Preferred orientation question
Dear All, Could anybody help me with a question I have related to preferred orientation? I have collected some spectra of a sample, on a D4 using flat plate geometry, that I suspect is showing preferred orientation effects. I was under the impression that a way of testing for this is to re-pack the sample, re-run and compare the spectra, as the level of preferred orientation should change between packings and so the spectra should differ slightly. Despite re-packing and comparing spectra from up to 8 scans the spectra overlay perfectly (within noise). This suggests to me that the refinement residuals are probably not due to preferred orientation. I am using Topas to refine the data and despite the comment above, the residuals seem best fitted using a spherical harmonic-prefered orientation model. I have also tried using other parameters to fit the residuals such as the occupancy of some of the sites, using anisotropic displacement parameters or anisotropic broadening effects, but the SH-PO fits best and seems the most physically reasonable treatment. As a test, I have also run the sample in capillary transmission geometry on another instrument, and the refined value of the SH-PO parameter is reduced. This seems to confirm that PO is the problem, but the question I have is how effective the re-packing comparison method is for confirming PO? If I see no difference in the spectra does it confirm that PO is NOT the problem or can I still have PO effects that are very repeatable upon repeat packing? If PO is not the problem in this case, are there any other structural or instrument effects that could lead to refinement residuals that would be well treated with a SH-PO model? Thank you all very much for any information or light you can shed on the subject. Ross Colman
Re: Instrumental parameters file
Dear Upakul, I would recommend downloading and installing the modified Jedit software from John Evans site: http://www.dur.ac.uk/john.evans/topas_academic/topas_main.htm I have never needed an instrument parameter file with TA because it is possible to set all of your instrument parameters within the inp file. The plugins that come with John Evans Jedit install make setting up the input files extremely clear and considerably easier than going through the manuals for all of the keywords. There are also several instrument-set ups already programmed into the plugin for Johns diffractometers, including a D8. You will need to change the emmission profile wavelength and parameters to a Co source though as (if I am remembering correctly) it is set up with a Cu source. I hope this was helpful. Best regards Ross Colman Hi All, I am an absolute beginner to this community and Rietveld. I have been trying to get a grip on TOPAS-Academic (v4). I was wondering if anyone could let me know where to get hold of an instrumental parameter file for a Bruker D8 advance (Co source). We use this in our laboratory. I have been trying to search for this without much success. Of course I could create one myself, but if one is already available, it saves us some time. Thanks in advance. Best regards Upakul Deka Inorganic Chemistry and Catalysis Debye Institute for Nanomaterials Science Utrecht University Sorbonnelaan 16 3584 CA Utrecht The Netherlands Tel. 00 31 (0) 30 253 6769
Re: How to calculate Occupation number in FullProf
Dear Huy,
In order to minimise the information needed to describe a crystal
structure, we use space groups that define the symmetry of the unit cell.
Each space group has a different set of symmetry opperators that can
generate multiple atoms in the unit cell when you only give the atomic
coordinates of one of the atoms, as they are all related by the inherent
symmetry of the space group.
For most of the unit cell ('general positions'), you can apply all of the
symmetry opperators and generate all of the related positions but on
'special sites' applying all of the symmetry opperators will generate more
than one atom at a position. The easy way of visuallising this is by
having an atom one side of a mirror plane. The mirror plane generates a
second atom, equal distance from the opposite face of the mirror plane. As
you move the first atom closer and closer to the mirror plane the two
atoms get closer until they sit on top of each other, when the atom
resides on the plane itself. Obviously in a real system two atoms do not
sit on top of each other but in fact there is just one atom. This is known
as overgeneration, as the symmetry opperators of the space group have
gnereated more atoms than there actually are.
Some refinement programs deal with overgeneration internally, such as
GSAS, but fullprof requires you to correct for overgeneration. The way you
do this is to look up the multiplicity of the specific atomic site for
that atom in the International Tables for Crystallography, then divide it
by the multiplicity of the general position and put this value into
fulprof as the the occupation number. i.e. fullprof would generate two
atoms on the mirror plane so you must set the occupancy to 0.5. That way
the total number of atoms on the site is 2 x 0.5 = 1.
This complicates things when a site in your crystal is also deficient. If
you do not have unity occupancy then you must multiply the occupancy (SOF)
that you do have by the correction value for overgeneration.
So for your Mg2Sn you are right that the occupancies that you need to put
in for Mg and Sn are 8/192 and 4/192 respectively if you have unity
occupancy on the sites but if you also need to take into account any site
deficiencies then you must further multiply these values by your SOF
values.
