Introducing myself
Hi All, This is just to introduce myself to the members of the mailing list. My name is Nandini Devi Radhamonyamma and I am currently working in St. Andrews University, Scotland with Dr. Paul Wright. I am relatively new to structure solution from powder data and hope to get all the help I can to get a grip on it. Thank you nandini __ Do you Yahoo!? Get better spam protection with Yahoo! Mail. http://antispam.yahoo.com/tools
Bragg R and GSAS
Hi All, How important is Rbragg in powder data structure solution? Does GSAS suit give this parameter? __ Do you Yahoo!? Get better spam protection with Yahoo! Mail. http://antispam.yahoo.com/tools
RE: RE: Re: thermal parameters at low temperature
Title: RE: Re: thermal parameters at low temperature ï Liliana, OK, they should vibrate less... but are they good neutron scatterers or poor? If they are poorly scattering, the thermal factors won't be as meaningful. - Kurt ---Kurt LeinenweberDepartment of ChemistryArizona State UniversityTempe, AZ 85287-1604Phone: (480)-965-8853Fax: (480)-965-2747--- -Original Message-From: Marilena L Viciu [mailto:[EMAIL PROTECTED]Sent: Thursday, February 26, 2004 1:27 PMTo: [EMAIL PROTECTED]Subject: RE: RE: Re: thermal parameters at low temperature Kurt, I mean heavy in the atomic number. Liliana -Original Message- From: Kurt Leinenweber [mailto:[EMAIL PROTECTED] Sent: Thu 2/26/2004 2:21 PM To: [EMAIL PROTECTED] Cc: Subject: RE: Re: thermal parameters at low temperature Wait! I have to mention - the "heaviness" of atoms (atomic number Z) isimportant in x-ray diffraction, but is uncorrelated with the neutronscattering factor for the nuclei. When you say heavy, do you mean thehighly scattering ones for neutrons, or the high-Z ones? - Kurt---Kurt LeinenweberDepartment of ChemistryArizona State UniversityTempe, AZ 85287-1604Phone: (480)-965-8853Fax: (480)-965-2747Original Message-From: Maxim V. Lobanov [mailto:[EMAIL PROTECTED]]Sent: Thursday, February 26, 2004 12:59 PMTo: [EMAIL PROTECTED]>Sorry for the ambiguous information I gave previously. The data at>room temperature were taken with a variable wavelength (TOF) whether>at low temperature the data were recorded with constant wavelength.>There is no magnetic contribution on the pattern. The negative thermal>parameters are for the heaviest atoms in the crystal.>Then it seems that you really overlooked some instrumental issue that canaffect thermal factors. As pointed out by Andreas, indeed it would be mostcritical for heavy atoms, with intrinsically low thermal factors at low T.For example, absorprion. It is typically not very significant for neutrons,but anyway I would calculate it (for example, usinghttp://www.ncnr.nist.gov/instruments/bt1/neutron.html), then fix in therefinement and look if it would "cure" the thermal factors.According to GSAS manual,"For constant wavelength data the absorption coefficient, Ah, is related tothe value for 1Ð neutrons; the correction is indistinguishable from thermalmotion effects and should not be refined. "By the way, I would be grateful if one could share the knowledge about someother important instrumental factors, relevant for thermal factors inneutrons, and ways to estimate reasonable correction values.Sincerely, Maxim.__Maxim V. LobanovDepartment of ChemistryRutgers University610 Taylor RdPiscataway, NJ 08854Phone: (732) 445-3811 <>
Re: Bragg R and GSAS
Thank you. In parallel with single crystal analysis, is there an accepted limit for R(F2) or any other parameter like Rexp to follow? I'm using synchrotron data. nandini --- "Von Dreele, Robert B." <[EMAIL PROTECTED]> wrote: > Nandini, > GSAS gives R(F^2) which is sometimes defined for > single crystal structure analysis. It can be used in > the same way as RBragg. Neither is statistically > related to the minimization process in a Rietveld > least squares refinement, but can be a useful > diagnostic for the quality of the structural fit to > the reflection intensities. > Bob Von Dreele > > > -Original Message- > From: Nandini Devi Radhamonyamma > [mailto:[EMAIL PROTECTED] > Sent: Thu 2/26/2004 5:15 AM > To: [EMAIL PROTECTED] > > Hi All, > > How important is Rbragg in powder data structure > solution? Does GSAS suit give this parameter? > > __ __ Do you Yahoo!? Get better spam protection with Yahoo! Mail. http://antispam.yahoo.com/tools
