, I realized that alll of them tend to 20, so after all refinements I put them to 20, and refine all over again. I don´t care that much for atoms positions, I´m only using them because refining only lattice, thermal and cry size wasn´t enough to make a good calculated pattern to compare with the measured one. In the calcite and dolomite I refine: lattice parameters, cry size and thermal factors. And use on both a preferred orientation correction (spherical harmonics 4 th order). The RWP is about 16. I´d to hear some opinions about this strategy of refinement, if you think that I can spare some refining cycles or even fix some values to reduce erros in the refinement. _ Descubra como mandar Torpedos SMS do seu Messenger para o celular dos seus amigos. http://mobile.msn.com/
RE: Problems using TOPAS R (Rietveld refinement)
Leandro Not sure what the purpose of your refinement is but if it's quantification then your results would probably be in error to a large extent. The references given by Alan Hewat and Lubo Smrcok is probably a good starting point. Data quality and model errors typically mean that atomic positions should not be refined for clays; especially for Kaolinite. Also, use a common beq value for all sites or take them from literature. A gobal beq could then be superimposed using something like prm b 0 scale_pks = Exp(-b / D_spacing^2);. For quantification try spiking the sample with a standard to determine the amorphous content. It is possible to get the peak shapes without changing peak intensities; if you need assistance then contact me off the list. Cheers Alan -Original Message- From: Leandro Bravo [mailto:[EMAIL PROTECTED] Sent: Friday, 16 March 2007 9:15 AM To: rietveld_l@ill.fr Subject: Re: Problems using TOPAS R (Rietveld refinement) Ok, I´m starting to have sucess in the kaolinite refinement, the quantification is giving me reasonable values. I´m refining the thermal factors, all the atoms positions in the kaolinite, the lattice parameters and the cystallite size. Lattice parameters and crystallite size are giving me very good numbers, with very low errors (about 0,09). In the thermal factors, I realized that alll of them tend to 20, so after all refinements I put them to 20, and refine all over again. I don´t care that much for atoms positions, I´m only using them because refining only lattice, thermal and cry size wasn´t enough to make a good calculated pattern to compare with the measured one. In the calcite and dolomite I refine: lattice parameters, cry size and thermal factors. And use on both a preferred orientation correction (spherical harmonics 4 th order). The RWP is about 16. I´d to hear some opinions about this strategy of refinement, if you think that I can spare some refining cycles or even fix some values to reduce erros in the refinement. _ Descubra como mandar Torpedos SMS do seu Messenger para o celular dos seus amigos. http://mobile.msn.com/
RE: Problems using TOPAS R (Rietveld refinement)
I know that refining the atoms positions is ´´too much´´, exagerated. But is the only way I can make the calculated DRX pattern fit with the measured one. There must a problem in the instrument details since I´m using Fundamental Parameters (FP) for peak shape, the values I put in the instrument description play a major role in FP, am I right? I made a new scan, of the same sample, with range from 10° to 80°, step size 0,02 and count time 4 seconds. The old one was from 5° to 120,° maybe it is prejudicing the background refining. Tomorrow I´m gonna to scrap this old pattern and work with the new one. I´m having a good response refining the calcite and teh dolomite in the sample only refining lattice parameters, cry size and beq. I think that refining this is what we can call a ´´normal refining method``. Now the kaolinite... The major problem is that I have a sample from a laterite with hydroxyapatite, calcite, dolomite, vermiculite and other phases. The vermiculite is very alterated and in the DRX pattern we can confuse it with other ``layered silicates``, it will be a huge problem. But I will only put my hands on these samples after finishing with the kaolinite. One question, these ´´models`` and ´´trials`` that you talk about regarding the kaolinite is used in the CIF part of the refinement, am I right?! It´s not a part of the TOPAS itself. right? Thank you, Leandro _ Chegou o Windows Live Spaces com rede social. Confira http://spaces.live.com/
Re: Problems using TOPAS R (Rietveld refinement)
Reinhard Kleeberg said: There are not so much trials published to find a working solution for practical Rietveld quantification of clays. One would be a self-citation of a paper, so I can't do this here in the list. A good one is :-) Pitfalls in Rietveld Phase Quantification of Complex Samples R. Kleeberg (2005) Microstructure Analysis in Materials Science http://www.ww.tu-freiberg.de/mk/bht/Abstracts/kleeberg.pdf _ Dr Alan Hewat, ILL Grenoble, FRANCE [EMAIL PROTECTED]fax+33.476.20.76.48 +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/people/hewat/ _