I hope that answered your question, and am sure that Juan (that wrote
fullprof, just over the road from you) has probably already replied with a
better answer.
Ross
Dear all,
As a newbie in FullProf (and also in crystallography) I'm being
confused with the parameter Occupation number (Occ).
In fact, as indicated in the FullProf Manual:
/Occupation number i.e. chemical occupancy × site multiplicity (can be
normalised to the multiplicity of the general position of the group)./
What is the meaning of this Occupation number and difference between
Occupation number and SOF ?
Could anyone help me to explain how to find the value of chemical
occupancy, site multiplicity ? And how can the Occupation number be
/normalised to the multiplicity of the general position of the group/ ?
I have tried to calculate for Mg2Sn (Fm3m), with Mg at the site 8c and
Sn at 4a, then Occupation number of Mg is 8/192 and that of Sn is 4/192.
Is this right ?
Thanks in advance for your any help.
Huy LE-QUOC,
LPSC/CRPMN - CNRS
53 rue des Martyrs, Grenoble 38026, FRANCE
Dummy pattern within TOPAS
Dear Rietvelders, I am looking to generate a number of 'dummy' powder neutron diffraction patterns within TOPAS for comparison purposes. I know that this can be done within Fulprof using the Job=3 mode but could not find anything within the TOPAS manual/examples about generation of simulated patterns. If it is possible could someone send me the command/macro or an example of its use in an INP file? Thank you in advance for any help you may have. Best regards Ross Colman
Re: about background substraction
Dear Wahyu, As well as the points that David has pointed out, the background could be due to fluorescence from elements in your sample. For example iron fluoresces under excitation from copper x-rays and so if you have access to another wavelength / source then it may be more successfull. Or if you have the facility for a secondary monochromator in your setup? Regards Ross Colman David Lee wrote: I would suggest that you do the background refinement with GSAS. Try using Expgui, a graphical interface to gsas written by Brian Toby, to select background points and do a background fit. There are excellent tutorials on doing this available at: http://www.ncnr.nist.gov/xtal/software/expgui/ Also, you need to find out why your background is so high and rough. Do you have other phases present? Is your material not fully crystallized? Is your sample (if a powder) ground finely enough? Is your sample surface smooth and flat? Good Luck, David Lee, Ph.D. DTLee Scientific, llc http://www.dtlee.com 614-562-6230 On May 19, 2009, at 6:16 AM, wahyu bambang wrote: Dear all rietvelder, Please give me a suggestion about my problem. I want to do quantitative analysis using GSAS, however my diffraction pattern has very high and rough background which makes me difficult to do preliminary qualitative works to determine the available phases. Is it alright if I substract the background and refine it a little first using another refinement software before I go through GSAS? I really appreciate your kindness to answer. regards, wahyu -- Ross Colman G19 Christopher Ingold Laboratories University College London Department of Chemistry 20 Gordon Street London WC1H 0AJ Phone: +44 (0)20 7679 4636 Internal: 24636 Email: ross.col...@ucl.ac.uk mailto:ross.col...@ucl.ac.uk
Anisotropic strain
Dear Rietvelders, I am a PhD student working at UCL (UK) and was wondering if anyone out there could help me with a diffraction related problem: I am attempting to refine some neutron diffraction data on a powder sample that has a very laminar structure. The refinement is acceptable but close inspection shows that some peaks are modelled poorly compared to others. The relative intensity of each peak appears to be a good fit but some peaks are sharper than others whilst some are noticably broadened. The instrument responsible suggested using anisotropic strain within Fullprof to attempt to model the peak shape anisotropies (as an ILL instrument was used to collect the data). This worked quite well and when considering the crystallite morphologies it seems physically reasonable. I have also been using TOPAS to refine the some of the data for comparison and as a new user have not found a way of including this kind of anisotropic strain into the refinement. Is it possible? If so does anybody have an example? Many thanks for your help Ross Colman p.s If it helps in the discussion, I am analysing a crystal structure with P -3 m 1 symmetry and so the refinable parameters within Fullprof are s_400, s_004 and s_112. From a chemical point of view the c direction is only weekly hydrogen bonded and so the laminar structure seen in SEM should be within the a-b plane. Ross Colman G19 Christopher Ingold Laboratories University College London Department of Chemistry 20 Gordon Street London WC1H 0AJ Phone: +44 (0)20 7679 4636 Internal: 24636 Email: ross.col...@ucl.ac.uk mailto:ross.col...@ucl.ac.uk