RE: Re: thermal parameters at low temperature
Liliana, GSAS will refine the value of the absorption coefficient for neutron TOF data quite easily (I recall one message of yours mentioned that your data was of this "flavor"). Just turn on the flag. Your Uiso's should rise for all atoms making those for the heavy atoms positive. The ABS value will be a small positive value. You didn't mention the composition but there must be a neutron absorber of some sort in your sample. BTW one always should refine ABS for neutron TOF data - it is almost always there (might be negative since the incident spectrum is frequently not corrected for it's own absorption). Bob Von Dreele -Original Message- From: Marilena L Viciu [mailto:[EMAIL PROTECTED] Sent: Thu 2/26/2004 2:30 PM To: [EMAIL PROTECTED] Maxim, I looked quickly in GSAS manual and I colud not find the path of setting the absorption correction. Do you know the way of fixing these terms, or is there anybody out there willing to tell me the way of doing it? Thank you very much, Liliana -Original Message- From: Maxim V. Lobanov [mailto:[EMAIL PROTECTED] Sent: Thu 2/26/2004 1:59 PM To: [EMAIL PROTECTED] Cc: >Sorry for the ambiguous information I gave previously. The data at >room temperature were taken with a variable wavelength (TOF) whether >at low temperature the data were recorded with constant wavelength. >There is no magnetic contribution on the pattern. The negative thermal >parameters are for the heaviest atoms in the crystal. > Then it seems that you really overlooked some instrumental issue that can affect thermal factors. As pointed out by Andreas, indeed it would be most critical for heavy atoms, with intrinsically low thermal factors at low T. For example, absorprion. It is typically not very significant for neutrons, but anyway I would calculate it (for example, using http://www.ncnr.nist.gov/instruments/bt1/neutron.html), then fix in the refinement and look if it would "cure" the thermal factors. According to GSAS manual, "For constant wavelength data the absorption coefficient, Ah, is related to the value for 1? neutrons; the correction is indistinguishable from thermal motion effects and should not be refined. " By the way, I would be grateful if one could share the knowledge about some other important instrumental factors, relevant for thermal factors in neutrons, and ways to estimate reasonable correction values. Sincerely, Maxim. __ Maxim V. Lobanov Department of Chemistry Rutgers University 610 Taylor Rd Piscataway, NJ 08854 Phone: (732) 445-3811
thermal parameters at low temperature
Dear all, I am refining a powder neutron data at low temperature (50K). I got some of the thermal parameters negative although the model seems to be quite right (the data at room temperature behaved well with the same model). From your experience, is this the case of a wrong model? I really appreciate any comment! Thank you! Liliana
RE: RE: Re: thermal parameters at low temperature
Dear Dr Von Dreele, The structure at room temperature was refined from neutron TOF. Now, I am using this model to refine low temperature data from neutron CW. My sample has Cu-Cl-La-Nb-O. Sincerely, Liliana -Original Message- From: Von Dreele, Robert B. [mailto:[EMAIL PROTECTED] Sent: Thu 2/26/2004 2:59 PM To: [EMAIL PROTECTED] Cc: Subject: RE: Re: thermal parameters at low temperature Liliana, GSAS will refine the value of the absorption coefficient for neutron TOF data quite easily (I recall one message of yours mentioned that your data was of this "flavor"). Just turn on the flag. Your Uiso's should rise for all atoms making those for the heavy atoms positive. The ABS value will be a small positive value. You didn't mention the composition but there must be a neutron absorber of some sort in your sample. BTW one always should refine ABS for neutron TOF data - it is almost always there (might be negative since the incident spectrum is frequently not corrected for it's own absorption). Bob Von Dreele -Original