Re: Problems using TOPAS R (Rietveld refinement)
Or, to see how bad the results from Rietveld refinements of kaolintes are try review paper in Zeitschrift fuer Kristallographie 210(3) 177-183, 1997 lubo smrcok On Wed, 14 Mar 2007, Alan Hewat wrote: Reinhard Kleeberg said: There are not so much trials published to find a working solution for practical Rietveld quantification of clays. One would be a self-citation of a paper, so I can't do this here in the list. A good one is :-) Pitfalls in Rietveld Phase Quantification of Complex Samples R. Kleeberg (2005) Microstructure Analysis in Materials Science http://www.ww.tu-freiberg.de/mk/bht/Abstracts/kleeberg.pdf _ Dr Alan Hewat, ILL Grenoble, FRANCE [EMAIL PROTECTED]fax+33.476.20.76.48 +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/people/hewat/ _
Re: Problems using TOPAS R (Rietveld refinement)
Ok... another problem... I don´t think that the kaolinite CIF that I´m using is working well, I´m refining the temperature factors and it´s giving me non realistic numbers. Can somebody send me a trustable kaolinite CIF, with good temperature factors?! Other doubt... I´m making my scans from 5 (2-theta) to 120 (2-theta), and I´m realizing that above 80° I´m getting unecessary data (basically just backgorund). The question is how this ´´unecessary data`` affect the quantification?!?! From: Leandro Bravo [EMAIL PROTECTED] Reply-To: rietveld_l@ill.fr To: rietveld_l@ill.fr Subject: Re: Problems using TOPAS R (Rietveld refinement) Date: Mon, 12 Mar 2007 13:35:54 -0300 I think that I just did a good job in my quantification: 50,2% calcite and 49,8% dolomite. Now I´m moving foward to a sinthetic mixture of calcite, dolomite and kaolinite. I have other questin, how can I determine a trustable value to the Full Axial Model?! Especially the these paramters: sample lenght, source lenght and RS lenght?!?! I´m starting to realize that the temperature factors are the key to the refinement! They change the calculated pattern so much!!! From: jilin_zhang_Houston [EMAIL PROTECTED] Reply-To: rietveld_l@ill.fr To: rietveld_l@ill.fr rietveld_l@ill.fr Subject: Re: Problems using TOPAS R (Rietveld refinement) Date: Mon, 12 Mar 2007 10:39:41 -0600 Leandro : here is an example of calcite I used. You can use min and max to confine the parameters. One way to know whether it is right is to mix a known fraction of a compound, e.g. ZnO with a ratio of original sample/ZnO=100/15. At the end of the refinement, you have N components with N corrected(with volume and density) scalefactor, S(i), Weight(i)=S(i)/S(ZnO)*15 the sum of all weight(i) should be close to 100 if the whole thing is crystalline. str phase_name calcite scale sc_calcite 0.0001813894308 space_group R-3c r_bragg 5.769971925 Crystallite_Size(cs_calcite, 100 min =100; max =1000;) Trigonal(a_calcite 4.995096119 min =4.95; max =5.2;,c_calcite 17.08621648 min =16.9; max =17.1;) site Ca num_posns 6 x 0 y 0 z 0 occ Ca+2 1 beq 0.95 site C num_posns 6 x 0 y 0 z =1/4; : 0.25 occ C 1 beq 0.9 site O1 num_posns 18 x 0.257 y 0 z =1/4; : 0.25 occ O-2 1 beq 0.94 PO_Spherical_Harmonics(sh_calcite, 2 ) Cheers J Hi, guys, I´m having some trouble using the Bruker software TOPAS R, right now I´m quantifying a sinthetic sample with 50% of calcite and 50% of dolomite. Check the following questions an help me if you can. 1) I´m using the CIF files from ICSD, but when I put it in the software it gives me a temperature factor (beq.) of 1. Is there anyway I can check some good temperature factors?! When i put then to refine, sometimes they become negative, but the calculated - observed pattern is just good. 2) I´m using Fundamental Paramaters and for these I must have acknowledge of my instrument, well I have, minus sample lenght... and stuff like that... is there anyway I can determine these values with accuacy and use them with sure?! 3) In TOPAS how do I know if the refinement is good?! Because each time I refine the 50%/50% mixture I have different results and I don´t know wich one gives me a result that I can trust. Thank ou in advance, Leandro Bravo Ferreira da Costa Student, UFRJ - Universidade Federal do Rio de Janeiro - BR CETEM - RJ _ Inscreva-se no novo Windows Live Mail beta e seja um dos primeiros a testar as novidades-grátis. Saiba mais: http://www.ideas.live.com/programpage.aspx?versionId=5d21c51a-b161-4314-9b0e-4911fb2b2e6d _ Seja um dos primeiros a testar o novo Windows Live Mail Beta- grátis. Acesse http://www.ideas.live.com/programpage.aspx?versionId=5d21c51a-b161-4314-9b0e-4911fb2b2e6d _ Verificador de Segurança do Windows Live OneCare: combata já vírus e outras ameaças! http://onecare.live.com/site/pt-br/default.htm
Re: Problems using TOPAS R (Rietveld refinement)