Message- From: Marilena L Viciu [mailto:[EMAIL PROTECTED] Sent: Thu 2/26/2004 2:30 PM To: [EMAIL PROTECTED] Maxim, I looked quickly in GSAS manual and I colud not find the path of setting the absorption correction. Do you know the way of fixing these terms, or is there anybody out there willing to tell me the way of doing it? Thank you very much, Liliana -Original Message- From: Maxim V. Lobanov [mailto:[EMAIL PROTECTED] Sent: Thu 2/26/2004 1:59 PM To: [EMAIL PROTECTED] Cc: >Sorry for the ambiguous information I gave previously. The data at >room temperature were taken with a variable wavelength (TOF) whether >at low temperature the data were recorded with constant wavelength. >There is no magnetic contribution on the pattern. The negative thermal >parameters are for the heaviest atoms in the crystal. > Then it seems that you really overlooked some instrumental issue that can affect thermal factors. As pointed out by Andreas, indeed it would be most critical for heavy atoms, with intrinsically low thermal factors at low T. For example, absorprion. It is typically not very significant for neutrons, but anyway I would calculate it (for example, using http://www.ncnr.nist.gov/instruments/bt1/neutron.html), then fix in the refinement and look if it would "cure" the thermal factors. According to GSAS manual, "For constant wavelength data the absorption coefficient, Ah, is related to the value for 1? neutrons; the correction is indistinguishable from thermal motion effects and should not be refined. " By the way, I would be grateful if one could share the knowledge about some other important instrumental factors, relevant for thermal factors in neutrons, and ways to estimate reasonable correction values. Sincerely, Maxim. __ Maxim V. Lobanov Department of Chemistry Rutgers University 610 Taylor Rd Piscataway, NJ 08854 Phone: (732) 445-3811 <>
RE: RE: Re: thermal parameters at low temperature
> ... the path of > setting the absorption correction. > In expedt (after choosing the file): L, O, A, C In EXPGUI: input window is behind "Globally Edit Absorption" buttom in the Histogram panel. Best Regards, Markus -- Markus Valkeapää, [EMAIL PROTECTED] Inorganic Chemistry, Göteborg University tel: +46 (0)31 772 2857; fax: +46 (0)31 772 2853 mail: Oorganisk kemi GU, SE-412 96 Gothenburg, Sweden
Re: thermal parameters at low temperature
Dear Liliana, if the model is correct, and variable site occupancies can be excluded and the chosen scattering lengths are correect, it is likely that some 2theta-dependent or time-flight-dependent (if time of flight diffractometer was used) effects (e.g. absorption, Lorentz factors) are not correctly considered, although neutron diffraction is less sensitive than X-ray diffraction. Best regards Andreas Marilena L Viciu schrieb: Dear all, urn:schemas-microsoft-com:office:office" /> I am refining a powder neutron data at low temperature (50K). I got some of the thermal parameters negative although the model seems to be quite right (the data at room temperature behaved well with the same model). From your experience, is this the case of a wrong model? I really appreciate any comment! Thank you! Liliana -- Dr. Andreas Leineweber Max-Planck-Institut fuer Metallforschung Heisenbergstrasse 3 70569 Stuttgart Germany Tel. +49 711 689 3365 Fax. +49 711 689 3312 e-mail: [EMAIL PROTECTED] home page of department: http://www.mf.mpg.de/de/abteilungen/mittemeijer/english/index_english.htm
Re: Bragg R and GSAS
Nandini, I suggest you look at the paper "Rietveld refinement guidelines", J. Appl. Cryst. (1999) 32, 36-50. Bob Von Dreele -Original Message- From: Nandini Devi Radhamonyamma [mailto:[EMAIL PROTECTED] Sent: Thu 2/26/2004 8:38 AM To: [EMAIL PROTECTED] Thank you. In parallel with single crystal analysis, is there an accepted limit for R(F2) or any other parameter like Rexp to follow? I'm using synchrotron data. nandini --- "Von Dreele, Robert B." <[EMAIL PROTECTED]> wrote: > Nandini, > GSAS gives R(F^2) which is sometimes defined for > single crystal structure analysis. It can be used in > the same way as RBragg. Neither is statistically > related to the minimization process in a Rietveld > least squares refinement, but can be a useful > diagnostic for the quality of the structural fit to > the reflection intensities. > Bob Von Dreele > > > -Original Message- > From: Nandini Devi Radhamonyamma > [mailto:[EMAIL PROTECTED] > Sent: Thu 2/26/2004 5:15 AM > To: [EMAIL PROTECTED] > > Hi All, > > How important is Rbragg in powder data structure > solution? Does GSAS suit give this parameter? > > __ __ Do you Yahoo!? Get better spam protection with Yahoo! Mail. http://antispam.yahoo.com/tools
Single crystal data setup
Hello, Can I insert a single crystal data set into GSAS for a refinement without having to reduce the data? Can I start the refinement from the hkl intensity data file (ASCII), without entering the intrument specifics? ie orientation angles, attenuation and wavelength? My data set has already been reduced - I would just like to try the refinement. Jennifer -- Jennifer L. Anderson Ph.D. Candidate - Mineralogy Department of Geological Sciences Miller Hall (312), Queen's University Kingston, ON K7L 3N6 Tel: 613 483-7097
Re: thermal parameters at low temperature
Dear Liliana, To guess what could be a possible answer one would probably need a little more information. Is the RT dataset collected with the same instrument and setup? Is it constant-wavelength of TOF? Do you have any magnetic contribution at 50K, and how do you treat it? Sincerely, Maxim. __ Maxim V. Lobanov Department of Chemistry Rutgers University 610 Taylor Rd Piscataway, NJ 08854 Phone: (732) 445-3811
Re: Bragg R and GSAS
In comparing refinements with different powder datasets there is no "number of observations" in common usage and no 10:1 rule of thumb. Broadly, this means "crappy" data with a chemically unreasonable model can sometimes give much better figures of merit than a good structure with "good" data. Sad, isn't it? Jon Von Dreele, Robert B. wrote: Nandini, I suggest you look at the paper "Rietveld refinement guidelines", J. Appl. Cryst. (1999) 32, 36-50. Bob Von Dreele -Original Message- From: Nandini Devi Radhamonyamma [mailto:[EMAIL PROTECTED] Sent: Thu 2/26/2004 8:38 AM To: [EMAIL PROTECTED] Thank you. In parallel with single crystal analysis, is there an accepted limit for R(F2) or any other parameter like Rexp to follow? I'm using synchrotron data. nandini
Re: Bragg R and GSAS
I tend to use bond lengths to check refinements. If bond lengths - and thermal parameters too - aren't physically reasonable, it can mean that the structure is correct but the refinement is bad, that the structure is somehow wrong, or the atom assignments are wrong. Bond-valence sums are great for this purpose. I use Eutax by Mike O'Keeffe for this, but there are many other programs for bond-valence sums as well. Philosophically, though, I sometimes get disturbed by the fact that the structure has to agree with what we already know in order to be published. It might be better not to think about this too much when doing crystallography. - Kurt --- Kurt Leinenweber Department of Chemistry Arizona State University Tempe, AZ 85287-1604 Phone: (480)-965-8853 Fax: (480)-965-2747 --- -Original Message- From: Jon Wright [mailto:[EMAIL PROTECTED] Sent: Thursday, February 26, 2004 8:28 AM To: [EMAIL PROTECTED] In comparing refinements with different powder datasets there is no "number of observations" in common usage and no 10:1 rule of thumb. Broadly, this means "crappy" data with a chemically unreasonable model can sometimes give much better figures of merit than a good structure with "good" data. Sad, isn't it? Jon Von Dreele, Robert B. wrote: >Nandini, >I suggest you look at the paper "Rietveld refinement guidelines", J. Appl. Cryst. (1999) 32, 36-50. >Bob Von Dreele > > >-Original Message- >From: Nandini Devi Radhamonyamma [mailto:[EMAIL PROTECTED] >Sent: Thu 2/26/2004 8:38 AM >To: [EMAIL PROTECTED] > >Thank you. >In parallel with single crystal analysis, is there an >accepted limit for R(F2) or any other parameter like >Rexp to follow? I'm using synchrotron data. >nandini > > >
RE: Re: thermal parameters at low temperature