Leandro Bravo said: I don´t think that the kaolinite CIF that I´m using is working well, I´m refining the temperature factors and it´s giving me non realistic numbers. Can somebody send me a trustable kaolinite CIF, with good temperature factors?! You will find a dozen papers on the structure of kaolinite in ICSD. You should be able to download for free the ones in Clays and Clay Minerals by constructing URLs like this: http://www.crossref.org/openurl?aulast=Nedertitle=Clays%20and%20Clay%20Mineralsvolume=47spage=487year=1999 Other doubt... I´m making my scans from 5 (2-theta) to 120 (2-theta), and I´m realizing that above 80° I´m getting unecessary data (basically just backgorund). The question is how this ´´unecessary data`` affect the quantification?!?! I guess you may well have trouble refining realistic temperature factors if you are also refining the background and you can see no peaks above 80°. Clays are often not well ordered. You can't blame TOPAS or the CIF for that :-) Try fixing the background and/or temperature factors. Neder, R.B.;Burghammer, M.;Grasl, T.;Schulz, H.;Bram, A.;Fiedler, S. Refinement of the kaolinite structure from single-crystal synchrotron data (1999) Clays and Clay Minerals 47, 487-494 Akiba, E.; Hayakawa, H.; Hayashi, S.; Miyawaki, R.; Tomura, S.; Shibasaki, Y.; Izumi, F.; Asano, H.; Kamiyama, T. Structure refinement of synthetic deuterated kaolinite by Rietveld analysis using time-of-flight neutron powder diffraction data (1997) Clays and Clay Minerals 45, 781-788 Bish, D.L. Rietveld refinement of the kaolinite structure at 1.5K (1993) Clays and Clay Minerals 41, 738-744 Bish, D.L.;von Dreele, R.B. Rietveld refinement of non-hydrogen atomic positions in kaolinite (1989) Clays and Clay Minerals 37, 289-296 Young, R.A.;Hewat, A.W. Verification of the Triclinic Crystal Structure of Kaolinite (1988) Clays and Clay Minerals 36, 225-232 _ Dr Alan Hewat, ILL Grenoble, FRANCE [EMAIL PROTECTED]fax+33.476.20.76.48 +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/people/hewat/ _
Re: Problems using TOPAS R (Rietveld refinement)
I think that I just did a good job in my quantification: 50,2% calcite and 49,8% dolomite. Now I´m moving foward to a sinthetic mixture of calcite, dolomite and kaolinite. I have other questin, how can I determine a trustable value to the Full Axial Model?! Especially the these paramters: sample lenght, source lenght and RS lenght?!?! I´m starting to realize that the temperature factors are the key to the refinement! They change the calculated pattern so much!!! From: jilin_zhang_Houston [EMAIL PROTECTED] Reply-To: rietveld_l@ill.fr To: rietveld_l@ill.fr rietveld_l@ill.fr Subject: Re: Problems using TOPAS R (Rietveld refinement) Date: Mon, 12 Mar 2007 10:39:41 -0600 Leandro : here is an example of calcite I used. You can use min and max to confine the parameters. One way to know whether it is right is to mix a known fraction of a compound, e.g. ZnO with a ratio of original sample/ZnO=100/15. At the end of the refinement, you have N components with N corrected(with volume and density) scalefactor, S(i), Weight(i)=S(i)/S(ZnO)*15 the sum of all weight(i) should be close to 100 if the whole thing is crystalline. str phase_name calcite scale sc_calcite 0.0001813894308 space_group R-3c r_bragg 5.769971925 Crystallite_Size(cs_calcite, 100 min =100; max =1000;) Trigonal(a_calcite 4.995096119 min =4.95; max =5.2;,c_calcite 17.08621648 min =16.9; max =17.1;) site Ca num_posns 6 x 0 y 0 z 0 occ Ca+2 1 beq 0.95 site C num_posns 6 x 0 y 0 z =1/4; : 0.25 occ C 1 beq 0.9 site O1 num_posns 18 x 0.257 y 0 z =1/4; : 0.25 occ O-2 1 beq 0.94 PO_Spherical_Harmonics(sh_calcite, 2 ) Cheers J Hi, guys, I´m having some trouble using the Bruker software TOPAS R, right now I´m quantifying a sinthetic sample with 50% of calcite and 50% of dolomite. Check the following questions an help me if you can. 1) I´m using the CIF files from ICSD, but when I put it in the software it gives me a temperature factor (beq.) of 1. Is there anyway I can check some good temperature factors?! When i put then to refine, sometimes they become negative, but the calculated - observed pattern is just good. 2) I´m using Fundamental Paramaters and for these I must have acknowledge of my instrument, well I have, minus sample lenght... and stuff like that... is there anyway I can determine these values with accuacy and use them with sure?! 3) In TOPAS how do I know if the refinement is good?! Because each time I refine the 50%/50% mixture I have different results and I don´t know wich one gives me a result that I can trust. Thank ou in advance, Leandro Bravo Ferreira da Costa Student, UFRJ - Universidade Federal do Rio de Janeiro - BR CETEM - RJ _ Inscreva-se no novo Windows Live Mail beta e seja um dos primeiros a testar as novidades-grátis. Saiba mais: http://www.ideas.live.com/programpage.aspx?versionId=5d21c51a-b161-4314-9b0e-4911fb2b2e6d _ Seja um dos primeiros a testar o novo Windows Live Mail Beta- grátis. Acesse http://www.ideas.live.com/programpage.aspx?versionId=5d21c51a-b161-4314-9b0e-4911fb2b2e6d