>Sorry for the ambiguous information I gave previously. The data at >room temperature were taken with a variable wavelength (TOF) whether >at low temperature the data were recorded with constant wavelength. >There is no magnetic contribution on the pattern. The negative thermal >parameters are for the heaviest atoms in the crystal. > Then it seems that you really overlooked some instrumental issue that can affect thermal factors. As pointed out by Andreas, indeed it would be most critical for heavy atoms, with intrinsically low thermal factors at low T. For example, absorprion. It is typically not very significant for neutrons, but anyway I would calculate it (for example, using http://www.ncnr.nist.gov/instruments/bt1/neutron.html), then fix in the refinement and look if it would "cure" the thermal factors. According to GSAS manual, "For constant wavelength data the absorption coefficient, Ah, is related to the value for 1е neutrons; the correction is indistinguishable from thermal motion effects and should not be refined. " By the way, I would be grateful if one could share the knowledge about some other important instrumental factors, relevant for thermal factors in neutrons, and ways to estimate reasonable correction values. Sincerely, Maxim. __ Maxim V. Lobanov Department of Chemistry Rutgers University 610 Taylor Rd Piscataway, NJ 08854 Phone: (732) 445-3811
Single crystal data setup
Jennifer, Yes. Start with SXTLDATA to read in the hkl file. It will ask for lots of stuff but you will only really need h,k,l,Fo & sig(Fo). Then go to EXPEDT to put in the rest of the stuff (atom positions, etc.). Bob Von Dreele -Original Message- From: Jennifer Anderson [mailto:[EMAIL PROTECTED] Sent: Thu 2/26/2004 9:14 AM To: [EMAIL PROTECTED] Hello, Can I insert a single crystal data set into GSAS for a refinement without having to reduce the data? Can I start the refinement from the hkl intensity data file (ASCII), without entering the intrument specifics? ie orientation angles, attenuation and wavelength? My data set has already been reduced - I would just like to try the refinement. Jennifer -- Jennifer L. Anderson Ph.D. Candidate - Mineralogy Department of Geological Sciences Miller Hall (312), Queen's University Kingston, ON K7L 3N6 Tel: 613 483-7097
RE: Re: thermal parameters at low temperature
Liliana, You can calculate the absorption coefficient for your CW neutron experiment. GSAS wants mu*R/lambda. Find a table of "true" neutron absorption cross sections for your elements & calculate mu from them in cm-1. R is the radius of your sample can in cm. Divide by 2 to correct for packing efficiency. Finally divide by your CW neutron wavelength. Put it into GSAS but don't refine it. Your scale factor will shift and so will the Uiso's. Bob Von Dreele -Original Message- From: Marilena L Viciu [mailto:[EMAIL PROTECTED] Sent: Thu 2/26/2004 3:14 PM To: [EMAIL PROTECTED] Dear Dr Von Dreele, The structure at room temperature was refined from neutron TOF. Now, I am using this model to refine low temperature data from neutron CW. My sample has Cu-Cl-La-Nb-O. Sincerely, Liliana -Original Message- From: Von Dreele, Robert B. [mailto:[EMAIL PROTECTED] Sent: Thu 2/26/2004 2:59 PM To: [EMAIL PROTECTED] Cc: Liliana, GSAS will refine the value of the absorption coefficient for neutron TOF data quite easily (I recall one message of yours mentioned that your data was of this "flavor"). Just turn on the flag. Your Uiso's should rise for all atoms making those for the heavy atoms positive. The ABS value will be a small positive value. You didn't mention the composition but there must be a neutron absorber of some sort in your sample. BTW one always should refine ABS for neutron TOF data - it is almost always there (might be negative since the incident spectrum is frequently not corrected for it's own absorption). Bob Von Dreele -Original Message- From: Marilena L Viciu [mailto:[EMAIL PROTECTED] Sent: Thu 2/26/2004 2:30 PM To: [EMAIL PROTECTED] Maxim, I looked quickly in GSAS manual and I colud not find the path of setting the absorption correction. Do you know the way of fixing these terms, or is there anybody out there willing to tell me the way of doing it? Thank you very much, Liliana -Original Message- From: Maxim V. Lobanov [mailto:[EMAIL PROTECTED] Sent: Thu 2/26/2004 1:59 PM To: [EMAIL PROTECTED] Cc: >Sorry for the ambiguous information I gave previously. The data at >room temperature were taken with a variable wavelength (TOF) whether >at low temperature the data were recorded with constant wavelength. >There is no magnetic contribution on the pattern. The negative thermal >parameters are for the heaviest atoms in the crystal. > Then it seems that you really overlooked some instrumental issue that can affect thermal factors. As pointed out by Andreas, indeed it would be most critical for heavy atoms, with intrinsically low thermal factors at low T. For example, absorprion. It is typically not very significant for neutrons, but anyway I would calculate it (for example, using http://www.ncnr.nist.gov/instruments/bt1/neutron.html), then fix in the refinement and look if it would "cure" the thermal factors. According to GSAS manual, "For constant wavelength data the absorption coefficient, Ah, is related to the value for 1? neutrons; the correction is indistinguishable from thermal motion effects and should not be refined. " By the way, I would be grateful if one could share the knowledge about some other important instrumental factors, relevant for thermal factors in neutrons, and ways to estimate reasonable correction values. Sincerely, Maxim. __ Maxim V. Lobanov Department of Chemistry Rutgers University 610 Taylor Rd Piscataway, NJ 08854 Phone: (732) 445-3811
Re: thermal parameters at low temperature
Dear Liliana, of course the remarks of Maxim are correct, the experimental conditions are very important. Just additionally: Very important is also the range of d* which is covered experimentally for the accuracy of the displacement parameters. Of importance is also the mass of the atom. Heavy atoms (in a soft portential) can get really small ADP whereas for light atoms a considerable ADP should even be found at 0 K (Debye theory). Andreas > Marilena L Viciu schrieb: > > Dear all, > > > > I am refining a powder neutron data at low temperature (50K). I got some of the > thermal parameters negative although the model seems to be quite right (the data at > room temperature behaved well with the same model). From your experience, is this > the case of a wrong model? > > > > I really appreciate any comment! > > Thank you! > > Liliana -- Dr. Andreas Leineweber Max-Planck-Institut fuer Metallforschung Heisenbergstrasse 3 70569 Stuttgart Germany Tel. +49 711 689 3365 Fax. +49 711 689 3312 e-mail: [EMAIL PROTECTED] home page of department: http://www.mf.mpg.de/de/abteilungen/mittemeijer/english/index_english.htm
RE: Re: thermal parameters at low temperature
Wait! I have to mention - the "heaviness" of atoms (atomic number Z) is important in x-ray diffraction, but is uncorrelated with the neutron scattering factor for the nuclei. When you say heavy, do you mean the highly scattering ones for neutrons, or the high-Z ones? - Kurt --- Kurt Leinenweber Department of Chemistry Arizona State University Tempe, AZ 85287-1604 Phone: (480)-965-8853 Fax: (480)-965-2747 --- -Original Message- From: Maxim V. Lobanov [mailto:[EMAIL PROTECTED] Sent: Thursday, February 26, 2004 12:59 PM To: [EMAIL PROTECTED] >Sorry for the ambiguous information I gave previously. The data at >room temperature were taken with a variable wavelength (TOF) whether >at low temperature the data were recorded with constant wavelength. >There is no magnetic contribution on the pattern. The negative thermal >parameters are for the heaviest atoms in the crystal. > Then it seems that you really overlooked some instrumental issue that can affect thermal factors. As pointed out by Andreas, indeed it would be most critical for heavy atoms, with intrinsically low thermal factors at low T. For example, absorprion. It is typically not very significant for neutrons, but anyway I would calculate it (for example, using http://www.ncnr.nist.gov/instruments/bt1/neutron.html), then fix in the refinement and look if it would "cure" the thermal factors. According to GSAS manual, "For constant wavelength data the absorption coefficient, Ah, is related to the value for 1е neutrons; the correction is indistinguishable from thermal motion effects and should not be refined. " By the way, I would be grateful if one could share the knowledge about some other important instrumental factors, relevant for thermal factors in neutrons, and ways to estimate reasonable correction values. Sincerely, Maxim. __ Maxim V. Lobanov Department of Chemistry Rutgers University 610 Taylor Rd Piscataway, NJ 08854 Phone: (732) 445-3811
RE: RE: Re: thermal parameters at low temperature
Kurt, I mean heavy in the atomic number. Liliana -Original Message- From: Kurt Leinenweber [mailto:[EMAIL PROTECTED] Sent: Thu 2/26/2004 2:21 PM To: [EMAIL PROTECTED] Cc: Subject: RE: Re: thermal parameters at low temperature Wait! I have to mention - the "heaviness" of atoms (atomic number Z) is important in x-ray diffraction, but is uncorrelated with the neutron scattering factor for the nuclei. When you say heavy, do you mean the highly scattering ones for neutrons, or the high-Z ones? - Kurt --- Kurt Leinenweber Department of Chemistry Arizona State University Tempe, AZ 85287-1604 Phone: (480)-965-8853 Fax: (480)-965-2747 --- -Original Message- From: Maxim V. Lobanov [mailto:[EMAIL PROTECTED] Sent: Thursday, February 26, 2004 12:59 PM To: [EMAIL PROTECTED] >Sorry for the ambiguous information I gave previously. The data at >room temperature were taken with a variable wavelength (TOF) whether >at low temperature the data were recorded with constant wavelength. >There is no magnetic contribution on the pattern. The negative thermal >parameters are for the heaviest atoms in the crystal. > Then it seems that you really overlooked some instrumental issue that can affect thermal factors. As pointed out by Andreas, indeed it would be most critical for heavy atoms, with intrinsically low thermal factors at low T. For example, absorprion. It is typically not very significant for neutrons, but anyway I would calculate it (for example, using http://www.ncnr.nist.gov/instruments/bt1/neutron.html), then fix in the refinement and look if it would "cure" the thermal factors. According to GSAS manual, "For constant wavelength data the absorption coefficient, Ah, is related to the value for 1Ð neutrons; the correction is indistinguishable from thermal motion effects and should not be refined. " By the way, I would be grateful if one could share the knowledge about some other important instrumental factors, relevant for thermal factors in neutrons, and ways to estimate reasonable correction values. Sincerely, Maxim. __ Maxim V. Lobanov Department of Chemistry Rutgers University 610 Taylor Rd Piscataway, NJ 08854 Phone: (732) 445-3811 <>
RE: RE: Re: thermal parameters at low temperature
Maxim, I looked quickly in GSAS manual and I colud not find the path of setting the absorption correction. Do you know the way of fixing these terms, or is there anybody out there willing to tell me the way of doing it? Thank you very much, Liliana -Original Message- From: Maxim V. Lobanov [mailto:[EMAIL PROTECTED] Sent: Thu 2/26/2004 1:59 PM To: [EMAIL PROTECTED] Cc: Subject: RE: Re: thermal parameters at low temperature >Sorry for the ambiguous information I gave previously. The data at >room temperature were taken with a variable wavelength (TOF) whether >at low temperature the data were recorded with constant wavelength. >There is no magnetic contribution on the pattern. The negative thermal >parameters are for the heaviest atoms in the crystal. > Then it seems that you really overlooked some instrumental issue that can affect thermal factors. As pointed out by Andreas, indeed it would be most critical for heavy atoms, with intrinsically low thermal factors at low T. For example, absorprion. It is typically not very significant for neutrons, but anyway I would calculate it (for example, using http://www.ncnr.nist.gov/instruments/bt1/neutron.html), then fix in the refinement and look if it would "cure" the thermal factors. According to GSAS manual, "For constant wavelength data the absorption coefficient, Ah, is related to the value for 1Ð neutrons; the correction is indistinguishable from thermal motion effects and should not be refined. " By the way, I would be grateful if one could share the knowledge about some other important instrumental factors, relevant for thermal factors in neutrons, and ways to estimate reasonable correction values. Sincerely, Maxim. __ Maxim V. Lobanov Department of Chemistry Rutgers University 610 Taylor Rd Piscataway, NJ 08854 Phone: (732) 445-3811 <>
Re: thermal parameters at low temperature
In EXPGUI it is in the "Histogram" panel. Or, in "Expedt" go to l - o(overall)-a(absorption). Choose function number 0 (Debye-Scherrer)... > >I looked quickly in GSAS manual and I colud not find the path of >setting the absorption correction. Do you know the way of fixing these >terms, or is there anybody out there willing to tell me the way of >doing it? __ Maxim V. Lobanov Department of Chemistry Rutgers University 610 Taylor Rd Piscataway, NJ 08854 Phone: (732) 445-3811
Re: Bragg R and GSAS
At 16:28 26/02/2004, Jon Wright wrote: >Broadly, this means "crappy" data with a chemically unreasonable model can sometimes >give much better figures of merit than a good structure with "good" data. True, with enough parameters you can fit an elephant, but the calculated errors in your structure co-ordinates should reflect the fact that they are poorly determined (unless you have introduced too many constraints, which can make calculated errors meaningless). A low R-factor is not in itself a guarantee that you have a good structure - you need to look at the bond lengths and atom co-ordination, calculate Brown-Shannon valence sums where applicable etc... Alan Hewat, ILL Grenoble, FRANCE <[EMAIL PROTECTED]> fax (33) 4.76.20.76.48 (33) 4.76.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/AlanHewat.htm ___
RE: Re: thermal parameters at low temperature
Sorry for the ambiguous information I gave previously. The data at room temperature were taken with a variable wavelength (TOF) whether at low temperature the data were recorded with constant wavelength. There is no magnetic contribution on the pattern. The negative thermal parameters are for the heaviest atoms in the crystal. I hope that this is a bit clearer than the first e-mail. Thank you, Liliana -Original Message- From: Andreas Leineweber [mailto:[EMAIL PROTECTED] Sent: Thu 2/26/2004 1:06 PM To: [EMAIL PROTECTED] Cc: Subject: Re: thermal parameters at low temperature Dear Liliana, of course the remarks of Maxim are correct, the experimental conditions are very important. Just additionally: Very important is also the range of d* which is covered experimentally for the accuracy of the displacement parameters. Of importance is also the mass of the atom. Heavy atoms (in a soft portential) can get really small ADP whereas for light atoms a considerable ADP should even be found at 0 K (Debye theory). Andreas > Marilena L Viciu schrieb: > > Dear all, > > > > I am refining a powder neutron data at low temperature (50K). I got some of the thermal parameters negative although the model seems to be quite right (the data at room temperature behaved well with the same model). From your experience, is this the case of a wrong model? > > > > I really appreciate any comment! > > Thank you! > > Liliana -- Dr. Andreas Leineweber Max-Planck-Institut fuer Metallforschung Heisenbergstrasse 3 70569 Stuttgart Germany Tel. +49 711 689 3365 Fax. +49 711 689 3312 e-mail: [EMAIL PROTECTED] home page of department: http://www.mf.mpg.de/de/abteilungen/mittemeijer/english/index_english. htm <>
Bragg R and GSAS
Nandini, GSAS gives R(F^2) which is sometimes defined for single crystal structure analysis. It can be used in the same way as RBragg. Neither is statistically related to the minimization process in a Rietveld least squares refinement, but can be a useful diagnostic for the quality of the structural fit to the reflection intensities. Bob Von Dreele -Original Message- From: Nandini Devi Radhamonyamma [mailto:[EMAIL PROTECTED] Sent: Thu 2/26/2004 5:15 AM To: [EMAIL PROTECTED] Hi All, How important is Rbragg in powder data structure solution? Does GSAS suit give this parameter? __ Do you Yahoo!? Get better spam protection with Yahoo! Mail. http://antispam.yahoo.com/tools
